#Contains_Novel_or_Only_Known(Annotated)_Junctions	as_event_type	gene_name	chr	strand	exclusion_junctions	inclusion_junctions	exclusion_exons	inclusion_exons	intron-exon_junctions	neighboring_constitutive_exons	sample	
K	alternative_last_exon	CUFF.254	chr13	-	chr13:101129697-101132514	chr13:101132018-101132514	chr13:101129583-101129696	chr13:101131726-101132017			183;259
K	alternative_acceptor	CUFF.250	chr13	+	chr13:52028466-52034807	chr13:52028466-52034620		chr13:52034621-52034807	chr13:52034807-52034808		46;148
K	jcn_only_AA	CUFF.244,CUFF.249	chr13	+	chr13:21205242-21228014	chr13:21205242-21212470					462;109
K	alternative_last_exon	CUFF.246	chr13	-	chr13:25525627-25541529	chr13:25539719-25541529	chr13:25525432-25525626	chr13:25539638-25539718			25;359
K	alternative_first_exon	CUFF.253	chr13	-	chr13:97644827-97646822	chr13:97644827-97646551	chr13:97646823-97647081	chr13:97646552-97646800			28;58
K	alternative_first_exon	CUFF.253,CUFF.254	chr13	-	chr13:101132618-101133373	chr13:101132618-101133233	chr13:101133374-101133506	chr13:101133234-101133348			37;118
K	alternative_first_exon	CUFF.256	chr13	+	chr13:103498705-103504467	chr13:103501545-103504467	chr13:103497194-103498704	chr13:103501468-103501544			321;570
K	intron_retention	CUFF.256	chr13	+	chr13:103518262-103518611				chr13:103518261-103518262;chr13:103518611-103518612		10;92
K	jcn_only_AA	CUFF.253	chr13	-	chr13:97640030-97642011	chr13:97640088-97642011		chr13:97640030-97640087	chr13:97640029-97640030		73;43
K	alternative_first_exon	CUFF.244	chr13	+	chr13:21141396-21148518	chr13:21142137-21148518	chr13:21140530-21141395	chr13:21141809-21142136			18;36
N	alternative_donor	CUFF.248	chr13	+	chr13:33629453-33634815	chr13:33629503-33634815		chr13:33629453-33629502	chr13:33629452-33629453		10;121
N	alternative_donor	CUFF.256	chr13	+	chr13:103525694-103527656	chr13:103527209-103527656		chr13:103525694-103527208	chr13:103525693-103525694		22;4
K	alternative_last_exon	CUFF.244,CUFF.256	chr13	+	chr13:103510769-103513856	chr13:103510769-103511260	chr13:103513857-103514064	chr13:103511261-103511386			5;201
K	jcn_only_AD	CUFF.252,CUFF.253	chr13	-	chr13:78492760-78493531	chr13:78492760-78493141		chr13:78493142-78493531	chr13:78493531-78493532		11;48
N	alternative_donor	CUFF.248	chr13	+	chr13:33590452-33627903	chr13:33591398-33627903		chr13:33590452-33591397	chr13:33590451-33590452		178;15
K	alternative_acceptor	CUFF.253	chr13	-	chr13:97640030-97642011	chr13:97640088-97642011		chr13:97640030-97640087	chr13:97640029-97640030		73;29
N	jcn_only_AD	CUFF.256	chr13	+	chr13:103525694-103527656	chr13:103527209-103527656		chr13:103525694-103527208	chr13:103525693-103525694		22;20
K	alternative_first_exon	CUFF.252,CUFF.255	chr13	-	chr13:102527647-103053820	chr13:102527647-102568802	chr13:103053821-103054124	chr13:102568803-102569074			12;24
K	jcn_only_AD	CUFF.244	chr13	+	chr13:21205242-21228014	chr13:21219098-21228014					462;126
N	intron_retention		chr13	+	chr13:21141925-21142023				chr13:21141924-21141925;chr13:21142023-21142024		13;23
N	jcn_only_AD		chr13	-	chr13:24334357-24380088	chr13:24334357-24334671		chr13:24334672-24380088	chr13:24380088-24380089		18;626
K	alternative_donor	CUFF.253	chr13	-	chr13:97642064-97644761	chr13:97642064-97644675		chr13:97644676-97644761	chr13:97644761-97644762		9;70
K	cassette	CUFF.244	chr13	+	chr13:21230570-21237636	chr13:21230570-21237401;chr13:21237526-21237636		chr13:21237402-21237525			106;323
K	jcn_only_AA	CUFF.246	chr13	-	chr13:25507675-25525534	chr13:25517160-25525534					25;249
N	alternative_donor		chr13	-	chr13:24334357-24380088	chr13:24334357-24334671		chr13:24334672-24380088	chr13:24380088-24380089		18;3
N	jcn_only_AD	CUFF.248	chr13	+	chr13:33629453-33634815	chr13:33629503-33634815		chr13:33629453-33629502	chr13:33629452-33629453		10;196
N	jcn_only_AD	CUFF.254	chr13	-	chr13:24460646-24463270	chr13:24460646-24462816					11;93
K	intron_retention	CUFF.244	chr13	+	chr13:21237526-21237636				chr13:21237525-21237526;chr13:21237636-21237637		401;26
K	alternative_donor	CUFF.252,CUFF.253	chr13	-	chr13:78492760-78493531	chr13:78492760-78493141		chr13:78493142-78493531	chr13:78493531-78493532		11;47
K	cassette	CUFF.249	chr13	+	chr13:51805516-51825603	chr13:51805516-51819447;chr13:51819556-51825603		chr13:51819448-51819555			1;14
N	alternative_acceptor	CUFF.245	chr13	-	chr13:24415628-24432998	chr13:24416709-24432998		chr13:24415628-24416708	chr13:24415627-24415628		13;132
K	cassette	CUFF.244	chr13	+	chr13:21179245-21189931	chr13:21179245-21188495;chr13:21188575-21189931		chr13:21188496-21188574			78;38
K	jcn_only_AA	CUFF.252	chr13	-	chr13:78470694-78473993	chr13:78472470-78473993		chr13:78470694-78472469	chr13:78470693-78470694		23;24
N	jcn_only_AD	CUFF.248	chr13	+	chr13:33590452-33627903	chr13:33591398-33627903		chr13:33590452-33591397	chr13:33590451-33590452		178;12
K	jcn_only_AA	CUFF.250	chr13	+	chr13:52028466-52034807	chr13:52028466-52034620		chr13:52034621-52034807	chr13:52034807-52034808		46;76
N	jcn_only_AA	CUFF.245	chr13	-	chr13:24415628-24432998	chr13:24416709-24432998		chr13:24415628-24416708	chr13:24415627-24415628		13;224
K	jcn_only_AD	CUFF.253	chr13	-	chr13:97642064-97644761	chr13:97642064-97644675		chr13:97644676-97644761	chr13:97644761-97644762		9;115
K	cassette	CUFF.244	chr13	+	chr13:21157159-21165105	chr13:21157159-21163949;chr13:21164007-21165105		chr13:21163950-21164006			19;39
K	cassette	CUFF.247	chr13	+	chr13:31192194-31195900	chr13:31192194-31195209;chr13:31195377-31195900		chr13:31195210-31195376			20;4
K	alternative_first_exon	CUFF.246	chr13	-	chr13:25525627-25542343	chr13:25525627-25541529	chr13:25542344-25542719	chr13:25541530-25541650			306;15
K	jcn_only_AA	CUFF.249	chr13	+	chr13:51796706-51805483	chr13:51796706-51799256					18;70
K	alternative_acceptor	CUFF.252	chr13	-	chr13:78470694-78473993	chr13:78472470-78473993		chr13:78470694-78472469	chr13:78470693-78470694		23;63
K	jcn_only_AA	CUFF.244	chr13	+	chr13:21141396-21148518	chr13:21141396-21141808					40;38
K	alternative_last_exon	CUFF.246	chr13	-	chr13:25525627-25542343	chr13:25541592-25542343	chr13:25525432-25525626	chr13:25541530-25541591			402;56
K	intron_retention	CUFF.252	chr13	-	chr13:78492760-78493531				chr13:78492759-78492760;chr13:78493531-78493532		11;11
K	alternative_acceptor	CUFF.195,CUFF.220	chr12	+	chr12:53861628-53862563	chr12:53861628-53862560		chr12:53862561-53862563	chr12:53862563-53862564		113;386
N	jcn_only_AD	CUFF.236	chr12	-	chr12:102869578-102874096	chr12:102869578-102872264		chr12:102872265-102874096	chr12:102874096-102874097		166;14
N	intron_retention	CUFF.220	chr12	+	chr12:53854928-53856264				chr12:53854927-53854928;chr12:53856264-53856265	chr12:53853584-53854927	580;109
N	cassette	CUFF.200	chr12	-	chr12:7088742-7090755	chr12:7088742-7090165;chr12:7090345-7090755		chr12:7090166-7090344			47;279
K	cassette	CUFF.240	chr12	-	chr12:120146124-120148344	chr12:120146124-120148055;chr12:120148192-120148344		chr12:120148056-120148191			119;165
K	intron_retention	CUFF.194	chr12	-	chr12:346457-347091				chr12:346456-346457;chr12:347091-347092		474;70
K	jcn_only_AA	CUFF.205	chr12	+	chr12:13366756-13367504	chr12:13366756-13367467		chr12:13367468-13367504	chr12:13367504-13367505		794;303
K	jcn_only_AA	CUFF.206	chr12	+	chr12:21200152-21207512	chr12:21200152-21201645					31;51
K	intron_retention	CUFF.207	chr12	-	chr12:22666314-22672048				chr12:22666313-22666314;chr12:22672048-22672049		207;15
K	intron_retention	CUFF.229	chr12	+	chr12:58018390-58018506				chr12:58018389-58018390;chr12:58018506-58018507		30;912
K	alternative_first_exon	CUFF.238	chr12	-	chr12:113618864-113623082	chr12:113618864-113621527	chr12:113623083-113623371	chr12:113621528-113621658			55;28
K	cassette	CUFF.223	chr12	-	chr12:56575864-56577958	chr12:56575864-56577644;chr12:56577715-56577958		chr12:56577645-56577714			52;321
K	intron_retention	CUFF.229	chr12	+	chr12:58018577-58018648				chr12:58018576-58018577;chr12:58018648-58018649		26;960
K	alternative_acceptor	CUFF.240	chr12	-	chr12:120172163-120172964	chr12:120172212-120172964		chr12:120172163-120172211	chr12:120172162-120172163		64;35
K	intron_retention	CUFF.223	chr12	-	chr12:56574886-56575265				chr12:56574885-56574886;chr12:56575265-56575266		150;199
N	alternative_donor	CUFF.200	chr12	-	chr12:113617811-113618785	chr12:113617811-113618733		chr12:113618734-113618785	chr12:113618785-113618786		32;40
K	cassette	CUFF.223	chr12	-	chr12:56565217-56566211	chr12:56565217-56565462;chr12:56565722-56566211		chr12:56565463-56565721			105;420
K	cassette	CUFF.229	chr12	+	chr12:58018940-58019192	chr12:58018940-58019018;chr12:58019114-58019192		chr12:58019019-58019113			57;791
N	cassette	CUFF.207	chr12	-	chr12:22610096-22612425	chr12:22610096-22611417;chr12:22611490-22612425		chr12:22611418-22611489			46;256
K	intron_retention	CUFF.229	chr12	+	chr12:58019248-58019364				chr12:58019247-58019248;chr12:58019364-58019365		1333;21
K	cassette	CUFF.218	chr12	-	chr12:52981636-52985247	chr12:52981636-52984619;chr12:52984746-52985247		chr12:52984620-52984745			47;361
N	jcn_only_AA	CUFF.220	chr12	+	chr12:53853188-53854798;chr12:53853188-53853583	chr12:53853188-53854114		chr12:53853584-53854114;chr12:53854115-53854798	chr12:53854114-53854115;chr12:53854798-53854799	chr12:53853056-53853187;chr12:53854799-53854970	888;213
N	alternative_donor		chr12	+	chr12:4653071-4654384	chr12:4653078-4654384		chr12:4653071-4653077	chr12:4653070-4653071		241;17
K	jcn_only_AA	CUFF.239	chr12	-	chr12:113646065-113658801	chr12:113646315-113658801		chr12:113646065-113646314	chr12:113646064-113646065		44;56
N	cassette	CUFF.207	chr12	-	chr12:22646272-22666227	chr12:22646272-22659644;chr12:22659754-22666227		chr12:22659645-22659753			35;224
K	intron_retention	CUFF.233	chr12	+	chr12:69237613-69237713				chr12:69237612-69237613;chr12:69237713-69237714		119;171
K	intron_retention	CUFF.236	chr12	-	chr12:102874179-102874364				chr12:102874178-102874179;chr12:102874364-102874365		40;33
N	jcn_only_AD	CUFF.194	chr12	-	chr12:335681-336730	chr12:335681-335818		chr12:335819-336730	chr12:336730-336731		203;65
K	intron_retention		chr12	+	chr12:53861078-53861588				chr12:53861077-53861078;chr12:53861588-53861589		794;140
K	cassette	CUFF.213	chr12	-	chr12:49334972-49351092	chr12:49334972-49349880;chr12:49350319-49351092		chr12:49349881-49350318			82;180
N	coord_cassette	CUFF.233	chr12	+	chr12:69214155-69233053	chr12:69214155-69218142;chr12:69218211-69218334;chr12:69218432-69233053		chr12:69218143-69218210;chr12:69218335-69218431			68;154
K	intron_retention	CUFF.205	chr12	+	chr12:13364523-13366412				chr12:13364522-13364523;chr12:13366412-13366413		1204;122
N	alternative_last_exon	CUFF.236	chr12	-	chr12:102796345-102813286	chr12:102811782-102813286	chr12:102789546-102796344	chr12:102811188-102811781			6;128
N	cassette	CUFF.240	chr12	-	chr12:120204987-120210573	chr12:120204987-120208588;chr12:120208715-120210573		chr12:120208589-120208714			4;25
N	coord_cassette	CUFF.233	chr12	+	chr12:69203073-69229608	chr12:69203073-69218142;chr12:69218211-69218334;chr12:69218432-69222550;chr12:69222712-69229608		chr12:69218143-69218210;chr12:69218335-69218431;chr12:69222551-69222711			369;157
N	alternative_donor	CUFF.220	chr12	+	chr12:53853188-53854798	chr12:53854210-53854798		chr12:53853188-53854209	chr12:53853187-53853188	chr12:53854799-53854970;chr12:53853056-53853187	779;114
N	coord_cassette	CUFF.233	chr12	+	chr12:69218432-69233053	chr12:69218432-69222550;chr12:69222712-69229608;chr12:69229765-69233053		chr12:69222551-69222711;chr12:69229609-69229764			64;172
K	cassette	CUFF.213	chr12	-	chr12:49334972-49349880	chr12:49334972-49349477;chr12:49349544-49349880		chr12:49349478-49349543			93;36
K	intron_retention	CUFF.234	chr12	+	chr12:72094806-72097756				chr12:72094805-72094806;chr12:72097756-72097757		1178;30
N	coord_cassette	CUFF.233	chr12	+	chr12:69207409-69233053	chr12:69207409-69222550;chr12:69222712-69229608;chr12:69229765-69233053		chr12:69222551-69222711;chr12:69229609-69229764			70;100
K	alternative_first_exon	CUFF.220	chr12	+	chr12:53846760-53848509,chr12:53847068-53848509;chr12:53837558-53848509	chr12:53846161-53848509	chr12:53837175-53837557	chr12:53845800-53846160		chr12:53848510-53848653	103;368
K	intron_retention		chr12	-	chr12:48392215-48393701				chr12:48392214-48392215;chr12:48393701-48393702		47;39
N	cassette	CUFF.208	chr12	-	chr12:25679890-25801427	chr12:25679890-25699307;chr12:25699489-25801427		chr12:25699308-25699488			28;158
K	intron_retention	CUFF.205	chr12	+	chr12:13366756-13367504				chr12:13366755-13366756;chr12:13367504-13367505		794;321
N	coord_cassette	CUFF.208	chr12	-	chr12:25699489-25801427	chr12:25699489-25700158;chr12:25700286-25702259;chr12:25702481-25801427		chr12:25700159-25700285;chr12:25702260-25702480			16;25
K	jcn_only_AD	CUFF.229	chr12	+	chr12:58019102-58019192	chr12:58019114-58019192		chr12:58019102-58019113	chr12:58019101-58019102		1926;59
N	cassette	CUFF.233	chr12	+	chr12:69207409-69222550;chr12:69207409-69233053;chr12:69207409-69218142;chr12:69203073-69218142;chr12:69203073-69233053	chr12:69207409-69214104,chr12:69203073-69214104;chr12:69214155-69233053,chr12:69214155-69222550,chr12:69214155-69218142		chr12:69214105-69214154			278;354
K	intron_retention	CUFF.229	chr12	+	chr12:58017882-58018648				chr12:58017881-58017882;chr12:58018648-58018649		13;875
K	alternative_last_exon	CUFF.208	chr12	-	chr12:25655973-25656671,chr12:25650729-25656671;chr12:25652931-25656671;chr12:25629395-25656671	chr12:25562365-25656671	chr12:25652712-25652930;chr12:25628950-25629394	chr12:25562142-25562364			237;92
N	coord_cassette	CUFF.210	chr12	+	chr12:27628665-27648612	chr12:27628665-27641392;chr12:27641481-27647232;chr12:27647290-27648612		chr12:27641393-27641480;chr12:27647233-27647289			30;320
K	alternative_last_exon	CUFF.206	chr12	+	chr12:21242864-21279041	chr12:21242864-21245446	chr12:21279042-21279191	chr12:21245447-21245766			216;317
K	intron_retention	CUFF.240	chr12	-	chr12:120156667-120158282				chr12:120156666-120156667;chr12:120158282-120158283		3;50
K	intron_retention	CUFF.229	chr12	+	chr12:58016425-58016569				chr12:58016424-58016425;chr12:58016569-58016570		85;36
K	jcn_only_AA	CUFF.240	chr12	-	chr12:120128257-120135463	chr12:120128260-120135463		chr12:120128257-120128259	chr12:120128256-120128257		291;270
K	jcn_only_AA	CUFF.240	chr12	-	chr12:120172163-120172964	chr12:120172212-120172964		chr12:120172163-120172211	chr12:120172162-120172163		64;62
N	jcn_only_AA		chr12	-	chr12:56706670-56708634;chr12:56705238-56708634;chr12:56705199-56708634	chr12:56705180-56708634					240;32
K	jcn_only_AD	CUFF.211	chr12	-	chr12:48258961-48272750	chr12:48258961-48272598		chr12:48272599-48272750	chr12:48272750-48272751		644;163
K	cassette	CUFF.233	chr12	+	chr12:69207409-69210591	chr12:69207409-69209407;chr12:69209501-69210591		chr12:69209408-69209500			381;99
N	jcn_only_AD	CUFF.220	chr12	+	chr12:53853188-53854798	chr12:53854210-53854798		chr12:53853188-53854209	chr12:53853187-53853188	chr12:53854799-53854970;chr12:53853056-53853187	779;62
N	alternative_acceptor		chr12	+	chr12:26205536-26208211	chr12:26205536-26208168		chr12:26208169-26208211	chr12:26208211-26208212		20;56
K	alternative_last_exon	CUFF.208	chr12	-	chr12:25655973-25656671,chr12:25650729-25656671;chr12:25562365-25656671;chr12:25629395-25656671	chr12:25652931-25656671	chr12:25562142-25562364;chr12:25628950-25629394	chr12:25652712-25652930			279;50
K	intron_retention	CUFF.229	chr12	+	chr12:58013662-58014124				chr12:58013661-58013662;chr12:58014124-58014125		20;25
K	cassette	CUFF.207	chr12	-	chr12:22659754-22666227	chr12:22659754-22665580;chr12:22665614-22666227		chr12:22665581-22665613			218;198
K	intron_retention	CUFF.208	chr12	-	chr12:25679153-25679702				chr12:25679152-25679153;chr12:25679702-25679703		131;38
K	cassette	CUFF.217	chr12	-	chr12:52962174-52963642	chr12:52962174-52963273;chr12:52963316-52963642		chr12:52963274-52963315			80;13
N	cassette	CUFF.194	chr12	-	chr12:352980-371954	chr12:352980-369016;chr12:369224-371954		chr12:369017-369223			86;420
N	alternative_donor	CUFF.236	chr12	-	chr12:102869578-102874096	chr12:102869578-102872264		chr12:102872265-102874096	chr12:102874096-102874097		166;4
N	alternative_first_exon	CUFF.209	chr12	+	chr12:26148064-26173077	chr12:26164755-26173077	chr12:26147970-26148063	chr12:26164623-26164754			45;257
N	cassette	CUFF.211	chr12	-	chr12:48272899-48293619;chr12:48272899-48298737	chr12:48272899-48276476;chr12:48276558-48293619,chr12:48276558-48298737		chr12:48276477-48276557			200;380
N	intron_retention		chr12	-	chr12:7088742-7090755				chr12:7088741-7088742;chr12:7090755-7090756		47;252
K	alternative_last_exon	CUFF.208	chr12	-	chr12:25655973-25656671,chr12:25650729-25656671;chr12:25652931-25656671;chr12:25562365-25656671	chr12:25629395-25656671	chr12:25652712-25652930;chr12:25562142-25562364	chr12:25628950-25629394			208;121
N	jcn_only_AD	CUFF.195	chr12	+	chr12:1742072-1754959;chr12:1749143-1754959	chr12:1754228-1754959					234;326
K	intron_retention	CUFF.229	chr12	+	chr12:58019471-58019780				chr12:58019470-58019471;chr12:58019780-58019781		38;542
N	intron_retention	CUFF.194	chr12	-	chr12:335681-335818				chr12:335680-335681;chr12:335818-335819		65;820
N	intron_retention		chr12	-	chr12:56705238-56708634				chr12:56705237-56705238;chr12:56708634-56708635		69;268
K	intron_retention	CUFF.229	chr12	+	chr12:58015211-58015472				chr12:58015210-58015211;chr12:58015472-58015473		124;38
N	jcn_only_AD	CUFF.195	chr12	+	chr12:1754228-1754959;chr12:1749143-1754959	chr12:1742072-1754959					454;105
K	jcn_only_AD	CUFF.235	chr12	-	chr12:77260042-77272742	chr12:77260042-77272717		chr12:77272718-77272742	chr12:77272742-77272743		464;697
N	alternative_acceptor	CUFF.194	chr12	-	chr12:347177-369016	chr12:352980-369016		chr12:347177-352979	chr12:347176-347177		437;24
K	intron_retention	CUFF.222	chr12	-	chr12:54757644-54758176				chr12:54757643-54757644;chr12:54758176-54758177		69;28
K	jcn_only_AD	CUFF.206	chr12	+	chr12:21011506-21174394	chr12:21172315-21174394					35;8
K	alternative_donor	CUFF.234	chr12	+	chr12:72094659-72097756	chr12:72094806-72097756		chr12:72094659-72094805	chr12:72094658-72094659		501;833
K	intron_retention	CUFF.223	chr12	-	chr12:56558153-56558431				chr12:56558152-56558153;chr12:56558431-56558432		37;92
K	cassette	CUFF.200	chr12	-	chr12:7092701-7125577	chr12:7092701-7108732;chr12:7108792-7125577		chr12:7108733-7108791			221;54
N	intron_retention		chr12	-	chr12:56708751-56709604				chr12:56708750-56708751;chr12:56709604-56709605		33;37
K	alternative_donor	CUFF.211	chr12	-	chr12:48258961-48272750	chr12:48258961-48272598		chr12:48272599-48272750	chr12:48272750-48272751		644;150
K	alternative_first_exon	CUFF.216	chr12	+	chr12:52403024-52404664	chr12:52404347-52404664	chr12:52402974-52403023	chr12:52404232-52404346			95;270
N	cassette	CUFF.212	chr12	-	chr12:48392215-48398019	chr12:48392215-48393701;chr12:48393909-48398019		chr12:48393702-48393908			30;93
N	alternative_first_exon	CUFF.236	chr12	-	chr12:102796345-102811732;chr12:102796345-102813286	chr12:102796345-102809481	chr12:102811733-102811781;chr12:102813287-102813468	chr12:102809482-102809579			101;63
K	cassette	CUFF.218	chr12	-	chr12:52992897-52994810	chr12:52992897-52993054;chr12:52993194-52994810		chr12:52993055-52993193			281;123
K	cassette	CUFF.229	chr12	+	chr12:58017882-58018648	chr12:58017882-58018282;chr12:58018390-58018648		chr12:58018283-58018389			13;349
N	alternative_acceptor	CUFF.213	chr12	-	chr12:49335361-49351092;chr12:49350319-49351092;chr12:49349981-49351092	chr12:49332631-49351092		chr12:49332631-49335360;chr12:49335361-49349980;chr12:49349981-49350318	chr12:49332630-49332631;chr12:49335360-49335361;chr12:49349980-49349981		29;27
K	cassette	CUFF.201	chr12	+	chr12:9723489-9725598	chr12:9723489-9724056;chr12:9724170-9725598		chr12:9724057-9724169			42;30
K	alternative_first_exon	CUFF.233	chr12	+	chr12:69202272-69202987	chr12:69202867-69202987	chr12:69201924-69202271	chr12:69202722-69202866			89;253
N	jcn_only_AD	CUFF.239,CUFF.240	chr12	-	chr12:120148426-120149982	chr12:120148426-120148853		chr12:120148854-120149982	chr12:120149982-120149983		140;31
K	intron_retention	CUFF.205	chr12	+	chr12:13366756-13367467				chr12:13366755-13366756;chr12:13367467-13367468		303;284
N	alternative_acceptor	CUFF.219	chr12	-	chr12:53471046-53473094	chr12:53471956-53473094		chr12:53471046-53471955	chr12:53471045-53471046		265;5
N	cassette	CUFF.207	chr12	-	chr12:22610096-22612425	chr12:22610096-22611417;chr12:22611520-22612425		chr12:22611418-22611519			46;212
N	jcn_only_AA		chr12	-	chr12:56705180-56708634;chr12:56706670-56708634;chr12:56705238-56708634	chr12:56705199-56708634					157;116
K	cassette	CUFF.234	chr12	+	chr12:72083485-72090215	chr12:72083485-72084118;chr12:72084211-72090215		chr12:72084119-72084210			102;53
K	jcn_only_AA	CUFF.218	chr12	-	chr12:52993087-52994810	chr12:52993194-52994810		chr12:52993087-52993193	chr12:52993086-52993087		31;118
N	cassette	CUFF.213	chr12	-	chr12:49334972-49350767	chr12:49334972-49349880;chr12:49350134-49350767		chr12:49349881-49350133			26;163
N	alternative_acceptor		chr12	+	chr12:26148064-26208211	chr12:26148064-26208168		chr12:26208169-26208211	chr12:26208211-26208212		90;35
K	jcn_only_AD	CUFF.206	chr12	+	chr12:21229504-21294447	chr12:21284171-21294447					31;315
N	mutually_exclusive	CUFF.200	chr12	-	chr12:7088742-7090755,chr12:7090794-7090971	chr12:7088742-7090165,chr12:7090345-7090971	chr12:7090756-7090793	chr12:7090166-7090344			86;180
K	intron_retention	CUFF.233	chr12	+	chr12:69237045-69237520				chr12:69237044-69237045;chr12:69237520-69237521		66;145
N	coord_cassette	CUFF.213	chr12	-	chr12:49334972-49350767	chr12:49334972-49346895;chr12:49347058-49349880;chr12:49350134-49350767		chr12:49346896-49347057;chr12:49349881-49350133			26;212
N	alternative_first_exon	CUFF.209	chr12	+	chr12:26205536-26208211;chr12:26148064-26208211	chr12:26205930-26208211	chr12:26147970-26148063	chr12:26205426-26205929			80;179
N	intron_retention		chr12	-	chr12:56705199-56708634				chr12:56705198-56705199;chr12:56708634-56708635		116;275
K	alternative_donor	CUFF.235	chr12	-	chr12:77260042-77272742	chr12:77260042-77272717		chr12:77272718-77272742	chr12:77272742-77272743		464;372
N	cassette	CUFF.199	chr12	+	chr12:4654479-4655474;chr12:4653071-4655474	chr12:4654479-4654947,chr12:4653071-4654947;chr12:4654999-4655474		chr12:4654948-4654998			1157;212
N	intron_retention		chr12	+	chr12:53846760-53848509				chr12:53846759-53846760;chr12:53848509-53848510	chr12:53848510-53848653	34;261
K	intron_retention	CUFF.240	chr12	-	chr12:120220442-120221711				chr12:120220441-120220442;chr12:120221711-120221712		16;56
K	cassette	CUFF.233	chr12	+	chr12:69229765-69233053	chr12:69229765-69230451;chr12:69230530-69233053		chr12:69230452-69230529			245;549
K	intron_retention	CUFF.240	chr12	-	chr12:120151454-120152001				chr12:120151453-120151454;chr12:120152001-120152002		118;123
N	jcn_only_AA	CUFF.206,CUFF.220	chr12	+	chr12:53853188-53854114;chr12:53853188-53854798	chr12:53853188-53853583		chr12:53853584-53854114;chr12:53854115-53854798	chr12:53854114-53854115;chr12:53854798-53854799	chr12:53853056-53853187;chr12:53854799-53854970	992;110
N	jcn_only_AD	CUFF.200	chr12	-	chr12:113617811-113618785	chr12:113617811-113618733		chr12:113618734-113618785	chr12:113618785-113618786		32;68
K	alternative_acceptor	CUFF.238	chr12	-	chr12:113596915-113599074	chr12:113596918-113599074		chr12:113596915-113596917	chr12:113596914-113596915		74;936
K	cassette	CUFF.207	chr12	-	chr12:22646272-22659644	chr12:22646272-22655672;chr12:22655739-22659644		chr12:22655673-22655738			309;176
K	intron_retention	CUFF.234	chr12	+	chr12:72094659-72097756				chr12:72094658-72094659;chr12:72097756-72097757		501;297
K	intron_retention	CUFF.229	chr12	+	chr12:58018390-58018648				chr12:58018389-58018390;chr12:58018648-58018649		674;943
N	cassette	CUFF.233	chr12	+	chr12:69207409-69214104;chr12:69203073-69214104	chr12:69207409-69210591,chr12:69203073-69210591;chr12:69210726-69214104		chr12:69210592-69210725			245;292
N	jcn_only_AD		chr12	-	chr12:7086688-7087582	chr12:7086688-7086759		chr12:7086760-7087582	chr12:7087582-7087583		28;10
N	alternative_first_exon	CUFF.209	chr12	+	chr12:26205536-26208168,chr12:26174452-26208168;chr12:26205930-26208168;chr12:26164755-26208168	chr12:26148064-26208168	chr12:26205426-26205929;chr12:26164623-26164754	chr12:26147970-26148063			228;4
K	coord_cassette	CUFF.213	chr12	-	chr12:49334972-49351092	chr12:49334972-49349477;chr12:49349544-49349880;chr12:49350319-49351092		chr12:49349478-49349543;chr12:49349881-49350318			82;29
K	jcn_only_AD	CUFF.234	chr12	+	chr12:72094659-72097756	chr12:72094806-72097756		chr12:72094659-72094805	chr12:72094658-72094659		501;1178
K	jcn_only_AD	CUFF.243	chr12	-	chr12:133181171-133181291	chr12:133181171-133181286		chr12:133181287-133181291	chr12:133181291-133181292		21;432
N	cassette	CUFF.220	chr12	+	chr12:53848654-53849244	chr12:53848654-53849130;chr12:53849155-53849244		chr12:53849131-53849154		chr12:53848510-53848653;chr12:53849245-53849277	201;917
N	intron_retention		chr12	-	chr12:7086688-7087582				chr12:7086687-7086688;chr12:7087582-7087583		28;150
N	intron_retention		chr12	-	chr12:56578877-56579938				chr12:56578876-56578877;chr12:56579938-56579939		80;120
K	intron_retention	CUFF.240	chr12	-	chr12:120135644-120135780				chr12:120135643-120135644;chr12:120135780-120135781		511;53
K	intron_retention	CUFF.203	chr12	+	chr12:11709019-11709869				chr12:11709018-11709019;chr12:11709869-11709870		50;37
N	jcn_only_AD	CUFF.219	chr12	-	chr12:53471046-53473094	chr12:53471046-53471844		chr12:53471845-53473094	chr12:53473094-53473095		265;25
N	alternative_acceptor	CUFF.213	chr12	-	chr12:49350319-49351092;chr12:49349981-49351092;chr12:49332631-49351092	chr12:49335361-49351092		chr12:49332631-49335360;chr12:49335361-49349980;chr12:49349981-49350318	chr12:49332630-49332631;chr12:49335360-49335361;chr12:49349980-49349981		52;4
K	jcn_only_AA	CUFF.238	chr12	-	chr12:113596915-113599074	chr12:113596918-113599074		chr12:113596915-113596917	chr12:113596914-113596915		74;1886
N	jcn_only_AD	CUFF.225	chr12	-	chr12:56709027-56709604;chr12:56709027-56709500	chr12:56709027-56709690		chr12:56709501-56709604;chr12:56709605-56709690	chr12:56709604-56709605;chr12:56709690-56709691		596;109
K	cassette	CUFF.212	chr12	-	chr12:48393909-48398019	chr12:48393909-48394767;chr12:48394878-48398019		chr12:48394768-48394877			102;35
K	intron_retention	CUFF.223	chr12	-	chr12:56577715-56577958				chr12:56577714-56577715;chr12:56577958-56577959		581;103
N	alternative_acceptor	CUFF.209,CUFF.228	chr12	+	chr12:57857575-57858485	chr12:57857575-57857781		chr12:57857782-57858485	chr12:57858485-57858486		51;11
N	alternative_acceptor	CUFF.209	chr12	+	chr12:26205930-26208211	chr12:26205930-26208168		chr12:26208169-26208211	chr12:26208211-26208212		134;60
K	mutually_exclusive	CUFF.207	chr12	-	chr12:22666314-22672048,chr12:22672174-22676359	chr12:22666314-22670919,chr12:22671072-22676359	chr12:22672049-22672173	chr12:22670920-22671071			187;80
N	alternative_first_exon	CUFF.236	chr12	-	chr12:102796345-102809481;chr12:102796345-102811732	chr12:102796345-102813286	chr12:102809482-102809579;chr12:102811733-102811781	chr12:102813287-102813468			142;22
N	coord_cassette	CUFF.207	chr12	-	chr12:22646272-22666227	chr12:22646272-22659644;chr12:22659754-22665580;chr12:22665614-22666227		chr12:22659645-22659753;chr12:22665581-22665613			35;192
N	alternative_donor	CUFF.238	chr12	-	chr12:113599803-113600736	chr12:113599803-113600700		chr12:113600701-113600736	chr12:113600736-113600737		107;384
N	coord_cassette	CUFF.233	chr12	+	chr12:69203073-69229608	chr12:69203073-69218142;chr12:69218211-69218334;chr12:69218432-69229608		chr12:69218143-69218210;chr12:69218335-69218431			369;133
K	cassette	CUFF.233	chr12	+	chr12:69218211-69222550	chr12:69218211-69218334;chr12:69218432-69222550		chr12:69218335-69218431			95;330
N	jcn_only_AA	CUFF.198,CUFF.228	chr12	+	chr12:57853985-57858455	chr12:57853985-57857447					139;37
N	intron_retention	CUFF.240	chr12	-	chr12:120148426-120148853				chr12:120148425-120148426;chr12:120148853-120148854		31;77
K	cassette	CUFF.213	chr12	-	chr12:49334972-49351092	chr12:49334972-49349880;chr12:49349981-49351092		chr12:49349881-49349980			82;171
N	intron_retention		chr12	+	chr12:26205536-26208211				chr12:26205535-26205536;chr12:26208211-26208212		20;125
N	alternative_donor	CUFF.198	chr12	+	chr12:4430470-4440445	chr12:4433930-4440445		chr12:4430470-4433929	chr12:4430469-4430470		119;7
K	cassette	CUFF.210	chr12	+	chr12:27627847-27641392	chr12:27627847-27628514;chr12:27628665-27641392		chr12:27628515-27628664			129;291
K	alternative_acceptor	CUFF.205	chr12	+	chr12:13366756-13367504	chr12:13366756-13367467		chr12:13367468-13367504	chr12:13367504-13367505		794;243
K	cassette	CUFF.194	chr12	-	chr12:332401-333157	chr12:332401-332911;chr12:333012-333157		chr12:332912-333011			210;25
N	alternative_acceptor	CUFF.220	chr12	+	chr12:53853188-53854114;chr12:53853188-53853583	chr12:53853188-53854798		chr12:53853584-53854114;chr12:53854115-53854798	chr12:53854114-53854115;chr12:53854798-53854799	chr12:53853056-53853187;chr12:53854799-53854970	389;779
N	jcn_only_AD		chr12	-	chr12:56709027-56709690;chr12:56709027-56709500	chr12:56709027-56709604		chr12:56709501-56709604;chr12:56709605-56709690	chr12:56709604-56709605;chr12:56709690-56709691		146;559
N	intron_retention	CUFF.194	chr12	-	chr12:347177-347336				chr12:347176-347177;chr12:347336-347337		95;68
N	jcn_only_AD	CUFF.211,CUFF.225	chr12	-	chr12:56709027-56709604;chr12:56709027-56709690	chr12:56709027-56709500		chr12:56709501-56709604;chr12:56709605-56709690	chr12:56709604-56709605;chr12:56709690-56709691		668;37
N	coord_cassette	CUFF.212	chr12	-	chr12:48392215-48398019	chr12:48392215-48393701;chr12:48393909-48394767;chr12:48394878-48398019		chr12:48393702-48393908;chr12:48394768-48394877			30;33
N	jcn_only_AD	CUFF.195	chr12	+	chr12:1742072-1754959;chr12:1754228-1754959	chr12:1749143-1754959					431;128
N	jcn_only_AA	CUFF.209	chr12	+	chr12:13366510-13369377	chr12:13366510-13366614		chr12:13366615-13369377	chr12:13369377-13369378		66;1797
N	alternative_donor	CUFF.194	chr12	-	chr12:335681-336730	chr12:335681-335818		chr12:335819-336730	chr12:336730-336731		203;39
K	intron_retention	CUFF.211	chr12	-	chr12:48276558-48298737				chr12:48276557-48276558;chr12:48298737-48298738		448;10
N	coord_cassette	CUFF.233	chr12	+	chr12:69203073-69233053	chr12:69203073-69218142;chr12:69218211-69218334;chr12:69218432-69233053		chr12:69218143-69218210;chr12:69218335-69218431			66;59
K	alternative_donor	CUFF.243	chr12	-	chr12:133181171-133181291	chr12:133181171-133181286		chr12:133181287-133181291	chr12:133181291-133181292		21;213
N	alternative_donor	CUFF.229	chr12	+	chr12:58014837-58015045	chr12:58014876-58015045		chr12:58014837-58014875	chr12:58014836-58014837		26;66
K	coord_cassette	CUFF.220	chr12	+	chr12:53856352-53861004	chr12:53856352-53858543;chr12:53858637-53859715;chr12:53859758-53861004		chr12:53858544-53858636;chr12:53859716-53859757			124;306
K	jcn_only_AA	CUFF.195,CUFF.220	chr12	+	chr12:53861628-53862563	chr12:53861628-53862560		chr12:53862561-53862563	chr12:53862563-53862564		113;680
K	alternative_first_exon	CUFF.195	chr12	+	chr12:1726310-1740463,chr12:1684008-1740463,chr12:1640117-1740463,chr12:1738538-1740463;chr12:1639176-1740463	chr12:1739393-1740463	chr12:1639057-1639175	chr12:1739027-1739392			620;518
N	alternative_first_exon	CUFF.236	chr12	-	chr12:102796345-102809481;chr12:102796345-102813286	chr12:102796345-102811732	chr12:102809482-102809579;chr12:102813287-102813468	chr12:102811733-102811781			85;79
K	intron_retention	CUFF.200	chr12	-	chr12:7090345-7090971				chr12:7090344-7090345;chr12:7090971-7090972		166;181
K	intron_retention	CUFF.223	chr12	-	chr12:56578896-56579938				chr12:56578895-56578896;chr12:56579938-56579939		91;165
N	alternative_acceptor	CUFF.213	chr12	-	chr12:49335361-49351092;chr12:49350319-49351092;chr12:49332631-49351092	chr12:49349981-49351092		chr12:49332631-49335360;chr12:49335361-49349980;chr12:49349981-49350318	chr12:49332630-49332631;chr12:49335360-49335361;chr12:49349980-49349981		40;16
N	coord_cassette	CUFF.208	chr12	-	chr12:25702481-25801427	chr12:25702481-25710172;chr12:25710304-25735355;chr12:25735398-25801427		chr12:25710173-25710303;chr12:25735356-25735397			68;33
K	cassette	CUFF.223	chr12	-	chr12:56566489-56567479	chr12:56566489-56566720;chr12:56566814-56567479		chr12:56566721-56566813			501;132
K	alternative_acceptor	CUFF.218	chr12	-	chr12:52993087-52994810	chr12:52993194-52994810		chr12:52993087-52993193	chr12:52993086-52993087		31;65
K	alternative_first_exon	CUFF.221	chr12	+	chr12:54388801-54396213	chr12:54394511-54396213	chr12:54388679-54388800	chr12:54393881-54394510			110;114
K	alternative_acceptor	CUFF.207	chr12	-	chr12:22611490-22612425	chr12:22611520-22612425		chr12:22611490-22611519	chr12:22611489-22611490		196;88
K	cassette	CUFF.223	chr12	-	chr12:56557550-56558431	chr12:56557550-56558086;chr12:56558153-56558431		chr12:56558087-56558152			235;95
K	intron_retention		chr12	-	chr12:56708751-56708913				chr12:56708750-56708751;chr12:56708913-56708914		830;47
K	cassette	CUFF.213	chr12	-	chr12:49334972-49349880	chr12:49334972-49346895;chr12:49347058-49349880		chr12:49346896-49347057			93;288
N	coord_cassette	CUFF.233	chr12	+	chr12:69207409-69233053	chr12:69207409-69218142;chr12:69218211-69218334;chr12:69218432-69222550;chr12:69222712-69233053		chr12:69218143-69218210;chr12:69218335-69218431;chr12:69222551-69222711			70;98
N	jcn_only_AA		chr12	+	chr12:57854339-57858455	chr12:57854339-57857447					40;22
N	cassette	CUFF.199	chr12	+	chr12:4653078-4657257;chr12:4653071-4657257	chr12:4653078-4655474,chr12:4653071-4655474;chr12:4655585-4657257		chr12:4655475-4655584			1154;920
K	cassette	CUFF.204	chr12	+	chr12:12765122-12788710	chr12:12765122-12785422;chr12:12785526-12788710		chr12:12785423-12785525			6;38
N	cassette	CUFF.220	chr12	+	chr12:53856352-53859715;chr12:53856352-53861004	chr12:53856352-53858543;chr12:53858637-53859715,chr12:53858637-53861004		chr12:53858544-53858636			656;361
N	cassette	CUFF.208	chr12	-	chr12:25699489-25801427	chr12:25699489-25702259;chr12:25702481-25801427		chr12:25702260-25702480			16;203
K	alternative_first_exon	CUFF.198	chr12	+	chr12:4440484-4446204	chr12:4444818-4446204	chr12:4440446-4440483	chr12:4444656-4444817			64;68
K	alternative_acceptor	CUFF.239	chr12	-	chr12:113646065-113658801	chr12:113646315-113658801		chr12:113646065-113646314	chr12:113646064-113646065		44;58
N	jcn_only_AD	CUFF.199	chr12	+	chr12:4658003-4662148	chr12:4659714-4662148		chr12:4658003-4659713	chr12:4658002-4658003		1855;19
N	intron_retention		chr12	-	chr12:120156622-120158282				chr12:120156621-120156622;chr12:120158282-120158283		70;52
N	coord_cassette	CUFF.207	chr12	-	chr12:22643153-22659644	chr12:22643153-22646156;chr12:22646272-22655672;chr12:22655739-22659644		chr12:22646157-22646271;chr12:22655673-22655738			34;175
K	intron_retention	CUFF.220	chr12	+	chr12:53854928-53856276				chr12:53854927-53854928;chr12:53856276-53856277	chr12:53853584-53854927	366;109
K	alternative_first_exon	CUFF.200	chr12	-	chr12:7091066-7125577	chr12:7091066-7091836	chr12:7125578-7125909	chr12:7091837-7091995			260;557
K	intron_retention	CUFF.216	chr12	+	chr12:52407565-52407660				chr12:52407564-52407565;chr12:52407660-52407661		719;273
N	jcn_only_AA	CUFF.240	chr12	-	chr12:120156622-120158282	chr12:120156667-120158282		chr12:120156622-120156666	chr12:120156621-120156622		70;3
N	jcn_only_AA		chr12	+	chr12:26205536-26208211	chr12:26205536-26208168		chr12:26208169-26208211	chr12:26208211-26208212		20;54
N	coord_cassette	CUFF.233	chr12	+	chr12:69207409-69222550	chr12:69207409-69214104;chr12:69214155-69218142;chr12:69218211-69222550		chr12:69214105-69214154;chr12:69218143-69218210			21;94
N	intron_retention		chr12	-	chr12:22643153-22659644				chr12:22643152-22643153;chr12:22659644-22659645		34;18
N	jcn_only_AA	CUFF.209	chr12	+	chr12:26205930-26208211	chr12:26205930-26208168		chr12:26208169-26208211	chr12:26208211-26208212		134;62
N	cassette	CUFF.208	chr12	-	chr12:25702481-25706002	chr12:25702481-25705804;chr12:25705924-25706002		chr12:25705805-25705923			18;56
N	cassette	CUFF.225	chr12	-	chr12:56708751-56709604	chr12:56708751-56708913;chr12:56709027-56709604		chr12:56708914-56709026			33;583
N	cassette	CUFF.205	chr12	+	chr12:13349807-13366412	chr12:13349807-13364402;chr12:13364523-13366412		chr12:13364403-13364522			101;1373
N	coord_cassette	CUFF.207	chr12	-	chr12:22646272-22666227	chr12:22646272-22655672;chr12:22655739-22659644;chr12:22659754-22665580;chr12:22665614-22666227		chr12:22655673-22655738;chr12:22659645-22659753;chr12:22665581-22665613			35;168
N	alternative_last_exon	CUFF.209,CUFF.220	chr12	+	chr12:26148064-26208211,chr12:26148064-26208168	chr12:26148064-26173077	chr12:26208212-26208379	chr12:26173078-26173530			87;96
N	coord_cassette	CUFF.233	chr12	+	chr12:69207409-69222550	chr12:69207409-69218142;chr12:69218211-69218334;chr12:69218432-69222550		chr12:69218143-69218210;chr12:69218335-69218431			21;143
K	cassette	CUFF.199	chr12	+	chr12:4662314-4668022	chr12:4662314-4665518;chr12:4665669-4668022		chr12:4665519-4665668			29;899
N	coord_cassette	CUFF.233	chr12	+	chr12:69203073-69233053	chr12:69203073-69218142;chr12:69218211-69218334;chr12:69218432-69222550;chr12:69222712-69233053		chr12:69218143-69218210;chr12:69218335-69218431;chr12:69222551-69222711			66;107
N	alternative_donor	CUFF.219	chr12	-	chr12:53471046-53473094	chr12:53471046-53471844		chr12:53471845-53473094	chr12:53473094-53473095		265;3
N	jcn_only_AA	CUFF.220	chr12	+	chr12:53853188-53854114;chr12:53853188-53853583	chr12:53853188-53854798		chr12:53853584-53854114;chr12:53854115-53854798	chr12:53854114-53854115;chr12:53854798-53854799	chr12:53853056-53853187;chr12:53854799-53854970	323;779
N	cassette	CUFF.233	chr12	+	chr12:69207409-69222550;chr12:69214155-69222550	chr12:69207409-69218142,chr12:69214155-69218142;chr12:69218211-69222550		chr12:69218143-69218210			51;249
N	coord_cassette	CUFF.233	chr12	+	chr12:69214155-69222550	chr12:69214155-69218142;chr12:69218211-69218334;chr12:69218432-69222550		chr12:69218143-69218210;chr12:69218335-69218431			30;253
K	intron_retention	CUFF.240	chr12	-	chr12:120172163-120172964				chr12:120172162-120172163;chr12:120172964-120172965		64;35
K	jcn_only_AA	CUFF.207	chr12	-	chr12:22611490-22612425	chr12:22611520-22612425		chr12:22611490-22611519	chr12:22611489-22611490		196;118
K	alternative_donor	CUFF.229	chr12	+	chr12:58019102-58019192	chr12:58019114-58019192		chr12:58019102-58019113	chr12:58019101-58019102		1926;29
N	intron_retention		chr12	+	chr12:69236305-69237543				chr12:69236304-69236305;chr12:69237543-69237544		45;140
N	jcn_only_AD	CUFF.229	chr12	+	chr12:58014837-58015045	chr12:58014876-58015045		chr12:58014837-58014875	chr12:58014836-58014837		26;120
K	intron_retention	CUFF.219	chr12	-	chr12:53468569-53468878				chr12:53468568-53468569;chr12:53468878-53468879		225;77
K	intron_retention		chr12	-	chr12:7088742-7090165				chr12:7088741-7088742;chr12:7090165-7090166		313;53
N	jcn_only_AA		chr12	-	chr12:56705180-56708634;chr12:56705238-56708634;chr12:56705199-56708634	chr12:56706670-56708634					217;56
K	alternative_acceptor	CUFF.243	chr12	-	chr12:133181418-133182732	chr12:133181605-133182732		chr12:133181418-133181604	chr12:133181417-133181418		103;294
K	intron_retention	CUFF.207	chr12	-	chr12:22697114-22697253				chr12:22697113-22697114;chr12:22697253-22697254		219;71
K	intron_retention	CUFF.220	chr12	+	chr12:53849278-53849668				chr12:53849277-53849278;chr12:53849668-53849669	chr12:53849245-53849277;chr12:53849669-53849785	1963;28
K	cassette	CUFF.206	chr12	+	chr12:21229504-21279041	chr12:21229504-21272537;chr12:21272562-21279041		chr12:21272538-21272561			40;91
N	jcn_only_AA	CUFF.213	chr12	-	chr12:49335361-49351092;chr12:49350319-49351092;chr12:49332631-49351092	chr12:49349981-49351092		chr12:49332631-49335360;chr12:49335361-49349980;chr12:49349981-49350318	chr12:49332630-49332631;chr12:49335360-49335361;chr12:49349980-49349981		94;332
N	coord_cassette	CUFF.233	chr12	+	chr12:69207409-69229608	chr12:69207409-69218142;chr12:69218211-69218334;chr12:69218432-69222550;chr12:69222712-69229608		chr12:69218143-69218210;chr12:69218335-69218431;chr12:69222551-69222711			237;148
K	alternative_first_exon	CUFF.237	chr12	+	chr12:111809875-111840941	chr12:111834678-111840941	chr12:111809773-111809874	chr12:111834567-111834677			34;87
K	jcn_only_AA	CUFF.194	chr12	-	chr12:333283-333566	chr12:333296-333566		chr12:333283-333295	chr12:333282-333283		1040;226
K	jcn_only_AD	CUFF.239	chr12	-	chr12:113633695-113645242	chr12:113633695-113635345					30;15
N	alternative_first_exon	CUFF.209	chr12	+	chr12:26205536-26208168,chr12:26174452-26208168;chr12:26148064-26208168;chr12:26205930-26208168	chr12:26164755-26208168	chr12:26147970-26148063;chr12:26205426-26205929	chr12:26164623-26164754			199;33
K	intron_retention	CUFF.219	chr12	-	chr12:53459059-53459485				chr12:53459058-53459059;chr12:53459485-53459486		57;169
N	jcn_only_AA		chr12	-	chr12:56705180-56708634;chr12:56706670-56708634;chr12:56705199-56708634	chr12:56705238-56708634					204;69
K	intron_retention	CUFF.220	chr12	+	chr12:53861628-53862563				chr12:53861627-53861628;chr12:53862563-53862564		113;92
N	cassette	CUFF.207	chr12	-	chr12:22643153-22659644	chr12:22643153-22646156;chr12:22646272-22659644		chr12:22646157-22646271			34;386
K	coord_cassette	CUFF.213	chr12	-	chr12:49334972-49351092	chr12:49334972-49346895;chr12:49347058-49349880;chr12:49349981-49351092		chr12:49346896-49347057;chr12:49349881-49349980			82;235
N	intron_retention		chr12	+	chr12:69210619-69233541				chr12:69210618-69210619;chr12:69233541-69233542		282;644
N	jcn_only_AA	CUFF.208	chr12	-	chr12:25673010-25679702	chr12:25679153-25679702					52;131
N	jcn_only_AD		chr12	+	chr12:4653071-4654384	chr12:4653078-4654384		chr12:4653071-4653077	chr12:4653070-4653071		241;36
N	jcn_only_AD	CUFF.212	chr12	-	chr12:48381493-48383010	chr12:48381493-48382208		chr12:48382209-48383010	chr12:48383010-48383011		46;4
K	intron_retention	CUFF.205	chr12	+	chr12:13364475-13367969				chr12:13364474-13364475;chr12:13367969-13367970		1474;155
N	alternative_acceptor	CUFF.206	chr12	+	chr12:21220318-21229385	chr12:21220318-21228193		chr12:21228194-21229385	chr12:21229385-21229386		734;39
K	intron_retention	CUFF.243	chr12	-	chr12:133181418-133182732				chr12:133181417-133181418;chr12:133182732-133182733		103;204
N	jcn_only_AA	CUFF.220	chr12	+	chr12:53854928-53856276	chr12:53854928-53856264		chr12:53856265-53856276	chr12:53856276-53856277	chr12:53853584-53854927	366;580
N	coord_cassette	CUFF.233	chr12	+	chr12:69214155-69233053	chr12:69214155-69218142;chr12:69218211-69218334;chr12:69218432-69222550;chr12:69222712-69233053		chr12:69218143-69218210;chr12:69218335-69218431;chr12:69222551-69222711			68;172
N	intron_retention		chr12	-	chr12:56705180-56708634				chr12:56705179-56705180;chr12:56708634-56708635		32;290
N	jcn_only_AA	CUFF.213	chr12	-	chr12:49335361-49351092;chr12:49350319-49351092;chr12:49349981-49351092	chr12:49332631-49351092		chr12:49332631-49335360;chr12:49335361-49349980;chr12:49349981-49350318	chr12:49332630-49332631;chr12:49335360-49335361;chr12:49349980-49349981		399;27
N	jcn_only_AD	CUFF.209	chr12	+	chr12:26112082-26147969	chr12:26126821-26147969		chr12:26112082-26126820	chr12:26112081-26112082		110;48
N	intron_retention	CUFF.199	chr12	+	chr12:4662314-4665596				chr12:4662313-4662314;chr12:4665596-4665597		30;326
K	intron_retention	CUFF.216	chr12	+	chr12:52404992-52407470				chr12:52404991-52404992;chr12:52407470-52407471		341;75
K	alternative_first_exon	CUFF.207	chr12	-	chr12:22627826-22631246	chr12:22627826-22630195	chr12:22631247-22631411	chr12:22630196-22630294			302;62
K	intron_retention	CUFF.234	chr12	+	chr12:72080101-72080439				chr12:72080100-72080101;chr12:72080439-72080440		27;26
N	alternative_acceptor	CUFF.220	chr12	+	chr12:53853188-53854798;chr12:53853188-53853583	chr12:53853188-53854114		chr12:53853584-53854114;chr12:53854115-53854798	chr12:53854114-53854115;chr12:53854798-53854799	chr12:53853056-53853187;chr12:53854799-53854970	933;235
N	cassette	CUFF.238	chr12	-	chr12:113601080-113603448	chr12:113601080-113601871;chr12:113602091-113603448		chr12:113601872-113602090			18;396
K	cassette	CUFF.218	chr12	-	chr12:52992897-52994810	chr12:52992897-52993054;chr12:52993087-52994810		chr12:52993055-52993086			281;91
N	jcn_only_AA		chr12	+	chr12:26148064-26208211	chr12:26148064-26208168		chr12:26208169-26208211	chr12:26208211-26208212		90;6
K	intron_retention	CUFF.229	chr12	+	chr12:58019248-58019407				chr12:58019247-58019248;chr12:58019407-58019408		545;270
N	mutually_exclusive	CUFF.220	chr12	+	chr12:53856352-53859715,chr12:53859758-53861004	chr12:53856352-53858543,chr12:53858637-53861004	chr12:53859716-53859757	chr12:53858544-53858636			498;63
N	alternative_last_exon	CUFF.205	chr12	+	chr12:1742072-1754959	chr12:1742072-1748849	chr12:1754960-1756508	chr12:1748850-1749142			82;535
K	intron_retention		chr12	-	chr12:7086688-7086759				chr12:7086687-7086688;chr12:7086759-7086760		10;48
N	jcn_only_AA		chr12	-	chr12:351921-352844	chr12:351932-352844					143;84
N	alternative_donor	CUFF.199	chr12	+	chr12:4653071-4654947	chr12:4654479-4654947		chr12:4653071-4654478	chr12:4653070-4653071		121;15
N	cassette	CUFF.233	chr12	+	chr12:69207409-69233053;chr12:69214155-69233053;chr12:69207409-69229608;chr12:69218432-69233053;chr12:69218432-69229608	chr12:69207409-69222550,chr12:69218432-69222550,chr12:69214155-69222550;chr12:69222712-69233053,chr12:69222712-69229608		chr12:69222551-69222711			632;267
N	cassette	CUFF.211	chr12	-	chr12:48276558-48298737;chr12:48272899-48298737	chr12:48276558-48293619,chr12:48272899-48293619;chr12:48293742-48298737		chr12:48293620-48293741			635;78
K	intron_retention		chr12	-	chr12:56709027-56709604				chr12:56709026-56709027;chr12:56709604-56709605		559;9
N	cassette	CUFF.233	chr12	+	chr12:69207409-69233053;chr12:69222712-69233053;chr12:69203073-69233053;chr12:69218432-69233053	chr12:69203073-69229608,chr12:69222712-69229608,chr12:69207409-69229608,chr12:69218432-69229608;chr12:69229765-69233053		chr12:69229609-69229764			271;602
K	intron_retention	CUFF.223	chr12	-	chr12:56578721-56578813				chr12:56578720-56578721;chr12:56578813-56578814		480;65
N	alternative_donor		chr12	-	chr12:7086688-7087582	chr12:7086688-7086759		chr12:7086760-7087582	chr12:7087582-7087583		28;180
N	coord_cassette	CUFF.199	chr12	+	chr12:4653071-4657257	chr12:4653071-4654947;chr12:4654999-4655474;chr12:4655585-4657257		chr12:4654948-4654998;chr12:4655475-4655584			169;144
K	jcn_only_AA	CUFF.243	chr12	-	chr12:133181418-133182732	chr12:133181605-133182732		chr12:133181418-133181604	chr12:133181417-133181418		103;237
N	jcn_only_AD	CUFF.198	chr12	+	chr12:4430470-4440445	chr12:4433930-4440445		chr12:4430470-4433929	chr12:4430469-4430470		119;55
K	intron_retention	CUFF.215	chr12	+	chr12:50357440-50357874				chr12:50357439-50357440;chr12:50357874-50357875		189;49
K	intron_retention	CUFF.200	chr12	-	chr12:7086908-7087502				chr12:7086907-7086908;chr12:7087502-7087503		289;70
N	coord_cassette	CUFF.233	chr12	+	chr12:69207409-69214104	chr12:69207409-69209407;chr12:69209501-69210591;chr12:69210726-69214104		chr12:69209408-69209500;chr12:69210592-69210725			164;82
N	alternative_first_exon	CUFF.228	chr12	+	chr12:57853985-57857447	chr12:57854339-57857447	chr12:57853825-57853984	chr12:57854241-57854338			24;15
K	coord_cassette	CUFF.213	chr12	-	chr12:49334972-49351092	chr12:49334972-49349477;chr12:49349544-49349880;chr12:49349981-49351092		chr12:49349478-49349543;chr12:49349881-49349980			82;32
N	alternative_acceptor	CUFF.240	chr12	-	chr12:120156622-120158282	chr12:120156667-120158282		chr12:120156622-120156666	chr12:120156621-120156622		70;14
N	alternative_donor	CUFF.240	chr12	-	chr12:120221856-120222763	chr12:120221856-120221992		chr12:120221993-120222763	chr12:120222763-120222764		50;5
N	alternative_donor		chr12	-	chr12:56709027-56709690;chr12:56709027-56709500	chr12:56709027-56709604		chr12:56709501-56709604;chr12:56709605-56709690	chr12:56709604-56709605;chr12:56709690-56709691		125;353
N	jcn_only_AD	CUFF.199	chr12	+	chr12:4653071-4654947	chr12:4654479-4654947		chr12:4653071-4654478	chr12:4653070-4653071		121;140
K	alternative_last_exon	CUFF.209	chr12	+	chr12:26220647-26231965	chr12:26220647-26221629	chr12:26231966-26232921	chr12:26221630-26224588			25;109
K	alternative_acceptor	CUFF.194	chr12	-	chr12:333283-333566	chr12:333296-333566		chr12:333283-333295	chr12:333282-333283		1040;117
N	alternative_donor	CUFF.212	chr12	-	chr12:48375613-48375889	chr12:48375613-48375727		chr12:48375728-48375889	chr12:48375889-48375890		182;5
K	alternative_last_exon	CUFF.203	chr12	+	chr12:11712317-11743183	chr12:11712317-11716634	chr12:11743184-11743401	chr12:11716635-11717337			194;48
K	intron_retention	CUFF.218	chr12	-	chr12:52979620-52979746				chr12:52979619-52979620;chr12:52979746-52979747		282;180
K	intron_retention	CUFF.220	chr12	+	chr12:53861628-53862560				chr12:53861627-53861628;chr12:53862560-53862561		680;95
K	intron_retention	CUFF.194	chr12	-	chr12:333283-333566				chr12:333282-333283;chr12:333566-333567		1040;16
K	intron_retention	CUFF.200	chr12	-	chr12:7090794-7090971				chr12:7090793-7090794;chr12:7090971-7090972		613;276
K	alternative_acceptor	CUFF.229	chr12	+	chr12:58019248-58019407	chr12:58019248-58019364		chr12:58019365-58019407	chr12:58019407-58019408		545;834
K	cassette	CUFF.229	chr12	+	chr12:58018940-58019192	chr12:58018940-58019018;chr12:58019102-58019192		chr12:58019019-58019101			57;1576
N	jcn_only_AD	CUFF.240	chr12	-	chr12:120221856-120222763	chr12:120221856-120221992		chr12:120221993-120222763	chr12:120222763-120222764		50;6
K	cassette	CUFF.229	chr12	+	chr12:58018390-58018648	chr12:58018390-58018506;chr12:58018577-58018648		chr12:58018507-58018576			674;24
K	intron_retention	CUFF.235	chr12	-	chr12:77254194-77256955				chr12:77254193-77254194;chr12:77256955-77256956		700;7
N	alternative_first_exon		chr12	-	chr12:25673010-25679702	chr12:25673010-25679032	chr12:25679703-25679889	chr12:25679033-25679152			60;155
N	alternative_acceptor		chr12	-	chr12:347177-351779	chr12:347510-351779		chr12:347177-347509	chr12:347176-347177		174;111
N	alternative_first_exon	CUFF.209	chr12	+	chr12:26205536-26208168,chr12:26174452-26208168;chr12:26148064-26208168;chr12:26164755-26208168	chr12:26205930-26208168	chr12:26147970-26148063;chr12:26164623-26164754	chr12:26205426-26205929			149;83
N	alternative_first_exon	CUFF.228	chr12	+	chr12:57857875-57858455;chr12:57853985-57858455	chr12:57854339-57858455	chr12:57853825-57853984	chr12:57854241-57854338			126;27
N	intron_retention		chr12	+	chr12:26221857-26224588				chr12:26221856-26221857;chr12:26224588-26224589		26;108
K	alternative_donor	CUFF.229	chr12	+	chr12:58019471-58019780	chr12:58019536-58019780		chr12:58019471-58019535	chr12:58019470-58019471		38;1247
N	alternative_donor	CUFF.225	chr12	-	chr12:56709027-56709604;chr12:56709027-56709500	chr12:56709027-56709690		chr12:56709501-56709604;chr12:56709605-56709690	chr12:56709604-56709605;chr12:56709690-56709691		369;109
N	intron_retention		chr12	+	chr12:53854210-53854798				chr12:53854209-53854210;chr12:53854798-53854799	chr12:53853584-53854209;chr12:53854799-53854970	62;257
N	cassette	CUFF.213	chr12	-	chr12:49333563-49334730	chr12:49333563-49333779;chr12:49333891-49334730		chr12:49333780-49333890			20;232
K	intron_retention	CUFF.197	chr12	+	chr12:3432619-3434255				chr12:3432618-3432619;chr12:3434255-3434256		93;223
K	jcn_only_AD	CUFF.216	chr12	+	chr12:52404926-52407470	chr12:52404992-52407470		chr12:52404926-52404991	chr12:52404925-52404926		428;341
N	jcn_only_AA	CUFF.194	chr12	-	chr12:347177-369016	chr12:352980-369016		chr12:347177-352979	chr12:347176-347177		437;207
K	coord_cassette	CUFF.229	chr12	+	chr12:58017882-58018648	chr12:58017882-58018282;chr12:58018390-58018506;chr12:58018577-58018648		chr12:58018283-58018389;chr12:58018507-58018576			13;16
N	intron_retention		chr12	+	chr12:69218349-69233554				chr12:69218348-69218349;chr12:69233554-69233555		58;620
N	alternative_acceptor	CUFF.213	chr12	-	chr12:49335361-49351092;chr12:49349981-49351092;chr12:49332631-49351092	chr12:49350319-49351092		chr12:49332631-49335360;chr12:49335361-49349980;chr12:49349981-49350318	chr12:49332630-49332631;chr12:49335360-49335361;chr12:49349980-49349981		47;9
K	cassette	CUFF.208	chr12	-	chr12:25699489-25702259	chr12:25699489-25700158;chr12:25700286-25702259		chr12:25700159-25700285			260;22
N	coord_cassette	CUFF.207	chr12	-	chr12:22646272-22666227	chr12:22646272-22655672;chr12:22655739-22659644;chr12:22659754-22666227		chr12:22655673-22655738;chr12:22659645-22659753			35;148
N	jcn_only_AD	CUFF.212	chr12	-	chr12:48375613-48375889	chr12:48375613-48375727		chr12:48375728-48375889	chr12:48375889-48375890		182;3
N	jcn_only_AA		chr12	-	chr12:347177-351779	chr12:347510-351779		chr12:347177-347509	chr12:347176-347177		174;101
N	jcn_only_AA	CUFF.209,CUFF.228	chr12	+	chr12:57857575-57858485	chr12:57857575-57857781		chr12:57857782-57858485	chr12:57858485-57858486		51;24
K	intron_retention	CUFF.235	chr12	-	chr12:77257125-77259928				chr12:77257124-77257125;chr12:77259928-77259929		570;143
N	intron_retention		chr12	+	chr12:53861078-53862560				chr12:53861077-53861078;chr12:53862560-53862561		140;126
N	alternative_donor	CUFF.209	chr12	+	chr12:26112082-26147969	chr12:26126821-26147969		chr12:26112082-26126820	chr12:26112081-26112082		110;2
K	intron_retention	CUFF.238	chr12	-	chr12:113599188-113599697				chr12:113599187-113599188;chr12:113599697-113599698		86;1305
N	alternative_donor	CUFF.239,CUFF.240	chr12	-	chr12:120148426-120149982	chr12:120148426-120148853		chr12:120148854-120149982	chr12:120149982-120149983		140;4
N	jcn_only_AA	CUFF.206	chr12	+	chr12:21220318-21229385	chr12:21220318-21228193		chr12:21228194-21229385	chr12:21229385-21229386		734;48
K	intron_retention	CUFF.235	chr12	-	chr12:77254194-77256589				chr12:77254193-77254194;chr12:77256589-77256590		21;7
N	coord_cassette	CUFF.213	chr12	-	chr12:49334972-49350767	chr12:49334972-49349477;chr12:49349544-49349880;chr12:49350134-49350767		chr12:49349478-49349543;chr12:49349881-49350133			26;29
N	cassette	CUFF.220	chr12	+	chr12:53861078-53862560	chr12:53861078-53861588;chr12:53861628-53862560		chr12:53861589-53861627			140;668
K	intron_retention	CUFF.229	chr12	+	chr12:58019536-58019780				chr12:58019535-58019536;chr12:58019780-58019781		1904;64
K	alternative_donor	CUFF.214	chr12	-	chr12:50232799-50236636	chr12:50232799-50236168		chr12:50236169-50236636	chr12:50236636-50236637		263;232
N	jcn_only_AA	CUFF.219	chr12	-	chr12:53471046-53473094	chr12:53471956-53473094		chr12:53471046-53471955	chr12:53471045-53471046		265;31
K	mutually_exclusive	CUFF.211	chr12	-	chr12:48272899-48293619,chr12:48293742-48298737	chr12:48272899-48276476,chr12:48276558-48298737	chr12:48293620-48293741	chr12:48276477-48276557			12;324
N	coord_cassette	CUFF.211	chr12	-	chr12:48272899-48298737	chr12:48272899-48276476;chr12:48276558-48293619;chr12:48293742-48298737		chr12:48276477-48276557;chr12:48293620-48293741			186;57
K	intron_retention	CUFF.220	chr12	+	chr12:53849155-53849244				chr12:53849154-53849155;chr12:53849244-53849245	chr12:53849131-53849154;chr12:53849245-53849277	643;213
N	alternative_acceptor	CUFF.220	chr12	+	chr12:53854928-53856276	chr12:53854928-53856264		chr12:53856265-53856276	chr12:53856276-53856277	chr12:53853584-53854927	366;285
N	coord_cassette	CUFF.233	chr12	+	chr12:69207409-69229608	chr12:69207409-69218142;chr12:69218211-69218334;chr12:69218432-69229608		chr12:69218143-69218210;chr12:69218335-69218431			237;119
N	cassette	CUFF.207	chr12	-	chr12:22610096-22622642	chr12:22610096-22612425;chr12:22612477-22622642		chr12:22612426-22612476			76;179
N	alternative_donor	CUFF.199	chr12	+	chr12:4658003-4662148	chr12:4659714-4662148		chr12:4658003-4659713	chr12:4658002-4658003		1855;8
K	jcn_only_AA	CUFF.229	chr12	+	chr12:58019248-58019407	chr12:58019248-58019364		chr12:58019365-58019407	chr12:58019407-58019408		545;1333
N	alternative_donor	CUFF.211,CUFF.225	chr12	-	chr12:56709027-56709604;chr12:56709027-56709690	chr12:56709027-56709500		chr12:56709501-56709604;chr12:56709605-56709690	chr12:56709604-56709605;chr12:56709690-56709691		462;16
K	alternative_last_exon	CUFF.239	chr12	-	chr12:113633695-113645242	chr12:113638619-113645242	chr12:113633148-113633694	chr12:113637755-113638618			47;120
K	intron_retention	CUFF.200	chr12	-	chr12:7090345-7090755				chr12:7090344-7090345;chr12:7090755-7090756		161;239
N	jcn_only_AD		chr12	-	chr12:120158391-120287977	chr12:120158391-120159113					187;85
N	jcn_only_AD	CUFF.238	chr12	-	chr12:113599803-113600736	chr12:113599803-113600700		chr12:113600701-113600736	chr12:113600736-113600737		107;174
N	alternative_acceptor	CUFF.206,CUFF.220	chr12	+	chr12:53853188-53854114;chr12:53853188-53854798	chr12:53853188-53853583		chr12:53853584-53854114;chr12:53854115-53854798	chr12:53854114-53854115;chr12:53854798-53854799	chr12:53853056-53853187;chr12:53854799-53854970	1014;154
N	cassette	CUFF.220	chr12	+	chr12:53858637-53861004;chr12:53856352-53861004	chr12:53858637-53859715,chr12:53856352-53859715;chr12:53859758-53861004		chr12:53859716-53859757			201;838
K	coord_cassette	CUFF.213	chr12	-	chr12:49334972-49351092	chr12:49334972-49346895;chr12:49347058-49349880;chr12:49350319-49351092		chr12:49346896-49347057;chr12:49349881-49350318			82;202
N	cassette	CUFF.205	chr12	+	chr12:13349807-13366614	chr12:13349807-13366412;chr12:13366510-13366614		chr12:13366413-13366509			14;755
K	cassette	CUFF.235	chr12	-	chr12:77254194-77256955	chr12:77254194-77256589;chr12:77256740-77256955		chr12:77256590-77256739			700;21
N	jcn_only_AA	CUFF.213	chr12	-	chr12:49335361-49351092;chr12:49349981-49351092;chr12:49332631-49351092	chr12:49350319-49351092		chr12:49332631-49335360;chr12:49335361-49349980;chr12:49349981-49350318	chr12:49332630-49332631;chr12:49335360-49335361;chr12:49349980-49349981		374;52
K	alternative_acceptor	CUFF.240	chr12	-	chr12:120128257-120135463	chr12:120128260-120135463		chr12:120128257-120128259	chr12:120128256-120128257		291;134
K	intron_retention		chr12	+	chr12:69214155-69218142				chr12:69214154-69214155;chr12:69218142-69218143		459;18
K	jcn_only_AD	CUFF.214	chr12	-	chr12:50232799-50236636	chr12:50232799-50236168		chr12:50236169-50236636	chr12:50236636-50236637		263;194
N	cassette	CUFF.219	chr12	-	chr12:53467256-53468878	chr12:53467256-53468432;chr12:53468569-53468878		chr12:53468433-53468568			49;282
K	intron_retention	CUFF.216	chr12	+	chr12:52404926-52407470				chr12:52404925-52404926;chr12:52407470-52407471		428;126
N	alternative_acceptor	CUFF.209	chr12	+	chr12:13366510-13369377	chr12:13366510-13366614		chr12:13366615-13369377	chr12:13369377-13369378		66;295
K	intron_retention	CUFF.194	chr12	-	chr12:347177-369016				chr12:347176-347177;chr12:369016-369017		437;97
K	jcn_only_AD	CUFF.229	chr12	+	chr12:58019471-58019780	chr12:58019536-58019780		chr12:58019471-58019535	chr12:58019470-58019471		38;1904
N	alternative_last_exon		chr12	+	chr12:26164755-26208168	chr12:26164755-26173077	chr12:26208169-26208379	chr12:26173078-26173530			66;549
N	coord_cassette	CUFF.233	chr12	+	chr12:69214155-69233053	chr12:69214155-69222550;chr12:69222712-69229608;chr12:69229765-69233053		chr12:69222551-69222711;chr12:69229609-69229764			68;103
K	intron_retention	CUFF.229	chr12	+	chr12:58017882-58018282				chr12:58017881-58017882;chr12:58018282-58018283		84;932
N	intron_retention		chr12	-	chr12:56709027-56709690				chr12:56709026-56709027;chr12:56709690-56709691		109;173
N	alternative_acceptor	CUFF.223	chr12	-	chr12:56578877-56579938	chr12:56578896-56579938		chr12:56578877-56578895	chr12:56578876-56578877		80;149
K	alternative_first_exon	CUFF.205	chr12	+	chr12:13349807-13364402	chr12:13352468-13364402	chr12:13349562-13349806	chr12:13352370-13352467			2031;13
K	intron_retention	CUFF.223	chr12	-	chr12:56572319-56572593				chr12:56572318-56572319;chr12:56572593-56572594		148;248
K	intron_retention	CUFF.202	chr12	-	chr12:11461376-11461582				chr12:11461375-11461376;chr12:11461582-11461583		272;77
N	cassette	CUFF.233	chr12	+	chr12:69203073-69229608;chr12:69203073-69214104;chr12:69203073-69210591;chr12:69203073-69233053;chr12:69203073-69218142	chr12:69203073-69207333;chr12:69207409-69210591,chr12:69207409-69233053,chr12:69207409-69214104,chr12:69207409-69218142,chr12:69207409-69229608		chr12:69207334-69207408			622;881
N	coord_cassette	CUFF.233	chr12	+	chr12:69207409-69233053	chr12:69207409-69218142;chr12:69218211-69218334;chr12:69218432-69233053		chr12:69218143-69218210;chr12:69218335-69218431			70;45
K	alternative_donor	CUFF.216	chr12	+	chr12:52404926-52407470	chr12:52404992-52407470		chr12:52404926-52404991	chr12:52404925-52404926		428;195
N	alternative_donor	CUFF.212	chr12	-	chr12:48381493-48383010	chr12:48381493-48382208		chr12:48382209-48383010	chr12:48383010-48383011		46;1
K	alternative_last_exon	CUFF.220	chr12	+	chr12:53865592-53873189	chr12:53865592-53868652	chr12:53873190-53875044	chr12:53868653-53869905			688;373
N	jcn_only_AA	CUFF.223	chr12	-	chr12:56578877-56579938	chr12:56578896-56579938		chr12:56578877-56578895	chr12:56578876-56578877		80;91
N	jcn_only_AA	CUFF.213	chr12	-	chr12:49350319-49351092;chr12:49349981-49351092;chr12:49332631-49351092	chr12:49335361-49351092		chr12:49332631-49335360;chr12:49335361-49349980;chr12:49349981-49350318	chr12:49332630-49332631;chr12:49335360-49335361;chr12:49349980-49349981		411;15
K	intron_retention	CUFF.223	chr12	-	chr12:56578029-56578627				chr12:56578028-56578029;chr12:56578627-56578628		628;98
K	intron_retention	CUFF.229	chr12	+	chr12:58017697-58017785				chr12:58017696-58017697;chr12:58017785-58017786		87;938
N	jcn_only_AA	CUFF.194	chr12	-	chr12:332401-344255	chr12:336835-344255					31;170
K	cassette	CUFF.186	chr11	+	chr11:119057400-119058272	chr11:119057400-119057978;chr11:119058169-119058272		chr11:119057979-119058168			212;354
K	jcn_only_AD	CUFF.146	chr11	-	chr11:10821304-10821790	chr11:10821304-10821636		chr11:10821637-10821790	chr11:10821790-10821791		224;84
N	intron_retention		chr11	+	chr11:118403177-118404134				chr11:118403176-118403177;chr11:118404134-118404135		160;184
N	alternative_donor	CUFF.160	chr11	+	chr11:65480527-65480818	chr11:65480530-65480818		chr11:65480527-65480529	chr11:65480526-65480527		183;1159
N	jcn_only_AD	CUFF.174	chr11	-	chr11:102960048-102962412;chr11:102960048-102962244	chr11:102960048-102962515		chr11:102962245-102962412;chr11:102962413-102962515	chr11:102962412-102962413;chr11:102962515-102962516		129;77
K	intron_retention	CUFF.136	chr11	-	chr11:2906697-2906863				chr11:2906696-2906697;chr11:2906863-2906864		87;188
K	intron_retention	CUFF.142	chr11	-	chr11:6637735-6637891				chr11:6637734-6637735;chr11:6637891-6637892		220;199
N	alternative_acceptor	CUFF.157	chr11	+	chr11:63998413-63999342	chr11:63998413-63998503		chr11:63998504-63999342	chr11:63999342-63999343		133;430
K	intron_retention	CUFF.146	chr11	-	chr11:10822635-10823595				chr11:10822634-10822635;chr11:10823595-10823596		76;80
N	intron_retention		chr11	-	chr11:10821716-10821790				chr11:10821715-10821716;chr11:10821790-10821791		31;157
N	jcn_only_AA	CUFF.134	chr11	-	chr11:2188716-2189095	chr11:2188747-2189095		chr11:2188716-2188746	chr11:2188715-2188716		528;41
K	mutually_exclusive	CUFF.137	chr11	+	chr11:3239790-3241456,chr11:3241590-3242799	chr11:3239790-3240929,chr11:3241019-3242799	chr11:3241457-3241589	chr11:3240930-3241018			45;23
K	alternative_first_exon	CUFF.179	chr11	+	chr11:117072658-117073717;chr11:117070149-117073717,chr11:117070546-117073717	chr11:117071059-117073717	chr11:117070037-117070148	chr11:117070960-117071058			171;22
K	jcn_only_AD	CUFF.132	chr11	+	chr11:827319-828259	chr11:827460-828259		chr11:827319-827459	chr11:827318-827319		339;68
N	jcn_only_AD	CUFF.157	chr11	+	chr11:63998413-63999342	chr11:63998620-63999342		chr11:63998413-63998619	chr11:63998412-63998413		133;29
K	jcn_only_AD	CUFF.179	chr11	+	chr11:117070149-117073717	chr11:117070546-117073717		chr11:117070149-117070545	chr11:117070148-117070149		22;199
K	intron_retention	CUFF.157	chr11	+	chr11:64000338-64001365				chr11:64000337-64000338;chr11:64001365-64001366		426;647
N	jcn_only_AD	CUFF.140	chr11	-	chr11:10819429-10823840	chr11:10819429-10820538					110;518
K	intron_retention	CUFF.175	chr11	-	chr11:104915386-104916017				chr11:104915385-104915386;chr11:104916017-104916018		205;23
N	alternative_donor	CUFF.146,CUFF.171	chr11	-	chr11:94705358-94706452;chr11:94705358-94706661	chr11:94705358-94706436		chr11:94706437-94706452;chr11:94706453-94706661	chr11:94706452-94706453;chr11:94706661-94706662		391;16
K	alternative_first_exon	CUFF.175	chr11	-	chr11:104915386-104915917;chr11:104915386-104972134	chr11:104915386-104916017	chr11:104915918-104916016;chr11:104972135-104972250	chr11:104916018-104916042			31;181
N	alternative_acceptor	CUFF.175	chr11	-	chr11:104915386-104916017	chr11:104915659-104916017		chr11:104915386-104915658	chr11:104915385-104915386		205;30
K	jcn_only_AA	CUFF.157	chr11	+	chr11:63999437-63999981	chr11:63999437-63999901		chr11:63999902-63999981	chr11:63999981-63999982		355;276
K	alternative_first_exon	CUFF.140	chr11	-	chr11:5701469-5705215;chr11:5701469-5958630	chr11:5701469-5706245,chr11:5701469-5706097	chr11:5958631-5958735	chr11:5706246-5706624			64;66
N	alternative_acceptor		chr11	-	chr11:8496614-8502080;chr11:8498831-8502080	chr11:8496364-8502080		chr11:8496364-8496613;chr11:8496614-8498830	chr11:8496363-8496364;chr11:8496613-8496614		313;15
N	intron_retention		chr11	+	chr11:3427946-3428851				chr11:3427945-3427946;chr11:3428851-3428852		18;122
N	intron_retention		chr11	-	chr11:8949230-8950923				chr11:8949229-8949230;chr11:8950923-8950924		43;292
K	intron_retention	CUFF.182	chr11	-	chr11:118923542-118924832				chr11:118923541-118923542;chr11:118924832-118924833		118;29
K	jcn_only_AD	CUFF.153	chr11	+	chr11:61588941-61593754	chr11:61593610-61593754					1334;125
N	intron_retention		chr11	+	chr11:63999437-64001365				chr11:63999436-63999437;chr11:64001365-64001366		72;393
N	cassette	CUFF.143	chr11	-	chr11:8496614-8615290	chr11:8496614-8602360;chr11:8602508-8615290		chr11:8602361-8602507			27;393
K	intron_retention	CUFF.132	chr11	+	chr11:828964-829359				chr11:828963-828964;chr11:829359-829360		199;272
N	jcn_only_AD	CUFF.171	chr11	-	chr11:94705358-94706436;chr11:94705358-94706661	chr11:94705358-94706452		chr11:94706437-94706452;chr11:94706453-94706661	chr11:94706452-94706453;chr11:94706661-94706662		175;321
N	mutually_exclusive	CUFF.130	chr11	-	chr11:407958-408694,chr11:408894-414822	chr11:407958-408072,chr11:408207-414822	chr11:408695-408893	chr11:408073-408206			70;265
K	cassette	CUFF.130	chr11	-	chr11:407958-408694	chr11:407958-408072;chr11:408207-408694		chr11:408073-408206			74;683
K	jcn_only_AA	CUFF.149,CUFF.153	chr11	+	chr11:61584169-61605249	chr11:61584169-61588852					196;774
K	intron_retention	CUFF.160	chr11	+	chr11:65482382-65484137				chr11:65482381-65482382;chr11:65484137-65484138		1748;89
N	intron_retention		chr11	-	chr11:6632684-6633294				chr11:6632683-6632684;chr11:6633294-6633295		222;119
N	jcn_only_AD	CUFF.188	chr11	-	chr11:119291640-119292320;chr11:119291640-119293822	chr11:119291640-119295607		chr11:119292321-119293822;chr11:119293823-119295607	chr11:119293822-119293823;chr11:119295607-119295608		4109;102
N	intron_retention		chr11	+	chr11:118403177-118403804				chr11:118403176-118403177;chr11:118403804-118403805		527;952
N	jcn_only_AA		chr11	-	chr11:8496614-8498796	chr11:8498299-8498796		chr11:8496614-8498298	chr11:8496613-8496614		43;32
K	intron_retention	CUFF.180	chr11	+	chr11:118403923-118404571				chr11:118403922-118403923;chr11:118404571-118404572		625;284
K	alternative_last_exon	CUFF.167	chr11	+	chr11:74108951-74195221	chr11:74108951-74139377	chr11:74195222-74195293	chr11:74139378-74139610			12;71
N	jcn_only_AA	CUFF.190	chr11	-	chr11:124767529-124767621;chr11:124767158-124767621	chr11:124766952-124767621		chr11:124766952-124767157;chr11:124767158-124767528	chr11:124766951-124766952;chr11:124767157-124767158		463;13
N	alternative_acceptor	CUFF.188	chr11	-	chr11:119291089-119291578;chr11:119291046-119291578;chr11:119291159-119291578	chr11:119291097-119291578		chr11:119291046-119291088;chr11:119291089-119291096;chr11:119291097-119291158	chr11:119291045-119291046;chr11:119291088-119291089;chr11:119291096-119291097		295;1337
K	intron_retention	CUFF.182	chr11	-	chr11:118923142-118923348				chr11:118923141-118923142;chr11:118923348-118923349		132;38
K	alternative_first_exon	CUFF.130,CUFF.175	chr11	-	chr11:104915386-104916017;chr11:104915386-104915917	chr11:104915386-104972134	chr11:104916018-104916042;chr11:104915918-104916016	chr11:104972135-104972250			192;20
K	alternative_donor	CUFF.140	chr11	-	chr11:5685404-5686885	chr11:5685404-5686398		chr11:5686399-5686885	chr11:5686885-5686886		107;165
K	intron_retention	CUFF.155	chr11	-	chr11:62365863-62365993				chr11:62365862-62365863;chr11:62365993-62365994		266;29
K	intron_retention	CUFF.131	chr11	-	chr11:556376-556491				chr11:556375-556376;chr11:556491-556492		12;49
K	cassette	CUFF.175	chr11	-	chr11:104912447-104915118	chr11:104912447-104914209;chr11:104914273-104915118		chr11:104914210-104914272			183;104
N	alternative_donor		chr11	-	chr11:10828929-10829080;chr11:10828929-10829720;chr11:10828929-10829291	chr11:10828929-10829095		chr11:10829081-10829095;chr11:10829096-10829291;chr11:10829292-10829720	chr11:10829095-10829096;chr11:10829291-10829292;chr11:10829720-10829721		190;18
K	intron_retention	CUFF.164	chr11	+	chr11:67788996-67795518				chr11:67788995-67788996;chr11:67795518-67795519		688;412
N	alternative_acceptor	CUFF.186	chr11	+	chr11:119056220-119056633;chr11:119056220-119056557	chr11:119056220-119056630		chr11:119056558-119056630;chr11:119056631-119056633	chr11:119056630-119056631;chr11:119056633-119056634		561;70
N	jcn_only_AA	CUFF.180	chr11	+	chr11:118405071-118405221;chr11:118405071-118406222	chr11:118405071-118416833		chr11:118405222-118406222;chr11:118406223-118416833	chr11:118406222-118406223;chr11:118416833-118416834		882;87
K	intron_retention	CUFF.179	chr11	+	chr11:117070149-117073717				chr11:117070148-117070149;chr11:117073717-117073718		22;117
N	jcn_only_AD		chr11	-	chr11:8496364-8502080;chr11:8496364-8615290	chr11:8496364-8588797		chr11:8502081-8588797;chr11:8588798-8615290	chr11:8588797-8588798;chr11:8615290-8615291		110;23
K	intron_retention	CUFF.179	chr11	+	chr11:117074601-117074930				chr11:117074600-117074601;chr11:117074930-117074931		371;26
N	cassette	CUFF.149	chr11	+	chr11:36459027-36472758	chr11:36459027-36467849;chr11:36467991-36472758		chr11:36467850-36467990			17;204
K	alternative_acceptor	CUFF.152	chr11	-	chr11:61514596-61514822	chr11:61514614-61514822		chr11:61514596-61514613	chr11:61514595-61514596		47;11
K	mutually_exclusive	CUFF.177	chr11	+	chr11:107904638-107920616,chr11:107920794-107923386	chr11:107904638-107916996,chr11:107917097-107923386	chr11:107920617-107920793	chr11:107916997-107917096			57;212
N	intron_retention		chr11	+	chr11:119056338-119056557				chr11:119056337-119056338;chr11:119056557-119056558		14;14
N	alternative_donor	CUFF.153	chr11	+	chr11:61594904-61605249;chr11:61583899-61605249;chr11:61596070-61605249	chr11:61584169-61605249		chr11:61583899-61584168;chr11:61584169-61594903;chr11:61594904-61596069	chr11:61583898-61583899;chr11:61584168-61584169;chr11:61594903-61594904		106;368
K	intron_retention	CUFF.182	chr11	-	chr11:118919083-118919187				chr11:118919082-118919083;chr11:118919187-118919188		214;135
K	alternative_last_exon	CUFF.174	chr11	-	chr11:102933144-102936997	chr11:102935107-102936997	chr11:102932706-102933143	chr11:102934992-102935106			238;250
N	cassette	CUFF.182	chr11	-	chr11:118926880-118927785;chr11:118926880-118927730	chr11:118926880-118926990;chr11:118927130-118927730,chr11:118927130-118927785		chr11:118926991-118927129			327;940
N	jcn_only_AD	CUFF.133,CUFF.174	chr11	-	chr11:102960048-102962412;chr11:102960048-102962515	chr11:102960048-102962244		chr11:102962245-102962412;chr11:102962413-102962515	chr11:102962412-102962413;chr11:102962515-102962516		157;48
N	alternative_first_exon	CUFF.132	chr11	+	chr11:827712-828259;chr11:827319-828259,chr11:827460-828259	chr11:826267-828259	chr11:827558-827711;chr11:827206-827318	chr11:826053-826266			297;42
K	intron_retention	CUFF.155	chr11	-	chr11:62363810-62363929				chr11:62363809-62363810;chr11:62363929-62363930		84;16
N	alternative_donor		chr11	+	chr11:118402242-118402489;chr11:118401950-118402489	chr11:118402317-118402489		chr11:118401950-118402241;chr11:118402242-118402316	chr11:118401949-118401950;chr11:118402241-118402242		1226;124
N	alternative_first_exon	CUFF.157	chr11	+	chr11:63999437-64001365	chr11:64000338-64001365	chr11:63999007-63999436	chr11:64000176-64000337			75;889
N	alternative_first_exon	CUFF.132	chr11	+	chr11:826267-828259;chr11:827319-828259,chr11:827460-828259	chr11:827712-828259	chr11:826053-826266;chr11:827206-827318	chr11:827558-827711			309;30
K	intron_retention	CUFF.178	chr11	+	chr11:115268247-115268300				chr11:115268246-115268247;chr11:115268300-115268301		149;84
K	intron_retention	ENSG00000134817.9	chr11	-	chr11:57001333-57003265				chr11:57001332-57001333;chr11:57003265-57003266		315;11
N	jcn_only_AA	CUFF.131	chr11	-	chr11:558767-558855	chr11:558785-558855		chr11:558767-558784	chr11:558766-558767		52;36
K	intron_retention		chr11	+	chr11:118402587-118402864				chr11:118402586-118402587;chr11:118402864-118402865		1429;294
N	alternative_last_exon	CUFF.187	chr11	-	chr11:119230945-119252182	chr11:119244232-119252182	chr11:119230894-119230944	chr11:119243545-119244231			12;19
N	alternative_acceptor	CUFF.164	chr11	+	chr11:67790230-67793476	chr11:67790230-67791675		chr11:67791676-67793476	chr11:67793476-67793477		534;17
N	cassette	CUFF.164	chr11	+	chr11:67782930-67786241	chr11:67782930-67785996;chr11:67786107-67786241		chr11:67785997-67786106			39;1159
N	intron_retention		chr11	-	chr11:5687312-5699433				chr11:5687311-5687312;chr11:5699433-5699434		233;40
K	jcn_only_AA	CUFF.156	chr11	+	chr11:63669803-63670075	chr11:63669803-63670072		chr11:63670073-63670075	chr11:63670075-63670076		305;129
N	jcn_only_AA		chr11	+	chr11:118404845-118404983	chr11:118404845-118404980		chr11:118404981-118404983	chr11:118404983-118404984		220;736
K	intron_retention	CUFF.132	chr11	+	chr11:830133-830249				chr11:830132-830133;chr11:830249-830250		368;7
K	intron_retention	CUFF.168	chr11	+	chr11:74624828-74630577				chr11:74624827-74624828;chr11:74630577-74630578		22;57
N	jcn_only_AD	CUFF.149	chr11	+	chr11:36397709-36440804	chr11:36424929-36440804		chr11:36397709-36424928	chr11:36397708-36397709		11;395
K	intron_retention	CUFF.186	chr11	+	chr11:119059261-119059348				chr11:119059260-119059261;chr11:119059348-119059349		274;18
N	jcn_only_AA	CUFF.190	chr11	-	chr11:124766952-124767621;chr11:124767158-124767621	chr11:124767529-124767621		chr11:124766952-124767157;chr11:124767158-124767528	chr11:124766951-124766952;chr11:124767157-124767158		363;113
K	jcn_only_AA	CUFF.149,CUFF.157	chr11	+	chr11:64000087-64000175	chr11:64000087-64000172		chr11:64000173-64000175	chr11:64000175-64000176		1648;118
K	alternative_donor	CUFF.132	chr11	+	chr11:828964-829359	chr11:829184-829359		chr11:828964-829183	chr11:828963-828964		199;165
N	alternative_donor	CUFF.160	chr11	+	chr11:65486221-65486343	chr11:65486247-65486343		chr11:65486221-65486246	chr11:65486220-65486221		2144;35
K	intron_retention	CUFF.160	chr11	+	chr11:65482215-65482291				chr11:65482214-65482215;chr11:65482291-65482292		1777;50
K	intron_retention	CUFF.186	chr11	+	chr11:119056875-119057187				chr11:119056874-119056875;chr11:119057187-119057188		286;233
N	jcn_only_AD	CUFF.146	chr11	-	chr11:10828929-10829080;chr11:10828929-10829720;chr11:10828929-10829095	chr11:10828929-10829291		chr11:10829081-10829095;chr11:10829096-10829291;chr11:10829292-10829720	chr11:10829095-10829096;chr11:10829291-10829292;chr11:10829720-10829721		64;21
K	jcn_only_AA	CUFF.145	chr11	-	chr11:8950976-8953688	chr11:8951081-8953688		chr11:8950976-8951080	chr11:8950975-8950976		379;1077
N	cassette	CUFF.173	chr11	+	chr11:101852696-101863508	chr11:101852696-101857562;chr11:101857773-101863508		chr11:101857563-101857772			64;473
K	jcn_only_AA	CUFF.132,CUFF.157	chr11	+	chr11:829541-829985	chr11:829541-829967		chr11:829968-829985	chr11:829985-829986		247;124
K	intron_retention	CUFF.171	chr11	-	chr11:94704230-94704538				chr11:94704229-94704230;chr11:94704538-94704539		120;286
K	intron_retention	CUFF.161	chr11	-	chr11:67766776-67766988				chr11:67766775-67766776;chr11:67766988-67766989		639;663
N	cassette	CUFF.131	chr11	-	chr11:558980-560682	chr11:558980-559346;chr11:559499-560682		chr11:559347-559498			11;20
K	intron_retention		chr11	-	chr11:406060-406141				chr11:406059-406060;chr11:406141-406142		280;114
N	alternative_donor	CUFF.188	chr11	-	chr11:119291640-119292320;chr11:119291640-119293822	chr11:119291640-119295607		chr11:119292321-119293822;chr11:119293823-119295607	chr11:119293822-119293823;chr11:119295607-119295608		476;102
K	alternative_first_exon	CUFF.165	chr11	+	chr11:67818400-67820446	chr11:67819909-67820446	chr11:67818207-67818399	chr11:67819519-67819908			175;171
N	jcn_only_AA	CUFF.164	chr11	+	chr11:67786363-67786638	chr11:67786363-67786534		chr11:67786535-67786638	chr11:67786638-67786639		1196;35
N	jcn_only_AD		chr11	-	chr11:102960048-102962515;chr11:102960048-102962244	chr11:102960048-102962412		chr11:102962245-102962412;chr11:102962413-102962515	chr11:102962412-102962413;chr11:102962515-102962516		126;80
N	alternative_acceptor	CUFF.140	chr11	-	chr11:5687504-5699433	chr11:5691178-5699433		chr11:5687504-5691177	chr11:5687503-5687504		15;2
N	intron_retention		chr11	-	chr11:8496364-8502080				chr11:8496363-8496364;chr11:8502080-8502081		15;319
N	jcn_only_AD	CUFF.134,CUFF.182	chr11	-	chr11:118927130-118927785	chr11:118927130-118927730		chr11:118927731-118927785	chr11:118927785-118927786		422;5
K	intron_retention	CUFF.186	chr11	+	chr11:119058410-119058648				chr11:119058409-119058410;chr11:119058648-119058649		366;51
K	intron_retention	CUFF.132	chr11	+	chr11:829184-829359				chr11:829183-829184;chr11:829359-829360		57;190
K	cassette	CUFF.143	chr11	-	chr11:8414258-8457040	chr11:8414258-8435041;chr11:8435240-8457040		chr11:8435042-8435239			104;244
N	jcn_only_AD	CUFF.186	chr11	+	chr11:119058368-119058648	chr11:119058410-119058648		chr11:119058368-119058409	chr11:119058367-119058368		45;366
K	intron_retention	CUFF.182	chr11	-	chr11:118926052-118926204				chr11:118926051-118926052;chr11:118926204-118926205		2596;27
K	alternative_first_exon	CUFF.190	chr11	-	chr11:124767158-124767483;chr11:124767158-124768293	chr11:124767158-124767621	chr11:124768294-124768494	chr11:124767622-124768177			157;233
N	alternative_acceptor	CUFF.186	chr11	+	chr11:119056220-119056557;chr11:119056220-119056630	chr11:119056220-119056633		chr11:119056558-119056630;chr11:119056631-119056633	chr11:119056630-119056631;chr11:119056633-119056634		96;535
K	intron_retention	CUFF.141	chr11	-	chr11:6621496-6621715				chr11:6621495-6621496;chr11:6621715-6621716		572;62
K	jcn_only_AA	CUFF.174	chr11	-	chr11:102937297-102953984	chr11:102953569-102953984					213;294
N	jcn_only_AD	CUFF.146,CUFF.171	chr11	-	chr11:94705358-94706452;chr11:94705358-94706661	chr11:94705358-94706436		chr11:94706437-94706452;chr11:94706453-94706661	chr11:94706452-94706453;chr11:94706661-94706662		469;27
N	alternative_donor	CUFF.149	chr11	+	chr11:36383732-36415395;chr11:36398255-36415395	chr11:36322621-36415395		chr11:36322621-36383731;chr11:36383732-36398254	chr11:36322620-36322621;chr11:36383731-36383732		5;30
K	intron_retention	CUFF.161	chr11	-	chr11:67766846-67766988				chr11:67766845-67766846;chr11:67766988-67766989		32;648
N	cassette	CUFF.146	chr11	-	chr11:10828929-10830251;chr11:10828433-10830251	chr11:10828433-10829823,chr11:10828929-10829823;chr11:10830056-10830251		chr11:10829824-10830055			415;69
N	intron_retention		chr11	-	chr11:10827558-10828801				chr11:10827557-10827558;chr11:10828801-10828802		23;145
K	intron_retention	CUFF.188	chr11	-	chr11:119291097-119291578				chr11:119291096-119291097;chr11:119291578-119291579		2213;475
N	jcn_only_AA		chr11	+	chr11:827712-828259	chr11:827712-828229		chr11:828230-828259	chr11:828259-828260		23;87
N	cassette	CUFF.134	chr11	-	chr11:2187780-2188664	chr11:2187780-2187862;chr11:2187999-2188664		chr11:2187863-2187998			162;286
N	alternative_donor		chr11	+	chr11:118402242-118402489;chr11:118402317-118402489	chr11:118401950-118402489		chr11:118401950-118402241;chr11:118402242-118402316	chr11:118401949-118401950;chr11:118402241-118402242		201;1149
K	alternative_first_exon	CUFF.168	chr11	+	chr11:74630071-74630577;chr11:74624828-74630577	chr11:74622471-74630577	chr11:74629826-74630070;chr11:74624740-74624827	chr11:74622307-74622470			81;62
K	intron_retention	CUFF.188	chr11	-	chr11:119290231-119290760				chr11:119290230-119290231;chr11:119290760-119290761		581;48
K	intron_retention	CUFF.160	chr11	+	chr11:65484454-65486060				chr11:65484453-65484454;chr11:65486060-65486061		1848;76
N	jcn_only_AA		chr11	+	chr11:65481320-65482130	chr11:65481320-65481965		chr11:65481966-65482130	chr11:65482130-65482131		70;1911
N	intron_retention		chr11	-	chr11:102960039-102962412				chr11:102960038-102960039;chr11:102962412-102962413		47;68
K	alternative_acceptor	CUFF.190	chr11	-	chr11:124766952-124768293	chr11:124767158-124768293		chr11:124766952-124767157	chr11:124766951-124766952		86;558
K	cassette	CUFF.132	chr11	+	chr11:830714-831223	chr11:830714-830865;chr11:831033-831223		chr11:830866-831032			237;125
N	jcn_only_AD	CUFF.160	chr11	+	chr11:65486221-65486343	chr11:65486247-65486343		chr11:65486221-65486246	chr11:65486220-65486221		2144;69
N	intron_retention		chr11	-	chr11:119291046-119291578				chr11:119291045-119291046;chr11:119291578-119291579		34;919
K	intron_retention		chr11	-	chr11:118919599-118919729				chr11:118919598-118919599;chr11:118919729-118919730		113;9
K	cassette	CUFF.174	chr11	-	chr11:102937297-102953476	chr11:102937297-102950637;chr11:102950727-102953476		chr11:102950638-102950726			448;462
N	intron_retention		chr11	+	chr11:63670605-63671569				chr11:63670604-63670605;chr11:63671569-63671570		60;93
K	intron_retention	CUFF.160	chr11	+	chr11:65479917-65480236				chr11:65479916-65479917;chr11:65480236-65480237		1845;167
N	jcn_only_AA	CUFF.190	chr11	-	chr11:124766952-124767621;chr11:124767529-124767621	chr11:124767158-124767621		chr11:124766952-124767157;chr11:124767158-124767528	chr11:124766951-124766952;chr11:124767157-124767158		126;350
N	alternative_donor	CUFF.153	chr11	+	chr11:61594904-61605249;chr11:61584169-61605249;chr11:61596070-61605249	chr11:61583899-61605249		chr11:61583899-61584168;chr11:61584169-61594903;chr11:61594904-61596069	chr11:61583898-61583899;chr11:61584168-61584169;chr11:61594903-61594904		436;38
K	cassette	CUFF.160	chr11	+	chr11:65480530-65481063	chr11:65480530-65480818;chr11:65480975-65481063		chr11:65480819-65480974			445;2076
N	jcn_only_AA	CUFF.146	chr11	-	chr11:10821157-10821636	chr11:10821304-10821636		chr11:10821157-10821303	chr11:10821156-10821157		52;84
N	alternative_first_exon	CUFF.132	chr11	+	chr11:827712-828229;chr11:826267-828229	chr11:827460-828229	chr11:827558-827711;chr11:826053-826266	chr11:827206-827459			210;36
K	intron_retention	CUFF.146	chr11	-	chr11:10823322-10823595				chr11:10823321-10823322;chr11:10823595-10823596		41;61
N	jcn_only_AA	CUFF.188	chr11	-	chr11:119291089-119291578;chr11:119291097-119291578;chr11:119291046-119291578	chr11:119291159-119291578		chr11:119291046-119291088;chr11:119291089-119291096;chr11:119291097-119291158	chr11:119291045-119291046;chr11:119291088-119291089;chr11:119291096-119291097		2280;185
N	alternative_acceptor	CUFF.160	chr11	+	chr11:65479751-65479849	chr11:65479751-65479820		chr11:65479821-65479849	chr11:65479849-65479850		319;536
N	coord_cassette	CUFF.182	chr11	-	chr11:118926556-118927785	chr11:118926556-118926781;chr11:118926880-118926990;chr11:118927130-118927785		chr11:118926782-118926879;chr11:118926991-118927129			48;1052
N	alternative_acceptor	CUFF.180	chr11	+	chr11:118405071-118405221;chr11:118405071-118406222	chr11:118405071-118416833		chr11:118405222-118406222;chr11:118406223-118416833	chr11:118406222-118406223;chr11:118416833-118416834		165;87
K	cassette	CUFF.138	chr11	+	chr11:3405515-3422988	chr11:3405515-3418346;chr11:3418637-3422988		chr11:3418347-3418636		chr11:3405397-3405514	13;239
N	intron_retention		chr11	+	chr11:118401950-118402489				chr11:118401949-118401950;chr11:118402489-118402490		1149;180
N	intron_retention		chr11	+	chr11:118402317-118402489				chr11:118402316-118402317;chr11:118402489-118402490		122;307
N	alternative_first_exon	CUFF.132	chr11	+	chr11:827712-828259;chr11:826267-828259	chr11:827319-828259,chr11:827460-828259	chr11:827558-827711;chr11:826053-826266	chr11:827206-827318			72;267
N	intron_retention		chr11	-	chr11:102960048-102962515				chr11:102960047-102960048;chr11:102962515-102962516		77;142
K	intron_retention	CUFF.136	chr11	-	chr11:2905365-2905899				chr11:2905364-2905365;chr11:2905899-2905900		275;19
N	alternative_donor		chr11	-	chr11:102960048-102962515;chr11:102960048-102962244	chr11:102960048-102962412		chr11:102962245-102962412;chr11:102962413-102962515	chr11:102962412-102962413;chr11:102962515-102962516		116;77
N	alternative_donor	CUFF.146	chr11	-	chr11:10828929-10829080;chr11:10828929-10829291;chr11:10828929-10829095	chr11:10828929-10829720		chr11:10829081-10829095;chr11:10829096-10829291;chr11:10829292-10829720	chr11:10829095-10829096;chr11:10829291-10829292;chr11:10829720-10829721		184;24
N	alternative_acceptor	CUFF.180	chr11	+	chr11:118405071-118416833;chr11:118405071-118405221	chr11:118405071-118406222		chr11:118405222-118406222;chr11:118406223-118416833	chr11:118406222-118406223;chr11:118416833-118416834		244;8
N	jcn_only_AD	CUFF.160	chr11	+	chr11:65479917-65480236	chr11:65480069-65480236		chr11:65479917-65480068	chr11:65479916-65479917		1845;126
N	intron_retention		chr11	-	chr11:10821157-10821636				chr11:10821156-10821157;chr11:10821636-10821637		52;243
N	jcn_only_AA	CUFF.133	chr11	-	chr11:1775369-1776135	chr11:1775486-1776135		chr11:1775369-1775485	chr11:1775368-1775369		126;28
K	intron_retention	CUFF.130	chr11	-	chr11:410028-417324				chr11:410027-410028;chr11:417324-417325		33;73
N	cassette	CUFF.146	chr11	-	chr11:10825966-10827453	chr11:10825966-10826459;chr11:10826563-10827453		chr11:10826460-10826562			53;465
N	jcn_only_AD		chr11	-	chr11:10828929-10829080;chr11:10828929-10829720;chr11:10828929-10829291	chr11:10828929-10829095		chr11:10829081-10829095;chr11:10829096-10829291;chr11:10829292-10829720	chr11:10829095-10829096;chr11:10829291-10829292;chr11:10829720-10829721		80;5
N	alternative_acceptor	CUFF.143	chr11	-	chr11:8502162-8615629;chr11:8486370-8615629;chr11:8474454-8615629	chr11:8588841-8615629		chr11:8474454-8486369;chr11:8486370-8502161;chr11:8502162-8588840	chr11:8474453-8474454;chr11:8486369-8486370;chr11:8502161-8502162		63;2
N	cassette	CUFF.180	chr11	+	chr11:118403177-118404571;chr11:118403177-118404134	chr11:118403177-118403631;chr11:118403923-118404571,chr11:118403923-118404134		chr11:118403632-118403922			224;1875
K	jcn_only_AA	CUFF.165	chr11	+	chr11:67820553-67820828	chr11:67820553-67820825		chr11:67820826-67820828	chr11:67820828-67820829		64;373
K	intron_retention		chr11	-	chr11:2187999-2188116				chr11:2187998-2187999;chr11:2188116-2188117		274;100
N	alternative_acceptor	CUFF.143	chr11	-	chr11:8588841-8615629;chr11:8486370-8615629;chr11:8474454-8615629	chr11:8502162-8615629		chr11:8474454-8486369;chr11:8486370-8502161;chr11:8502162-8588840	chr11:8474453-8474454;chr11:8486369-8486370;chr11:8502161-8502162		48;17
N	alternative_donor	CUFF.188	chr11	-	chr11:119291640-119293822;chr11:119291640-119295607	chr11:119291640-119292320		chr11:119292321-119293822;chr11:119293823-119295607	chr11:119293822-119293823;chr11:119295607-119295608		546;32
K	intron_retention	CUFF.132	chr11	+	chr11:828773-828851				chr11:828772-828773;chr11:828851-828852		501;211
K	intron_retention	CUFF.132	chr11	+	chr11:827319-828259				chr11:827318-827319;chr11:828259-828260		339;76
K	intron_retention	CUFF.142	chr11	-	chr11:6640147-6640426				chr11:6640146-6640147;chr11:6640426-6640427		401;163
N	alternative_donor	CUFF.186	chr11	+	chr11:119058368-119058648	chr11:119058410-119058648		chr11:119058368-119058409	chr11:119058367-119058368		45;289
K	intron_retention	CUFF.151	chr11	+	chr11:59861032-59861436				chr11:59861031-59861032;chr11:59861436-59861437		25;134
N	jcn_only_AD	CUFF.186	chr11	+	chr11:119056875-119057187	chr11:119056951-119057187		chr11:119056875-119056950	chr11:119056874-119056875		286;60
K	cassette	CUFF.130	chr11	-	chr11:408894-409867	chr11:408894-409216;chr11:409309-409867		chr11:409217-409308			412;31
K	jcn_only_AD	CUFF.140	chr11	-	chr11:5701469-5706245	chr11:5701469-5706097		chr11:5706098-5706245	chr11:5706245-5706246		30;93
K	jcn_only_AA	CUFF.190	chr11	-	chr11:124766952-124768293	chr11:124767158-124768293		chr11:124766952-124767157	chr11:124766951-124766952		86;86
K	alternative_donor	CUFF.150	chr11	+	chr11:57310815-57311096	chr11:57310848-57311096		chr11:57310815-57310847	chr11:57310814-57310815		11;264
N	jcn_only_AA	CUFF.167,CUFF.178	chr11	+	chr11:115267610-115267986	chr11:115267610-115267983		chr11:115267984-115267986	chr11:115267986-115267987		23;47
N	intron_retention		chr11	+	chr11:65480527-65480818				chr11:65480526-65480527;chr11:65480818-65480819		183;116
K	coord_cassette	CUFF.170	chr11	-	chr11:77885630-77899618	chr11:77885630-77887933;chr11:77888032-77888784;chr11:77889032-77899618		chr11:77887934-77888031;chr11:77888785-77889031			6;27
K	intron_retention	CUFF.186	chr11	+	chr11:119058854-119059063				chr11:119058853-119058854;chr11:119059063-119059064		237;50
K	intron_retention	CUFF.140	chr11	-	chr11:5686626-5686885				chr11:5686625-5686626;chr11:5686885-5686886		236;61
N	jcn_only_AD	CUFF.149	chr11	+	chr11:36383732-36415395;chr11:36322621-36415395	chr11:36398255-36415395		chr11:36322621-36383731;chr11:36383732-36398254	chr11:36322620-36322621;chr11:36383731-36383732		107;317
K	intron_retention	CUFF.132	chr11	+	chr11:830714-830865				chr11:830713-830714;chr11:830865-830866		109;113
N	alternative_acceptor	CUFF.143	chr11	-	chr11:8588841-8615629;chr11:8502162-8615629;chr11:8474454-8615629	chr11:8486370-8615629		chr11:8474454-8486369;chr11:8486370-8502161;chr11:8502162-8588840	chr11:8474453-8474454;chr11:8486369-8486370;chr11:8502161-8502162		64;1
N	intron_retention		chr11	+	chr11:118402915-118403049				chr11:118402914-118402915;chr11:118403049-118403050		133;1506
N	intron_retention		chr11	+	chr11:61595697-61595966				chr11:61595696-61595697;chr11:61595966-61595967		20;17
N	jcn_only_AA	CUFF.132,CUFF.179	chr11	+	chr11:117070149-117073717	chr11:117070149-117070348		chr11:117070349-117073717	chr11:117073717-117073718		22;40
K	intron_retention	CUFF.134	chr11	-	chr11:2188716-2189095				chr11:2188715-2188716;chr11:2189095-2189096		528;85
K	jcn_only_AA	CUFF.136	chr11	-	chr11:2905141-2905228	chr11:2905146-2905228		chr11:2905141-2905145	chr11:2905140-2905141		35;331
K	alternative_donor	CUFF.146	chr11	-	chr11:10821304-10821790	chr11:10821304-10821636		chr11:10821637-10821790	chr11:10821790-10821791		224;125
N	alternative_acceptor		chr11	+	chr11:827712-828259	chr11:827712-828229		chr11:828230-828259	chr11:828259-828260		23;59
N	intron_retention		chr11	+	chr11:117073889-117074022				chr11:117073888-117073889;chr11:117074022-117074023		37;47
N	jcn_only_AD		chr11	+	chr11:36475657-36483891;chr11:36476369-36483891	chr11:36476997-36483891					79;30
N	alternative_donor		chr11	-	chr11:407569-407851	chr11:407569-407816		chr11:407817-407851	chr11:407851-407852		269;699
N	jcn_only_AD		chr11	+	chr11:118402242-118402489;chr11:118401950-118402489	chr11:118402317-118402489		chr11:118401950-118402241;chr11:118402242-118402316	chr11:118401949-118401950;chr11:118402241-118402242		1245;122
K	cassette	CUFF.170	chr11	-	chr11:77885630-77899618	chr11:77885630-77888784;chr11:77889032-77899618		chr11:77888785-77889031			6;55
K	alternative_last_exon	CUFF.152	chr11	-	chr11:61517215-61523106	chr11:61521918-61523106	chr11:61516015-61517214	chr11:61521403-61521917			36;136
N	alternative_acceptor	CUFF.164	chr11	+	chr11:67786363-67786638	chr11:67786363-67786534		chr11:67786535-67786638	chr11:67786638-67786639		1196;41
N	alternative_acceptor		chr11	+	chr11:36415562-36415945;chr11:36415562-36417663	chr11:36415562-36422546		chr11:36415946-36417663;chr11:36417664-36422546	chr11:36417663-36417664;chr11:36422546-36422547		16;249
K	intron_retention	CUFF.134	chr11	-	chr11:2186994-2187231				chr11:2186993-2186994;chr11:2187231-2187232		570;51
N	alternative_acceptor		chr11	+	chr11:119056662-119057324	chr11:119056662-119056800		chr11:119056801-119057324	chr11:119057324-119057325		34;560
K	intron_retention	CUFF.140	chr11	-	chr11:5685404-5686398				chr11:5685403-5685404;chr11:5686398-5686399		117;181
N	jcn_only_AA	CUFF.131	chr11	-	chr11:558980-559346	chr11:559063-559346		chr11:558980-559062	chr11:558979-558980		21;24
N	alternative_acceptor	CUFF.132,CUFF.179	chr11	+	chr11:117070149-117073717	chr11:117070149-117070348		chr11:117070349-117073717	chr11:117073717-117073718		22;15
N	jcn_only_AA	CUFF.132	chr11	+	chr11:827460-828259	chr11:827460-828229		chr11:828230-828259	chr11:828259-828260		68;32
N	alternative_donor	CUFF.149	chr11	+	chr11:36322621-36415395;chr11:36398255-36415395	chr11:36383732-36415395		chr11:36322621-36383731;chr11:36383732-36398254	chr11:36322620-36322621;chr11:36383731-36383732		35;0
N	alternative_first_exon		chr11	-	chr11:119244232-119246933;chr11:119244232-119252182	chr11:119244232-119249716	chr11:119252183-119252421	chr11:119249717-119249894			41;68
K	intron_retention	CUFF.177	chr11	+	chr11:107925520-107925601				chr11:107925519-107925520;chr11:107925601-107925602		73;137
K	coord_cassette	CUFF.134	chr11	-	chr11:2187780-2188664	chr11:2187780-2187862;chr11:2187999-2188116;chr11:2188263-2188664		chr11:2187863-2187998;chr11:2188117-2188262			162;318
N	intron_retention		chr11	+	chr11:65480069-65480236				chr11:65480068-65480069;chr11:65480236-65480237		126;256
N	intron_retention		chr11	+	chr11:107975630-107976933				chr11:107975629-107975630;chr11:107976933-107976934		9;31
K	intron_retention	CUFF.147	chr11	+	chr11:18477626-18478218				chr11:18477625-18477626;chr11:18478218-18478219		19;301
K	mutually_exclusive	CUFF.170	chr11	-	chr11:77885630-77897726,chr11:77897863-77899618	chr11:77885630-77888784,chr11:77889032-77899618	chr11:77897727-77897862	chr11:77888785-77889031			89;35
N	alternative_acceptor	CUFF.188	chr11	-	chr11:119291097-119291578;chr11:119291046-119291578;chr11:119291159-119291578	chr11:119291089-119291578		chr11:119291046-119291088;chr11:119291089-119291096;chr11:119291097-119291158	chr11:119291045-119291046;chr11:119291088-119291089;chr11:119291096-119291097		1607;25
N	jcn_only_AD	CUFF.153	chr11	+	chr11:61560501-61593503	chr11:61583899-61593503		chr11:61560501-61583898	chr11:61560500-61560501		38;131
N	alternative_donor		chr11	-	chr11:119291640-119292320;chr11:119291640-119295607	chr11:119291640-119293822		chr11:119292321-119293822;chr11:119293823-119295607	chr11:119293822-119293823;chr11:119295607-119295608		134;444
K	intron_retention	CUFF.171	chr11	-	chr11:94703261-94704140				chr11:94703260-94703261;chr11:94704140-94704141		78;177
K	intron_retention	CUFF.187	chr11	-	chr11:119229845-119229940				chr11:119229844-119229845;chr11:119229940-119229941		221;20
K	intron_retention		chr11	+	chr11:118401950-118402492				chr11:118401949-118401950;chr11:118402492-118402493		1184;182
N	jcn_only_AA	CUFF.188	chr11	-	chr11:119291097-119291578;chr11:119291046-119291578;chr11:119291159-119291578	chr11:119291089-119291578		chr11:119291046-119291088;chr11:119291089-119291096;chr11:119291097-119291158	chr11:119291045-119291046;chr11:119291088-119291089;chr11:119291096-119291097		2432;33
N	alternative_acceptor	CUFF.153	chr11	+	chr11:61615757-61624482	chr11:61615757-61616152		chr11:61616153-61624482	chr11:61624482-61624483		463;34
N	alternative_donor	CUFF.153	chr11	+	chr11:61594904-61605249;chr11:61584169-61605249;chr11:61583899-61605249	chr11:61596070-61605249		chr11:61583899-61584168;chr11:61584169-61594903;chr11:61594904-61596069	chr11:61583898-61583899;chr11:61584168-61584169;chr11:61594903-61594904		448;26
N	intron_retention		chr11	+	chr11:118404267-118404571				chr11:118404266-118404267;chr11:118404571-118404572		330;334
N	intron_retention		chr11	+	chr11:118402587-118403004				chr11:118402586-118402587;chr11:118403004-118403005		130;1173
N	alternative_acceptor		chr11	+	chr11:118404845-118404983	chr11:118404845-118404980		chr11:118404981-118404983	chr11:118404983-118404984		220;365
N	jcn_only_AD	CUFF.153	chr11	+	chr11:61594904-61605249;chr11:61584169-61605249;chr11:61583899-61605249	chr11:61596070-61605249		chr11:61583899-61584168;chr11:61584169-61594903;chr11:61594904-61596069	chr11:61583898-61583899;chr11:61584168-61584169;chr11:61594903-61594904		315;51
N	cassette	CUFF.156	chr11	+	chr11:63672516-63676348;chr11:63673587-63676348	chr11:63672516-63675731,chr11:63673587-63675731;chr11:63675777-63676348		chr11:63675732-63675776			80;409
N	mutually_exclusive	CUFF.146	chr11	-	chr11:10827595-10828801,chr11:10828929-10829823	chr11:10827595-10828366,chr11:10828433-10829823	chr11:10828802-10828928	chr11:10828367-10828432			116;65
K	alternative_last_exon	CUFF.177	chr11	+	chr11:107944225-107948902	chr11:107944225-107944526	chr11:107948903-107948967	chr11:107944527-107944891			11;151
N	alternative_first_exon	CUFF.132	chr11	+	chr11:827712-828229;chr11:827460-828229	chr11:826267-828229	chr11:827558-827711;chr11:827206-827459	chr11:826053-826266			145;101
N	alternative_donor		chr11	+	chr11:118402317-118402489;chr11:118401950-118402489	chr11:118402242-118402489		chr11:118401950-118402241;chr11:118402242-118402316	chr11:118401949-118401950;chr11:118402241-118402242		1273;77
N	jcn_only_AD		chr11	-	chr11:406060-406348	chr11:406060-406141		chr11:406142-406348	chr11:406348-406349		557;280
K	alternative_first_exon	CUFF.135	chr11	+	chr11:2798263-2799205	chr11:2799044-2799205	chr11:2798216-2798262	chr11:2798728-2799043			34;106
N	jcn_only_AA		chr11	+	chr11:61583899-61605249	chr11:61583899-61593503					38;131
K	alternative_first_exon	CUFF.168	chr11	+	chr11:74630071-74630577;chr11:74622471-74630577	chr11:74624828-74630577	chr11:74629826-74630070;chr11:74622307-74622470	chr11:74624740-74624827			128;15
K	intron_retention	CUFF.153	chr11	+	chr11:61608004-61608095				chr11:61608003-61608004;chr11:61608095-61608096		352;32
N	alternative_donor		chr11	-	chr11:8496364-8502080;chr11:8496364-8588797	chr11:8496364-8615290		chr11:8502081-8588797;chr11:8588798-8615290	chr11:8588797-8588798;chr11:8615290-8615291		1;95
N	jcn_only_AD		chr11	-	chr11:406539-407061	chr11:406539-406842					266;250
K	cassette	CUFF.156	chr11	+	chr11:63670631-63672257	chr11:63670631-63671457;chr11:63671620-63672257		chr11:63671458-63671619			134;272
N	intron_retention		chr11	+	chr11:118402587-118403631				chr11:118402586-118402587;chr11:118403631-118403632		36;185
N	jcn_only_AA		chr11	+	chr11:118402587-118402960;chr11:118402587-118402811;chr11:118402587-118403004	chr11:118402587-118403124					330;235
K	intron_retention	CUFF.190	chr11	-	chr11:124757110-124757253				chr11:124757109-124757110;chr11:124757253-124757254		121;16
N	jcn_only_AA		chr11	-	chr11:8496364-8502080;chr11:8496614-8502080	chr11:8498831-8502080		chr11:8496364-8496613;chr11:8496614-8498830	chr11:8496363-8496364;chr11:8496613-8496614		47;31
K	cassette	CUFF.145	chr11	-	chr11:8948722-8950923	chr11:8948722-8949049;chr11:8949256-8950923		chr11:8949050-8949255			43;411
N	alternative_donor	CUFF.143	chr11	-	chr11:8483457-8494709	chr11:8483457-8486255		chr11:8486256-8494709	chr11:8494709-8494710		43;29
N	jcn_only_AA		chr11	+	chr11:118402587-118402960;chr11:118402587-118403124;chr11:118402587-118402811	chr11:118402587-118403004					434;130
K	intron_retention	CUFF.182	chr11	-	chr11:118925773-118925896				chr11:118925772-118925773;chr11:118925896-118925897		651;179
N	cassette	CUFF.156	chr11	+	chr11:63672516-63676348;chr11:63672516-63675731	chr11:63672516-63673559;chr11:63673587-63676348,chr11:63673587-63675731		chr11:63673560-63673586			380;146
N	jcn_only_AD		chr11	+	chr11:118402242-118402489;chr11:118402317-118402489	chr11:118401950-118402489		chr11:118401950-118402241;chr11:118402242-118402316	chr11:118401949-118401950;chr11:118402241-118402242		218;1149
K	intron_retention	CUFF.134	chr11	-	chr11:2190926-2192926				chr11:2190925-2190926;chr11:2192926-2192927		84;59
K	intron_retention	CUFF.150	chr11	+	chr11:57310654-57310731				chr11:57310653-57310654;chr11:57310731-57310732		12;369
K	intron_retention	CUFF.132	chr11	+	chr11:829541-829985				chr11:829540-829541;chr11:829985-829986		247;44
N	jcn_only_AD	CUFF.142	chr11	-	chr11:6633050-6633604	chr11:6633050-6633188		chr11:6633189-6633604	chr11:6633604-6633605		94;153
N	intron_retention	CUFF.160	chr11	+	chr11:65479751-65479820				chr11:65479750-65479751;chr11:65479820-65479821		90;1510
N	alternative_acceptor	CUFF.190	chr11	-	chr11:124767529-124767621;chr11:124767158-124767621	chr11:124766952-124767621		chr11:124766952-124767157;chr11:124767158-124767528	chr11:124766951-124766952;chr11:124767157-124767158		598;13
K	alternative_acceptor	CUFF.161	chr11	-	chr11:67766776-67766988	chr11:67766846-67766988		chr11:67766776-67766845	chr11:67766775-67766776		639;100
N	cassette	CUFF.182	chr11	-	chr11:118919599-118920267	chr11:118919599-118919729;chr11:118919916-118920267		chr11:118919730-118919915			72;85
N	alternative_donor	CUFF.174	chr11	-	chr11:102960048-102962412;chr11:102960048-102962244	chr11:102960048-102962515		chr11:102962245-102962412;chr11:102962413-102962515	chr11:102962412-102962413;chr11:102962515-102962516		116;77
N	jcn_only_AA		chr11	+	chr11:36317989-36422546	chr11:36317989-36318920					101;12
N	intron_retention	CUFF.146	chr11	-	chr11:10828929-10829291				chr11:10828928-10828929;chr11:10829291-10829292		21;393
K	intron_retention	CUFF.189	chr11	+	chr11:124078396-124078521				chr11:124078395-124078396;chr11:124078521-124078522		24;57
N	cassette	CUFF.182	chr11	-	chr11:118926556-118927785	chr11:118926556-118926781;chr11:118926880-118927785		chr11:118926782-118926879			48;1143
N	alternative_donor		chr11	-	chr11:2192001-2192926	chr11:2192001-2192914		chr11:2192915-2192926	chr11:2192926-2192927		36;19
N	alternative_acceptor	CUFF.130	chr11	-	chr11:406539-407061	chr11:406994-407061		chr11:406539-406993	chr11:406538-406539		266;488
K	intron_retention	CUFF.138	chr11	+	chr11:3405515-3418346				chr11:3405514-3405515;chr11:3418346-3418347	chr11:3405397-3405514;chr11:3418347-3419385	205;33
K	intron_retention	CUFF.132	chr11	+	chr11:829541-829967				chr11:829540-829541;chr11:829967-829968		124;34
K	alternative_acceptor	CUFF.165	chr11	+	chr11:67820553-67820828	chr11:67820553-67820825		chr11:67820826-67820828	chr11:67820828-67820829		64;185
K	cassette	CUFF.170	chr11	-	chr11:77885630-77899618	chr11:77885630-77897726;chr11:77897863-77899618		chr11:77897727-77897862			6;99
N	jcn_only_AD		chr11	+	chr11:36397709-36398178	chr11:36397788-36398178					50;42
N	jcn_only_AD	CUFF.179	chr11	+	chr11:117073889-117074022	chr11:117073910-117074022		chr11:117073889-117073909	chr11:117073888-117073889		37;337
N	alternative_acceptor	CUFF.132	chr11	+	chr11:827460-828259	chr11:827460-828229		chr11:828230-828259	chr11:828259-828260		68;34
N	jcn_only_AA	CUFF.140	chr11	-	chr11:5701469-5706097	chr11:5705370-5706097		chr11:5701469-5705369	chr11:5701468-5701469		93;30
N	alternative_donor		chr11	-	chr11:6632684-6633294	chr11:6632684-6632894		chr11:6632895-6633294	chr11:6633294-6633295		222;124
N	jcn_only_AA	CUFF.143	chr11	-	chr11:8588841-8615629;chr11:8486370-8615629;chr11:8474454-8615629	chr11:8502162-8615629		chr11:8474454-8486369;chr11:8486370-8502161;chr11:8502162-8588840	chr11:8474453-8474454;chr11:8486369-8486370;chr11:8502161-8502162		85;49
K	intron_retention		chr11	+	chr11:63999437-63999981				chr11:63999436-63999437;chr11:63999981-63999982		355;1040
N	jcn_only_AA	CUFF.186	chr11	+	chr11:119056220-119056633;chr11:119056220-119056630	chr11:119056220-119056557		chr11:119056558-119056630;chr11:119056631-119056633	chr11:119056630-119056631;chr11:119056633-119056634		670;74
N	jcn_only_AA	CUFF.140	chr11	-	chr11:5687504-5699433	chr11:5691178-5699433		chr11:5687504-5691177	chr11:5687503-5687504		15;40
K	jcn_only_AA	CUFF.140	chr11	-	chr11:5685404-5686885	chr11:5686626-5686885		chr11:5685404-5686625	chr11:5685403-5685404		107;236
K	cassette	CUFF.137	chr11	+	chr11:3239790-3242799	chr11:3239790-3241456;chr11:3241590-3242799		chr11:3241457-3241589			66;44
N	intron_retention		chr11	-	chr11:10827595-10828801				chr11:10827594-10827595;chr11:10828801-10828802		179;36
N	intron_retention		chr11	-	chr11:10827572-10828856				chr11:10827571-10827572;chr11:10828856-10828857		34;329
N	coord_cassette	CUFF.138	chr11	+	chr11:3424187-3427728	chr11:3424187-3424822;chr11:3424883-3426083;chr11:3426194-3427728		chr11:3424823-3424882;chr11:3426084-3426193			110;126
K	coord_cassette	CUFF.130	chr11	-	chr11:408894-414822	chr11:408894-409216;chr11:409309-409867;chr11:410028-414822		chr11:409217-409308;chr11:409868-410027			40;36
K	intron_retention	CUFF.190	chr11	-	chr11:124756719-124756872				chr11:124756718-124756719;chr11:124756872-124756873		107;20
N	jcn_only_AA	CUFF.182	chr11	-	chr11:118927117-118927730	chr11:118927130-118927730		chr11:118927117-118927129	chr11:118927116-118927117		1181;5
K	intron_retention	CUFF.132	chr11	+	chr11:830714-831223				chr11:830713-830714;chr11:831223-831224		237;131
N	intron_retention		chr11	-	chr11:10827488-10828835				chr11:10827487-10827488;chr11:10828835-10828836		51;280
K	intron_retention	CUFF.134	chr11	-	chr11:2187289-2187709				chr11:2187288-2187289;chr11:2187709-2187710		620;50
N	intron_retention		chr11	+	chr11:119056338-119056630				chr11:119056337-119056338;chr11:119056630-119056631		28;10
N	jcn_only_AA	CUFF.169	chr11	-	chr11:75520420-75522468;chr11:75514563-75522468	chr11:75514771-75522468		chr11:75514563-75514770;chr11:75514771-75520419	chr11:75514562-75514563;chr11:75514770-75514771		371;208
N	alternative_donor	CUFF.179	chr11	+	chr11:117073889-117074022	chr11:117073910-117074022		chr11:117073889-117073909	chr11:117073888-117073889		37;194
K	alternative_first_exon	CUFF.133	chr11	-	chr11:1782699-1785021	chr11:1782699-1783362	chr11:1785022-1785299	chr11:1783363-1783715			24;50
K	alternative_donor	CUFF.136	chr11	-	chr11:2905365-2906431	chr11:2905365-2905899		chr11:2905900-2906431	chr11:2906431-2906432		56;338
N	mutually_exclusive	CUFF.140	chr11	-	chr11:5686913-5688918,chr11:5688942-5699433	chr11:5686913-5687210,chr11:5687312-5699433	chr11:5688919-5688941	chr11:5687211-5687311			30;192
K	intron_retention	CUFF.146	chr11	-	chr11:10821304-10821636				chr11:10821303-10821304;chr11:10821636-10821637		84;76
K	cassette	CUFF.149	chr11	+	chr11:36398255-36422546	chr11:36398255-36415395;chr11:36415562-36422546		chr11:36415396-36415561			270;320
N	jcn_only_AA	CUFF.180	chr11	+	chr11:118405071-118416833;chr11:118405071-118405221	chr11:118405071-118406222		chr11:118405222-118406222;chr11:118406223-118416833	chr11:118406222-118406223;chr11:118416833-118416834		876;93
N	jcn_only_AA	CUFF.149	chr11	+	chr11:36415562-36415945;chr11:36415562-36422546	chr11:36415562-36417663		chr11:36415946-36417663;chr11:36417664-36422546	chr11:36417663-36417664;chr11:36422546-36422547		540;36
N	jcn_only_AA		chr11	+	chr11:118405071-118416833;chr11:118405071-118406222	chr11:118405071-118405221		chr11:118405222-118406222;chr11:118406223-118416833	chr11:118406222-118406223;chr11:118416833-118416834		180;789
N	jcn_only_AD		chr11	-	chr11:10823983-10827453	chr11:10823983-10824576					66;137
N	jcn_only_AD		chr11	-	chr11:2192001-2192926	chr11:2192001-2192914		chr11:2192915-2192926	chr11:2192926-2192927		36;15
N	jcn_only_AA	CUFF.169	chr11	-	chr11:75514771-75522468;chr11:75520420-75522468	chr11:75514563-75522468		chr11:75514563-75514770;chr11:75514771-75520419	chr11:75514562-75514563;chr11:75514770-75514771		270;310
N	mutually_exclusive	CUFF.180	chr11	+	chr11:118402587-118403631,chr11:118403923-118404134	chr11:118402587-118402864,chr11:118403177-118404134	chr11:118403632-118403922	chr11:118402865-118403176			42;164
K	coord_cassette	CUFF.156	chr11	+	chr11:63672516-63676348	chr11:63672516-63673559;chr11:63673587-63675731;chr11:63675777-63676348		chr11:63673560-63673586;chr11:63675732-63675776			28;94
N	alternative_acceptor	CUFF.133	chr11	-	chr11:1775369-1776135	chr11:1775486-1776135		chr11:1775369-1775485	chr11:1775368-1775369		126;18
N	mutually_exclusive	CUFF.149	chr11	+	chr11:36459027-36472758,chr11:36472886-36483891	chr11:36459027-36467849,chr11:36467991-36483891	chr11:36472759-36472885	chr11:36467850-36467990			16;182
K	intron_retention	CUFF.157	chr11	+	chr11:64001453-64001544				chr11:64001452-64001453;chr11:64001544-64001545		382;110
K	intron_retention	CUFF.142	chr11	-	chr11:6640499-6640614				chr11:6640498-6640499;chr11:6640614-6640615		722;166
K	intron_retention	CUFF.130	chr11	-	chr11:407165-407424				chr11:407164-407165;chr11:407424-407425		623;523
K	intron_retention	CUFF.190	chr11	-	chr11:124757396-124757628				chr11:124757395-124757396;chr11:124757628-124757629		99;13
K	cassette	CUFF.137	chr11	+	chr11:3239790-3242799	chr11:3239790-3240929;chr11:3241019-3242799		chr11:3240930-3241018			66;23
K	intron_retention	CUFF.146	chr11	-	chr11:10825751-10825833				chr11:10825750-10825751;chr11:10825833-10825834		661;59
K	alternative_acceptor	CUFF.149,CUFF.157	chr11	+	chr11:64000087-64000175	chr11:64000087-64000172		chr11:64000173-64000175	chr11:64000175-64000176		1648;59
K	intron_retention	CUFF.140	chr11	-	chr11:5685404-5686885				chr11:5685403-5685404;chr11:5686885-5686886		107;112
K	intron_retention	CUFF.153	chr11	+	chr11:61615757-61624482				chr11:61615756-61615757;chr11:61624482-61624483		463;30
K	intron_retention	CUFF.181	chr11	-	chr11:118531625-118531868				chr11:118531624-118531625;chr11:118531868-118531869		788;17
N	intron_retention		chr11	+	chr11:118402549-118403062				chr11:118402548-118402549;chr11:118403062-118403063		131;1184
N	jcn_only_AA	CUFF.169	chr11	-	chr11:75514771-75522468;chr11:75514563-75522468	chr11:75520420-75522468		chr11:75514563-75514770;chr11:75514771-75520419	chr11:75514562-75514563;chr11:75514770-75514771		518;62
K	intron_retention		chr11	+	chr11:119056220-119056630				chr11:119056219-119056220;chr11:119056630-119056631		135;42
K	intron_retention	CUFF.140	chr11	-	chr11:5701469-5706245				chr11:5701468-5701469;chr11:5706245-5706246		30;80
K	alternative_acceptor	CUFF.145	chr11	-	chr11:8950976-8953688	chr11:8951081-8953688		chr11:8950976-8951080	chr11:8950975-8950976		379;678
K	intron_retention		chr11	+	chr11:119056220-119056557				chr11:119056219-119056220;chr11:119056557-119056558		74;46
K	intron_retention	CUFF.142	chr11	-	chr11:6637735-6638589				chr11:6637734-6637735;chr11:6638589-6638590		29;197
N	jcn_only_AD	CUFF.186	chr11	+	chr11:119056220-119056630	chr11:119056338-119056630		chr11:119056220-119056337	chr11:119056219-119056220		135;28
N	coord_cassette	CUFF.130	chr11	-	chr11:408207-409867	chr11:408207-408694;chr11:408894-409216;chr11:409309-409867		chr11:408695-408893;chr11:409217-409308			325;37
N	alternative_donor	CUFF.142	chr11	-	chr11:6633050-6633604	chr11:6633050-6633188		chr11:6633189-6633604	chr11:6633604-6633605		94;123
N	mutually_exclusive	CUFF.146	chr11	-	chr11:10827595-10828801,chr11:10828929-10830251	chr11:10827595-10828366,chr11:10828433-10830251	chr11:10828802-10828928	chr11:10828367-10828432			116;65
N	cassette	CUFF.140	chr11	-	chr11:5687312-5699433	chr11:5687312-5688918;chr11:5688942-5699433		chr11:5688919-5688941			233;178
N	alternative_acceptor	CUFF.140	chr11	-	chr11:5701469-5706097	chr11:5705370-5706097		chr11:5701469-5705369	chr11:5701468-5701469		93;3
N	cassette	CUFF.130	chr11	-	chr11:408207-414822;chr11:408207-409867	chr11:408207-408694;chr11:408894-409867,chr11:408894-414822		chr11:408695-408893			457;543
N	jcn_only_AD	CUFF.160	chr11	+	chr11:65480527-65480818	chr11:65480530-65480818		chr11:65480527-65480529	chr11:65480526-65480527		183;2216
K	alternative_first_exon	CUFF.164	chr11	+	chr11:67782546-67782766;chr11:67776163-67782766	chr11:67777863-67782766	chr11:67775960-67776162	chr11:67777709-67777862			264;734
N	intron_retention		chr11	+	chr11:118403177-118404571				chr11:118403176-118403177;chr11:118404571-118404572		64;172
N	jcn_only_AA	CUFF.143	chr11	-	chr11:8483457-8494709	chr11:8486370-8494709		chr11:8483457-8486369	chr11:8483456-8483457		43;289
K	intron_retention	CUFF.151	chr11	+	chr11:59856135-59856222				chr11:59856134-59856135;chr11:59856222-59856223		572;116
K	cassette	CUFF.172	chr11	+	chr11:94707233-94730187	chr11:94707233-94708817;chr11:94708913-94730187		chr11:94708818-94708912			6;94
K	cassette	CUFF.170	chr11	-	chr11:77885630-77888784	chr11:77885630-77887933;chr11:77888032-77888784		chr11:77887934-77888031			43;26
K	intron_retention	CUFF.190	chr11	-	chr11:124766567-124766827				chr11:124766566-124766567;chr11:124766827-124766828		363;279
K	cassette	CUFF.182	chr11	-	chr11:118926284-118926781	chr11:118926284-118926461;chr11:118926556-118926781		chr11:118926462-118926555			76;2049
K	intron_retention	CUFF.161	chr11	-	chr11:67771269-67771417				chr11:67771268-67771269;chr11:67771417-67771418		270;865
N	jcn_only_AD	CUFF.143	chr11	-	chr11:8483457-8494709	chr11:8483457-8486255		chr11:8486256-8494709	chr11:8494709-8494710		43;374
N	jcn_only_AD		chr11	-	chr11:119291640-119292320;chr11:119291640-119295607	chr11:119291640-119293822		chr11:119292321-119293822;chr11:119293823-119295607	chr11:119293822-119293823;chr11:119295607-119295608		181;4030
N	alternative_acceptor	CUFF.169	chr11	-	chr11:75514771-75522468;chr11:75520420-75522468	chr11:75514563-75522468		chr11:75514563-75514770;chr11:75514771-75520419	chr11:75514562-75514563;chr11:75514770-75514771		253;310
N	alternative_acceptor	CUFF.146	chr11	-	chr11:10821157-10821636	chr11:10821304-10821636		chr11:10821157-10821303	chr11:10821156-10821157		52;234
N	alternative_acceptor	CUFF.190	chr11	-	chr11:124766952-124767621;chr11:124767529-124767621	chr11:124767158-124767621		chr11:124766952-124767157;chr11:124767158-124767528	chr11:124766951-124766952;chr11:124767157-124767158		98;513
N	intron_retention		chr11	-	chr11:406060-406348				chr11:406059-406060;chr11:406348-406349		557;238
N	alternative_acceptor	CUFF.169	chr11	-	chr11:75520420-75522468;chr11:75514563-75522468	chr11:75514771-75522468		chr11:75514563-75514770;chr11:75514771-75520419	chr11:75514562-75514563;chr11:75514770-75514771		319;244
N	cassette	CUFF.138	chr11	+	chr11:3423960-3424822	chr11:3423960-3424144;chr11:3424187-3424822		chr11:3424145-3424186			196;66
K	jcn_only_AA	CUFF.161	chr11	-	chr11:67766776-67766988	chr11:67766846-67766988		chr11:67766776-67766845	chr11:67766775-67766776		639;32
K	alternative_first_exon	CUFF.141	chr11	-	chr11:6622006-6624633	chr11:6622006-6622155	chr11:6624634-6624921	chr11:6622156-6622285			518;54
N	alternative_acceptor	CUFF.131	chr11	-	chr11:558767-558855	chr11:558785-558855		chr11:558767-558784	chr11:558766-558767		52;18
N	alternative_donor	CUFF.157	chr11	+	chr11:63998413-63999342	chr11:63998620-63999342		chr11:63998413-63998619	chr11:63998412-63998413		133;11
N	alternative_first_exon	CUFF.174,CUFF.190	chr11	-	chr11:124766952-124768293	chr11:124766952-124767621	chr11:124768294-124768494	chr11:124767622-124768177			69;9
N	cassette	CUFF.140	chr11	-	chr11:5686913-5688918	chr11:5686913-5687210;chr11:5687312-5688918		chr11:5687211-5687311			31;246
N	cassette	CUFF.134	chr11	-	chr11:2191102-2192914;chr11:2191102-2192926	chr11:2191102-2191919;chr11:2192001-2192914,chr11:2192001-2192926		chr11:2191920-2192000			97;45
N	alternative_first_exon	CUFF.142	chr11	-	chr11:8486370-8615629	chr11:8486370-8494709	chr11:8615630-8615903	chr11:8494710-8494823			11;203
K	jcn_only_AA	CUFF.188	chr11	-	chr11:119290142-119290760	chr11:119290231-119290760		chr11:119290142-119290230	chr11:119290141-119290142		2513;581
K	intron_retention	CUFF.130	chr11	-	chr11:407535-407816				chr11:407534-407535;chr11:407816-407817		219;215
N	alternative_acceptor		chr11	+	chr11:65481320-65482130	chr11:65481320-65481965		chr11:65481966-65482130	chr11:65482130-65482131		70;1618
K	intron_retention	CUFF.178	chr11	+	chr11:115267610-115267986				chr11:115267609-115267610;chr11:115267986-115267987		23;124
N	alternative_donor	CUFF.149	chr11	+	chr11:36383732-36415395;chr11:36322621-36415395	chr11:36398255-36415395		chr11:36322621-36383731;chr11:36383732-36398254	chr11:36322620-36322621;chr11:36383731-36383732		30;5
K	alternative_first_exon	CUFF.174	chr11	-	chr11:102954056-102962515	chr11:102954056-102959955	chr11:102962516-102963031	chr11:102959956-102960047			275;293
N	mutually_exclusive	CUFF.182	chr11	-	chr11:118926284-118926781,chr11:118926880-118927785	chr11:118926284-118926461,chr11:118926556-118927785	chr11:118926782-118926879	chr11:118926462-118926555			58;38
N	jcn_only_AA		chr11	+	chr11:61608198-61615630	chr11:61608198-61615292		chr11:61615293-61615630	chr11:61615630-61615631		368;40
K	intron_retention	CUFF.155	chr11	-	chr11:62365614-62365798				chr11:62365613-62365614;chr11:62365798-62365799		79;152
N	intron_retention		chr11	-	chr11:8486370-8615629				chr11:8486369-8486370;chr11:8615629-8615630		13;24
K	alternative_first_exon	CUFF.187	chr11	-	chr11:119230945-119243416;chr11:119230945-119252182	chr11:119230945-119234558	chr11:119252183-119252421	chr11:119234559-119234996			21;203
N	jcn_only_AA	CUFF.143	chr11	-	chr11:8502162-8615629;chr11:8486370-8615629;chr11:8474454-8615629	chr11:8588841-8615629		chr11:8474454-8486369;chr11:8486370-8502161;chr11:8502162-8588840	chr11:8474453-8474454;chr11:8486369-8486370;chr11:8502161-8502162		107;27
N	intron_retention		chr11	+	chr11:118402587-118403124				chr11:118402586-118402587;chr11:118403124-118403125		235;781
N	alternative_donor	CUFF.171	chr11	-	chr11:94705358-94706436;chr11:94705358-94706661	chr11:94705358-94706452		chr11:94706437-94706452;chr11:94706453-94706661	chr11:94706452-94706453;chr11:94706661-94706662		164;243
K	cassette	CUFF.135	chr11	+	chr11:2466715-2549157	chr11:2466715-2542708;chr11:2542801-2549157		chr11:2542709-2542800			48;122
N	intron_retention		chr11	+	chr11:118402587-118402811				chr11:118402586-118402587;chr11:118402811-118402812		54;314
K	jcn_only_AA	CUFF.141	chr11	-	chr11:6623446-6624633;chr11:6623495-6624633	chr11:6622006-6624633					129;449
K	intron_retention	CUFF.146	chr11	-	chr11:10822635-10823207				chr11:10822634-10822635;chr11:10823207-10823208		85;40
K	intron_retention	CUFF.142	chr11	-	chr11:6638385-6638531				chr11:6638384-6638385;chr11:6638531-6638532		302;182
N	intron_retention		chr11	+	chr11:119056662-119057324				chr11:119056661-119056662;chr11:119057324-119057325		34;293
K	cassette	CUFF.182	chr11	-	chr11:118926880-118927730	chr11:118926880-118926990;chr11:118927117-118927730		chr11:118926991-118927116			120;1234
N	jcn_only_AA	CUFF.157	chr11	+	chr11:63998413-63999342	chr11:63998413-63998503		chr11:63998504-63999342	chr11:63999342-63999343		133;28
N	alternative_donor	CUFF.138	chr11	+	chr11:3427841-3428851	chr11:3427946-3428851		chr11:3427841-3427945	chr11:3427840-3427841		200;61
N	jcn_only_AD		chr11	-	chr11:407569-407851	chr11:407569-407816		chr11:407817-407851	chr11:407851-407852		269;1218
N	mutually_exclusive	CUFF.156	chr11	+	chr11:63672516-63675731,chr11:63675777-63676348	chr11:63672516-63673559,chr11:63673587-63676348	chr11:63675732-63675776	chr11:63673560-63673586			313;47
K	cassette	CUFF.143	chr11	-	chr11:8457687-8474368	chr11:8457687-8462224;chr11:8462301-8474368		chr11:8462225-8462300			38;331
K	jcn_only_AD	CUFF.174	chr11	-	chr11:102933144-102936997	chr11:102933144-102935003					216;322
N	jcn_only_AA	CUFF.175	chr11	-	chr11:104915386-104916017	chr11:104915659-104916017		chr11:104915386-104915658	chr11:104915385-104915386		205;31
N	intron_retention		chr11	+	chr11:117072658-117073717				chr11:117072657-117072658;chr11:117073717-117073718		22;45
K	intron_retention	CUFF.161	chr11	-	chr11:67770646-67771126				chr11:67770645-67770646;chr11:67771126-67771127		1609;159
K	intron_retention	CUFF.169	chr11	-	chr11:75522615-75524647				chr11:75522614-75522615;chr11:75524647-75524648		187;602
K	intron_retention	CUFF.169	chr11	-	chr11:75522582-75524647				chr11:75522581-75522582;chr11:75524647-75524648		220;689
N	alternative_donor	CUFF.136	chr11	-	chr11:8496364-8615290;chr11:8496364-8588797	chr11:8496364-8502080		chr11:8502081-8588797;chr11:8588798-8615290	chr11:8588797-8588798;chr11:8615290-8615291		96;0
K	intron_retention	CUFF.182	chr11	-	chr11:118926284-118926461				chr11:118926283-118926284;chr11:118926461-118926462		2449;63
N	intron_retention		chr11	+	chr11:118402587-118402960				chr11:118402586-118402587;chr11:118402960-118402961		146;1079
K	alternative_acceptor	CUFF.140	chr11	-	chr11:5685404-5686885	chr11:5686626-5686885		chr11:5685404-5686625	chr11:5685403-5685404		107;308
N	alternative_acceptor	CUFF.149	chr11	+	chr11:36415562-36422546;chr11:36415562-36417663	chr11:36415562-36415945		chr11:36415946-36417663;chr11:36417664-36422546	chr11:36417663-36417664;chr11:36422546-36422547		251;14
K	intron_retention	CUFF.146	chr11	-	chr11:10825138-10825445				chr11:10825137-10825138;chr11:10825445-10825446		246;99
K	cassette	CUFF.142	chr11	-	chr11:6639008-6640426	chr11:6639008-6640006;chr11:6640147-6640426		chr11:6640007-6640146			136;429
N	cassette	CUFF.130	chr11	-	chr11:408207-414822;chr11:408894-414822	chr11:408894-409867,chr11:408207-409867;chr11:410028-414822		chr11:409868-410027			172;768
K	jcn_only_AA	CUFF.152	chr11	-	chr11:61514596-61514822	chr11:61514614-61514822		chr11:61514596-61514613	chr11:61514595-61514596		47;19
K	alternative_first_exon	CUFF.175	chr11	-	chr11:104915386-104916017;chr11:104915386-104972134	chr11:104915386-104915917	chr11:104916018-104916042;chr11:104972135-104972250	chr11:104915918-104916016			201;11
K	alternative_acceptor	CUFF.132,CUFF.157	chr11	+	chr11:829541-829985	chr11:829541-829967		chr11:829968-829985	chr11:829985-829986		247;71
N	alternative_donor	CUFF.153	chr11	+	chr11:61560501-61593503	chr11:61583899-61593503		chr11:61560501-61583898	chr11:61560500-61560501		38;2
K	intron_retention	CUFF.136	chr11	-	chr11:2905365-2906431				chr11:2905364-2905365;chr11:2906431-2906432		56;118
K	jcn_only_AD	CUFF.132	chr11	+	chr11:828964-829359	chr11:829184-829359		chr11:828964-829183	chr11:828963-828964		199;57
K	intron_retention	CUFF.146	chr11	-	chr11:10825598-10825683				chr11:10825597-10825598;chr11:10825683-10825684		288;215
K	jcn_only_AD	CUFF.181	chr11	-	chr11:118532439-118533496	chr11:118532439-118532598					562;49
N	jcn_only_AA	CUFF.164	chr11	+	chr11:67790230-67793476	chr11:67790230-67791675		chr11:67791676-67793476	chr11:67793476-67793477		534;33
N	alternative_donor	CUFF.153	chr11	+	chr11:61584169-61605249;chr11:61583899-61605249;chr11:61596070-61605249	chr11:61594904-61605249		chr11:61583899-61584168;chr11:61584169-61594903;chr11:61594904-61596069	chr11:61583898-61583899;chr11:61584168-61584169;chr11:61594903-61594904		432;42
N	intron_retention		chr11	+	chr11:118401950-118403631				chr11:118401949-118401950;chr11:118403631-118403632		157;56
K	cassette	CUFF.188	chr11	-	chr11:119291097-119293822	chr11:119291097-119291578;chr11:119291640-119293822		chr11:119291579-119291639			65;2686
K	intron_retention	CUFF.155	chr11	-	chr11:62364888-62365081				chr11:62364887-62364888;chr11:62365081-62365082		73;28
N	alternative_first_exon	CUFF.132	chr11	+	chr11:826267-828229;chr11:827460-828229	chr11:827712-828229	chr11:826053-826266;chr11:827206-827459	chr11:827558-827711			137;109
N	cassette	CUFF.149	chr11	+	chr11:36424929-36453402	chr11:36424929-36440804;chr11:36440854-36453402		chr11:36440805-36440853			126;321
K	intron_retention	CUFF.160	chr11	+	chr11:65479751-65479849				chr11:65479750-65479751;chr11:65479849-65479850		319;1254
N	jcn_only_AA	CUFF.188	chr11	-	chr11:119291089-119291578;chr11:119291046-119291578;chr11:119291159-119291578	chr11:119291097-119291578		chr11:119291046-119291088;chr11:119291089-119291096;chr11:119291097-119291158	chr11:119291045-119291046;chr11:119291088-119291089;chr11:119291096-119291097		252;2213
K	jcn_only_AA	CUFF.130	chr11	-	chr11:407535-407816	chr11:407569-407816		chr11:407535-407568	chr11:407534-407535		219;1218
K	jcn_only_AD	CUFF.140	chr11	-	chr11:5685404-5686885	chr11:5685404-5686398		chr11:5686399-5686885	chr11:5686885-5686886		107;117
K	cassette	CUFF.149	chr11	+	chr11:36467991-36483891	chr11:36467991-36472758;chr11:36472886-36483891		chr11:36472759-36472885			209;112
K	alternative_acceptor	CUFF.188	chr11	-	chr11:119290142-119290760	chr11:119290231-119290760		chr11:119290142-119290230	chr11:119290141-119290142		2513;446
N	alternative_acceptor	CUFF.169	chr11	-	chr11:75514771-75522468;chr11:75514563-75522468	chr11:75520420-75522468		chr11:75514563-75514770;chr11:75514771-75520419	chr11:75514562-75514563;chr11:75514770-75514771		554;9
N	alternative_acceptor	CUFF.149	chr11	+	chr11:36415562-36415945;chr11:36415562-36422546	chr11:36415562-36417663		chr11:36415946-36417663;chr11:36417664-36422546	chr11:36417663-36417664;chr11:36422546-36422547		263;2
N	alternative_last_exon	CUFF.160	chr11	+	chr11:63999437-63999865;chr11:63999437-64001365	chr11:63999437-63999981,chr11:63999437-63999901	chr11:64001366-64001857	chr11:63999982-64000086			503;482
N	alternative_donor	CUFF.171	chr11	-	chr11:94705358-94706452;chr11:94705358-94706436	chr11:94705358-94706661		chr11:94706437-94706452;chr11:94706453-94706661	chr11:94706452-94706453;chr11:94706661-94706662		259;148
K	alternative_acceptor	CUFF.157	chr11	+	chr11:63999437-63999981	chr11:63999437-63999901		chr11:63999902-63999981	chr11:63999981-63999982		355;668
K	intron_retention	CUFF.160	chr11	+	chr11:65480530-65480818				chr11:65480529-65480530;chr11:65480818-65480819		2216;117
N	jcn_only_AA	CUFF.132	chr11	+	chr11:826267-828259	chr11:826267-828229		chr11:828230-828259	chr11:828259-828260		43;104
N	alternative_acceptor		chr11	-	chr11:8496614-8498796	chr11:8498299-8498796		chr11:8496614-8498298	chr11:8496613-8496614		43;17
N	alternative_acceptor		chr11	+	chr11:61608198-61615630	chr11:61608198-61615292		chr11:61615293-61615630	chr11:61615630-61615631		368;243
N	alternative_last_exon	CUFF.146	chr11	-	chr11:10819429-10823840	chr11:10823757-10823840	chr11:10818498-10819428	chr11:10823596-10823756			100;191
N	alternative_acceptor		chr11	+	chr11:119056338-119056630	chr11:119056338-119056557		chr11:119056558-119056630	chr11:119056630-119056631		28;10
N	jcn_only_AD	CUFF.134	chr11	-	chr11:2190926-2192926	chr11:2190926-2192914		chr11:2192915-2192926	chr11:2192926-2192927		84;36
N	alternative_first_exon	CUFF.161	chr11	-	chr11:8502162-8587256;chr11:8502162-8615629	chr11:8502162-8615290	chr11:8615630-8615903	chr11:8615291-8615625			60;25
K	alternative_donor	CUFF.132	chr11	+	chr11:827319-828259	chr11:827460-828259		chr11:827319-827459	chr11:827318-827319		339;74
N	jcn_only_AA		chr11	-	chr11:8496364-8502080;chr11:8498831-8502080	chr11:8496614-8502080		chr11:8496364-8496613;chr11:8496614-8498830	chr11:8496363-8496364;chr11:8496613-8496614		46;32
K	intron_retention	CUFF.161	chr11	-	chr11:67758834-67764242				chr11:67758833-67758834;chr11:67764242-67764243		72;34
K	intron_retention		chr11	-	chr11:6632684-6632894				chr11:6632683-6632684;chr11:6632894-6632895		201;117
K	alternative_acceptor	CUFF.169	chr11	-	chr11:75522582-75524647	chr11:75522615-75524647		chr11:75522582-75522614	chr11:75522581-75522582		220;237
K	alternative_first_exon	CUFF.148,CUFF.181	chr11	-	chr11:34226238-34378247	chr11:34226238-34264021	chr11:34378248-34379555	chr11:34264022-34264158			24;63
K	jcn_only_AA	CUFF.141	chr11	-	chr11:6623446-6624633;chr11:6622006-6624633	chr11:6623495-6624633					474;104
K	cassette	CUFF.181	chr11	-	chr11:118533906-118550247	chr11:118533906-118534047;chr11:118534149-118550247		chr11:118534048-118534148			612;79
N	alternative_acceptor	CUFF.174	chr11	-	chr11:102960039-102962412	chr11:102960048-102962412		chr11:102960039-102960047	chr11:102960038-102960039		47;90
K	intron_retention	CUFF.160	chr11	+	chr11:65480306-65480392				chr11:65480305-65480306;chr11:65480392-65480393		2518;18
N	alternative_acceptor	CUFF.188	chr11	-	chr11:119291089-119291578;chr11:119291097-119291578;chr11:119291046-119291578	chr11:119291159-119291578		chr11:119291046-119291088;chr11:119291089-119291096;chr11:119291097-119291158	chr11:119291045-119291046;chr11:119291088-119291089;chr11:119291096-119291097		1396;236
K	intron_retention		chr11	+	chr11:63999437-63999901				chr11:63999436-63999437;chr11:63999901-63999902		276;766
K	cassette	CUFF.174	chr11	-	chr11:102937297-102962515	chr11:102937297-102953984;chr11:102954056-102962515		chr11:102953985-102954055			19;151
K	alternative_last_exon	CUFF.168	chr11	+	chr11:74622471-74630577	chr11:74622471-74624739	chr11:74630578-74631166	chr11:74624740-74624827			133;93
N	jcn_only_AD	CUFF.186	chr11	+	chr11:119056220-119056557	chr11:119056338-119056557		chr11:119056220-119056337	chr11:119056219-119056220		74;14
N	jcn_only_AA	CUFF.143	chr11	-	chr11:8588841-8615629;chr11:8502162-8615629;chr11:8474454-8615629	chr11:8486370-8615629		chr11:8474454-8486369;chr11:8486370-8502161;chr11:8502162-8588840	chr11:8474453-8474454;chr11:8486369-8486370;chr11:8502161-8502162		121;13
N	alternative_acceptor		chr11	-	chr11:8496364-8502080;chr11:8498831-8502080	chr11:8496614-8502080		chr11:8496364-8496613;chr11:8496614-8498830	chr11:8496363-8496364;chr11:8496613-8496614		76;252
K	cassette	CUFF.145	chr11	-	chr11:8941998-8947009	chr11:8941998-8942840;chr11:8943063-8947009		chr11:8942841-8943062			35;38
N	jcn_only_AA		chr11	-	chr11:8496614-8502080;chr11:8498831-8502080	chr11:8496364-8502080		chr11:8496364-8496613;chr11:8496614-8498830	chr11:8496363-8496364;chr11:8496613-8496614		63;15
N	alternative_donor	CUFF.186	chr11	+	chr11:119056220-119056557	chr11:119056338-119056557		chr11:119056220-119056337	chr11:119056219-119056220		74;38
N	alternative_donor	CUFF.134,CUFF.182	chr11	-	chr11:118927130-118927785	chr11:118927130-118927730		chr11:118927731-118927785	chr11:118927785-118927786		422;409
K	intron_retention	CUFF.146	chr11	-	chr11:10821304-10821790				chr11:10821303-10821304;chr11:10821790-10821791		224;111
N	intron_retention		chr11	+	chr11:63999437-63999865				chr11:63999436-63999437;chr11:63999865-63999866		446;718
N	jcn_only_AA	CUFF.186	chr11	+	chr11:119056220-119056633;chr11:119056220-119056557	chr11:119056220-119056630		chr11:119056558-119056630;chr11:119056631-119056633	chr11:119056630-119056631;chr11:119056633-119056634		609;135
N	jcn_only_AA		chr11	+	chr11:118402587-118403124;chr11:118402587-118402811;chr11:118402587-118403004	chr11:118402587-118402960					419;146
N	intron_retention		chr11	+	chr11:119056220-119056633				chr11:119056219-119056220;chr11:119056633-119056634		535;42
N	alternative_acceptor	CUFF.143	chr11	-	chr11:8483457-8494709	chr11:8486370-8494709		chr11:8483457-8486369	chr11:8483456-8483457		43;21
K	intron_retention	CUFF.146	chr11	-	chr11:10820972-10821098				chr11:10820971-10820972;chr11:10821098-10821099		470;285
N	alternative_acceptor	CUFF.190	chr11	-	chr11:124766952-124767621;chr11:124767158-124767621	chr11:124767529-124767621		chr11:124766952-124767157;chr11:124767158-124767528	chr11:124766951-124766952;chr11:124767157-124767158		526;85
K	intron_retention	CUFF.155	chr11	-	chr11:62364005-62364108				chr11:62364004-62364005;chr11:62364108-62364109		89;20
N	alternative_acceptor	CUFF.186	chr11	+	chr11:119056220-119056633;chr11:119056220-119056630	chr11:119056220-119056557		chr11:119056558-119056630;chr11:119056631-119056633	chr11:119056630-119056631;chr11:119056633-119056634		605;26
N	jcn_only_AD		chr11	-	chr11:6632684-6633294	chr11:6632684-6632894		chr11:6632895-6633294	chr11:6633294-6633295		222;201
N	jcn_only_AA	CUFF.143	chr11	-	chr11:8588841-8615629;chr11:8502162-8615629;chr11:8486370-8615629	chr11:8474454-8615629		chr11:8474454-8486369;chr11:8486370-8502161;chr11:8502162-8588840	chr11:8474453-8474454;chr11:8486369-8486370;chr11:8502161-8502162		88;45
N	jcn_only_AD	CUFF.153	chr11	+	chr11:61594904-61605249;chr11:61584169-61605249;chr11:61596070-61605249	chr11:61583899-61605249		chr11:61583899-61584168;chr11:61584169-61594903;chr11:61594904-61596069	chr11:61583898-61583899;chr11:61584168-61584169;chr11:61594903-61594904		327;38
K	intron_retention		chr11	-	chr11:102960048-102962412				chr11:102960047-102960048;chr11:102962412-102962413		80;69
N	jcn_only_AA	CUFF.174	chr11	-	chr11:102960039-102962412	chr11:102960048-102962412		chr11:102960039-102960047	chr11:102960038-102960039		47;80
K	intron_retention	CUFF.146	chr11	-	chr11:10828929-10829095				chr11:10828928-10828929;chr11:10829095-10829096		5;532
N	alternative_acceptor	CUFF.167,CUFF.178	chr11	+	chr11:115267610-115267986	chr11:115267610-115267983		chr11:115267984-115267986	chr11:115267986-115267987		23;79
N	intron_retention		chr11	-	chr11:2188747-2189095				chr11:2188746-2188747;chr11:2189095-2189096		41;108
N	jcn_only_AA	CUFF.188	chr11	-	chr11:119291089-119291578;chr11:119291097-119291578;chr11:119291159-119291578	chr11:119291046-119291578		chr11:119291046-119291088;chr11:119291089-119291096;chr11:119291097-119291158	chr11:119291045-119291046;chr11:119291088-119291089;chr11:119291096-119291097		2431;34
N	alternative_acceptor		chr11	-	chr11:8496364-8502080;chr11:8496614-8502080	chr11:8498831-8502080		chr11:8496364-8496613;chr11:8496614-8498830	chr11:8496363-8496364;chr11:8496613-8496614		267;61
N	alternative_acceptor	CUFF.134	chr11	-	chr11:2188716-2189095	chr11:2188747-2189095		chr11:2188716-2188746	chr11:2188715-2188716		528;59
N	mutually_exclusive	CUFF.130	chr11	-	chr11:407958-408694,chr11:408894-409867	chr11:407958-408072,chr11:408207-409867	chr11:408695-408893	chr11:408073-408206			70;265
N	alternative_donor	CUFF.146,CUFF.174	chr11	-	chr11:10828929-10829720;chr11:10828929-10829291;chr11:10828929-10829095	chr11:10828929-10829080		chr11:10829081-10829095;chr11:10829096-10829291;chr11:10829292-10829720	chr11:10829095-10829096;chr11:10829291-10829292;chr11:10829720-10829721		61;147
N	alternative_donor	CUFF.133,CUFF.174	chr11	-	chr11:102960048-102962412;chr11:102960048-102962515	chr11:102960048-102962244		chr11:102962245-102962412;chr11:102962413-102962515	chr11:102962412-102962413;chr11:102962515-102962516		154;39
K	alternative_acceptor	CUFF.156	chr11	+	chr11:63669803-63670075	chr11:63669803-63670072		chr11:63670073-63670075	chr11:63670075-63670076		305;64
N	alternative_acceptor	CUFF.143	chr11	-	chr11:8588841-8615629;chr11:8502162-8615629;chr11:8486370-8615629	chr11:8474454-8615629		chr11:8474454-8486369;chr11:8486370-8502161;chr11:8502162-8588840	chr11:8474453-8474454;chr11:8486369-8486370;chr11:8502161-8502162		20;45
K	cassette	CUFF.164	chr11	+	chr11:67786725-67788953	chr11:67786725-67787183;chr11:67787266-67788953		chr11:67787184-67787265			142;1025
N	jcn_only_AA	CUFF.186	chr11	+	chr11:119056220-119056557;chr11:119056220-119056630	chr11:119056220-119056633		chr11:119056558-119056630;chr11:119056631-119056633	chr11:119056630-119056631;chr11:119056633-119056634		209;535
N	jcn_only_AD	CUFF.149	chr11	+	chr11:36383732-36415395;chr11:36398255-36415395	chr11:36322621-36415395		chr11:36322621-36383731;chr11:36383732-36398254	chr11:36322620-36322621;chr11:36383731-36383732		394;30
N	cassette	CUFF.181	chr11	-	chr11:118532219-118532598	chr11:118532219-118532345;chr11:118532439-118532598		chr11:118532346-118532438			63;297
K	alternative_first_exon	CUFF.141,CUFF.161	chr11	-	chr11:67771269-67772276	chr11:67771269-67771417	chr11:67772277-67772546	chr11:67771418-67771625			367;680
K	intron_retention	CUFF.138	chr11	+	chr11:3427841-3428851				chr11:3427840-3427841;chr11:3428851-3428852		200;132
N	alternative_donor	CUFF.160	chr11	+	chr11:65479917-65480236	chr11:65480069-65480236		chr11:65479917-65480068	chr11:65479916-65479917		1845;74
N	intron_retention	CUFF.178	chr11	+	chr11:115267610-115267983				chr11:115267609-115267610;chr11:115267983-115267984		47;124
N	intron_retention		chr11	-	chr11:8496614-8502080				chr11:8496613-8496614;chr11:8502080-8502081		32;16
K	intron_retention		chr11	+	chr11:119056662-119056800				chr11:119056661-119056662;chr11:119056800-119056801		752;48
K	intron_retention	CUFF.133	chr11	-	chr11:1775132-1775223				chr11:1775131-1775132;chr11:1775223-1775224		68;63
K	intron_retention		chr11	-	chr11:10827595-10828366				chr11:10827594-10827595;chr11:10828366-10828367		470;184
N	intron_retention		chr11	+	chr11:119056951-119057187				chr11:119056950-119056951;chr11:119057187-119057188		60;258
K	alternative_first_exon	CUFF.130,CUFF.155	chr11	-	chr11:410028-417293;chr11:410028-417324	chr11:410028-414822	chr11:417325-417545	chr11:414823-415071			186;586
N	alternative_donor	CUFF.149	chr11	+	chr11:36397709-36440804	chr11:36424929-36440804		chr11:36397709-36424928	chr11:36397708-36397709		11;18
K	alternative_first_exon	CUFF.148,CUFF.155	chr11	-	chr11:62366112-62367637	chr11:62366112-62366689	chr11:62367638-62367812	chr11:62366690-62366788			139;28
K	intron_retention	CUFF.179	chr11	+	chr11:117073910-117074022				chr11:117073909-117073910;chr11:117074022-117074023		337;21
N	intron_retention		chr11	-	chr11:555504-555733				chr11:555503-555504;chr11:555733-555734		13;72
K	intron_retention	CUFF.180	chr11	+	chr11:118403923-118404134				chr11:118403922-118403923;chr11:118404134-118404135		985;295
N	cassette	CUFF.156	chr11	+	chr11:63656437-63662630	chr11:63656437-63657693;chr11:63657768-63662630		chr11:63657694-63657767			28;174
N	jcn_only_AD	CUFF.188	chr11	-	chr11:119291640-119293822;chr11:119291640-119295607	chr11:119291640-119292320		chr11:119292321-119293822;chr11:119293823-119295607	chr11:119293822-119293823;chr11:119295607-119295608		4132;79
N	alternative_acceptor		chr11	+	chr11:118405071-118416833;chr11:118405071-118406222	chr11:118405071-118405221		chr11:118405222-118406222;chr11:118406223-118416833	chr11:118406222-118406223;chr11:118416833-118416834		95;157
N	cassette	CUFF.134	chr11	-	chr11:2187999-2188664	chr11:2187999-2188116;chr11:2188263-2188664		chr11:2188117-2188262			101;338
N	jcn_only_AA		chr11	+	chr11:36415562-36415945;chr11:36415562-36417663	chr11:36415562-36422546		chr11:36415946-36417663;chr11:36417664-36422546	chr11:36417663-36417664;chr11:36422546-36422547		327;249
N	intron_retention		chr11	+	chr11:118402242-118402489				chr11:118402241-118402242;chr11:118402489-118402490		96;280
N	jcn_only_AA	CUFF.130	chr11	-	chr11:406539-407061	chr11:406994-407061		chr11:406539-406993	chr11:406538-406539		266;475
K	jcn_only_AD	CUFF.136	chr11	-	chr11:2905365-2906431	chr11:2905365-2905899		chr11:2905900-2906431	chr11:2906431-2906432		56;275
K	intron_retention	CUFF.138	chr11	+	chr11:3418637-3422988				chr11:3418636-3418637;chr11:3422988-3422989	chr11:3418319-3418636	115;75
N	jcn_only_AD	CUFF.153	chr11	+	chr11:61594904-61605249;chr11:61583899-61605249;chr11:61596070-61605249	chr11:61584169-61605249		chr11:61583899-61584168;chr11:61584169-61594903;chr11:61594904-61596069	chr11:61583898-61583899;chr11:61584168-61584169;chr11:61594903-61594904		170;196
N	alternative_donor		chr11	-	chr11:8496364-8502080;chr11:8496364-8615290	chr11:8496364-8588797		chr11:8502081-8588797;chr11:8588798-8615290	chr11:8588797-8588798;chr11:8615290-8615291		95;1
N	jcn_only_AA		chr11	+	chr11:119056662-119057324	chr11:119056662-119056800		chr11:119056801-119057324	chr11:119057324-119057325		34;752
K	alternative_first_exon	CUFF.155	chr11	-	chr11:62368162-62368894	chr11:62368162-62368494	chr11:62368895-62369406	chr11:62368495-62368588			71;19
K	intron_retention	CUFF.146	chr11	-	chr11:10830291-10830428				chr11:10830290-10830291;chr11:10830428-10830429		23;269
N	jcn_only_AD	CUFF.171	chr11	-	chr11:94705358-94706452;chr11:94705358-94706436	chr11:94705358-94706661		chr11:94706437-94706452;chr11:94706453-94706661	chr11:94706452-94706453;chr11:94706661-94706662		347;148
K	intron_retention		chr11	-	chr11:10825966-10826459				chr11:10825965-10825966;chr11:10826459-10826460		458;210
N	jcn_only_AA	CUFF.160	chr11	+	chr11:65479751-65479849	chr11:65479751-65479820		chr11:65479821-65479849	chr11:65479849-65479850		319;90
N	jcn_only_AD	CUFF.153	chr11	+	chr11:61584169-61605249;chr11:61583899-61605249;chr11:61596070-61605249	chr11:61594904-61605249		chr11:61583899-61584168;chr11:61584169-61594903;chr11:61594904-61596069	chr11:61583898-61583899;chr11:61584168-61584169;chr11:61594903-61594904		285;81
K	intron_retention	CUFF.174	chr11	-	chr11:102937103-102937187				chr11:102937102-102937103;chr11:102937187-102937188		594;417
K	jcn_only_AA	CUFF.193	chr11	-	chr11:133710705-133711924	chr11:133710819-133711924		chr11:133710705-133710818	chr11:133710704-133710705		31;123
N	jcn_only_AA	CUFF.168	chr11	+	chr11:118402587-118402960;chr11:118402587-118403124;chr11:118402587-118403004	chr11:118402587-118402811					511;54
N	jcn_only_AA		chr11	+	chr11:119056338-119056630	chr11:119056338-119056557		chr11:119056558-119056630	chr11:119056630-119056631		28;14
K	intron_retention	CUFF.133	chr11	-	chr11:1776259-1778553				chr11:1776258-1776259;chr11:1778553-1778554		111;39
K	intron_retention	CUFF.143	chr11	-	chr11:8474454-8476290				chr11:8474453-8474454;chr11:8476290-8476291		387;37
N	intron_retention		chr11	-	chr11:119291089-119291578				chr11:119291088-119291089;chr11:119291578-119291579		33;491
N	alternative_donor	CUFF.134	chr11	-	chr11:2190926-2192926	chr11:2190926-2192914		chr11:2192915-2192926	chr11:2192926-2192927		84;30
N	jcn_only_AD		chr11	+	chr11:36475657-36483891;chr11:36476997-36483891	chr11:36476369-36483891					66;43
K	intron_retention	CUFF.143	chr11	-	chr11:8474454-8615629				chr11:8474453-8474454;chr11:8615629-8615630		45;7
N	jcn_only_AD	CUFF.138	chr11	+	chr11:3427841-3428851	chr11:3427946-3428851		chr11:3427841-3427945	chr11:3427840-3427841		200;18
K	intron_retention	CUFF.132	chr11	+	chr11:831033-831223				chr11:831032-831033;chr11:831223-831224		69;163
K	cassette	CUFF.146	chr11	-	chr11:10822635-10823595	chr11:10822635-10823207;chr11:10823322-10823595		chr11:10823208-10823321			76;55
N	alternative_donor	CUFF.186	chr11	+	chr11:119056220-119056630	chr11:119056338-119056630		chr11:119056220-119056337	chr11:119056219-119056220		135;44
N	jcn_only_AA	CUFF.153	chr11	+	chr11:61615757-61624482	chr11:61615757-61616152		chr11:61616153-61624482	chr11:61624482-61624483		463;279
K	intron_retention		chr11	+	chr11:118403177-118403631				chr11:118403176-118403177;chr11:118403631-118403632		1477;192
K	alternative_acceptor	CUFF.130	chr11	-	chr11:407535-407816	chr11:407569-407816		chr11:407535-407568	chr11:407534-407535		219;750
N	jcn_only_AD	CUFF.146,CUFF.174	chr11	-	chr11:10828929-10829720;chr11:10828929-10829291;chr11:10828929-10829095	chr11:10828929-10829080		chr11:10829081-10829095;chr11:10829096-10829291;chr11:10829292-10829720	chr11:10829095-10829096;chr11:10829291-10829292;chr11:10829720-10829721		49;36
N	alternative_acceptor	CUFF.146	chr11	-	chr11:10821304-10821790	chr11:10821716-10821790		chr11:10821304-10821715	chr11:10821303-10821304		224;84
N	intron_retention		chr11	-	chr11:119291159-119291578				chr11:119291158-119291159;chr11:119291578-119291579		185;418
N	alternative_donor	CUFF.186	chr11	+	chr11:119056875-119057187	chr11:119056951-119057187		chr11:119056875-119056950	chr11:119056874-119056875		286;123
N	jcn_only_AD		chr11	+	chr11:118402317-118402489;chr11:118401950-118402489	chr11:118402242-118402489		chr11:118401950-118402241;chr11:118402242-118402316	chr11:118401949-118401950;chr11:118402241-118402242		1271;96
K	intron_retention	CUFF.153	chr11	+	chr11:61630542-61630753				chr11:61630541-61630542;chr11:61630753-61630754		513;103
K	alternative_acceptor	CUFF.193	chr11	-	chr11:133710705-133711924	chr11:133710819-133711924		chr11:133710705-133710818	chr11:133710704-133710705		31;100
K	jcn_only_AD	CUFF.142,CUFF.187	chr11	-	chr11:6637735-6638589	chr11:6637735-6637891					29;220
N	intron_retention		chr11	+	chr11:828260-828574				chr11:828259-828260;chr11:828574-828575		40;414
N	intron_retention		chr11	+	chr11:36397709-36398178				chr11:36397708-36397709;chr11:36398178-36398179		50;257
K	jcn_only_AA	CUFF.169	chr11	-	chr11:75522582-75524647	chr11:75522615-75524647		chr11:75522582-75522614	chr11:75522581-75522582		220;187
K	alternative_first_exon	CUFF.135	chr11	+	chr11:2466715-2542708	chr11:2483208-2542708	chr11:2466423-2466714	chr11:2483037-2483207			29;200
K	intron_retention	CUFF.130	chr11	-	chr11:406994-407061				chr11:406993-406994;chr11:407061-407062		475;143
N	jcn_only_AD	CUFF.146	chr11	-	chr11:10828929-10829080;chr11:10828929-10829291;chr11:10828929-10829095	chr11:10828929-10829720		chr11:10829081-10829095;chr11:10829096-10829291;chr11:10829292-10829720	chr11:10829095-10829096;chr11:10829291-10829292;chr11:10829720-10829721		61;24
N	intron_retention		chr11	+	chr11:119058368-119058648				chr11:119058367-119058368;chr11:119058648-119058649		45;146
N	jcn_only_AD	CUFF.136	chr11	-	chr11:8496364-8615290;chr11:8496364-8588797	chr11:8496364-8502080		chr11:8502081-8588797;chr11:8588798-8615290	chr11:8588797-8588798;chr11:8615290-8615291		118;15
K	alternative_donor	CUFF.140	chr11	-	chr11:5701469-5706245	chr11:5701469-5706097		chr11:5706098-5706245	chr11:5706245-5706246		30;93
K	alternative_first_exon	CUFF.168	chr11	+	chr11:74624828-74630577;chr11:74622471-74630577	chr11:74630071-74630577	chr11:74624740-74624827;chr11:74622307-74622470	chr11:74629826-74630070			77;66
N	alternative_donor		chr11	-	chr11:406060-406348	chr11:406060-406141		chr11:406142-406348	chr11:406348-406349		557;319
N	jcn_only_AA	CUFF.146	chr11	-	chr11:10821304-10821790	chr11:10821716-10821790		chr11:10821304-10821715	chr11:10821303-10821304		224;31
K	intron_retention		chr11	-	chr11:406539-406842				chr11:406538-406539;chr11:406842-406843		250;344
K	jcn_only_AA	CUFF.141	chr11	-	chr11:6622006-6624633;chr11:6623495-6624633	chr11:6623446-6624633					553;26
K	intron_retention	CUFF.143	chr11	-	chr11:8476380-8478887				chr11:8476379-8476380;chr11:8478887-8478888		397;14
K	cassette	CUFF.177	chr11	+	chr11:107917097-107923386	chr11:107917097-107920616;chr11:107920794-107923386		chr11:107920617-107920793			233;41
K	intron_retention	CUFF.186	chr11	+	chr11:119059577-119059713				chr11:119059576-119059577;chr11:119059713-119059714		286;8
K	intron_retention	CUFF.188	chr11	-	chr11:119290142-119290760				chr11:119290141-119290142;chr11:119290760-119290761		2513;279
N	alternative_acceptor	CUFF.182	chr11	-	chr11:118927117-118927730	chr11:118927130-118927730		chr11:118927117-118927129	chr11:118927116-118927117		1181;16
N	intron_retention	CUFF.146	chr11	-	chr11:10828929-10829080				chr11:10828928-10828929;chr11:10829080-10829081		36;513
N	alternative_acceptor	CUFF.188	chr11	-	chr11:119291089-119291578;chr11:119291097-119291578;chr11:119291159-119291578	chr11:119291046-119291578		chr11:119291046-119291088;chr11:119291089-119291096;chr11:119291097-119291158	chr11:119291045-119291046;chr11:119291088-119291089;chr11:119291096-119291097		1598;34
K	intron_retention	CUFF.132	chr11	+	chr11:830338-830620				chr11:830337-830338;chr11:830620-830621		316;69
N	alternative_acceptor	CUFF.132	chr11	+	chr11:826267-828259	chr11:826267-828229		chr11:828230-828259	chr11:828259-828260		43;67
N	alternative_donor	CUFF.146	chr11	-	chr11:10828929-10829080;chr11:10828929-10829720;chr11:10828929-10829095	chr11:10828929-10829291		chr11:10829081-10829095;chr11:10829096-10829291;chr11:10829292-10829720	chr11:10829095-10829096;chr11:10829291-10829292;chr11:10829720-10829721		189;19
K	alternative_acceptor	CUFF.136	chr11	-	chr11:2905141-2905228	chr11:2905146-2905228		chr11:2905141-2905145	chr11:2905140-2905141		35;163
N	jcn_only_AD		chr11	+	chr11:36476997-36483891;chr11:36476369-36483891	chr11:36475657-36483891					73;36
N	intron_retention	CUFF.179	chr11	+	chr11:117070149-117070348				chr11:117070148-117070149;chr11:117070348-117070349		40;193
K	alternative_donor	CUFF.179	chr11	+	chr11:117070149-117073717	chr11:117070546-117073717		chr11:117070149-117070545	chr11:117070148-117070149		22;227
N	jcn_only_AA	CUFF.149	chr11	+	chr11:36415562-36422546;chr11:36415562-36417663	chr11:36415562-36415945		chr11:36415946-36417663;chr11:36417664-36422546	chr11:36417663-36417664;chr11:36422546-36422547		286;291
K	intron_retention	CUFF.182	chr11	-	chr11:118927117-118927730				chr11:118927116-118927117;chr11:118927730-118927731		1181;30
N	alternative_acceptor	CUFF.131	chr11	-	chr11:558980-559346	chr11:559063-559346		chr11:558980-559062	chr11:558979-558980		21;15
N	jcn_only_AD	CUFF.149	chr11	+	chr11:36322621-36415395;chr11:36398255-36415395	chr11:36383732-36415395		chr11:36322621-36383731;chr11:36383732-36398254	chr11:36322620-36322621;chr11:36383731-36383732		347;77
K	intron_retention	CUFF.138	chr11	+	chr11:3405515-3422988				chr11:3405514-3405515;chr11:3422988-3422989	chr11:3405397-3405514	13;68
N	jcn_only_AD		chr11	-	chr11:8496364-8502080;chr11:8496364-8588797	chr11:8496364-8615290		chr11:8502081-8588797;chr11:8588798-8615290	chr11:8588797-8588798;chr11:8615290-8615291		38;95
N	intron_retention		chr11	-	chr11:406539-407061				chr11:406538-406539;chr11:407061-407062		266;242
K	alternative_first_exon	CUFF.143	chr11	-	chr11:8474454-8615629	chr11:8474454-8476290	chr11:8615630-8615903	chr11:8476291-8476379			40;262
K	jcn_only_AD	CUFF.150	chr11	+	chr11:57310815-57311096	chr11:57310848-57311096		chr11:57310815-57310847	chr11:57310814-57310815		11;461
K	intron_retention	CUFF.146	chr11	-	chr11:10828929-10829823				chr11:10828928-10828929;chr11:10829823-10829824		30;372
K	intron_retention	CUFF.142	chr11	-	chr11:6636561-6636672				chr11:6636560-6636561;chr11:6636672-6636673		319;128
K	intron_retention	CUFF.106	chr10	+	chr10:70673036-70673105				chr10:70673035-70673036;chr10:70673105-70673106		70;57
K	coord_cassette	CUFF.125	chr10	+	chr10:124157491-124172435	chr10:124157491-124159858;chr10:124159905-124166091;chr10:124166190-124172435		chr10:124159859-124159904;chr10:124166092-124166189			27;223
K	alternative_first_exon	CUFF.120	chr10	+	chr10:103113986-103190101	chr10:103114367-103190101	chr10:103113820-103113985	chr10:103114273-103114366			96;26
N	jcn_only_AA	CUFF.114	chr10	-	chr10:80825577-80827144	chr10:80826344-80827144		chr10:80825577-80826343	chr10:80825576-80825577		699;10
K	intron_retention	CUFF.110	chr10	-	chr10:74094376-74095537				chr10:74094375-74094376;chr10:74095537-74095538	chr10:74092489-74094375;chr10:74095538-74095689	138;95
K	cassette	CUFF.106	chr10	+	chr10:70679738-70694554	chr10:70679738-70693954;chr10:70694117-70694554		chr10:70693955-70694116			529;31
K	jcn_only_AD	CUFF.100	chr10	-	chr10:46159291-46168126;chr10:46159291-46167719	chr10:46159291-46167697		chr10:46167698-46167719;chr10:46167720-46168126	chr10:46167719-46167720;chr10:46168126-46168127	chr10:46158990-46159290	74;344
K	alternative_first_exon	CUFF.108	chr10	-	chr10:73973090-73975534;chr10:73973090-73976578;chr10:73973090-73975964	chr10:73973090-73975539	chr10:73976579-73976983;chr10:73975965-73976127	chr10:73975540-73975867			365;222
K	jcn_only_AA	CUFF.108	chr10	-	chr10:73963283-73970489	chr10:73964264-73970489					909;148
N	jcn_only_AA	CUFF.108	chr10	-	chr10:73973036-73975964;chr10:73973090-73975964;chr10:73975868-73975964;chr10:73973110-73975964	chr10:73975613-73975964					762;70
K	cassette	CUFF.108	chr10	-	chr10:73956748-73963184	chr10:73956748-73958206;chr10:73958424-73963184		chr10:73958207-73958423			848;256
K	alternative_first_exon	CUFF.119	chr10	+	chr10:101492318-101496002;chr10:101482868-101496002	chr10:101492167-101496002	chr10:101482675-101482867	chr10:101491904-101492166			46;523
K	coord_cassette	CUFF.100	chr10	-	chr10:46113709-46143741	chr10:46113709-46120030;chr10:46120086-46121398;chr10:46122554-46135263;chr10:46135412-46143741		chr10:46120031-46120085;chr10:46121399-46122553;chr10:46135264-46135411		chr10:46113588-46113708;chr10:46143742-46143982	30;268
N	coord_cassette	CUFF.91	chr10	-	chr10:27040713-27054146	chr10:27040713-27044583;chr10:27044671-27047990;chr10:27048168-27054146		chr10:27044584-27044670;chr10:27047991-27048167			53;222
N	jcn_only_AD	CUFF.107,CUFF.113	chr10	-	chr10:78709125-78713558	chr10:78709125-78711794		chr10:78711795-78713558	chr10:78713558-78713559		403;10
N	alternative_acceptor	CUFF.113	chr10	-	chr10:78831404-78832854;chr10:78823902-78832854	chr10:78799396-78832854		chr10:78799396-78823901;chr10:78823902-78831403	chr10:78799395-78799396;chr10:78823901-78823902		8;388
N	alternative_acceptor	CUFF.113	chr10	-	chr10:78669855-78674693	chr10:78673896-78674693		chr10:78669855-78673895	chr10:78669854-78669855		527;1
K	coord_cassette	CUFF.83	chr10	+	chr10:5120170-5138601	chr10:5120170-5122937;chr10:5123094-5123873;chr10:5124078-5138601		chr10:5122938-5123093;chr10:5123874-5124077			224;102
N	alternative_acceptor	CUFF.114	chr10	-	chr10:80810175-80825503	chr10:80814486-80825503		chr10:80810175-80814485	chr10:80810174-80810175		410;0
N	intron_retention		chr10	-	chr10:78644776-78647048				chr10:78644775-78644776;chr10:78647048-78647049		51;249
K	cassette	CUFF.88	chr10	+	chr10:18280233-18284584	chr10:18280233-18282109;chr10:18282221-18284584		chr10:18282110-18282220			13;58
N	jcn_only_AA	CUFF.108	chr10	-	chr10:73973036-73975964;chr10:73973090-73975964;chr10:73975868-73975964;chr10:73975613-73975964	chr10:73973110-73975964					746;86
K	coord_cassette	CUFF.108	chr10	-	chr10:73857209-73887839	chr10:73857209-73862091;chr10:73862171-73862607;chr10:73862726-73887839		chr10:73862092-73862170;chr10:73862608-73862725			240;105
N	alternative_acceptor	CUFF.113	chr10	-	chr10:79396328-79397022;chr10:79163782-79397022	chr10:79396274-79397022		chr10:79163782-79396273;chr10:79396274-79396327	chr10:79163781-79163782;chr10:79396273-79396274		153;0
K	intron_retention	CUFF.94	chr10	-	chr10:30301980-30302411				chr10:30301979-30301980;chr10:30302411-30302412		22;16
K	alternative_first_exon	CUFF.93	chr10	+	chr10:28033878-28056286	chr10:28053703-28056286	chr10:28033715-28033877	chr10:28053580-28053702			101;44
N	jcn_only_AA	CUFF.108	chr10	-	chr10:73973036-73975964;chr10:73973090-73975964;chr10:73975613-73975964;chr10:73973110-73975964	chr10:73975868-73975964					727;106
N	jcn_only_AA	CUFF.114	chr10	-	chr10:80810175-80825503	chr10:80814486-80825503		chr10:80810175-80814485	chr10:80810174-80810175		410;10
K	cassette	CUFF.117	chr10	+	chr10:96972698-96979647	chr10:96972698-96974608;chr10:96974733-96979647		chr10:96974609-96974732			94;421
K	alternative_donor	CUFF.117	chr10	+	chr10:96961943-96966964	chr10:96961953-96966964		chr10:96961943-96961952	chr10:96961942-96961943		13;219
K	alternative_donor	CUFF.100	chr10	-	chr10:46159291-46167697;chr10:46159291-46167719	chr10:46159291-46168126		chr10:46167698-46167719;chr10:46167720-46168126	chr10:46167719-46167720;chr10:46168126-46168127	chr10:46158990-46159290	119;52
K	cassette	CUFF.100	chr10	-	chr10:46148508-46158989	chr10:46148508-46158027;chr10:46158130-46158989		chr10:46158028-46158129		chr10:46148432-46148507;chr10:46158990-46159290	80;248
N	cassette	CUFF.91	chr10	-	chr10:27040713-27047990;chr10:27040713-27054146	chr10:27040713-27044583;chr10:27044671-27047990,chr10:27044671-27054146		chr10:27044584-27044670			138;264
N	jcn_only_AA	CUFF.113	chr10	-	chr10:78637649-78647048;chr10:78637652-78647048	chr10:78644776-78647048		chr10:78637649-78637651;chr10:78637652-78644775	chr10:78637648-78637649;chr10:78637651-78637652		173;51
N	cassette	CUFF.91	chr10	-	chr10:27044671-27054146;chr10:27040713-27054146	chr10:27044671-27047990,chr10:27040713-27047990;chr10:27048165-27054146		chr10:27047991-27048164			96;243
N	alternative_acceptor	CUFF.113	chr10	-	chr10:78709125-78713558	chr10:78711918-78713558		chr10:78709125-78711917	chr10:78709124-78709125		403;0
K	intron_retention	CUFF.108	chr10	-	chr10:73964264-73970489				chr10:73964263-73964264;chr10:73970489-73970490		148;78
N	jcn_only_AD	CUFF.119	chr10	+	chr10:101507148-101514285	chr10:101510154-101514285		chr10:101507148-101510153	chr10:101507147-101507148		626;140
N	coord_cassette	CUFF.91	chr10	-	chr10:27040713-27054146	chr10:27040713-27044583;chr10:27044671-27047990;chr10:27048165-27054146		chr10:27044584-27044670;chr10:27047991-27048164			53;189
N	alternative_acceptor	CUFF.113	chr10	-	chr10:78799396-78832854;chr10:78831404-78832854	chr10:78823902-78832854		chr10:78799396-78823901;chr10:78823902-78831403	chr10:78799395-78799396;chr10:78823901-78823902		393;3
N	coord_cassette	CUFF.121	chr10	+	chr10:106937932-106970894	chr10:106937932-106959756;chr10:106959875-106960877;chr10:106961012-106970894		chr10:106959757-106959874;chr10:106960878-106961011			24;26
N	cassette	CUFF.96	chr10	+	chr10:35464634-35468061	chr10:35464634-35467816;chr10:35467915-35468061		chr10:35467817-35467914			34;1117
K	coord_cassette	CUFF.84	chr10	+	chr10:6263491-6265920	chr10:6263491-6263603;chr10:6263709-6264817;chr10:6264948-6265920		chr10:6263604-6263708;chr10:6264818-6264947			6;524
N	alternative_donor	CUFF.107,CUFF.113	chr10	-	chr10:78709125-78713558	chr10:78709125-78711794		chr10:78711795-78713558	chr10:78713558-78713559		403;1
K	cassette	CUFF.117	chr10	+	chr10:96954435-96961741	chr10:96954435-96961197;chr10:96961279-96961741		chr10:96961198-96961278			454;12
K	cassette	CUFF.84	chr10	+	chr10:6266177-6268154	chr10:6266177-6267123;chr10:6267212-6268154		chr10:6267124-6267211			518;211
K	cassette	CUFF.83	chr10	+	chr10:5077809-5138601	chr10:5077809-5120061;chr10:5120170-5138601		chr10:5120062-5120169			198;172
K	jcn_only_AA	CUFF.113	chr10	-	chr10:78778858-78787580	chr10:78782695-78787580					253;151
N	jcn_only_AA	CUFF.108	chr10	-	chr10:73973036-73975964;chr10:73975868-73975964;chr10:73975613-73975964;chr10:73973110-73975964	chr10:73973090-73975964					588;244
N	jcn_only_AD	CUFF.114,CUFF.87	chr10	-	chr10:80825577-80827144	chr10:80825577-80826204		chr10:80826205-80827144	chr10:80827144-80827145		699;7
K	intron_retention	CUFF.87	chr10	-	chr10:17645648-17645724				chr10:17645647-17645648;chr10:17645724-17645725		90;15
K	alternative_acceptor	CUFF.96	chr10	+	chr10:35495980-35500583	chr10:35495980-35500181		chr10:35500182-35500583	chr10:35500583-35500584		2801;832
N	cassette	CUFF.91	chr10	-	chr10:27059275-27112066	chr10:27059275-27065993;chr10:27066171-27112066		chr10:27065994-27066170			34;260
K	alternative_first_exon	CUFF.125	chr10	+	chr10:124134323-124152696,chr10:124134364-124152696	chr10:124151889-124152696	chr10:124134212-124134322	chr10:124151819-124151888			34;152
K	alternative_first_exon	CUFF.108	chr10	-	chr10:73963283-73970489	chr10:73963283-73964179	chr10:73970490-73970589	chr10:73964180-73964278			599;240
K	intron_retention	CUFF.125	chr10	+	chr10:124134323-124152696				chr10:124134322-124134323;chr10:124152696-124152697		21;31
K	intron_retention	CUFF.123	chr10	-	chr10:119774622-119798482				chr10:119774621-119774622;chr10:119798482-119798483		3;15
K	cassette	CUFF.91	chr10	-	chr10:27059275-27065993	chr10:27059275-27059451;chr10:27059470-27065993		chr10:27059452-27059469			32;90
N	intron_retention		chr10	-	chr10:80721165-80721655				chr10:80721164-80721165;chr10:80721655-80721656		6;38
N	alternative_donor	CUFF.91	chr10	-	chr10:27112235-27149675	chr10:27112235-27128661		chr10:27128662-27149675	chr10:27149675-27149676		366;0
N	alternative_acceptor	CUFF.91	chr10	-	chr10:27112235-27149675	chr10:27128713-27149675		chr10:27112235-27128712	chr10:27112234-27112235		366;0
N	jcn_only_AA	CUFF.91	chr10	-	chr10:27112235-27149675	chr10:27128713-27149675		chr10:27112235-27128712	chr10:27112234-27112235		366;6
K	cassette	CUFF.103	chr10	+	chr10:60029065-60036876	chr10:60029065-60035877;chr10:60035973-60036876		chr10:60035878-60035972			58;17
N	alternative_donor	CUFF.100,CUFF.113	chr10	-	chr10:78637649-78647048	chr10:78637649-78644746		chr10:78644747-78647048	chr10:78647048-78647049		41;126
N	coord_cassette	CUFF.91	chr10	-	chr10:27059275-27112066	chr10:27059275-27059451;chr10:27059470-27065993;chr10:27066171-27112066		chr10:27059452-27059469;chr10:27065994-27066170			34;100
N	alternative_acceptor	CUFF.95	chr10	-	chr10:35351991-35360126	chr10:35353045-35360126		chr10:35351991-35353044	chr10:35351990-35351991		265;43
N	jcn_only_AA	CUFF.108	chr10	-	chr10:73973090-73975964;chr10:73975868-73975964;chr10:73975613-73975964;chr10:73973110-73975964	chr10:73973036-73975964					506;326
K	cassette	CUFF.82	chr10	-	chr10:518490-532398	chr10:518490-530720;chr10:530889-532398		chr10:530721-530888		chr10:518379-518489;chr10:532399-532470	6;113
N	mutually_exclusive	CUFF.124	chr10	-	chr10:123670667-123681863,chr10:123681927-123683780	chr10:123670667-123673304,chr10:123673409-123683780	chr10:123681864-123681926	chr10:123673305-123673408			35;52
K	cassette	CUFF.82	chr10	-	chr10:410523-412214	chr10:410523-410754;chr10:410962-412214		chr10:410755-410961		chr10:410314-410522;chr10:412215-412351	15;38
N	cassette	CUFF.108	chr10	-	chr10:73857209-73862607;chr10:73857209-73887839	chr10:73857209-73862091;chr10:73862171-73862607,chr10:73862171-73887839		chr10:73862092-73862170			276;154
K	cassette	CUFF.108	chr10	-	chr10:73970590-73972944	chr10:73970590-73971945;chr10:73972044-73972944		chr10:73971946-73972043			836;80
N	alternative_acceptor	CUFF.113	chr10	-	chr10:79396274-79397022;chr10:79163782-79397022	chr10:79396328-79397022		chr10:79163782-79396273;chr10:79396274-79396327	chr10:79163781-79163782;chr10:79396273-79396274		153;0
N	jcn_only_AA	CUFF.113	chr10	-	chr10:78709125-78713558	chr10:78711918-78713558		chr10:78709125-78711917	chr10:78709124-78709125		403;6
N	jcn_only_AA	CUFF.113	chr10	-	chr10:78669855-78674693	chr10:78673896-78674693		chr10:78669855-78673895	chr10:78669854-78669855		527;23
N	jcn_only_AD	CUFF.82	chr10	-	chr10:532471-735433	chr10:532471-629528		chr10:629529-735433	chr10:735433-735434	chr10:532399-532470;chr10:735434-735606	147;4
N	cassette	CUFF.124	chr10	-	chr10:123673409-123683780	chr10:123673409-123681863;chr10:123681927-123683780		chr10:123681864-123681926			60;148
N	alternative_donor	CUFF.96	chr10	+	chr10:35437420-35464780	chr10:35464634-35464780		chr10:35437420-35464633	chr10:35437419-35437420		332;24
K	intron_retention	CUFF.96	chr10	+	chr10:35495980-35500583				chr10:35495979-35495980;chr10:35500583-35500584		2801;286
K	alternative_first_exon	CUFF.128,CUFF.82	chr10	-	chr10:127541212-127548171	chr10:127541212-127542529	chr10:127548172-127548544	chr10:127542530-127543428			38;31
N	cassette	CUFF.124	chr10	-	chr10:123673409-123687358	chr10:123673409-123683780;chr10:123683845-123687358		chr10:123683781-123683844			27;72
N	jcn_only_AD		chr10	+	chr10:35426808-35437295;chr10:35416496-35437295	chr10:35416122-35437295		chr10:35416122-35416495;chr10:35416496-35426807	chr10:35416121-35416122;chr10:35416495-35416496		971;706
K	alternative_first_exon	CUFF.89	chr10	-	chr10:18831107-18834393	chr10:18831107-18833252	chr10:18834394-18834580	chr10:18833253-18833402			25;42
N	cassette	CUFF.96	chr10	+	chr10:35464634-35477127	chr10:35464634-35468061;chr10:35468205-35477127		chr10:35468062-35468204			415;1103
K	cassette	CUFF.84	chr10	+	chr10:6266177-6274857	chr10:6266177-6268154;chr10:6268329-6274857		chr10:6268155-6268328			96;469
N	alternative_acceptor	CUFF.113	chr10	-	chr10:78637649-78647048;chr10:78637652-78647048	chr10:78644776-78647048		chr10:78637649-78637651;chr10:78637652-78644775	chr10:78637648-78637649;chr10:78637651-78637652		106;18
K	mutually_exclusive	CUFF.91	chr10	-	chr10:27040713-27047990,chr10:27048165-27054146	chr10:27040713-27044583,chr10:27044671-27054146	chr10:27047991-27048164	chr10:27044584-27044670			58;36
N	coord_cassette	CUFF.96	chr10	+	chr10:35416122-35495822	chr10:35416122-35467816;chr10:35467915-35468061;chr10:35468205-35495822		chr10:35467817-35467914;chr10:35468062-35468204			80;396
K	cassette	CUFF.125	chr10	+	chr10:124186548-124189139	chr10:124186548-124187791;chr10:124187937-124189139		chr10:124187792-124187936			55;61
K	cassette	CUFF.101	chr10	+	chr10:48231815-48235818	chr10:48231815-48235121;chr10:48235174-48235818		chr10:48235122-48235173			71;14
K	cassette	CUFF.84	chr10	+	chr10:6263491-6264817	chr10:6263491-6263603;chr10:6263709-6264817		chr10:6263604-6263708			22;501
K	cassette	CUFF.101	chr10	+	chr10:48221540-48231778	chr10:48221540-48229090;chr10:48229192-48231778		chr10:48229091-48229191			74;13
K	intron_retention	CUFF.110	chr10	-	chr10:74094376-74095591				chr10:74094375-74094376;chr10:74095591-74095592	chr10:74092489-74094375;chr10:74095592-74095689	11;127
K	alternative_first_exon	CUFF.125	chr10	+	chr10:124147500-124151818;chr10:124134478-124151818	chr10:124145704-124151818	chr10:124134127-124134477	chr10:124145561-124145703			132;40
K	alternative_last_exon	CUFF.111	chr10	-	chr10:75476951-75478917	chr10:75477924-75478917	chr10:75476801-75476950	chr10:75477773-75477923			33;56
K	alternative_first_exon	CUFF.100,CUFF.95	chr10	-	chr10:35360268-35378823,chr10:35360268-35379357;chr10:35360268-35379106	chr10:35360268-35363119	chr10:35379107-35379354	chr10:35363120-35363277			156;125
K	cassette	CUFF.84	chr10	+	chr10:6265984-6268154	chr10:6265984-6266111;chr10:6266177-6268154		chr10:6266112-6266176			7;550
N	jcn_only_AA	CUFF.113	chr10	-	chr10:78644776-78647048;chr10:78637652-78647048	chr10:78637649-78647048		chr10:78637649-78637651;chr10:78637652-78644775	chr10:78637648-78637649;chr10:78637651-78637652		183;41
K	alternative_last_exon	CUFF.124	chr10	-	chr10:123503374-123549683	chr10:123542215-123549683	chr10:123499845-123503373	chr10:123541934-123542214			167;172
N	jcn_only_AD	CUFF.113,CUFF.87	chr10	-	chr10:78669855-78674693	chr10:78669855-78673814		chr10:78673815-78674693	chr10:78674693-78674694		527;23
K	cassette	CUFF.106	chr10	+	chr10:70661228-70666466	chr10:70661228-70665981;chr10:70666094-70666466		chr10:70665982-70666093			25;168
N	jcn_only_AD	CUFF.120	chr10	+	chr10:103190210-103221737	chr10:103213314-103221737		chr10:103190210-103213313	chr10:103190209-103190210		24;35
N	coord_cassette	CUFF.96	chr10	+	chr10:35464634-35477127	chr10:35464634-35467816;chr10:35467915-35468061;chr10:35468205-35477127		chr10:35467817-35467914;chr10:35468062-35468204			415;1063
K	alternative_last_exon	CUFF.82	chr10	-	chr10:356033-372945	chr10:370960-372945	chr10:355971-356032	chr10:370480-370959		chr10:372946-373116	3;238
K	mutually_exclusive	CUFF.113	chr10	-	chr10:78729826-78761164,chr10:78761339-78771724	chr10:78729826-78734244,chr10:78734332-78771724	chr10:78761165-78761338	chr10:78734245-78734331			206;80
K	cassette	CUFF.121	chr10	+	chr10:106976881-106982873	chr10:106976881-106977601;chr10:106977724-106982873		chr10:106977602-106977723			19;25
K	jcn_only_AA	CUFF.84	chr10	+	chr10:6259155-6261531	chr10:6259155-6261481		chr10:6261482-6261531	chr10:6261531-6261532		531;4
K	alternative_first_exon	CUFF.84	chr10	+	chr10:6188460-6255585;chr10:6186977-6255585	chr10:6245300-6255585	chr10:6186826-6186976	chr10:6244735-6245299			23;673
K	jcn_only_AA	CUFF.95	chr10	-	chr10:35349853-35351887	chr10:35349897-35351887		chr10:35349853-35349896	chr10:35349852-35349853		35;203
K	cassette	CUFF.84	chr10	+	chr10:6263491-6265920	chr10:6263491-6264817;chr10:6264948-6265920		chr10:6264818-6264947			6;373
N	jcn_only_AA	CUFF.114	chr10	-	chr10:80722644-80808530	chr10:80804270-80808530		chr10:80722644-80804269	chr10:80722643-80722644		9;574
K	intron_retention	CUFF.106	chr10	+	chr10:70673036-70673146				chr10:70673035-70673036;chr10:70673146-70673147		31;119
K	jcn_only_AD	CUFF.100	chr10	-	chr10:46159291-46167697;chr10:46159291-46167719	chr10:46159291-46168126		chr10:46167698-46167719;chr10:46167720-46168126	chr10:46167719-46167720;chr10:46168126-46168127	chr10:46158990-46159290	366;52
N	jcn_only_AA		chr10	+	chr10:103113986-103213257	chr10:103113986-103190101		chr10:103190102-103213257	chr10:103213257-103213258		48;97
N	intron_retention		chr10	-	chr10:35360268-35379357				chr10:35360267-35360268;chr10:35379357-35379358		52;10
K	alternative_acceptor	CUFF.106	chr10	+	chr10:70673036-70673146	chr10:70673036-70673105		chr10:70673106-70673146	chr10:70673146-70673147		31;93
K	alternative_first_exon	CUFF.100,CUFF.110	chr10	-	chr10:46143983-46147413	chr10:46143983-46145179	chr10:46147414-46147481	chr10:46145180-46145275		chr10:46143742-46143982	302;29
N	alternative_donor		chr10	+	chr10:35426808-35437295;chr10:35416122-35437295	chr10:35416496-35437295		chr10:35416122-35416495;chr10:35416496-35426807	chr10:35416121-35416122;chr10:35416495-35416496		726;66
K	coord_cassette	CUFF.84	chr10	+	chr10:6266177-6274857	chr10:6266177-6267123;chr10:6267212-6268154;chr10:6268329-6274857		chr10:6267124-6267211;chr10:6268155-6268328			96;180
N	jcn_only_AA	CUFF.95	chr10	-	chr10:35351991-35360126	chr10:35353045-35360126		chr10:35351991-35353044	chr10:35351990-35351991		265;96
K	jcn_only_AD	CUFF.90	chr10	+	chr10:25305622-25310670	chr10:25305719-25310670		chr10:25305622-25305718	chr10:25305621-25305622		2;2
N	alternative_donor		chr10	+	chr10:35437420-35467799	chr10:35464634-35467799		chr10:35437420-35464633	chr10:35437419-35437420		229;24
N	intron_retention		chr10	-	chr10:73973110-73975964				chr10:73973109-73973110;chr10:73975964-73975965		86;29
K	cassette	CUFF.84	chr10	+	chr10:6266177-6268154	chr10:6266177-6266468;chr10:6266587-6268154		chr10:6266469-6266586			518;28
N	jcn_only_AD		chr10	-	chr10:78637652-78647048	chr10:78637652-78644746		chr10:78644747-78647048	chr10:78647048-78647049		132;16
K	cassette	CUFF.84	chr10	+	chr10:6270182-6274857	chr10:6270182-6273225;chr10:6273278-6274857		chr10:6273226-6273277			85;354
K	coord_cassette	CUFF.101	chr10	+	chr10:48216059-48221504	chr10:48216059-48216427;chr10:48216497-48218794;chr10:48218864-48221504		chr10:48216428-48216496;chr10:48218795-48218863			63;17
N	intron_retention		chr10	+	chr10:35437420-35464780				chr10:35437419-35437420;chr10:35464780-35464781		332;126
N	cassette	CUFF.91	chr10	-	chr10:27044671-27054146;chr10:27040713-27054146	chr10:27044671-27047990,chr10:27040713-27047990;chr10:27048168-27054146		chr10:27047991-27048167			96;294
N	cassette	CUFF.114	chr10	-	chr10:80705747-80721010	chr10:80705747-80720261;chr10:80720474-80721010		chr10:80720262-80720473			9;44
K	cassette	CUFF.129	chr10	-	chr10:135060555-135061294	chr10:135060555-135061057;chr10:135061206-135061294		chr10:135061058-135061205			20;380
K	alternative_first_exon	CUFF.98	chr10	+	chr10:43572780-43607546	chr10:43606914-43607546	chr10:43572428-43572779	chr10:43606655-43606913			56;17
N	cassette	CUFF.124	chr10	-	chr10:123629554-123661905	chr10:123629554-123658355;chr10:123658485-123661905		chr10:123658356-123658484			38;99
K	cassette	CUFF.91	chr10	-	chr10:27059275-27065993	chr10:27059275-27060003;chr10:27060019-27065993		chr10:27060004-27060018			32;186
N	cassette	CUFF.83	chr10	+	chr10:5123094-5138601	chr10:5123094-5123873;chr10:5124078-5138601		chr10:5123874-5124077			48;112
N	jcn_only_AD	CUFF.113,CUFF.128	chr10	-	chr10:78647274-78649208	chr10:78647274-78647552		chr10:78647553-78649208	chr10:78649208-78649209		670;16
K	jcn_only_AD	CUFF.117	chr10	+	chr10:96961943-96966964	chr10:96961953-96966964		chr10:96961943-96961952	chr10:96961942-96961943		13;435
K	alternative_acceptor	CUFF.95	chr10	-	chr10:35349853-35351887	chr10:35349897-35351887		chr10:35349853-35349896	chr10:35349852-35349853		35;101
K	intron_retention	CUFF.108	chr10	-	chr10:73892940-73912626				chr10:73892939-73892940;chr10:73912626-73912627		394;95
K	alternative_donor	CUFF.100	chr10	-	chr10:46159291-46168126;chr10:46159291-46167719	chr10:46159291-46167697		chr10:46167698-46167719;chr10:46167720-46168126	chr10:46167719-46167720;chr10:46168126-46168127	chr10:46158990-46159290	61;110
N	cassette	CUFF.124	chr10	-	chr10:123629554-123661905	chr10:123629554-123659380;chr10:123659510-123661905		chr10:123659381-123659509			38;124
N	alternative_acceptor	CUFF.119,CUFF.96	chr10	+	chr10:101507148-101514285	chr10:101507148-101510125		chr10:101510126-101514285	chr10:101514285-101514286		626;5
K	jcn_only_AA	CUFF.104	chr10	-	chr10:69575888-69583071	chr10:69575892-69583071		chr10:69575888-69575891	chr10:69575887-69575888		32;382
K	intron_retention	CUFF.108	chr10	-	chr10:73892940-73921295				chr10:73892939-73892940;chr10:73921295-73921296		93;78
N	cassette	CUFF.96	chr10	+	chr10:35468205-35490378;chr10:35468205-35495822	chr10:35468205-35477127;chr10:35477317-35495822,chr10:35477317-35490378		chr10:35477128-35477316			760;1711
N	alternative_donor	CUFF.120	chr10	+	chr10:103190210-103221737	chr10:103213314-103221737		chr10:103190210-103213313	chr10:103190209-103190210		24;0
K	jcn_only_AA	CUFF.88	chr10	+	chr10:18280233-18282112	chr10:18280233-18282109		chr10:18282110-18282112	chr10:18282112-18282113		16;57
N	jcn_only_AA		chr10	-	chr10:78637649-78644746	chr10:78637652-78644746		chr10:78637649-78637651	chr10:78637648-78637649		35;16
K	mutually_exclusive	CUFF.124	chr10	-	chr10:123629554-123659380,chr10:123659510-123661905	chr10:123629554-123658355,chr10:123658485-123661905	chr10:123659381-123659509	chr10:123658356-123658484			91;99
N	jcn_only_AD	CUFF.100,CUFF.113	chr10	-	chr10:78637649-78647048	chr10:78637649-78644746		chr10:78644747-78647048	chr10:78647048-78647049		41;35
N	alternative_acceptor	CUFF.113	chr10	-	chr10:79396328-79397022;chr10:79396274-79397022	chr10:79163782-79397022		chr10:79163782-79396273;chr10:79396274-79396327	chr10:79163781-79163782;chr10:79396273-79396274		0;153
K	intron_retention	CUFF.108	chr10	-	chr10:73975868-73975964				chr10:73975867-73975868;chr10:73975964-73975965		106;35
N	intron_retention		chr10	-	chr10:73975613-73975964				chr10:73975612-73975613;chr10:73975964-73975965		70;95
N	alternative_first_exon		chr10	-	chr10:17636383-17645558	chr10:17636383-17641288	chr10:17645559-17645858	chr10:17641289-17641410			14;52
K	jcn_only_AD	CUFF.125	chr10	+	chr10:124187833-124189139	chr10:124187937-124189139		chr10:124187833-124187936	chr10:124187832-124187833		38;52
K	alternative_donor	CUFF.100	chr10	-	chr10:46159291-46167697;chr10:46159291-46168126	chr10:46159291-46167719		chr10:46167698-46167719;chr10:46167720-46168126	chr10:46167719-46167720;chr10:46168126-46168127	chr10:46158990-46159290	162;9
K	alternative_last_exon	CUFF.105	chr10	+	chr10:69918385-69925239	chr10:69918385-69921485	chr10:69925240-69925255	chr10:69921486-69922020			25;219
K	jcn_only_AA	CUFF.118,CUFF.120	chr10	+	chr10:98092354-98095650	chr10:98092354-98095647		chr10:98095648-98095650	chr10:98095650-98095651		61;106
N	jcn_only_AA	CUFF.113	chr10	-	chr10:78799396-78832854;chr10:78831404-78832854	chr10:78823902-78832854		chr10:78799396-78823901;chr10:78823902-78831403	chr10:78799395-78799396;chr10:78823901-78823902		483;106
K	cassette	CUFF.104	chr10	-	chr10:69571422-69583071	chr10:69571422-69575797;chr10:69575892-69583071		chr10:69575798-69575891			354;370
N	alternative_last_exon	CUFF.87	chr10	-	chr10:17636383-17645558	chr10:17641411-17645558	chr10:17636204-17636382	chr10:17641003-17641410			23;53
K	coord_cassette	CUFF.100	chr10	-	chr10:46147482-46158989	chr10:46147482-46148431;chr10:46148508-46158027;chr10:46158130-46158989		chr10:46148432-46148507;chr10:46158028-46158129		chr10:46147414-46147481;chr10:46158990-46159290	39;231
N	alternative_donor	CUFF.108	chr10	-	chr10:73912747-73921295	chr10:73912747-73918703		chr10:73918704-73921295	chr10:73921295-73921296		418;71
N	jcn_only_AD	CUFF.106	chr10	+	chr10:70679738-70695761	chr10:70694675-70695761					33;45
K	cassette	CUFF.103	chr10	+	chr10:60037083-60047320	chr10:60037083-60042658;chr10:60042843-60047320		chr10:60042659-60042842			116;282
N	alternative_donor	CUFF.82	chr10	-	chr10:532471-735433	chr10:532471-629528		chr10:629529-735433	chr10:735433-735434	chr10:532399-532470;chr10:735434-735606	147;0
K	cassette	CUFF.95	chr10	-	chr10:35299371-35302626	chr10:35299371-35300775;chr10:35300893-35302626		chr10:35300776-35300892			63;186
N	jcn_only_AD	CUFF.96	chr10	+	chr10:35437420-35464780	chr10:35464634-35464780		chr10:35437420-35464633	chr10:35437419-35437420		332;56
K	alternative_donor	CUFF.90	chr10	+	chr10:25305622-25310670	chr10:25305719-25310670		chr10:25305622-25305718	chr10:25305621-25305622		2;3
N	alternative_donor	CUFF.124	chr10	-	chr10:80808690-80814352	chr10:80808690-80810038		chr10:80810039-80814352	chr10:80814352-80814353		6;44
K	jcn_only_AD	CUFF.125	chr10	+	chr10:124134323-124152696	chr10:124134364-124152696		chr10:124134323-124134363	chr10:124134322-124134323		21;27
N	alternative_donor		chr10	+	chr10:35416122-35426709	chr10:35416496-35426709		chr10:35416122-35416495	chr10:35416121-35416122		562;116
N	jcn_only_AA	CUFF.113	chr10	-	chr10:79396328-79397022;chr10:79396274-79397022	chr10:79163782-79397022		chr10:79163782-79396273;chr10:79396274-79396327	chr10:79163781-79163782;chr10:79396273-79396274		270;153
N	jcn_only_AA		chr10	+	chr10:35416496-35437295	chr10:35416496-35426709					202;167
N	cassette	CUFF.83	chr10	+	chr10:5120170-5138601	chr10:5120170-5122937;chr10:5123094-5138601		chr10:5122938-5123093			224;98
K	cassette	CUFF.108	chr10	-	chr10:73892940-73921295	chr10:73892940-73912626;chr10:73912747-73921295		chr10:73912627-73912746			93;362
K	alternative_first_exon	CUFF.108	chr10	-	chr10:73973090-73975534;chr10:73973090-73976578;chr10:73973090-73975539	chr10:73973090-73975964	chr10:73976579-73976983;chr10:73975540-73975867	chr10:73975965-73976127			412;175
N	alternative_acceptor		chr10	+	chr10:103113986-103213257	chr10:103113986-103190101		chr10:103190102-103213257	chr10:103213257-103213258		48;1
K	alternative_donor	CUFF.121	chr10	+	chr10:106937825-106959756	chr10:106937932-106959756		chr10:106937825-106937931	chr10:106937824-106937825		30;8
N	coord_cassette	CUFF.96	chr10	+	chr10:35437420-35495822	chr10:35437420-35467816;chr10:35467915-35468061;chr10:35468205-35495822		chr10:35467817-35467914;chr10:35468062-35468204			260;484
N	jcn_only_AA	CUFF.113	chr10	-	chr10:78831404-78832854;chr10:78823902-78832854	chr10:78799396-78832854		chr10:78799396-78823901;chr10:78823902-78831403	chr10:78799395-78799396;chr10:78823901-78823902		201;388
K	alternative_first_exon	CUFF.112,CUFF.89	chr10	-	chr10:76287751-76290264	chr10:76287751-76289050	chr10:76290265-76290405	chr10:76289051-76289159			67;82
K	alternative_last_exon	CUFF.100	chr10	-	chr10:46143983-46147413	chr10:46147074-46147413	chr10:46143742-46143982	chr10:46146988-46147073		chr10:46147414-46147481	413;11
N	jcn_only_AA	CUFF.95	chr10	-	chr10:35360268-35379106	chr10:35378930-35379106		chr10:35360268-35378929	chr10:35360267-35360268		29;19
N	alternative_donor	CUFF.119	chr10	+	chr10:101507148-101514285	chr10:101510154-101514285		chr10:101507148-101510153	chr10:101507147-101507148		626;8
K	alternative_acceptor	CUFF.105,CUFF.120	chr10	+	chr10:103190210-103221737	chr10:103190210-103221720		chr10:103221721-103221737	chr10:103221737-103221738		24;87
N	cassette	CUFF.96	chr10	+	chr10:35437420-35467816;chr10:35464634-35467816	chr10:35464634-35464780,chr10:35437420-35464780;chr10:35464928-35467816		chr10:35464781-35464927			630;468
K	cassette	CUFF.125	chr10	+	chr10:124186548-124189139	chr10:124186548-124187791;chr10:124187833-124189139		chr10:124187792-124187832			55;59
K	cassette	CUFF.100	chr10	-	chr10:46135412-46143741	chr10:46135412-46135688;chr10:46135870-46143741		chr10:46135689-46135869		chr10:46135264-46135411;chr10:46143742-46143982	175;30
K	alternative_donor	CUFF.110,CUFF.112	chr10	-	chr10:74094376-74095591	chr10:74094376-74095537		chr10:74095538-74095591	chr10:74095591-74095592	chr10:74092489-74094375;chr10:74095592-74095689	11;146
N	cassette	CUFF.108	chr10	-	chr10:73862171-73887839;chr10:73857209-73887839	chr10:73862171-73862607,chr10:73857209-73862607;chr10:73862726-73887839		chr10:73862608-73862725			331;162
N	alternative_donor		chr10	+	chr10:35426808-35437295;chr10:35416496-35437295	chr10:35416122-35437295		chr10:35416122-35416495;chr10:35416496-35426807	chr10:35416121-35416122;chr10:35416495-35416496		86;706
K	alternative_first_exon	CUFF.99	chr10	-	chr10:44273299-44274154	chr10:44273299-44274029	chr10:44274155-44274351	chr10:44274030-44274074			25;25
K	cassette	CUFF.112	chr10	-	chr10:76269268-76287523	chr10:76269268-76276480;chr10:76276660-76287523		chr10:76276481-76276659			96;46
N	jcn_only_AD		chr10	+	chr10:35437420-35467799	chr10:35464634-35467799		chr10:35437420-35464633	chr10:35437419-35437420		229;70
N	coord_cassette	CUFF.91	chr10	-	chr10:27059275-27112066	chr10:27059275-27060003;chr10:27060019-27065993;chr10:27066171-27112066		chr10:27060004-27060018;chr10:27065994-27066170			34;206
K	alternative_acceptor	CUFF.88	chr10	+	chr10:18280233-18282112	chr10:18280233-18282109		chr10:18282110-18282112	chr10:18282112-18282113		16;28
N	alternative_acceptor		chr10	-	chr10:78637649-78644746	chr10:78637652-78644746		chr10:78637649-78637651	chr10:78637648-78637649		35;8
N	alternative_acceptor	CUFF.113	chr10	-	chr10:78644776-78647048;chr10:78637649-78647048	chr10:78637652-78647048		chr10:78637649-78637651;chr10:78637652-78644775	chr10:78637648-78637649;chr10:78637651-78637652		59;65
K	jcn_only_AD	CUFF.121	chr10	+	chr10:106937825-106959756	chr10:106937932-106959756		chr10:106937825-106937931	chr10:106937824-106937825		30;13
N	jcn_only_AD	CUFF.91	chr10	-	chr10:27112235-27149675	chr10:27112235-27128661		chr10:27128662-27149675	chr10:27149675-27149676		366;7
N	cassette	CUFF.96	chr10	+	chr10:35485071-35495822;chr10:35484143-35495822;chr10:35485028-35495822;chr10:35477317-35495822;chr10:35468205-35495822	chr10:35468205-35490378,chr10:35485071-35490378,chr10:35477317-35490378,chr10:35485028-35490378,chr10:35484143-35490378;chr10:35490415-35495822		chr10:35490379-35490414			2084;1147
K	alternative_donor	CUFF.125	chr10	+	chr10:124134323-124152696	chr10:124134364-124152696		chr10:124134323-124134363	chr10:124134322-124134323		21;34
K	intron_retention		chr10	-	chr10:73956748-73963184				chr10:73956747-73956748;chr10:73963184-73963185		848;70
K	alternative_first_exon	CUFF.116	chr10	+	chr10:94833592-94834064	chr10:94833881-94834064	chr10:94833232-94833591	chr10:94833616-94833880			101;34
K	intron_retention	CUFF.103	chr10	+	chr10:60047518-60048035				chr10:60047517-60047518;chr10:60048035-60048036		26;196
N	coord_cassette	CUFF.96	chr10	+	chr10:35416122-35495822	chr10:35416122-35467816;chr10:35467915-35468061;chr10:35468205-35477127;chr10:35477317-35495822		chr10:35467817-35467914;chr10:35468062-35468204;chr10:35477128-35477316			80;961
N	mutually_exclusive	CUFF.124	chr10	-	chr10:123629554-123661905,chr10:123662136-123670420	chr10:123629554-123659380,chr10:123659510-123670420	chr10:123661906-123662135	chr10:123659381-123659509			41;58
K	jcn_only_AA	CUFF.98	chr10	+	chr10:43572780-43607546	chr10:43572780-43595906					65;11
K	coord_cassette	CUFF.83	chr10	+	chr10:5138770-5141518	chr10:5138770-5139625;chr10:5139743-5140993;chr10:5141072-5141518		chr10:5139626-5139742;chr10:5140994-5141071			109;433
N	jcn_only_AA	CUFF.113	chr10	-	chr10:79396328-79397022;chr10:79163782-79397022	chr10:79396274-79397022		chr10:79163782-79396273;chr10:79396274-79396327	chr10:79163781-79163782;chr10:79396273-79396274		249;174
K	jcn_only_AD	CUFF.110,CUFF.112	chr10	-	chr10:74094376-74095591	chr10:74094376-74095537		chr10:74095538-74095591	chr10:74095591-74095592	chr10:74092489-74094375;chr10:74095592-74095689	11;138
K	alternative_acceptor	CUFF.84	chr10	+	chr10:6259155-6261531	chr10:6259155-6261481		chr10:6261482-6261531	chr10:6261531-6261532		531;3
K	cassette	CUFF.104	chr10	-	chr10:69583151-69597691	chr10:69583151-69587299;chr10:69587442-69597691		chr10:69587300-69587441			549;72
N	alternative_acceptor	CUFF.114	chr10	-	chr10:80825577-80827144	chr10:80826344-80827144		chr10:80825577-80826343	chr10:80825576-80825577		699;3
N	alternative_donor	CUFF.113,CUFF.128	chr10	-	chr10:78647274-78649208	chr10:78647274-78647552		chr10:78647553-78649208	chr10:78649208-78649209		670;4
N	coord_cassette	CUFF.96	chr10	+	chr10:35437420-35495822	chr10:35437420-35467816;chr10:35467915-35468061;chr10:35468205-35477127;chr10:35477317-35495822		chr10:35467817-35467914;chr10:35468062-35468204;chr10:35477128-35477316			260;1021
N	alternative_acceptor	CUFF.113	chr10	-	chr10:78799396-78832854;chr10:78823902-78832854	chr10:78831404-78832854		chr10:78799396-78823901;chr10:78823902-78831403	chr10:78799395-78799396;chr10:78823901-78823902		391;5
K	alternative_first_exon	CUFF.124	chr10	-	chr10:123683845-123687861	chr10:123683845-123687358	chr10:123687862-123688409	chr10:123687359-123687551			145;88
N	jcn_only_AD	CUFF.124	chr10	-	chr10:80808690-80814352	chr10:80808690-80810038		chr10:80810039-80814352	chr10:80814352-80814353		6;843
K	alternative_last_exon	CUFF.118,CUFF.84	chr10	+	chr10:6268329-6274857	chr10:6268329-6270158	chr10:6274858-6277594	chr10:6270159-6270315			51;406
K	alternative_first_exon	CUFF.108	chr10	-	chr10:73973090-73975534;chr10:73973090-73975539;chr10:73973090-73975964	chr10:73973090-73976578	chr10:73975540-73975867;chr10:73975965-73976127	chr10:73976579-73976983			449;138
K	jcn_only_AA	CUFF.106	chr10	+	chr10:70673036-70673146	chr10:70673036-70673105		chr10:70673106-70673146	chr10:70673146-70673147		31;70
K	intron_retention	CUFF.123	chr10	-	chr10:119765350-119768592				chr10:119765349-119765350;chr10:119768592-119768593		24;23
K	cassette	CUFF.100	chr10	-	chr10:46147482-46158989	chr10:46147482-46148431;chr10:46148508-46158989		chr10:46148432-46148507		chr10:46147414-46147481;chr10:46158990-46159290	39;185
K	alternative_acceptor	CUFF.118,CUFF.120	chr10	+	chr10:98092354-98095650	chr10:98092354-98095647		chr10:98095648-98095650	chr10:98095650-98095651		61;53
K	cassette	CUFF.113	chr10	-	chr10:78729826-78771724	chr10:78729826-78734244;chr10:78734332-78771724		chr10:78734245-78734331			80;86
N	alternative_acceptor	CUFF.114	chr10	-	chr10:80722644-80808530	chr10:80804270-80808530		chr10:80722644-80804269	chr10:80722643-80722644		9;7
N	alternative_acceptor	CUFF.95	chr10	-	chr10:35360268-35379106	chr10:35378930-35379106		chr10:35360268-35378929	chr10:35360267-35360268		29;1
K	alternative_donor	CUFF.125	chr10	+	chr10:124187833-124189139	chr10:124187937-124189139		chr10:124187833-124187936	chr10:124187832-124187833		38;29
K	alternative_acceptor	CUFF.104	chr10	-	chr10:69575888-69583071	chr10:69575892-69583071		chr10:69575888-69575891	chr10:69575887-69575888		32;189
N	jcn_only_AA	CUFF.113	chr10	-	chr10:78644776-78647048;chr10:78637649-78647048	chr10:78637652-78647048		chr10:78637649-78637651;chr10:78637652-78644775	chr10:78637648-78637649;chr10:78637651-78637652		93;132
N	alternative_donor	CUFF.114,CUFF.87	chr10	-	chr10:80825577-80827144	chr10:80825577-80826204		chr10:80826205-80827144	chr10:80827144-80827145		699;1
N	jcn_only_AA	CUFF.119,CUFF.96	chr10	+	chr10:101507148-101514285	chr10:101507148-101510125		chr10:101510126-101514285	chr10:101514285-101514286		626;131
N	alternative_acceptor	CUFF.113	chr10	-	chr10:78771802-78778770	chr10:78772316-78778770		chr10:78771802-78772315	chr10:78771801-78771802		479;35
K	jcn_only_AA	CUFF.128	chr10	-	chr10:127541212-127548171	chr10:127542773-127548171					31;24
N	jcn_only_AD		chr10	+	chr10:35426808-35437295;chr10:35416122-35437295	chr10:35416496-35437295		chr10:35416122-35416495;chr10:35416496-35426807	chr10:35416121-35416122;chr10:35416495-35416496		1476;202
K	cassette	CUFF.88	chr10	+	chr10:18280233-18284584	chr10:18280233-18282112;chr10:18282221-18284584		chr10:18282113-18282220			13;42
N	jcn_only_AD		chr10	+	chr10:35416122-35426709	chr10:35416496-35426709		chr10:35416122-35416495	chr10:35416121-35416122		562;167
K	alternative_last_exon	CUFF.87	chr10	-	chr10:17646047-17659081	chr10:17657964-17659081	chr10:17645929-17646046	chr10:17657406-17657963			45;57
K	coord_cassette	CUFF.84	chr10	+	chr10:6265984-6268154	chr10:6265984-6266111;chr10:6266177-6266468;chr10:6266587-6268154		chr10:6266112-6266176;chr10:6266469-6266586			7;27
N	alternative_acceptor	CUFF.113	chr10	-	chr10:78644776-78647048;chr10:78637652-78647048	chr10:78637649-78647048		chr10:78637649-78637651;chr10:78637652-78644775	chr10:78637648-78637649;chr10:78637651-78637652		83;41
N	jcn_only_AD	CUFF.108	chr10	-	chr10:73912747-73921295	chr10:73912747-73918703		chr10:73918704-73921295	chr10:73921295-73921296		418;198
N	alternative_donor		chr10	-	chr10:78637652-78647048	chr10:78637652-78644746		chr10:78644747-78647048	chr10:78647048-78647049		132;125
K	jcn_only_AD	CUFF.100	chr10	-	chr10:46159291-46167697;chr10:46159291-46168126	chr10:46159291-46167719		chr10:46167698-46167719;chr10:46167720-46168126	chr10:46167719-46167720;chr10:46168126-46168127	chr10:46158990-46159290	395;23
N	mutually_exclusive	CUFF.108	chr10	-	chr10:73857209-73862607,chr10:73862726-73887839	chr10:73857209-73862091,chr10:73862171-73887839	chr10:73862608-73862725	chr10:73862092-73862170			33;60
N	alternative_donor		chr10	+	chr10:35416496-35437295;chr10:35416122-35437295	chr10:35426808-35437295		chr10:35416122-35416495;chr10:35416496-35426807	chr10:35416121-35416122;chr10:35416495-35416496		772;20
K	alternative_last_exon	CUFF.115,CUFF.98	chr10	+	chr10:88993347-88994873	chr10:88993347-88993679	chr10:88994874-88996759	chr10:88993680-88994735			20;41
N	intron_retention		chr10	+	chr10:35437420-35467816				chr10:35437419-35437420;chr10:35467816-35467817		552;77
K	intron_retention	CUFF.105	chr10	+	chr10:69921510-69925458				chr10:69921509-69921510;chr10:69925458-69925459		17;14
K	jcn_only_AA	CUFF.105,CUFF.120	chr10	+	chr10:103190210-103221737	chr10:103190210-103221720		chr10:103221721-103221737	chr10:103221737-103221738		24;182
K	alternative_first_exon	CUFF.110,CUFF.82	chr10	-	chr10:415574-428586	chr10:415574-418952	chr10:428587-428701	chr10:418953-419152		chr10:415434-415573	41;16
K	cassette	CUFF.88	chr10	+	chr10:18240955-18250509	chr10:18240955-18242119;chr10:18242467-18250509		chr10:18242120-18242466			40;40
N	coord_cassette	CUFF.124	chr10	-	chr10:123673409-123687358	chr10:123673409-123681863;chr10:123681927-123683780;chr10:123683845-123687358		chr10:123681864-123681926;chr10:123683781-123683844			27;104
K	cassette	CUFF.104	chr10	-	chr10:69571422-69583071	chr10:69571422-69575797;chr10:69575888-69583071		chr10:69575798-69575887			354;232
N	jcn_only_AD		chr10	+	chr10:35416496-35437295;chr10:35416122-35437295	chr10:35426808-35437295		chr10:35416122-35416495;chr10:35416496-35426807	chr10:35416121-35416122;chr10:35416495-35416496		908;770
K	intron_retention	CUFF.125	chr10	+	chr10:124134364-124152696				chr10:124134363-124134364;chr10:124152696-124152697		27;68
K	intron_retention	CUFF.108	chr10	-	chr10:73973090-73975964				chr10:73973089-73973090;chr10:73975964-73975965		244;39
K	mutually_exclusive	CUFF.91	chr10	-	chr10:27040713-27047990,chr10:27048168-27054146	chr10:27040713-27044583,chr10:27044671-27054146	chr10:27047991-27048167	chr10:27044584-27044670			74;36
N	jcn_only_AA	CUFF.113	chr10	-	chr10:78771802-78778770	chr10:78772316-78778770		chr10:78771802-78772315	chr10:78771801-78771802		479;31
N	coord_cassette	CUFF.83	chr10	+	chr10:5077809-5138601	chr10:5077809-5120061;chr10:5120170-5122937;chr10:5123094-5138601		chr10:5120062-5120169;chr10:5122938-5123093			198;48
N	jcn_only_AA	CUFF.113	chr10	-	chr10:79396274-79397022;chr10:79163782-79397022	chr10:79396328-79397022		chr10:79163782-79396273;chr10:79396274-79396327	chr10:79163781-79163782;chr10:79396273-79396274		327;96
N	jcn_only_AA	CUFF.113	chr10	-	chr10:78799396-78832854;chr10:78823902-78832854	chr10:78831404-78832854		chr10:78799396-78823901;chr10:78823902-78831403	chr10:78799395-78799396;chr10:78823901-78823902		494;95
K	coord_cassette	CUFF.96	chr10	+	chr10:35468205-35495822	chr10:35468205-35477127;chr10:35477317-35490378;chr10:35490415-35495822		chr10:35477128-35477316;chr10:35490379-35490414			555;798
K	intron_retention	CUFF.108	chr10	-	chr10:73973036-73975964				chr10:73973035-73973036;chr10:73975964-73975965		326;199
K	jcn_only_AA	CUFF.96	chr10	+	chr10:35495980-35500583	chr10:35495980-35500181		chr10:35500182-35500583	chr10:35500583-35500584		2801;767
K	jcn_only_AD	CUFF.105	chr10	+	chr10:69866559-69902696	chr10:69882098-69902696					3;151
K	cassette	CUFF.124	chr10	-	chr10:123670667-123681863	chr10:123670667-123673304;chr10:123673409-123681863		chr10:123673305-123673408			47;194
K	cassette	CUFF.111	chr10	-	chr10:75479058-75480295	chr10:75479058-75479764;chr10:75479953-75480295		chr10:75479765-75479952			63;38
N	jcn_only_AA		chr10	-	chr10:78737397-78771724	chr10:78755467-78771724					15;21
K	alternative_first_exon	CUFF.107,CUFF.108	chr10	-	chr10:73515224-73520624	chr10:73515224-73517334	chr10:73520625-73520681	chr10:73517335-73517478			4;25
K	alternative_first_exon	CUFF.110	chr10	-	chr10:74103270-74113099	chr10:74103270-74104707	chr10:74113100-74113198	chr10:74104708-74104885		chr10:74103124-74103269	11;119
K	cassette	CUFF.124	chr10	-	chr10:123659510-123670420	chr10:123659510-123661905;chr10:123662136-123670420		chr10:123661906-123662135			70;234
N	coord_cassette	CUFF.96	chr10	+	chr10:35464634-35468061	chr10:35464634-35464780;chr10:35464928-35467816;chr10:35467915-35468061		chr10:35464781-35464927;chr10:35467817-35467914			34;304
K	cassette	CUFF.123	chr10	-	chr10:119774622-119798482	chr10:119774622-119793492;chr10:119793553-119798482		chr10:119793493-119793552			3;29
K	cassette	CUFF.113	chr10	-	chr10:78729826-78771724	chr10:78729826-78761164;chr10:78761339-78771724		chr10:78761165-78761338			80;206
N	alternative_donor	CUFF.113,CUFF.87	chr10	-	chr10:78669855-78674693	chr10:78669855-78673814		chr10:78673815-78674693	chr10:78674693-78674694		527;3
K	cassette	CUFF.456	chr17	-	chr17:76994046-76996181;chr17:76994046-77005745	chr17:76994046-76994229;chr17:76994369-76996181,chr17:76994369-77005745		chr17:76994230-76994368			1162;294
N	intron_retention		chr17	-	chr17:15586686-15587509				chr17:15586685-15586686;chr17:15587509-15587510		41;62
N	coord_cassette	CUFF.456	chr17	-	chr17:76993727-77005745	chr17:76993727-76993921;chr17:76994046-76994229;chr17:76994369-77005745		chr17:76993922-76994045;chr17:76994230-76994368			27;112
N	jcn_only_AD	CUFF.452	chr17	+	chr17:66511708-66518896	chr17:66511718-66518896		chr17:66511708-66511717	chr17:66511707-66511708		22;867
N	jcn_only_AA	CUFF.457	chr17	-	chr17:79250934-79254408	chr17:79253961-79254408		chr17:79250934-79253960	chr17:79250933-79250934		187;89
K	coord_cassette	CUFF.459	chr17	-	chr17:79354385-79358928	chr17:79354385-79355676;chr17:79355741-79358745;chr17:79358833-79358928		chr17:79355677-79355740;chr17:79358746-79358832			71;838
N	jcn_only_AD	CUFF.413	chr17	+	chr17:6349508-6350782;chr17:6348663-6350782	chr17:6348725-6350782		chr17:6348663-6348724;chr17:6348725-6349507	chr17:6348662-6348663;chr17:6348724-6348725		278;561
N	jcn_only_AD	CUFF.461	chr17	-	chr17:79894738-79895137;chr17:79894738-79895133;chr17:79894738-79895055;chr17:79894738-79895068;chr17:79894738-79894845;chr17:79894738-79895103	chr17:79894738-79895403		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		992;39
N	jcn_only_AD	CUFF.413	chr17	+	chr17:6352728-6353347	chr17:6353099-6353347		chr17:6352728-6353098	chr17:6352727-6352728		491;64
K	intron_retention	CUFF.452	chr17	+	chr17:66511261-66511534				chr17:66511260-66511261;chr17:66511534-66511535		179;141
K	jcn_only_AA	CUFF.412	chr17	-	chr17:5405193-5421065;chr17:5418838-5421065	chr17:5409298-5421065				chr17:5421066-5421207	316;5
N	jcn_only_AA		chr17	+	chr17:61574347-61584416	chr17:61574347-61574497		chr17:61574498-61584416	chr17:61584416-61584417		7;397
N	jcn_only_AA	CUFF.412	chr17	-	chr17:5487280-5487612	chr17:5487424-5487612		chr17:5487280-5487423	chr17:5487279-5487280	chr17:5487613-5487820;chr17:5487007-5487279	2;61
K	intron_retention		chr17	-	chr17:57775340-57776231				chr17:57775339-57775340;chr17:57776231-57776232		48;25
K	intron_retention		chr17	+	chr17:25969375-25972886				chr17:25969374-25969375;chr17:25972886-25972887		189;50
N	jcn_only_AA	CUFF.413	chr17	+	chr17:6348725-6350782	chr17:6348725-6349414		chr17:6349415-6350782	chr17:6350782-6350783		561;48
K	jcn_only_AD	CUFF.410	chr17	-	chr17:1615694-1617149	chr17:1615694-1616996		chr17:1616997-1617149	chr17:1617149-1617150		84;59
N	intron_retention		chr17	+	chr17:66508637-66511534				chr17:66508636-66508637;chr17:66511534-66511535		62;164
N	cassette	CUFF.409	chr17	-	chr17:651273-655372	chr17:651273-653053;chr17:653150-655372		chr17:653054-653149			57;109
N	alternative_donor	CUFF.452	chr17	+	chr17:66509413-66511534;chr17:66511261-66511534;chr17:66511294-66511534;chr17:66508637-66511534	chr17:66508721-66511534		chr17:66508637-66508720;chr17:66508721-66509412;chr17:66509413-66511260;chr17:66511261-66511293	chr17:66508636-66508637;chr17:66508720-66508721;chr17:66509412-66509413;chr17:66511260-66511261		140;30
N	cassette	CUFF.435	chr17	-	chr17:40738156-40739851	chr17:40738156-40738782;chr17:40738910-40739851		chr17:40738783-40738909			41;200
K	intron_retention	CUFF.450	chr17	+	chr17:61908977-61909083				chr17:61908976-61908977;chr17:61909083-61909084		962;75
N	jcn_only_AD		chr17	+	chr17:29706376-29708890;chr17:29707246-29708890	chr17:29706042-29708890					77;84
N	alternative_acceptor	CUFF.460	chr17	-	chr17:79479142-79479257	chr17:79479169-79479257		chr17:79479142-79479168	chr17:79479141-79479142		37;720
N	intron_retention		chr17	-	chr17:79894738-79895068				chr17:79894737-79894738;chr17:79895068-79895069		143;174
K	alternative_acceptor	CUFF.415	chr17	-	chr17:15498141-15499827	chr17:15498205-15499827		chr17:15498141-15498204	chr17:15498140-15498141		115;127
N	alternative_donor	CUFF.461	chr17	-	chr17:79894738-79895137;chr17:79894738-79895403;chr17:79894738-79895055;chr17:79894738-79895068;chr17:79894738-79894845;chr17:79894738-79895103	chr17:79894738-79895133		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		310;63
K	jcn_only_AD	CUFF.412,CUFF.456	chr17	-	chr17:5436305-5436623	chr17:5436305-5436611		chr17:5436612-5436623	chr17:5436623-5436624	chr17:5436142-5436304;chr17:5436624-5436704	269;26
K	alternative_first_exon	CUFF.409,CUFF.465	chr17	-	chr17:79993940-79994066,chr17:79993940-79994057	chr17:79993940-79994022	chr17:79994067-79994184	chr17:79994023-79994057			1041;37
N	alternative_donor	CUFF.443	chr17	-	chr17:56082403-56082774;chr17:56082403-56082758	chr17:56082403-56083870		chr17:56082759-56082774;chr17:56082775-56083870	chr17:56082774-56082775;chr17:56083870-56083871		191;90
K	intron_retention		chr17	-	chr17:1616199-1616996				chr17:1616198-1616199;chr17:1616996-1616997		459;292
N	cassette	CUFF.456	chr17	-	chr17:76994046-77001453;chr17:76994369-77005745;chr17:76994046-77005745	chr17:76994369-76996181,chr17:76994046-76996181;chr17:76996353-77001453,chr17:76996353-77005745		chr17:76996182-76996352			385;1012
K	intron_retention	CUFF.452	chr17	+	chr17:66521100-66521894				chr17:66521099-66521100;chr17:66521894-66521895		434;37
K	alternative_first_exon	CUFF.441	chr17	-	chr17:47304121-47307938	chr17:47304121-47307829	chr17:47307939-47308214	chr17:47307830-47307890			95;105
K	alternative_last_exon	CUFF.452	chr17	+	chr17:66526143-66547224	chr17:66526143-66526417	chr17:66547225-66547559	chr17:66526418-66529036			50;503
K	cassette	CUFF.412	chr17	-	chr17:5421208-5424843	chr17:5421208-5424200;chr17:5424333-5424843		chr17:5424201-5424332		chr17:5421066-5421207;chr17:5424844-5425106	169;129
K	alternative_donor	CUFF.465	chr17	-	chr17:79993940-79994066	chr17:79993940-79994057		chr17:79994058-79994066	chr17:79994066-79994067		1081;171
N	jcn_only_AD	CUFF.413	chr17	+	chr17:6352728-6353681	chr17:6353393-6353681					111;325
N	intron_retention	CUFF.450	chr17	+	chr17:61908296-61908379				chr17:61908295-61908296;chr17:61908379-61908380		144;119
N	alternative_donor	CUFF.426	chr17	+	chr17:29626625-29652837;chr17:29592358-29652837	chr17:29645583-29652837		chr17:29592358-29626624;chr17:29626625-29645582	chr17:29592357-29592358;chr17:29626624-29626625		28;0
N	alternative_donor	CUFF.452	chr17	+	chr17:66511708-66518896	chr17:66511718-66518896		chr17:66511708-66511717	chr17:66511707-66511708		22;483
N	jcn_only_AA	CUFF.411	chr17	+	chr17:1939386-1939822	chr17:1939386-1939722		chr17:1939723-1939822	chr17:1939822-1939823		347;18
N	alternative_acceptor	CUFF.416	chr17	-	chr17:15580592-15580888	chr17:15580595-15580888		chr17:15580592-15580594	chr17:15580591-15580592		210;27
N	jcn_only_AA	CUFF.457	chr17	-	chr17:79258696-79263490	chr17:79262746-79263490		chr17:79258696-79262745	chr17:79258695-79258696		85;134
N	jcn_only_AA	CUFF.413	chr17	+	chr17:6352728-6353681	chr17:6352728-6353347		chr17:6353348-6353681	chr17:6353681-6353682		111;491
N	alternative_donor	CUFF.452	chr17	+	chr17:66508721-66511534;chr17:66511261-66511534;chr17:66511294-66511534;chr17:66508637-66511534	chr17:66509413-66511534		chr17:66508637-66508720;chr17:66508721-66509412;chr17:66509413-66511260;chr17:66511261-66511293	chr17:66508636-66508637;chr17:66508720-66508721;chr17:66509412-66509413;chr17:66511260-66511261		154;16
N	coord_cassette	CUFF.456	chr17	-	chr17:76993727-77005745	chr17:76993727-76993921;chr17:76994046-76994229;chr17:76994369-76996181;chr17:76996353-77005745		chr17:76993922-76994045;chr17:76994230-76994368;chr17:76996182-76996352			27;188
N	jcn_only_AA	CUFF.413	chr17	+	chr17:6353393-6353681	chr17:6353393-6353558		chr17:6353559-6353681	chr17:6353681-6353682		325;65
K	intron_retention	CUFF.435	chr17	-	chr17:40738910-40744073				chr17:40738909-40738910;chr17:40744073-40744074		217;44
K	intron_retention	CUFF.466	chr17	+	chr17:80416707-80417875				chr17:80416706-80416707;chr17:80417875-80417876		61;4
K	intron_retention	CUFF.457	chr17	-	chr17:79220859-79225292				chr17:79220858-79220859;chr17:79225292-79225293		63;113
N	alternative_acceptor	CUFF.457	chr17	-	chr17:79258696-79263490	chr17:79262746-79263490		chr17:79258696-79262745	chr17:79258695-79258696		85;30
N	jcn_only_AD	CUFF.450	chr17	+	chr17:61907862-61908395	chr17:61908296-61908395					42;2601
N	intron_retention	CUFF.460	chr17	-	chr17:79479387-79479631				chr17:79479386-79479387;chr17:79479631-79479632		6;37
N	coord_cassette	CUFF.456	chr17	-	chr17:76994046-77001453	chr17:76994046-76994229;chr17:76994369-76996181;chr17:76996353-77001453		chr17:76994230-76994368;chr17:76996182-76996352			79;201
N	cassette	CUFF.426	chr17	+	chr17:29576138-29585361	chr17:29576138-29584704;chr17:29584745-29585361		chr17:29584705-29584744			27;230
K	intron_retention	CUFF.423	chr17	+	chr17:26554520-26554633				chr17:26554519-26554520;chr17:26554633-26554634		54;31
K	intron_retention		chr17	-	chr17:79894738-79894845				chr17:79894737-79894738;chr17:79894845-79894846		166;102
N	cassette	CUFF.465	chr17	-	chr17:79994890-79995506	chr17:79994890-79995325;chr17:79995424-79995506		chr17:79995326-79995423			164;348
N	jcn_only_AD	CUFF.461	chr17	-	chr17:79894738-79895137;chr17:79894738-79895403;chr17:79894738-79895055;chr17:79894738-79895068;chr17:79894738-79894845;chr17:79894738-79895103	chr17:79894738-79895133		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		805;226
N	jcn_only_AA	CUFF.410	chr17	-	chr17:1616350-1617149;chr17:1616190-1617149;chr17:1615694-1617149;chr17:1615941-1617149	chr17:1616199-1617149		chr17:1615694-1615940;chr17:1615941-1616189;chr17:1616190-1616198;chr17:1616199-1616349	chr17:1615693-1615694;chr17:1615940-1615941;chr17:1616189-1616190;chr17:1616198-1616199		559;144
K	intron_retention	CUFF.450	chr17	+	chr17:61904875-61905497				chr17:61904874-61904875;chr17:61905497-61905498		568;113
K	intron_retention	CUFF.441	chr17	-	chr17:47304121-47307938				chr17:47304120-47304121;chr17:47307938-47307939		38;52
K	coord_cassette	CUFF.426	chr17	+	chr17:29576138-29585361	chr17:29576138-29579955;chr17:29580019-29584704;chr17:29584745-29585361		chr17:29579956-29580018;chr17:29584705-29584744			27;371
N	mutually_exclusive	CUFF.459	chr17	-	chr17:79354385-79358745,chr17:79358833-79358928	chr17:79354385-79355676,chr17:79355741-79358928	chr17:79358746-79358832	chr17:79355677-79355740			25;69
N	alternative_acceptor	CUFF.461	chr17	-	chr17:79893021-79893998	chr17:79893393-79893998		chr17:79893021-79893392	chr17:79893020-79893021		57;662
K	intron_retention	CUFF.450	chr17	+	chr17:61904875-61905033				chr17:61904874-61904875;chr17:61905033-61905034		65;111
N	jcn_only_AA	CUFF.410	chr17	-	chr17:1616350-1617149;chr17:1616199-1617149;chr17:1616190-1617149;chr17:1615694-1617149	chr17:1615941-1617149		chr17:1615694-1615940;chr17:1615941-1616189;chr17:1616190-1616198;chr17:1616199-1616349	chr17:1615693-1615694;chr17:1615940-1615941;chr17:1616189-1616190;chr17:1616198-1616199		649;54
K	intron_retention		chr17	+	chr17:25970647-25972339				chr17:25970646-25970647;chr17:25972339-25972340		263;53
N	intron_retention		chr17	-	chr17:56082403-56082758				chr17:56082402-56082403;chr17:56082758-56082759		45;196
K	intron_retention	CUFF.456	chr17	-	chr17:76991304-76993073				chr17:76991303-76991304;chr17:76993073-76993074		285;13
N	alternative_donor	CUFF.461	chr17	-	chr17:79894738-79895137;chr17:79894738-79895403;chr17:79894738-79895133;chr17:79894738-79895055;chr17:79894738-79895068;chr17:79894738-79895103	chr17:79894738-79894845		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		283;90
N	alternative_donor	CUFF.435	chr17	-	chr17:40738910-40744073	chr17:40738910-40739851		chr17:40739852-40744073	chr17:40744073-40744074		217;6
K	intron_retention	CUFF.462	chr17	-	chr17:79916872-79917346				chr17:79916871-79916872;chr17:79917346-79917347	chr17:79916811-79916871;chr17:79917347-79917442	466;58
K	alternative_last_exon	CUFF.418,CUFF.447	chr17	+	chr17:17380580-17394592	chr17:17380580-17388613	chr17:17394593-17396639	chr17:17388614-17388989			10;50
N	intron_retention		chr17	-	chr17:15517057-15517146				chr17:15517056-15517057;chr17:15517146-15517147		10;89
N	alternative_acceptor	CUFF.416	chr17	-	chr17:15586472-15587509	chr17:15586686-15587509		chr17:15586472-15586685	chr17:15586471-15586472		664;142
N	intron_retention		chr17	+	chr17:1945170-1946269				chr17:1945169-1945170;chr17:1946269-1946270		174;243
N	alternative_donor		chr17	-	chr17:79263609-79269221	chr17:79263609-79268622		chr17:79268623-79269221	chr17:79269221-79269222		35;76
N	jcn_only_AA	CUFF.454	chr17	+	chr17:29706042-29708890	chr17:29706042-29706123					84;16
N	jcn_only_AD		chr17	-	chr17:1616190-1617149	chr17:1616190-1616996		chr17:1616997-1617149	chr17:1617149-1617150		106;165
N	cassette	CUFF.416	chr17	-	chr17:15580595-15584178	chr17:15580595-15580888;chr17:15581036-15584178		chr17:15580889-15581035			80;197
N	cassette	CUFF.450	chr17	+	chr17:61904875-61905478;chr17:61904875-61905497	chr17:61904875-61905210;chr17:61905284-61905478,chr17:61905284-61905497		chr17:61905211-61905283			632;253
K	intron_retention	CUFF.410	chr17	-	chr17:1615694-1616996				chr17:1615693-1615694;chr17:1616996-1616997		59;210
K	alternative_donor	CUFF.440	chr17	+	chr17:46990328-46993437	chr17:46990384-46993437		chr17:46990328-46990383	chr17:46990327-46990328		115;119
N	intron_retention	CUFF.411	chr17	+	chr17:1939386-1939722				chr17:1939385-1939386;chr17:1939722-1939723		18;50
N	intron_retention		chr17	+	chr17:6353099-6353347				chr17:6353098-6353099;chr17:6353347-6353348		64;159
K	jcn_only_AA	CUFF.421	chr17	-	chr17:21437283-21438688	chr17:21437833-21438688		chr17:21437283-21437832	chr17:21437282-21437283	chr17:21438689-21438799;chr17:21435641-21437282	24;6
N	jcn_only_AA	CUFF.416	chr17	-	chr17:15580592-15580888	chr17:15580595-15580888		chr17:15580592-15580594	chr17:15580591-15580592		210;55
N	cassette	CUFF.416	chr17	-	chr17:15584268-15586349;chr17:15584537-15586349	chr17:15584537-15586167,chr17:15584268-15586167;chr17:15586266-15586349		chr17:15586168-15586265			466;378
N	alternative_acceptor	CUFF.422	chr17	+	chr17:25967800-25969263	chr17:25967800-25967990		chr17:25967991-25969263	chr17:25969263-25969264		839;11
N	alternative_acceptor	CUFF.412	chr17	-	chr17:5487280-5487612	chr17:5487424-5487612		chr17:5487280-5487423	chr17:5487279-5487280	chr17:5487613-5487820;chr17:5487007-5487279	2;167
K	intron_retention	CUFF.452	chr17	+	chr17:66522054-66523980				chr17:66522053-66522054;chr17:66523980-66523981		699;54
K	intron_retention	CUFF.460	chr17	-	chr17:79478653-79478788				chr17:79478652-79478653;chr17:79478788-79478789		112;85
N	jcn_only_AD		chr17	-	chr17:1616199-1617149	chr17:1616199-1616996		chr17:1616997-1617149	chr17:1617149-1617150		144;459
N	intron_retention		chr17	-	chr17:79994890-79995489				chr17:79994889-79994890;chr17:79995489-79995490		110;432
N	jcn_only_AD	CUFF.413	chr17	+	chr17:6349508-6350782;chr17:6348725-6350782	chr17:6348663-6350782		chr17:6348663-6348724;chr17:6348725-6349507	chr17:6348662-6348663;chr17:6348724-6348725		610;230
N	alternative_first_exon	CUFF.441	chr17	-	chr17:15492542-15499827	chr17:15492542-15496650	chr17:15499828-15499976	chr17:15496651-15496809			51;110
N	alternative_last_exon	CUFF.413	chr17	+	chr17:6352728-6353681,chr17:6352728-6353347	chr17:6352728-6353023	chr17:6353682-6354789	chr17:6353024-6353342			273;516
N	jcn_only_AA	CUFF.465	chr17	-	chr17:79994185-79994259	chr17:79994199-79994259		chr17:79994185-79994198	chr17:79994184-79994185		1440;62
K	intron_retention	CUFF.466	chr17	+	chr17:80438421-80438957				chr17:80438420-80438421;chr17:80438957-80438958		12;38
N	intron_retention	CUFF.416	chr17	-	chr17:15546131-15580489				chr17:15546130-15546131;chr17:15580489-15580490		60;109
N	jcn_only_AD	CUFF.452	chr17	+	chr17:66508721-66511534;chr17:66509413-66511534;chr17:66511261-66511534;chr17:66508637-66511534	chr17:66511294-66511534		chr17:66508637-66508720;chr17:66508721-66509412;chr17:66509413-66511260;chr17:66511261-66511293	chr17:66508636-66508637;chr17:66508720-66508721;chr17:66509412-66509413;chr17:66511260-66511261		340;107
N	jcn_only_AA	CUFF.466	chr17	+	chr17:80430575-80436675	chr17:80430575-80436446		chr17:80436447-80436675	chr17:80436675-80436676		541;16
N	cassette	CUFF.452	chr17	+	chr17:66509120-66511534;chr17:66508690-66511534;chr17:66508284-66511534	chr17:66509120-66511127,chr17:66508690-66511127,chr17:66508284-66511127;chr17:66511294-66511534		chr17:66511128-66511293			264;127
N	intron_retention		chr17	+	chr17:61555152-61555291				chr17:61555151-61555152;chr17:61555291-61555292		35;632
K	cassette	CUFF.433	chr17	-	chr17:37599882-37604050	chr17:37599882-37601663;chr17:37601823-37604050		chr17:37601664-37601822			65;209
N	jcn_only_AD	CUFF.426	chr17	+	chr17:29626625-29652837;chr17:29645583-29652837	chr17:29592358-29652837		chr17:29592358-29626624;chr17:29626625-29645582	chr17:29592357-29592358;chr17:29626624-29626625		34;28
K	cassette	CUFF.417	chr17	+	chr17:15603092-15604465	chr17:15603092-15603361;chr17:15603483-15604465		chr17:15603362-15603482			28;90
K	intron_retention	CUFF.411	chr17	+	chr17:1944476-1944774				chr17:1944475-1944476;chr17:1944774-1944775		489;57
N	intron_retention		chr17	-	chr17:1616190-1617149				chr17:1616189-1616190;chr17:1617149-1617150		106;883
N	intron_retention		chr17	+	chr17:66509120-66511534				chr17:66509119-66509120;chr17:66511534-66511535		56;95
N	alternative_first_exon	CUFF.409	chr17	-	chr17:653150-655857;chr17:653150-654890	chr17:653150-655372	chr17:655858-656061;chr17:654891-655341	chr17:655373-655501			247;19
K	alternative_first_exon	CUFF.418	chr17	+	chr17:17380580-17394592	chr17:17388748-17394592	chr17:17380222-17380579	chr17:17388614-17388747			18;30
K	intron_retention	CUFF.411	chr17	+	chr17:1939386-1939822				chr17:1939385-1939386;chr17:1939822-1939823		347;60
N	intron_retention		chr17	+	chr17:61562331-61562596				chr17:61562330-61562331;chr17:61562596-61562597		77;91
K	cassette	CUFF.414	chr17	-	chr17:8638573-8644791	chr17:8638573-8638707;chr17:8638930-8644791		chr17:8638708-8638929		chr17:8638414-8638572;chr17:8644792-8644989	29;45
K	cassette	CUFF.452	chr17	+	chr17:66524042-66525010	chr17:66524042-66524771;chr17:66524861-66525010		chr17:66524772-66524860			522;195
K	intron_retention	CUFF.450	chr17	+	chr17:61907310-61907630				chr17:61907309-61907310;chr17:61907630-61907631		100;51
K	intron_retention	CUFF.450	chr17	+	chr17:61904875-61905478				chr17:61904874-61904875;chr17:61905478-61905479		64;122
N	jcn_only_AD	CUFF.461	chr17	-	chr17:79894738-79895137;chr17:79894738-79895403;chr17:79894738-79895133;chr17:79894738-79895055;chr17:79894738-79895068;chr17:79894738-79894845	chr17:79894738-79895103		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		888;144
K	intron_retention	CUFF.411	chr17	+	chr17:1943669-1943798				chr17:1943668-1943669;chr17:1943798-1943799		287;79
N	jcn_only_AA	CUFF.410	chr17	-	chr17:1616220-1616996;chr17:1615694-1616996;chr17:1616190-1616996;chr17:1616199-1616996	chr17:1616350-1616996		chr17:1615694-1616189;chr17:1616190-1616198;chr17:1616199-1616219;chr17:1616220-1616349	chr17:1615693-1615694;chr17:1616189-1616190;chr17:1616198-1616199;chr17:1616219-1616220		703;110
N	jcn_only_AD	CUFF.413	chr17	+	chr17:6348725-6350782;chr17:6348663-6350782	chr17:6349508-6350782		chr17:6348663-6348724;chr17:6348725-6349507	chr17:6348662-6348663;chr17:6348724-6348725		791;48
K	intron_retention	CUFF.431	chr17	-	chr17:34499761-34500203				chr17:34499760-34499761;chr17:34500203-34500204		383;103
N	jcn_only_AA	CUFF.410	chr17	-	chr17:1616220-1616996;chr17:1615694-1616996;chr17:1616350-1616996;chr17:1616199-1616996	chr17:1616190-1616996		chr17:1615694-1616189;chr17:1616190-1616198;chr17:1616199-1616219;chr17:1616220-1616349	chr17:1615693-1615694;chr17:1616189-1616190;chr17:1616198-1616199;chr17:1616219-1616220		648;165
N	coord_cassette	CUFF.422	chr17	+	chr17:25969375-25974055	chr17:25969375-25972886;chr17:25972938-25973572;chr17:25973615-25974055		chr17:25972887-25972937;chr17:25973573-25973614			44;560
K	jcn_only_AD	CUFF.465	chr17	-	chr17:79994185-79994289	chr17:79994185-79994259		chr17:79994260-79994289	chr17:79994289-79994290		111;1440
N	alternative_acceptor	CUFF.466	chr17	+	chr17:80430575-80436675	chr17:80430575-80436446		chr17:80436447-80436675	chr17:80436675-80436676		541;5
K	intron_retention	CUFF.426	chr17	+	chr17:29684388-29685497				chr17:29684387-29684388;chr17:29685497-29685498		366;6
N	jcn_only_AA	CUFF.410	chr17	-	chr17:1616350-1617149;chr17:1616199-1617149;chr17:1616190-1617149;chr17:1615941-1617149	chr17:1615694-1617149		chr17:1615694-1615940;chr17:1615941-1616189;chr17:1616190-1616198;chr17:1616199-1616349	chr17:1615693-1615694;chr17:1615940-1615941;chr17:1616189-1616190;chr17:1616198-1616199		619;84
N	alternative_first_exon	CUFF.409	chr17	-	chr17:653150-655857;chr17:653150-655372	chr17:653150-654890	chr17:655858-656061;chr17:655373-655501	chr17:654891-655341			83;183
K	cassette	CUFF.410	chr17	-	chr17:1617309-1619423	chr17:1617309-1617664;chr17:1617748-1619423		chr17:1617665-1617747			837;646
K	intron_retention	CUFF.450	chr17	+	chr17:61908786-61908865				chr17:61908785-61908786;chr17:61908865-61908866		2191;97
K	cassette	CUFF.416	chr17	-	chr17:15535029-15539349	chr17:15535029-15535822;chr17:15535989-15539349		chr17:15535823-15535988			88;346
K	intron_retention	CUFF.450	chr17	+	chr17:61907310-61907492				chr17:61907309-61907310;chr17:61907492-61907493		1047;64
K	jcn_only_AA	CUFF.412	chr17	-	chr17:5409298-5421065;chr17:5418838-5421065	chr17:5405193-5421065				chr17:5421066-5421207	287;35
N	jcn_only_AD	CUFF.457	chr17	-	chr17:79220862-79225292	chr17:79220862-79223869		chr17:79223870-79225292	chr17:79225292-79225293		62;32
K	intron_retention	CUFF.416	chr17	-	chr17:15535029-15535822				chr17:15535028-15535029;chr17:15535822-15535823		273;120
N	jcn_only_AD	CUFF.415	chr17	-	chr17:15562191-15584178	chr17:15562191-15580489					124;64
N	intron_retention		chr17	-	chr17:79994199-79994259				chr17:79994198-79994199;chr17:79994259-79994260		62;282
N	cassette	CUFF.422	chr17	+	chr17:25958331-25967597	chr17:25958331-25965288;chr17:25965381-25967597		chr17:25965289-25965380			24;422
N	intron_retention		chr17	-	chr17:76993412-76993572				chr17:76993411-76993412;chr17:76993572-76993573		154;662
K	intron_retention	CUFF.450	chr17	+	chr17:61908587-61908686				chr17:61908586-61908587;chr17:61908686-61908687		2120;47
N	jcn_only_AA	CUFF.424,CUFF.452	chr17	+	chr17:66519068-66519865	chr17:66519068-66519854		chr17:66519855-66519865	chr17:66519865-66519866		675;42
N	alternative_donor	CUFF.461	chr17	-	chr17:79894738-79895137;chr17:79894738-79895403;chr17:79894738-79895133;chr17:79894738-79895068;chr17:79894738-79894845;chr17:79894738-79895103	chr17:79894738-79895055		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		366;7
N	mutually_exclusive	CUFF.416	chr17	-	chr17:15584268-15586167,chr17:15586266-15586349	chr17:15584268-15584364,chr17:15584537-15586349	chr17:15586168-15586265	chr17:15584365-15584536			355;23
K	intron_retention	CUFF.426	chr17	+	chr17:29685641-29685986				chr17:29685640-29685641;chr17:29685986-29685987		442;10
N	intron_retention		chr17	-	chr17:56081080-56082283				chr17:56081079-56081080;chr17:56082283-56082284		55;192
K	cassette	CUFF.460	chr17	-	chr17:79478653-79478928	chr17:79478653-79478788;chr17:79478830-79478928		chr17:79478789-79478829			1207;122
N	alternative_last_exon	CUFF.444	chr17	-	chr17:57777551-57784731,chr17:57777238-57784731;chr17:57756906-57784731	chr17:57775340-57784731	chr17:57756728-57756905	chr17:57774636-57775339			543;44
N	cassette	CUFF.450	chr17	+	chr17:61904875-61905478;chr17:61904875-61905497	chr17:61904875-61905033;chr17:61905284-61905478,chr17:61905284-61905497		chr17:61905034-61905283			632;271
N	intron_retention		chr17	+	chr17:25969375-25972339				chr17:25969374-25969375;chr17:25972339-25972340		76;79
N	jcn_only_AD	CUFF.461	chr17	-	chr17:79894738-79895137;chr17:79894738-79895403;chr17:79894738-79895133;chr17:79894738-79895055;chr17:79894738-79894845;chr17:79894738-79895103	chr17:79894738-79895068		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		889;143
N	cassette	CUFF.447	chr17	+	chr17:61555460-61557129	chr17:61555460-61556367;chr17:61556462-61557129		chr17:61556368-61556461			52;670
K	jcn_only_AA	CUFF.412	chr17	-	chr17:5405193-5421065;chr17:5409298-5421065	chr17:5418838-5421065				chr17:5421066-5421207	39;282
N	jcn_only_AD	CUFF.411	chr17	+	chr17:1945170-1945898	chr17:1945526-1945898		chr17:1945170-1945525	chr17:1945169-1945170		620;30
N	jcn_only_AD	CUFF.426	chr17	+	chr17:29667602-29670026	chr17:29667664-29670026		chr17:29667602-29667663	chr17:29667601-29667602		60;294
K	alternative_last_exon	CUFF.454	chr17	+	chr17:75543175-75557026	chr17:75543175-75544052	chr17:75557027-75559423	chr17:75544053-75544076			57;43
K	intron_retention	CUFF.443	chr17	-	chr17:56081363-56082283				chr17:56081362-56081363;chr17:56082283-56082284		134;189
N	alternative_acceptor	CUFF.410	chr17	-	chr17:1616350-1617149;chr17:1616199-1617149;chr17:1616190-1617149;chr17:1615694-1617149	chr17:1615941-1617149		chr17:1615694-1615940;chr17:1615941-1616189;chr17:1616190-1616198;chr17:1616199-1616349	chr17:1615693-1615694;chr17:1615940-1615941;chr17:1616189-1616190;chr17:1616198-1616199		682;33
K	intron_retention	CUFF.450	chr17	+	chr17:61908296-61908395				chr17:61908295-61908296;chr17:61908395-61908396		2601;130
K	cassette	CUFF.424	chr17	+	chr17:29490395-29508439	chr17:29490395-29496908;chr17:29497016-29508439		chr17:29496909-29497015			27;111
K	jcn_only_AD	CUFF.440	chr17	+	chr17:46990328-46993437	chr17:46990384-46993437		chr17:46990328-46990383	chr17:46990327-46990328		115;190
N	alternative_donor	CUFF.426	chr17	+	chr17:29592358-29652837;chr17:29645583-29652837	chr17:29626625-29652837		chr17:29592358-29626624;chr17:29626625-29645582	chr17:29592357-29592358;chr17:29626624-29626625		28;0
K	intron_retention	CUFF.465	chr17	-	chr17:79994520-79994596				chr17:79994519-79994520;chr17:79994596-79994597		1688;94
K	alternative_last_exon	CUFF.465	chr17	-	chr17:79993122-79994066	chr17:79993940-79994066	chr17:79992914-79993121	chr17:79993656-79993939			57;1196
N	jcn_only_AD	CUFF.461	chr17	-	chr17:79894738-79895137;chr17:79894738-79895403;chr17:79894738-79895133;chr17:79894738-79895055;chr17:79894738-79895068;chr17:79894738-79895103	chr17:79894738-79894845		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		865;166
N	cassette	CUFF.447	chr17	+	chr17:61571832-61574158	chr17:61571832-61573754;chr17:61573878-61574158		chr17:61573755-61573877			63;340
K	intron_retention		chr17	+	chr17:35378314-35388910				chr17:35378313-35378314;chr17:35388910-35388911		25;33
N	alternative_acceptor		chr17	+	chr17:61562734-61563652;chr17:61562734-61563719	chr17:61562734-61563917		chr17:61563653-61563719;chr17:61563720-61563917	chr17:61563719-61563720;chr17:61563917-61563918		48;305
K	intron_retention		chr17	+	chr17:25969375-25970550				chr17:25969374-25969375;chr17:25970550-25970551		329;64
N	jcn_only_AD	CUFF.443	chr17	-	chr17:56082403-56083870;chr17:56082403-56082774	chr17:56082403-56082758		chr17:56082759-56082774;chr17:56082775-56083870	chr17:56082774-56082775;chr17:56083870-56083871		190;45
N	jcn_only_AA	CUFF.457	chr17	-	chr17:79220041-79220684	chr17:79220474-79220684		chr17:79220041-79220473	chr17:79220040-79220041		28;179
N	cassette	CUFF.426	chr17	+	chr17:29677337-29683477	chr17:29677337-29679274;chr17:29679433-29683477		chr17:29679275-29679432			62;203
N	intron_retention		chr17	-	chr17:79477356-79477504				chr17:79477355-79477356;chr17:79477504-79477505		81;727
K	cassette	CUFF.466	chr17	+	chr17:80417949-80426639	chr17:80417949-80422162;chr17:80422307-80426639		chr17:80422163-80422306			440;943
N	alternative_donor	CUFF.416,CUFF.444	chr17	-	chr17:15555261-15580489	chr17:15555261-15562115		chr17:15562116-15580489	chr17:15580489-15580490		84;0
K	intron_retention	CUFF.460	chr17	-	chr17:79479169-79479257				chr17:79479168-79479169;chr17:79479257-79479258		937;134
K	intron_retention	CUFF.461	chr17	-	chr17:79890840-79891182				chr17:79890839-79890840;chr17:79891182-79891183		68;194
N	intron_retention	CUFF.450	chr17	+	chr17:61904875-61905188				chr17:61904874-61904875;chr17:61905188-61905189		60;198
K	intron_retention		chr17	+	chr17:1945170-1945898				chr17:1945169-1945170;chr17:1945898-1945899		620;35
K	intron_retention	CUFF.416	chr17	-	chr17:15584268-15584364				chr17:15584267-15584268;chr17:15584364-15584365		29;20
N	alternative_first_exon		chr17	-	chr17:57775340-57784731	chr17:57775340-57776231	chr17:57784732-57784776	chr17:57776232-57776329			15;32
N	cassette	CUFF.447	chr17	+	chr17:61560051-61560820	chr17:61560051-61560389;chr17:61560535-61560820		chr17:61560390-61560534			96;142
N	intron_retention		chr17	+	chr17:80441619-80446077				chr17:80441618-80441619;chr17:80446077-80446078		27;365
N	jcn_only_AD	CUFF.461	chr17	-	chr17:79894738-79895403;chr17:79894738-79895133;chr17:79894738-79895055;chr17:79894738-79895068;chr17:79894738-79894845;chr17:79894738-79895103	chr17:79894738-79895137		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		735;296
N	mutually_exclusive	CUFF.416	chr17	-	chr17:15584268-15586174,chr17:15586266-15586349	chr17:15584268-15584364,chr17:15584537-15586349	chr17:15586175-15586265	chr17:15584365-15584536			190;23
N	intron_retention		chr17	+	chr17:25965381-25967668				chr17:25965380-25965381;chr17:25967668-25967669		197;255
K	intron_retention	CUFF.411	chr17	+	chr17:1940251-1943048				chr17:1940250-1940251;chr17:1943048-1943049		333;134
N	intron_retention		chr17	+	chr17:61568730-61571282				chr17:61568729-61568730;chr17:61571282-61571283		65;72
N	jcn_only_AA	CUFF.457	chr17	-	chr17:79223894-79225292;chr17:79220862-79225292	chr17:79220859-79225292		chr17:79220859-79220861;chr17:79220862-79223893	chr17:79220858-79220859;chr17:79220861-79220862		90;63
N	alternative_donor	CUFF.454	chr17	+	chr17:75543175-75557026	chr17:75556926-75557026		chr17:75543175-75556925	chr17:75543174-75543175		14;1
N	jcn_only_AA		chr17	+	chr17:1945170-1946269	chr17:1945170-1945898		chr17:1945899-1946269	chr17:1946269-1946270		174;620
N	alternative_acceptor		chr17	+	chr17:1945170-1946269	chr17:1945170-1945898		chr17:1945899-1946269	chr17:1946269-1946270		174;681
N	cassette	CUFF.459	chr17	-	chr17:79354385-79358928;chr17:79355741-79358928	chr17:79355741-79358745,chr17:79354385-79358745;chr17:79358833-79358928		chr17:79358746-79358832			137;824
N	cassette	CUFF.456	chr17	-	chr17:76993727-77005745	chr17:76993727-76993921;chr17:76994046-77005745		chr17:76993922-76994045			27;645
K	intron_retention	CUFF.452	chr17	+	chr17:66509112-66511127				chr17:66509111-66509112;chr17:66511127-66511128		76;68
K	cassette	CUFF.441	chr17	-	chr17:47302494-47304008	chr17:47302494-47303017;chr17:47303140-47304008		chr17:47303018-47303139		chr17:47300627-47302493;chr17:47304009-47304116	109;26
N	alternative_donor		chr17	-	chr17:56082403-56083870;chr17:56082403-56082758	chr17:56082403-56082774		chr17:56082759-56082774;chr17:56082775-56083870	chr17:56082774-56082775;chr17:56083870-56083871		158;123
N	alternative_acceptor	CUFF.410	chr17	-	chr17:1616220-1616996;chr17:1616190-1616996;chr17:1616350-1616996;chr17:1616199-1616996	chr17:1615694-1616996		chr17:1615694-1616189;chr17:1616190-1616198;chr17:1616199-1616219;chr17:1616220-1616349	chr17:1615693-1615694;chr17:1616189-1616190;chr17:1616198-1616199;chr17:1616219-1616220		835;59
K	intron_retention	CUFF.413	chr17	+	chr17:6348663-6350782				chr17:6348662-6348663;chr17:6350782-6350783		230;273
N	jcn_only_AD	CUFF.443	chr17	-	chr17:56082403-56082774;chr17:56082403-56082758	chr17:56082403-56083870		chr17:56082759-56082774;chr17:56082775-56083870	chr17:56082774-56082775;chr17:56083870-56083871		145;90
N	jcn_only_AA	CUFF.450	chr17	+	chr17:61905284-61905497	chr17:61905284-61905478		chr17:61905479-61905497	chr17:61905497-61905498		337;44
N	alternative_acceptor	CUFF.443	chr17	-	chr17:56081080-56082283	chr17:56081363-56082283		chr17:56081080-56081362	chr17:56081079-56081080		55;186
K	jcn_only_AA	CUFF.430	chr17	+	chr17:33640726-33648755	chr17:33640726-33648753		chr17:33648754-33648755	chr17:33648755-33648756		140;254
K	intron_retention	CUFF.465	chr17	-	chr17:79995424-79995506				chr17:79995423-79995424;chr17:79995506-79995507		362;314
N	jcn_only_AD	CUFF.447	chr17	+	chr17:61568730-61571282;chr17:61567390-61571282	chr17:61571021-61571282		chr17:61567390-61568729;chr17:61568730-61571020	chr17:61567389-61567390;chr17:61568729-61568730		126;301
K	cassette	CUFF.431	chr17	-	chr17:34500807-34502089	chr17:34500807-34501765;chr17:34501989-34502089		chr17:34501766-34501988			66;378
K	jcn_only_AD	CUFF.465	chr17	-	chr17:79993940-79994066	chr17:79993940-79994057		chr17:79994058-79994066	chr17:79994066-79994067		1081;293
N	intron_retention		chr17	+	chr17:1939948-1940128				chr17:1939947-1939948;chr17:1940128-1940129		16;75
N	alternative_donor	CUFF.426	chr17	+	chr17:29667602-29670026	chr17:29667664-29670026		chr17:29667602-29667663	chr17:29667601-29667602		60;173
N	cassette	CUFF.426	chr17	+	chr17:29576138-29584704	chr17:29576138-29579955;chr17:29580019-29584704		chr17:29579956-29580018			35;375
N	jcn_only_AA	CUFF.426	chr17	+	chr17:29687722-29701030	chr17:29687722-29694242		chr17:29694243-29701030	chr17:29701030-29701031		303;77
N	jcn_only_AD	CUFF.466	chr17	+	chr17:80417949-80422162	chr17:80418200-80422162		chr17:80417949-80418199	chr17:80417948-80417949		986;30
N	jcn_only_AD	CUFF.447	chr17	+	chr17:61562734-61563917	chr17:61563733-61563917		chr17:61562734-61563732	chr17:61562733-61562734		305;160
K	cassette	CUFF.440	chr17	+	chr17:46988243-46993437	chr17:46988243-46990195;chr17:46990328-46993437		chr17:46990196-46990327			124;167
K	cassette	CUFF.446	chr17	+	chr17:60783831-60813446	chr17:60783831-60784792;chr17:60784969-60813446		chr17:60784793-60784968			49;230
N	intron_retention		chr17	-	chr17:650523-650784				chr17:650522-650523;chr17:650784-650785		60;145
N	intron_retention	CUFF.460	chr17	-	chr17:79479387-79479640				chr17:79479386-79479387;chr17:79479640-79479641		41;38
N	alternative_acceptor	CUFF.450	chr17	+	chr17:61908296-61908395	chr17:61908296-61908379		chr17:61908380-61908395	chr17:61908395-61908396		2601;112
K	intron_retention	CUFF.450	chr17	+	chr17:61904567-61904777				chr17:61904566-61904567;chr17:61904777-61904778		74;157
N	jcn_only_AA	CUFF.461	chr17	-	chr17:79893021-79893998	chr17:79893393-79893998		chr17:79893021-79893392	chr17:79893020-79893021		57;1290
N	cassette	CUFF.459	chr17	-	chr17:79354385-79358928;chr17:79354385-79358745	chr17:79354385-79355676;chr17:79355741-79358745,chr17:79355741-79358928		chr17:79355677-79355740			97;950
N	jcn_only_AD		chr17	+	chr17:29706042-29708890;chr17:29707246-29708890	chr17:29706376-29708890					135;27
K	alternative_first_exon	CUFF.412,CUFF.438	chr17	-	chr17:42339005-42340003	chr17:42339005-42339394	chr17:42340004-42340094	chr17:42339395-42339515			39;176
N	alternative_last_exon	CUFF.415	chr17	-	chr17:15492542-15499827	chr17:15498141-15499827,chr17:15498205-15499827	chr17:15491610-15492541	chr17:15498062-15498140			58;207
N	jcn_only_AD	CUFF.452	chr17	+	chr17:66509413-66511534;chr17:66511261-66511534;chr17:66511294-66511534;chr17:66508637-66511534	chr17:66508721-66511534		chr17:66508637-66508720;chr17:66508721-66509412;chr17:66509413-66511260;chr17:66511261-66511293	chr17:66508636-66508637;chr17:66508720-66508721;chr17:66509412-66509413;chr17:66511260-66511261		399;49
N	jcn_only_AA	CUFF.450	chr17	+	chr17:61904875-61905210;chr17:61904875-61905188	chr17:61904875-61905033		chr17:61905034-61905188;chr17:61905189-61905210	chr17:61905188-61905189;chr17:61905210-61905211		285;65
K	intron_retention		chr17	+	chr17:61905570-61906853				chr17:61905569-61905570;chr17:61906853-61906854		673;210
N	cassette	CUFF.417	chr17	+	chr17:15611562-15638243	chr17:15611562-15619372;chr17:15620628-15638243		chr17:15619373-15620627			129;139
K	alternative_first_exon	CUFF.439	chr17	-	chr17:46685458-46687880;chr17:46685458-46710875	chr17:46685458-46685590	chr17:46687881-46688379;chr17:46710876-46711031	chr17:46685591-46685764			48;69
K	cassette	CUFF.440	chr17	+	chr17:46988243-46993437	chr17:46988243-46990195;chr17:46990384-46993437		chr17:46990196-46990383			124;206
K	coord_cassette	CUFF.435	chr17	-	chr17:40744181-40761103	chr17:40744181-40748550;chr17:40748646-40757265;chr17:40757310-40761103		chr17:40748551-40748645;chr17:40757266-40757309			401;284
K	alternative_first_exon	CUFF.424	chr17	+	chr17:29422388-29483000	chr17:29455526-29483000	chr17:29421849-29422387	chr17:29455427-29455525			120;34
N	alternative_donor	CUFF.413	chr17	+	chr17:6349508-6350782;chr17:6348725-6350782	chr17:6348663-6350782		chr17:6348663-6348724;chr17:6348725-6349507	chr17:6348662-6348663;chr17:6348724-6348725		440;230
N	intron_retention		chr17	+	chr17:35378314-35413900				chr17:35378313-35378314;chr17:35413900-35413901		90;105
N	intron_retention	CUFF.416	chr17	-	chr17:15584268-15586167				chr17:15584267-15584268;chr17:15586167-15586168		512;32
N	intron_retention		chr17	-	chr17:1615941-1617149				chr17:1615940-1615941;chr17:1617149-1617150		54;875
K	intron_retention		chr17	+	chr17:80441656-80442688				chr17:80441655-80441656;chr17:80442688-80442689		468;257
N	intron_retention		chr17	+	chr17:61573785-61574893				chr17:61573784-61573785;chr17:61574893-61574894		46;229
N	alternative_donor	CUFF.443	chr17	-	chr17:56082403-56083870;chr17:56082403-56082774	chr17:56082403-56082758		chr17:56082759-56082774;chr17:56082775-56083870	chr17:56082774-56082775;chr17:56083870-56083871		213;68
N	intron_retention		chr17	-	chr17:1616350-1617149				chr17:1616349-1616350;chr17:1617149-1617150		315;727
K	intron_retention	CUFF.440	chr17	+	chr17:46990328-46993437				chr17:46990327-46990328;chr17:46993437-46993438		115;99
N	intron_retention		chr17	-	chr17:5487424-5487612				chr17:5487423-5487424;chr17:5487612-5487613	chr17:5487007-5487423;chr17:5487613-5487820	61;298
N	cassette	CUFF.447	chr17	+	chr17:61566153-61568314	chr17:61566153-61566301;chr17:61566494-61568314		chr17:61566302-61566493			39;406
N	alternative_donor	CUFF.411	chr17	+	chr17:1945170-1945898	chr17:1945526-1945898		chr17:1945170-1945525	chr17:1945169-1945170		620;55
K	intron_retention	CUFF.416	chr17	-	chr17:15531376-15532187				chr17:15531375-15531376;chr17:15532187-15532188		69;397
K	intron_retention	CUFF.450	chr17	+	chr17:61904884-61907492				chr17:61904883-61904884;chr17:61907492-61907493		57;103
N	intron_retention		chr17	-	chr17:76988223-76988491				chr17:76988222-76988223;chr17:76988491-76988492		30;236
K	intron_retention	CUFF.447	chr17	+	chr17:61566494-61568314				chr17:61566493-61566494;chr17:61568314-61568315		337;38
N	jcn_only_AD	CUFF.411	chr17	+	chr17:1939948-1940128	chr17:1939981-1940128		chr17:1939948-1939980	chr17:1939947-1939948		16;471
N	intron_retention		chr17	+	chr17:80442807-80446096				chr17:80442806-80442807;chr17:80446096-80446097		38;412
N	intron_retention		chr17	+	chr17:61904973-61906217				chr17:61904972-61904973;chr17:61906217-61906218		23;153
N	jcn_only_AA	CUFF.450	chr17	+	chr17:61904875-61905033;chr17:61904875-61905210	chr17:61904875-61905188		chr17:61905034-61905188;chr17:61905189-61905210	chr17:61905188-61905189;chr17:61905210-61905211		290;60
N	jcn_only_AD	CUFF.443	chr17	-	chr17:56083889-56084304	chr17:56083889-56084267		chr17:56084268-56084304	chr17:56084304-56084305		427;49
K	intron_retention	CUFF.452	chr17	+	chr17:66508690-66509050				chr17:66508689-66508690;chr17:66509050-66509051		62;40
K	intron_retention	CUFF.426	chr17	+	chr17:29686034-29687504				chr17:29686033-29686034;chr17:29687504-29687505		439;9
K	jcn_only_AD	CUFF.466	chr17	+	chr17:80439088-80441591	chr17:80441181-80441591					500;517
K	cassette	CUFF.451	chr17	-	chr17:66268909-66274229	chr17:66268909-66270067;chr17:66270212-66274229		chr17:66270068-66270211			20;72
K	intron_retention	CUFF.452	chr17	+	chr17:66511294-66511534				chr17:66511293-66511294;chr17:66511534-66511535		107;131
N	alternative_acceptor	CUFF.447	chr17	+	chr17:61564435-61566008	chr17:61564435-61565930		chr17:61565931-61566008	chr17:61566008-61566009		377;75
N	alternative_donor	CUFF.411	chr17	+	chr17:1939948-1940128	chr17:1939981-1940128		chr17:1939948-1939980	chr17:1939947-1939948		16;285
K	intron_retention		chr17	-	chr17:76993727-76993921				chr17:76993726-76993727;chr17:76993921-76993922		1123;274
N	intron_retention		chr17	+	chr17:25970647-25972886				chr17:25970646-25970647;chr17:25972886-25972887		106;24
K	intron_retention	CUFF.465	chr17	-	chr17:79994758-79994964				chr17:79994757-79994758;chr17:79994964-79994965		47;352
N	alternative_acceptor	CUFF.413	chr17	+	chr17:6348725-6350782	chr17:6348725-6349414		chr17:6349415-6350782	chr17:6350782-6350783		561;14
N	jcn_only_AA	CUFF.457	chr17	-	chr17:79220859-79225292;chr17:79220862-79225292	chr17:79223894-79225292		chr17:79220859-79220861;chr17:79220862-79223893	chr17:79220858-79220859;chr17:79220861-79220862		126;28
K	alternative_first_exon	CUFF.439	chr17	-	chr17:46685458-46687880;chr17:46685458-46685590	chr17:46685458-46710875	chr17:46687881-46688379;chr17:46685591-46685764	chr17:46710876-46711031			92;25
N	alternative_acceptor		chr17	+	chr17:25965381-25967668	chr17:25965381-25967597		chr17:25967598-25967668	chr17:25967668-25967669		197;319
K	intron_retention	CUFF.413	chr17	+	chr17:6353393-6353681				chr17:6353392-6353393;chr17:6353681-6353682		325;111
N	jcn_only_AD	CUFF.426	chr17	+	chr17:29687722-29701030	chr17:29694297-29701030		chr17:29687722-29694296	chr17:29687721-29687722		303;82
N	jcn_only_AA	CUFF.450	chr17	+	chr17:61904875-61905033;chr17:61904875-61905188	chr17:61904875-61905210		chr17:61905034-61905188;chr17:61905189-61905210	chr17:61905188-61905189;chr17:61905210-61905211		125;225
K	intron_retention	CUFF.447	chr17	+	chr17:61564435-61566008				chr17:61564434-61564435;chr17:61566008-61566009		377;101
K	cassette	CUFF.450	chr17	+	chr17:61907310-61907630	chr17:61907310-61907492;chr17:61907550-61907630		chr17:61907493-61907549			100;940
K	intron_retention	CUFF.417	chr17	+	chr17:15603483-15603586				chr17:15603482-15603483;chr17:15603586-15603587		62;37
K	cassette	CUFF.451	chr17	-	chr17:66279265-66287226	chr17:66279265-66281685;chr17:66281784-66287226		chr17:66281686-66281783			11;27
K	intron_retention	CUFF.434	chr17	+	chr17:37822033-37822104				chr17:37822032-37822033;chr17:37822104-37822105		49;22
K	intron_retention	CUFF.419	chr17	-	chr17:20279149-20279443				chr17:20279148-20279149;chr17:20279443-20279444		207;253
N	jcn_only_AD	CUFF.452	chr17	+	chr17:66508721-66511534;chr17:66509413-66511534;chr17:66511294-66511534;chr17:66508637-66511534	chr17:66511261-66511534		chr17:66508637-66508720;chr17:66508721-66509412;chr17:66509413-66511260;chr17:66511261-66511293	chr17:66508636-66508637;chr17:66508720-66508721;chr17:66509412-66509413;chr17:66511260-66511261		269;179
K	intron_retention	CUFF.416	chr17	-	chr17:15586472-15587509				chr17:15586471-15586472;chr17:15587509-15587510		664;102
N	jcn_only_AA	CUFF.447	chr17	+	chr17:61562734-61563652;chr17:61562734-61563917	chr17:61562734-61563719		chr17:61563653-61563719;chr17:61563720-61563917	chr17:61563719-61563720;chr17:61563917-61563918		337;126
N	jcn_only_AD	CUFF.426	chr17	+	chr17:29626625-29652837;chr17:29592358-29652837	chr17:29645583-29652837		chr17:29592358-29626624;chr17:29626625-29645582	chr17:29592357-29592358;chr17:29626624-29626625		51;11
N	jcn_only_AD		chr17	-	chr17:56082403-56083870;chr17:56082403-56082758	chr17:56082403-56082774		chr17:56082759-56082774;chr17:56082775-56083870	chr17:56082774-56082775;chr17:56083870-56083871		136;100
N	jcn_only_AD	CUFF.416,CUFF.444	chr17	-	chr17:15555261-15580489	chr17:15555261-15562115		chr17:15562116-15580489	chr17:15580489-15580490		84;25
N	alternative_acceptor	CUFF.457	chr17	-	chr17:79220859-79225292;chr17:79220862-79225292	chr17:79223894-79225292		chr17:79220859-79220861;chr17:79220862-79223893	chr17:79220858-79220859;chr17:79220861-79220862		101;11
N	jcn_only_AD	CUFF.411	chr17	+	chr17:1937137-1939263	chr17:1938315-1939263		chr17:1937137-1938314	chr17:1937136-1937137		377;64
N	jcn_only_AD	CUFF.454	chr17	+	chr17:75543175-75557026	chr17:75556926-75557026		chr17:75543175-75556925	chr17:75543174-75543175		14;5
N	intron_retention		chr17	-	chr17:79479142-79479257				chr17:79479141-79479142;chr17:79479257-79479258		37;308
N	alternative_acceptor	CUFF.410	chr17	-	chr17:1616220-1616996;chr17:1615694-1616996;chr17:1616190-1616996;chr17:1616199-1616996	chr17:1616350-1616996		chr17:1615694-1616189;chr17:1616190-1616198;chr17:1616199-1616219;chr17:1616220-1616349	chr17:1615693-1615694;chr17:1616189-1616190;chr17:1616198-1616199;chr17:1616219-1616220		714;180
K	intron_retention	CUFF.457	chr17	-	chr17:79220862-79225292				chr17:79220861-79220862;chr17:79225292-79225293		62;113
N	jcn_only_AA	CUFF.416	chr17	-	chr17:15586472-15587509	chr17:15586686-15587509		chr17:15586472-15586685	chr17:15586471-15586472		664;41
K	jcn_only_AA	CUFF.465	chr17	-	chr17:79994890-79995325	chr17:79994965-79995325		chr17:79994890-79994964	chr17:79994889-79994890		516;361
K	jcn_only_AA	CUFF.440,CUFF.452	chr17	+	chr17:46986183-46993437	chr17:46986183-46988169					39;108
K	alternative_donor	CUFF.410	chr17	-	chr17:1615694-1617149	chr17:1615694-1616996		chr17:1616997-1617149	chr17:1617149-1617150		84;731
N	alternative_acceptor		chr17	+	chr17:61574347-61584416	chr17:61574347-61574497		chr17:61574498-61584416	chr17:61584416-61584417		7;38
N	alternative_donor	CUFF.426	chr17	+	chr17:29687722-29701030	chr17:29694297-29701030		chr17:29687722-29694296	chr17:29687721-29687722		303;11
N	alternative_acceptor	CUFF.426	chr17	+	chr17:29592358-29652837	chr17:29592358-29626527		chr17:29626528-29652837	chr17:29652837-29652838		28;0
K	intron_retention	CUFF.452	chr17	+	chr17:66508690-66511534				chr17:66508689-66508690;chr17:66511534-66511535		171;72
N	jcn_only_AA	CUFF.447	chr17	+	chr17:61564435-61566008	chr17:61564435-61565930		chr17:61565931-61566008	chr17:61566008-61566009		377;90
N	jcn_only_AA	CUFF.410	chr17	-	chr17:1616220-1616996;chr17:1616190-1616996;chr17:1616350-1616996;chr17:1616199-1616996	chr17:1615694-1616996		chr17:1615694-1616189;chr17:1616190-1616198;chr17:1616199-1616219;chr17:1616220-1616349	chr17:1615693-1615694;chr17:1616189-1616190;chr17:1616198-1616199;chr17:1616219-1616220		755;59
K	alternative_donor	CUFF.412,CUFF.456	chr17	-	chr17:5436305-5436623	chr17:5436305-5436611		chr17:5436612-5436623	chr17:5436623-5436624	chr17:5436142-5436304;chr17:5436624-5436704	269;12
N	alternative_acceptor	CUFF.410	chr17	-	chr17:1616220-1616996;chr17:1615694-1616996;chr17:1616350-1616996;chr17:1616199-1616996	chr17:1616190-1616996		chr17:1615694-1616189;chr17:1616190-1616198;chr17:1616199-1616219;chr17:1616220-1616349	chr17:1615693-1615694;chr17:1616189-1616190;chr17:1616198-1616199;chr17:1616219-1616220		720;174
N	cassette	CUFF.466	chr17	+	chr17:80426773-80436675;chr17:80426773-80436446	chr17:80426773-80430439;chr17:80430575-80436446,chr17:80430575-80436675		chr17:80430440-80430574			451;538
N	intron_retention	CUFF.460	chr17	-	chr17:79479387-79479489				chr17:79479386-79479387;chr17:79479489-79479490		34;41
N	coord_cassette	CUFF.456	chr17	-	chr17:76994046-77005745	chr17:76994046-76996181;chr17:76996353-77001453;chr17:77001564-77005745		chr17:76996182-76996352;chr17:77001454-77001563			184;234
N	cassette	CUFF.452	chr17	+	chr17:66509120-66511534;chr17:66508690-66511534;chr17:66508284-66511534	chr17:66509120-66511127,chr17:66508690-66511127,chr17:66508284-66511127;chr17:66511261-66511534		chr17:66511128-66511260			264;136
N	cassette	CUFF.422	chr17	+	chr17:25969375-25972886;chr17:25969375-25972339	chr17:25969375-25970550;chr17:25970647-25972886,chr17:25970647-25972339		chr17:25970551-25970646			264;278
N	alternative_acceptor	CUFF.447	chr17	+	chr17:61562734-61563652;chr17:61562734-61563917	chr17:61562734-61563719		chr17:61563653-61563719;chr17:61563720-61563917	chr17:61563719-61563720;chr17:61563917-61563918		312;41
N	alternative_last_exon		chr17	+	chr17:61907862-61908395	chr17:61907862-61908168	chr17:61908396-61908586	chr17:61908169-61908295			41;1220
K	alternative_acceptor	CUFF.421	chr17	-	chr17:21437283-21438688	chr17:21437833-21438688		chr17:21437283-21437832	chr17:21437282-21437283	chr17:21438689-21438799;chr17:21435641-21437282	24;11
N	alternative_acceptor	CUFF.410	chr17	-	chr17:1616350-1617149;chr17:1616199-1617149;chr17:1615694-1617149;chr17:1615941-1617149	chr17:1616190-1617149		chr17:1615694-1615940;chr17:1615941-1616189;chr17:1616190-1616198;chr17:1616199-1616349	chr17:1615693-1615694;chr17:1615940-1615941;chr17:1616189-1616190;chr17:1616198-1616199		601;114
N	alternative_acceptor	CUFF.426	chr17	+	chr17:29687722-29701030	chr17:29687722-29694242		chr17:29694243-29701030	chr17:29701030-29701031		303;2
N	intron_retention		chr17	-	chr17:79478605-79478952				chr17:79478604-79478605;chr17:79478952-79478953		68;455
K	cassette	CUFF.417	chr17	+	chr17:15603483-15604465	chr17:15603483-15603586;chr17:15603681-15604465		chr17:15603587-15603680			23;84
K	intron_retention	CUFF.450	chr17	+	chr17:61905284-61905497				chr17:61905283-61905284;chr17:61905497-61905498		337;150
K	coord_cassette	CUFF.452	chr17	+	chr17:66508690-66511534	chr17:66508690-66509050;chr17:66509112-66511127;chr17:66511294-66511534		chr17:66509051-66509111;chr17:66511128-66511293			171;61
N	intron_retention		chr17	+	chr17:66509120-66511127				chr17:66509119-66509120;chr17:66511127-66511128		44;67
N	jcn_only_AA	CUFF.457	chr17	-	chr17:79220859-79225292;chr17:79223894-79225292	chr17:79220862-79225292		chr17:79220859-79220861;chr17:79220862-79223893	chr17:79220858-79220859;chr17:79220861-79220862		91;62
K	intron_retention	CUFF.452	chr17	+	chr17:66508690-66511127				chr17:66508689-66508690;chr17:66511127-66511128		8;44
N	alternative_donor	CUFF.426	chr17	+	chr17:29626625-29652837;chr17:29645583-29652837	chr17:29592358-29652837		chr17:29592358-29626624;chr17:29626625-29645582	chr17:29592357-29592358;chr17:29626624-29626625		0;28
K	cassette	CUFF.412	chr17	-	chr17:5437309-5442734	chr17:5437309-5440170;chr17:5440261-5442734		chr17:5440171-5440260		chr17:5437217-5437308;chr17:5442735-5442905	109;143
N	jcn_only_AD		chr17	+	chr17:29706376-29708890;chr17:29706042-29708890	chr17:29707246-29708890					111;51
K	jcn_only_AA	CUFF.466	chr17	+	chr17:80416707-80417875	chr17:80416707-80417867		chr17:80417868-80417875	chr17:80417875-80417876		61;823
N	intron_retention		chr17	+	chr17:61905570-61907211				chr17:61905569-61905570;chr17:61907211-61907212		47;95
K	cassette	CUFF.416	chr17	-	chr17:15584268-15586349	chr17:15584268-15586174;chr17:15586266-15586349		chr17:15586175-15586265			436;190
K	cassette	CUFF.451	chr17	-	chr17:66274469-66287226	chr17:66274469-66279137;chr17:66279265-66287226		chr17:66279138-66279264			49;26
N	jcn_only_AA	CUFF.411	chr17	+	chr17:80416385-80417867	chr17:80416385-80417150		chr17:80417151-80417867	chr17:80417867-80417868		104;33
K	alternative_first_exon	CUFF.460	chr17	-	chr17:79479387-79479489,chr17:79479387-79479631,chr17:79479387-79479640,chr17:79479387-79481572;chr17:79479387-79490667	chr17:79479387-79479759	chr17:79490668-79490972	chr17:79479760-79479900			500;311
K	alternative_acceptor	CUFF.465	chr17	-	chr17:79994890-79995325	chr17:79994965-79995325		chr17:79994890-79994964	chr17:79994889-79994890		516;359
K	intron_retention	CUFF.450	chr17	+	chr17:61904875-61905210				chr17:61904874-61904875;chr17:61905210-61905211		225;184
K	alternative_donor	CUFF.465	chr17	-	chr17:79994185-79994289	chr17:79994185-79994259		chr17:79994260-79994289	chr17:79994289-79994290		111;805
K	alternative_first_exon	CUFF.416	chr17	-	chr17:15532513-15539349	chr17:15532513-15534932	chr17:15539350-15539583	chr17:15534933-15535384			192;360
K	intron_retention	CUFF.460	chr17	-	chr17:79479387-79479759				chr17:79479386-79479387;chr17:79479759-79479760		456;95
K	alternative_acceptor	CUFF.466	chr17	+	chr17:80416707-80417875	chr17:80416707-80417867		chr17:80417868-80417875	chr17:80417875-80417876		61;404
K	alternative_last_exon	CUFF.412	chr17	-	chr17:5425107-5433800	chr17:5433379-5433800	chr17:5424844-5425106	chr17:5433166-5433378		chr17:5433801-5434024	301;84
K	alternative_first_exon	CUFF.461	chr17	-	chr17:79894070-79898625;chr17:79894070-79900171	chr17:79894070-79894623	chr17:79900172-79900378	chr17:79894624-79894845			46;610
K	coord_cassette	CUFF.456	chr17	-	chr17:76994046-77005745	chr17:76994046-76994229;chr17:76994369-76996181;chr17:76996353-77005745		chr17:76994230-76994368;chr17:76996182-76996352			184;201
K	cassette	CUFF.422	chr17	+	chr17:25974145-25975861	chr17:25974145-25974295;chr17:25974459-25975861		chr17:25974296-25974458			284;497
N	alternative_acceptor	CUFF.424,CUFF.452	chr17	+	chr17:66519068-66519865	chr17:66519068-66519854		chr17:66519855-66519865	chr17:66519865-66519866		675;20
N	intron_retention		chr17	-	chr17:1616350-1616996				chr17:1616349-1616350;chr17:1616996-1616997		110;151
K	cassette	CUFF.417	chr17	+	chr17:15638385-15638910	chr17:15638385-15638661;chr17:15638738-15638910		chr17:15638662-15638737			101;52
N	jcn_only_AD	CUFF.426	chr17	+	chr17:29657517-29661855	chr17:29661749-29661855		chr17:29657517-29661748	chr17:29657516-29657517		78;37
N	alternative_acceptor	CUFF.411	chr17	+	chr17:1939386-1939822	chr17:1939386-1939722		chr17:1939723-1939822	chr17:1939822-1939823		347;39
N	mutually_exclusive	CUFF.461	chr17	-	chr17:79891253-79892528,chr17:79892622-79892801	chr17:79891253-79892201,chr17:79892366-79892801	chr17:79892529-79892621	chr17:79892202-79892365			21;15
N	jcn_only_AA		chr17	+	chr17:61562734-61563652;chr17:61562734-61563719	chr17:61562734-61563917		chr17:61563653-61563719;chr17:61563720-61563917	chr17:61563719-61563720;chr17:61563917-61563918		158;305
N	alternative_donor	CUFF.413	chr17	+	chr17:6348725-6350782;chr17:6348663-6350782	chr17:6349508-6350782		chr17:6348663-6348724;chr17:6348725-6349507	chr17:6348662-6348663;chr17:6348724-6348725		659;11
K	intron_retention	CUFF.465	chr17	-	chr17:79994325-79994419				chr17:79994324-79994325;chr17:79994419-79994420		1199;421
N	alternative_acceptor	CUFF.410	chr17	-	chr17:1615694-1616996;chr17:1616190-1616996;chr17:1616350-1616996;chr17:1616199-1616996	chr17:1616220-1616996		chr17:1615694-1616189;chr17:1616190-1616198;chr17:1616199-1616219;chr17:1616220-1616349	chr17:1615693-1615694;chr17:1616189-1616190;chr17:1616198-1616199;chr17:1616219-1616220		867;27
K	intron_retention	CUFF.457	chr17	-	chr17:79225413-79225994				chr17:79225412-79225413;chr17:79225994-79225995		233;184
K	intron_retention	CUFF.422	chr17	+	chr17:25974145-25974295				chr17:25974144-25974145;chr17:25974295-25974296		616;53
N	alternative_donor	CUFF.452	chr17	+	chr17:66508721-66511534;chr17:66509413-66511534;chr17:66511261-66511534;chr17:66508637-66511534	chr17:66511294-66511534		chr17:66508637-66508720;chr17:66508721-66509412;chr17:66509413-66511260;chr17:66511261-66511293	chr17:66508636-66508637;chr17:66508720-66508721;chr17:66509412-66509413;chr17:66511260-66511261		142;28
N	alternative_acceptor	CUFF.410	chr17	-	chr17:1616199-1617149;chr17:1616190-1617149;chr17:1615694-1617149;chr17:1615941-1617149	chr17:1616350-1617149		chr17:1615694-1615940;chr17:1615941-1616189;chr17:1616190-1616198;chr17:1616199-1616349	chr17:1615693-1615694;chr17:1615940-1615941;chr17:1616189-1616190;chr17:1616198-1616199		380;335
N	alternative_acceptor	CUFF.410	chr17	-	chr17:1617309-1617664	chr17:1617340-1617664		chr17:1617309-1617339	chr17:1617308-1617309		599;100
N	intron_retention		chr17	-	chr17:56082403-56083870				chr17:56082402-56082403;chr17:56083870-56083871		90;140
N	cassette	CUFF.435	chr17	-	chr17:40744181-40762554	chr17:40744181-40748550;chr17:40748646-40762554		chr17:40748551-40748645			59;138
K	coord_cassette	CUFF.451	chr17	-	chr17:66274469-66287226	chr17:66274469-66279137;chr17:66279265-66281685;chr17:66281784-66287226		chr17:66279138-66279264;chr17:66281686-66281783			49;27
N	alternative_first_exon		chr17	-	chr17:77001564-77005745	chr17:77001564-77004144	chr17:77005746-77006044	chr17:77004145-77004234			178;27
N	intron_retention		chr17	+	chr17:6352728-6353681				chr17:6352727-6352728;chr17:6353681-6353682		111;93
N	alternative_acceptor	CUFF.410	chr17	-	chr17:1616350-1617149;chr17:1616199-1617149;chr17:1616190-1617149;chr17:1615941-1617149	chr17:1615694-1617149		chr17:1615694-1615940;chr17:1615941-1616189;chr17:1616190-1616198;chr17:1616199-1616349	chr17:1615693-1615694;chr17:1615940-1615941;chr17:1616189-1616190;chr17:1616198-1616199		631;84
K	coord_cassette	CUFF.452	chr17	+	chr17:66508690-66511534	chr17:66508690-66509050;chr17:66509112-66511127;chr17:66511261-66511534		chr17:66509051-66509111;chr17:66511128-66511260			171;65
N	jcn_only_AA	CUFF.422	chr17	+	chr17:25967800-25969263	chr17:25967800-25967990		chr17:25967991-25969263	chr17:25969263-25969264		839;62
N	cassette	CUFF.461	chr17	-	chr17:79892366-79892801;chr17:79891253-79892801	chr17:79892366-79892528,chr17:79891253-79892528;chr17:79892622-79892801		chr17:79892529-79892621			110;571
N	alternative_acceptor	CUFF.450	chr17	+	chr17:61904875-61905033;chr17:61904875-61905210	chr17:61904875-61905188		chr17:61905034-61905188;chr17:61905189-61905210	chr17:61905188-61905189;chr17:61905210-61905211		383;82
N	jcn_only_AD	CUFF.435	chr17	-	chr17:40738910-40744073	chr17:40738910-40739851		chr17:40739852-40744073	chr17:40744073-40744074		217;105
K	intron_retention		chr17	+	chr17:61571832-61573754				chr17:61571831-61571832;chr17:61573754-61573755		380;110
N	alternative_donor		chr17	-	chr17:1616190-1617149	chr17:1616190-1616996		chr17:1616997-1617149	chr17:1617149-1617150		106;769
N	alternative_donor	CUFF.413	chr17	+	chr17:6352728-6353347	chr17:6353099-6353347		chr17:6352728-6353098	chr17:6352727-6352728		491;32
N	intron_retention		chr17	-	chr17:40738156-40761103				chr17:40738155-40738156;chr17:40761103-40761104		31;152
N	cassette	CUFF.450	chr17	+	chr17:61905570-61907211	chr17:61905570-61906853;chr17:61906924-61907211		chr17:61906854-61906923			47;746
K	intron_retention	CUFF.415	chr17	-	chr17:15501968-15508536				chr17:15501967-15501968;chr17:15508536-15508537		11;70
K	intron_retention		chr17	+	chr17:25965381-25967597				chr17:25965380-25965381;chr17:25967597-25967598		352;71
N	jcn_only_AD	CUFF.461	chr17	-	chr17:79894738-79895137;chr17:79894738-79895403;chr17:79894738-79895133;chr17:79894738-79895068;chr17:79894738-79894845;chr17:79894738-79895103	chr17:79894738-79895055		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		1014;17
K	intron_retention	CUFF.465	chr17	-	chr17:79994640-79994734				chr17:79994639-79994640;chr17:79994734-79994735		1581;162
K	cassette	CUFF.436	chr17	-	chr17:41719401-41738433	chr17:41719401-41720855;chr17:41721029-41738433		chr17:41720856-41721028			86;151
N	alternative_acceptor	CUFF.465	chr17	-	chr17:79994185-79994259	chr17:79994199-79994259		chr17:79994185-79994198	chr17:79994184-79994185		1440;154
N	cassette	CUFF.466	chr17	+	chr17:80441656-80443372	chr17:80441656-80442688;chr17:80442807-80443372		chr17:80442689-80442806			46;266
N	alternative_donor	CUFF.447	chr17	+	chr17:61571021-61571282;chr17:61567390-61571282	chr17:61568730-61571282		chr17:61567390-61568729;chr17:61568730-61571020	chr17:61567389-61567390;chr17:61568729-61568730		125;21
N	cassette	CUFF.416	chr17	-	chr17:15546131-15562115;chr17:15546131-15580489	chr17:15546131-15554404;chr17:15555261-15580489,chr17:15555261-15562115		chr17:15554405-15555260			128;143
K	cassette	CUFF.466	chr17	+	chr17:80436795-80438957	chr17:80436795-80438282;chr17:80438421-80438957		chr17:80438283-80438420			937;12
N	jcn_only_AD	CUFF.452	chr17	+	chr17:66508721-66511534;chr17:66511261-66511534;chr17:66511294-66511534;chr17:66508637-66511534	chr17:66509413-66511534		chr17:66508637-66508720;chr17:66508721-66509412;chr17:66509413-66511260;chr17:66511261-66511293	chr17:66508636-66508637;chr17:66508720-66508721;chr17:66509412-66509413;chr17:66511260-66511261		397;51
N	alternative_donor	CUFF.466	chr17	+	chr17:80417949-80422162	chr17:80418200-80422162		chr17:80417949-80418199	chr17:80417948-80417949		986;136
K	intron_retention	CUFF.465	chr17	-	chr17:79994185-79994289				chr17:79994184-79994185;chr17:79994289-79994290		111;278
K	intron_retention	CUFF.410	chr17	-	chr17:1615694-1617149				chr17:1615693-1615694;chr17:1617149-1617150		84;786
K	jcn_only_AD	CUFF.450	chr17	+	chr17:61904884-61907492	chr17:61907310-61907492					57;1047
K	intron_retention	CUFF.459	chr17	-	chr17:79358833-79358928				chr17:79358832-79358833;chr17:79358928-79358929		1161;22
N	alternative_donor	CUFF.452	chr17	+	chr17:66508721-66511534;chr17:66509413-66511534;chr17:66511294-66511534;chr17:66508637-66511534	chr17:66511261-66511534		chr17:66508637-66508720;chr17:66508721-66509412;chr17:66509413-66511260;chr17:66511261-66511293	chr17:66508636-66508637;chr17:66508720-66508721;chr17:66509412-66509413;chr17:66511260-66511261		136;34
N	intron_retention		chr17	+	chr17:1945526-1945898				chr17:1945525-1945526;chr17:1945898-1945899		30;30
N	alternative_acceptor	CUFF.457	chr17	-	chr17:79223894-79225292;chr17:79220862-79225292	chr17:79220859-79225292		chr17:79220859-79220861;chr17:79220862-79223893	chr17:79220858-79220859;chr17:79220861-79220862		49;63
N	alternative_donor	CUFF.461	chr17	-	chr17:79894738-79895403;chr17:79894738-79895133;chr17:79894738-79895055;chr17:79894738-79895068;chr17:79894738-79894845;chr17:79894738-79895103	chr17:79894738-79895137		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		281;92
N	cassette	CUFF.432	chr17	+	chr17:35378314-35413900	chr17:35378314-35388910;chr17:35388983-35413900		chr17:35388911-35388982			90;53
K	intron_retention	CUFF.465	chr17	-	chr17:79994965-79995325				chr17:79994964-79994965;chr17:79995325-79995326		361;102
N	intron_retention		chr17	-	chr17:79894738-79895055				chr17:79894737-79894738;chr17:79895055-79895056		17;171
N	jcn_only_AA	CUFF.426	chr17	+	chr17:29657517-29661855	chr17:29657517-29661681		chr17:29661682-29661855	chr17:29661855-29661856		78;22
K	intron_retention		chr17	+	chr17:61574347-61574497				chr17:61574346-61574347;chr17:61574497-61574498		397;64
K	intron_retention	CUFF.460	chr17	-	chr17:79478653-79478928				chr17:79478652-79478653;chr17:79478928-79478929		1207;52
K	intron_retention	CUFF.466	chr17	+	chr17:80417949-80426639				chr17:80417948-80417949;chr17:80426639-80426640		440;99
N	intron_retention	CUFF.413	chr17	+	chr17:6353393-6353558				chr17:6353392-6353393;chr17:6353558-6353559		65;102
N	intron_retention		chr17	-	chr17:1616220-1616996				chr17:1616219-1616220;chr17:1616996-1616997		21;289
N	jcn_only_AD	CUFF.447	chr17	+	chr17:61554705-61555291	chr17:61555152-61555291		chr17:61554705-61555151	chr17:61554704-61554705		459;35
N	alternative_acceptor	CUFF.450	chr17	+	chr17:61904875-61905033;chr17:61904875-61905188	chr17:61904875-61905210		chr17:61905034-61905188;chr17:61905189-61905210	chr17:61905188-61905189;chr17:61905210-61905211		240;225
N	jcn_only_AD	CUFF.452	chr17	+	chr17:66508721-66511534;chr17:66509413-66511534;chr17:66511261-66511534;chr17:66511294-66511534	chr17:66508637-66511534		chr17:66508637-66508720;chr17:66508721-66509412;chr17:66509413-66511260;chr17:66511261-66511293	chr17:66508636-66508637;chr17:66508720-66508721;chr17:66509412-66509413;chr17:66511260-66511261		386;62
N	jcn_only_AD	CUFF.447	chr17	+	chr17:61568730-61571282;chr17:61571021-61571282	chr17:61567390-61571282		chr17:61567390-61568729;chr17:61568730-61571020	chr17:61567389-61567390;chr17:61568729-61568730		366;60
N	jcn_only_AD		chr17	-	chr17:79263609-79269221	chr17:79263609-79268622		chr17:79268623-79269221	chr17:79269221-79269222		35;169
K	alternative_first_exon	CUFF.466	chr17	+	chr17:80417325-80417867,chr17:80417000-80417867,chr17:80416385-80417867;chr17:80416394-80417867	chr17:80416707-80417867	chr17:80416056-80416393	chr17:80416472-80416706			593;910
N	alternative_donor		chr17	-	chr17:1616350-1617149	chr17:1616350-1616996		chr17:1616997-1617149	chr17:1617149-1617150		315;749
N	alternative_donor	CUFF.443	chr17	-	chr17:56083889-56084304	chr17:56083889-56084267		chr17:56084268-56084304	chr17:56084304-56084305		427;32
N	alternative_acceptor	CUFF.410	chr17	-	chr17:1616220-1616996;chr17:1615694-1616996;chr17:1616190-1616996;chr17:1616350-1616996	chr17:1616199-1616996		chr17:1615694-1616189;chr17:1616190-1616198;chr17:1616199-1616219;chr17:1616220-1616349	chr17:1615693-1615694;chr17:1616189-1616190;chr17:1616198-1616199;chr17:1616219-1616220		440;454
K	intron_retention	CUFF.416	chr17	-	chr17:15584268-15586174				chr17:15584267-15584268;chr17:15586174-15586175		64;32
N	alternative_acceptor	CUFF.457	chr17	-	chr17:79250934-79254408	chr17:79253961-79254408		chr17:79250934-79253960	chr17:79250933-79250934		187;34
K	intron_retention	CUFF.460	chr17	-	chr17:79478830-79478928				chr17:79478829-79478830;chr17:79478928-79478929		157;38
K	cassette	CUFF.433	chr17	-	chr17:37595447-37596875	chr17:37595447-37596638;chr17:37596772-37596875		chr17:37596639-37596771			5;44
N	jcn_only_AD	CUFF.426	chr17	+	chr17:29592358-29652837;chr17:29645583-29652837	chr17:29626625-29652837		chr17:29592358-29626624;chr17:29626625-29645582	chr17:29592357-29592358;chr17:29626624-29626625		38;23
N	jcn_only_AA	CUFF.410	chr17	-	chr17:1616350-1617149;chr17:1616199-1617149;chr17:1615694-1617149;chr17:1615941-1617149	chr17:1616190-1617149		chr17:1615694-1615940;chr17:1615941-1616189;chr17:1616190-1616198;chr17:1616199-1616349	chr17:1615693-1615694;chr17:1615940-1615941;chr17:1616189-1616190;chr17:1616198-1616199		596;106
N	intron_retention	CUFF.435	chr17	-	chr17:40738910-40739851				chr17:40738909-40738910;chr17:40739851-40739852		105;28
N	alternative_donor	CUFF.457	chr17	-	chr17:79220862-79225292	chr17:79220862-79223869		chr17:79223870-79225292	chr17:79225292-79225293		62;179
N	alternative_acceptor	CUFF.450	chr17	+	chr17:61905284-61905497	chr17:61905284-61905478		chr17:61905479-61905497	chr17:61905497-61905498		337;68
N	alternative_donor	CUFF.461	chr17	-	chr17:79894738-79895137;chr17:79894738-79895133;chr17:79894738-79895055;chr17:79894738-79895068;chr17:79894738-79894845;chr17:79894738-79895103	chr17:79894738-79895403		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		334;39
N	jcn_only_AA		chr17	+	chr17:25965381-25967668	chr17:25965381-25967597		chr17:25967598-25967668	chr17:25967668-25967669		197;352
K	intron_retention	CUFF.450	chr17	+	chr17:61906924-61907211				chr17:61906923-61906924;chr17:61907211-61907212		1096;56
N	jcn_only_AA	CUFF.426	chr17	+	chr17:29592358-29652837	chr17:29592358-29626527		chr17:29626528-29652837	chr17:29652837-29652838		28;18
K	coord_cassette	CUFF.416	chr17	-	chr17:15584268-15586349	chr17:15584268-15584364;chr17:15584537-15586167;chr17:15586266-15586349		chr17:15584365-15584536;chr17:15586168-15586265			436;21
K	intron_retention	CUFF.450	chr17	+	chr17:61907550-61907630				chr17:61907549-61907550;chr17:61907630-61907631		1118;56
N	intron_retention		chr17	-	chr17:79894738-79895103				chr17:79894737-79894738;chr17:79895103-79895104		144;161
K	intron_retention	CUFF.440	chr17	+	chr17:46993550-46998521				chr17:46993549-46993550;chr17:46998521-46998522		447;44
N	jcn_only_AA		chr17	+	chr17:80442807-80446096	chr17:80442807-80443372		chr17:80443373-80446096	chr17:80446096-80446097		38;80
K	cassette	CUFF.457	chr17	-	chr17:79244825-79249768	chr17:79244825-79246315;chr17:79246428-79249768		chr17:79246316-79246427			174;62
K	alternative_acceptor	CUFF.430	chr17	+	chr17:33640726-33648755	chr17:33640726-33648753		chr17:33648754-33648755	chr17:33648755-33648756		140;126
N	jcn_only_AA	CUFF.443	chr17	-	chr17:56081080-56082283	chr17:56081363-56082283		chr17:56081080-56081362	chr17:56081079-56081080		55;134
N	alternative_acceptor	CUFF.457	chr17	-	chr17:79220041-79220684	chr17:79220474-79220684		chr17:79220041-79220473	chr17:79220040-79220041		28;177
K	intron_retention	CUFF.460	chr17	-	chr17:79478135-79478213				chr17:79478134-79478135;chr17:79478213-79478214		951;47
N	coord_cassette	CUFF.456	chr17	-	chr17:76994369-77005745	chr17:76994369-76996181;chr17:76996353-77001453;chr17:77001564-77005745		chr17:76996182-76996352;chr17:77001454-77001563			122;210
K	cassette	CUFF.452	chr17	+	chr17:66508690-66511127	chr17:66508690-66509050;chr17:66509112-66511127		chr17:66509051-66509111			8;59
K	intron_retention	CUFF.465	chr17	-	chr17:79994185-79994259				chr17:79994184-79994185;chr17:79994259-79994260		1440;274
N	alternative_acceptor	CUFF.413	chr17	+	chr17:6353393-6353681	chr17:6353393-6353558		chr17:6353559-6353681	chr17:6353681-6353682		325;108
K	intron_retention	CUFF.438	chr17	-	chr17:42340095-42340219				chr17:42340094-42340095;chr17:42340219-42340220		25;21
K	jcn_only_AA	CUFF.415	chr17	-	chr17:15498141-15499827	chr17:15498205-15499827		chr17:15498141-15498204	chr17:15498140-15498141		115;180
K	alternative_first_exon	CUFF.412,CUFF.460	chr17	-	chr17:5403271-5405056	chr17:5403271-5403350	chr17:5405057-5409297	chr17:5403351-5404514		chr17:5402649-5403270	104;307
N	cassette	CUFF.456	chr17	-	chr17:76996353-77005745;chr17:76994046-77005745	chr17:76996353-77001453,chr17:76994046-77001453;chr17:77001564-77005745		chr17:77001454-77001563			909;241
K	alternative_first_exon	CUFF.439	chr17	-	chr17:46685458-46710875;chr17:46685458-46685590	chr17:46685458-46687880	chr17:46710876-46711031;chr17:46685591-46685764	chr17:46687881-46688379			94;23
N	jcn_only_AA	CUFF.410	chr17	-	chr17:1616220-1616996;chr17:1615694-1616996;chr17:1616190-1616996;chr17:1616350-1616996	chr17:1616199-1616996		chr17:1615694-1616189;chr17:1616190-1616198;chr17:1616199-1616219;chr17:1616220-1616349	chr17:1615693-1615694;chr17:1616189-1616190;chr17:1616198-1616199;chr17:1616219-1616220		354;459
K	intron_retention		chr17	-	chr17:40738156-40738782				chr17:40738155-40738156;chr17:40738782-40738783		319;167
N	coord_cassette	CUFF.426	chr17	+	chr17:29664899-29667522	chr17:29664899-29665042;chr17:29665158-29665721;chr17:29665824-29667522		chr17:29665043-29665157;chr17:29665722-29665823			71;168
N	alternative_donor	CUFF.461	chr17	-	chr17:79894738-79895137;chr17:79894738-79895403;chr17:79894738-79895133;chr17:79894738-79895055;chr17:79894738-79895068;chr17:79894738-79894845	chr17:79894738-79895103		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		334;39
N	alternative_first_exon	CUFF.409	chr17	-	chr17:653150-654890;chr17:653150-655372	chr17:653150-655857	chr17:654891-655341;chr17:655373-655501	chr17:655858-656061			202;64
N	alternative_donor	CUFF.447	chr17	+	chr17:61568730-61571282;chr17:61571021-61571282	chr17:61567390-61571282		chr17:61567390-61568729;chr17:61568730-61571020	chr17:61567389-61567390;chr17:61568729-61568730		86;60
N	alternative_donor	CUFF.447	chr17	+	chr17:61554705-61555291	chr17:61555152-61555291		chr17:61554705-61555151	chr17:61554704-61554705		459;401
N	alternative_acceptor	CUFF.450	chr17	+	chr17:61904875-61905210;chr17:61904875-61905188	chr17:61904875-61905033		chr17:61905034-61905188;chr17:61905189-61905210	chr17:61905188-61905189;chr17:61905210-61905211		307;158
K	intron_retention		chr17	-	chr17:79894738-79895133				chr17:79894737-79894738;chr17:79895133-79895134		226;135
K	cassette	CUFF.411	chr17	+	chr17:1937137-1939822	chr17:1937137-1939263;chr17:1939386-1939822		chr17:1939264-1939385			110;313
N	intron_retention		chr17	-	chr17:1616190-1616996				chr17:1616189-1616190;chr17:1616996-1616997		165;306
N	cassette	CUFF.416	chr17	-	chr17:15584268-15586349;chr17:15584268-15586167	chr17:15584268-15584364;chr17:15584537-15586167,chr17:15584537-15586349		chr17:15584365-15584536			948;47
N	alternative_acceptor	CUFF.426	chr17	+	chr17:29657517-29661855	chr17:29657517-29661681		chr17:29661682-29661855	chr17:29661855-29661856		78;7
N	jcn_only_AA	CUFF.410	chr17	-	chr17:1617309-1617664	chr17:1617340-1617664		chr17:1617309-1617339	chr17:1617308-1617309		599;29
N	alternative_acceptor	CUFF.413	chr17	+	chr17:6352728-6353681	chr17:6352728-6353347		chr17:6353348-6353681	chr17:6353681-6353682		111;275
N	alternative_donor	CUFF.447	chr17	+	chr17:61562734-61563917	chr17:61563733-61563917		chr17:61562734-61563732	chr17:61562733-61562734		305;94
N	jcn_only_AD		chr17	-	chr17:1616350-1617149	chr17:1616350-1616996		chr17:1616997-1617149	chr17:1617149-1617150		315;110
K	intron_retention	CUFF.426	chr17	+	chr17:29684109-29684286				chr17:29684108-29684109;chr17:29684286-29684287		346;3
N	alternative_donor	CUFF.426	chr17	+	chr17:29657517-29661855	chr17:29661749-29661855		chr17:29657517-29661748	chr17:29657516-29657517		78;16
N	alternative_donor	CUFF.452	chr17	+	chr17:66508721-66511534;chr17:66509413-66511534;chr17:66511261-66511534;chr17:66511294-66511534	chr17:66508637-66511534		chr17:66508637-66508720;chr17:66508721-66509412;chr17:66509413-66511260;chr17:66511261-66511293	chr17:66508636-66508637;chr17:66508720-66508721;chr17:66509412-66509413;chr17:66511260-66511261		108;62
N	alternative_donor	CUFF.411	chr17	+	chr17:1937137-1939263	chr17:1938315-1939263		chr17:1937137-1938314	chr17:1937136-1937137		377;23
K	intron_retention	CUFF.466	chr17	+	chr17:80436795-80438957				chr17:80436794-80436795;chr17:80438957-80438958		937;44
N	intron_retention		chr17	+	chr17:35307565-35311097				chr17:35307564-35307565;chr17:35311097-35311098		28;5
N	alternative_acceptor	CUFF.413,CUFF.447	chr17	+	chr17:61562734-61563917;chr17:61562734-61563719	chr17:61562734-61563652		chr17:61563653-61563719;chr17:61563720-61563917	chr17:61563719-61563720;chr17:61563917-61563918		346;7
K	intron_retention	CUFF.422	chr17	+	chr17:25972376-25972886				chr17:25972375-25972376;chr17:25972886-25972887		534;12
K	intron_retention	CUFF.414	chr17	-	chr17:8648039-8648146				chr17:8648038-8648039;chr17:8648146-8648147	chr17:8647845-8648038;chr17:8648147-8648236	36;48
N	alternative_donor		chr17	-	chr17:1616199-1617149	chr17:1616199-1616996		chr17:1616997-1617149	chr17:1617149-1617150		144;873
N	jcn_only_AA	CUFF.450	chr17	+	chr17:61908296-61908395	chr17:61908296-61908379		chr17:61908380-61908395	chr17:61908395-61908396		2601;144
K	intron_retention	CUFF.452	chr17	+	chr17:66526143-66526417				chr17:66526142-66526143;chr17:66526417-66526418		603;59
N	alternative_donor	CUFF.413	chr17	+	chr17:6349508-6350782;chr17:6348663-6350782	chr17:6348725-6350782		chr17:6348663-6348724;chr17:6348725-6349507	chr17:6348662-6348663;chr17:6348724-6348725		241;429
K	alternative_last_exon	CUFF.431	chr17	-	chr17:34497370-34497912	chr17:34497494-34497912	chr17:34497249-34497369	chr17:34497372-34497493			64;31
N	intron_retention		chr17	+	chr17:29701148-29705905				chr17:29701147-29701148;chr17:29705905-29705906		58;174
N	jcn_only_AA	CUFF.413,CUFF.447	chr17	+	chr17:61562734-61563917;chr17:61562734-61563719	chr17:61562734-61563652		chr17:61563653-61563719;chr17:61563720-61563917	chr17:61563719-61563720;chr17:61563917-61563918		430;32
K	intron_retention		chr17	-	chr17:56082403-56082774				chr17:56082402-56082403;chr17:56082774-56082775		100;199
N	alternative_acceptor		chr17	+	chr17:80442807-80446096	chr17:80442807-80443372		chr17:80443373-80446096	chr17:80446096-80446097		38;158
N	intron_retention	CUFF.450	chr17	+	chr17:61904884-61904979				chr17:61904883-61904884;chr17:61904979-61904980		94;85
N	cassette	CUFF.447	chr17	+	chr17:61561903-61562596	chr17:61561903-61562330;chr17:61562428-61562596		chr17:61562331-61562427			206;90
K	coord_cassette	CUFF.417	chr17	+	chr17:15603092-15604465	chr17:15603092-15603361;chr17:15603483-15603586;chr17:15603681-15604465		chr17:15603362-15603482;chr17:15603587-15603680			28;88
N	alternative_donor	CUFF.461	chr17	-	chr17:79894738-79895137;chr17:79894738-79895403;chr17:79894738-79895133;chr17:79894738-79895055;chr17:79894738-79894845;chr17:79894738-79895103	chr17:79894738-79895068		chr17:79894846-79895055;chr17:79895056-79895068;chr17:79895069-79895103;chr17:79895104-79895133;chr17:79895134-79895137;chr17:79895138-79895403	chr17:79895055-79895056;chr17:79895068-79895069;chr17:79895103-79895104;chr17:79895133-79895134;chr17:79895137-79895138;chr17:79895403-79895404		330;43
K	intron_retention	CUFF.411	chr17	+	chr17:1944916-1945061				chr17:1944915-1944916;chr17:1945061-1945062		718;154
N	jcn_only_AD	CUFF.447	chr17	+	chr17:61571021-61571282;chr17:61567390-61571282	chr17:61568730-61571282		chr17:61567390-61568729;chr17:61568730-61571020	chr17:61567389-61567390;chr17:61568729-61568730		361;65
K	intron_retention	CUFF.447	chr17	+	chr17:61571021-61571282				chr17:61571020-61571021;chr17:61571282-61571283		301;110
N	intron_retention		chr17	-	chr17:40738156-40739851				chr17:40738155-40738156;chr17:40739851-40739852		41;151
N	intron_retention		chr17	-	chr17:79995418-79995506				chr17:79995417-79995418;chr17:79995506-79995507		341;312
N	jcn_only_AA	CUFF.410	chr17	-	chr17:1615694-1616996;chr17:1616190-1616996;chr17:1616350-1616996;chr17:1616199-1616996	chr17:1616220-1616996		chr17:1615694-1616189;chr17:1616190-1616198;chr17:1616199-1616219;chr17:1616220-1616349	chr17:1615693-1615694;chr17:1616189-1616190;chr17:1616198-1616199;chr17:1616219-1616220		793;21
N	alternative_acceptor	CUFF.410	chr17	-	chr17:1616350-1617149;chr17:1616190-1617149;chr17:1615694-1617149;chr17:1615941-1617149	chr17:1616199-1617149		chr17:1615694-1615940;chr17:1615941-1616189;chr17:1616190-1616198;chr17:1616199-1616349	chr17:1615693-1615694;chr17:1615940-1615941;chr17:1616189-1616190;chr17:1616198-1616199		566;149
N	jcn_only_AA	CUFF.460	chr17	-	chr17:79479142-79479257	chr17:79479169-79479257		chr17:79479142-79479168	chr17:79479141-79479142		37;937
K	intron_retention		chr17	-	chr17:79994890-79995325				chr17:79994889-79994890;chr17:79995325-79995326		516;259
N	intron_retention		chr17	-	chr17:1616199-1617149				chr17:1616198-1616199;chr17:1617149-1617150		144;869
K	cassette	CUFF.449	chr17	-	chr17:61843555-61850771	chr17:61843555-61850136;chr17:61850224-61850771		chr17:61850137-61850223			122;43
K	intron_retention	CUFF.447	chr17	+	chr17:61562428-61562596				chr17:61562427-61562428;chr17:61562596-61562597		114;114
N	intron_retention		chr17	-	chr17:79994890-79995506				chr17:79994889-79994890;chr17:79995506-79995507		164;453
K	intron_retention	CUFF.443	chr17	-	chr17:56082962-56083161				chr17:56082961-56082962;chr17:56083161-56083162		252;79
N	alternative_donor	CUFF.447	chr17	+	chr17:61568730-61571282;chr17:61567390-61571282	chr17:61571021-61571282		chr17:61567390-61568729;chr17:61568730-61571020	chr17:61567389-61567390;chr17:61568729-61568730		81;65
N	alternative_acceptor	CUFF.457	chr17	-	chr17:79220859-79225292;chr17:79223894-79225292	chr17:79220862-79225292		chr17:79220859-79220861;chr17:79220862-79223893	chr17:79220858-79220859;chr17:79220861-79220862		74;38
K	intron_retention		chr17	-	chr17:79894738-79895137				chr17:79894737-79894738;chr17:79895137-79895138		296;130
K	alternative_last_exon	CUFF.415	chr17	-	chr17:15472345-15496650	chr17:15492542-15496650	chr17:15472205-15472344	chr17:15491610-15492541			14;126
N	jcn_only_AA	CUFF.410	chr17	-	chr17:1616199-1617149;chr17:1616190-1617149;chr17:1615694-1617149;chr17:1615941-1617149	chr17:1616350-1617149		chr17:1615694-1615940;chr17:1615941-1616189;chr17:1616190-1616198;chr17:1616199-1616349	chr17:1615693-1615694;chr17:1615940-1615941;chr17:1616189-1616190;chr17:1616198-1616199		388;315
K	intron_retention		chr17	+	chr17:6352728-6353347				chr17:6352727-6352728;chr17:6353347-6353348		491;24
N	alternative_acceptor	CUFF.411	chr17	+	chr17:80416385-80417867	chr17:80416385-80417150		chr17:80417151-80417867	chr17:80417867-80417868		104;15
K	coord_cassette	CUFF.431	chr17	-	chr17:34500807-34503839	chr17:34500807-34502089;chr17:34502176-34502338;chr17:34502412-34503839		chr17:34502090-34502175;chr17:34502339-34502411			199;181
K	intron_retention	CUFF.412	chr17	-	chr17:5487280-5487612				chr17:5487279-5487280;chr17:5487612-5487613	chr17:5487007-5487279;chr17:5487613-5487820	2;271
N	intron_retention	CUFF.450	chr17	+	chr17:61905284-61905478				chr17:61905283-61905284;chr17:61905478-61905479		44;158
K	intron_retention	CUFF.436	chr17	-	chr17:41738762-41739238				chr17:41738761-41738762;chr17:41739238-41739239		139;94
K	alternative_first_exon	CUFF.440	chr17	+	chr17:46986183-46993437	chr17:46990328-46993437,chr17:46990384-46993437	chr17:46985638-46986182	chr17:46990196-46990327			31;241
K	cassette	CUFF.437	chr17	-	chr17:42113669-42114779	chr17:42113669-42114229;chr17:42114471-42114779		chr17:42114230-42114470		chr17:42111904-42113668;chr17:42114780-42114906	99;160
K	coord_cassette	CUFF.378	chr16	+	chr16:21969921-21973780	chr16:21969921-21970659;chr16:21970877-21972648;chr16:21972787-21973780		chr16:21970660-21970876;chr16:21972649-21972786			811;103
K	cassette	CUFF.393	chr16	-	chr16:63565209-63651596	chr16:63565209-63566720;chr16:63566836-63651596		chr16:63566721-63566835			292;38
K	cassette	CUFF.364	chr16	+	chr16:3194326-3194743	chr16:3194326-3194453;chr16:3194649-3194743		chr16:3194454-3194648			72;151
N	alternative_donor	CUFF.366,CUFF.404	chr16	-	chr16:4411471-4411985	chr16:4411471-4411749		chr16:4411750-4411985	chr16:4411985-4411986		685;244
N	jcn_only_AD	CUFF.373	chr16	-	chr16:15186472-15188001	chr16:15186472-15187808		chr16:15187809-15188001	chr16:15188001-15188002		122;128
K	intron_retention	CUFF.375	chr16	+	chr16:21712349-21716489				chr16:21712348-21712349;chr16:21716489-21716490		294;36
K	intron_retention	CUFF.400	chr16	+	chr16:70399035-70399835				chr16:70399034-70399035;chr16:70399835-70399836		111;2
K	intron_retention	CUFF.387	chr16	+	chr16:31371785-31372383				chr16:31371784-31371785;chr16:31372383-31372384		9;2
K	jcn_only_AD	CUFF.375	chr16	+	chr16:21716614-21721208	chr16:21716766-21721208		chr16:21716614-21716765	chr16:21716613-21716614		330;71
K	cassette	CUFF.395	chr16	-	chr16:67218508-67218804	chr16:67218508-67218588;chr16:67218714-67218804		chr16:67218589-67218713			212;150
N	jcn_only_AD		chr16	+	chr16:3115496-3115781;chr16:3115712-3115781	chr16:3115689-3115781		chr16:3115496-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115688-3115689		262;21
K	alternative_first_exon	CUFF.374	chr16	+	chr16:19613046-19619499	chr16:19619184-19619499	chr16:19612986-19613045	chr16:19619043-19619183			389;749
K	intron_retention	CUFF.386	chr16	-	chr16:30004879-30004960				chr16:30004878-30004879;chr16:30004960-30004961		207;68
N	intron_retention	CUFF.366	chr16	-	chr16:4411471-4411749				chr16:4411470-4411471;chr16:4411749-4411750		197;137
N	intron_retention		chr16	-	chr16:70253699-70253814				chr16:70253698-70253699;chr16:70253814-70253815		40;27
N	intron_retention		chr16	+	chr16:3115712-3115781				chr16:3115711-3115712;chr16:3115781-3115782		34;432
N	cassette	CUFF.378	chr16	+	chr16:21969921-21973780	chr16:21969921-21972648;chr16:21972787-21973780		chr16:21972649-21972786			811;107
N	cassette	CUFF.363	chr16	+	chr16:3118012-3118990	chr16:3118012-3118180;chr16:3118241-3118990		chr16:3118181-3118240			291;2903
N	intron_retention		chr16	-	chr16:4463406-4465766				chr16:4463405-4463406;chr16:4465766-4465767		21;98
N	intron_retention		chr16	-	chr16:4445341-4466459				chr16:4445340-4445341;chr16:4466459-4466460		269;45
K	intron_retention	CUFF.375	chr16	+	chr16:21716359-21716489				chr16:21716358-21716359;chr16:21716489-21716490		13;76
N	alternative_donor	CUFF.391	chr16	-	chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57514241		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		205;13
N	jcn_only_AA	CUFF.400	chr16	+	chr16:105550-105793	chr16:105550-105776		chr16:105777-105793	chr16:105793-105794		65;858
N	alternative_acceptor	CUFF.366	chr16	-	chr16:4445341-4455491	chr16:4447452-4455491		chr16:4445341-4447451	chr16:4445340-4445341		933;15
N	alternative_donor	CUFF.363	chr16	+	chr16:3115689-3115784;chr16:3115496-3115784;chr16:3115657-3115784	chr16:3115712-3115784		chr16:3115496-3115656;chr16:3115657-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115656-3115657;chr16:3115688-3115689		1206;151
K	alternative_first_exon	CUFF.408	chr16	+	chr16:89788254-89788938;chr16:89786991-89788938	chr16:89787685-89788938	chr16:89787907-89788253;chr16:89786808-89786990	chr16:89787360-89787684			340;139
K	alternative_first_exon	CUFF.365	chr16	-	chr16:4254636-4289634;chr16:4254636-4256727	chr16:4254636-4292007	chr16:4289635-4289824;chr16:4256728-4258105	chr16:4292008-4292171			60;5
N	alternative_acceptor	CUFF.355	chr16	+	chr16:586143-596816	chr16:586143-587133		chr16:587134-596816	chr16:596816-596817		7;13
K	alternative_last_exon	CUFF.371	chr16	-	chr16:5651666-5661235	chr16:5660676-5661235	chr16:5651170-5651665	chr16:5660204-5660675			41;339
K	intron_retention	CUFF.408	chr16	+	chr16:89804314-89804383				chr16:89804313-89804314;chr16:89804383-89804384		672;133
K	intron_retention	CUFF.408	chr16	+	chr16:89799821-89799889				chr16:89799820-89799821;chr16:89799889-89799890		675;83
N	intron_retention	CUFF.354	chr16	+	chr16:105883-106320				chr16:105882-105883;chr16:106320-106321		42;132
K	jcn_only_AD	CUFF.400	chr16	+	chr16:70395414-70398445	chr16:70395540-70398445		chr16:70395414-70395539	chr16:70395413-70395414		257;27
N	coord_cassette	CUFF.400	chr16	+	chr16:70390151-70398445	chr16:70390151-70390748;chr16:70390810-70394679;chr16:70394798-70395320;chr16:70395414-70398445		chr16:70390749-70390809;chr16:70394680-70394797;chr16:70395321-70395413			24;44
K	alternative_acceptor	CUFF.407	chr16	-	chr16:87807148-87811473	chr16:87807196-87811473		chr16:87807148-87807195	chr16:87807147-87807148		72;18
N	jcn_only_AD	CUFF.374	chr16	+	chr16:19621738-19637498	chr16:19628131-19637498					70;232
K	intron_retention		chr16	-	chr16:30006165-30006423				chr16:30006164-30006165;chr16:30006423-30006424		40;355
N	jcn_only_AD		chr16	+	chr16:105543-105793	chr16:105550-105793		chr16:105543-105549	chr16:105542-105543		177;65
N	cassette	CUFF.366	chr16	-	chr16:4458253-4466459	chr16:4458253-4462356;chr16:4462432-4466459		chr16:4462357-4462431			133;483
N	coord_cassette	CUFF.374	chr16	+	chr16:19613046-19621643	chr16:19613046-19619499;chr16:19619597-19620295;chr16:19620344-19621643		chr16:19619500-19619596;chr16:19620296-19620343			60;790
K	intron_retention	CUFF.366	chr16	-	chr16:4465854-4466459				chr16:4465853-4465854;chr16:4466459-4466460		172;94
N	intron_retention		chr16	+	chr16:3115496-3115642				chr16:3115495-3115496;chr16:3115642-3115643		120;237
N	alternative_donor	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57517869		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		218;0
N	cassette	CUFF.400	chr16	+	chr16:70390151-70398445	chr16:70390151-70395320;chr16:70395540-70398445		chr16:70395321-70395539			24;132
K	intron_retention		chr16	+	chr16:70389439-70390031				chr16:70389438-70389439;chr16:70390031-70390032		37;73
K	intron_retention	CUFF.382	chr16	-	chr16:23504780-23505619				chr16:23504779-23504780;chr16:23505619-23505620		254;384
K	intron_retention	CUFF.400	chr16	+	chr16:70400166-70400526				chr16:70400165-70400166;chr16:70400526-70400527		334;78
N	intron_retention		chr16	-	chr16:30006165-30006861				chr16:30006164-30006165;chr16:30006861-30006862		116;169
K	cassette	CUFF.366	chr16	-	chr16:4463406-4466459	chr16:4463406-4465715;chr16:4465854-4466459		chr16:4465716-4465853			591;249
K	cassette	CUFF.400	chr16	+	chr16:70380952-70384459	chr16:70380952-70381777;chr16:70381894-70384459		chr16:70381778-70381893			256;36
N	jcn_only_AD		chr16	-	chr16:57513598-57513772;chr16:57513598-57517869	chr16:57513598-57513756					185;70
N	jcn_only_AA	CUFF.363	chr16	+	chr16:603042-604553	chr16:603042-603338		chr16:603339-604553	chr16:604553-604554		63;111
N	alternative_acceptor	CUFF.391	chr16	-	chr16:57509870-57513353	chr16:57512575-57513353		chr16:57509870-57512574	chr16:57509869-57509870		2209;10
N	alternative_acceptor	CUFF.406	chr16	+	chr16:19710971-19716437	chr16:19710971-19711699		chr16:19711700-19716437	chr16:19716437-19716438		7;73
N	intron_retention		chr16	-	chr16:57513601-57521042				chr16:57513600-57513601;chr16:57521042-57521043		45;104
K	intron_retention		chr16	+	chr16:3115496-3115784				chr16:3115495-3115496;chr16:3115784-3115785		695;146
N	jcn_only_AD		chr16	-	chr16:57513598-57513756;chr16:57513598-57517869	chr16:57513598-57513772					89;165
K	intron_retention	CUFF.386	chr16	-	chr16:30006539-30006663				chr16:30006538-30006539;chr16:30006663-30006664		462;115
K	cassette	CUFF.375	chr16	+	chr16:21737980-21739561	chr16:21737980-21738432;chr16:21738481-21739561		chr16:21738433-21738480			435;8
N	jcn_only_AA		chr16	+	chr16:3194833-3195668	chr16:3194833-3194984		chr16:3194985-3195668	chr16:3195668-3195669		20;169
N	alternative_donor	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57521007		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		147;71
K	intron_retention		chr16	+	chr16:70389439-70390014				chr16:70389438-70389439;chr16:70390014-70390015		413;46
N	jcn_only_AD	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756	chr16:57513601-57514206		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		1440;32
K	intron_retention		chr16	-	chr16:23505700-23507014				chr16:23505699-23505700;chr16:23507014-23507015		682;46
K	alternative_last_exon	CUFF.355	chr16	+	chr16:583999-586028;chr16:583999-597558	chr16:583999-596816	chr16:597559-598302	chr16:596817-597392			242;59
K	jcn_only_AA	CUFF.387	chr16	+	chr16:31368423-31368654	chr16:31368423-31368573		chr16:31368574-31368654	chr16:31368654-31368655		132;10
N	alternative_donor		chr16	+	chr16:3115689-3115781;chr16:3115712-3115781	chr16:3115496-3115781		chr16:3115496-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115688-3115689		244;228
N	jcn_only_AA	CUFF.354,CUFF.387	chr16	+	chr16:105883-106538	chr16:105883-106320		chr16:106321-106538	chr16:106538-106539		797;42
K	alternative_first_exon	CUFF.375	chr16	+	chr16:21693147-21696550	chr16:21695874-21696550	chr16:21693059-21693146	chr16:21695668-21695873			25;202
K	alternative_acceptor	CUFF.399	chr16	-	chr16:70267574-70268076	chr16:70267606-70268076		chr16:70267574-70267605	chr16:70267573-70267574		8;72
K	cassette	CUFF.396	chr16	+	chr16:67233905-67234353	chr16:67233905-67234094;chr16:67234265-67234353		chr16:67234095-67234264			56;918
N	alternative_donor	CUFF.355	chr16	+	chr16:583999-596816	chr16:586143-596816		chr16:583999-586142	chr16:583998-583999		41;1
K	alternative_acceptor	CUFF.408	chr16	+	chr16:89789592-89789686	chr16:89789592-89789667		chr16:89789668-89789686	chr16:89789686-89789687		107;245
N	alternative_acceptor	CUFF.389	chr16	+	chr16:56226529-56309842;chr16:56226529-56247183	chr16:56226529-56268924		chr16:56247184-56268924;chr16:56268925-56309842	chr16:56268924-56268925;chr16:56309842-56309843		23;0
K	intron_retention	CUFF.386	chr16	-	chr16:30006785-30006861				chr16:30006784-30006785;chr16:30006861-30006862		687;21
K	alternative_donor	CUFF.408	chr16	+	chr16:89793734-89795642	chr16:89793766-89795642		chr16:89793734-89793765	chr16:89793733-89793734		407;129
K	jcn_only_AA	CUFF.399	chr16	-	chr16:70267574-70268076	chr16:70267606-70268076		chr16:70267574-70267605	chr16:70267573-70267574		8;156
K	jcn_only_AD	CUFF.395,CUFF.407	chr16	-	chr16:67221042-67222922	chr16:67221042-67221127					97;129
K	jcn_only_AA	CUFF.374	chr16	+	chr16:19576273-19580745	chr16:19576273-19580565		chr16:19580566-19580745	chr16:19580745-19580746		455;116
N	jcn_only_AD	CUFF.355	chr16	+	chr16:583999-596816	chr16:586143-596816		chr16:583999-586142	chr16:583998-583999		41;7
K	jcn_only_AD	CUFF.404	chr16	-	chr16:75575354-75576499	chr16:75575354-75576452		chr16:75576453-75576499	chr16:75576499-75576500	chr16:75575248-75575353;chr16:75576500-75576581	170;56
N	cassette	CUFF.404	chr16	-	chr16:75576582-75589701	chr16:75576582-75579723;chr16:75579853-75589701		chr16:75579724-75579852		chr16:75576500-75576581;chr16:75589702-75590255	57;75
N	intron_retention		chr16	-	chr16:4411805-4411985				chr16:4411804-4411805;chr16:4411985-4411986		172;238
N	alternative_first_exon	CUFF.381	chr16	+	chr16:22448814-22466022	chr16:22462980-22466022	chr16:22448329-22448813	chr16:22462915-22462979			5;191
K	alternative_first_exon	CUFF.389	chr16	+	chr16:56269297-56309842;chr16:56227625-56309842;chr16:56260484-56309842	chr16:56226529-56309842	chr16:56227496-56227624;chr16:56260385-56260483	chr16:56226486-56226528			390;17
K	intron_retention	CUFF.357	chr16	-	chr16:1370460-1372488				chr16:1370459-1370460;chr16:1372488-1372489		174;107
K	intron_retention	CUFF.381	chr16	+	chr16:22494549-22494716				chr16:22494548-22494549;chr16:22494716-22494717		43;210
K	intron_retention	CUFF.404	chr16	-	chr16:75589872-75589968				chr16:75589871-75589872;chr16:75589968-75589969	chr16:75589702-75589871;chr16:75589969-75590255	135;62
N	jcn_only_AD	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57521042		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		1427;45
N	jcn_only_AA	CUFF.389	chr16	+	chr16:56226529-56309842;chr16:56226529-56247183	chr16:56226529-56268924		chr16:56247184-56268924;chr16:56268925-56309842	chr16:56268924-56268925;chr16:56309842-56309843		195;44
N	coord_cassette	CUFF.400	chr16	+	chr16:70390151-70395320	chr16:70390151-70390748;chr16:70390810-70394679;chr16:70394798-70395320		chr16:70390749-70390809;chr16:70394680-70394797			145;20
K	alternative_acceptor	CUFF.374	chr16	+	chr16:19576273-19580745	chr16:19576273-19580565		chr16:19580566-19580745	chr16:19580745-19580746		455;152
K	intron_retention	CUFF.378	chr16	+	chr16:21976827-21979948				chr16:21976826-21976827;chr16:21979948-21979949		167;273
K	intron_retention	CUFF.366	chr16	-	chr16:4410365-4410444				chr16:4410364-4410365;chr16:4410444-4410445		1003;51
N	jcn_only_AD	CUFF.382,CUFF.399	chr16	-	chr16:70254784-70255156	chr16:70254784-70255152		chr16:70255153-70255156	chr16:70255156-70255157		66;14
N	jcn_only_AD	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57520216		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		1468;4
K	alternative_first_exon	CUFF.365	chr16	-	chr16:4254636-4289634;chr16:4254636-4292007	chr16:4254636-4256727	chr16:4289635-4289824;chr16:4292008-4292171	chr16:4256728-4258105			27;38
K	intron_retention	CUFF.408	chr16	+	chr16:89789243-89789544				chr16:89789242-89789243;chr16:89789544-89789545		404;51
N	alternative_donor	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57520216		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		218;0
N	mutually_exclusive	CUFF.363	chr16	+	chr16:3117615-3118180,chr16:3118241-3118990	chr16:3117615-3117984,chr16:3118012-3118990	chr16:3118181-3118240	chr16:3117985-3118011			72;270
N	coord_cassette	CUFF.363	chr16	+	chr16:3117417-3118180	chr16:3117417-3117554;chr16:3117615-3117984;chr16:3118012-3118180		chr16:3117555-3117614;chr16:3117985-3118011			78;2556
K	jcn_only_AA	CUFF.407	chr16	-	chr16:87807148-87811473	chr16:87807196-87811473		chr16:87807148-87807195	chr16:87807147-87807148		72;28
N	alternative_donor	CUFF.404	chr16	-	chr16:75579853-75589701	chr16:75579853-75589116		chr16:75589117-75589701	chr16:75589701-75589702	chr16:75579724-75579852;chr16:75589702-75590255	157;5
N	alternative_last_exon		chr16	+	chr16:77759482-77775478	chr16:77759482-77769724	chr16:77775479-77776256	chr16:77769725-77770226			109;360
N	coord_cassette	CUFF.378	chr16	+	chr16:21983444-21991867	chr16:21983444-21985216;chr16:21985298-21987487;chr16:21987565-21991867		chr16:21985217-21985297;chr16:21987488-21987564			40;48
N	jcn_only_AD	CUFF.399	chr16	-	chr16:70266708-70267326	chr16:70266708-70267315		chr16:70267316-70267326	chr16:70267326-70267327		124;7
K	alternative_acceptor	CUFF.396	chr16	+	chr16:67234872-67235311	chr16:67234872-67235287		chr16:67235288-67235311	chr16:67235311-67235312		63;550
N	cassette	CUFF.373	chr16	-	chr16:15170508-15177369	chr16:15170508-15173854;chr16:15173954-15177369		chr16:15173855-15173953			65;247
N	alternative_donor	CUFF.381	chr16	+	chr16:22466187-22470675	chr16:22466927-22470675		chr16:22466187-22466926	chr16:22466186-22466187		293;1
K	jcn_only_AD	CUFF.375	chr16	+	chr16:21712349-21716489	chr16:21712391-21716489		chr16:21712349-21712390	chr16:21712348-21712349		294;4
N	mutually_exclusive	CUFF.386	chr16	-	chr16:30005130-30006423,chr16:30006785-30006861	chr16:30005130-30005226,chr16:30006165-30006861	chr16:30006424-30006784	chr16:30005227-30006164			328;57
N	jcn_only_AA		chr16	-	chr16:57513598-57513756	chr16:57513601-57513756		chr16:57513598-57513600	chr16:57513597-57513598		70;163
N	intron_retention		chr16	+	chr16:3117615-3118180				chr16:3117614-3117615;chr16:3118180-3118181		82;285
K	cassette	CUFF.374	chr16	+	chr16:19592976-19612985	chr16:19592976-19603111;chr16:19603197-19612985		chr16:19603112-19603196			18;246
K	alternative_acceptor	CUFF.396,CUFF.400	chr16	+	chr16:70399035-70399987	chr16:70399035-70399835		chr16:70399836-70399987	chr16:70399987-70399988		296;102
K	jcn_only_AD	CUFF.375	chr16	+	chr16:21756358-21763255	chr16:21760282-21763255					748;17
N	alternative_donor		chr16	-	chr16:23505700-23507009;chr16:23505700-23507034	chr16:23505700-23507014		chr16:23507010-23507014;chr16:23507015-23507034	chr16:23507014-23507015;chr16:23507034-23507035		382;333
N	intron_retention		chr16	-	chr16:57513601-57514241				chr16:57513600-57513601;chr16:57514241-57514242		372;97
N	cassette	CUFF.387	chr16	+	chr16:31383106-31383917	chr16:31383106-31383698;chr16:31383831-31383917		chr16:31383699-31383830			10;42
K	jcn_only_AA	CUFF.396	chr16	+	chr16:67234872-67235311	chr16:67234872-67235287		chr16:67235288-67235311	chr16:67235311-67235312		63;1169
N	cassette	CUFF.373	chr16	-	chr16:15180116-15185171	chr16:15180116-15180221;chr16:15180312-15185171		chr16:15180222-15180311			23;245
K	intron_retention	CUFF.361	chr16	+	chr16:2202887-2202989				chr16:2202886-2202887;chr16:2202989-2202990		335;106
N	alternative_donor		chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57515373		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		215;3
K	alternative_donor	CUFF.375	chr16	+	chr16:21716614-21721208	chr16:21716766-21721208		chr16:21716614-21716765	chr16:21716613-21716614		330;71
N	cassette	CUFF.404	chr16	-	chr16:75576582-75589701	chr16:75576582-75579723;chr16:75579976-75589701		chr16:75579724-75579975		chr16:75576500-75576581;chr16:75589702-75590255	57;52
K	alternative_first_exon	CUFF.385	chr16	-	chr16:28515372-28523148	chr16:28515372-28518101	chr16:28523149-28523453	chr16:28518102-28518155			32;52
K	intron_retention	CUFF.382	chr16	-	chr16:23504780-23505623				chr16:23504779-23504780;chr16:23505623-23505624		489;384
N	alternative_acceptor	CUFF.354,CUFF.387	chr16	+	chr16:105883-106538	chr16:105883-106320		chr16:106321-106538	chr16:106538-106539		797;106
N	jcn_only_AD	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57521007		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		1217;255
N	alternative_acceptor	CUFF.363	chr16	+	chr16:603042-604553	chr16:603042-603338		chr16:603339-604553	chr16:604553-604554		63;208
K	alternative_last_exon	CUFF.394	chr16	+	chr16:66613796-66620899	chr16:66613796-66613928	chr16:66620900-66621001	chr16:66613929-66614027			52;57
N	alternative_donor	CUFF.373	chr16	-	chr16:15186472-15188001	chr16:15186472-15187808		chr16:15187809-15188001	chr16:15188001-15188002		122;49
N	intron_retention		chr16	-	chr16:23505700-23507034				chr16:23505699-23505700;chr16:23507034-23507035		58;38
K	coord_cassette	CUFF.378	chr16	+	chr16:21964778-21974081	chr16:21964778-21968737;chr16:21968888-21969855;chr16:21969921-21973780;chr16:21973838-21974081		chr16:21968738-21968887;chr16:21969856-21969920;chr16:21973781-21973837			239;562
N	alternative_first_exon	CUFF.369	chr16	+	chr16:4552961-4555484,chr16:4533756-4555484,chr16:4538744-4555484,chr16:4533740-4555484,chr16:4526489-4555484,chr16:4526667-4555484;chr16:4524849-4555484;chr16:4526419-4555484	chr16:4546029-4555484	chr16:4524691-4524848;chr16:4526289-4526418	chr16:4545844-4546028			509;64
N	cassette	CUFF.378	chr16	+	chr16:21987565-21994408	chr16:21987565-21991867;chr16:21992022-21994408		chr16:21991868-21992021			81;84
K	alternative_acceptor	CUFF.395	chr16	-	chr16:67223587-67223873	chr16:67223671-67223873		chr16:67223587-67223670	chr16:67223586-67223587		130;296
K	alternative_last_exon	CUFF.405	chr16	-	chr16:76170264-76181457	chr16:76174302-76181457	chr16:76170165-76170263	chr16:76174260-76174301			76;763
K	alternative_donor	CUFF.382	chr16	-	chr16:23504780-23505623	chr16:23504780-23505619		chr16:23505620-23505623	chr16:23505623-23505624		489;145
K	cassette	CUFF.406	chr16	+	chr16:77769884-77775478	chr16:77769884-77770546;chr16:77770641-77775478		chr16:77770547-77770640			212;32
K	intron_retention	CUFF.387	chr16	+	chr16:31368423-31368573				chr16:31368422-31368423;chr16:31368573-31368574		10;23
N	jcn_only_AA		chr16	+	chr16:56226529-56268924;chr16:56226529-56247183	chr16:56226529-56309842		chr16:56247184-56268924;chr16:56268925-56309842	chr16:56268924-56268925;chr16:56309842-56309843		218;21
K	cassette	CUFF.374	chr16	+	chr16:19621738-19627435	chr16:19621738-19623049;chr16:19623121-19627435		chr16:19623050-19623120			249;875
K	intron_retention	CUFF.381	chr16	+	chr16:22477140-22477517				chr16:22477139-22477140;chr16:22477517-22477518		68;18
N	cassette	CUFF.369	chr16	+	chr16:4526489-4556895	chr16:4526489-4555484;chr16:4555612-4556895		chr16:4555485-4555611			27;349
K	intron_retention	CUFF.395	chr16	-	chr16:67223671-67223873				chr16:67223670-67223671;chr16:67223873-67223874		421;48
N	jcn_only_AD		chr16	+	chr16:3115689-3115781;chr16:3115712-3115781	chr16:3115496-3115781		chr16:3115496-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115688-3115689		55;228
N	jcn_only_AD	CUFF.391	chr16	-	chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57514241		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		1101;372
N	cassette	CUFF.363	chr16	+	chr16:3117615-3118180;chr16:3117417-3118180	chr16:3117615-3117984,chr16:3117417-3117984;chr16:3118012-3118180		chr16:3117985-3118011			160;3169
N	jcn_only_AD	CUFF.366,CUFF.404	chr16	-	chr16:4411471-4411985	chr16:4411471-4411749		chr16:4411750-4411985	chr16:4411985-4411986		685;197
N	cassette	CUFF.400	chr16	+	chr16:70389439-70395320	chr16:70389439-70390014;chr16:70390151-70395320		chr16:70390015-70390150			146;274
N	jcn_only_AD	CUFF.363	chr16	+	chr16:3115712-3115784;chr16:3115689-3115784;chr16:3115657-3115784	chr16:3115496-3115784		chr16:3115496-3115656;chr16:3115657-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115656-3115657;chr16:3115688-3115689		1339;695
K	intron_retention	CUFF.366	chr16	-	chr16:4408485-4409296				chr16:4408484-4408485;chr16:4409296-4409297		1371;97
N	alternative_donor	CUFF.399	chr16	-	chr16:70265062-70265339	chr16:70265062-70265225		chr16:70265226-70265339	chr16:70265339-70265340		169;6
K	intron_retention	CUFF.397	chr16	-	chr16:67970389-67970596				chr16:67970388-67970389;chr16:67970596-67970597		61;60
N	intron_retention		chr16	-	chr16:4466602-4466785				chr16:4466601-4466602;chr16:4466785-4466786		140;547
N	coord_cassette	CUFF.366	chr16	-	chr16:4455569-4462356	chr16:4455569-4457501;chr16:4457686-4458181;chr16:4458253-4462356		chr16:4457502-4457685;chr16:4458182-4458252			181;850
N	jcn_only_AD	CUFF.399	chr16	-	chr16:70265062-70265339	chr16:70265062-70265225		chr16:70265226-70265339	chr16:70265339-70265340		169;10
N	cassette	CUFF.387	chr16	+	chr16:31374696-31382404	chr16:31374696-31381301;chr16:31381420-31382404		chr16:31381302-31381419			19;2
N	intron_retention		chr16	+	chr16:3117417-3117984				chr16:3117416-3117417;chr16:3117984-3117985		191;188
N	coord_cassette	CUFF.400	chr16	+	chr16:70390151-70398445	chr16:70390151-70394679;chr16:70394798-70395320;chr16:70395414-70398445		chr16:70394680-70394797;chr16:70395321-70395413			24;88
K	intron_retention		chr16	+	chr16:21987565-21991867				chr16:21987564-21987565;chr16:21991867-21991868		15;53
N	intron_retention		chr16	+	chr16:602531-602604				chr16:602530-602531;chr16:602604-602605		22;96
K	jcn_only_AA	CUFF.395	chr16	-	chr16:67223587-67223873	chr16:67223671-67223873		chr16:67223587-67223670	chr16:67223586-67223587		130;421
K	alternative_first_exon	CUFF.374	chr16	+	chr16:19566643-19576172	chr16:19567069-19576172	chr16:19566465-19566642	chr16:19566683-19567068			134;332
N	alternative_first_exon		chr16	-	chr16:4445341-4447318,chr16:4445341-4466785;chr16:4445341-4466459	chr16:4445341-4455491	chr16:4466460-4466785	chr16:4455492-4455568			425;662
K	jcn_only_AA	CUFF.400	chr16	+	chr16:70389439-70390031	chr16:70389439-70390014		chr16:70390015-70390031	chr16:70390031-70390032		37;413
K	jcn_only_AD	CUFF.396	chr16	+	chr16:67234710-67234792	chr16:67234712-67234792		chr16:67234710-67234711	chr16:67234709-67234710		894;234
N	cassette	CUFF.400	chr16	+	chr16:70390151-70398445	chr16:70390151-70395320;chr16:70395414-70398445		chr16:70395321-70395413			24;161
N	jcn_only_AA	CUFF.391	chr16	-	chr16:57509870-57513353	chr16:57512575-57513353		chr16:57509870-57512574	chr16:57509869-57509870		2209;29
K	intron_retention	CUFF.408	chr16	+	chr16:89789592-89789667				chr16:89789591-89789592;chr16:89789667-89789668		446;12
K	alternative_last_exon	CUFF.384	chr16	-	chr16:25098045-25114671;chr16:25112007-25114671	chr16:25097094-25114671	chr16:25097563-25098044;chr16:25111788-25112006	chr16:25096913-25097093			631;52
N	jcn_only_AA	CUFF.382	chr16	-	chr16:23504843-23505623;chr16:23504909-23505623	chr16:23504780-23505623		chr16:23504780-23504842;chr16:23504843-23504908	chr16:23504779-23504780;chr16:23504842-23504843		964;489
N	alternative_first_exon	CUFF.369	chr16	+	chr16:4552961-4555484,chr16:4533756-4555484,chr16:4538744-4555484,chr16:4533740-4555484,chr16:4526489-4555484,chr16:4526667-4555484;chr16:4524849-4555484;chr16:4546029-4555484	chr16:4526419-4555484	chr16:4524691-4524848;chr16:4545844-4546028	chr16:4526289-4526418			462;111
N	jcn_only_AA	CUFF.366	chr16	-	chr16:4445341-4455491	chr16:4447452-4455491		chr16:4445341-4447451	chr16:4445340-4445341		933;150
N	cassette	CUFF.404	chr16	-	chr16:75576582-75579723	chr16:75576582-75579249;chr16:75579394-75579723		chr16:75579250-75579393		chr16:75576500-75576581;chr16:75579724-75579975	23;106
K	intron_retention	CUFF.397	chr16	-	chr16:67970007-67970117				chr16:67970006-67970007;chr16:67970117-67970118		88;71
K	jcn_only_AD	CUFF.366,CUFF.399	chr16	-	chr16:70268196-70274909	chr16:70268196-70268899					5;137
N	intron_retention		chr16	-	chr16:57513598-57513756				chr16:57513597-57513598;chr16:57513756-57513757		70;101
N	jcn_only_AA	CUFF.355	chr16	+	chr16:586143-596816	chr16:586143-587133		chr16:587134-596816	chr16:596816-596817		7;11
K	alternative_donor	CUFF.400	chr16	+	chr16:70395414-70398445	chr16:70395540-70398445		chr16:70395414-70395539	chr16:70395413-70395414		257;98
K	jcn_only_AA	CUFF.404	chr16	-	chr16:75579853-75589701	chr16:75579976-75589701		chr16:75579853-75579975	chr16:75579852-75579853	chr16:75589702-75590255;chr16:75579724-75579852	157;59
N	jcn_only_AA	CUFF.395	chr16	-	chr16:67223084-67223533	chr16:67223099-67223533		chr16:67223084-67223098	chr16:67223083-67223084		952;24
N	alternative_donor	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756	chr16:57513601-57514206		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		217;1
K	jcn_only_AA	CUFF.395	chr16	-	chr16:67221042-67222922	chr16:67222844-67222922					97;632
K	intron_retention	CUFF.366	chr16	-	chr16:4409623-4410278				chr16:4409622-4409623;chr16:4410278-4410279		889;157
K	cassette	CUFF.361	chr16	+	chr16:2200053-2201569	chr16:2200053-2201130;chr16:2201317-2201569		chr16:2201131-2201316			224;137
N	intron_retention		chr16	-	chr16:57513601-57521157				chr16:57513600-57513601;chr16:57521157-57521158		91;121
N	intron_retention		chr16	-	chr16:23478152-23478309				chr16:23478151-23478152;chr16:23478309-23478310		150;42
N	cassette	CUFF.363	chr16	+	chr16:3117417-3118180;chr16:3117417-3117984	chr16:3117417-3117554;chr16:3117615-3118180,chr16:3117615-3117984		chr16:3117555-3117614			269;2508
N	alternative_donor	CUFF.382,CUFF.399	chr16	-	chr16:70254784-70255156	chr16:70254784-70255152		chr16:70255153-70255156	chr16:70255156-70255157		66;7
N	jcn_only_AD	CUFF.382	chr16	-	chr16:23505700-23507034;chr16:23505700-23507014	chr16:23505700-23507009		chr16:23507010-23507014;chr16:23507015-23507034	chr16:23507014-23507015;chr16:23507034-23507035		740;927
K	cassette	CUFF.362	chr16	+	chr16:2653729-2663960	chr16:2653729-2660462;chr16:2661054-2663960		chr16:2660463-2661053			221;20
K	intron_retention	CUFF.400	chr16	+	chr16:70399035-70399987				chr16:70399034-70399035;chr16:70399987-70399988		296;56
N	jcn_only_AD	CUFF.404	chr16	-	chr16:75579853-75589701	chr16:75579853-75589116		chr16:75589117-75589701	chr16:75589701-75589702	chr16:75579724-75579852;chr16:75589702-75590255	157;23
K	intron_retention	CUFF.400	chr16	+	chr16:70398549-70398919				chr16:70398548-70398549;chr16:70398919-70398920		339;19
K	coord_cassette	CUFF.400	chr16	+	chr16:70380952-70389387	chr16:70380952-70381777;chr16:70381894-70384459;chr16:70384509-70389387		chr16:70381778-70381893;chr16:70384460-70384508			88;42
N	alternative_donor	CUFF.399	chr16	-	chr16:70266708-70267326	chr16:70266708-70267315		chr16:70267316-70267326	chr16:70267326-70267327		124;4
N	alternative_acceptor		chr16	+	chr16:56226529-56268924;chr16:56226529-56247183	chr16:56226529-56309842		chr16:56247184-56268924;chr16:56268925-56309842	chr16:56268924-56268925;chr16:56309842-56309843		2;21
K	alternative_first_exon	CUFF.408	chr16	+	chr16:89787685-89788938;chr16:89786991-89788938	chr16:89788254-89788938	chr16:89787360-89787684;chr16:89786808-89786990	chr16:89787907-89788253			259;220
N	jcn_only_AD	CUFF.381	chr16	+	chr16:22448814-22462940	chr16:22449059-22462940		chr16:22448814-22449058	chr16:22448813-22448814		195;37
N	alternative_acceptor	CUFF.366	chr16	-	chr16:4412133-4445289	chr16:4438633-4445289		chr16:4412133-4438632	chr16:4412132-4412133		68;31
N	jcn_only_AA	CUFF.406	chr16	+	chr16:19710971-19716437	chr16:19710971-19711699		chr16:19711700-19716437	chr16:19716437-19716438		7;326
N	alternative_donor		chr16	+	chr16:3115496-3115781;chr16:3115689-3115781	chr16:3115712-3115781		chr16:3115496-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115688-3115689		278;194
K	intron_retention		chr16	-	chr16:4463406-4466459				chr16:4463405-4463406;chr16:4466459-4466460		591;68
K	alternative_first_exon	CUFF.365	chr16	-	chr16:4254636-4256727;chr16:4254636-4292007	chr16:4254636-4289634	chr16:4256728-4258105;chr16:4292008-4292171	chr16:4289635-4289824			43;22
N	jcn_only_AD	CUFF.382	chr16	-	chr16:23505700-23507009;chr16:23505700-23507014	chr16:23505700-23507034		chr16:23507010-23507014;chr16:23507015-23507034	chr16:23507014-23507015;chr16:23507034-23507035		1609;58
N	intron_retention		chr16	-	chr16:23505700-23507009				chr16:23505699-23505700;chr16:23507009-23507010		927;47
K	intron_retention		chr16	+	chr16:3117615-3117984				chr16:3117614-3117615;chr16:3117984-3117985		3330;256
N	alternative_donor	CUFF.363	chr16	+	chr16:3115712-3115784;chr16:3115689-3115784;chr16:3115657-3115784	chr16:3115496-3115784		chr16:3115496-3115656;chr16:3115657-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115656-3115657;chr16:3115688-3115689		662;695
N	alternative_acceptor		chr16	+	chr16:2203224-2203578	chr16:2203224-2203319		chr16:2203320-2203578	chr16:2203578-2203579		27;242
N	coord_cassette	CUFF.400	chr16	+	chr16:70390151-70398445	chr16:70390151-70390748;chr16:70390810-70394679;chr16:70394798-70395320;chr16:70395540-70398445		chr16:70390749-70390809;chr16:70394680-70394797;chr16:70395321-70395539			24;40
N	coord_cassette	CUFF.386	chr16	-	chr16:30006165-30006861	chr16:30006165-30006423;chr16:30006539-30006663;chr16:30006785-30006861		chr16:30006424-30006538;chr16:30006664-30006784			116;308
K	jcn_only_AD	CUFF.382	chr16	-	chr16:23504780-23505623	chr16:23504780-23505619		chr16:23505620-23505623	chr16:23505623-23505624		489;254
N	alternative_acceptor		chr16	-	chr16:57513598-57517869	chr16:57513601-57517869		chr16:57513598-57513600	chr16:57513597-57513598		20;99
N	jcn_only_AD	CUFF.381	chr16	+	chr16:22466187-22470675	chr16:22466927-22470675		chr16:22466187-22466926	chr16:22466186-22466187		293;3
N	intron_retention		chr16	-	chr16:57507408-57507524				chr16:57507407-57507408;chr16:57507524-57507525		27;32
N	jcn_only_AA	CUFF.389	chr16	+	chr16:56226529-56309842;chr16:56226529-56268924	chr16:56226529-56247183		chr16:56247184-56268924;chr16:56268925-56309842	chr16:56268924-56268925;chr16:56309842-56309843		65;174
N	cassette	CUFF.389	chr16	+	chr16:56370773-56388777	chr16:56370773-56385295;chr16:56385450-56388777		chr16:56385296-56385449			32;26
N	alternative_donor	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57513772		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		203;15
K	coord_cassette	CUFF.378	chr16	+	chr16:21964778-21974081	chr16:21964778-21968555;chr16:21968640-21968737;chr16:21968888-21969855;chr16:21969921-21973780;chr16:21973838-21974081		chr16:21968556-21968639;chr16:21968738-21968887;chr16:21969856-21969920;chr16:21973781-21973837			239;407
K	alternative_donor	CUFF.396	chr16	+	chr16:67234710-67234792	chr16:67234712-67234792		chr16:67234710-67234711	chr16:67234709-67234710		894;116
N	jcn_only_AA		chr16	-	chr16:57513598-57513772	chr16:57513601-57513772		chr16:57513598-57513600	chr16:57513597-57513598		165;407
N	cassette	CUFF.391	chr16	-	chr16:57509132-57509761	chr16:57509132-57509417;chr16:57509533-57509761		chr16:57509418-57509532			155;1368
N	alternative_donor	CUFF.363	chr16	+	chr16:3115712-3115784;chr16:3115496-3115784;chr16:3115657-3115784	chr16:3115689-3115784		chr16:3115496-3115656;chr16:3115657-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115656-3115657;chr16:3115688-3115689		1098;259
N	intron_retention		chr16	+	chr16:3115689-3115784				chr16:3115688-3115689;chr16:3115784-3115785		591;393
N	intron_retention		chr16	+	chr16:3119111-3119281				chr16:3119110-3119111;chr16:3119281-3119282		1019;2376
K	intron_retention	CUFF.387	chr16	+	chr16:31382819-31382950				chr16:31382818-31382819;chr16:31382950-31382951		24;20
K	alternative_acceptor	CUFF.400	chr16	+	chr16:70389439-70390031	chr16:70389439-70390014		chr16:70390015-70390031	chr16:70390031-70390032		37;263
N	coord_cassette	CUFF.366	chr16	-	chr16:4455569-4462356	chr16:4455569-4457562;chr16:4457686-4458181;chr16:4458253-4462356		chr16:4457563-4457685;chr16:4458182-4458252			181;805
N	jcn_only_AA	CUFF.375	chr16	+	chr16:21756358-21763255	chr16:21756358-21758618		chr16:21758619-21763255	chr16:21763255-21763256		748;8
N	alternative_acceptor	CUFF.389	chr16	+	chr16:56226529-56309842;chr16:56226529-56268924	chr16:56226529-56247183		chr16:56247184-56268924;chr16:56268925-56309842	chr16:56268924-56268925;chr16:56309842-56309843		21;2
K	cassette	CUFF.374	chr16	+	chr16:19586445-19590373	chr16:19586445-19589625;chr16:19589681-19590373		chr16:19589626-19589680			244;155
K	intron_retention	CUFF.395	chr16	-	chr16:67218714-67218804				chr16:67218713-67218714;chr16:67218804-67218805		99;131
K	alternative_donor	CUFF.366	chr16	-	chr16:4455569-4457562	chr16:4455569-4457501		chr16:4457502-4457562	chr16:4457562-4457563		639;460
N	intron_retention		chr16	+	chr16:3115657-3115784				chr16:3115656-3115657;chr16:3115784-3115785		627;330
N	alternative_acceptor	CUFF.382	chr16	-	chr16:23504780-23505623;chr16:23504909-23505623	chr16:23504843-23505623		chr16:23504780-23504842;chr16:23504843-23504908	chr16:23504779-23504780;chr16:23504842-23504843		1034;81
N	jcn_only_AD	CUFF.395	chr16	-	chr16:4466963-4475478	chr16:4466963-4470359					64;71
N	jcn_only_AD		chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57515373		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		1382;90
K	intron_retention	CUFF.400	chr16	+	chr16:70395414-70398445				chr16:70395413-70395414;chr16:70398445-70398446		257;138
N	alternative_acceptor		chr16	-	chr16:57513598-57513772	chr16:57513601-57513772		chr16:57513598-57513600	chr16:57513597-57513598		165;295
K	alternative_donor	CUFF.404	chr16	-	chr16:75575354-75576499	chr16:75575354-75576452		chr16:75576453-75576499	chr16:75576499-75576500	chr16:75575248-75575353;chr16:75576500-75576581	170;31
K	intron_retention	CUFF.366	chr16	-	chr16:4408105-4408367				chr16:4408104-4408105;chr16:4408367-4408368		1343;43
N	intron_retention		chr16	-	chr16:23504843-23505623				chr16:23504842-23504843;chr16:23505623-23505624		109;273
K	intron_retention	CUFF.381	chr16	+	chr16:22493214-22493764				chr16:22493213-22493214;chr16:22493764-22493765		41;81
K	alternative_first_exon	CUFF.389	chr16	+	chr16:56269297-56309842;chr16:56260484-56309842;chr16:56226529-56309842	chr16:56227625-56309842	chr16:56260385-56260483;chr16:56226486-56226528	chr16:56227496-56227624			90;317
N	jcn_only_AA	CUFF.381,CUFF.400	chr16	+	chr16:22466187-22470675	chr16:22466187-22466770		chr16:22466771-22470675	chr16:22470675-22470676		293;4
N	intron_retention		chr16	+	chr16:3115689-3115781				chr16:3115688-3115689;chr16:3115781-3115782		21;403
N	cassette	CUFF.400	chr16	+	chr16:70390151-70395320;chr16:70390810-70395320	chr16:70390151-70394679,chr16:70390810-70394679;chr16:70394798-70395320		chr16:70394680-70394797			268;131
K	alternative_first_exon	CUFF.394	chr16	+	chr16:66613796-66620899	chr16:66614088-66620899	chr16:66613259-66613795	chr16:66614042-66614087			264;785
N	alternative_donor	CUFF.363	chr16	+	chr16:3115712-3115784;chr16:3115689-3115784;chr16:3115496-3115784	chr16:3115657-3115784		chr16:3115496-3115656;chr16:3115657-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115656-3115657;chr16:3115688-3115689		1105;252
K	intron_retention	CUFF.354	chr16	+	chr16:106421-106538				chr16:106420-106421;chr16:106538-106539		37;128
N	jcn_only_AA	CUFF.366	chr16	-	chr16:4412133-4445289	chr16:4438633-4445289		chr16:4412133-4438632	chr16:4412132-4412133		68;1269
N	alternative_acceptor		chr16	+	chr16:3194833-3195668	chr16:3194833-3194984		chr16:3194985-3195668	chr16:3195668-3195669		20;153
N	jcn_only_AD		chr16	-	chr16:67221741-67222806	chr16:67221741-67222623		chr16:67222624-67222806	chr16:67222806-67222807		77;666
K	intron_retention	CUFF.382	chr16	-	chr16:23504909-23505623				chr16:23504908-23504909;chr16:23505623-23505624		855;30
K	cassette	CUFF.386	chr16	-	chr16:30005130-30006423	chr16:30005130-30005226;chr16:30006165-30006423		chr16:30005227-30006164			246;59
N	jcn_only_AA		chr16	+	chr16:14020614-14021978	chr16:14020614-14021884		chr16:14021885-14021978	chr16:14021978-14021979		71;293
N	alternative_donor	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57521157		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		127;91
K	alternative_donor	CUFF.407	chr16	-	chr16:87811607-87812592	chr16:87811607-87812413		chr16:87812414-87812592	chr16:87812592-87812593		73;25
K	alternative_last_exon	CUFF.384	chr16	-	chr16:25097094-25114671;chr16:25112007-25114671	chr16:25098045-25114671	chr16:25096913-25097093;chr16:25111788-25112006	chr16:25097563-25098044			573;110
N	intron_retention		chr16	-	chr16:4412133-4445289				chr16:4412132-4412133;chr16:4445289-4445290		68;135
K	alternative_last_exon	CUFF.374	chr16	+	chr16:19663413-19680481	chr16:19663413-19663676	chr16:19680482-19680621	chr16:19663677-19664095			197;219
K	jcn_only_AA	CUFF.408	chr16	+	chr16:89789592-89789686	chr16:89789592-89789667		chr16:89789668-89789686	chr16:89789686-89789687		107;446
K	intron_retention	CUFF.366	chr16	-	chr16:4411471-4411985				chr16:4411470-4411471;chr16:4411985-4411986		685;123
N	intron_retention		chr16	-	chr16:4445341-4466785				chr16:4445340-4445341;chr16:4466785-4466786		21;61
K	intron_retention	CUFF.366	chr16	-	chr16:4414415-4414597				chr16:4414414-4414415;chr16:4414597-4414598		651;88
N	intron_retention		chr16	-	chr16:57513601-57513772				chr16:57513600-57513601;chr16:57513772-57513773		407;101
K	intron_retention	CUFF.354	chr16	+	chr16:105883-106538				chr16:105882-105883;chr16:106538-106539		797;118
K	intron_retention	CUFF.372	chr16	+	chr16:14024748-14026013				chr16:14024747-14024748;chr16:14026013-14026014		449;53
N	jcn_only_AD	CUFF.363	chr16	+	chr16:3115689-3115784;chr16:3115496-3115784;chr16:3115657-3115784	chr16:3115712-3115784		chr16:3115496-3115656;chr16:3115657-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115656-3115657;chr16:3115688-3115689		1913;121
K	intron_retention	CUFF.374	chr16	+	chr16:19592976-19612985				chr16:19592975-19592976;chr16:19612985-19612986		18;140
N	jcn_only_AD	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57513772		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		1065;407
N	intron_retention		chr16	+	chr16:14020614-14021978				chr16:14020613-14020614;chr16:14021978-14021979		71;284
K	intron_retention		chr16	-	chr16:4445341-4455491				chr16:4445340-4445341;chr16:4455491-4455492		933;84
K	alternative_donor	CUFF.354	chr16	+	chr16:105883-106538	chr16:106421-106538		chr16:105883-106420	chr16:105882-105883		797;168
K	alternative_first_exon	CUFF.361	chr16	+	chr16:2190951-2199941	chr16:2198980-2199941	chr16:2190708-2190950	chr16:2198574-2198979			81;249
K	intron_retention	CUFF.378	chr16	+	chr16:21973838-21974081				chr16:21973837-21973838;chr16:21974081-21974082		852;47
N	jcn_only_AD		chr16	+	chr16:3115496-3115781;chr16:3115689-3115781	chr16:3115712-3115781		chr16:3115496-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115688-3115689		249;34
N	alternative_acceptor	CUFF.400	chr16	+	chr16:105550-105793	chr16:105550-105776		chr16:105777-105793	chr16:105793-105794		65;439
K	intron_retention		chr16	+	chr16:3117417-3117554				chr16:3117416-3117417;chr16:3117554-3117555		2404;622
K	cassette	CUFF.366	chr16	-	chr16:4407261-4408367	chr16:4407261-4407968;chr16:4408105-4408367		chr16:4407969-4408104			126;1121
N	jcn_only_AD		chr16	-	chr16:23505700-23507009;chr16:23505700-23507034	chr16:23505700-23507014		chr16:23507010-23507014;chr16:23507015-23507034	chr16:23507014-23507015;chr16:23507034-23507035		985;682
K	jcn_only_AD	CUFF.407	chr16	-	chr16:87811607-87812592	chr16:87811607-87812413		chr16:87812414-87812592	chr16:87812592-87812593		73;29
N	alternative_donor	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57521042		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		200;18
K	jcn_only_AA	CUFF.396,CUFF.400	chr16	+	chr16:70399035-70399987	chr16:70399035-70399835		chr16:70399836-70399987	chr16:70399987-70399988		296;111
K	jcn_only_AA	CUFF.397	chr16	-	chr16:67968575-67968699	chr16:67968598-67968699		chr16:67968575-67968597	chr16:67968574-67968575		185;132
N	intron_retention		chr16	-	chr16:57513598-57513772				chr16:57513597-57513598;chr16:57513772-57513773		165;101
N	jcn_only_AD	CUFF.363	chr16	+	chr16:3115712-3115784;chr16:3115496-3115784;chr16:3115657-3115784	chr16:3115689-3115784		chr16:3115496-3115656;chr16:3115657-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115656-3115657;chr16:3115688-3115689		1443;591
K	intron_retention	CUFF.369	chr16	+	chr16:4559540-4559629				chr16:4559539-4559540;chr16:4559629-4559630		522;123
N	intron_retention		chr16	-	chr16:4463406-4466785				chr16:4463405-4463406;chr16:4466785-4466786		15;83
N	alternative_acceptor	CUFF.366	chr16	-	chr16:4411471-4411985	chr16:4411805-4411985		chr16:4411471-4411804	chr16:4411470-4411471		685;189
K	alternative_acceptor	CUFF.397	chr16	-	chr16:67968575-67968699	chr16:67968598-67968699		chr16:67968575-67968597	chr16:67968574-67968575		185;69
N	jcn_only_AA		chr16	+	chr16:3115828-3117443	chr16:3115828-3117377		chr16:3117378-3117443	chr16:3117443-3117444		24;3170
N	intron_retention		chr16	-	chr16:23478100-23478752				chr16:23478099-23478100;chr16:23478752-23478753		36;92
N	jcn_only_AA	CUFF.382	chr16	-	chr16:23504780-23505623;chr16:23504909-23505623	chr16:23504843-23505623		chr16:23504780-23504842;chr16:23504843-23504908	chr16:23504779-23504780;chr16:23504842-23504843		1344;109
N	alternative_donor	CUFF.382	chr16	-	chr16:23505700-23507009;chr16:23505700-23507014	chr16:23505700-23507034		chr16:23507010-23507014;chr16:23507015-23507034	chr16:23507014-23507015;chr16:23507034-23507035		657;58
K	intron_retention		chr16	+	chr16:2203224-2203319				chr16:2203223-2203224;chr16:2203319-2203320		242;69
K	jcn_only_AD	CUFF.354	chr16	+	chr16:105883-106538	chr16:106421-106538		chr16:105883-106420	chr16:105882-105883		797;37
K	intron_retention	CUFF.389	chr16	+	chr16:56368770-56370642				chr16:56368769-56368770;chr16:56370642-56370643		29;205
N	alternative_acceptor	CUFF.381,CUFF.400	chr16	+	chr16:22466187-22470675	chr16:22466187-22466770		chr16:22466771-22470675	chr16:22470675-22470676		293;0
N	intron_retention		chr16	-	chr16:57513601-57513756				chr16:57513600-57513601;chr16:57513756-57513757		163;100
N	intron_retention		chr16	+	chr16:31393218-31393788				chr16:31393217-31393218;chr16:31393788-31393789		15;32
K	cassette	CUFF.378	chr16	+	chr16:21964778-21968737	chr16:21964778-21968555;chr16:21968640-21968737		chr16:21968556-21968639			598;196
N	jcn_only_AD	CUFF.391	chr16	-	chr16:57509870-57513353	chr16:57509870-57512455		chr16:57512456-57513353	chr16:57513353-57513354		2209;21
N	alternative_acceptor	CUFF.375	chr16	+	chr16:21756358-21763255	chr16:21756358-21758618		chr16:21758619-21763255	chr16:21763255-21763256		748;6
N	alternative_acceptor	CUFF.382	chr16	-	chr16:23504843-23505623;chr16:23504909-23505623	chr16:23504780-23505623		chr16:23504780-23504842;chr16:23504843-23504908	chr16:23504779-23504780;chr16:23504842-23504843		626;489
N	jcn_only_AA	CUFF.382	chr16	-	chr16:23504843-23505623;chr16:23504780-23505623	chr16:23504909-23505623		chr16:23504780-23504842;chr16:23504843-23504908	chr16:23504779-23504780;chr16:23504842-23504843		597;855
K	cassette	CUFF.374	chr16	+	chr16:19659205-19663297	chr16:19659205-19661703;chr16:19661782-19663297		chr16:19661704-19661781			97;222
K	intron_retention	CUFF.373	chr16	-	chr16:15154031-15155645				chr16:15154030-15154031;chr16:15155645-15155646		19;163
N	jcn_only_AD	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57521157		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		1381;91
K	intron_retention	CUFF.408	chr16	+	chr16:89789592-89789686				chr16:89789591-89789592;chr16:89789686-89789687		107;38
K	intron_retention		chr16	+	chr16:3118012-3118180				chr16:3118011-3118012;chr16:3118180-3118181		3272;89
N	mutually_exclusive	CUFF.363	chr16	+	chr16:3117417-3117984,chr16:3118012-3118180	chr16:3117417-3117554,chr16:3117615-3118180	chr16:3117985-3118011	chr16:3117555-3117614			181;61
K	alternative_first_exon	CUFF.375	chr16	+	chr16:21712349-21716489,chr16:21712391-21716489	chr16:21716359-21716489	chr16:21712209-21712348	chr16:21716263-21716358			245;8
N	jcn_only_AA	CUFF.374	chr16	+	chr16:22448814-22466022	chr16:22448814-22462940					3;195
N	jcn_only_AA		chr16	-	chr16:57513598-57517869	chr16:57513601-57517869		chr16:57513598-57513600	chr16:57513597-57513598		20;11
N	alternative_donor	CUFF.399	chr16	-	chr16:70255305-70256273	chr16:70255305-70256269		chr16:70256270-70256273	chr16:70256273-70256274		42;7
N	alternative_donor		chr16	+	chr16:105543-105793	chr16:105550-105793		chr16:105543-105549	chr16:105542-105543		177;32
K	alternative_last_exon	CUFF.384	chr16	-	chr16:25098045-25114671;chr16:25097094-25114671	chr16:25112007-25114671	chr16:25097563-25098044;chr16:25096913-25097093	chr16:25111788-25112006			162;521
K	jcn_only_AD	CUFF.408	chr16	+	chr16:89793734-89795642	chr16:89793766-89795642		chr16:89793734-89793765	chr16:89793733-89793734		407;280
N	cassette	CUFF.363	chr16	+	chr16:3115496-3117377	chr16:3115496-3115784;chr16:3115828-3117377		chr16:3115785-3115827			253;1734
N	alternative_donor	CUFF.381	chr16	+	chr16:22448814-22462940	chr16:22449059-22462940		chr16:22448814-22449058	chr16:22448813-22448814		195;34
K	intron_retention		chr16	+	chr16:19584564-19586419				chr16:19584563-19584564;chr16:19586419-19586420		447;36
N	intron_retention		chr16	+	chr16:3117417-3118180				chr16:3117416-3117417;chr16:3118180-3118181		78;217
K	jcn_only_AD	CUFF.366	chr16	-	chr16:4455569-4457562	chr16:4455569-4457501		chr16:4457502-4457562	chr16:4457562-4457563		639;624
K	alternative_donor	CUFF.360	chr16	+	chr16:2141610-2142889	chr16:2141616-2142889		chr16:2141610-2141615	chr16:2141609-2141610		183;290
N	alternative_acceptor		chr16	+	chr16:3115828-3117443	chr16:3115828-3117377		chr16:3117378-3117443	chr16:3117443-3117444		24;1602
N	alternative_donor		chr16	+	chr16:3115496-3115781;chr16:3115712-3115781	chr16:3115689-3115781		chr16:3115496-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115688-3115689		422;50
N	cassette	CUFF.387	chr16	+	chr16:31383992-31388119	chr16:31383992-31384569;chr16:31384712-31388119		chr16:31384570-31384711			6;22
K	intron_retention	CUFF.361	chr16	+	chr16:2203047-2203146				chr16:2203046-2203047;chr16:2203146-2203147		154;200
K	intron_retention	CUFF.400	chr16	+	chr16:70404289-70405274				chr16:70404288-70404289;chr16:70405274-70405275		312;45
N	alternative_acceptor	CUFF.395	chr16	-	chr16:67223084-67223533	chr16:67223099-67223533		chr16:67223084-67223098	chr16:67223083-67223084		952;12
N	cassette	CUFF.400	chr16	+	chr16:70390151-70394679;chr16:70390151-70395320	chr16:70390151-70390748;chr16:70390810-70394679,chr16:70390810-70395320		chr16:70390749-70390809			296;90
N	coord_cassette	CUFF.400	chr16	+	chr16:70390151-70398445	chr16:70390151-70394679;chr16:70394798-70395320;chr16:70395540-70398445		chr16:70394680-70394797;chr16:70395321-70395539			24;76
K	intron_retention	CUFF.364	chr16	+	chr16:3196087-3197258				chr16:3196086-3196087;chr16:3197258-3197259		24;45
N	alternative_donor	CUFF.382	chr16	-	chr16:23505700-23507034;chr16:23505700-23507014	chr16:23505700-23507009		chr16:23507010-23507014;chr16:23507015-23507034	chr16:23507014-23507015;chr16:23507034-23507035		391;324
N	intron_retention		chr16	-	chr16:4458199-4466480				chr16:4458198-4458199;chr16:4466480-4466481		74;181
N	cassette	CUFF.366	chr16	-	chr16:4462432-4466459	chr16:4462432-4463308;chr16:4463406-4466459		chr16:4463309-4463405			57;714
K	intron_retention		chr16	+	chr16:14020614-14021884				chr16:14020613-14020614;chr16:14021884-14021885		293;129
N	alternative_donor	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57514206	chr16:57513601-57513756		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		212;6
N	jcn_only_AA		chr16	+	chr16:2203224-2203578	chr16:2203224-2203319		chr16:2203320-2203578	chr16:2203578-2203579		27;242
K	alternative_donor	CUFF.396	chr16	+	chr16:67233486-67233586	chr16:67233497-67233586		chr16:67233486-67233496	chr16:67233485-67233486		78;95
N	alternative_acceptor		chr16	-	chr16:57513598-57513756	chr16:57513601-57513756		chr16:57513598-57513600	chr16:57513597-57513598		70;174
K	intron_retention	CUFF.375	chr16	+	chr16:21730513-21730707				chr16:21730512-21730513;chr16:21730707-21730708		415;4
K	cassette	CUFF.400	chr16	+	chr16:70380952-70389387	chr16:70380952-70384459;chr16:70384509-70389387		chr16:70384460-70384508			88;279
N	intron_retention		chr16	+	chr16:14026262-14028048				chr16:14026261-14026262;chr16:14028048-14028049		50;202
K	intron_retention	CUFF.395	chr16	-	chr16:67223587-67223873				chr16:67223586-67223587;chr16:67223873-67223874		130;167
K	alternative_first_exon	CUFF.382	chr16	-	chr16:23507100-23530907	chr16:23507100-23521641	chr16:23530908-23530960	chr16:23521642-23521877			292;970
K	alternative_first_exon	CUFF.389	chr16	+	chr16:56269297-56309842;chr16:56227625-56309842;chr16:56226529-56309842	chr16:56260484-56309842	chr16:56227496-56227624;chr16:56226486-56226528	chr16:56260385-56260483			383;24
N	mutually_exclusive	CUFF.363	chr16	+	chr16:3117417-3118180,chr16:3118241-3118990	chr16:3117417-3117984,chr16:3118012-3118990	chr16:3118181-3118240	chr16:3117985-3118011			72;270
N	alternative_donor		chr16	-	chr16:67221741-67222806	chr16:67221741-67222623		chr16:67222624-67222806	chr16:67222806-67222807		77;482
N	jcn_only_AD	CUFF.399	chr16	-	chr16:70255305-70256273	chr16:70255305-70256269		chr16:70256270-70256273	chr16:70256273-70256274		42;14
K	intron_retention	CUFF.397	chr16	-	chr16:67969382-67969484				chr16:67969381-67969382;chr16:67969484-67969485		249;109
N	cassette	CUFF.406	chr16	+	chr16:77756515-77775478	chr16:77756515-77759327;chr16:77759482-77775478		chr16:77759328-77759481			50;252
N	alternative_acceptor	CUFF.374	chr16	+	chr16:19580914-19584445	chr16:19580914-19584440		chr16:19584441-19584445	chr16:19584445-19584446		198;277
N	intron_retention		chr16	-	chr16:4438624-4457652				chr16:4438623-4438624;chr16:4457652-4457653		137;191
K	jcn_only_AD	CUFF.360	chr16	+	chr16:2141610-2142889	chr16:2141616-2142889		chr16:2141610-2141615	chr16:2141609-2141610		183;588
K	cassette	CUFF.395	chr16	-	chr16:67220561-67220923	chr16:67220561-67220661;chr16:67220788-67220923		chr16:67220662-67220787			121;62
K	mutually_exclusive	CUFF.396	chr16	+	chr16:67233660-67234094,chr16:67234265-67234353	chr16:67233660-67233853,chr16:67233905-67234353	chr16:67234095-67234264	chr16:67233854-67233904			45;28
K	intron_retention	CUFF.366	chr16	-	chr16:4405165-4405286				chr16:4405164-4405165;chr16:4405286-4405287		1018;205
N	coord_cassette	CUFF.374	chr16	+	chr16:19584564-19590373	chr16:19584564-19586419;chr16:19586445-19589625;chr16:19589681-19590373		chr16:19586420-19586444;chr16:19589626-19589680			80;145
N	alternative_acceptor		chr16	+	chr16:14020614-14021978	chr16:14020614-14021884		chr16:14021885-14021978	chr16:14021978-14021979		71;262
K	alternative_acceptor	CUFF.387	chr16	+	chr16:31368423-31368654	chr16:31368423-31368573		chr16:31368574-31368654	chr16:31368654-31368655		132;16
N	cassette	CUFF.374	chr16	+	chr16:19584564-19590373	chr16:19584564-19586419;chr16:19586445-19590373		chr16:19586420-19586444			80;324
K	alternative_first_exon	CUFF.408	chr16	+	chr16:89787685-89788938;chr16:89788254-89788938	chr16:89786991-89788938	chr16:89787360-89787684;chr16:89787907-89788253	chr16:89786808-89786990			359;120
N	jcn_only_AD	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57517869		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		1461;11
N	cassette	CUFF.378	chr16	+	chr16:21969921-21972648	chr16:21969921-21970659;chr16:21970877-21972648		chr16:21970660-21970876			54;107
N	jcn_only_AD	CUFF.363	chr16	+	chr16:3115712-3115784;chr16:3115689-3115784;chr16:3115496-3115784	chr16:3115657-3115784		chr16:3115496-3115656;chr16:3115657-3115688;chr16:3115689-3115711	chr16:3115495-3115496;chr16:3115656-3115657;chr16:3115688-3115689		1407;627
K	intron_retention	CUFF.404	chr16	-	chr16:75575354-75576499				chr16:75575353-75575354;chr16:75576499-75576500	chr16:75575248-75575353;chr16:75576500-75576581	170;31
K	intron_retention	CUFF.374	chr16	+	chr16:19592976-19603111				chr16:19592975-19592976;chr16:19603111-19603112		267;78
N	jcn_only_AD		chr16	-	chr16:57513598-57513772;chr16:57513598-57513756	chr16:57513598-57517869					235;20
N	jcn_only_AD	CUFF.391	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57520216;chr16:57513601-57521007;chr16:57513601-57514206	chr16:57513601-57513756		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57520216;chr16:57520217-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57520216-57520217;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		1309;163
N	alternative_first_exon	CUFF.369	chr16	+	chr16:4552961-4555484,chr16:4533756-4555484,chr16:4538744-4555484,chr16:4533740-4555484,chr16:4526489-4555484,chr16:4526667-4555484;chr16:4526419-4555484;chr16:4546029-4555484	chr16:4524849-4555484	chr16:4526289-4526418;chr16:4545844-4546028	chr16:4524691-4524848			482;91
K	intron_retention	CUFF.394	chr16	+	chr16:66613602-66614041				chr16:66613601-66613602;chr16:66614041-66614042		769;124
K	intron_retention	CUFF.387	chr16	+	chr16:31368423-31368654				chr16:31368422-31368423;chr16:31368654-31368655		132;24
N	jcn_only_AA	CUFF.374	chr16	+	chr16:19580914-19584445	chr16:19580914-19584440		chr16:19584441-19584445	chr16:19584445-19584446		198;562
N	intron_retention		chr16	+	chr16:3115496-3115621				chr16:3115495-3115496;chr16:3115621-3115622		82;215
K	alternative_donor	CUFF.375	chr16	+	chr16:21712349-21716489	chr16:21712391-21716489		chr16:21712349-21712390	chr16:21712348-21712349		294;3
N	intron_retention		chr16	+	chr16:19584564-19590373				chr16:19584563-19584564;chr16:19590373-19590374		80;73
K	jcn_only_AD	CUFF.396	chr16	+	chr16:67233486-67233586	chr16:67233497-67233586		chr16:67233486-67233496	chr16:67233485-67233486		78;191
N	intron_retention		chr16	+	chr16:3115712-3115784				chr16:3115711-3115712;chr16:3115784-3115785		121;422
N	jcn_only_AD		chr16	+	chr16:586143-587133	chr16:586896-587133					11;20
N	alternative_donor	CUFF.391	chr16	-	chr16:57509870-57513353	chr16:57509870-57512455		chr16:57512456-57513353	chr16:57513353-57513354		2209;4
N	cassette	CUFF.400	chr16	+	chr16:70390151-70398919	chr16:70390151-70398445;chr16:70398549-70398919		chr16:70398446-70398548			88;148
N	intron_retention		chr16	+	chr16:3115496-3115781				chr16:3115495-3115496;chr16:3115781-3115782		228;157
N	alternative_acceptor	CUFF.382	chr16	-	chr16:23504843-23505623;chr16:23504780-23505623	chr16:23504909-23505623		chr16:23504780-23504842;chr16:23504843-23504908	chr16:23504779-23504780;chr16:23504842-23504843		570;545
N	jcn_only_AA		chr16	-	chr16:4466963-4475478	chr16:4470555-4475478					64;65
N	jcn_only_AA	CUFF.366	chr16	-	chr16:4411471-4411985	chr16:4411805-4411985		chr16:4411471-4411804	chr16:4411470-4411471		685;172
N	intron_retention		chr16	+	chr16:2203224-2203578				chr16:2203223-2203224;chr16:2203578-2203579		27;108
K	alternative_acceptor	CUFF.404	chr16	-	chr16:75579853-75589701	chr16:75579976-75589701		chr16:75579853-75579975	chr16:75579852-75579853	chr16:75589702-75590255;chr16:75579724-75579852	157;47
N	cassette	CUFF.372	chr16	+	chr16:14031716-14038579	chr16:14031716-14037830;chr16:14037953-14038579		chr16:14037831-14037952			57;193
N	cassette	CUFF.400	chr16	+	chr16:70389439-70395320	chr16:70389439-70390031;chr16:70390151-70395320		chr16:70390032-70390150			146;111
K	cassette	CUFF.314	chr15	-	chr15:50831049-50838669	chr15:50831049-50833245;chr15:50833462-50838669		chr15:50833246-50833461			421;92
K	jcn_only_AD	CUFF.351	chr15	+	chr15:97326820-97327382;chr15:97326975-97327382	chr15:97327061-97327382		chr15:97326820-97326974;chr15:97326975-97327060	chr15:97326819-97326820;chr15:97326974-97326975		199;59
N	alternative_donor	CUFF.323	chr15	+	chr15:63128273-63131054	chr15:63128318-63131054		chr15:63128273-63128317	chr15:63128272-63128273		260;6
N	alternative_first_exon		chr15	-	chr15:84873728-84898603	chr15:84873728-84873982	chr15:84898604-84898984	chr15:84873983-84874117			185;768
K	intron_retention	CUFF.335	chr15	+	chr15:77771664-77775311				chr15:77771663-77771664;chr15:77775311-77775312		67;117
N	jcn_only_AD	CUFF.319	chr15	+	chr15:57211105-57212089	chr15:57211427-57212089		chr15:57211105-57211426	chr15:57211104-57211105		1565;68
K	alternative_first_exon	CUFF.311	chr15	-	chr15:45470505-45490969;chr15:45470505-45473304;chr15:45470505-45492924	chr15:45470505-45479651	chr15:45473305-45473403;chr15:45492925-45493462	chr15:45479652-45480189			440;260
N	alternative_donor	CUFF.310	chr15	-	chr15:44892831-44898222	chr15:44892831-44896302		chr15:44896303-44898222	chr15:44898222-44898223		257;2
N	intron_retention		chr15	-	chr15:83355772-83357487				chr15:83355771-83355772;chr15:83357487-83357488		44;424
N	cassette	CUFF.337	chr15	-	chr15:78487069-78526712	chr15:78487069-78518796;chr15:78518948-78526712		chr15:78518797-78518947			24;141
K	jcn_only_AD	CUFF.324	chr15	+	chr15:64445539-64445850	chr15:64445586-64445850		chr15:64445539-64445585	chr15:64445538-64445539		90;12
K	alternative_acceptor	CUFF.319	chr15	+	chr15:57211105-57212099	chr15:57211105-57212089		chr15:57212090-57212099	chr15:57212099-57212100		23;833
N	jcn_only_AD		chr15	+	chr15:24820151-24832713	chr15:24825478-24832713					86;16
K	intron_retention		chr15	+	chr15:40531337-40532799				chr15:40531336-40531337;chr15:40532799-40532800		461;57
K	intron_retention	CUFF.324	chr15	+	chr15:64444526-64444836				chr15:64444525-64444526;chr15:64444836-64444837		34;50
N	coord_cassette	CUFF.315	chr15	-	chr15:55485032-55488550	chr15:55485032-55486350;chr15:55486382-55486493;chr15:55486558-55488550		chr15:55486351-55486381;chr15:55486494-55486557			35;31
N	jcn_only_AD	CUFF.295	chr15	+	chr15:24758885-24778841	chr15:24766978-24778841		chr15:24758885-24766977	chr15:24758884-24758885		391;2003
N	alternative_donor	CUFF.331	chr15	+	chr15:74771620-74773391	chr15:74773256-74773391		chr15:74771620-74773255	chr15:74771619-74771620		120;15
N	cassette	CUFF.310	chr15	-	chr15:44862857-44876011	chr15:44862857-44864880;chr15:44865019-44876011		chr15:44864881-44865018			28;244
N	alternative_acceptor	CUFF.332	chr15	-	chr15:75772256-75782548	chr15:75780119-75782548		chr15:75772256-75780118	chr15:75772255-75772256		37;9
N	cassette	CUFF.337	chr15	-	chr15:78487069-78526712	chr15:78487069-78500343;chr15:78500445-78526712		chr15:78500344-78500444			24;133
N	alternative_donor	CUFF.298	chr15	+	chr15:29283000-29287955;chr15:29213922-29287955;chr15:29253788-29287955	chr15:29213953-29287955		chr15:29213922-29213952;chr15:29213953-29253787;chr15:29253788-29282999	chr15:29213921-29213922;chr15:29213952-29213953;chr15:29253787-29253788	chr15:29287956-29288009;chr15:29213843-29213921	22;383
K	cassette	CUFF.313	chr15	-	chr15:47652295-47687757	chr15:47652295-47672653;chr15:47672793-47687757		chr15:47672654-47672792			26;60
N	alternative_acceptor	CUFF.319	chr15	+	chr15:57574797-57578354;chr15:57574797-57591423	chr15:57574797-57583026		chr15:57578355-57583026;chr15:57583027-57591423	chr15:57583026-57583027;chr15:57591423-57591424		231;15
N	alternative_acceptor	CUFF.311	chr15	-	chr15:45491299-45492924;chr15:45491319-45492924	chr15:45470505-45492924		chr15:45470505-45491298;chr15:45491299-45491318	chr15:45470504-45470505;chr15:45491298-45491299		0;310
N	jcn_only_AA		chr15	+	chr15:24811948-24813043;chr15:24811948-24813677;chr15:24811948-24813038	chr15:24811948-24814929					96;37
N	cassette	CUFF.315	chr15	-	chr15:55485032-55488550	chr15:55485032-55486493;chr15:55486558-55488550		chr15:55486494-55486557			35;25
K	alternative_last_exon	CUFF.353	chr15	-	chr15:102239639-102241288;chr15:102226266-102241288	chr15:102236243-102241288	chr15:102226099-102226265	chr15:102235864-102236242			90;773
N	jcn_only_AA	CUFF.342	chr15	-	chr15:83331986-83332311	chr15:83332048-83332311		chr15:83331986-83332047	chr15:83331985-83331986		152;119
N	jcn_only_AA	CUFF.319	chr15	+	chr15:57574797-57578354;chr15:57574797-57583026	chr15:57574797-57591423		chr15:57578355-57583026;chr15:57583027-57591423	chr15:57583026-57583027;chr15:57591423-57591424		2358;34
N	jcn_only_AA	CUFF.311	chr15	-	chr15:45491299-45492924;chr15:45491319-45492924	chr15:45470505-45492924		chr15:45470505-45491298;chr15:45491299-45491318	chr15:45470504-45470505;chr15:45491298-45491299		37;310
N	cassette	CUFF.310	chr15	-	chr15:44859791-44864880	chr15:44859791-44862722;chr15:44862857-44864880		chr15:44862723-44862856			145;243
K	cassette	CUFF.353	chr15	-	chr15:102194934-102197124	chr15:102194934-102196069;chr15:102196224-102197124		chr15:102196070-102196223			147;37
K	coord_cassette	CUFF.313	chr15	-	chr15:47652295-47687757	chr15:47652295-47672653;chr15:47672793-47685518;chr15:47685683-47687757		chr15:47672654-47672792;chr15:47685519-47685682			26;17
K	intron_retention	CUFF.345	chr15	-	chr15:84874072-84898653				chr15:84874071-84874072;chr15:84898653-84898654		45;243
N	jcn_only_AD	CUFF.331	chr15	+	chr15:74771620-74773391	chr15:74773256-74773391		chr15:74771620-74773255	chr15:74771619-74771620		120;24
K	alternative_last_exon	CUFF.330	chr15	+	chr15:69576672-69587411	chr15:69576672-69580746	chr15:69587412-69587760	chr15:69580747-69580903			113;39
K	intron_retention	CUFF.319	chr15	+	chr15:57565461-57574642				chr15:57565460-57565461;chr15:57574642-57574643		1607;193
K	jcn_only_AA	CUFF.314	chr15	-	chr15:50793035-50821993	chr15:50793249-50821993		chr15:50793035-50793248	chr15:50793034-50793035		138;352
N	cassette	CUFF.325	chr15	-	chr15:64669105-64673524	chr15:64669105-64673156;chr15:64673238-64673524		chr15:64673157-64673237			70;174
N	alternative_acceptor	CUFF.311	chr15	-	chr15:45470505-45492924;chr15:45491319-45492924	chr15:45491299-45492924		chr15:45470505-45491298;chr15:45491299-45491318	chr15:45470504-45470505;chr15:45491298-45491299		310;0
K	coord_cassette	CUFF.344	chr15	-	chr15:83687606-83698887	chr15:83687606-83689426;chr15:83689515-83697367;chr15:83697481-83698887		chr15:83689427-83689514;chr15:83697368-83697480			90;44
N	cassette	CUFF.311	chr15	-	chr15:45464277-45467416	chr15:45464277-45464344;chr15:45464517-45467416		chr15:45464345-45464516			55;178
N	cassette	CUFF.325	chr15	-	chr15:64658275-64673156	chr15:64658275-64668941;chr15:64669105-64673156		chr15:64668942-64669104			12;345
N	jcn_only_AD	CUFF.342	chr15	-	chr15:83333696-83334208	chr15:83333696-83333998		chr15:83333999-83334208	chr15:83334208-83334209		107;26
N	alternative_acceptor	CUFF.310	chr15	-	chr15:44892831-44898222	chr15:44896396-44898222		chr15:44892831-44896395	chr15:44892830-44892831		257;1
N	jcn_only_AA	CUFF.345	chr15	-	chr15:84871760-84872928	chr15:84871773-84872928		chr15:84871760-84871772	chr15:84871759-84871760		40;149
K	jcn_only_AD	CUFF.328	chr15	-	chr15:66786891-66787667	chr15:66786891-66787240		chr15:66787241-66787667	chr15:66787667-66787668		781;164
K	alternative_first_exon	CUFF.305	chr15	+	chr15:40732165-40750649	chr15:40733468-40750649	chr15:40731920-40732164	chr15:40733358-40733467			5;4
K	intron_retention	CUFF.324	chr15	+	chr15:64447103-64447305				chr15:64447102-64447103;chr15:64447305-64447306		10;37
K	intron_retention	CUFF.324	chr15	+	chr15:64444050-64444836				chr15:64444049-64444050;chr15:64444836-64444837		7;35
K	cassette	CUFF.317	chr15	-	chr15:55783455-55789909	chr15:55783455-55787325;chr15:55787401-55789909		chr15:55787326-55787400			416;32
K	alternative_last_exon	CUFF.300,CUFF.331	chr15	+	chr15:74771620-74773391	chr15:74771620-74772961	chr15:74773392-74773742	chr15:74772962-74773057			186;18
K	alternative_donor	CUFF.335	chr15	+	chr15:77750839-77756581	chr15:77750901-77756581		chr15:77750839-77750900	chr15:77750838-77750839		292;676
K	intron_retention	CUFF.310	chr15	-	chr15:44889142-44890462				chr15:44889141-44889142;chr15:44890462-44890463		135;30
N	cassette	CUFF.333	chr15	-	chr15:77578847-77712347	chr15:77578847-77657504;chr15:77657568-77712347		chr15:77657505-77657567			80;382
N	alternative_donor	CUFF.348	chr15	+	chr15:91304486-91306195	chr15:91305653-91306195		chr15:91304486-91305652	chr15:91304485-91304486		38;8
K	cassette	CUFF.307	chr15	-	chr15:41108452-41120584	chr15:41108452-41109429;chr15:41109546-41120584		chr15:41109430-41109545			294;123
N	jcn_only_AD		chr15	-	chr15:45460332-45467416	chr15:45460332-45464080					12;246
K	alternative_first_exon	CUFF.335	chr15	+	chr15:77740154-77750745,chr15:77750627-77750745;chr15:77713080-77750745;chr15:77713437-77750745	chr15:77713347-77750745	chr15:77712666-77713079;chr15:77713347-77713436	chr15:77713177-77713346			167;922
N	alternative_donor	CUFF.328	chr15	-	chr15:66787758-66789979	chr15:66787758-66789827		chr15:66789828-66789979	chr15:66789979-66789980		714;29
N	intron_retention	CUFF.303	chr15	+	chr15:40558697-40559123				chr15:40558696-40558697;chr15:40559123-40559124		31;20
N	alternative_acceptor	CUFF.347	chr15	-	chr15:90432369-90437112	chr15:90432373-90437112		chr15:90432369-90432372	chr15:90432368-90432369		59;462
N	alternative_acceptor	CUFF.310	chr15	-	chr15:44878049-44881449	chr15:44880837-44881449		chr15:44878049-44880836	chr15:44878048-44878049		356;9
K	jcn_only_AD	CUFF.296	chr15	+	chr15:25223466-25225093	chr15:25224790-25225093					118;202
K	alternative_first_exon	CUFF.332	chr15	-	chr15:75762341-75766029	chr15:75762341-75763020	chr15:75766030-75766108	chr15:75763021-75763286			127;168
K	alternative_acceptor	CUFF.305,CUFF.312	chr15	+	chr15:40752096-40754113	chr15:40752096-40754110		chr15:40754111-40754113	chr15:40754113-40754114		14;24
N	jcn_only_AD	CUFF.328	chr15	-	chr15:66787758-66789979	chr15:66787758-66789827		chr15:66789828-66789979	chr15:66789979-66789980		714;23
N	jcn_only_AD	CUFF.319	chr15	+	chr15:57426699-57458599;chr15:57401516-57458599;chr15:57422171-57458599	chr15:57384090-57458599					2336;328
N	cassette	CUFF.298	chr15	+	chr15:29131425-29213842	chr15:29131425-29140665;chr15:29140756-29213842		chr15:29140666-29140755		chr15:29213843-29213921	11;317
K	alternative_last_exon	CUFF.312	chr15	+	chr15:45768751-45789310;chr15:45768751-45804570	chr15:45768751-45769966	chr15:45804571-45804647	chr15:45769967-45772030			109;129
K	cassette	CUFF.317	chr15	-	chr15:55742566-55783320	chr15:55742566-55759127;chr15:55759360-55783320		chr15:55759128-55759359			62;295
K	alternative_first_exon	CUFF.335	chr15	+	chr15:77740154-77750745,chr15:77750627-77750745;chr15:77713080-77750745;chr15:77713347-77750745	chr15:77713437-77750745	chr15:77712666-77713079;chr15:77713177-77713346	chr15:77713347-77713436			1028;61
N	cassette	CUFF.328	chr15	-	chr15:66786891-66789979;chr15:66786891-66789827	chr15:66786891-66787667;chr15:66787758-66789979,chr15:66787758-66789827		chr15:66787668-66787757			129;613
K	cassette	CUFF.319	chr15	+	chr15:57543622-57545459	chr15:57543622-57544618;chr15:57544691-57545459		chr15:57544619-57544690			909;214
K	intron_retention	CUFF.346	chr15	+	chr15:89878601-89878879				chr15:89878600-89878601;chr15:89878879-89878880		32;72
N	jcn_only_AD	CUFF.312	chr15	+	chr15:45741000-45752643	chr15:45751249-45752643		chr15:45741000-45751248	chr15:45740999-45741000		45;31
N	jcn_only_AD		chr15	+	chr15:24813330-24814929;chr15:24811948-24814929	chr15:24813711-24814929					54;26
K	intron_retention	CUFF.303	chr15	+	chr15:40545216-40545378				chr15:40545215-40545216;chr15:40545378-40545379		761;17
K	alternative_first_exon	CUFF.306	chr15	+	chr15:40780407-40800530	chr15:40800267-40800530	chr15:40780240-40780406	chr15:40800135-40800266			15;73
N	jcn_only_AD	CUFF.347	chr15	-	chr15:90380955-90395592;chr15:90380955-90414706;chr15:90380955-90381260	chr15:90380955-90391824		chr15:90381261-90391824;chr15:90391825-90395592;chr15:90395593-90414706	chr15:90391824-90391825;chr15:90395592-90395593;chr15:90414706-90414707		860;31
K	intron_retention	CUFF.308	chr15	+	chr15:41222881-41223700				chr15:41222880-41222881;chr15:41223700-41223701		49;62
K	alternative_first_exon	CUFF.327	chr15	-	chr15:66645294-66678757;chr15:66645294-66678987,chr15:66645294-66678944	chr15:66645294-66648976	chr15:66678988-66679149	chr15:66648977-66649054			61;91
N	jcn_only_AD	CUFF.319	chr15	+	chr15:57490024-57523349;chr15:57506595-57523349	chr15:57511789-57523349		chr15:57490024-57506594;chr15:57506595-57511788	chr15:57490023-57490024;chr15:57506594-57506595		428;225
N	jcn_only_AD		chr15	+	chr15:24813330-24814929;chr15:24813711-24814929	chr15:24811948-24814929					42;37
K	intron_retention	CUFF.337	chr15	-	chr15:78474958-78475046				chr15:78474957-78474958;chr15:78475046-78475047		184;105
N	jcn_only_AD		chr15	-	chr15:90380955-90391824;chr15:90380955-90395592;chr15:90380955-90381260	chr15:90380955-90414706		chr15:90381261-90391824;chr15:90391825-90395592;chr15:90395593-90414706	chr15:90391824-90391825;chr15:90395592-90395593;chr15:90414706-90414707		96;795
K	alternative_first_exon	CUFF.331	chr15	+	chr15:74754369-74758376,chr15:74754373-74758376	chr15:74754440-74758376	chr15:74754224-74754368	chr15:74754374-74754439			227;12
N	jcn_only_AA	CUFF.311	chr15	-	chr15:45464201-45464344	chr15:45464277-45464344		chr15:45464201-45464276	chr15:45464200-45464201		187;31
N	intron_retention		chr15	+	chr15:40568307-40569316				chr15:40568306-40568307;chr15:40569316-40569317		53;155
N	alternative_donor	CUFF.347	chr15	-	chr15:90380955-90391824;chr15:90380955-90414706;chr15:90380955-90381260	chr15:90380955-90395592		chr15:90381261-90391824;chr15:90391825-90395592;chr15:90395593-90414706	chr15:90391824-90391825;chr15:90395592-90395593;chr15:90414706-90414707		799;1
K	cassette	CUFF.337	chr15	-	chr15:78500445-78537610	chr15:78500445-78501486;chr15:78501592-78537610		chr15:78501487-78501591			164;41
K	alternative_acceptor	CUFF.314	chr15	-	chr15:50793035-50821993	chr15:50793249-50821993		chr15:50793035-50793248	chr15:50793034-50793035		138;298
N	jcn_only_AA	CUFF.342	chr15	-	chr15:83358206-83378345	chr15:83358687-83378345		chr15:83358206-83358686	chr15:83358205-83358206		2391;262
K	intron_retention	CUFF.310	chr15	-	chr15:44912602-44913956				chr15:44912601-44912602;chr15:44913956-44913957		32;34
N	alternative_acceptor	CUFF.342	chr15	-	chr15:83358206-83378345	chr15:83358687-83378345		chr15:83358206-83358686	chr15:83358205-83358206		2391;96
K	cassette	CUFF.341	chr15	-	chr15:82981344-82982924	chr15:82981344-82982303;chr15:82982498-82982924		chr15:82982304-82982497			105;244
K	alternative_first_exon	CUFF.311	chr15	-	chr15:45470505-45490969;chr15:45470505-45479651;chr15:45470505-45492924	chr15:45470505-45473304	chr15:45479652-45480189;chr15:45492925-45493462	chr15:45473305-45473403			682;18
N	jcn_only_AD	CUFF.319	chr15	+	chr15:57384090-57458599;chr15:57426699-57458599;chr15:57401516-57458599	chr15:57422171-57458599					593;2071
K	intron_retention	CUFF.324	chr15	+	chr15:64446202-64446585				chr15:64446201-64446202;chr15:64446585-64446586		105;40
N	jcn_only_AA		chr15	+	chr15:24811948-24814929;chr15:24811948-24813043;chr15:24811948-24813677	chr15:24811948-24813038					81;53
N	cassette	CUFF.310	chr15	-	chr15:44859791-44862722	chr15:44859791-44861595;chr15:44861704-44862722		chr15:44861596-44861703			97;224
N	intron_retention		chr15	+	chr15:77713177-77750795				chr15:77713176-77713177;chr15:77750795-77750796		109;159
N	jcn_only_AA	CUFF.331	chr15	+	chr15:57574797-57583026;chr15:57574797-57591423	chr15:57574797-57578354		chr15:57578355-57583026;chr15:57583027-57591423	chr15:57583026-57583027;chr15:57591423-57591424		405;1987
K	coord_cassette	CUFF.310	chr15	-	chr15:44859791-44864880	chr15:44859791-44861595;chr15:44861704-44862722;chr15:44862857-44864880		chr15:44861596-44861703;chr15:44862723-44862856			145;240
N	jcn_only_AD	CUFF.348	chr15	+	chr15:91290721-91292596	chr15:91290892-91292596		chr15:91290721-91290891	chr15:91290720-91290721		11;26
K	cassette	CUFF.353	chr15	-	chr15:102197240-102201914	chr15:102197240-102197987;chr15:102198061-102201914		chr15:102197988-102198060			119;40
K	alternative_donor	CUFF.328	chr15	-	chr15:66786891-66787667	chr15:66786891-66787240		chr15:66787241-66787667	chr15:66787667-66787668		781;190
K	jcn_only_AA	CUFF.296	chr15	+	chr15:25207357-25222924	chr15:25207357-25213078					89;165
K	intron_retention	CUFF.310	chr15	-	chr15:44865019-44865744				chr15:44865018-44865019;chr15:44865744-44865745		399;260
K	alternative_first_exon	CUFF.320,CUFF.340	chr15	-	chr15:61931912-62007313	chr15:61931912-61945387	chr15:62007314-62007469	chr15:61945388-61945400			289;131
K	jcn_only_AD	CUFF.331	chr15	+	chr15:74754369-74758376	chr15:74754373-74758376		chr15:74754369-74754372	chr15:74754368-74754369		40;238
K	jcn_only_AA	CUFF.331,CUFF.335	chr15	+	chr15:74758472-74771400	chr15:74758472-74771384		chr15:74771385-74771400	chr15:74771400-74771401		242;45
N	jcn_only_AD	CUFF.315	chr15	-	chr15:83350333-83357909	chr15:83350333-83357487		chr15:83357488-83357909	chr15:83357909-83357910		9;1014
K	intron_retention	CUFF.351	chr15	+	chr15:97326820-97327382				chr15:97326819-97326820;chr15:97327382-97327383		160;56
N	alternative_acceptor	CUFF.342	chr15	-	chr15:83333696-83334208	chr15:83334056-83334208		chr15:83333696-83334055	chr15:83333695-83333696		107;7
K	jcn_only_AD	CUFF.311,CUFF.315	chr15	-	chr15:55483246-55484917	chr15:55483246-55484600		chr15:55484601-55484917	chr15:55484917-55484918		56;46
N	alternative_donor	CUFF.319	chr15	+	chr15:57490024-57523349;chr15:57506595-57523349	chr15:57511789-57523349		chr15:57490024-57506594;chr15:57506595-57511788	chr15:57490023-57490024;chr15:57506594-57506595		366;10
N	alternative_last_exon	CUFF.345	chr15	-	chr15:84871760-84872928,chr15:84871773-84872928	chr15:84872839-84872928	chr15:84871622-84871759	chr15:84872530-84872838			144;1002
N	cassette	CUFF.303	chr15	+	chr15:40565878-40568127	chr15:40565878-40566342;chr15:40566478-40568127		chr15:40566343-40566477			55;115
K	intron_retention	CUFF.308	chr15	+	chr15:41222315-41222822				chr15:41222314-41222315;chr15:41222822-41222823		51;77
N	jcn_only_AA	CUFF.335,CUFF.350	chr15	+	chr15:77713347-77750745	chr15:77713347-77740060		chr15:77740061-77750745	chr15:77750745-77750746		1257;10
N	mutually_exclusive	CUFF.325	chr15	-	chr15:64658275-64673156,chr15:64673238-64673524	chr15:64658275-64668941,chr15:64669105-64673524	chr15:64673157-64673237	chr15:64668942-64669104			9;62
K	cassette	CUFF.296	chr15	+	chr15:25225232-25244116	chr15:25225232-25226921;chr15:25227585-25244116		chr15:25226922-25227584			120;309
N	jcn_only_AD		chr15	+	chr15:24819892-24820053	chr15:24819961-24820053					60;37
K	intron_retention	CUFF.310	chr15	-	chr15:44858208-44858414				chr15:44858207-44858208;chr15:44858414-44858415		262;9
K	alternative_first_exon	CUFF.335	chr15	+	chr15:77740154-77750745,chr15:77750627-77750745;chr15:77713347-77750745;chr15:77713437-77750745	chr15:77713080-77750745	chr15:77713177-77713346;chr15:77713347-77713436	chr15:77712666-77713079			1039;50
N	jcn_only_AD	CUFF.348	chr15	+	chr15:91304486-91306195	chr15:91305653-91306195		chr15:91304486-91305652	chr15:91304485-91304486		38;57
K	cassette	CUFF.341	chr15	-	chr15:82978166-82980083	chr15:82978166-82978266;chr15:82978466-82980083		chr15:82978267-82978465			278;157
K	intron_retention	CUFF.345	chr15	-	chr15:84869961-84871621				chr15:84869960-84869961;chr15:84871621-84871622		676;161
N	alternative_last_exon	CUFF.333	chr15	-	chr15:77544869-77577299	chr15:77576373-77577299	chr15:77544709-77544868	chr15:77576079-77576372			43;483
K	alternative_donor	CUFF.324	chr15	+	chr15:64445539-64445850	chr15:64445586-64445850		chr15:64445539-64445585	chr15:64445538-64445539		90;12
K	alternative_last_exon	CUFF.332	chr15	-	chr15:75762341-75766029	chr15:75763172-75766029	chr15:75762060-75762340	chr15:75763021-75763171			242;66
N	alternative_donor	CUFF.315	chr15	-	chr15:83350333-83357909	chr15:83350333-83357487		chr15:83357488-83357909	chr15:83357909-83357910		9;1043
K	intron_retention	CUFF.324	chr15	+	chr15:64445884-64446133				chr15:64445883-64445884;chr15:64446133-64446134		120;11
K	alternative_first_exon	CUFF.300	chr15	+	chr15:30771397-30776704	chr15:30773111-30776704	chr15:30771218-30771396	chr15:30772945-30773110			17;88
K	alternative_donor	CUFF.311,CUFF.345	chr15	-	chr15:84874072-84898653	chr15:84874072-84898603		chr15:84898604-84898653	chr15:84898653-84898654		45;110
N	jcn_only_AA	CUFF.303	chr15	+	chr15:40558697-40564424	chr15:40558697-40559123		chr15:40559124-40564424	chr15:40564424-40564425		120;31
K	alternative_first_exon	CUFF.342	chr15	-	chr15:83358206-83358514,chr15:83358206-83366608;chr15:83358206-83378345	chr15:83358206-83377523	chr15:83378346-83378734	chr15:83377524-83377621			2360;24
N	cassette	CUFF.303	chr15	+	chr15:40509869-40545378;chr15:40531337-40545378	chr15:40509869-40532799,chr15:40531337-40532799;chr15:40532883-40545378		chr15:40532800-40532882			138;495
N	jcn_only_AD	CUFF.347	chr15	-	chr15:90420657-90431752	chr15:90420657-90421496		chr15:90421497-90431752	chr15:90431752-90431753		178;368
K	alternative_acceptor	CUFF.319,CUFF.335	chr15	+	chr15:77756730-77759524	chr15:77756730-77759436		chr15:77759437-77759524	chr15:77759524-77759525		1051;256
K	cassette	CUFF.319	chr15	+	chr15:57213297-57355947	chr15:57213297-57293546;chr15:57293583-57355947		chr15:57293547-57293582			118;954
N	jcn_only_AA		chr15	+	chr15:24825478-24869114	chr15:24825478-24832713					15;16
N	jcn_only_AD	CUFF.319	chr15	+	chr15:57213297-57565227	chr15:57555473-57565227					304;1210
N	cassette	CUFF.327	chr15	-	chr15:66641776-66644466	chr15:66641776-66643862;chr15:66643939-66644466		chr15:66643863-66643938			104;100
K	alternative_first_exon	CUFF.303	chr15	+	chr15:40532297-40532799,chr15:40532004-40532799;chr15:40509869-40532799	chr15:40531337-40532799	chr15:40509629-40509868	chr15:40530867-40531336			47;517
N	alternative_donor		chr15	-	chr15:90380955-90391824;chr15:90380955-90395592;chr15:90380955-90381260	chr15:90380955-90414706		chr15:90381261-90391824;chr15:90391825-90395592;chr15:90395593-90414706	chr15:90391824-90391825;chr15:90395592-90395593;chr15:90414706-90414707		5;795
N	jcn_only_AD	CUFF.319	chr15	+	chr15:57490024-57523349;chr15:57511789-57523349	chr15:57506595-57523349		chr15:57490024-57506594;chr15:57506595-57511788	chr15:57490023-57490024;chr15:57506594-57506595		590;63
K	alternative_acceptor	CUFF.305	chr15	+	chr15:40756747-40757542	chr15:40756747-40757533		chr15:40757534-40757542	chr15:40757542-40757543		47;41
K	jcn_only_AD	CUFF.311,CUFF.345	chr15	-	chr15:84874072-84898653	chr15:84874072-84898603		chr15:84898604-84898653	chr15:84898653-84898654		45;147
K	intron_retention	CUFF.324	chr15	+	chr15:64445586-64445850				chr15:64445585-64445586;chr15:64445850-64445851		12;10
N	coord_cassette	CUFF.348	chr15	+	chr15:91341568-91352366	chr15:91341568-91346750;chr15:91346951-91347396;chr15:91347590-91352366		chr15:91346751-91346950;chr15:91347397-91347589			15;260
N	cassette	CUFF.303	chr15	+	chr15:40545491-40555999	chr15:40545491-40549043;chr15:40549288-40555999		chr15:40549044-40549287			65;199
N	intron_retention		chr15	-	chr15:90378746-90380846				chr15:90378745-90378746;chr15:90380846-90380847		57;304
N	alternative_donor	CUFF.303	chr15	+	chr15:40558697-40564424	chr15:40559199-40564424		chr15:40558697-40559198	chr15:40558696-40558697		120;28
K	jcn_only_AD	CUFF.327	chr15	-	chr15:66645294-66678987	chr15:66645294-66678944		chr15:66678945-66678987	chr15:66678987-66678988		32;13
K	alternative_first_exon	CUFF.310,CUFF.347	chr15	-	chr15:44884637-44888257	chr15:44884637-44887456	chr15:44888258-44888599	chr15:44887457-44887657			338;131
K	cassette	CUFF.311	chr15	-	chr15:45464517-45467416	chr15:45464517-45465773;chr15:45465915-45467416		chr15:45465774-45465914			182;165
K	alternative_last_exon	CUFF.339	chr15	+	chr15:78819906-78829641	chr15:78819906-78825551	chr15:78829642-78829714	chr15:78825552-78826098			67;152
K	alternative_donor	CUFF.311,CUFF.315	chr15	-	chr15:55483246-55484917	chr15:55483246-55484600		chr15:55484601-55484917	chr15:55484917-55484918		56;71
K	cassette	CUFF.324	chr15	+	chr15:64444050-64444836	chr15:64444050-64444441;chr15:64444526-64444836		chr15:64444442-64444525			7;44
N	jcn_only_AD	CUFF.319	chr15	+	chr15:57384090-57458599;chr15:57401516-57458599;chr15:57422171-57458599	chr15:57426699-57458599					2639;24
K	jcn_only_AD	CUFF.335	chr15	+	chr15:77750839-77756581	chr15:77750901-77756581		chr15:77750839-77750900	chr15:77750838-77750839		292;1204
N	jcn_only_AD	CUFF.298	chr15	+	chr15:29283000-29287955;chr15:29213922-29287955;chr15:29253788-29287955	chr15:29213953-29287955		chr15:29213922-29213952;chr15:29213953-29253787;chr15:29253788-29282999	chr15:29213921-29213922;chr15:29213952-29213953;chr15:29253787-29253788	chr15:29287956-29288009;chr15:29213843-29213921	85;761
N	jcn_only_AD	CUFF.319	chr15	+	chr15:57565461-57574642	chr15:57573991-57574642		chr15:57565461-57573990	chr15:57565460-57565461		1607;146
K	alternative_donor	CUFF.328,CUFF.337	chr15	-	chr15:66783056-66786752	chr15:66783056-66786614		chr15:66786615-66786752	chr15:66786752-66786753		444;461
N	jcn_only_AA	CUFF.347	chr15	-	chr15:90432369-90437112	chr15:90432373-90437112		chr15:90432369-90432372	chr15:90432368-90432369		59;627
K	intron_retention	CUFF.336	chr15	+	chr15:78080488-78080722				chr15:78080487-78080488;chr15:78080722-78080723		137;60
N	jcn_only_AD	CUFF.298	chr15	+	chr15:29283000-29287955;chr15:29213953-29287955;chr15:29213922-29287955	chr15:29253788-29287955		chr15:29213922-29213952;chr15:29213953-29253787;chr15:29253788-29282999	chr15:29213921-29213922;chr15:29213952-29213953;chr15:29253787-29253788	chr15:29287956-29288009;chr15:29213843-29213921	810;37
K	alternative_last_exon	CUFF.333	chr15	-	chr15:77451039-77471131	chr15:77470366-77471131	chr15:77447443-77451038	chr15:77470070-77470365			115;166
N	alternative_donor	CUFF.319	chr15	+	chr15:57490024-57523349;chr15:57511789-57523349	chr15:57506595-57523349		chr15:57490024-57506594;chr15:57506595-57511788	chr15:57490023-57490024;chr15:57506594-57506595		375;1
N	alternative_donor	CUFF.298	chr15	+	chr15:29283000-29287955;chr15:29213953-29287955;chr15:29213922-29287955	chr15:29253788-29287955		chr15:29213922-29213952;chr15:29213953-29253787;chr15:29253788-29282999	chr15:29213921-29213922;chr15:29213952-29213953;chr15:29253787-29253788	chr15:29287956-29288009;chr15:29213843-29213921	405;0
K	alternative_last_exon	CUFF.312	chr15	+	chr15:45741000-45753476	chr15:45741000-45752643	chr15:45753477-45753588	chr15:45752644-45752767			181;32
N	alternative_donor	CUFF.310	chr15	-	chr15:44907765-44912387	chr15:44907765-44912322		chr15:44912323-44912387	chr15:44912387-44912388		80;19
K	jcn_only_AA	CUFF.319,CUFF.335	chr15	+	chr15:77756730-77759524	chr15:77756730-77759436		chr15:77759437-77759524	chr15:77759524-77759525		1051;380
N	alternative_donor	CUFF.319	chr15	+	chr15:57506595-57523349;chr15:57511789-57523349	chr15:57490024-57523349		chr15:57490024-57506594;chr15:57506595-57511788	chr15:57490023-57490024;chr15:57506594-57506595		11;365
N	alternative_acceptor	CUFF.319	chr15	+	chr15:57574797-57578354;chr15:57574797-57583026	chr15:57574797-57591423		chr15:57578355-57583026;chr15:57583027-57591423	chr15:57583026-57583027;chr15:57591423-57591424		212;34
K	intron_retention	CUFF.345	chr15	-	chr15:84873269-84873351				chr15:84873268-84873269;chr15:84873351-84873352		343;237
K	cassette	CUFF.344	chr15	-	chr15:83710678-83725140	chr15:83710678-83718824;chr15:83718931-83725140		chr15:83718825-83718930			71;84
K	jcn_only_AD	CUFF.351	chr15	+	chr15:97326820-97327382;chr15:97327061-97327382	chr15:97326975-97327382		chr15:97326820-97326974;chr15:97326975-97327060	chr15:97326819-97326820;chr15:97326974-97326975		219;39
N	jcn_only_AD	CUFF.329	chr15	-	chr15:67700814-67713672	chr15:67700814-67705840		chr15:67705841-67713672	chr15:67713672-67713673		4;37
N	jcn_only_AD	CUFF.298	chr15	+	chr15:29288010-29346047	chr15:29336632-29346047		chr15:29288010-29336631	chr15:29288009-29288010	chr15:29346048-29347038;chr15:29287956-29288009	882;73
K	intron_retention	CUFF.335	chr15	+	chr15:77756730-77759524				chr15:77756729-77756730;chr15:77759524-77759525		1051;144
N	jcn_only_AD	CUFF.347	chr15	-	chr15:90380955-90391824;chr15:90380955-90414706;chr15:90380955-90381260	chr15:90380955-90395592		chr15:90381261-90391824;chr15:90391825-90395592;chr15:90395593-90414706	chr15:90391824-90391825;chr15:90395592-90395593;chr15:90414706-90414707		864;26
K	alternative_last_exon	CUFF.327	chr15	-	chr15:66645294-66678987	chr15:66672279-66678987	chr15:66645153-66645293	chr15:66671511-66672278			24;170
K	intron_retention		chr15	-	chr15:83350333-83357487				chr15:83350332-83350333;chr15:83357487-83357488		1014;474
K	intron_retention	CUFF.310	chr15	-	chr15:44876134-44876362				chr15:44876133-44876134;chr15:44876362-44876363		69;202
K	alternative_last_exon	CUFF.342	chr15	-	chr15:83355772-83357487;chr15:83350333-83357487	chr15:83357251-83357487	chr15:83350172-83350332	chr15:83357093-83357250			999;360
N	jcn_only_AD	CUFF.319	chr15	+	chr15:57506595-57523349;chr15:57511789-57523349	chr15:57490024-57523349		chr15:57490024-57506594;chr15:57506595-57511788	chr15:57490023-57490024;chr15:57506594-57506595		288;365
K	alternative_first_exon	CUFF.311,CUFF.332	chr15	-	chr15:45470505-45490969;chr15:45470505-45473304;chr15:45470505-45479651	chr15:45470505-45492924	chr15:45473305-45473403;chr15:45479652-45480189	chr15:45492925-45493462			315;385
N	cassette	CUFF.347	chr15	-	chr15:90414779-90431752;chr15:90414779-90421496	chr15:90414779-90420537;chr15:90420657-90421496,chr15:90420657-90431752		chr15:90420538-90420656			484;428
K	intron_retention	CUFF.319	chr15	+	chr15:57535749-57543547				chr15:57535748-57535749;chr15:57543547-57543548		357;119
K	alternative_first_exon	CUFF.337	chr15	-	chr15:78501592-78537610	chr15:78501592-78504890	chr15:78537611-78538123	chr15:78504891-78505068			43;36
K	intron_retention	CUFF.310	chr15	-	chr15:44888554-44888981				chr15:44888553-44888554;chr15:44888981-44888982		143;64
K	alternative_acceptor	CUFF.331,CUFF.335	chr15	+	chr15:74758472-74771400	chr15:74758472-74771384		chr15:74771385-74771400	chr15:74771400-74771401		242;23
K	alternative_last_exon	CUFF.300	chr15	+	chr15:30771397-30776704	chr15:30771397-30772944	chr15:30776705-30776892	chr15:30772945-30773361			20;200
N	cassette	CUFF.348	chr15	+	chr15:91306388-91310139	chr15:91306388-91308525;chr15:91308645-91310139		chr15:91308526-91308644			22;58
N	alternative_donor	CUFF.329	chr15	-	chr15:67700814-67713672	chr15:67700814-67705840		chr15:67705841-67713672	chr15:67713672-67713673		4;16
N	jcn_only_AD	CUFF.310	chr15	-	chr15:44881613-44884528	chr15:44881613-44882618		chr15:44882619-44884528	chr15:44884528-44884529		355;98
N	alternative_donor	CUFF.312	chr15	+	chr15:45741000-45752643	chr15:45751249-45752643		chr15:45741000-45751248	chr15:45740999-45741000		45;4
N	jcn_only_AD		chr15	+	chr15:24811948-24814929;chr15:24813711-24814929	chr15:24813330-24814929					63;16
K	intron_retention	CUFF.342	chr15	-	chr15:83357251-83357487				chr15:83357250-83357251;chr15:83357487-83357488		9;861
K	alternative_last_exon	CUFF.314	chr15	-	chr15:50793035-50821993,chr15:50793249-50821993	chr15:50805710-50821993	chr15:50792660-50793034	chr15:50805612-50805709			255;26
K	alternative_first_exon	CUFF.333	chr15	-	chr15:77474383-77578764	chr15:77474383-77544708	chr15:77578765-77578846	chr15:77544709-77544873			49;173
K	intron_retention	CUFF.331	chr15	+	chr15:74753977-74773545				chr15:74753976-74753977;chr15:74773545-74773546		226;128
K	jcn_only_AA	CUFF.305	chr15	+	chr15:40756747-40757542	chr15:40756747-40757533		chr15:40757534-40757542	chr15:40757542-40757543		47;38
K	intron_retention	CUFF.310	chr15	-	chr15:44890572-44890828				chr15:44890571-44890572;chr15:44890828-44890829		222;54
N	jcn_only_AA		chr15	+	chr15:57555473-57565230	chr15:57555473-57565227		chr15:57565228-57565230	chr15:57565230-57565231		73;1210
K	alternative_first_exon	CUFF.319	chr15	+	chr15:57535749-57543547	chr15:57540280-57543547	chr15:57535670-57535748	chr15:57540142-57540279			252;760
N	jcn_only_AD	CUFF.298	chr15	+	chr15:29213953-29287955;chr15:29213922-29287955;chr15:29253788-29287955	chr15:29283000-29287955		chr15:29213922-29213952;chr15:29213953-29253787;chr15:29253788-29282999	chr15:29213921-29213922;chr15:29213952-29213953;chr15:29253787-29253788	chr15:29287956-29288009;chr15:29213843-29213921	820;26
K	intron_retention	CUFF.302	chr15	+	chr15:33022996-33023116				chr15:33022995-33022996;chr15:33023116-33023117		25;31
N	coord_cassette	CUFF.298	chr15	+	chr15:29131425-29213842	chr15:29131425-29139019;chr15:29139191-29140665;chr15:29140756-29213842		chr15:29139020-29139190;chr15:29140666-29140755		chr15:29213843-29213921	11;582
N	intron_retention	CUFF.345	chr15	-	chr15:84871760-84872928				chr15:84871759-84871760;chr15:84872928-84872929		40;80
N	jcn_only_AA	CUFF.310	chr15	-	chr15:44878049-44881449	chr15:44880837-44881449		chr15:44878049-44880836	chr15:44878048-44878049		356;153
K	jcn_only_AA	CUFF.319	chr15	+	chr15:57211105-57212099	chr15:57211105-57212089		chr15:57212090-57212099	chr15:57212099-57212100		23;1565
N	jcn_only_AA		chr15	+	chr15:24811948-24814929;chr15:24811948-24813043;chr15:24811948-24813038	chr15:24811948-24813677					111;23
N	jcn_only_AD	CUFF.353	chr15	-	chr15:102226266-102241288	chr15:102226266-102239533		chr15:102239534-102241288	chr15:102241288-102241289		32;67
N	jcn_only_AA	CUFF.311	chr15	-	chr15:45470505-45492924;chr15:45491319-45492924	chr15:45491299-45492924		chr15:45470505-45491298;chr15:45491299-45491318	chr15:45470504-45470505;chr15:45491298-45491299		337;10
N	jcn_only_AA		chr15	+	chr15:24803469-24811802	chr15:24803469-24811235					59;27
K	intron_retention	CUFF.333	chr15	-	chr15:77470366-77471131				chr15:77470365-77470366;chr15:77471131-77471132		142;26
N	jcn_only_AD		chr15	+	chr15:24811360-24811802;chr15:24780954-24811802	chr15:24803469-24811802					197;59
K	cassette	CUFF.344	chr15	-	chr15:83687606-83698887	chr15:83687606-83689426;chr15:83689515-83698887		chr15:83689427-83689514			90;123
N	jcn_only_AA	CUFF.310	chr15	-	chr15:44892831-44898222	chr15:44896396-44898222		chr15:44892831-44896395	chr15:44892830-44892831		257;27
N	jcn_only_AD	CUFF.303	chr15	+	chr15:40558697-40564424	chr15:40559199-40564424		chr15:40558697-40559198	chr15:40558696-40558697		120;33
N	jcn_only_AA	CUFF.319	chr15	+	chr15:57574797-57578354;chr15:57574797-57591423	chr15:57574797-57583026		chr15:57578355-57583026;chr15:57583027-57591423	chr15:57583026-57583027;chr15:57591423-57591424		2021;371
K	alternative_last_exon	CUFF.347	chr15	-	chr15:90380955-90414706	chr15:90408926-90414706	chr15:90380847-90380954	chr15:90408663-90408925			556;175
K	intron_retention	CUFF.331	chr15	+	chr15:74753760-74754223				chr15:74753759-74753760;chr15:74754223-74754224		102;173
K	cassette	CUFF.348	chr15	+	chr15:91298169-91303823	chr15:91298169-91303376;chr15:91303510-91303823		chr15:91303377-91303509			116;21
K	cassette	CUFF.349	chr15	+	chr15:94408878-94421262	chr15:94408878-94412919;chr15:94413063-94421262		chr15:94412920-94413062			109;25
N	cassette	CUFF.328	chr15	-	chr15:66786891-66789979;chr15:66786891-66789827	chr15:66786891-66787240;chr15:66787758-66789979,chr15:66787758-66789827		chr15:66787241-66787757			129;330
N	jcn_only_AD	CUFF.298	chr15	+	chr15:29283000-29287955;chr15:29213953-29287955;chr15:29253788-29287955	chr15:29213922-29287955		chr15:29213922-29213952;chr15:29213953-29253787;chr15:29253788-29282999	chr15:29213921-29213922;chr15:29213952-29213953;chr15:29253787-29253788	chr15:29287956-29288009;chr15:29213843-29213921	824;22
K	alternative_last_exon	CUFF.350	chr15	+	chr15:94449519-94527014	chr15:94449519-94512822	chr15:94527015-94527478	chr15:94512823-94512924			56;27
N	jcn_only_AD	CUFF.310	chr15	-	chr15:44892831-44898222	chr15:44892831-44896302		chr15:44896303-44898222	chr15:44898222-44898223		257;26
K	intron_retention	CUFF.324	chr15	+	chr15:64444942-64445443				chr15:64444941-64444942;chr15:64445443-64445444		119;8
N	intron_retention		chr15	-	chr15:84869629-84871621				chr15:84869628-84869629;chr15:84871621-84871622		31;390
K	alternative_donor	CUFF.351	chr15	+	chr15:97327061-97327382;chr15:97326975-97327382	chr15:97326820-97327382		chr15:97326820-97326974;chr15:97326975-97327060	chr15:97326819-97326820;chr15:97326974-97326975		94;160
K	cassette	CUFF.313	chr15	-	chr15:47672793-47687757	chr15:47672793-47685518;chr15:47685683-47687757		chr15:47685519-47685682			52;17
K	cassette	CUFF.352	chr15	-	chr15:99514388-99548657	chr15:99514388-99544415;chr15:99544509-99548657		chr15:99544416-99544508			7;54
N	jcn_only_AA	CUFF.311	chr15	-	chr15:45470505-45492924;chr15:45491299-45492924	chr15:45491319-45492924		chr15:45470505-45491298;chr15:45491299-45491318	chr15:45470504-45470505;chr15:45491298-45491299		319;28
K	alternative_first_exon	CUFF.312	chr15	+	chr15:45742489-45768276	chr15:45752768-45768276	chr15:45742303-45742488	chr15:45752644-45752767			128;22
K	jcn_only_AA	CUFF.305,CUFF.312	chr15	+	chr15:40752096-40754113	chr15:40752096-40754110		chr15:40754111-40754113	chr15:40754113-40754114		14;48
N	alternative_donor	CUFF.316	chr15	+	chr15:55700985-55710420	chr15:55709958-55710420		chr15:55700985-55709957	chr15:55700984-55700985		54;6
K	cassette	CUFF.345	chr15	-	chr15:84873269-84873538	chr15:84873269-84873351;chr15:84873444-84873538		chr15:84873352-84873443			1039;275
K	jcn_only_AD	CUFF.328,CUFF.337	chr15	-	chr15:66783056-66786752	chr15:66783056-66786614		chr15:66786615-66786752	chr15:66786752-66786753		444;259
N	alternative_acceptor	CUFF.311	chr15	-	chr15:45464201-45464344	chr15:45464277-45464344		chr15:45464201-45464276	chr15:45464200-45464201		187;39
N	alternative_first_exon		chr15	-	chr15:55486558-55488550	chr15:55486558-55487501	chr15:55488551-55488886	chr15:55487502-55487789			27;52
N	alternative_donor	CUFF.298	chr15	+	chr15:29213953-29287955;chr15:29213922-29287955;chr15:29253788-29287955	chr15:29283000-29287955		chr15:29213922-29213952;chr15:29213953-29253787;chr15:29253788-29282999	chr15:29213921-29213922;chr15:29213952-29213953;chr15:29253787-29253788	chr15:29287956-29288009;chr15:29213843-29213921	405;0
K	jcn_only_AA	CUFF.317	chr15	-	chr15:55790009-55790404	chr15:55790058-55790404		chr15:55790009-55790057	chr15:55790008-55790009		27;288
N	alternative_acceptor	CUFF.347	chr15	-	chr15:90378746-90380846	chr15:90378876-90380846		chr15:90378746-90378875	chr15:90378745-90378746		57;337
N	coord_cassette	CUFF.337	chr15	-	chr15:78475128-78526712	chr15:78475128-78485847;chr15:78485969-78486273;chr15:78486363-78486847;chr15:78487069-78526712		chr15:78485848-78485968;chr15:78486274-78486362;chr15:78486848-78487068			29;128
K	cassette	CUFF.329	chr15	-	chr15:67713837-67752029	chr15:67713837-67722658;chr15:67722739-67752029		chr15:67722659-67722738			2;224
N	alternative_donor	CUFF.333,CUFF.347	chr15	-	chr15:90380955-90391824;chr15:90380955-90395592;chr15:90380955-90414706	chr15:90380955-90381260		chr15:90381261-90391824;chr15:90391825-90395592;chr15:90395593-90414706	chr15:90391824-90391825;chr15:90395592-90395593;chr15:90414706-90414707		798;2
K	alternative_donor	CUFF.351	chr15	+	chr15:97326820-97327382;chr15:97327061-97327382	chr15:97326975-97327382		chr15:97326820-97326974;chr15:97326975-97327060	chr15:97326819-97326820;chr15:97326974-97326975		217;37
K	cassette	CUFF.314	chr15	-	chr15:50822127-50830905	chr15:50822127-50824208;chr15:50824425-50830905		chr15:50824209-50824424			436;37
N	jcn_only_AD	CUFF.319	chr15	+	chr15:57384090-57458599;chr15:57426699-57458599;chr15:57422171-57458599	chr15:57401516-57458599					2424;240
N	alternative_acceptor		chr15	+	chr15:57555473-57565230	chr15:57555473-57565227		chr15:57565228-57565230	chr15:57565230-57565231		73;600
N	jcn_only_AD	CUFF.316	chr15	+	chr15:55700985-55710420	chr15:55709958-55710420		chr15:55700985-55709957	chr15:55700984-55700985		54;43
N	jcn_only_AA	CUFF.345	chr15	-	chr15:84873728-84898603	chr15:84874072-84898603					186;147
N	alternative_donor	CUFF.298	chr15	+	chr15:29283000-29287955;chr15:29213953-29287955;chr15:29253788-29287955	chr15:29213922-29287955		chr15:29213922-29213952;chr15:29213953-29253787;chr15:29253788-29282999	chr15:29213921-29213922;chr15:29213952-29213953;chr15:29253787-29253788	chr15:29287956-29288009;chr15:29213843-29213921	383;22
N	alternative_donor	CUFF.310,CUFF.327	chr15	-	chr15:44878049-44881449	chr15:44878049-44880764		chr15:44880765-44881449	chr15:44881449-44881450		356;25
N	alternative_last_exon	CUFF.342	chr15	-	chr15:83350333-83357909	chr15:83357584-83357909	chr15:83350172-83350332	chr15:83357093-83357583			8;1387
N	alternative_acceptor	CUFF.335,CUFF.350	chr15	+	chr15:77713347-77750745	chr15:77713347-77740060		chr15:77740061-77750745	chr15:77750745-77750746		1257;0
N	intron_retention	CUFF.345	chr15	-	chr15:84873269-84873347				chr15:84873268-84873269;chr15:84873347-84873348		36;243
K	cassette	CUFF.298	chr15	+	chr15:29131425-29140665	chr15:29131425-29139019;chr15:29139191-29140665		chr15:29139020-29139190			41;633
K	coord_cassette	CUFF.314	chr15	-	chr15:50833462-50838669	chr15:50833462-50835794;chr15:50835991-50836783;chr15:50836979-50838669		chr15:50835795-50835990;chr15:50836784-50836978			26;72
K	alternative_first_exon	CUFF.340	chr15	-	chr15:80200027-80215793	chr15:80200027-80206929	chr15:80215794-80216139	chr15:80206930-80207640			43;35
K	intron_retention	CUFF.351	chr15	+	chr15:97326975-97327382				chr15:97326974-97326975;chr15:97327382-97327383		39;55
N	jcn_only_AA	CUFF.342	chr15	-	chr15:83333696-83334208	chr15:83334056-83334208		chr15:83333696-83334055	chr15:83333695-83333696		107;27
N	cassette	CUFF.315	chr15	-	chr15:55485032-55486493	chr15:55485032-55486350;chr15:55486382-55486493		chr15:55486351-55486381			30;46
K	alternative_first_exon	CUFF.301	chr15	+	chr15:31294234-31327955	chr15:31327860-31327955	chr15:31294216-31294233	chr15:31327773-31327859			39;61
N	alternative_donor	CUFF.353	chr15	-	chr15:102226266-102241288	chr15:102226266-102239533		chr15:102239534-102241288	chr15:102241288-102241289		32;6
N	alternative_donor	CUFF.319	chr15	+	chr15:57565461-57574642	chr15:57573991-57574642		chr15:57565461-57573990	chr15:57565460-57565461		1607;9
N	jcn_only_AD	CUFF.310	chr15	-	chr15:44907765-44912387	chr15:44907765-44912322		chr15:44912323-44912387	chr15:44912387-44912388		80;29
N	cassette	CUFF.298	chr15	+	chr15:29385424-29390692	chr15:29385424-29386480;chr15:29386517-29390692		chr15:29386481-29386516		chr15:29385278-29385423;chr15:29390693-29390779	66;74
K	cassette	CUFF.339	chr15	+	chr15:78807450-78819721	chr15:78807450-78810929;chr15:78811116-78819721		chr15:78810930-78811115			224;37
N	mutually_exclusive	CUFF.310	chr15	-	chr15:44859791-44864880,chr15:44865019-44876011	chr15:44859791-44862722,chr15:44862857-44876011	chr15:44864881-44865018	chr15:44862723-44862856			53;23
K	alternative_first_exon	CUFF.353	chr15	-	chr15:102202020-102211688	chr15:102202020-102204372	chr15:102211689-102211789	chr15:102204373-102204654			84;48
N	alternative_acceptor	CUFF.303	chr15	+	chr15:40558697-40564424	chr15:40558697-40559123		chr15:40559124-40564424	chr15:40564424-40564425		120;2
K	alternative_last_exon	CUFF.332	chr15	-	chr15:75801369-75809599	chr15:75805780-75809599	chr15:75801258-75801368	chr15:75805440-75805779			25;121
K	intron_retention	CUFF.324	chr15	+	chr15:64445539-64445850				chr15:64445538-64445539;chr15:64445850-64445851		90;14
N	alternative_acceptor	CUFF.331	chr15	+	chr15:57574797-57583026;chr15:57574797-57591423	chr15:57574797-57578354		chr15:57578355-57583026;chr15:57583027-57591423	chr15:57583026-57583027;chr15:57591423-57591424		49;197
N	alternative_donor	CUFF.348	chr15	+	chr15:91290721-91292596	chr15:91290892-91292596		chr15:91290721-91290891	chr15:91290720-91290721		11;21
N	cassette	CUFF.303	chr15	+	chr15:40545491-40556981	chr15:40545491-40555999;chr15:40556121-40556981		chr15:40556000-40556120			2045;166
K	intron_retention	CUFF.342	chr15	-	chr15:83348982-83349223				chr15:83348981-83348982;chr15:83349223-83349224		34;12
N	alternative_last_exon	CUFF.317	chr15	-	chr15:55703354-55724694	chr15:55722978-55724694	chr15:55703307-55703353	chr15:55722410-55722977			52;32
K	intron_retention	CUFF.324	chr15	+	chr15:64446952-64447589				chr15:64446951-64446952;chr15:64447589-64447590		18;75
K	intron_retention	CUFF.310	chr15	-	chr15:44876757-44877833				chr15:44876756-44876757;chr15:44877833-44877834		223;12
N	intron_retention		chr15	-	chr15:83350333-83357909				chr15:83350332-83350333;chr15:83357909-83357910		9;327
N	jcn_only_AD		chr15	+	chr15:24825478-24869114	chr15:24832883-24869114					15;42
N	jcn_only_AD		chr15	+	chr15:24811360-24811802;chr15:24803469-24811802	chr15:24780954-24811802					230;27
N	jcn_only_AD	CUFF.345	chr15	-	chr15:64658275-64665896	chr15:64658275-64665354					18;47
N	jcn_only_AD		chr15	+	chr15:24793618-24811235	chr15:24803469-24811235					92;27
K	intron_retention	CUFF.324	chr15	+	chr15:64444050-64444441				chr15:64444049-64444050;chr15:64444441-64444442		74;11
N	jcn_only_AD	CUFF.310,CUFF.327	chr15	-	chr15:44878049-44881449	chr15:44878049-44880764		chr15:44880765-44881449	chr15:44881449-44881450		356;139
K	cassette	CUFF.319	chr15	+	chr15:57213297-57383986	chr15:57213297-57355947;chr15:57356022-57383986		chr15:57355948-57356021			178;556
N	alternative_donor	CUFF.347	chr15	-	chr15:90380955-90395592;chr15:90380955-90414706;chr15:90380955-90381260	chr15:90380955-90391824		chr15:90381261-90391824;chr15:90391825-90395592;chr15:90395593-90414706	chr15:90391824-90391825;chr15:90395592-90395593;chr15:90414706-90414707		798;2
N	jcn_only_AA		chr15	+	chr15:24820151-24832713	chr15:24820151-24825373					86;48
N	jcn_only_AA	CUFF.332	chr15	-	chr15:75772256-75782548	chr15:75780119-75782548		chr15:75772256-75780118	chr15:75772255-75772256		37;60
N	cassette	CUFF.317	chr15	-	chr15:55722978-55727102	chr15:55722978-55724694;chr15:55724801-55727102		chr15:55724695-55724800			213;46
N	alternative_donor	CUFF.295	chr15	+	chr15:24758885-24778841	chr15:24766978-24778841		chr15:24758885-24766977	chr15:24758884-24758885		391;127
K	alternative_donor	CUFF.331	chr15	+	chr15:74754369-74758376	chr15:74754373-74758376		chr15:74754369-74754372	chr15:74754368-74754369		40;127
K	intron_retention	CUFF.300	chr15	+	chr15:30773111-30776704				chr15:30773110-30773111;chr15:30776704-30776705		71;86
K	alternative_acceptor	CUFF.317	chr15	-	chr15:55790009-55790404	chr15:55790058-55790404		chr15:55790009-55790057	chr15:55790008-55790009		27;200
K	intron_retention	CUFF.342	chr15	-	chr15:83331005-83331445				chr15:83331004-83331005;chr15:83331445-83331446		187;83
N	alternative_donor	CUFF.298	chr15	+	chr15:29288010-29346047	chr15:29336632-29346047		chr15:29288010-29336631	chr15:29288009-29288010	chr15:29346048-29347038;chr15:29287956-29288009	882;0
N	jcn_only_AA	CUFF.345	chr15	-	chr15:84869629-84871621	chr15:84869961-84871621		chr15:84869629-84869960	chr15:84869628-84869629		31;676
K	coord_cassette	CUFF.319	chr15	+	chr15:57213297-57383986	chr15:57213297-57293546;chr15:57293583-57355947;chr15:57356022-57383986		chr15:57293547-57293582;chr15:57355948-57356021			178;886
K	alternative_donor	CUFF.327	chr15	-	chr15:66645294-66678987	chr15:66645294-66678944		chr15:66678945-66678987	chr15:66678987-66678988		32;21
K	intron_retention	CUFF.351	chr15	+	chr15:97327061-97327382				chr15:97327060-97327061;chr15:97327382-97327383		59;28
N	alternative_acceptor	CUFF.345	chr15	-	chr15:84869629-84871621	chr15:84869961-84871621		chr15:84869629-84869960	chr15:84869628-84869629		31;672
K	coord_cassette	CUFF.310	chr15	-	chr15:44855500-44859621	chr15:44855500-44856744;chr15:44856897-44858051;chr15:44858208-44858414;chr15:44858504-44859621		chr15:44856745-44856896;chr15:44858052-44858207;chr15:44858415-44858503			126;217
N	intron_retention		chr15	+	chr15:40531337-40545378				chr15:40531336-40531337;chr15:40545378-40545379		130;26
K	cassette	CUFF.344	chr15	-	chr15:83689515-83698887	chr15:83689515-83697367;chr15:83697481-83698887		chr15:83697368-83697480			194;58
N	cassette	CUFF.333	chr15	-	chr15:77544869-77578764	chr15:77544869-77577299;chr15:77577398-77578764		chr15:77577300-77577397			5;37
N	alternative_acceptor	CUFF.342	chr15	-	chr15:83331986-83332311	chr15:83332048-83332311		chr15:83331986-83332047	chr15:83331985-83331986		152;91
N	alternative_acceptor	CUFF.311	chr15	-	chr15:45470505-45492924;chr15:45491299-45492924	chr15:45491319-45492924		chr15:45470505-45491298;chr15:45491299-45491318	chr15:45470504-45470505;chr15:45491298-45491299		310;0
N	alternative_donor	CUFF.319	chr15	+	chr15:57211105-57212089	chr15:57211427-57212089		chr15:57211105-57211426	chr15:57211104-57211105		1565;25
N	jcn_only_AD	CUFF.333,CUFF.347	chr15	-	chr15:90380955-90391824;chr15:90380955-90395592;chr15:90380955-90414706	chr15:90380955-90381260		chr15:90381261-90391824;chr15:90391825-90395592;chr15:90395593-90414706	chr15:90391824-90391825;chr15:90395592-90395593;chr15:90414706-90414707		852;39
N	jcn_only_AD	CUFF.323	chr15	+	chr15:63128273-63131054	chr15:63128318-63131054		chr15:63128273-63128317	chr15:63128272-63128273		260;9
N	jcn_only_AD		chr15	+	chr15:24780954-24811802;chr15:24803469-24811802	chr15:24811360-24811802					86;171
N	cassette	CUFF.319	chr15	+	chr15:57523456-57524909	chr15:57523456-57524488;chr15:57524629-57524909		chr15:57524489-57524628			303;322
N	intron_retention		chr15	+	chr15:24819892-24820053				chr15:24819891-24819892;chr15:24820053-24820054		60;13
N	coord_cassette	CUFF.311	chr15	-	chr15:45464277-45467416	chr15:45464277-45464344;chr15:45464517-45465773;chr15:45465915-45467416		chr15:45464345-45464516;chr15:45465774-45465914			55;114
N	jcn_only_AD	CUFF.298	chr15	+	chr15:29347039-29367123	chr15:29363303-29367123		chr15:29347039-29363302	chr15:29347038-29347039	chr15:29367124-29367204;chr15:29346048-29347038	111;13
N	alternative_acceptor	CUFF.345	chr15	-	chr15:84871760-84872928	chr15:84871773-84872928		chr15:84871760-84871772	chr15:84871759-84871760		40;99
K	alternative_first_exon	CUFF.342,CUFF.347	chr15	-	chr15:90432373-90437112	chr15:90432373-90437108	chr15:90437113-90437574	chr15:90437109-90437109			349;15
K	coord_cassette	CUFF.303	chr15	+	chr15:40545491-40556981	chr15:40545491-40549043;chr15:40549288-40555999;chr15:40556121-40556981		chr15:40549044-40549287;chr15:40556000-40556120			2045;190
N	alternative_donor	CUFF.310	chr15	-	chr15:44881613-44884528	chr15:44881613-44882618		chr15:44882619-44884528	chr15:44884528-44884529		355;21
K	intron_retention	CUFF.302	chr15	+	chr15:33023006-33023128				chr15:33023005-33023006;chr15:33023128-33023129		172;27
N	cassette	CUFF.345	chr15	-	chr15:84871760-84873177;chr15:84871773-84873177	chr15:84871773-84872928,chr15:84871760-84872928;chr15:84873084-84873177		chr15:84872929-84873083			711;643
K	jcn_only_AD	CUFF.351	chr15	+	chr15:97327061-97327382;chr15:97326975-97327382	chr15:97326820-97327382		chr15:97326820-97326974;chr15:97326975-97327060	chr15:97326819-97326820;chr15:97326974-97326975		97;160
N	jcn_only_AA	CUFF.347	chr15	-	chr15:90378746-90380846	chr15:90378876-90380846		chr15:90378746-90378875	chr15:90378745-90378746		57;511
K	alternative_first_exon	CUFF.323	chr15	+	chr15:63047893-63053879	chr15:63050859-63053879	chr15:63046548-63047892	chr15:63050751-63050858			25;19
K	alternative_first_exon	CUFF.294	chr15	-	chr15:23114293-23115116	chr15:23114293-23114585	chr15:23115117-23115256	chr15:23114586-23114684			241;207
N	jcn_only_AA		chr15	+	chr15:24811948-24814929;chr15:24811948-24813677;chr15:24811948-24813038	chr15:24811948-24813043					113;21
K	intron_retention	CUFF.342	chr15	-	chr15:83357584-83357909				chr15:83357583-83357584;chr15:83357909-83357910		1016;678
N	alternative_donor	CUFF.347	chr15	-	chr15:90420657-90431752	chr15:90420657-90421496		chr15:90421497-90431752	chr15:90431752-90431753		178;11
K	alternative_donor	CUFF.351	chr15	+	chr15:97326820-97327382;chr15:97326975-97327382	chr15:97327061-97327382		chr15:97326820-97326974;chr15:97326975-97327060	chr15:97326819-97326820;chr15:97326974-97326975		197;57
K	alternative_last_exon	CUFF.337	chr15	-	chr15:78471174-78471891	chr15:78471323-78471891	chr15:78470956-78471173	chr15:78471225-78471322			131;21
N	alternative_donor	CUFF.298	chr15	+	chr15:29347039-29367123	chr15:29363303-29367123		chr15:29347039-29363302	chr15:29347038-29347039	chr15:29367124-29367204;chr15:29346048-29347038	111;1
N	alternative_donor	CUFF.342	chr15	-	chr15:83333696-83334208	chr15:83333696-83333998		chr15:83333999-83334208	chr15:83334208-83334209		107;8
K	alternative_last_exon	CUFF.269	chr14	+	chr14:58979346-59003724;chr14:58979346-59014498;chr14:58979346-58987639	chr14:58979346-59006788	chr14:59003725-59003983;chr14:59014499-59015315;chr14:58987640-58987981	chr14:59006789-59006854			615;51
K	intron_retention		chr14	-	chr14:75152364-75158743				chr14:75152363-75152364;chr14:75158743-75158744		75;47
K	cassette	CUFF.273	chr14	+	chr14:61512886-61517229	chr14:61512886-61514868;chr14:61515016-61517229		chr14:61514869-61515015			478;142
K	alternative_last_exon	CUFF.269	chr14	+	chr14:58979346-59014498;chr14:58979346-59006788;chr14:58979346-58987639	chr14:58979346-59003724	chr14:59014499-59015315;chr14:59006789-59006854;chr14:58987640-58987981	chr14:59003725-59003983			572;94
K	alternative_acceptor	CUFF.260,CUFF.279	chr14	+	chr14:24572465-24573050	chr14:24572465-24572718		chr14:24572719-24573050	chr14:24573050-24573051		45;668
N	mutually_exclusive	CUFF.277	chr14	-	chr14:75143456-75151156,chr14:75151384-75152302	chr14:75143456-75149998,chr14:75150237-75152302	chr14:75151157-75151383	chr14:75149999-75150236			136;57
N	intron_retention		chr14	-	chr14:52481981-52485962				chr14:52481980-52481981;chr14:52485962-52485963		23;29
K	cassette	CUFF.280	chr14	-	chr14:77270256-77272758	chr14:77270256-77270717;chr14:77270759-77272758		chr14:77270718-77270758			4;101
K	alternative_acceptor	CUFF.262	chr14	-	chr14:31358462-31358589	chr14:31358484-31358589		chr14:31358462-31358483	chr14:31358461-31358462		273;119
N	cassette	CUFF.290	chr14	-	chr14:104251252-104263707	chr14:104251252-104260913;chr14:104261001-104263707		chr14:104260914-104261000			509;718
N	alternative_donor	CUFF.271,CUFF.277	chr14	-	chr14:75138187-75139533	chr14:75138187-75138671		chr14:75138672-75139533	chr14:75139533-75139534		99;10
N	jcn_only_AA	CUFF.282	chr14	+	chr14:77934852-77935419	chr14:77934852-77934932		chr14:77934933-77935419	chr14:77935419-77935420		211;78
N	cassette	CUFF.277	chr14	-	chr14:75150237-75152302	chr14:75150237-75151156;chr14:75151384-75152302		chr14:75151157-75151383			56;141
K	cassette	CUFF.264	chr14	+	chr14:50065922-50069087	chr14:50065922-50068259;chr14:50068368-50069087		chr14:50068260-50068367			54;104
K	intron_retention	CUFF.273	chr14	+	chr14:61504402-61509864				chr14:61504401-61504402;chr14:61509864-61509865		546;27
N	alternative_donor	CUFF.279	chr14	+	chr14:76201633-76211437	chr14:76203951-76211437		chr14:76201633-76203950	chr14:76201632-76201633		32;3
K	intron_retention	CUFF.261	chr14	-	chr14:24683358-24683515				chr14:24683357-24683358;chr14:24683515-24683516		12;10
K	intron_retention	CUFF.280	chr14	-	chr14:77270256-77270717				chr14:77270255-77270256;chr14:77270717-77270718		91;15
K	alternative_last_exon	CUFF.271	chr14	-	chr14:59939809-59942586;chr14:59941245-59942586	chr14:59927892-59942586	chr14:59939243-59939808;chr14:59941157-59941244	chr14:59927690-59927891			211;31
N	coord_cassette	CUFF.277	chr14	-	chr14:75159032-75179635	chr14:75159032-75165466;chr14:75165560-75168371;chr14:75168478-75179635		chr14:75165467-75165559;chr14:75168372-75168477			194;37
N	alternative_donor	CUFF.279	chr14	+	chr14:76373021-76420766;chr14:76407838-76420766	chr14:76368568-76420766		chr14:76368568-76373020;chr14:76373021-76407837	chr14:76368567-76368568;chr14:76373020-76373021		21;18
N	alternative_last_exon	CUFF.271	chr14	-	chr14:59939809-59941445	chr14:59941245-59941445	chr14:59939243-59939808	chr14:59941157-59941244			38;150
K	jcn_only_AD	CUFF.272,CUFF.277	chr14	-	chr14:75140815-75142443	chr14:75140815-75142401		chr14:75142402-75142443	chr14:75142443-75142444		65;134
N	intron_retention		chr14	-	chr14:106208297-106208401				chr14:106208296-106208297;chr14:106208401-106208402		349;217
N	alternative_acceptor		chr14	+	chr14:76201633-76203908;chr14:76201633-76210719	chr14:76201633-76211437		chr14:76203909-76210719;chr14:76210720-76211437	chr14:76210719-76210720;chr14:76211437-76211438		96;32
N	jcn_only_AD	CUFF.262	chr14	-	chr14:31355533-31358348	chr14:31355533-31358325		chr14:31358326-31358348	chr14:31358348-31358349		444;28
K	cassette	CUFF.277	chr14	-	chr14:75136830-75138110	chr14:75136830-75137464;chr14:75137575-75138110		chr14:75137465-75137574			12;92
K	cassette	CUFF.275	chr14	-	chr14:71200060-71201102	chr14:71200060-71200473;chr14:71200516-71201102		chr14:71200474-71200515			6;33
K	alternative_first_exon	CUFF.282	chr14	+	chr14:77924326-77925958	chr14:77924613-77925958	chr14:77924140-77924325	chr14:77924328-77924612			11;157
N	jcn_only_AD	CUFF.290	chr14	-	chr14:104224089-104245081;chr14:104224089-104230199	chr14:104224089-104225527		chr14:104225528-104230199;chr14:104230200-104245081	chr14:104230199-104230200;chr14:104245081-104245082		547;248
K	alternative_first_exon	CUFF.264	chr14	+	chr14:50070337-50074117;chr14:50067416-50074117	chr14:50069187-50074117	chr14:50067123-50067415	chr14:50069088-50069186			66;84
N	jcn_only_AD		chr14	-	chr14:104263856-104313344;chr14:104263856-104313111;chr14:104263856-104306415	chr14:104263856-104313635		chr14:104306416-104313111;chr14:104313112-104313344;chr14:104313345-104313635	chr14:104313111-104313112;chr14:104313344-104313345;chr14:104313635-104313636		829;724
N	jcn_only_AA	CUFF.279	chr14	+	chr14:76201633-76203908;chr14:76201633-76211437	chr14:76201633-76210719		chr14:76203909-76210719;chr14:76210720-76211437	chr14:76210719-76210720;chr14:76211437-76211438		55;136
K	alternative_donor	CUFF.275	chr14	-	chr14:71205116-71206758	chr14:71205116-71206614		chr14:71206615-71206758	chr14:71206758-71206759		24;7
K	cassette	CUFF.263	chr14	+	chr14:39944160-39961458	chr14:39944160-39954220;chr14:39954462-39961458		chr14:39954221-39954461			224;2047
K	alternative_last_exon	CUFF.269	chr14	+	chr14:58979346-59003724;chr14:58979346-59006788;chr14:58979346-58987639	chr14:58979346-59014498	chr14:59003725-59003983;chr14:59006789-59006854;chr14:58987640-58987981	chr14:59014499-59015315			346;320
N	jcn_only_AA	CUFF.264	chr14	+	chr14:50074840-50080973	chr14:50074840-50079189		chr14:50079190-50080973	chr14:50080973-50080974		171;17
N	alternative_donor	CUFF.273	chr14	+	chr14:61497242-61503776	chr14:61500832-61503776		chr14:61497242-61500831	chr14:61497241-61497242		336;53
K	alternative_first_exon	CUFF.286	chr14	+	chr14:92788980-92792211	chr14:92790305-92792211	chr14:92788925-92788979	chr14:92789867-92790304			3;82
K	alternative_first_exon	CUFF.291	chr14	+	chr14:105046341-105052751	chr14:105047963-105052751	chr14:105046021-105046340	chr14:105047406-105047962			92;310
K	intron_retention	CUFF.266	chr14	-	chr14:52478402-52481004				chr14:52478401-52478402;chr14:52481004-52481005		123;75
K	alternative_last_exon	CUFF.291,CUFF.293	chr14	+	chr14:106944969-106950170	chr14:106944969-106946393	chr14:106950171-106951526	chr14:106946394-106946583			53;85
K	alternative_first_exon	CUFF.269	chr14	+	chr14:58894576-58896080;chr14:58894532-58896080	chr14:58895182-58896080	chr14:58894356-58894531	chr14:58894956-58895181			557;6
K	jcn_only_AA	CUFF.273	chr14	+	chr14:61545646-61550272	chr14:61545646-61550267		chr14:61550268-61550272	chr14:61550272-61550273		66;436
K	intron_retention	CUFF.265	chr14	+	chr14:50241397-50244556				chr14:50241396-50241397;chr14:50244556-50244557		725;189
N	alternative_acceptor	CUFF.279	chr14	+	chr14:76201633-76211437;chr14:76201633-76210719	chr14:76201633-76203908		chr14:76203909-76210719;chr14:76210720-76211437	chr14:76210719-76210720;chr14:76211437-76211438		125;3
N	jcn_only_AA		chr14	-	chr14:104213110-104213269;chr14:104213198-104213269	chr14:104212891-104213269		chr14:104212891-104213109;chr14:104213110-104213197	chr14:104212890-104212891;chr14:104213109-104213110		70;32
N	alternative_donor	CUFF.275	chr14	-	chr14:71216799-71227718	chr14:71216799-71219654		chr14:71219655-71227718	chr14:71227718-71227719		23;0
K	jcn_only_AA	CUFF.279	chr14	+	chr14:76174051-76184203	chr14:76174051-76175521					9;46
N	jcn_only_AD	CUFF.283	chr14	-	chr14:81864925-81893445	chr14:81864925-81884506		chr14:81884507-81893445	chr14:81893445-81893446	chr14:81864639-81864924;chr14:81893446-81893556	169;240
K	cassette	CUFF.273	chr14	+	chr14:61497242-61504342	chr14:61497242-61503776;chr14:61503860-61504342		chr14:61503777-61503859			127;315
N	alternative_acceptor	CUFF.283	chr14	-	chr14:81728276-81737013	chr14:81734842-81737013		chr14:81728276-81734841	chr14:81728275-81728276	chr14:81737014-81737216;chr14:81727000-81728275	10;7
N	cassette	CUFF.260	chr14	+	chr14:24563464-24566100;chr14:24563644-24566100	chr14:24563464-24563974,chr14:24563644-24563974;chr14:24564055-24566100		chr14:24563975-24564054			315;433
N	alternative_donor	CUFF.290	chr14	-	chr14:104224089-104245081;chr14:104224089-104225527	chr14:104224089-104230199		chr14:104225528-104230199;chr14:104230200-104245081	chr14:104230199-104230200;chr14:104245081-104245082		489;4
N	intron_retention		chr14	+	chr14:92915504-92920243				chr14:92915503-92915504;chr14:92920243-92920244		29;52
N	alternative_acceptor		chr14	+	chr14:76368568-76372897;chr14:76368568-76407766	chr14:76368568-76420766		chr14:76372898-76407766;chr14:76407767-76420766	chr14:76407766-76407767;chr14:76420766-76420767		1;18
N	alternative_donor	CUFF.262	chr14	-	chr14:31355533-31358348	chr14:31355533-31358325		chr14:31358326-31358348	chr14:31358348-31358349		444;17
N	alternative_acceptor	CUFF.279	chr14	+	chr14:76201633-76203908;chr14:76201633-76211437	chr14:76201633-76210719		chr14:76203909-76210719;chr14:76210720-76211437	chr14:76210719-76210720;chr14:76211437-76211438		35;93
K	alternative_first_exon	CUFF.265	chr14	+	chr14:50235340-50238311	chr14:50235810-50238311	chr14:50234229-50235339	chr14:50235512-50235809			717;214
K	alternative_acceptor	CUFF.273	chr14	+	chr14:61545646-61550272	chr14:61545646-61550267		chr14:61550268-61550272	chr14:61550272-61550273		66;215
N	cassette	CUFF.277	chr14	-	chr14:75143456-75149998	chr14:75143456-75144881;chr14:75145033-75149998		chr14:75144882-75145032			45;37
N	alternative_acceptor	CUFF.290	chr14	-	chr14:104230817-104245081;chr14:104225643-104245081	chr14:104224089-104245081		chr14:104224089-104225642;chr14:104225643-104230816	chr14:104224088-104224089;chr14:104225642-104225643		40;480
N	jcn_only_AA	CUFF.290	chr14	-	chr14:104230817-104245081;chr14:104224089-104245081	chr14:104225643-104245081		chr14:104224089-104225642;chr14:104225643-104230816	chr14:104224088-104224089;chr14:104225642-104225643		523;286
N	alternative_donor	CUFF.283	chr14	-	chr14:81745084-81837331	chr14:81745084-81772975		chr14:81772976-81837331	chr14:81837331-81837332	chr14:81743245-81745083;chr14:81837332-81837529	196;0
N	alternative_acceptor	CUFF.274	chr14	-	chr14:69542129-69558390	chr14:69557874-69558390		chr14:69542129-69557873	chr14:69542128-69542129		532;11
K	intron_retention	CUFF.290	chr14	-	chr14:104201001-104201336				chr14:104201000-104201001;chr14:104201336-104201337		15;343
N	cassette	CUFF.258	chr14	+	chr14:23390330-23393509	chr14:23390330-23392287;chr14:23392414-23393509		chr14:23392288-23392413			35;131
K	intron_retention	CUFF.259	chr14	+	chr14:24470143-24470241				chr14:24470142-24470143;chr14:24470241-24470242		437;23
K	jcn_only_AA	CUFF.279	chr14	+	chr14:76241974-76243089	chr14:76241974-76243047		chr14:76243048-76243089	chr14:76243089-76243090		71;32
N	alternative_donor	CUFF.283	chr14	-	chr14:81864925-81893445	chr14:81864925-81884506		chr14:81884507-81893445	chr14:81893445-81893446	chr14:81864639-81864924;chr14:81893446-81893556	169;7
N	mutually_exclusive	CUFF.263	chr14	+	chr14:39944160-39961458,chr14:39961761-39982820	chr14:39944160-39954220,chr14:39954462-39982820	chr14:39961459-39961760	chr14:39954221-39954461			182;165
N	alternative_acceptor		chr14	-	chr14:104212891-104213269;chr14:104213110-104213269	chr14:104213198-104213269		chr14:104212891-104213109;chr14:104213110-104213197	chr14:104212890-104212891;chr14:104213109-104213110		52;13
N	alternative_acceptor	CUFF.279	chr14	+	chr14:76249874-76259258	chr14:76249874-76259255		chr14:76259256-76259258	chr14:76259258-76259259		83;5
N	jcn_only_AA	CUFF.279,CUFF.286	chr14	+	chr14:92922953-92949023	chr14:92922953-92923597		chr14:92923598-92949023	chr14:92949023-92949024		269;105
N	alternative_acceptor	CUFF.290	chr14	-	chr14:104225643-104245081;chr14:104224089-104245081	chr14:104230817-104245081		chr14:104224089-104225642;chr14:104225643-104230816	chr14:104224088-104224089;chr14:104225642-104225643		512;8
N	jcn_only_AA	CUFF.270	chr14	+	chr14:55494190-55498606	chr14:55494190-55498580		chr14:55498581-55498606	chr14:55498606-55498607		93;14
K	intron_retention	CUFF.265	chr14	+	chr14:50246394-50246465				chr14:50246393-50246394;chr14:50246465-50246466		617;393
K	cassette	CUFF.275	chr14	-	chr14:71227900-71249939	chr14:71227900-71232158;chr14:71232205-71249939		chr14:71232159-71232204			6;12
K	intron_retention	CUFF.277	chr14	-	chr14:75136830-75137464				chr14:75136829-75136830;chr14:75137464-75137465		63;17
K	alternative_acceptor	CUFF.272	chr14	-	chr14:60018141-60027836	chr14:60018155-60027836		chr14:60018141-60018154	chr14:60018140-60018141		150;29
K	alternative_first_exon	CUFF.262	chr14	-	chr14:31353881-31354618	chr14:31353881-31354173	chr14:31354619-31355532	chr14:31354174-31354429			509;230
N	alternative_donor	CUFF.286	chr14	+	chr14:92792323-92900255	chr14:92874779-92900255		chr14:92792323-92874778	chr14:92792322-92792323		95;0
N	cassette	CUFF.290	chr14	-	chr14:104245159-104263707	chr14:104245159-104251131;chr14:104251252-104263707		chr14:104251132-104251251			162;912
N	jcn_only_AD	CUFF.279	chr14	+	chr14:76373021-76420766;chr14:76407838-76420766	chr14:76368568-76420766		chr14:76368568-76373020;chr14:76373021-76407837	chr14:76368567-76368568;chr14:76373020-76373021		146;18
K	jcn_only_AD	CUFF.279	chr14	+	chr14:76187047-76198680	chr14:76198577-76198680					79;30
N	coord_cassette	CUFF.260	chr14	+	chr14:24563464-24566100	chr14:24563464-24563974;chr14:24564055-24564351;chr14:24564588-24566100		chr14:24563975-24564054;chr14:24564352-24564587			229;388
K	cassette	CUFF.269	chr14	+	chr14:58899176-58909423	chr14:58899176-58906787;chr14:58906879-58909423		chr14:58906788-58906878			565;44
N	jcn_only_AD	CUFF.290	chr14	-	chr14:104209161-104212709	chr14:104209161-104210227		chr14:104210228-104212709	chr14:104212709-104212710		147;65
N	mutually_exclusive	CUFF.265	chr14	+	chr14:50247041-50249087,chr14:50249176-50249259	chr14:50247041-50247420,chr14:50247494-50249259	chr14:50249088-50249175	chr14:50247421-50247493			82;16
N	jcn_only_AA	CUFF.277	chr14	-	chr14:75136830-75137464	chr14:75136846-75137464		chr14:75136830-75136845	chr14:75136829-75136830		63;71
K	alternative_first_exon	CUFF.286	chr14	+	chr14:92915504-92920243;chr14:92915561-92920243	chr14:92918991-92920243	chr14:92915418-92915560	chr14:92916548-92918990			165;109
K	intron_retention	CUFF.260	chr14	+	chr14:24567597-24567683				chr14:24567596-24567597;chr14:24567683-24567684		581;84
K	intron_retention	CUFF.290	chr14	-	chr14:104209161-104212709				chr14:104209160-104209161;chr14:104212709-104212710		147;141
N	mutually_exclusive	CUFF.258	chr14	+	chr14:23390330-23393509,chr14:23393651-23395669	chr14:23390330-23392287,chr14:23392414-23395669	chr14:23393510-23393650	chr14:23392288-23392413			27;46
N	cassette	CUFF.259	chr14	+	chr14:24459569-24473545;chr14:24459569-24470071	chr14:24459569-24464240;chr14:24464343-24473545,chr14:24464343-24470071		chr14:24464241-24464342			89;310
K	alternative_first_exon	CUFF.279	chr14	+	chr14:76259444-76286349	chr14:76269597-76286349	chr14:76259259-76259443	chr14:76269467-76269596			192;86
K	intron_retention	CUFF.282	chr14	+	chr14:77929103-77930940				chr14:77929102-77929103;chr14:77930940-77930941		295;68
K	jcn_only_AA	CUFF.290	chr14	-	chr14:104202540-104205015	chr14:104204198-104205015					60;429
N	alternative_donor	CUFF.271,CUFF.290	chr14	-	chr14:104212891-104216130;chr14:104212891-104213269	chr14:104212891-104212988		chr14:104212989-104213269;chr14:104213270-104216130	chr14:104213269-104213270;chr14:104216130-104216131		128;22
K	coord_cassette	CUFF.269	chr14	+	chr14:58899176-58909423	chr14:58899176-58899829;chr14:58900063-58907938;chr14:58908062-58909423		chr14:58899830-58900062;chr14:58907939-58908061			565;108
N	alternative_acceptor	CUFF.282	chr14	+	chr14:77934852-77935419	chr14:77934852-77934932		chr14:77934933-77935419	chr14:77935419-77935420		211;46
K	alternative_last_exon	CUFF.269	chr14	+	chr14:58979346-59003724;chr14:58979346-59014498;chr14:58979346-59006788	chr14:58979346-58987639	chr14:59003725-59003983;chr14:59014499-59015315;chr14:59006789-59006854	chr14:58987640-58987981			465;201
N	cassette	CUFF.277	chr14	-	chr14:75143456-75151156	chr14:75143456-75149998;chr14:75150237-75151156		chr14:75149999-75150236			160;91
K	intron_retention	CUFF.269	chr14	+	chr14:58908062-58909423				chr14:58908061-58908062;chr14:58909423-58909424		90;24
K	intron_retention		chr14	+	chr14:24563644-24563974				chr14:24563643-24563644;chr14:24563974-24563975		783;91
N	jcn_only_AA		chr14	+	chr14:76201633-76203908;chr14:76201633-76210719	chr14:76201633-76211437		chr14:76203909-76210719;chr14:76210720-76211437	chr14:76210719-76210720;chr14:76211437-76211438		159;32
N	alternative_donor		chr14	-	chr14:104263856-104313344;chr14:104263856-104313111;chr14:104263856-104306415	chr14:104263856-104313635		chr14:104306416-104313111;chr14:104313112-104313344;chr14:104313345-104313635	chr14:104313111-104313112;chr14:104313344-104313345;chr14:104313635-104313636		193;724
K	jcn_only_AA	CUFF.260,CUFF.279	chr14	+	chr14:24572465-24573050	chr14:24572465-24572718		chr14:24572719-24573050	chr14:24573050-24573051		45;784
N	jcn_only_AD	CUFF.283	chr14	-	chr14:81745084-81837331	chr14:81745084-81772975		chr14:81772976-81837331	chr14:81837331-81837332	chr14:81743245-81745083;chr14:81837332-81837529	196;53
N	cassette	CUFF.279	chr14	+	chr14:76100040-76129397	chr14:76100040-76101252;chr14:76101357-76129397		chr14:76101253-76101356			38;34
N	cassette	CUFF.277	chr14	-	chr14:75127644-75130601	chr14:75127644-75130214;chr14:75130526-75130601		chr14:75130215-75130525			13;220
N	alternative_donor	CUFF.283	chr14	-	chr14:81893557-81893644;chr14:81893557-81902431	chr14:81893557-81902664		chr14:81893645-81902431;chr14:81902432-81902664	chr14:81902431-81902432;chr14:81902664-81902665	chr14:81893446-81893556	54;37
N	alternative_donor	CUFF.290	chr14	-	chr14:104224089-104245081;chr14:104224089-104230199	chr14:104224089-104225527		chr14:104225528-104230199;chr14:104230200-104245081	chr14:104230199-104230200;chr14:104245081-104245082		484;9
K	intron_retention	CUFF.282	chr14	+	chr14:77924326-77925958				chr14:77924325-77924326;chr14:77925958-77925959		11;16
K	jcn_only_AA	CUFF.293	chr14	+	chr14:106938645-106960260	chr14:106938645-106944774					87;96
N	alternative_acceptor	CUFF.277	chr14	-	chr14:75136830-75137464	chr14:75136846-75137464		chr14:75136830-75136845	chr14:75136829-75136830		63;36
K	intron_retention	CUFF.277	chr14	-	chr14:75130526-75130601				chr14:75130525-75130526;chr14:75130601-75130602		103;260
N	alternative_acceptor		chr14	-	chr14:104212891-104213269;chr14:104213198-104213269	chr14:104213110-104213269		chr14:104212891-104213109;chr14:104213110-104213197	chr14:104212890-104212891;chr14:104213109-104213110		45;20
K	intron_retention	CUFF.273	chr14	+	chr14:61448101-61449225				chr14:61448100-61448101;chr14:61449225-61449226		498;50
N	alternative_last_exon	CUFF.274	chr14	-	chr14:69522329-69542061	chr14:69529229-69542061	chr14:69517500-69522328	chr14:69529073-69529228			20;408
N	jcn_only_AD	CUFF.290	chr14	-	chr14:104263856-104313635;chr14:104263856-104313111;chr14:104263856-104306415	chr14:104263856-104313344		chr14:104306416-104313111;chr14:104313112-104313344;chr14:104313345-104313635	chr14:104313111-104313112;chr14:104313344-104313345;chr14:104313635-104313636		999;554
N	alternative_donor	CUFF.274	chr14	-	chr14:69589078-69619660	chr14:69589078-69619481		chr14:69619482-69619660	chr14:69619660-69619661		78;75
K	cassette	CUFF.260	chr14	+	chr14:24564055-24566100	chr14:24564055-24564351;chr14:24564588-24566100		chr14:24564352-24564587			223;544
N	jcn_only_AD	CUFF.271	chr14	-	chr14:59939809-59941445	chr14:59939809-59941156		chr14:59941157-59941445	chr14:59941445-59941446		51;731
N	jcn_only_AD	CUFF.290	chr14	-	chr14:104212891-104216130;chr14:104212891-104212988	chr14:104212891-104213269		chr14:104212989-104213269;chr14:104213270-104216130	chr14:104213269-104213270;chr14:104216130-104216131		170;32
K	cassette	CUFF.285	chr14	-	chr14:92185823-92191423	chr14:92185823-92189392;chr14:92189534-92191423		chr14:92189393-92189533			127;370
N	jcn_only_AD	CUFF.290	chr14	-	chr14:104224089-104245081;chr14:104224089-104225527	chr14:104224089-104230199		chr14:104225528-104230199;chr14:104230200-104245081	chr14:104230199-104230200;chr14:104245081-104245082		728;68
K	coord_cassette	CUFF.259	chr14	+	chr14:24459569-24470071	chr14:24459569-24459983;chr14:24460162-24464240;chr14:24464343-24470071		chr14:24459984-24460161;chr14:24464241-24464342			64;70
K	jcn_only_AA	CUFF.270	chr14	+	chr14:59377061-59475751	chr14:59377061-59415030					42;152
N	jcn_only_AD	CUFF.290	chr14	-	chr14:81893557-81902664;chr14:81893557-81902431	chr14:81893557-81893644		chr14:81893645-81902431;chr14:81902432-81902664	chr14:81902431-81902432;chr14:81902664-81902665	chr14:81893446-81893556	114;3
K	alternative_last_exon	CUFF.277	chr14	-	chr14:75152364-75158743	chr14:75157854-75158743	chr14:75152303-75152363	chr14:75157667-75157853			57;217
K	cassette	CUFF.264	chr14	+	chr14:50069187-50080973	chr14:50069187-50074117;chr14:50074840-50080973		chr14:50074118-50074839			22;235
N	jcn_only_AA		chr14	-	chr14:104212891-104213269;chr14:104213110-104213269	chr14:104213198-104213269		chr14:104212891-104213109;chr14:104213110-104213197	chr14:104212890-104212891;chr14:104213109-104213110		75;27
N	jcn_only_AD	CUFF.279	chr14	+	chr14:76368568-76420766;chr14:76373021-76420766	chr14:76407838-76420766		chr14:76368568-76373020;chr14:76373021-76407837	chr14:76368567-76368568;chr14:76373020-76373021		105;59
N	alternative_first_exon	CUFF.290	chr14	-	chr14:104202540-104205015	chr14:104202540-104204030	chr14:104205016-104205149	chr14:104204031-104204197			48;406
N	alternative_acceptor	CUFF.264	chr14	+	chr14:50074840-50080973	chr14:50074840-50079189		chr14:50079190-50080973	chr14:50080973-50080974		171;2
K	cassette	CUFF.269	chr14	+	chr14:58956959-58965500	chr14:58956959-58958861;chr14:58958994-58965500		chr14:58958862-58958993			386;101
N	alternative_donor	CUFF.279	chr14	+	chr14:76150000-76156534	chr14:76156205-76156534		chr14:76150000-76156204	chr14:76149999-76150000		64;17
K	alternative_last_exon	CUFF.279	chr14	+	chr14:76349246-76368484	chr14:76349246-76353042	chr14:76368485-76368940	chr14:76353043-76353697			284;136
K	jcn_only_AD	CUFF.282	chr14	+	chr14:77928586-77934425	chr14:77932011-77934425					19;364
N	cassette	CUFF.277	chr14	-	chr14:75165560-75179635	chr14:75165560-75168371;chr14:75168478-75179635		chr14:75168372-75168477			34;33
N	jcn_only_AD	CUFF.273	chr14	+	chr14:61497242-61503776	chr14:61500832-61503776		chr14:61497242-61500831	chr14:61497241-61497242		336;185
K	cassette	CUFF.273	chr14	+	chr14:61518854-61545527	chr14:61518854-61519066;chr14:61519704-61545527		chr14:61519067-61519703			104;502
K	intron_retention	CUFF.290	chr14	-	chr14:104200260-104200703				chr14:104200259-104200260;chr14:104200703-104200704		22;217
N	alternative_donor	CUFF.290	chr14	-	chr14:81893557-81902664;chr14:81893557-81902431	chr14:81893557-81893644		chr14:81893645-81902431;chr14:81902432-81902664	chr14:81902431-81902432;chr14:81902664-81902665	chr14:81893446-81893556	91;0
K	intron_retention	CUFF.266	chr14	-	chr14:52472568-52473254				chr14:52472567-52472568;chr14:52473254-52473255		199;28
K	coord_cassette	CUFF.273	chr14	+	chr14:61451522-61497162	chr14:61451522-61482621;chr14:61482675-61486258;chr14:61486299-61497162		chr14:61482622-61482674;chr14:61486259-61486298			20;755
N	jcn_only_AD	CUFF.271,CUFF.290	chr14	-	chr14:104212891-104216130;chr14:104212891-104213269	chr14:104212891-104212988		chr14:104212989-104213269;chr14:104213270-104216130	chr14:104213269-104213270;chr14:104216130-104216131		147;55
N	alternative_first_exon	CUFF.271,CUFF.274	chr14	-	chr14:59939809-59942586	chr14:59939809-59941445,chr14:59939809-59941156	chr14:59942587-59942724	chr14:59941446-59941982			77;485
N	jcn_only_AD		chr14	-	chr14:69522329-69542061	chr14:69522329-69529100					17;262
K	intron_retention	CUFF.273	chr14	+	chr14:61518854-61545547				chr14:61518853-61518854;chr14:61545547-61545548		161;281
N	cassette	CUFF.269	chr14	+	chr14:58925264-58927703	chr14:58925264-58926560;chr14:58926789-58927703		chr14:58926561-58926788			6;50
K	cassette	CUFF.288	chr14	+	chr14:103187422-103188523	chr14:103187422-103187656;chr14:103187715-103188523		chr14:103187657-103187714			39;15
N	coord_cassette	CUFF.277	chr14	-	chr14:75152364-75179635	chr14:75152364-75158743;chr14:75159032-75165466;chr14:75165560-75179635		chr14:75158744-75159031;chr14:75165467-75165559			19;76
N	cassette	CUFF.284	chr14	+	chr14:83117341-83153657	chr14:83117341-83151723;chr14:83151776-83153657		chr14:83151724-83151775			29;312
N	cassette	CUFF.260	chr14	+	chr14:24572100-24572718	chr14:24572100-24572368;chr14:24572465-24572718		chr14:24572369-24572464			16;578
N	intron_retention	CUFF.290	chr14	-	chr14:104212891-104212988				chr14:104212890-104212891;chr14:104212988-104212989		55;6
K	intron_retention	CUFF.290	chr14	-	chr14:104204198-104205015				chr14:104204197-104204198;chr14:104205015-104205016		429;32
N	jcn_only_AD	CUFF.290	chr14	-	chr14:104263856-104313344;chr14:104263856-104313635;chr14:104263856-104306415	chr14:104263856-104313111		chr14:104306416-104313111;chr14:104313112-104313344;chr14:104313345-104313635	chr14:104313111-104313112;chr14:104313344-104313345;chr14:104313635-104313636		1513;41
K	intron_retention	CUFF.273	chr14	+	chr14:61518854-61519066				chr14:61518853-61518854;chr14:61519066-61519067		454;495
N	jcn_only_AA	CUFF.283	chr14	-	chr14:81728276-81737013	chr14:81734842-81737013		chr14:81728276-81734841	chr14:81728275-81728276	chr14:81737014-81737216;chr14:81727000-81728275	10;47
K	intron_retention	CUFF.265	chr14	+	chr14:50246525-50246930				chr14:50246524-50246525;chr14:50246930-50246931		776;179
N	jcn_only_AD	CUFF.279	chr14	+	chr14:76368568-76420766;chr14:76407838-76420766	chr14:76373021-76420766		chr14:76368568-76373020;chr14:76373021-76407837	chr14:76368567-76368568;chr14:76373020-76373021		77;87
N	jcn_only_AA	CUFF.290	chr14	-	chr14:104225643-104245081;chr14:104224089-104245081	chr14:104230817-104245081		chr14:104224089-104225642;chr14:104225643-104230816	chr14:104224088-104224089;chr14:104225642-104225643		766;43
K	cassette	CUFF.275	chr14	-	chr14:71201216-71204961	chr14:71201216-71202677;chr14:71202747-71204961		chr14:71202678-71202746			36;8
N	jcn_only_AA	CUFF.279	chr14	+	chr14:76249874-76259258	chr14:76249874-76259255		chr14:76259256-76259258	chr14:76259258-76259259		83;10
N	alternative_donor	CUFF.279	chr14	+	chr14:76368568-76420766;chr14:76373021-76420766	chr14:76407838-76420766		chr14:76368568-76373020;chr14:76373021-76407837	chr14:76368567-76368568;chr14:76373020-76373021		38;1
K	alternative_first_exon	CUFF.271	chr14	-	chr14:59941245-59942586	chr14:59941245-59941445	chr14:59942587-59942724	chr14:59941446-59941982			191;350
N	alternative_donor	CUFF.271	chr14	-	chr14:59939809-59941445	chr14:59939809-59941156		chr14:59941157-59941445	chr14:59941445-59941446		51;294
K	cassette	CUFF.273	chr14	+	chr14:61451522-61482621	chr14:61451522-61453769;chr14:61453876-61482621		chr14:61453770-61453875			651;306
K	alternative_last_exon	CUFF.279,CUFF.293	chr14	+	chr14:76286505-76330009	chr14:76286505-76286945	chr14:76330010-76330205	chr14:76286946-76287205			105;408
N	jcn_only_AD		chr14	-	chr14:104212891-104212988;chr14:104212891-104213269	chr14:104212891-104216130		chr14:104212989-104213269;chr14:104213270-104216130	chr14:104213269-104213270;chr14:104216130-104216131		87;115
N	jcn_only_AD	CUFF.286	chr14	+	chr14:92792323-92900255	chr14:92874779-92900255		chr14:92792323-92874778	chr14:92792322-92792323		95;50
N	jcn_only_AD	CUFF.283	chr14	-	chr14:81893557-81893644;chr14:81893557-81902431	chr14:81893557-81902664		chr14:81893645-81902431;chr14:81902432-81902664	chr14:81902431-81902432;chr14:81902664-81902665	chr14:81893446-81893556	79;37
N	alternative_acceptor		chr14	-	chr14:104213110-104213269;chr14:104213198-104213269	chr14:104212891-104213269		chr14:104212891-104213109;chr14:104213110-104213197	chr14:104212890-104212891;chr14:104213109-104213110		33;32
K	alternative_first_exon	CUFF.259	chr14	+	chr14:24439542-24459390	chr14:24458285-24459390	chr14:24439060-24439541	chr14:24457947-24458284			51;1237
N	coord_cassette	CUFF.260	chr14	+	chr14:24564055-24567411	chr14:24564055-24564351;chr14:24564588-24566100;chr14:24566347-24567411		chr14:24564352-24564587;chr14:24566101-24566346			134;540
K	alternative_last_exon	CUFF.282	chr14	+	chr14:77929103-77935419	chr14:77929103-77930940	chr14:77935420-77935915	chr14:77930941-77931029			366;200
K	alternative_first_exon	CUFF.273	chr14	+	chr14:61448962-61449225,chr14:61448410-61449225;chr14:61448101-61449225	chr14:61448406-61449225	chr14:61447742-61448100	chr14:61448157-61448405			524;97
N	jcn_only_AD	CUFF.290	chr14	-	chr14:104263856-104313344;chr14:104263856-104313635;chr14:104263856-104313111	chr14:104263856-104306415		chr14:104306416-104313111;chr14:104313112-104313344;chr14:104313345-104313635	chr14:104313111-104313112;chr14:104313344-104313345;chr14:104313635-104313636		1320;234
N	jcn_only_AA	CUFF.279	chr14	+	chr14:76368568-76372897;chr14:76368568-76420766	chr14:76368568-76407766		chr14:76372898-76407766;chr14:76407767-76420766	chr14:76407766-76407767;chr14:76420766-76420767		64;101
K	cassette	CUFF.273	chr14	+	chr14:61509931-61512063	chr14:61509931-61510167;chr14:61510222-61512063		chr14:61510168-61510221			136;348
N	alternative_acceptor	CUFF.290	chr14	-	chr14:104230817-104245081;chr14:104224089-104245081	chr14:104225643-104245081		chr14:104224089-104225642;chr14:104225643-104230816	chr14:104224088-104224089;chr14:104225642-104225643		488;32
N	jcn_only_AD	CUFF.283	chr14	-	chr14:81893557-81902664;chr14:81893557-81893644	chr14:81893557-81902431		chr14:81893645-81902431;chr14:81902432-81902664	chr14:81902431-81902432;chr14:81902664-81902665	chr14:81893446-81893556	40;77
N	jcn_only_AA	CUFF.279	chr14	+	chr14:76201633-76211437;chr14:76201633-76210719	chr14:76201633-76203908		chr14:76203909-76210719;chr14:76210720-76211437	chr14:76210719-76210720;chr14:76211437-76211438		168;23
N	mutually_exclusive	CUFF.258	chr14	+	chr14:23390330-23393509,chr14:23393651-23395669	chr14:23390330-23392180,chr14:23392414-23395669	chr14:23393510-23393650	chr14:23392181-23392413			27;31
K	jcn_only_AA	CUFF.262	chr14	-	chr14:31358462-31358589	chr14:31358484-31358589		chr14:31358462-31358483	chr14:31358461-31358462		273;215
K	intron_retention	CUFF.261	chr14	-	chr14:24684869-24684942				chr14:24684868-24684869;chr14:24684942-24684943		11;3
N	intron_retention	CUFF.290	chr14	-	chr14:104202540-104204030				chr14:104202539-104202540;chr14:104204030-104204031		447;18
N	cassette	CUFF.285	chr14	-	chr14:92195824-92246919	chr14:92195824-92245318;chr14:92245415-92246919		chr14:92245319-92245414			113;40
K	intron_retention	CUFF.271	chr14	-	chr14:59941245-59942586				chr14:59941244-59941245;chr14:59942586-59942587		214;57
K	intron_retention	CUFF.260	chr14	+	chr14:24568930-24569203				chr14:24568929-24568930;chr14:24569203-24569204		309;128
N	jcn_only_AD	CUFF.279	chr14	+	chr14:76150000-76156534	chr14:76156205-76156534		chr14:76150000-76156204	chr14:76149999-76150000		64;69
N	alternative_donor	CUFF.290	chr14	-	chr14:104263856-104313344;chr14:104263856-104313635;chr14:104263856-104313111	chr14:104263856-104306415		chr14:104306416-104313111;chr14:104313112-104313344;chr14:104313345-104313635	chr14:104313111-104313112;chr14:104313344-104313345;chr14:104313635-104313636		909;8
N	jcn_only_AD	CUFF.274	chr14	-	chr14:69589078-69619660	chr14:69589078-69619481		chr14:69619482-69619660	chr14:69619660-69619661		78;49
K	alternative_last_exon	CUFF.282	chr14	+	chr14:77928586-77934425	chr14:77928586-77928984	chr14:77934426-77934716	chr14:77928985-77929102			11;365
N	cassette	CUFF.277	chr14	-	chr14:75159032-75179635	chr14:75159032-75165466;chr14:75165560-75179635		chr14:75165467-75165559			194;54
K	intron_retention	CUFF.290	chr14	-	chr14:104206401-104313878				chr14:104206400-104206401;chr14:104313878-104313879		24;204
K	intron_retention	CUFF.282	chr14	+	chr14:77929103-77935419				chr14:77929102-77929103;chr14:77935419-77935420		297;27
N	jcn_only_AA		chr14	-	chr14:104212891-104213269;chr14:104213198-104213269	chr14:104213110-104213269		chr14:104212891-104213109;chr14:104213110-104213197	chr14:104212890-104212891;chr14:104213109-104213110		59;43
K	alternative_donor	CUFF.272,CUFF.277	chr14	-	chr14:75140815-75142443	chr14:75140815-75142401		chr14:75142402-75142443	chr14:75142443-75142444		65;86
K	alternative_first_exon	CUFF.271	chr14	-	chr14:59946070-59950526;chr14:59946070-59950397	chr14:59946070-59950207	chr14:59950398-59951239	chr14:59950208-59950300			255;15
K	mutually_exclusive	CUFF.259	chr14	+	chr14:24459569-24473545,chr14:24473602-24475094	chr14:24459569-24470592,chr14:24470727-24475094	chr14:24473546-24473601	chr14:24470593-24470726			14;79
K	cassette	CUFF.259	chr14	+	chr14:24459569-24473545	chr14:24459569-24470592;chr14:24470727-24473545		chr14:24470593-24470726			25;1134
K	intron_retention	CUFF.290	chr14	-	chr14:104201417-104204030				chr14:104201416-104201417;chr14:104204030-104204031		17;268
K	cassette	CUFF.279	chr14	+	chr14:76219299-76230957	chr14:76219299-76224173;chr14:76224213-76230957		chr14:76224174-76224212			43;69
N	intron_retention		chr14	+	chr14:24563464-24563974				chr14:24563463-24563464;chr14:24563974-24563975		45;90
K	intron_retention	CUFF.282	chr14	+	chr14:77931030-77931881				chr14:77931029-77931030;chr14:77931881-77931882		328;37
N	mutually_exclusive	CUFF.265	chr14	+	chr14:50247494-50249259,chr14:50249313-50249547	chr14:50247494-50249087,chr14:50249176-50249547	chr14:50249260-50249312	chr14:50249088-50249175			15;130
K	intron_retention	CUFF.286	chr14	+	chr14:92909161-92909743				chr14:92909160-92909161;chr14:92909743-92909744		135;17
N	alternative_first_exon	CUFF.274	chr14	-	chr14:69589078-69616147,chr14:69589078-69619130;chr14:69589078-69619660,chr14:69589078-69619481	chr14:69589078-69619205	chr14:69619661-69619843	chr14:69619206-69619369			127;170
N	alternative_donor	CUFF.290	chr14	-	chr14:104263856-104313344;chr14:104263856-104313635;chr14:104263856-104306415	chr14:104263856-104313111		chr14:104306416-104313111;chr14:104313112-104313344;chr14:104313345-104313635	chr14:104313111-104313112;chr14:104313344-104313345;chr14:104313635-104313636		908;9
N	alternative_acceptor	CUFF.279	chr14	+	chr14:76368568-76372897;chr14:76368568-76420766	chr14:76368568-76407766		chr14:76372898-76407766;chr14:76407767-76420766	chr14:76407766-76407767;chr14:76420766-76420767		18;1
K	intron_retention	CUFF.261	chr14	-	chr14:24683602-24683697				chr14:24683601-24683602;chr14:24683697-24683698		11;11
N	jcn_only_AA		chr14	+	chr14:76368568-76372897;chr14:76368568-76407766	chr14:76368568-76420766		chr14:76372898-76407766;chr14:76407767-76420766	chr14:76407766-76407767;chr14:76420766-76420767		147;18
N	jcn_only_AD	CUFF.275	chr14	-	chr14:71216799-71227718	chr14:71216799-71219654		chr14:71219655-71227718	chr14:71227718-71227719		23;14
N	jcn_only_AD	CUFF.260	chr14	+	chr14:24563464-24563974	chr14:24563644-24563974		chr14:24563464-24563643	chr14:24563463-24563464		45;783
N	cassette	CUFF.265	chr14	+	chr14:50247494-50249259	chr14:50247494-50249087;chr14:50249176-50249259		chr14:50249088-50249175			19;652
K	cassette	CUFF.272	chr14	-	chr14:60010173-60018072	chr14:60010173-60011880;chr14:60012018-60018072		chr14:60011881-60012017			133;39
K	intron_retention	CUFF.279	chr14	+	chr14:76201633-76211437				chr14:76201632-76201633;chr14:76211437-76211438		32;18
N	alternative_donor		chr14	-	chr14:104224089-104230199;chr14:104224089-104225527	chr14:104224089-104245081		chr14:104225528-104230199;chr14:104230200-104245081	chr14:104230199-104230200;chr14:104245081-104245082		13;480
N	jcn_only_AD	CUFF.279	chr14	+	chr14:76201633-76211437	chr14:76203951-76211437		chr14:76201633-76203950	chr14:76201632-76201633		32;28
N	cassette	CUFF.260	chr14	+	chr14:24564055-24567411	chr14:24564055-24566100;chr14:24566347-24567411		chr14:24566101-24566346			134;918
K	intron_retention	CUFF.282	chr14	+	chr14:77934528-77935419				chr14:77934527-77934528;chr14:77935419-77935420		29;53
K	coord_cassette	CUFF.270	chr14	+	chr14:59295274-59360860	chr14:59295274-59355515;chr14:59355641-59357041;chr14:59357239-59360860		chr14:59355516-59355640;chr14:59357042-59357238			180;376
K	intron_retention	CUFF.266	chr14	-	chr14:52486897-52495439				chr14:52486896-52486897;chr14:52495439-52495440		76;33
N	cassette	CUFF.260	chr14	+	chr14:24567888-24568766	chr14:24567888-24568257;chr14:24568446-24568766		chr14:24568258-24568445			18;528
N	cassette	CUFF.274	chr14	-	chr14:69585948-69619660	chr14:69585948-69588933;chr14:69589078-69619660		chr14:69588934-69589077			271;240
K	cassette	CUFF.280	chr14	-	chr14:77275987-77279106	chr14:77275987-77276431;chr14:77276598-77279106		chr14:77276432-77276597			3;117
N	alternative_acceptor	CUFF.279,CUFF.286	chr14	+	chr14:92922953-92949023	chr14:92922953-92923597		chr14:92923598-92949023	chr14:92949023-92949024		269;4
K	jcn_only_AA	CUFF.279	chr14	+	chr14:76243194-76245921	chr14:76243194-76245917		chr14:76245918-76245921	chr14:76245921-76245922		31;66
K	intron_retention	CUFF.290	chr14	-	chr14:104202540-104205015				chr14:104202539-104202540;chr14:104205015-104205016		60;42
N	cassette	CUFF.277	chr14	-	chr14:75152364-75179635	chr14:75152364-75158743;chr14:75159032-75179635		chr14:75158744-75159031			19;340
K	coord_cassette	CUFF.273	chr14	+	chr14:61451522-61497162	chr14:61451522-61453769;chr14:61453876-61482621;chr14:61482675-61486258;chr14:61486299-61497162		chr14:61453770-61453875;chr14:61482622-61482674;chr14:61486259-61486298			20;548
K	intron_retention	CUFF.271	chr14	-	chr14:59941245-59941445				chr14:59941244-59941245;chr14:59941445-59941446		221;82
K	jcn_only_AA	CUFF.272	chr14	-	chr14:60018141-60027836	chr14:60018155-60027836		chr14:60018141-60018154	chr14:60018140-60018141		150;60
N	jcn_only_AD	CUFF.271,CUFF.277	chr14	-	chr14:75138187-75139533	chr14:75138187-75138671		chr14:75138672-75139533	chr14:75139533-75139534		99;64
K	intron_retention	CUFF.265	chr14	+	chr14:50249176-50249259				chr14:50249175-50249176;chr14:50249259-50249260		796;40
N	alternative_acceptor	CUFF.270	chr14	+	chr14:55494190-55498606	chr14:55494190-55498580		chr14:55498581-55498606	chr14:55498606-55498607		93;9
N	intron_retention		chr14	-	chr14:75152364-75179635				chr14:75152363-75152364;chr14:75179635-75179636		19;24
N	jcn_only_AA	CUFF.277	chr14	-	chr14:75138187-75139533	chr14:75138724-75139533		chr14:75138187-75138723	chr14:75138186-75138187		99;74
N	alternative_acceptor	CUFF.277	chr14	-	chr14:75138187-75139533	chr14:75138724-75139533		chr14:75138187-75138723	chr14:75138186-75138187		99;15
K	alternative_last_exon	CUFF.271	chr14	-	chr14:59939809-59942586;chr14:59927892-59942586	chr14:59941245-59942586	chr14:59939243-59939808;chr14:59927690-59927891	chr14:59941157-59941244			96;146
N	cassette	CUFF.259	chr14	+	chr14:24459569-24464240	chr14:24459569-24459983;chr14:24460162-24464240		chr14:24459984-24460161			312;74
N	cassette	CUFF.290	chr14	-	chr14:104208629-104212709	chr14:104208629-104208990;chr14:104209161-104212709		chr14:104208991-104209160			35;336
N	jcn_only_AA	CUFF.274	chr14	-	chr14:69542129-69558390	chr14:69557874-69558390		chr14:69542129-69557873	chr14:69542128-69542129		532;36
N	coord_cassette	CUFF.290	chr14	-	chr14:104245159-104263707	chr14:104245159-104251131;chr14:104251252-104260913;chr14:104261001-104263707		chr14:104251132-104251251;chr14:104260914-104261000			162;717
N	alternative_donor	CUFF.260	chr14	+	chr14:24563464-24563974	chr14:24563644-24563974		chr14:24563464-24563643	chr14:24563463-24563464		45;487
K	alternative_acceptor	CUFF.279	chr14	+	chr14:76243194-76245921	chr14:76243194-76245917		chr14:76245918-76245921	chr14:76245921-76245922		31;33
K	coord_cassette	CUFF.277	chr14	-	chr14:75143456-75151156	chr14:75143456-75144881;chr14:75145033-75149998;chr14:75150237-75151156		chr14:75144882-75145032;chr14:75149999-75150236			160;51
K	alternative_acceptor	CUFF.279	chr14	+	chr14:76241974-76243089	chr14:76241974-76243047		chr14:76243048-76243089	chr14:76243089-76243090		71;19
K	cassette	CUFF.265	chr14	+	chr14:50247041-50249087	chr14:50247041-50247420;chr14:50247494-50249087		chr14:50247421-50247493			98;684
N	jcn_only_AA	CUFF.274	chr14	-	chr14:69584993-69585910	chr14:69584996-69585910		chr14:69584993-69584995	chr14:69584992-69584993		134;539
N	jcn_only_AA	CUFF.279,CUFF.282	chr14	+	chr14:76368568-76420766;chr14:76368568-76407766	chr14:76368568-76372897		chr14:76372898-76407766;chr14:76407767-76420766	chr14:76407766-76407767;chr14:76420766-76420767		119;46
K	jcn_only_AA	CUFF.291	chr14	+	chr14:105054647-105054958	chr14:105054647-105054914		chr14:105054915-105054958	chr14:105054958-105054959		60;276
K	cassette	CUFF.265	chr14	+	chr14:50249176-50249547	chr14:50249176-50249259;chr14:50249313-50249547		chr14:50249260-50249312			165;647
N	coord_cassette	CUFF.260	chr14	+	chr14:24563644-24566100	chr14:24563644-24563974;chr14:24564055-24564351;chr14:24564588-24566100		chr14:24563975-24564054;chr14:24564352-24564587			86;465
K	cassette	CUFF.258	chr14	+	chr14:23392414-23395669	chr14:23392414-23393509;chr14:23393651-23395669		chr14:23393510-23393650			31;66
K	alternative_last_exon	CUFF.289	chr14	-	chr14:103236793-103240977	chr14:103237911-103240977	chr14:103236377-103236792	chr14:103237381-103237910			49;56
K	cassette	CUFF.269	chr14	+	chr14:59006855-59014498	chr14:59006855-59010600;chr14:59010686-59014498		chr14:59010601-59010685			146;13
N	alternative_donor	CUFF.279	chr14	+	chr14:76368568-76420766;chr14:76407838-76420766	chr14:76373021-76420766		chr14:76368568-76373020;chr14:76373021-76407837	chr14:76368567-76368568;chr14:76373020-76373021		19;20
N	jcn_only_AA	CUFF.290	chr14	-	chr14:104201417-104204030	chr14:104202540-104204030					17;447
N	jcn_only_AA	CUFF.290	chr14	-	chr14:104230817-104245081;chr14:104225643-104245081	chr14:104224089-104245081		chr14:104224089-104225642;chr14:104225643-104230816	chr14:104224088-104224089;chr14:104225642-104225643		329;480
K	cassette	CUFF.285	chr14	-	chr14:92105595-92136157	chr14:92105595-92126180;chr14:92126326-92136157		chr14:92126181-92126325		chr14:92105440-92105594;chr14:92136158-92136274	53;286
N	coord_cassette	CUFF.259	chr14	+	chr14:24459569-24473545	chr14:24459569-24459983;chr14:24460162-24464240;chr14:24464343-24473545		chr14:24459984-24460161;chr14:24464241-24464342			25;51
K	coord_cassette	CUFF.259	chr14	+	chr14:24459569-24470592	chr14:24459569-24470071;chr14:24470143-24470241;chr14:24470294-24470592		chr14:24470072-24470142;chr14:24470242-24470293			1138;244
K	alternative_first_exon	CUFF.272	chr14	-	chr14:60030578-60031764	chr14:60030578-60031075	chr14:60031765-60031993	chr14:60031076-60031247			33;120
N	alternative_donor	CUFF.283	chr14	-	chr14:81893557-81902664;chr14:81893557-81893644	chr14:81893557-81902431		chr14:81893645-81902431;chr14:81902432-81902664	chr14:81902431-81902432;chr14:81902664-81902665	chr14:81893446-81893556	37;54
N	alternative_donor	CUFF.290	chr14	-	chr14:104263856-104313635;chr14:104263856-104313111;chr14:104263856-104306415	chr14:104263856-104313344		chr14:104306416-104313111;chr14:104313112-104313344;chr14:104313345-104313635	chr14:104313111-104313112;chr14:104313344-104313345;chr14:104313635-104313636		741;176
K	alternative_acceptor	CUFF.291	chr14	+	chr14:105054647-105054958	chr14:105054647-105054914		chr14:105054915-105054958	chr14:105054958-105054959		60;173
N	alternative_acceptor	CUFF.279,CUFF.282	chr14	+	chr14:76368568-76420766;chr14:76368568-76407766	chr14:76368568-76372897		chr14:76372898-76407766;chr14:76407767-76420766	chr14:76407766-76407767;chr14:76420766-76420767		19;0
N	alternative_acceptor	CUFF.274	chr14	-	chr14:69584993-69585910	chr14:69584996-69585910		chr14:69584993-69584995	chr14:69584992-69584993		134;267
K	alternative_last_exon	CUFF.271	chr14	-	chr14:59927892-59942586;chr14:59941245-59942586	chr14:59939809-59942586	chr14:59927690-59927891;chr14:59941157-59941244	chr14:59939243-59939808			177;65
N	alternative_donor	CUFF.290	chr14	-	chr14:104212891-104216130;chr14:104212891-104212988	chr14:104212891-104213269		chr14:104212989-104213269;chr14:104213270-104216130	chr14:104213269-104213270;chr14:104216130-104216131		137;13
N	jcn_only_AD		chr14	-	chr14:104224089-104230199;chr14:104224089-104225527	chr14:104224089-104245081		chr14:104225528-104230199;chr14:104230200-104245081	chr14:104230199-104230200;chr14:104245081-104245082		316;480
K	intron_retention	CUFF.279	chr14	+	chr14:76156666-76165530				chr14:76156665-76156666;chr14:76165530-76165531		36;43
N	alternative_donor	CUFF.290	chr14	-	chr14:104209161-104212709	chr14:104209161-104210227		chr14:104210228-104212709	chr14:104212709-104212710		147;14
K	intron_retention	CUFF.260	chr14	+	chr14:24569423-24571961				chr14:24569422-24569423;chr14:24571961-24571962		325;325
K	jcn_only_AD	CUFF.275	chr14	-	chr14:71205116-71206758	chr14:71205116-71206614		chr14:71206615-71206758	chr14:71206758-71206759		24;6
K	jcn_only_AA	CUFF.273	chr14	+	chr14:61518650-61518758	chr14:61518650-61518723		chr14:61518724-61518758	chr14:61518758-61518759		728;366
K	alternative_acceptor	CUFF.273	chr14	+	chr14:61518650-61518758	chr14:61518650-61518723		chr14:61518724-61518758	chr14:61518758-61518759		728;206
K	intron_retention	CUFF.279	chr14	+	chr14:76129567-76135758				chr14:76129566-76129567;chr14:76135758-76135759		99;22
N	alternative_donor		chr14	-	chr14:104212891-104212988;chr14:104212891-104213269	chr14:104212891-104216130		chr14:104212989-104213269;chr14:104213270-104216130	chr14:104213269-104213270;chr14:104216130-104216131		35;115
K	cassette	CUFF.286	chr14	+	chr14:92958585-92959819	chr14:92958585-92959170;chr14:92959269-92959819		chr14:92959171-92959268			303;17
K	coord_cassette	CUFF.273	chr14	+	chr14:61518854-61545547	chr14:61518854-61519066;chr14:61519704-61540565;chr14:61540660-61545547		chr14:61519067-61519703;chr14:61540566-61540659			161;356
K	cassette	CUFF.282	chr14	+	chr14:77934528-77935419	chr14:77934528-77934799;chr14:77934852-77935419		chr14:77934800-77934851			29;215
K	cassette	CUFF.266	chr14	-	chr14:52486897-52495439	chr14:52486897-52493918;chr14:52494063-52495439		chr14:52493919-52494062			76;16
K	intron_retention	CUFF.551	chr19	-	chr19:51526485-51527300				chr19:51526484-51526485;chr19:51527300-51527301		303;22
N	alternative_donor	CUFF.520	chr19	+	chr19:17447967-17448682	chr19:17448474-17448682		chr19:17447967-17448473	chr19:17447966-17447967		160;179
K	cassette	CUFF.554	chr19	+	chr19:52264484-52271897	chr19:52264484-52266614;chr19:52266771-52271897		chr19:52266615-52266770			251;25
N	alternative_acceptor	CUFF.495	chr19	+	chr19:1438892-1439714;chr19:1438892-1440017;chr19:1438892-1439604;chr19:1438892-1440024;chr19:1438892-1439966	chr19:1438892-1439959		chr19:1439605-1439714;chr19:1439715-1439959;chr19:1439960-1439966;chr19:1439967-1440017;chr19:1440018-1440024	chr19:1439714-1439715;chr19:1439959-1439960;chr19:1439966-1439967;chr19:1440017-1440018;chr19:1440024-1440025		1062;26
N	alternative_donor	CUFF.516	chr19	+	chr19:16186520-16186856;chr19:16178773-16186856	chr19:16178549-16186856		chr19:16178549-16178772;chr19:16178773-16186519	chr19:16178548-16178549;chr19:16178772-16178773		98;213
N	alternative_donor	CUFF.558	chr19	+	chr19:54656737-54657451	chr19:54656820-54657451		chr19:54656737-54656819	chr19:54656736-54656737		87;23
K	intron_retention	CUFF.508	chr19	+	chr19:10394171-10394233				chr19:10394170-10394171;chr19:10394233-10394234		28;176
K	jcn_only_AA	CUFF.510	chr19	+	chr19:11467653-11468335	chr19:11467653-11468294		chr19:11468295-11468335	chr19:11468335-11468336		86;148
K	cassette	CUFF.511	chr19	-	chr19:11537392-11537692	chr19:11537392-11537502;chr19:11537605-11537692		chr19:11537503-11537604			125;116
K	intron_retention	CUFF.516	chr19	+	chr19:16212601-16213657				chr19:16212600-16212601;chr19:16213657-16213658		31;103
N	intron_retention		chr19	-	chr19:49310332-49314240				chr19:49310331-49310332;chr19:49314240-49314241		75;76
K	cassette	CUFF.499	chr19	-	chr19:5897009-5903622	chr19:5897009-5901345;chr19:5901466-5903622		chr19:5901346-5901465			64;412
N	alternative_acceptor	CUFF.529	chr19	-	chr19:33882386-33892626	chr19:33887062-33892626		chr19:33882386-33887061	chr19:33882385-33882386		572;3
N	jcn_only_AD	CUFF.529,CUFF.552	chr19	-	chr19:33878388-33878795	chr19:33878388-33878560		chr19:33878561-33878795	chr19:33878795-33878796		736;38
K	intron_retention	CUFF.520	chr19	+	chr19:17449551-17449931				chr19:17449550-17449551;chr19:17449931-17449932		18;433
N	cassette	CUFF.520	chr19	+	chr19:17445932-17448816	chr19:17445932-17447628;chr19:17448474-17448816		chr19:17447629-17448473			24;402
N	coord_cassette	CUFF.529	chr19	-	chr19:33984244-34003498	chr19:33984244-33991843;chr19:33991908-34001933;chr19:34002062-34003498		chr19:33991844-33991907;chr19:34001934-34002061			106;389
N	alternative_donor	CUFF.543	chr19	+	chr19:45261671-45261980	chr19:45261731-45261980		chr19:45261671-45261730	chr19:45261670-45261671		276;149
N	alternative_acceptor	CUFF.542	chr19	+	chr19:4304759-4306020;chr19:4304759-4305981	chr19:4304759-4305942		chr19:4305943-4305981;chr19:4305982-4306020	chr19:4305981-4305982;chr19:4306020-4306021		57;200
N	jcn_only_AD	CUFF.516	chr19	+	chr19:16199931-16204345	chr19:16203943-16204345		chr19:16199931-16203942	chr19:16199930-16199931		604;131
K	cassette	CUFF.562	chr19	+	chr19:55084903-55085542	chr19:55084903-55085164;chr19:55085380-55085542		chr19:55085165-55085379			173;344
K	alternative_acceptor	CUFF.538	chr19	-	chr19:41533165-41533447	chr19:41533170-41533447		chr19:41533165-41533169	chr19:41533164-41533165		16;22
K	jcn_only_AA	CUFF.535	chr19	+	chr19:40478152-40478368	chr19:40478152-40478275		chr19:40478276-40478368	chr19:40478368-40478369		31;209
K	cassette	CUFF.506	chr19	-	chr19:8161891-8165784	chr19:8161891-8162172;chr19:8162299-8165784		chr19:8162173-8162298			45;336
N	alternative_acceptor	CUFF.495	chr19	+	chr19:1438892-1439714;chr19:1438892-1440017;chr19:1438892-1439959;chr19:1438892-1440024;chr19:1438892-1439966	chr19:1438892-1439604		chr19:1439605-1439714;chr19:1439715-1439959;chr19:1439960-1439966;chr19:1439967-1440017;chr19:1440018-1440024	chr19:1439714-1439715;chr19:1439959-1439960;chr19:1439966-1439967;chr19:1440017-1440018;chr19:1440024-1440025		1041;47
K	cassette	CUFF.562	chr19	+	chr19:55087577-55098667	chr19:55087577-55088931;chr19:55089191-55098667		chr19:55088932-55089190			98;143
K	cassette	CUFF.554	chr19	+	chr19:52264484-52271897	chr19:52264484-52265669;chr19:52265789-52271897		chr19:52265670-52265788			251;56
K	cassette	CUFF.506	chr19	-	chr19:8154555-8154982	chr19:8154555-8154777;chr19:8154844-8154982		chr19:8154778-8154843			35;630
K	jcn_only_AD	CUFF.555	chr19	+	chr19:52901154-52901619;chr19:52901158-52901619	chr19:52901274-52901619		chr19:52901154-52901157;chr19:52901158-52901273	chr19:52901153-52901154;chr19:52901157-52901158		593;135
K	intron_retention	CUFF.510	chr19	+	chr19:11470397-11470496				chr19:11470396-11470397;chr19:11470496-11470497		61;144
K	intron_retention	CUFF.495	chr19	+	chr19:1438428-1438805				chr19:1438427-1438428;chr19:1438805-1438806		390;450
N	jcn_only_AA	CUFF.521	chr19	+	chr19:17581517-17594690;chr19:17581517-17597371	chr19:17581517-17598268					115;86
K	cassette	CUFF.515	chr19	-	chr19:14876617-14883153	chr19:14876617-14877789;chr19:14877922-14883153		chr19:14877790-14877921			21;259
K	intron_retention	CUFF.539	chr19	-	chr19:41937794-41938219				chr19:41937793-41937794;chr19:41938219-41938220		231;796
K	jcn_only_AA	CUFF.551	chr19	-	chr19:51525921-51526347	chr19:51525954-51526347		chr19:51525921-51525953	chr19:51525920-51525921		63;303
N	jcn_only_AA		chr19	+	chr19:17448474-17448816;chr19:17448474-17448682	chr19:17448474-17448707		chr19:17448683-17448707;chr19:17448708-17448816	chr19:17448707-17448708;chr19:17448816-17448817		784;144
N	alternative_donor	CUFF.510	chr19	+	chr19:11474496-11474836	chr19:11474512-11474836		chr19:11474496-11474511	chr19:11474495-11474496		23;1380
N	intron_retention		chr19	+	chr19:44764092-44768466				chr19:44764091-44764092;chr19:44768466-44768467		14;79
K	alternative_donor	CUFF.507	chr19	-	chr19:10204296-10204488	chr19:10204296-10204368		chr19:10204369-10204488	chr19:10204488-10204489		12;78
K	intron_retention	CUFF.500	chr19	-	chr19:6007814-6008116				chr19:6007813-6007814;chr19:6008116-6008117		354;87
K	coord_cassette	CUFF.551	chr19	-	chr19:51526485-51528847	chr19:51526485-51527300;chr19:51527567-51527889;chr19:51528051-51528847		chr19:51527301-51527566;chr19:51527890-51528050			35;148
K	intron_retention	CUFF.542	chr19	+	chr19:44771115-44777457				chr19:44771114-44771115;chr19:44777457-44777458		74;57
N	jcn_only_AD	CUFF.520	chr19	+	chr19:17447967-17448682	chr19:17448474-17448682		chr19:17447967-17448473	chr19:17447966-17447967		160;172
K	alternative_acceptor	CUFF.542,CUFF.555	chr19	+	chr19:52901158-52901706	chr19:52901158-52901619		chr19:52901620-52901706	chr19:52901706-52901707		69;247
K	intron_retention	CUFF.546	chr19	-	chr19:49311494-49314240				chr19:49311493-49311494;chr19:49314240-49314241		148;15
N	alternative_acceptor	CUFF.558	chr19	+	chr19:54648069-54649277;chr19:54648069-54649333	chr19:54648069-54649330		chr19:54649278-54649330;chr19:54649331-54649333	chr19:54649330-54649331;chr19:54649333-54649334		146;16
K	intron_retention	CUFF.515	chr19	-	chr19:14876617-14877046				chr19:14876616-14876617;chr19:14877046-14877047		128;23
N	jcn_only_AD	CUFF.520	chr19	+	chr19:17445921-17448816;chr19:17448386-17448816;chr19:17447844-17448816;chr19:17448457-17448816;chr19:17448474-17448816;chr19:17447967-17448816	chr19:17448079-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		1389;240
K	intron_retention	CUFF.548	chr19	+	chr19:50305399-50306205				chr19:50305398-50305399;chr19:50306205-50306206		1261;16
K	cassette	CUFF.562	chr19	+	chr19:55087577-55098667	chr19:55087577-55098476;chr19:55098528-55098667		chr19:55098477-55098527			98;90
N	alternative_acceptor	CUFF.520	chr19	+	chr19:17448474-17448682;chr19:17448474-17448707	chr19:17448474-17448816		chr19:17448683-17448707;chr19:17448708-17448816	chr19:17448707-17448708;chr19:17448816-17448817		254;611
K	intron_retention	CUFF.536	chr19	-	chr19:40903878-40904526				chr19:40903877-40903878;chr19:40904526-40904527		4;3
N	alternative_acceptor		chr19	+	chr19:11468416-11470146;chr19:11468416-11470282	chr19:11468416-11470207		chr19:11470147-11470207;chr19:11470208-11470282	chr19:11470207-11470208;chr19:11470282-11470283		61;103
K	alternative_first_exon	CUFF.541	chr19	-	chr19:43724395-43727042	chr19:43724395-43724782	chr19:43727043-43727110	chr19:43724783-43725058			52;48
N	jcn_only_AA	CUFF.520	chr19	+	chr19:17448474-17448682;chr19:17448474-17448707	chr19:17448474-17448816		chr19:17448683-17448707;chr19:17448708-17448816	chr19:17448707-17448708;chr19:17448816-17448817		316;611
N	jcn_only_AD	CUFF.520	chr19	+	chr19:17445921-17448816;chr19:17447844-17448816;chr19:17448457-17448816;chr19:17448079-17448816;chr19:17448474-17448816;chr19:17447967-17448816	chr19:17448386-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		1360;269
K	cassette	CUFF.511	chr19	-	chr19:11537861-11541718	chr19:11537861-11541518;chr19:11541597-11541718		chr19:11541519-11541596			103;156
K	intron_retention	CUFF.534	chr19	-	chr19:39924059-39924161				chr19:39924058-39924059;chr19:39924161-39924162		1498;50
N	alternative_donor	CUFF.515	chr19	-	chr19:14885119-14887537	chr19:14885119-14887215		chr19:14887216-14887537	chr19:14887537-14887538		401;19
N	alternative_donor		chr19	-	chr19:39924402-39926297	chr19:39924402-39926246		chr19:39926247-39926297	chr19:39926297-39926298		152;505
K	intron_retention	CUFF.548	chr19	+	chr19:50306634-50308709				chr19:50306633-50306634;chr19:50308709-50308710		1578;35
K	intron_retention	CUFF.555	chr19	+	chr19:52901158-52901706				chr19:52901157-52901158;chr19:52901706-52901707		69;289
N	alternative_acceptor	CUFF.521	chr19	+	chr19:10381903-10394804	chr19:10381903-10385440		chr19:10385441-10394804	chr19:10394804-10394805		21;23
N	intron_retention		chr19	+	chr19:18119038-18119262				chr19:18119037-18119038;chr19:18119262-18119263		27;270
K	intron_retention	ENSG00000269399.1	chr19	-	chr19:16654417-16655074				chr19:16654416-16654417;chr19:16655074-16655075		266;11
K	intron_retention	CUFF.534	chr19	-	chr19:39924059-39924133				chr19:39924058-39924059;chr19:39924133-39924134		28;58
K	alternative_acceptor	CUFF.495	chr19	+	chr19:1438428-1438809	chr19:1438428-1438805		chr19:1438806-1438809	chr19:1438809-1438810		49;351
N	cassette	CUFF.562	chr19	+	chr19:55085380-55085767	chr19:55085380-55085542;chr19:55085579-55085767		chr19:55085543-55085578			22;439
K	intron_retention	CUFF.520	chr19	+	chr19:17449065-17449173				chr19:17449064-17449065;chr19:17449173-17449174		1897;263
N	alternative_acceptor	CUFF.558	chr19	+	chr19:54657578-54657680;chr19:54657578-54658995	chr19:54657578-54659046		chr19:54657681-54658995;chr19:54658996-54659046	chr19:54658995-54658996;chr19:54659046-54659047		140;221
K	jcn_only_AD	CUFF.498	chr19	+	chr19:4323144-4323344;chr19:4323211-4323344	chr19:4323235-4323344		chr19:4323144-4323210;chr19:4323211-4323234	chr19:4323143-4323144;chr19:4323210-4323211		126;247
N	alternative_acceptor	CUFF.521	chr19	+	chr19:17597767-17597982	chr19:17597767-17597908		chr19:17597909-17597982	chr19:17597982-17597983		61;46
N	intron_retention		chr19	-	chr19:41938968-41939441				chr19:41938967-41938968;chr19:41939441-41939442		544;211
N	alternative_donor	CUFF.520	chr19	+	chr19:17445921-17448816;chr19:17448386-17448816;chr19:17447844-17448816;chr19:17448457-17448816;chr19:17448079-17448816;chr19:17448474-17448816	chr19:17447967-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		342;3
K	intron_retention	CUFF.548	chr19	+	chr19:50305399-50305790				chr19:50305398-50305399;chr19:50305790-50305791		71;31
K	cassette	CUFF.500	chr19	-	chr19:6002882-6007022	chr19:6002882-6004211;chr19:6004310-6007022		chr19:6004212-6004309			98;20
K	intron_retention	CUFF.548	chr19	+	chr19:50306447-50306543				chr19:50306446-50306447;chr19:50306543-50306544		1509;27
N	jcn_only_AA	CUFF.498	chr19	+	chr19:4304759-4305981;chr19:4304759-4305942	chr19:4304759-4306020		chr19:4305943-4305981;chr19:4305982-4306020	chr19:4305981-4305982;chr19:4306020-4306021		720;37
K	intron_retention	CUFF.513	chr19	+	chr19:12917615-12917821				chr19:12917614-12917615;chr19:12917821-12917822		4912;34
K	intron_retention	CUFF.552	chr19	-	chr19:51537897-51538061				chr19:51537896-51537897;chr19:51538061-51538062		623;11
N	intron_retention		chr19	+	chr19:17445921-17448816				chr19:17445920-17445921;chr19:17448816-17448817		38;182
K	alternative_acceptor	CUFF.547	chr19	-	chr19:49335990-49337532	chr19:49336010-49337532		chr19:49335990-49336009	chr19:49335989-49335990		74;17
K	intron_retention	CUFF.516	chr19	+	chr19:16198908-16199854				chr19:16198907-16198908;chr19:16199854-16199855		616;131
N	intron_retention		chr19	+	chr19:1438892-1439959				chr19:1438891-1438892;chr19:1439959-1439960		37;173
N	jcn_only_AD	CUFF.516	chr19	+	chr19:16178549-16186856;chr19:16178773-16186856	chr19:16186520-16186856		chr19:16178549-16178772;chr19:16178773-16186519	chr19:16178548-16178549;chr19:16178772-16178773		384;151
N	alternative_donor	CUFF.520	chr19	+	chr19:17445921-17448816;chr19:17448386-17448816;chr19:17447844-17448816;chr19:17448457-17448816;chr19:17448474-17448816;chr19:17447967-17448816	chr19:17448079-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		300;45
K	jcn_only_AA	CUFF.542,CUFF.558	chr19	+	chr19:44768529-44770350	chr19:44768529-44770307		chr19:44770308-44770350	chr19:44770350-44770351		206;91
K	intron_retention	CUFF.499	chr19	-	chr19:5894866-5896463				chr19:5894865-5894866;chr19:5896463-5896464		688;15
K	alternative_first_exon	CUFF.552	chr19	-	chr19:51537897-51538061	chr19:51537897-51538050	chr19:51538062-51538583	chr19:51538051-51538054			348;37
N	alternative_acceptor	CUFF.516	chr19	+	chr19:16204564-16212073	chr19:16204564-16206073		chr19:16206074-16212073	chr19:16212073-16212074		333;14
K	intron_retention	CUFF.502	chr19	-	chr19:6211077-6211308				chr19:6211076-6211077;chr19:6211308-6211309		73;88
N	cassette	CUFF.516	chr19	+	chr19:16186983-16197232	chr19:16186983-16192722;chr19:16192857-16197232		chr19:16192723-16192856			148;595
N	jcn_only_AD	CUFF.520	chr19	+	chr19:17448386-17448816;chr19:17447844-17448816;chr19:17448457-17448816;chr19:17448079-17448816;chr19:17448474-17448816;chr19:17447967-17448816	chr19:17445921-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		1591;38
N	jcn_only_AA	CUFF.520	chr19	+	chr19:17448474-17448816;chr19:17448474-17448707	chr19:17448474-17448682		chr19:17448683-17448707;chr19:17448708-17448816	chr19:17448707-17448708;chr19:17448816-17448817		755;172
N	jcn_only_AD	CUFF.520	chr19	+	chr19:17445921-17448816;chr19:17448386-17448816;chr19:17447844-17448816;chr19:17448457-17448816;chr19:17448079-17448816;chr19:17447967-17448816	chr19:17448474-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		1018;611
K	alternative_donor	CUFF.534,CUFF.552	chr19	-	chr19:51534178-51535131	chr19:51534178-51535035		chr19:51535036-51535131	chr19:51535131-51535132		78;127
K	intron_retention	CUFF.548	chr19	+	chr19:50308834-50308917				chr19:50308833-50308834;chr19:50308917-50308918		193;41
K	alternative_first_exon	CUFF.523,CUFF.564	chr19	-	chr19:56321705-56343328	chr19:56321705-56329269	chr19:56343329-56343460	chr19:56329270-56329603			178;107
N	jcn_only_AD	CUFF.542	chr19	+	chr19:44764362-44768466;chr19:44764092-44768466	chr19:44764156-44768466		chr19:44764092-44764155;chr19:44764156-44764361	chr19:44764091-44764092;chr19:44764155-44764156		143;146
N	alternative_acceptor	CUFF.495	chr19	+	chr19:1438892-1440017;chr19:1438892-1439604;chr19:1438892-1439959;chr19:1438892-1440024;chr19:1438892-1439966	chr19:1438892-1439714		chr19:1439605-1439714;chr19:1439715-1439959;chr19:1439960-1439966;chr19:1439967-1440017;chr19:1440018-1440024	chr19:1439714-1439715;chr19:1439959-1439960;chr19:1439966-1439967;chr19:1440017-1440018;chr19:1440024-1440025		972;116
K	intron_retention	CUFF.540	chr19	-	chr19:42734544-42734830				chr19:42734543-42734544;chr19:42734830-42734831		21;159
K	intron_retention	CUFF.555	chr19	+	chr19:52917622-52918376				chr19:52917621-52917622;chr19:52918376-52918377		16;6
K	alternative_first_exon	CUFF.500,CUFF.546	chr19	-	chr19:6047516-6049146,chr19:6047516-6072015,chr19:6047516-6148241;chr19:6047516-6110403	chr19:6047516-6057172	chr19:6110404-6110700	chr19:6057173-6057271			270;19
N	jcn_only_AD	CUFF.520	chr19	+	chr19:17445921-17448816;chr19:17448386-17448816;chr19:17447844-17448816;chr19:17448079-17448816;chr19:17448474-17448816;chr19:17447967-17448816	chr19:17448457-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		1602;27
N	alternative_acceptor	CUFF.542	chr19	+	chr19:44771115-44777457;chr19:44771115-44777051	chr19:44771115-44771532		chr19:44771533-44777051;chr19:44777052-44777457	chr19:44777051-44777052;chr19:44777457-44777458		162;10
K	intron_retention		chr19	+	chr19:16186983-16192722				chr19:16186982-16186983;chr19:16192722-16192723		290;82
K	alternative_donor	CUFF.498	chr19	+	chr19:4323144-4323344;chr19:4323211-4323344	chr19:4323235-4323344		chr19:4323144-4323210;chr19:4323211-4323234	chr19:4323143-4323144;chr19:4323210-4323211		132;208
N	cassette	CUFF.515	chr19	-	chr19:14876383-14883153	chr19:14876383-14876469;chr19:14876617-14883153		chr19:14876470-14876616			89;242
K	intron_retention	CUFF.513	chr19	+	chr19:12918144-12918232				chr19:12918143-12918144;chr19:12918232-12918233		7979;23
K	alternative_donor	CUFF.555	chr19	+	chr19:52901154-52901619;chr19:52901158-52901619	chr19:52901274-52901619		chr19:52901154-52901157;chr19:52901158-52901273	chr19:52901153-52901154;chr19:52901157-52901158		548;90
K	intron_retention	CUFF.552	chr19	-	chr19:51537897-51538050				chr19:51537896-51537897;chr19:51538050-51538051		38;10
K	alternative_first_exon	CUFF.529	chr19	-	chr19:33968997-33977808;chr19:33968997-33980901	chr19:33968997-33978155	chr19:33980902-33980963	chr19:33978156-33978380			710;5625
K	jcn_only_AA	CUFF.520	chr19	+	chr19:17450409-17451915	chr19:17450409-17451852		chr19:17451853-17451915	chr19:17451915-17451916		129;784
K	intron_retention	CUFF.539	chr19	-	chr19:41938314-41939176				chr19:41938313-41938314;chr19:41939176-41939177		719;264
N	jcn_only_AD	CUFF.495	chr19	+	chr19:1440241-1440347	chr19:1440253-1440347		chr19:1440241-1440252	chr19:1440240-1440241		126;1472
N	jcn_only_AA	CUFF.495	chr19	+	chr19:1438892-1439714;chr19:1438892-1440017;chr19:1438892-1439604;chr19:1438892-1439959;chr19:1438892-1440024	chr19:1438892-1439966		chr19:1439605-1439714;chr19:1439715-1439959;chr19:1439960-1439966;chr19:1439967-1440017;chr19:1440018-1440024	chr19:1439714-1439715;chr19:1439959-1439960;chr19:1439966-1439967;chr19:1440017-1440018;chr19:1440024-1440025		1461;232
N	jcn_only_AA	CUFF.526	chr19	-	chr19:21632180-21636351	chr19:21636082-21636351		chr19:21632180-21636081	chr19:21632179-21632180		13;90
N	alternative_donor	CUFF.521	chr19	+	chr19:17581517-17597371	chr19:17594931-17597371		chr19:17581517-17594930	chr19:17581516-17581517		92;1
N	coord_cassette	CUFF.515	chr19	-	chr19:14863339-14867049	chr19:14863339-14865765;chr19:14865940-14866465;chr19:14866657-14867049		chr19:14865766-14865939;chr19:14866466-14866656			62;257
N	mutually_exclusive	CUFF.500	chr19	-	chr19:6040253-6044203,chr19:6044294-6047417	chr19:6040253-6042054,chr19:6042135-6047417	chr19:6044204-6044293	chr19:6042055-6042134			122;13
N	jcn_only_AD	CUFF.542	chr19	+	chr19:44764156-44768466;chr19:44764362-44768466	chr19:44764092-44768466		chr19:44764092-44764155;chr19:44764156-44764361	chr19:44764091-44764092;chr19:44764155-44764156		274;14
N	cassette	CUFF.500	chr19	-	chr19:6042135-6047417	chr19:6042135-6044203;chr19:6044294-6047417		chr19:6044204-6044293			17;496
K	intron_retention	CUFF.522	chr19	+	chr19:18119587-18119779				chr19:18119586-18119587;chr19:18119779-18119780		1523;81
N	jcn_only_AA	CUFF.495	chr19	+	chr19:1438892-1439714;chr19:1438892-1440017;chr19:1438892-1439604;chr19:1438892-1440024;chr19:1438892-1439966	chr19:1438892-1439959		chr19:1439605-1439714;chr19:1439715-1439959;chr19:1439960-1439966;chr19:1439967-1440017;chr19:1440018-1440024	chr19:1439714-1439715;chr19:1439959-1439960;chr19:1439966-1439967;chr19:1440017-1440018;chr19:1440024-1440025		1656;37
N	alternative_donor	CUFF.529	chr19	-	chr19:33882386-33892626;chr19:33882386-33886015	chr19:33882386-33886995		chr19:33886016-33886995;chr19:33886996-33892626	chr19:33886995-33886996;chr19:33892626-33892627		573;3
K	intron_retention	CUFF.537	chr19	-	chr19:41350678-41351198				chr19:41350677-41350678;chr19:41351198-41351199		21;36
N	jcn_only_AA	CUFF.558	chr19	+	chr19:54648069-54649330;chr19:54648069-54649333	chr19:54648069-54649277		chr19:54649278-54649330;chr19:54649331-54649333	chr19:54649330-54649331;chr19:54649333-54649334		99;112
N	jcn_only_AD	CUFF.516	chr19	+	chr19:16186520-16186856;chr19:16178773-16186856	chr19:16178549-16186856		chr19:16178549-16178772;chr19:16178773-16186519	chr19:16178548-16178549;chr19:16178772-16178773		321;213
K	cassette	CUFF.566	chr19	+	chr19:58963072-58965062	chr19:58963072-58963494;chr19:58964150-58965062		chr19:58963495-58964149		chr19:58962971-58963071;chr19:58965063-58965189	173;2487
K	jcn_only_AD	CUFF.531	chr19	+	chr19:35642377-35642535	chr19:35642386-35642535		chr19:35642377-35642385	chr19:35642376-35642377		430;395
N	jcn_only_AD	CUFF.516	chr19	+	chr19:16186520-16186856;chr19:16178549-16186856	chr19:16178773-16186856		chr19:16178549-16178772;chr19:16178773-16186519	chr19:16178548-16178549;chr19:16178772-16178773		364;170
N	cassette	CUFF.515	chr19	-	chr19:14865940-14867049;chr19:14863339-14867049	chr19:14865940-14866465,chr19:14863339-14866465;chr19:14866690-14867049		chr19:14866466-14866689			217;253
K	intron_retention	CUFF.545	chr19	-	chr19:49117594-49117696				chr19:49117593-49117594;chr19:49117696-49117697		103;80
K	intron_retention		chr19	+	chr19:17448474-17448707				chr19:17448473-17448474;chr19:17448707-17448708		144;53
N	jcn_only_AA	CUFF.529	chr19	-	chr19:33882386-33892626	chr19:33887062-33892626		chr19:33882386-33887061	chr19:33882385-33882386		572;70
K	jcn_only_AA	CUFF.553	chr19	+	chr19:52085136-52092800	chr19:52085136-52089879		chr19:52089880-52092800	chr19:52092800-52092801		87;70
N	alternative_acceptor	CUFF.543	chr19	+	chr19:45251386-45254483	chr19:45251386-45251951		chr19:45251952-45254483	chr19:45254483-45254484		87;19
N	jcn_only_AA	CUFF.515	chr19	-	chr19:14847057-14854231	chr19:14852899-14854231		chr19:14847057-14852898	chr19:14847056-14847057		534;76
N	alternative_donor	CUFF.520	chr19	+	chr19:17448386-17448816;chr19:17447844-17448816;chr19:17448457-17448816;chr19:17448079-17448816;chr19:17448474-17448816;chr19:17447967-17448816	chr19:17445921-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		307;38
N	jcn_only_AD	CUFF.534	chr19	-	chr19:39924059-39924133;chr19:39924059-39924157	chr19:39924059-39924161		chr19:39924134-39924157;chr19:39924158-39924161	chr19:39924157-39924158;chr19:39924161-39924162		149;1498
N	intron_retention		chr19	+	chr19:1438892-1439714				chr19:1438891-1438892;chr19:1439714-1439715		120;176
K	alternative_first_exon	CUFF.516	chr19	+	chr19:16187508-16192722;chr19:16191886-16192722;chr19:16186983-16192722	chr19:16191253-16192722	chr19:16191725-16191885;chr19:16186857-16186982	chr19:16190850-16191252			559;126
N	intron_retention		chr19	+	chr19:1438892-1440024				chr19:1438891-1438892;chr19:1440024-1440025		60;228
N	jcn_only_AD		chr19	-	chr19:33882386-33886995;chr19:33882386-33886015	chr19:33882386-33892626		chr19:33886016-33886995;chr19:33886996-33892626	chr19:33886995-33886996;chr19:33892626-33892627		121;572
N	alternative_acceptor	CUFF.542	chr19	+	chr19:44771115-44777051;chr19:44771115-44771532	chr19:44771115-44777457		chr19:44771533-44777051;chr19:44777052-44777457	chr19:44777051-44777052;chr19:44777457-44777458		98;74
K	cassette	CUFF.552	chr19	-	chr19:51534178-51537235	chr19:51534178-51535131;chr19:51535392-51537235		chr19:51535132-51535391			460;242
K	alternative_acceptor	CUFF.510	chr19	+	chr19:11467653-11468335	chr19:11467653-11468294		chr19:11468295-11468335	chr19:11468335-11468336		86;83
K	jcn_only_AA	CUFF.542,CUFF.555	chr19	+	chr19:52901158-52901706	chr19:52901158-52901619		chr19:52901620-52901706	chr19:52901706-52901707		69;134
N	alternative_acceptor		chr19	+	chr19:1438892-1439714;chr19:1438892-1439604;chr19:1438892-1439959;chr19:1438892-1440024;chr19:1438892-1439966	chr19:1438892-1440017		chr19:1439605-1439714;chr19:1439715-1439959;chr19:1439960-1439966;chr19:1439967-1440017;chr19:1440018-1440024	chr19:1439714-1439715;chr19:1439959-1439960;chr19:1439966-1439967;chr19:1440017-1440018;chr19:1440024-1440025		378;710
N	cassette	CUFF.520	chr19	+	chr19:17445932-17448816	chr19:17445932-17447628;chr19:17447967-17448816		chr19:17447629-17447966			24;444
N	alternative_acceptor	CUFF.558	chr19	+	chr19:54657578-54657680;chr19:54657578-54659046	chr19:54657578-54658995		chr19:54657681-54658995;chr19:54658996-54659046	chr19:54658995-54658996;chr19:54659046-54659047		325;36
N	alternative_donor	CUFF.516	chr19	+	chr19:16186520-16186856;chr19:16178549-16186856	chr19:16178773-16186856		chr19:16178549-16178772;chr19:16178773-16186519	chr19:16178548-16178549;chr19:16178772-16178773		218;93
K	alternative_first_exon	CUFF.503	chr19	-	chr19:6216525-6217964	chr19:6216525-6216746	chr19:6217965-6218052	chr19:6216747-6216988			212;94
K	intron_retention		chr19	+	chr19:17447967-17448682				chr19:17447966-17447967;chr19:17448682-17448683		160;139
K	cassette	CUFF.552	chr19	-	chr19:51534178-51537235	chr19:51534178-51535035;chr19:51535392-51537235		chr19:51535036-51535391			460;277
N	cassette	CUFF.521	chr19	+	chr19:17611686-17615263	chr19:17611686-17612081;chr19:17612229-17615263		chr19:17612082-17612228			93;129
K	cassette	CUFF.506	chr19	-	chr19:8140075-8145886	chr19:8140075-8140166;chr19:8140296-8145886		chr19:8140167-8140295			85;1071
N	alternative_last_exon	CUFF.500	chr19	-	chr19:6027346-6039990;chr19:6016283-6039990	chr19:6026249-6039990	chr19:6016101-6016282	chr19:6026131-6026248			49;130
K	mutually_exclusive	CUFF.554	chr19	+	chr19:52264484-52266614,chr19:52266771-52271897	chr19:52264484-52265669,chr19:52265789-52271897	chr19:52266615-52266770	chr19:52265670-52265788			25;56
K	intron_retention	CUFF.520	chr19	+	chr19:17450409-17451915				chr19:17450408-17450409;chr19:17451915-17451916		129;340
N	alternative_donor	CUFF.520	chr19	+	chr19:17445921-17448816;chr19:17448386-17448816;chr19:17448457-17448816;chr19:17448079-17448816;chr19:17448474-17448816;chr19:17447967-17448816	chr19:17447844-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		273;72
K	intron_retention	CUFF.520	chr19	+	chr19:17449551-17449762				chr19:17449550-17449551;chr19:17449762-17449763		706;327
K	alternative_last_exon	CUFF.545	chr19	-	chr19:49116565-49117964	chr19:49117885-49117964	chr19:49116165-49116564	chr19:49117331-49117884			105;193
N	intron_retention		chr19	-	chr19:21636082-21636351				chr19:21636081-21636082;chr19:21636351-21636352		90;160
N	mutually_exclusive	CUFF.562	chr19	+	chr19:55084903-55085542,chr19:55085579-55085767	chr19:55084903-55085297,chr19:55085380-55085767	chr19:55085543-55085578	chr19:55085298-55085379			156;10
N	jcn_only_AD	CUFF.542	chr19	+	chr19:44771115-44777051	chr19:44771298-44777051		chr19:44771115-44771297	chr19:44771114-44771115		90;13
K	intron_retention	CUFF.558	chr19	+	chr19:54657578-54658995				chr19:54657577-54657578;chr19:54658995-54658996		32;86
N	intron_retention	CUFF.558	chr19	+	chr19:54657578-54657680				chr19:54657577-54657578;chr19:54657680-54657681		23;70
N	alternative_acceptor	CUFF.498	chr19	+	chr19:4304759-4306020;chr19:4304759-4305942	chr19:4304759-4305981		chr19:4305943-4305981;chr19:4305982-4306020	chr19:4305981-4305982;chr19:4306020-4306021		237;20
K	intron_retention	CUFF.516	chr19	+	chr19:16204409-16204493				chr19:16204408-16204409;chr19:16204493-16204494		432;57
K	intron_retention	CUFF.543	chr19	+	chr19:45261671-45261980				chr19:45261670-45261671;chr19:45261980-45261981		276;259
K	cassette	CUFF.537	chr19	-	chr19:41354669-41356151	chr19:41354669-41355722;chr19:41355886-41356151		chr19:41355723-41355885			22;147
K	cassette	CUFF.539	chr19	-	chr19:41939579-41944122	chr19:41939579-41942296;chr19:41942378-41944122		chr19:41942297-41942377			922;796
N	alternative_donor	CUFF.516	chr19	+	chr19:16199931-16204345	chr19:16203943-16204345		chr19:16199931-16203942	chr19:16199930-16199931		604;6
K	jcn_only_AA	CUFF.498	chr19	+	chr19:4317278-4318380	chr19:4317278-4318342		chr19:4318343-4318380	chr19:4318380-4318381		35;304
K	cassette	CUFF.500	chr19	-	chr19:6010263-6016100	chr19:6010263-6012996;chr19:6013117-6016100		chr19:6012997-6013116			323;448
K	intron_retention	CUFF.548	chr19	+	chr19:50306263-50306363				chr19:50306262-50306263;chr19:50306363-50306364		1431;25
N	cassette	CUFF.500	chr19	-	chr19:6044294-6110403	chr19:6044294-6047417;chr19:6047516-6110403		chr19:6047418-6047515			429;214
K	intron_retention	CUFF.520	chr19	+	chr19:17447844-17448816				chr19:17447843-17447844;chr19:17448816-17448817		428;466
K	cassette	CUFF.550	chr19	-	chr19:51483744-51485582	chr19:51483744-51485022;chr19:51485171-51485582		chr19:51485023-51485170			149;129
K	cassette	CUFF.546	chr19	-	chr19:49298722-49299684	chr19:49298722-49299403;chr19:49299587-49299684		chr19:49299404-49299586			234;154
N	jcn_only_AA	CUFF.558	chr19	+	chr19:54657578-54657680;chr19:54657578-54658995	chr19:54657578-54659046		chr19:54657681-54658995;chr19:54658996-54659046	chr19:54658995-54658996;chr19:54659046-54659047		55;221
N	intron_retention	CUFF.555	chr19	+	chr19:52917622-52918191				chr19:52917621-52917622;chr19:52918191-52918192		18;5
K	intron_retention		chr19	-	chr19:49310332-49311012				chr19:49310331-49310332;chr19:49311012-49311013		177;175
N	jcn_only_AD	CUFF.529	chr19	-	chr19:33882386-33892626;chr19:33882386-33886995	chr19:33882386-33886015		chr19:33886016-33886995;chr19:33886996-33892626	chr19:33886995-33886996;chr19:33892626-33892627		641;52
N	intron_retention		chr19	+	chr19:17448079-17448816				chr19:17448078-17448079;chr19:17448816-17448817		240;245
N	alternative_acceptor	CUFF.495	chr19	+	chr19:1438892-1439714;chr19:1438892-1440017;chr19:1438892-1439604;chr19:1438892-1439959;chr19:1438892-1440024	chr19:1438892-1439966		chr19:1439605-1439714;chr19:1439715-1439959;chr19:1439960-1439966;chr19:1439967-1440017;chr19:1440018-1440024	chr19:1439714-1439715;chr19:1439959-1439960;chr19:1439966-1439967;chr19:1440017-1440018;chr19:1440024-1440025		959;129
N	jcn_only_AA	CUFF.536	chr19	-	chr19:40909770-40913812	chr19:40913627-40913812		chr19:40909770-40913626	chr19:40909769-40909770		3;20
K	alternative_first_exon	CUFF.516	chr19	+	chr19:16187508-16192722;chr19:16191253-16192722;chr19:16191886-16192722	chr19:16186983-16192722	chr19:16190850-16191252;chr19:16191725-16191885	chr19:16186857-16186982			440;245
K	intron_retention	CUFF.516	chr19	+	chr19:16178549-16186856				chr19:16178548-16178549;chr19:16186856-16186857		213;70
N	jcn_only_AA	CUFF.558	chr19	+	chr19:54648069-54649330;chr19:54648069-54649277	chr19:54648069-54649333		chr19:54649278-54649330;chr19:54649331-54649333	chr19:54649330-54649331;chr19:54649333-54649334		134;78
K	intron_retention	CUFF.520	chr19	+	chr19:17452543-17452964				chr19:17452542-17452543;chr19:17452964-17452965		137;98
N	jcn_only_AA		chr19	-	chr19:6148341-6199486;chr19:6176455-6199486	chr19:6192041-6199486					82;24
N	alternative_acceptor		chr19	+	chr19:17447967-17448816	chr19:17447967-17448682		chr19:17448683-17448816	chr19:17448816-17448817		16;235
N	intron_retention		chr19	+	chr19:36139796-36142134				chr19:36139795-36139796;chr19:36142134-36142135		40;70
K	jcn_only_AA	CUFF.564	chr19	-	chr19:56321705-56343328	chr19:56329603-56343328					234;78
K	alternative_first_exon	CUFF.551	chr19	-	chr19:51528923-51529793;chr19:51528923-51529011;chr19:51528923-51531199	chr19:51528923-51530712	chr19:51529794-51530500;chr19:51529012-51529107;chr19:51531200-51531394	chr19:51530713-51530971			186;78
N	cassette	CUFF.515	chr19	-	chr19:14865940-14867049;chr19:14863339-14867049	chr19:14865940-14866465,chr19:14863339-14866465;chr19:14866657-14867049		chr19:14866466-14866656			217;240
K	alternative_first_exon	CUFF.532	chr19	+	chr19:36139796-36142134;chr19:36139306-36142134	chr19:36139811-36142134	chr19:36139125-36139305	chr19:36139501-36139810			91;208
K	alternative_acceptor	CUFF.535	chr19	+	chr19:40478152-40478368	chr19:40478152-40478275		chr19:40478276-40478368	chr19:40478368-40478369		31;203
K	cassette	CUFF.555	chr19	+	chr19:52901873-52905199	chr19:52901873-52904937;chr19:52905007-52905199		chr19:52904938-52905006			11;771
K	jcn_only_AD	CUFF.507	chr19	-	chr19:10204296-10204488	chr19:10204296-10204368		chr19:10204369-10204488	chr19:10204488-10204489		12;117
N	jcn_only_AA	CUFF.521	chr19	+	chr19:10381903-10394804	chr19:10381903-10385440		chr19:10385441-10394804	chr19:10394804-10394805		21;44
K	intron_retention	CUFF.548	chr19	+	chr19:50309199-50309375				chr19:50309198-50309199;chr19:50309375-50309376		1520;84
K	alternative_first_exon	CUFF.551	chr19	-	chr19:51528923-51530712;chr19:51528923-51529793;chr19:51528923-51529011	chr19:51528923-51531199	chr19:51530713-51530971;chr19:51529794-51530500;chr19:51529012-51529107	chr19:51531200-51531394			220;44
K	alternative_first_exon	CUFF.523	chr19	-	chr19:20243397-20351308;chr19:20243397-20349096	chr19:20243397-20261169	chr19:20349097-20349343	chr19:20261170-20261357			140;43
N	coord_cassette	CUFF.521	chr19	+	chr19:17611442-17615263	chr19:17611442-17611520;chr19:17611686-17612081;chr19:17612229-17615263		chr19:17611521-17611685;chr19:17612082-17612228			27;120
K	intron_retention	CUFF.504	chr19	-	chr19:6375628-6375712				chr19:6375627-6375628;chr19:6375712-6375713		27;65
N	cassette	CUFF.515	chr19	-	chr19:14854597-14857707	chr19:14854597-14857043;chr19:14857136-14857707		chr19:14857044-14857135			40;506
N	alternative_acceptor	CUFF.551	chr19	-	chr19:51528923-51529793	chr19:51528955-51529793		chr19:51528923-51528954	chr19:51528922-51528923		160;13
K	alternative_acceptor	CUFF.551	chr19	-	chr19:51525921-51526347	chr19:51525954-51526347		chr19:51525921-51525953	chr19:51525920-51525921		63;174
K	jcn_only_AD	CUFF.539	chr19	-	chr19:41938314-41939441	chr19:41938314-41939176					370;719
N	alternative_acceptor	CUFF.542	chr19	+	chr19:44771115-44777457;chr19:44771115-44771532	chr19:44771115-44777051		chr19:44771533-44777051;chr19:44777052-44777457	chr19:44777051-44777052;chr19:44777457-44777458		84;88
N	jcn_only_AA	CUFF.521	chr19	+	chr19:17597767-17597982	chr19:17597767-17597908		chr19:17597909-17597982	chr19:17597982-17597983		61;33
N	alternative_donor	CUFF.495	chr19	+	chr19:1440241-1440347	chr19:1440253-1440347		chr19:1440241-1440252	chr19:1440240-1440241		126;866
K	mutually_exclusive	CUFF.550	chr19	-	chr19:51483744-51485582,chr19:51485714-51487106	chr19:51483744-51485022,chr19:51485171-51487106	chr19:51485583-51485713	chr19:51485023-51485170			143;87
K	alternative_acceptor	CUFF.548	chr19	+	chr19:50308834-50308981	chr19:50308834-50308917		chr19:50308918-50308981	chr19:50308981-50308982		1385;118
N	jcn_only_AD		chr19	-	chr19:39924402-39926297	chr19:39924402-39926246		chr19:39926247-39926297	chr19:39926297-39926298		152;1068
K	intron_retention	CUFF.520	chr19	+	chr19:17449261-17449347				chr19:17449260-17449261;chr19:17449347-17449348		1983;63
K	alternative_donor	CUFF.498	chr19	+	chr19:4323144-4323344;chr19:4323235-4323344	chr19:4323211-4323344		chr19:4323144-4323210;chr19:4323211-4323234	chr19:4323143-4323144;chr19:4323210-4323211		290;50
K	cassette	CUFF.547	chr19	-	chr19:49316606-49316919	chr19:49316606-49316712;chr19:49316810-49316919		chr19:49316713-49316809			55;55
K	alternative_last_exon	CUFF.526	chr19	-	chr19:21627226-21637184	chr19:21636580-21637184	chr19:21627043-21627225	chr19:21634794-21636579			67;185
N	coord_cassette	CUFF.515	chr19	-	chr19:14862484-14867049	chr19:14862484-14863140;chr19:14863339-14865765;chr19:14865940-14867049		chr19:14863141-14863338;chr19:14865766-14865939			28;306
N	alternative_acceptor	CUFF.511	chr19	-	chr19:11541841-11545593	chr19:11545352-11545593		chr19:11541841-11545351	chr19:11541840-11541841		168;4
K	alternative_acceptor	CUFF.505,CUFF.555	chr19	+	chr19:7075117-7075686	chr19:7075117-7075665		chr19:7075666-7075686	chr19:7075686-7075687		10;12
N	intron_retention	CUFF.521	chr19	+	chr19:17597767-17597908				chr19:17597766-17597767;chr19:17597908-17597909		33;49
K	alternative_first_exon	CUFF.516	chr19	+	chr19:16187508-16192722;chr19:16191253-16192722;chr19:16186983-16192722	chr19:16191886-16192722	chr19:16190850-16191252;chr19:16186857-16186982	chr19:16191725-16191885			454;231
K	intron_retention	CUFF.498	chr19	+	chr19:4310594-4311838				chr19:4310593-4310594;chr19:4311838-4311839		244;130
K	cassette	CUFF.547	chr19	-	chr19:49316606-49316919	chr19:49316606-49316689;chr19:49316810-49316919		chr19:49316690-49316809			55;41
K	intron_retention	CUFF.520	chr19	+	chr19:17447537-17447628				chr19:17447536-17447537;chr19:17447628-17447629		44;369
K	jcn_only_AD	CUFF.498	chr19	+	chr19:4323144-4323344;chr19:4323235-4323344	chr19:4323211-4323344		chr19:4323144-4323210;chr19:4323211-4323234	chr19:4323143-4323144;chr19:4323210-4323211		329;43
N	intron_retention		chr19	+	chr19:17448474-17448682				chr19:17448473-17448474;chr19:17448682-17448683		172;24
N	intron_retention		chr19	-	chr19:39924402-39926297				chr19:39924401-39924402;chr19:39926297-39926298		152;97
N	alternative_acceptor	CUFF.526	chr19	-	chr19:21632180-21636351	chr19:21636082-21636351		chr19:21632180-21636081	chr19:21632179-21632180		13;33
N	cassette	CUFF.515	chr19	-	chr19:14863339-14866465;chr19:14863339-14867049	chr19:14863339-14865765;chr19:14865940-14866465,chr19:14865940-14867049		chr19:14865766-14865939			72;451
N	jcn_only_AA	CUFF.542	chr19	+	chr19:44771115-44777457;chr19:44771115-44777051	chr19:44771115-44771532		chr19:44771533-44777051;chr19:44777052-44777457	chr19:44777051-44777052;chr19:44777457-44777458		164;29
K	alternative_first_exon	CUFF.539,CUFF.551	chr19	-	chr19:41944320-41946385;chr19:41944320-41945786	chr19:41944320-41945378	chr19:41945787-41946383	chr19:41945379-41945477			401;168
K	alternative_first_exon	CUFF.511,CUFF.549	chr19	-	chr19:11541841-11546510	chr19:11541841-11545593	chr19:11546511-11546692	chr19:11545594-11545925			70;185
N	alternative_acceptor	CUFF.558	chr19	+	chr19:54648069-54649330;chr19:54648069-54649277	chr19:54648069-54649333		chr19:54649278-54649330;chr19:54649331-54649333	chr19:54649330-54649331;chr19:54649333-54649334		84;78
K	mutually_exclusive	CUFF.562	chr19	+	chr19:55087577-55098476,chr19:55098528-55098667	chr19:55087577-55088931,chr19:55089191-55098667	chr19:55098477-55098527	chr19:55088932-55089190			90;143
K	intron_retention	CUFF.548	chr19	+	chr19:50305857-50306205				chr19:50305856-50305857;chr19:50306205-50306206		179;16
K	alternative_first_exon	CUFF.514	chr19	-	chr19:14436244-14474683	chr19:14436244-14458126	chr19:14474684-14474802	chr19:14458127-14458221			25;70
N	jcn_only_AD	CUFF.529	chr19	-	chr19:33882386-33892626;chr19:33882386-33886015	chr19:33882386-33886995		chr19:33886016-33886995;chr19:33886996-33892626	chr19:33886995-33886996;chr19:33892626-33892627		624;69
N	jcn_only_AA	CUFF.495	chr19	+	chr19:1438892-1439714;chr19:1438892-1440017;chr19:1438892-1439604;chr19:1438892-1439959;chr19:1438892-1439966	chr19:1438892-1440024		chr19:1439605-1439714;chr19:1439715-1439959;chr19:1439960-1439966;chr19:1439967-1440017;chr19:1440018-1440024	chr19:1439714-1439715;chr19:1439959-1439960;chr19:1439966-1439967;chr19:1440017-1440018;chr19:1440024-1440025		1634;60
N	jcn_only_AD	CUFF.507,CUFF.529	chr19	-	chr19:33954969-33968951	chr19:33954969-33967985		chr19:33967986-33968951	chr19:33968951-33968952		5785;28
N	jcn_only_AD	CUFF.564	chr19	-	chr19:6176455-6199490	chr19:6176455-6199486					24;21
N	intron_retention		chr19	+	chr19:16212220-16212869				chr19:16212219-16212220;chr19:16212869-16212870		116;135
N	intron_retention		chr19	+	chr19:18119394-18119519				chr19:18119393-18119394;chr19:18119519-18119520		172;70
K	jcn_only_AA	CUFF.547	chr19	-	chr19:49335990-49337532	chr19:49336010-49337532		chr19:49335990-49336009	chr19:49335989-49335990		74;36
K	alternative_first_exon	CUFF.521	chr19	+	chr19:17581517-17598268	chr19:17598145-17598268	chr19:17581275-17581516	chr19:17597372-17598144			96;178
N	jcn_only_AD	CUFF.520	chr19	+	chr19:17445921-17448816;chr19:17448386-17448816;chr19:17447844-17448816;chr19:17448457-17448816;chr19:17448079-17448816;chr19:17448474-17448816	chr19:17447967-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		1612;16
K	intron_retention	CUFF.520	chr19	+	chr19:17449836-17449931				chr19:17449835-17449836;chr19:17449931-17449932		373;320
N	alternative_acceptor	CUFF.555	chr19	+	chr19:52917622-52918376	chr19:52917622-52918191		chr19:52918192-52918376	chr19:52918376-52918377		16;10
K	intron_retention	CUFF.495	chr19	+	chr19:1438428-1438809				chr19:1438427-1438428;chr19:1438809-1438810		49;451
K	jcn_only_AD	CUFF.555	chr19	+	chr19:52901274-52901619;chr19:52901158-52901619	chr19:52901154-52901619		chr19:52901154-52901157;chr19:52901158-52901273	chr19:52901153-52901154;chr19:52901157-52901158		269;459
N	cassette	CUFF.521	chr19	+	chr19:17611442-17615263	chr19:17611442-17611520;chr19:17611686-17615263		chr19:17611521-17611685			27;151
K	alternative_last_exon	CUFF.523	chr19	-	chr19:20243397-20349096;chr19:20339293-20349096	chr19:20287619-20349096	chr19:20243270-20243396;chr19:20338732-20339292	chr19:20286842-20287618			248;58
N	alternative_donor		chr19	-	chr19:33882386-33886995;chr19:33882386-33886015	chr19:33882386-33892626		chr19:33886016-33886995;chr19:33886996-33892626	chr19:33886995-33886996;chr19:33892626-33892627		4;572
N	intron_retention		chr19	+	chr19:17448457-17448816				chr19:17448456-17448457;chr19:17448816-17448817		27;261
K	cassette	CUFF.547	chr19	-	chr19:49318399-49335922	chr19:49318399-49334924;chr19:49335017-49335922		chr19:49334925-49335016			24;66
K	intron_retention	CUFF.510	chr19	+	chr19:11474496-11474836				chr19:11474495-11474496;chr19:11474836-11474837		23;2993
N	jcn_only_AD	CUFF.509	chr19	+	chr19:11041001-11044036	chr19:11042937-11044036		chr19:11041001-11042936	chr19:11041000-11041001		129;139
N	alternative_donor	CUFF.498	chr19	+	chr19:4306039-4306194	chr19:4306067-4306194		chr19:4306039-4306066	chr19:4306038-4306039		576;13
K	intron_retention		chr19	+	chr19:1438892-1440017				chr19:1438891-1438892;chr19:1440017-1440018		1220;211
K	cassette	CUFF.527	chr19	+	chr19:32851525-32873372	chr19:32851525-32871514;chr19:32871527-32873372		chr19:32871515-32871526			34;8
N	jcn_only_AA	CUFF.558	chr19	+	chr19:54657578-54657680;chr19:54657578-54659046	chr19:54657578-54658995		chr19:54657681-54658995;chr19:54658996-54659046	chr19:54658995-54658996;chr19:54659046-54659047		244;32
N	jcn_only_AD	CUFF.498	chr19	+	chr19:4306039-4306194	chr19:4306067-4306194		chr19:4306039-4306066	chr19:4306038-4306039		576;27
N	coord_cassette	CUFF.546	chr19	-	chr19:49303555-49314240	chr19:49303555-49309773;chr19:49309975-49310256;chr19:49310332-49314240		chr19:49309774-49309974;chr19:49310257-49310331			108;267
K	alternative_acceptor	CUFF.553	chr19	+	chr19:52085136-52092800	chr19:52085136-52089879		chr19:52089880-52092800	chr19:52092800-52092801		87;83
K	alternative_donor	CUFF.519	chr19	-	chr19:16593597-16594740	chr19:16593597-16594572		chr19:16594573-16594740	chr19:16594740-16594741		26;80
K	intron_retention	CUFF.548	chr19	+	chr19:50304879-50304978				chr19:50304878-50304879;chr19:50304978-50304979		1198;15
K	intron_retention	CUFF.548	chr19	+	chr19:50304257-50304659				chr19:50304256-50304257;chr19:50304659-50304660		1028;19
K	alternative_donor	CUFF.537	chr19	-	chr19:41355886-41356151	chr19:41355886-41356141		chr19:41356142-41356151	chr19:41356151-41356152		13;98
N	jcn_only_AD	CUFF.495	chr19	+	chr19:1438892-1440017	chr19:1439826-1440017		chr19:1438892-1439825	chr19:1438891-1438892		1220;166
K	intron_retention		chr19	-	chr19:6026249-6039990				chr19:6026248-6026249;chr19:6039990-6039991		197;44
N	cassette	CUFF.555	chr19	+	chr19:52909897-52918191;chr19:52909897-52918376	chr19:52909897-52917456;chr19:52917622-52918191,chr19:52917622-52918376		chr19:52917457-52917621			29;27
N	alternative_acceptor	CUFF.523	chr19	-	chr19:20236319-20243269	chr19:20236593-20243269		chr19:20236319-20236592	chr19:20236318-20236319		27;204
K	alternative_donor	CUFF.495	chr19	+	chr19:1438428-1438805	chr19:1438580-1438805		chr19:1438428-1438579	chr19:1438427-1438428		390;552
N	jcn_only_AD	CUFF.558	chr19	+	chr19:54656737-54657451	chr19:54656820-54657451		chr19:54656737-54656819	chr19:54656736-54656737		87;43
K	intron_retention	CUFF.546	chr19	-	chr19:49300591-49302931				chr19:49300590-49300591;chr19:49302931-49302932		334;155
N	intron_retention		chr19	+	chr19:44764092-44768480				chr19:44764091-44764092;chr19:44768480-44768481		38;79
K	jcn_only_AD	CUFF.564	chr19	-	chr19:56344282-56348075	chr19:56344282-56347701		chr19:56347702-56348075	chr19:56348075-56348076		172;52
K	alternative_first_exon	CUFF.551	chr19	-	chr19:51528923-51530712;chr19:51528923-51529793;chr19:51528923-51531199	chr19:51528923-51529011	chr19:51530713-51530971;chr19:51529794-51530500;chr19:51531200-51531394	chr19:51529012-51529107			213;51
K	jcn_only_AD	CUFF.537	chr19	-	chr19:41355886-41356151	chr19:41355886-41356141		chr19:41356142-41356151	chr19:41356151-41356152		13;198
N	alternative_donor	CUFF.516	chr19	+	chr19:16178549-16186856;chr19:16178773-16186856	chr19:16186520-16186856		chr19:16178549-16178772;chr19:16178773-16186519	chr19:16178548-16178549;chr19:16178772-16178773		306;5
N	intron_retention		chr19	-	chr19:6191606-6191875				chr19:6191605-6191606;chr19:6191875-6191876		76;64
K	intron_retention	CUFF.558	chr19	+	chr19:54657578-54659046				chr19:54657577-54657578;chr19:54659046-54659047		221;86
N	jcn_only_AA	CUFF.543	chr19	+	chr19:45251386-45254483	chr19:45251386-45251951		chr19:45251952-45254483	chr19:45254483-45254484		87;27
K	intron_retention	CUFF.522	chr19	+	chr19:18119928-18120400				chr19:18119927-18119928;chr19:18120400-18120401		213;98
N	alternative_donor	CUFF.507,CUFF.529	chr19	-	chr19:33954969-33968951	chr19:33954969-33967985		chr19:33967986-33968951	chr19:33968951-33968952		5785;11
K	jcn_only_AD	CUFF.552	chr19	-	chr19:51537396-51537840	chr19:51537396-51537680		chr19:51537681-51537840	chr19:51537840-51537841		401;202
K	alternative_donor	CUFF.507	chr19	-	chr19:10207250-10213243	chr19:10207250-10213227		chr19:10213228-10213243	chr19:10213243-10213244		41;32
N	alternative_acceptor	CUFF.558	chr19	+	chr19:54657578-54658995;chr19:54657578-54659046	chr19:54657578-54657680		chr19:54657681-54658995;chr19:54658996-54659046	chr19:54658995-54658996;chr19:54659046-54659047		257;104
N	alternative_donor	CUFF.520	chr19	+	chr19:17445921-17448816;chr19:17447844-17448816;chr19:17448457-17448816;chr19:17448079-17448816;chr19:17448474-17448816;chr19:17447967-17448816	chr19:17448386-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		296;49
K	intron_retention	CUFF.535	chr19	+	chr19:40486054-40486192				chr19:40486053-40486054;chr19:40486192-40486193		197;183
N	jcn_only_AA	CUFF.558	chr19	+	chr19:54657578-54658995;chr19:54657578-54659046	chr19:54657578-54657680		chr19:54657681-54658995;chr19:54658996-54659046	chr19:54658995-54658996;chr19:54659046-54659047		253;23
N	jcn_only_AA	CUFF.510	chr19	+	chr19:11468416-11470146;chr19:11468416-11470207	chr19:11468416-11470282		chr19:11470147-11470207;chr19:11470208-11470282	chr19:11470207-11470208;chr19:11470282-11470283		179;39
N	intron_retention		chr19	+	chr19:11474512-11474836				chr19:11474511-11474512;chr19:11474836-11474837		16;3019
K	intron_retention	CUFF.548	chr19	+	chr19:50308834-50308981				chr19:50308833-50308834;chr19:50308981-50308982		1385;63
N	alternative_donor	CUFF.542	chr19	+	chr19:44764362-44768466;chr19:44764092-44768466	chr19:44764156-44768466		chr19:44764092-44764155;chr19:44764156-44764361	chr19:44764091-44764092;chr19:44764155-44764156		102;96
N	jcn_only_AA	CUFF.520,CUFF.521	chr19	+	chr19:17581517-17597371;chr19:17581517-17598268	chr19:17581517-17594690					178;23
N	intron_retention	CUFF.534	chr19	-	chr19:39924059-39924157				chr19:39924058-39924059;chr19:39924157-39924158		121;51
K	intron_retention	CUFF.507	chr19	-	chr19:10207250-10213243				chr19:10207249-10207250;chr19:10213243-10213244		41;12
K	intron_retention	CUFF.520	chr19	+	chr19:17449381-17449989				chr19:17449380-17449381;chr19:17449989-17449990		520;415
N	alternative_donor	CUFF.495	chr19	+	chr19:1438892-1440017	chr19:1439826-1440017		chr19:1438892-1439825	chr19:1438891-1438892		1220;273
N	alternative_acceptor	CUFF.558	chr19	+	chr19:54648069-54649330;chr19:54648069-54649333	chr19:54648069-54649277		chr19:54649278-54649330;chr19:54649331-54649333	chr19:54649330-54649331;chr19:54649333-54649334		94;68
N	alternative_acceptor	CUFF.536	chr19	-	chr19:40909770-40913812	chr19:40913627-40913812		chr19:40909770-40913626	chr19:40909769-40909770		3;3
N	mutually_exclusive	CUFF.562	chr19	+	chr19:55084903-55085542,chr19:55085579-55085767	chr19:55084903-55085164,chr19:55085380-55085767	chr19:55085543-55085578	chr19:55085165-55085379			156;18
N	jcn_only_AD	CUFF.543	chr19	+	chr19:45254638-45259488	chr19:45258732-45259488		chr19:45254638-45258731	chr19:45254637-45254638		224;26
N	jcn_only_AA		chr19	+	chr19:11468416-11470146;chr19:11468416-11470282	chr19:11468416-11470207		chr19:11470147-11470207;chr19:11470208-11470282	chr19:11470207-11470208;chr19:11470282-11470283		73;145
K	intron_retention	CUFF.522	chr19	+	chr19:18120849-18121004				chr19:18120848-18120849;chr19:18121004-18121005		187;94
K	intron_retention	CUFF.500	chr19	-	chr19:6008236-6010146				chr19:6008235-6008236;chr19:6010146-6010147		477;106
K	intron_retention	CUFF.495	chr19	+	chr19:1438580-1438805				chr19:1438579-1438580;chr19:1438805-1438806		491;191
K	jcn_only_AA	CUFF.505,CUFF.555	chr19	+	chr19:7075117-7075686	chr19:7075117-7075665		chr19:7075666-7075686	chr19:7075686-7075687		10;25
N	jcn_only_AD	CUFF.529,CUFF.534	chr19	-	chr19:39924059-39924161;chr19:39924059-39924157	chr19:39924059-39924133		chr19:39924134-39924157;chr19:39924158-39924161	chr19:39924157-39924158;chr19:39924161-39924162		1620;28
N	alternative_donor	CUFF.534	chr19	-	chr19:39924059-39924161;chr19:39924059-39924133	chr19:39924059-39924157		chr19:39924134-39924157;chr19:39924158-39924161	chr19:39924157-39924158;chr19:39924161-39924162		1515;67
K	intron_retention	CUFF.539	chr19	-	chr19:41938314-41939441				chr19:41938313-41938314;chr19:41939441-41939442		370;48
N	jcn_only_AA	CUFF.555	chr19	+	chr19:52917622-52918376	chr19:52917622-52918191		chr19:52918192-52918376	chr19:52918376-52918377		16;18
K	alternative_acceptor	CUFF.515	chr19	-	chr19:14866657-14867049	chr19:14866690-14867049		chr19:14866657-14866689	chr19:14866656-14866657		131;94
N	jcn_only_AA		chr19	+	chr19:1438892-1439714;chr19:1438892-1439604;chr19:1438892-1439959;chr19:1438892-1440024;chr19:1438892-1439966	chr19:1438892-1440017		chr19:1439605-1439714;chr19:1439715-1439959;chr19:1439960-1439966;chr19:1439967-1440017;chr19:1440018-1440024	chr19:1439714-1439715;chr19:1439959-1439960;chr19:1439966-1439967;chr19:1440017-1440018;chr19:1440024-1440025		473;1220
N	alternative_donor	CUFF.542	chr19	+	chr19:44764156-44768466;chr19:44764362-44768466	chr19:44764092-44768466		chr19:44764092-44764155;chr19:44764156-44764361	chr19:44764091-44764092;chr19:44764155-44764156		184;14
N	jcn_only_AA		chr19	+	chr19:44764092-44768480	chr19:44764092-44768466		chr19:44768467-44768480	chr19:44768480-44768481		38;14
N	jcn_only_AA	CUFF.542	chr19	+	chr19:4304759-4306020;chr19:4304759-4305981	chr19:4304759-4305942		chr19:4305943-4305981;chr19:4305982-4306020	chr19:4305981-4305982;chr19:4306020-4306021		80;677
K	intron_retention	CUFF.548	chr19	+	chr19:50309035-50309128				chr19:50309034-50309035;chr19:50309128-50309129		1556;45
N	alternative_acceptor	CUFF.510	chr19	+	chr19:11468416-11470146;chr19:11468416-11470207	chr19:11468416-11470282		chr19:11470147-11470207;chr19:11470208-11470282	chr19:11470207-11470208;chr19:11470282-11470283		125;39
K	cassette	CUFF.555	chr19	+	chr19:52905282-52909159	chr19:52905282-52905681;chr19:52905799-52909159		chr19:52905682-52905798			699;162
K	cassette	CUFF.564	chr19	-	chr19:56307617-56312937	chr19:56307617-56309594;chr19:56309671-56312937		chr19:56309595-56309670			184;34
N	alternative_donor	CUFF.509	chr19	+	chr19:11041001-11044036	chr19:11042937-11044036		chr19:11041001-11042936	chr19:11041000-11041001		129;44
N	coord_cassette	CUFF.529	chr19	-	chr19:33904550-33968951	chr19:33904550-33953900;chr19:33953948-33954892;chr19:33954969-33968951		chr19:33953901-33953947;chr19:33954893-33954968			371;6674
K	intron_retention	CUFF.553	chr19	+	chr19:52076655-52084643				chr19:52076654-52076655;chr19:52084643-52084644		137;27
K	alternative_donor	CUFF.564	chr19	-	chr19:56344282-56348075	chr19:56344282-56347701		chr19:56347702-56348075	chr19:56348075-56348076		172;60
K	cassette	CUFF.521	chr19	+	chr19:17598339-17599816	chr19:17598339-17599656;chr19:17599749-17599816		chr19:17599657-17599748			51;226
N	jcn_only_AD	CUFF.515	chr19	-	chr19:14885119-14887537	chr19:14885119-14887215		chr19:14887216-14887537	chr19:14887537-14887538		401;23
K	intron_retention	CUFF.531	chr19	+	chr19:35642232-35642342				chr19:35642231-35642232;chr19:35642342-35642343		487;115
N	jcn_only_AA	CUFF.498	chr19	+	chr19:4304759-4306020;chr19:4304759-4305942	chr19:4304759-4305981		chr19:4305943-4305981;chr19:4305982-4306020	chr19:4305981-4305982;chr19:4306020-4306021		713;44
N	alternative_acceptor	CUFF.495	chr19	+	chr19:1438892-1439714;chr19:1438892-1440017;chr19:1438892-1439604;chr19:1438892-1439959;chr19:1438892-1439966	chr19:1438892-1440024		chr19:1439605-1439714;chr19:1439715-1439959;chr19:1439960-1439966;chr19:1439967-1440017;chr19:1440018-1440024	chr19:1439714-1439715;chr19:1439959-1439960;chr19:1439966-1439967;chr19:1440017-1440018;chr19:1440024-1440025		1028;60
N	cassette	CUFF.529	chr19	-	chr19:33984244-34001933	chr19:33984244-33991843;chr19:33991908-34001933		chr19:33991844-33991907			51;409
N	alternative_donor	CUFF.543	chr19	+	chr19:45254638-45259488	chr19:45258732-45259488		chr19:45254638-45258731	chr19:45254637-45254638		224;5
N	jcn_only_AA		chr19	-	chr19:6192041-6199486;chr19:6148341-6199486	chr19:6176455-6199486					86;21
N	jcn_only_AA		chr19	-	chr19:6192065-6199490;chr19:6176455-6199490	chr19:6192041-6199490					70;96
K	alternative_acceptor	CUFF.542,CUFF.558	chr19	+	chr19:44768529-44770350	chr19:44768529-44770307		chr19:44770308-44770350	chr19:44770350-44770351		206;51
N	cassette	CUFF.522	chr19	+	chr19:18118181-18119519	chr19:18118181-18118398;chr19:18118652-18119519		chr19:18118399-18118651			30;1438
N	alternative_donor	CUFF.542	chr19	+	chr19:44764156-44768466;chr19:44764092-44768466	chr19:44764362-44768466		chr19:44764092-44764155;chr19:44764156-44764361	chr19:44764091-44764092;chr19:44764155-44764156		110;88
K	alternative_last_exon	CUFF.523	chr19	-	chr19:20287619-20349096;chr19:20243397-20349096	chr19:20339293-20349096	chr19:20286842-20287618;chr19:20243270-20243396	chr19:20338732-20339292			135;171
K	cassette	CUFF.539	chr19	-	chr19:41939579-41945378	chr19:41939579-41944122;chr19:41944320-41945378		chr19:41944123-41944319			397;783
N	intron_retention		chr19	+	chr19:1440241-1440347				chr19:1440240-1440241;chr19:1440347-1440348		126;197
K	jcn_only_AA	CUFF.548	chr19	+	chr19:50308834-50308981	chr19:50308834-50308917		chr19:50308918-50308981	chr19:50308981-50308982		1385;193
N	jcn_only_AA	CUFF.511	chr19	-	chr19:11541841-11545593	chr19:11545352-11545593		chr19:11541841-11545351	chr19:11541840-11541841		168;31
N	jcn_only_AA	CUFF.516	chr19	+	chr19:16204564-16212073	chr19:16204564-16206073		chr19:16206074-16212073	chr19:16212073-16212074		333;111
K	alternative_donor	CUFF.531	chr19	+	chr19:35642377-35642535	chr19:35642386-35642535		chr19:35642377-35642385	chr19:35642376-35642377		430;197
N	jcn_only_AA	CUFF.521	chr19	+	chr19:17581517-17594690;chr19:17581517-17598268	chr19:17581517-17597371					109;92
N	jcn_only_AA	CUFF.495	chr19	+	chr19:1438892-1439714;chr19:1438892-1440017;chr19:1438892-1439959;chr19:1438892-1440024;chr19:1438892-1439966	chr19:1438892-1439604		chr19:1439605-1439714;chr19:1439715-1439959;chr19:1439960-1439966;chr19:1439967-1440017;chr19:1440018-1440024	chr19:1439714-1439715;chr19:1439959-1439960;chr19:1439966-1439967;chr19:1440017-1440018;chr19:1440024-1440025		1669;24
K	alternative_first_exon	CUFF.551	chr19	-	chr19:51528923-51530712;chr19:51528923-51529011;chr19:51528923-51531199	chr19:51528923-51529793	chr19:51530713-51530971;chr19:51529012-51529107;chr19:51531200-51531394	chr19:51529794-51530500			173;91
N	jcn_only_AA	CUFF.523	chr19	-	chr19:20236319-20243269	chr19:20236593-20243269		chr19:20236319-20236592	chr19:20236318-20236319		27;222
K	cassette	CUFF.520	chr19	+	chr19:17449551-17449931	chr19:17449551-17449762;chr19:17449836-17449931		chr19:17449763-17449835			18;452
K	jcn_only_AA	CUFF.495	chr19	+	chr19:1438428-1438809	chr19:1438428-1438805		chr19:1438806-1438809	chr19:1438809-1438810		49;390
K	cassette	CUFF.548	chr19	+	chr19:50305399-50306205	chr19:50305399-50305790;chr19:50305857-50306205		chr19:50305791-50305856			1261;106
K	intron_retention	CUFF.534	chr19	-	chr19:39924210-39924304				chr19:39924209-39924210;chr19:39924304-39924305		528;944
N	jcn_only_AA		chr19	-	chr19:6192041-6199486;chr19:6176455-6199486	chr19:6148341-6199486					45;61
N	intron_retention		chr19	+	chr19:4311877-4323568				chr19:4311876-4311877;chr19:4323568-4323569		41;157
K	cassette	CUFF.562	chr19	+	chr19:55084903-55085542	chr19:55084903-55085297;chr19:55085380-55085542		chr19:55085298-55085379			173;190
K	alternative_donor	CUFF.552	chr19	-	chr19:51537396-51537840	chr19:51537396-51537680		chr19:51537681-51537840	chr19:51537840-51537841		401;141
N	alternative_donor	CUFF.520	chr19	+	chr19:17445921-17448816;chr19:17448386-17448816;chr19:17447844-17448816;chr19:17448457-17448816;chr19:17448079-17448816;chr19:17447967-17448816	chr19:17448474-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		212;133
K	alternative_first_exon	CUFF.549	chr19	-	chr19:50548045-50554138	chr19:50548045-50551215	chr19:50554139-50554319	chr19:50551216-50551342			55;62
K	intron_retention	CUFF.521	chr19	+	chr19:17597767-17597982				chr19:17597766-17597767;chr19:17597982-17597983		61;65
N	alternative_acceptor	CUFF.520	chr19	+	chr19:17448474-17448816;chr19:17448474-17448707	chr19:17448474-17448682		chr19:17448683-17448707;chr19:17448708-17448816	chr19:17448707-17448708;chr19:17448816-17448817		738;127
K	jcn_only_AD	CUFF.495	chr19	+	chr19:1438428-1438805	chr19:1438580-1438805		chr19:1438428-1438579	chr19:1438427-1438428		390;491
K	jcn_only_AD	CUFF.507	chr19	-	chr19:10207250-10213243	chr19:10207250-10213227		chr19:10213228-10213243	chr19:10213243-10213244		41;59
N	intron_retention		chr19	+	chr19:1438892-1439604				chr19:1438891-1438892;chr19:1439604-1439605		24;163
N	jcn_only_AA	CUFF.551	chr19	-	chr19:51528923-51529793	chr19:51528955-51529793		chr19:51528923-51528954	chr19:51528922-51528923		160;28
N	jcn_only_AD	CUFF.542	chr19	+	chr19:44764156-44768466;chr19:44764092-44768466	chr19:44764362-44768466		chr19:44764092-44764155;chr19:44764156-44764361	chr19:44764091-44764092;chr19:44764155-44764156		161;128
N	intron_retention		chr19	+	chr19:17447967-17448816				chr19:17447966-17447967;chr19:17448816-17448817		16;307
N	alternative_donor	CUFF.542	chr19	+	chr19:44771115-44777051	chr19:44771298-44777051		chr19:44771115-44771297	chr19:44771114-44771115		90;24
N	alternative_donor	CUFF.529	chr19	-	chr19:33882386-33892626;chr19:33882386-33886995	chr19:33882386-33886015		chr19:33886016-33886995;chr19:33886996-33892626	chr19:33886995-33886996;chr19:33892626-33892627		575;1
N	jcn_only_AD	CUFF.543	chr19	+	chr19:45261671-45261980	chr19:45261731-45261980		chr19:45261671-45261730	chr19:45261670-45261671		276;61
N	coord_cassette	CUFF.500	chr19	-	chr19:6026249-6110403	chr19:6026249-6039990;chr19:6040253-6042054;chr19:6042135-6047417;chr19:6047516-6110403		chr19:6039991-6040252;chr19:6042055-6042134;chr19:6047418-6047515			331;208
K	intron_retention	CUFF.510	chr19	+	chr19:11470633-11471892				chr19:11470632-11470633;chr19:11471892-11471893		88;207
K	alternative_last_exon	CUFF.499	chr19	-	chr19:5893302-5896463	chr19:5894866-5896463	chr19:5891287-5893301	chr19:5894589-5894865			34;805
K	jcn_only_AD	CUFF.519	chr19	-	chr19:16593597-16594740	chr19:16593597-16594572		chr19:16594573-16594740	chr19:16594740-16594741		26;86
N	alternative_donor	CUFF.520	chr19	+	chr19:17445921-17448816;chr19:17448386-17448816;chr19:17447844-17448816;chr19:17448079-17448816;chr19:17448474-17448816;chr19:17447967-17448816	chr19:17448457-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		340;5
K	jcn_only_AD	CUFF.547	chr19	-	chr19:49316606-49316712	chr19:49316606-49316689		chr19:49316690-49316712	chr19:49316712-49316713		60;28
N	jcn_only_AD	CUFF.520	chr19	+	chr19:17445921-17448816;chr19:17448386-17448816;chr19:17448457-17448816;chr19:17448079-17448816;chr19:17448474-17448816;chr19:17447967-17448816	chr19:17447844-17448816		chr19:17445921-17447843;chr19:17447844-17447966;chr19:17447967-17448078;chr19:17448079-17448385;chr19:17448386-17448456;chr19:17448457-17448473	chr19:17445920-17445921;chr19:17447843-17447844;chr19:17447966-17447967;chr19:17448078-17448079;chr19:17448385-17448386;chr19:17448456-17448457		1201;428
N	alternative_donor	CUFF.534	chr19	-	chr19:39924059-39924133;chr19:39924059-39924157	chr19:39924059-39924161		chr19:39924134-39924157;chr19:39924158-39924161	chr19:39924157-39924158;chr19:39924161-39924162		84;1498
N	jcn_only_AA		chr19	-	chr19:6192041-6199490;chr19:6192065-6199490	chr19:6176455-6199490					141;24
K	cassette	CUFF.515	chr19	-	chr19:14876617-14877789	chr19:14876617-14877046;chr19:14877194-14877789		chr19:14877047-14877193			174;124
N	jcn_only_AA		chr19	-	chr19:6192041-6199490;chr19:6176455-6199490	chr19:6192065-6199490					121;45
N	jcn_only_AA	CUFF.510	chr19	+	chr19:11468416-11470282;chr19:11468416-11470207	chr19:11468416-11470146		chr19:11470147-11470207;chr19:11470208-11470282	chr19:11470207-11470208;chr19:11470282-11470283		184;35
K	intron_retention	CUFF.558	chr19	+	chr19:54647486-54647741				chr19:54647485-54647486;chr19:54647741-54647742		178;8
K	alternative_donor	CUFF.547	chr19	-	chr19:49316606-49316712	chr19:49316606-49316689		chr19:49316690-49316712	chr19:49316712-49316713		60;14
K	intron_retention	CUFF.515	chr19	-	chr19:14876617-14883153				chr19:14876616-14876617;chr19:14883153-14883154		21;32
K	alternative_donor	CUFF.497	chr19	-	chr19:2427323-2427456	chr19:2427323-2427411		chr19:2427412-2427456	chr19:2427456-2427457		45;9
K	intron_retention	CUFF.566	chr19	+	chr19:58965712-58966549				chr19:58965711-58965712;chr19:58966549-58966550	chr19:58965595-58965711;chr19:58966550-58969200	392;1011
N	jcn_only_AA		chr19	+	chr19:17447967-17448816	chr19:17447967-17448682		chr19:17448683-17448816	chr19:17448816-17448817		16;160
K	intron_retention	CUFF.516	chr19	+	chr19:16191886-16192722				chr19:16191885-16191886;chr19:16192722-16192723		268;115
K	alternative_acceptor	CUFF.498	chr19	+	chr19:4317278-4318380	chr19:4317278-4318342		chr19:4318343-4318380	chr19:4318380-4318381		35;191
K	alternative_donor	CUFF.555	chr19	+	chr19:52901274-52901619;chr19:52901158-52901619	chr19:52901154-52901619		chr19:52901154-52901157;chr19:52901158-52901273	chr19:52901153-52901154;chr19:52901157-52901158		179;459
K	cassette	CUFF.532	chr19	+	chr19:36142252-36149495	chr19:36142252-36145472;chr19:36145574-36149495		chr19:36145473-36145573			268;362
K	cassette	CUFF.519	chr19	-	chr19:16596069-16606561	chr19:16596069-16601177;chr19:16601382-16606561		chr19:16601178-16601381			16;30
K	alternative_first_exon	CUFF.543	chr19	+	chr19:45251386-45254483	chr19:45252304-45254483	chr19:45250962-45251385	chr19:45251753-45252303			111;108
N	jcn_only_AA	CUFF.558	chr19	+	chr19:54648069-54649277;chr19:54648069-54649333	chr19:54648069-54649330		chr19:54649278-54649330;chr19:54649331-54649333	chr19:54649330-54649331;chr19:54649333-54649334		189;22
K	intron_retention	CUFF.555	chr19	+	chr19:52909897-52917456				chr19:52909896-52909897;chr19:52917456-52917457		16;73
K	intron_retention	CUFF.543	chr19	+	chr19:45260673-45260902				chr19:45260672-45260673;chr19:45260902-45260903		218;111
N	intron_retention		chr19	+	chr19:17448474-17448816				chr19:17448473-17448474;chr19:17448816-17448817		611;192
K	intron_retention	CUFF.521	chr19	+	chr19:17599927-17608063				chr19:17599926-17599927;chr19:17608063-17608064		367;5
K	intron_retention	CUFF.535	chr19	+	chr19:40485892-40485976				chr19:40485891-40485892;chr19:40485976-40485977		433;21
N	intron_retention		chr19	+	chr19:45261731-45261980				chr19:45261730-45261731;chr19:45261980-45261981		61;258
K	alternative_last_exon	CUFF.523	chr19	-	chr19:20287619-20349096;chr19:20339293-20349096	chr19:20243397-20349096	chr19:20286842-20287618;chr19:20338732-20339292	chr19:20243270-20243396			229;77
K	alternative_donor	CUFF.498	chr19	+	chr19:4323235-4323344;chr19:4323211-4323344	chr19:4323144-4323344		chr19:4323144-4323210;chr19:4323211-4323234	chr19:4323143-4323144;chr19:4323210-4323211		258;82
K	intron_retention	CUFF.520	chr19	+	chr19:17450409-17451852				chr19:17450408-17450409;chr19:17451852-17451853		784;134
K	intron_retention	CUFF.548	chr19	+	chr19:50285228-50296292				chr19:50285227-50285228;chr19:50296292-50296293		624;6
K	jcn_only_AD	CUFF.534,CUFF.552	chr19	-	chr19:51534178-51535131	chr19:51534178-51535035		chr19:51535036-51535131	chr19:51535131-51535132		78;182
N	alternative_acceptor	CUFF.510	chr19	+	chr19:11468416-11470282;chr19:11468416-11470207	chr19:11468416-11470146		chr19:11470147-11470207;chr19:11470208-11470282	chr19:11470207-11470208;chr19:11470282-11470283		142;22
K	intron_retention	CUFF.555	chr19	+	chr19:52909897-52918376				chr19:52909896-52909897;chr19:52918376-52918377		14;70
N	jcn_only_AD		chr19	-	chr19:6192041-6199490	chr19:6192041-6199486					96;24
N	jcn_only_AD	CUFF.534	chr19	-	chr19:39924059-39924161;chr19:39924059-39924133	chr19:39924059-39924157		chr19:39924134-39924157;chr19:39924158-39924161	chr19:39924157-39924158;chr19:39924161-39924162		1526;121
K	cassette	CUFF.564	chr19	-	chr19:56313106-56320134	chr19:56313106-56319218;chr19:56319381-56320134		chr19:56319219-56319380			70;136
K	jcn_only_AD	CUFF.497	chr19	-	chr19:2427323-2427456	chr19:2427323-2427411		chr19:2427412-2427456	chr19:2427456-2427457		45;15
K	jcn_only_AA	CUFF.515	chr19	-	chr19:14866657-14867049	chr19:14866690-14867049		chr19:14866657-14866689	chr19:14866656-14866657		131;157
K	cassette	CUFF.558	chr19	+	chr19:54656737-54657233	chr19:54656737-54656917;chr19:54657131-54657233		chr19:54656918-54657130			49;241
K	intron_retention	CUFF.526	chr19	-	chr19:21636580-21637184				chr19:21636579-21636580;chr19:21637184-21637185		285;10
N	cassette	CUFF.515	chr19	-	chr19:14862484-14867049	chr19:14862484-14863140;chr19:14863339-14867049		chr19:14863141-14863338			28;426
N	intron_retention		chr19	+	chr19:1438892-1439966				chr19:1438891-1438892;chr19:1439966-1439967		232;176
K	intron_retention	CUFF.539	chr19	-	chr19:41939340-41939441				chr19:41939339-41939340;chr19:41939441-41939442		1098;67
K	intron_retention	CUFF.548	chr19	+	chr19:50303275-50303353				chr19:50303274-50303275;chr19:50303353-50303354		988;29
K	intron_retention	CUFF.548	chr19	+	chr19:50309511-50309937				chr19:50309510-50309511;chr19:50309937-50309938		1639;60
K	intron_retention		chr19	-	chr19:39924402-39926246				chr19:39924401-39924402;chr19:39926246-39926247		1068;68
K	alternative_first_exon	CUFF.546	chr19	-	chr19:49311494-49314240	chr19:49311494-49314065	chr19:49314241-49314385	chr19:49314066-49314211			92;29
K	intron_retention	CUFF.558	chr19	+	chr19:54652479-54653294				chr19:54652478-54652479;chr19:54653294-54653295		211;9
N	jcn_only_AD	CUFF.521	chr19	+	chr19:17608274-17611086	chr19:17610764-17611086		chr19:17608274-17610763	chr19:17608273-17608274		186;29
K	intron_retention	CUFF.498	chr19	+	chr19:4306210-4323020				chr19:4306209-4306210;chr19:4323020-4323021		313;92
K	intron_retention	CUFF.526	chr19	-	chr19:21637275-21639262				chr19:21637274-21637275;chr19:21639262-21639263		441;7
K	intron_retention	CUFF.552	chr19	-	chr19:51532469-51532597				chr19:51532468-51532469;chr19:51532597-51532598		403;286
N	alternative_acceptor		chr19	+	chr19:17448474-17448816;chr19:17448474-17448682	chr19:17448474-17448707		chr19:17448683-17448707;chr19:17448708-17448816	chr19:17448707-17448708;chr19:17448816-17448817		738;127
K	alternative_last_exon	CUFF.539	chr19	-	chr19:41938968-41939441;chr19:41938314-41939441	chr19:41939340-41939441	chr19:41937223-41938313	chr19:41938678-41939339			990;1093
K	intron_retention	CUFF.516	chr19	+	chr19:16197351-16198836				chr19:16197350-16197351;chr19:16198836-16198837		853;43
N	coord_cassette	CUFF.515	chr19	-	chr19:14863339-14867049	chr19:14863339-14865765;chr19:14865940-14866465;chr19:14866690-14867049		chr19:14865766-14865939;chr19:14866466-14866689			62;265
K	intron_retention	CUFF.522	chr19	+	chr19:18121168-18121380				chr19:18121167-18121168;chr19:18121380-18121381		109;134
N	intron_retention		chr19	+	chr19:17448386-17448816				chr19:17448385-17448386;chr19:17448816-17448817		269;473
K	intron_retention	CUFF.535	chr19	+	chr19:40486362-40486568				chr19:40486361-40486362;chr19:40486568-40486569		307;49
K	alternative_first_exon	CUFF.520	chr19	+	chr19:17445932-17447628	chr19:17447537-17447628	chr19:17445644-17445931	chr19:17447426-17447536			39;30
N	cassette	CUFF.500	chr19	-	chr19:6040253-6044203	chr19:6040253-6042054;chr19:6042135-6044203		chr19:6042055-6042134			176;701
K	intron_retention	CUFF.526	chr19	-	chr19:21638407-21639262				chr19:21638406-21638407;chr19:21639262-21639263		121;3
N	alternative_acceptor	CUFF.498	chr19	+	chr19:4304759-4305981;chr19:4304759-4305942	chr19:4304759-4306020		chr19:4305943-4305981;chr19:4305982-4306020	chr19:4305981-4305982;chr19:4306020-4306021		220;37
K	alternative_acceptor	CUFF.520	chr19	+	chr19:17450409-17451915	chr19:17450409-17451852		chr19:17451853-17451915	chr19:17451915-17451916		129;570
N	alternative_acceptor	CUFF.515	chr19	-	chr19:14847057-14854231	chr19:14852899-14854231		chr19:14847057-14852898	chr19:14847056-14847057		534;21
K	intron_retention	CUFF.522	chr19	+	chr19:18120504-18120591				chr19:18120503-18120504;chr19:18120591-18120592		254;61
K	alternative_donor	CUFF.555	chr19	+	chr19:52901274-52901619;chr19:52901154-52901619	chr19:52901158-52901619		chr19:52901154-52901157;chr19:52901158-52901273	chr19:52901153-52901154;chr19:52901157-52901158		549;89
N	alternative_donor	CUFF.521	chr19	+	chr19:17608274-17611086	chr19:17610764-17611086		chr19:17608274-17610763	chr19:17608273-17608274		186;225
N	jcn_only_AA	CUFF.542	chr19	+	chr19:44771115-44777457;chr19:44771115-44771532	chr19:44771115-44777051		chr19:44771533-44777051;chr19:44777052-44777457	chr19:44777051-44777052;chr19:44777457-44777458		104;90
N	alternative_donor	CUFF.529,CUFF.534	chr19	-	chr19:39924059-39924161;chr19:39924059-39924157	chr19:39924059-39924133		chr19:39924134-39924157;chr19:39924158-39924161	chr19:39924157-39924158;chr19:39924161-39924162		1565;17
N	coord_cassette	CUFF.500	chr19	-	chr19:6016283-6110403	chr19:6016283-6039990;chr19:6040253-6042054;chr19:6042135-6047417;chr19:6047516-6110403		chr19:6039991-6040252;chr19:6042055-6042134;chr19:6047418-6047515			238;19
K	intron_retention	CUFF.551	chr19	-	chr19:51525921-51526347				chr19:51525920-51525921;chr19:51526347-51526348		63;43
K	cassette	CUFF.512	chr19	+	chr19:11888553-11889144	chr19:11888553-11888930;chr19:11888995-11889144		chr19:11888931-11888994			27;69
K	jcn_only_AA	CUFF.538	chr19	-	chr19:41533165-41533447	chr19:41533170-41533447		chr19:41533165-41533169	chr19:41533164-41533165		16;45
N	alternative_acceptor		chr19	+	chr19:44764092-44768480	chr19:44764092-44768466		chr19:44768467-44768480	chr19:44768480-44768481		38;10
K	intron_retention	CUFF.558	chr19	+	chr19:54656737-54657451				chr19:54656736-54656737;chr19:54657451-54657452		87;128
K	coord_cassette	CUFF.515	chr19	-	chr19:14876617-14883153	chr19:14876617-14877046;chr19:14877194-14877789;chr19:14877922-14883153		chr19:14877047-14877193;chr19:14877790-14877921			21;131
N	intron_retention	CUFF.555	chr19	+	chr19:52909897-52918191				chr19:52909896-52909897;chr19:52918191-52918192		15;69
K	intron_retention	CUFF.546	chr19	-	chr19:49299587-49299684				chr19:49299586-49299587;chr19:49299684-49299685		57;237
N	jcn_only_AA	CUFF.495	chr19	+	chr19:1438892-1440017;chr19:1438892-1439604;chr19:1438892-1439959;chr19:1438892-1440024;chr19:1438892-1439966	chr19:1438892-1439714		chr19:1439605-1439714;chr19:1439715-1439959;chr19:1439960-1439966;chr19:1439967-1440017;chr19:1440018-1440024	chr19:1439714-1439715;chr19:1439959-1439960;chr19:1439966-1439967;chr19:1440017-1440018;chr19:1440024-1440025		1573;120
N	intron_retention		chr19	-	chr19:41942378-41944139				chr19:41942377-41942378;chr19:41944139-41944140		23;84
K	intron_retention	CUFF.495	chr19	+	chr19:1440253-1440347				chr19:1440252-1440253;chr19:1440347-1440348		1472;136
N	intron_retention		chr19	+	chr19:1439826-1440017				chr19:1439825-1439826;chr19:1440017-1440018		166;228
N	alternative_donor	CUFF.529,CUFF.552	chr19	-	chr19:33878388-33878795	chr19:33878388-33878560		chr19:33878561-33878795	chr19:33878795-33878796		736;15
K	intron_retention	CUFF.513	chr19	+	chr19:12917894-12918019				chr19:12917893-12917894;chr19:12918019-12918020		5593;16
N	jcn_only_AA	CUFF.542	chr19	+	chr19:44771115-44777051;chr19:44771115-44771532	chr19:44771115-44777457		chr19:44771533-44777051;chr19:44777052-44777457	chr19:44777051-44777052;chr19:44777457-44777458		119;74
K	alternative_last_exon	CUFF.526	chr19	-	chr19:21637275-21639262	chr19:21638407-21639262	chr19:21637185-21637274	chr19:21638091-21638406			299;132
N	jcn_only_AD	CUFF.521	chr19	+	chr19:17581517-17597371	chr19:17594931-17597371		chr19:17581517-17594930	chr19:17581516-17581517		92;26
K	intron_retention	CUFF.542	chr19	+	chr19:44764156-44768466				chr19:44764155-44764156;chr19:44768466-44768467		146;53
K	jcn_only_AD	CUFF.498	chr19	+	chr19:4323235-4323344;chr19:4323211-4323344	chr19:4323144-4323344		chr19:4323144-4323210;chr19:4323211-4323234	chr19:4323143-4323144;chr19:4323210-4323211		290;82
N	jcn_only_AD	CUFF.510	chr19	+	chr19:11474496-11474836	chr19:11474512-11474836		chr19:11474496-11474511	chr19:11474495-11474496		23;16
N	cassette	CUFF.546	chr19	-	chr19:49310332-49314065;chr19:49310332-49314240	chr19:49310332-49311012;chr19:49311494-49314065,chr19:49311494-49314240		chr19:49311013-49311493			121;285
K	intron_retention	CUFF.498	chr19	+	chr19:4318949-4322982				chr19:4318948-4318949;chr19:4322982-4322983		326;15
K	jcn_only_AD	CUFF.555	chr19	+	chr19:52901274-52901619;chr19:52901154-52901619	chr19:52901158-52901619		chr19:52901154-52901157;chr19:52901158-52901273	chr19:52901153-52901154;chr19:52901157-52901158		594;134
K	jcn_only_AA	CUFF.563	chr19	+	chr19:55255537-55275342	chr19:55255537-55258786					253;251
N	cassette	CUFF.529	chr19	-	chr19:33984244-34003498	chr19:33984244-34001933;chr19:34002062-34003498		chr19:34001934-34002061			106;268
N	jcn_only_AA	CUFF.488	chr18	-	chr18:67563282-67623990;chr18:67614670-67623990	chr18:67614769-67623990					57;107
K	alternative_acceptor	CUFF.477	chr18	-	chr18:44268831-44272131	chr18:44268883-44272131		chr18:44268831-44268882	chr18:44268830-44268831		22;191
K	cassette	CUFF.481	chr18	+	chr18:55919287-55989656	chr18:55919287-55983213;chr18:55983265-55989656		chr18:55983214-55983264			21;582
K	cassette	CUFF.468	chr18	+	chr18:180340-196636	chr18:180340-192841;chr18:192901-196636		chr18:192842-192900			157;202
K	alternative_first_exon	CUFF.468	chr18	+	chr18:158715-162982	chr18:159022-162982	chr18:158298-158714	chr18:158820-159021			55;122
N	cassette	CUFF.481	chr18	+	chr18:55862966-55912658;chr18:55888990-55912658;chr18:55833094-55912658	chr18:55833094-55895061,chr18:55888990-55895061,chr18:55862966-55895061;chr18:55895121-55912658		chr18:55895062-55895120			451;232
K	alternative_donor	CUFF.480	chr18	-	chr18:47329224-47340101	chr18:47329224-47339838		chr18:47339839-47340101	chr18:47340101-47340102		48;24
K	alternative_first_exon	CUFF.477,CUFF.478	chr18	-	chr18:44486279-44497964;chr18:44486279-44500021	chr18:44486279-44497284	chr18:44500022-44500217	chr18:44497285-44497500		chr18:44485642-44486278	195;176
K	jcn_only_AA	CUFF.488	chr18	-	chr18:67509632-67562936	chr18:67540483-67562936					68;166
N	cassette	CUFF.478	chr18	-	chr18:44471018-44483489	chr18:44471018-44473393;chr18:44473495-44483489		chr18:44473394-44473494			340;39
K	intron_retention	CUFF.468	chr18	+	chr18:210032-210385				chr18:210031-210032;chr18:210385-210386		295;130
N	jcn_only_AA	CUFF.473	chr18	+	chr18:55711941-56057877	chr18:55711941-55833019					244;49
N	jcn_only_AA	CUFF.471	chr18	+	chr18:12014373-12021700;chr18:12014373-12028041	chr18:12014373-12017612		chr18:12017613-12021700;chr18:12021701-12028041	chr18:12021700-12021701;chr18:12028041-12028042		971;38
N	alternative_acceptor	CUFF.478	chr18	-	chr18:44483599-44497284	chr18:44486279-44497284		chr18:44483599-44486278	chr18:44483598-44483599	chr18:44497285-44497500	43;92
N	jcn_only_AD	CUFF.493	chr18	+	chr18:77867357-77875412	chr18:77867906-77875412		chr18:77867357-77867905	chr18:77867356-77867357		34;206
N	cassette	CUFF.468	chr18	+	chr18:163454-180235	chr18:163454-166786;chr18:166820-180235		chr18:166787-166819			82;170
N	jcn_only_AA		chr18	+	chr18:14808579-14822603	chr18:14808579-14808670		chr18:14808671-14822603	chr18:14822603-14822604		8;186
N	jcn_only_AA	CUFF.486	chr18	+	chr18:63430289-63476939	chr18:63430289-63470350		chr18:63470351-63476939	chr18:63476939-63476940		274;32
N	coord_cassette	CUFF.481	chr18	+	chr18:56001125-56016768	chr18:56001125-56008909;chr18:56009030-56010137;chr18:56010336-56016768		chr18:56008910-56009029;chr18:56010138-56010335			11;345
K	jcn_only_AD	CUFF.473	chr18	+	chr18:12658205-12658572	chr18:12658343-12658572		chr18:12658205-12658342	chr18:12658204-12658205		45;59
K	intron_retention	CUFF.477	chr18	-	chr18:44268883-44272131				chr18:44268882-44268883;chr18:44272131-44272132		110;124
N	alternative_donor	CUFF.493	chr18	+	chr18:77867357-77875412	chr18:77867906-77875412		chr18:77867357-77867905	chr18:77867356-77867357		34;127
N	jcn_only_AA	CUFF.471	chr18	+	chr18:11999187-12009881	chr18:11999187-12008331		chr18:12008332-12009881	chr18:12009881-12009882		662;34
K	alternative_donor	CUFF.473	chr18	+	chr18:12658205-12658572	chr18:12658343-12658572		chr18:12658205-12658342	chr18:12658204-12658205		45;83
N	alternative_acceptor		chr18	+	chr18:55713021-55833023	chr18:55713021-55833019		chr18:55833020-55833023	chr18:55833023-55833024		334;69
K	intron_retention	CUFF.485	chr18	+	chr18:61826223-61826329				chr18:61826222-61826223;chr18:61826329-61826330		264;42
K	intron_retention	CUFF.471	chr18	+	chr18:12028151-12028840				chr18:12028150-12028151;chr18:12028840-12028841		527;364
K	alternative_first_exon	CUFF.480	chr18	-	chr18:47329224-47340051,chr18:47329224-47340186;chr18:47329224-47340101,chr18:47329224-47339838;chr18:47329224-47337765	chr18:47329224-47339094	chr18:47340102-47340330;chr18:47337766-47337886	chr18:47339095-47339492			143;267
K	jcn_only_AA	CUFF.488	chr18	-	chr18:67614007-67614596	chr18:67614306-67614596		chr18:67614007-67614305	chr18:67614006-67614007		27;257
K	mutually_exclusive	CUFF.468	chr18	+	chr18:163454-178932,chr18:179038-180235	chr18:163454-166786,chr18:166820-180235	chr18:178933-179037	chr18:166787-166819			67;170
N	cassette	CUFF.471	chr18	+	chr18:12009987-12014263	chr18:12009987-12012168;chr18:12012215-12014263		chr18:12012169-12012214			225;564
K	cassette	CUFF.482	chr18	-	chr18:57106811-57115214	chr18:57106811-57106908;chr18:57107049-57115214		chr18:57106909-57107048			93;14
N	mutually_exclusive	CUFF.478	chr18	-	chr18:44435579-44470542,chr18:44471018-44497284	chr18:44435579-44444126,chr18:44444212-44497284	chr18:44470543-44471017	chr18:44444127-44444211		chr18:44497285-44497500	107;11
N	jcn_only_AD	CUFF.489	chr18	-	chr18:72914296-72920374;chr18:72914296-72920315	chr18:72914296-72917147		chr18:72917148-72920315;chr18:72920316-72920374	chr18:72920315-72920316;chr18:72920374-72920375		397;37
N	alternative_acceptor		chr18	+	chr18:12014373-12021700;chr18:12014373-12017612	chr18:12014373-12028041		chr18:12017613-12021700;chr18:12021701-12028041	chr18:12021700-12021701;chr18:12028041-12028042		9;894
N	intron_retention		chr18	+	chr18:56002770-56008269				chr18:56002769-56002770;chr18:56008269-56008270		19;44
K	alternative_acceptor	CUFF.488	chr18	-	chr18:67614007-67614596	chr18:67614306-67614596		chr18:67614007-67614305	chr18:67614006-67614007		27;260
N	jcn_only_AD	CUFF.481	chr18	+	chr18:56033461-56034977	chr18:56034459-56034977		chr18:56033461-56034458	chr18:56033460-56033461		644;33
K	jcn_only_AA	CUFF.473	chr18	+	chr18:12658343-12658572	chr18:12658343-12658549		chr18:12658550-12658572	chr18:12658572-12658573		59;82
K	alternative_first_exon	CUFF.477	chr18	-	chr18:44301433-44336340	chr18:44301433-44310168	chr18:44336341-44337132	chr18:44310169-44310324			132;98
N	alternative_donor	CUFF.481	chr18	+	chr18:56001125-56008269	chr18:56002770-56008269		chr18:56001125-56002769	chr18:56001124-56001125		324;34
K	jcn_only_AD	CUFF.480	chr18	-	chr18:47329224-47340101	chr18:47329224-47339838		chr18:47339839-47340101	chr18:47340101-47340102		48;17
N	jcn_only_AA		chr18	+	chr18:12014373-12021700;chr18:12014373-12017612	chr18:12014373-12028041		chr18:12017613-12021700;chr18:12021701-12028041	chr18:12021700-12021701;chr18:12028041-12028042		115;894
K	intron_retention	CUFF.477	chr18	-	chr18:44268831-44272131				chr18:44268830-44268831;chr18:44272131-44272132		22;210
K	jcn_only_AA	CUFF.474	chr18	+	chr18:14797854-14808549	chr18:14797854-14799099					45;134
K	alternative_last_exon	CUFF.469	chr18	-	chr18:4775123-4946880	chr18:4807995-4946880	chr18:4775053-4775122	chr18:4807854-4807994			81;52
N	alternative_donor	CUFF.481	chr18	+	chr18:55912741-55916130	chr18:55914857-55916130		chr18:55912741-55914856	chr18:55912740-55912741		720;27
K	mutually_exclusive	CUFF.468	chr18	+	chr18:163454-178900,chr18:179038-180235	chr18:163454-166786,chr18:166820-180235	chr18:178901-179037	chr18:166787-166819			111;170
K	alternative_first_exon	CUFF.480	chr18	-	chr18:47329224-47340051,chr18:47329224-47340186;chr18:47329224-47339094;chr18:47329224-47337765	chr18:47329224-47340101,chr18:47329224-47339838	chr18:47339095-47339492;chr18:47337766-47337886	chr18:47340102-47340330			327;83
N	cassette	CUFF.468	chr18	+	chr18:163454-180235	chr18:163454-178900;chr18:179038-180235		chr18:178901-179037			82;111
N	jcn_only_AD	CUFF.471	chr18	+	chr18:11999187-12009881	chr18:12008591-12009881		chr18:11999187-12008590	chr18:11999186-11999187		662;33
N	alternative_first_exon	CUFF.481	chr18	+	chr18:55711941-56057877	chr18:56056425-56057877	chr18:55711599-55711940	chr18:56056317-56056424			248;621
N	jcn_only_AD	CUFF.481	chr18	+	chr18:55912741-55916130	chr18:55914857-55916130		chr18:55912741-55914856	chr18:55912740-55912741		720;30
K	intron_retention		chr18	+	chr18:56001125-56008269				chr18:56001124-56001125;chr18:56008269-56008270		324;99
N	jcn_only_AA	CUFF.488	chr18	-	chr18:67614769-67623990;chr18:67614670-67623990	chr18:67563282-67623990					117;47
K	alternative_last_exon	CUFF.483	chr18	-	chr18:61060783-61064266	chr18:61060800-61064266	chr18:61060590-61060782	chr18:61060783-61060799			412;54
N	alternative_donor	CUFF.486	chr18	+	chr18:63417617-63429882	chr18:63418387-63429882		chr18:63417617-63418386	chr18:63417616-63417617		5;198
K	jcn_only_AD	CUFF.474	chr18	+	chr18:14797854-14808549	chr18:14803824-14808549					45;160
N	jcn_only_AD	CUFF.489	chr18	-	chr18:72914296-72917147;chr18:72914296-72920315	chr18:72914296-72920374		chr18:72917148-72920315;chr18:72920316-72920374	chr18:72920315-72920316;chr18:72920374-72920375		373;61
N	cassette	CUFF.481	chr18	+	chr18:56001125-56010137	chr18:56001125-56008909;chr18:56009030-56010137		chr18:56008910-56009029			11;261
N	coord_cassette	CUFF.481	chr18	+	chr18:56001125-56010137	chr18:56001125-56008269;chr18:56008402-56008909;chr18:56009030-56010137		chr18:56008270-56008401;chr18:56008910-56009029			11;342
K	cassette	CUFF.493	chr18	+	chr18:77891076-77893494	chr18:77891076-77891574;chr18:77891690-77893494		chr18:77891575-77891689			218;26
K	jcn_only_AD	CUFF.484	chr18	+	chr18:61377596-61390228	chr18:61388221-61390228					25;299
N	jcn_only_AD	CUFF.486	chr18	+	chr18:63417617-63429882	chr18:63418387-63429882		chr18:63417617-63418386	chr18:63417616-63417617		5;205
N	jcn_only_AA	CUFF.478	chr18	-	chr18:44483599-44497284	chr18:44486279-44497284		chr18:44483599-44486278	chr18:44483598-44483599	chr18:44497285-44497500	43;227
N	jcn_only_AD	CUFF.489	chr18	-	chr18:72914296-72917147;chr18:72914296-72920374	chr18:72914296-72920315		chr18:72917148-72920315;chr18:72920316-72920374	chr18:72920315-72920316;chr18:72920374-72920375		97;337
N	alternative_acceptor		chr18	+	chr18:14808579-14822603	chr18:14808579-14808670		chr18:14808671-14822603	chr18:14822603-14822604		8;22
N	alternative_first_exon	CUFF.481	chr18	+	chr18:55862966-55895061;chr18:55833094-55895061	chr18:55888990-55895061	chr18:55833020-55833093	chr18:55888825-55888989			199;30
K	intron_retention		chr18	+	chr18:163454-178932				chr18:163453-163454;chr18:178932-178933		33;108
N	alternative_donor	CUFF.489	chr18	-	chr18:72914296-72917147;chr18:72914296-72920315	chr18:72914296-72920374		chr18:72917148-72920315;chr18:72920316-72920374	chr18:72920315-72920316;chr18:72920374-72920375		172;61
K	cassette	CUFF.477	chr18	-	chr18:44284628-44336340	chr18:44284628-44301324;chr18:44301433-44336340		chr18:44301325-44301432			14;115
N	cassette	CUFF.484	chr18	+	chr18:61379928-61387246	chr18:61379928-61383268;chr18:61383387-61387246		chr18:61383269-61383386			19;262
K	intron_retention	CUFF.476	chr18	-	chr18:14969572-14969674				chr18:14969571-14969572;chr18:14969674-14969675		60;47
K	alternative_first_exon	CUFF.474	chr18	+	chr18:14728514-14797659	chr18:14796415-14797659	chr18:14728271-14728513	chr18:14796342-14796414			43;104
N	cassette	CUFF.478	chr18	-	chr18:44444212-44497284	chr18:44444212-44470542;chr18:44471018-44497284		chr18:44470543-44471017		chr18:44497285-44497500	6;600
K	alternative_last_exon	CUFF.478	chr18	-	chr18:44395313-44400895	chr18:44398411-44400895	chr18:44395275-44395312	chr18:44398133-44398410			68;91
N	alternative_first_exon		chr18	-	chr18:44483597-44484064;chr18:44483597-44500021	chr18:44483597-44486189	chr18:44500022-44500217	chr18:44486190-44486278			250;18
K	alternative_first_exon	CUFF.481	chr18	+	chr18:56024485-56031499	chr18:56027291-56031499	chr18:56024426-56024484	chr18:56027109-56027290			472;109
N	alternative_acceptor	CUFF.486	chr18	+	chr18:63430289-63476939	chr18:63430289-63470350		chr18:63470351-63476939	chr18:63476939-63476940		274;7
N	jcn_only_AD	CUFF.481	chr18	+	chr18:55919287-55983213	chr18:55981822-55983213		chr18:55919287-55981821	chr18:55919286-55919287		651;71
N	alternative_donor	CUFF.481	chr18	+	chr18:55919287-55983213	chr18:55981822-55983213		chr18:55919287-55981821	chr18:55919286-55919287		651;0
K	alternative_first_exon	CUFF.492	chr18	+	chr18:77440262-77455224	chr18:77441518-77455224	chr18:77439711-77440261	chr18:77441398-77441517			24;37
N	cassette	CUFF.481	chr18	+	chr18:56001125-56016768	chr18:56001125-56010137;chr18:56010336-56016768		chr18:56010138-56010335			11;352
N	jcn_only_AD	CUFF.481	chr18	+	chr18:56001125-56008269	chr18:56002770-56008269		chr18:56001125-56002769	chr18:56001124-56001125		324;19
N	alternative_donor	CUFF.481	chr18	+	chr18:56033461-56034977	chr18:56034459-56034977		chr18:56033461-56034458	chr18:56033460-56033461		644;22
N	alternative_acceptor	CUFF.471	chr18	+	chr18:12014373-12021700;chr18:12014373-12028041	chr18:12014373-12017612		chr18:12017613-12021700;chr18:12021701-12028041	chr18:12021700-12021701;chr18:12028041-12028042		897;6
N	coord_cassette	CUFF.478	chr18	-	chr18:44471018-44500021	chr18:44471018-44473393;chr18:44473495-44483489;chr18:44483597-44500021		chr18:44473394-44473494;chr18:44483490-44483596			73;33
K	jcn_only_AA	CUFF.487	chr18	-	chr18:66567475-66569424	chr18:66567509-66569424		chr18:66567475-66567508	chr18:66567474-66567475		61;29
K	intron_retention	CUFF.481	chr18	+	chr18:55989719-55990463				chr18:55989718-55989719;chr18:55990463-55990464		442;67
K	alternative_first_exon	CUFF.491	chr18	-	chr18:76737430-76738785;chr18:76737430-76738462	chr18:76737430-76737554	chr18:76738463-76738843	chr18:76737555-76737959			113;101
N	alternative_donor	CUFF.471	chr18	+	chr18:11999187-12009881	chr18:12008591-12009881		chr18:11999187-12008590	chr18:11999186-11999187		662;2
K	intron_retention	CUFF.471	chr18	+	chr18:11981693-11999060				chr18:11981692-11981693;chr18:11999060-11999061		26;153
N	alternative_acceptor		chr18	+	chr18:77875534-77905317	chr18:77875534-77890985		chr18:77890986-77905317	chr18:77905317-77905318		31;3
K	alternative_donor	CUFF.493	chr18	+	chr18:77875468-77890985	chr18:77875534-77890985		chr18:77875468-77875533	chr18:77875467-77875468		35;109
K	jcn_only_AD	CUFF.493	chr18	+	chr18:77875468-77890985	chr18:77875534-77890985		chr18:77875468-77875533	chr18:77875467-77875468		35;198
K	intron_retention		chr18	-	chr18:44483597-44486189				chr18:44483596-44483597;chr18:44486189-44486190	chr18:44486190-44486278	27;93
N	jcn_only_AA		chr18	+	chr18:55713021-55833023	chr18:55713021-55833019		chr18:55833020-55833023	chr18:55833023-55833024		334;140
N	alternative_donor	CUFF.471	chr18	+	chr18:12014373-12028041	chr18:12021822-12028041		chr18:12014373-12021821	chr18:12014372-12014373		894;10
N	alternative_acceptor	CUFF.471	chr18	+	chr18:12014373-12017612;chr18:12014373-12028041	chr18:12014373-12021700		chr18:12017613-12021700;chr18:12021701-12028041	chr18:12021700-12021701;chr18:12028041-12028042		900;3
K	cassette	CUFF.483	chr18	-	chr18:61064487-61067280	chr18:61064487-61066474;chr18:61066557-61067280		chr18:61066475-61066556			366;66
K	intron_retention	CUFF.473	chr18	+	chr18:12658205-12658572				chr18:12658204-12658205;chr18:12658572-12658573		45;49
N	alternative_donor	CUFF.489	chr18	-	chr18:72914296-72920374;chr18:72914296-72920315	chr18:72914296-72917147		chr18:72917148-72920315;chr18:72920316-72920374	chr18:72920315-72920316;chr18:72920374-72920375		227;6
N	cassette	CUFF.478	chr18	-	chr18:44471018-44500021	chr18:44471018-44483489;chr18:44483597-44500021		chr18:44483490-44483596			73;183
K	alternative_first_exon	CUFF.480	chr18	-	chr18:47329224-47340051,chr18:47329224-47340186;chr18:47329224-47340101,chr18:47329224-47339838;chr18:47329224-47339094	chr18:47329224-47337765	chr18:47340102-47340330;chr18:47339095-47339492	chr18:47337766-47337886			380;30
K	jcn_only_AA	CUFF.492	chr18	+	chr18:77441518-77455224	chr18:77441518-77443042					59;75
K	cassette	CUFF.492	chr18	+	chr18:77478017-77496354	chr18:77478017-77488906;chr18:77489070-77496354		chr18:77488907-77489069			6;31
N	cassette	CUFF.477	chr18	-	chr18:44272219-44336340	chr18:44272219-44284534;chr18:44284628-44336340		chr18:44284535-44284627			38;89
K	cassette	CUFF.483	chr18	-	chr18:61071060-61077522	chr18:61071060-61074664;chr18:61074733-61077522		chr18:61074665-61074732			318;42
K	alternative_last_exon	CUFF.484	chr18	+	chr18:61377596-61390228	chr18:61377596-61378568	chr18:61390229-61391222	chr18:61378569-61378628			48;304
N	alternative_acceptor	CUFF.471	chr18	+	chr18:11999187-12009881	chr18:11999187-12008331		chr18:12008332-12009881	chr18:12009881-12009882		662;23
N	coord_cassette	CUFF.477	chr18	-	chr18:44272219-44336340	chr18:44272219-44284534;chr18:44284628-44301324;chr18:44301433-44336340		chr18:44284535-44284627;chr18:44301325-44301432			38;106
K	alternative_acceptor	CUFF.473	chr18	+	chr18:12658343-12658572	chr18:12658343-12658549		chr18:12658550-12658572	chr18:12658572-12658573		59;44
K	alternative_first_exon	CUFF.488	chr18	-	chr18:67614769-67623849;chr18:67614769-67628827	chr18:67614769-67623990	chr18:67628828-67629132	chr18:67623991-67624489			120;133
N	cassette	CUFF.468	chr18	+	chr18:163454-180235	chr18:163454-178932;chr18:179038-180235		chr18:178933-179037			82;67
N	jcn_only_AD	CUFF.471	chr18	+	chr18:12014373-12028041	chr18:12021822-12028041		chr18:12014373-12021821	chr18:12014372-12014373		894;90
K	alternative_acceptor	CUFF.487	chr18	-	chr18:66567475-66569424	chr18:66567509-66569424		chr18:66567475-66567508	chr18:66567474-66567475		61;14
N	jcn_only_AA	CUFF.471	chr18	+	chr18:12014373-12017612;chr18:12014373-12028041	chr18:12014373-12021700		chr18:12017613-12021700;chr18:12021701-12028041	chr18:12021700-12021701;chr18:12028041-12028042		932;77
K	cassette	CUFF.478	chr18	-	chr18:44435579-44470542	chr18:44435579-44444126;chr18:44444212-44470542		chr18:44444127-44444211			46;362
K	cassette	CUFF.468	chr18	+	chr18:158715-163307	chr18:158715-162982;chr18:163175-163307		chr18:162983-163174			194;190
N	jcn_only_AA	CUFF.488	chr18	-	chr18:67614769-67623990;chr18:67563282-67623990	chr18:67614670-67623990					155;10
K	intron_retention	CUFF.478	chr18	-	chr18:44424803-44426669				chr18:44424802-44424803;chr18:44426669-44426670		360;177
K	intron_retention	CUFF.481	chr18	+	chr18:56056425-56057877				chr18:56056424-56056425;chr18:56057877-56057878		886;47
K	cassette	CUFF.481	chr18	+	chr18:56001125-56008909	chr18:56001125-56008269;chr18:56008402-56008909		chr18:56008270-56008401			27;323
K	alternative_first_exon	CUFF.481	chr18	+	chr18:55758860-55833019,chr18:55816802-55833019,chr18:55816792-55833019,chr18:55713251-55833019,chr18:55712848-55833019,chr18:55722109-55833019,chr18:55713021-55833019;chr18:55711941-55833019	chr18:55714743-55833019	chr18:55711599-55711940	chr18:55713593-55714742			608;162
K	intron_retention	CUFF.483	chr18	-	chr18:61060783-61064266				chr18:61060782-61060783;chr18:61064266-61064267		410;24
K	cassette	CUFF.474	chr18	+	chr18:14791491-14796341	chr18:14791491-14796219;chr18:14796249-14796341		chr18:14796220-14796248			932;11
N	jcn_only_AA		chr18	+	chr18:77875534-77905317	chr18:77875534-77890985		chr18:77890986-77905317	chr18:77905317-77905318		31;198
N	alternative_donor	CUFF.489	chr18	-	chr18:72914296-72917147;chr18:72914296-72920374	chr18:72914296-72920315		chr18:72917148-72920315;chr18:72920316-72920374	chr18:72920315-72920316;chr18:72920374-72920375		67;166
K	alternative_first_exon	CUFF.471	chr18	+	chr18:11981130-11999052;chr18:11981205-11999052	chr18:11981765-11999052	chr18:11981024-11981204	chr18:11981385-11981764			80;349
K	cassette	CUFF.488	chr18	-	chr18:67563282-67613969	chr18:67563282-67611719;chr18:67611805-67613969		chr18:67611720-67611804			139;18
N	mutually_exclusive	CUFF.492	chr18	+	chr18:77478017-77496354,chr18:77496522-77513651	chr18:77478017-77488906,chr18:77489070-77513651	chr18:77496355-77496521	chr18:77488907-77489069			13;12
K	jcn_only_AD	CUFF.484	chr18	+	chr18:61323211-61377412	chr18:61370241-61377412					31;427
K	jcn_only_AA	CUFF.477	chr18	-	chr18:44268831-44272131	chr18:44268883-44272131		chr18:44268831-44268882	chr18:44268830-44268831		22;110
K	alternative_first_exon	CUFF.1102	chrX	+	chrX:15699171-15706783;chrX:15693696-15706783;chrX:15693092-15706783;chrX:15699311-15706783	chrX:15693902-15706783	chrX:15693598-15693695;chrX:15693055-15693091;chrX:15699124-15699310	chrX:15693813-15693901			211;90
N	jcn_only_AA		chrX	-	chrX:46360768-46387784;chrX:46384874-46387784	chrX:46382561-46387784		chrX:46360768-46382560;chrX:46382561-46384873	chrX:46360767-46360768;chrX:46382560-46382561		39;179
K	cassette	CUFF.1111	chrX	-	chrX:53570930-53571989	chrX:53570930-53571520;chrX:53571724-53571989		chrX:53571521-53571723			70;87
K	cassette	CUFF.1124	chrX	+	chrX:114536689-114540769	chrX:114536689-114537864;chrX:114537984-114540769		chrX:114537865-114537983			118;59
K	alternative_last_exon	CUFF.1102	chrX	+	chrX:15711182-15713793;chrX:15711182-15715362	chrX:15711182-15720904	chrX:15713794-15713856;chrX:15715363-15715978	chrX:15720905-15721946			236;176
K	alternative_acceptor	CUFF.1099	chrX	-	chrX:10417657-10422909	chrX:10417757-10422909		chrX:10417657-10417756	chrX:10417656-10417657		13;53
K	jcn_only_AD	CUFF.1110	chrX	+	chrX:47039437-47039610	chrX:47039440-47039610		chrX:47039437-47039439	chrX:47039436-47039437		79;21
K	intron_retention	CUFF.1103	chrX	-	chrX:19932545-19933056				chrX:19932544-19932545;chrX:19933056-19933057		508;12
N	cassette	CUFF.1095	chrX	+	chrX:1414350-1422815	chrX:1414350-1419383;chrX:1419520-1422815		chrX:1419384-1419519			124;557
K	intron_retention	CUFF.1098	chrX	-	chrX:8998402-9000170				chrX:8998401-8998402;chrX:9000170-9000171		84;25
K	alternative_first_exon	CUFF.1103,CUFF.1108	chrX	-	chrX:19954017-19955622	chrX:19954017-19955535	chrX:19955623-19955650	chrX:19955536-19955618			89;17
K	intron_retention	CUFF.1101	chrX	-	chrX:15343275-15349711				chrX:15343274-15343275;chrX:15349711-15349712		161;33
K	intron_retention	CUFF.1105	chrX	+	chrX:24382349-24382540				chrX:24382348-24382349;chrX:24382540-24382541		119;22
K	intron_retention	CUFF.1111	chrX	-	chrX:53563629-53564516				chrX:53563628-53563629;chrX:53564516-53564517		81;31
K	intron_retention	CUFF.1100	chrX	-	chrX:13791150-13794356				chrX:13791149-13791150;chrX:13794356-13794357		259;178
N	jcn_only_AD	CUFF.1101	chrX	-	chrX:15344169-15349995;chrX:15344169-15349711	chrX:15344169-15349337		chrX:15349338-15349711;chrX:15349712-15349995	chrX:15349711-15349712;chrX:15349995-15349996		79;6
K	cassette	CUFF.1113	chrX	+	chrX:78003532-78005670	chrX:78003532-78004459;chrX:78004728-78005670		chrX:78004460-78004727			75;47
K	alternative_first_exon	CUFF.1100	chrX	-	chrX:13798109-13801483	chrX:13798109-13799033	chrX:13801484-13801640	chrX:13799034-13799132			756;117
N	alternative_donor	CUFF.1103,CUFF.1134	chrX	-	chrX:19948059-19953926	chrX:19948059-19953475		chrX:19953476-19953926	chrX:19953926-19953927		141;19
K	cassette	CUFF.1101	chrX	-	chrX:15343275-15349711	chrX:15343275-15344035;chrX:15344169-15349711		chrX:15344036-15344168			161;88
K	cassette	CUFF.1104	chrX	-	chrX:20252933-20285156	chrX:20252933-20258686;chrX:20258788-20285156		chrX:20258687-20258787			83;35
K	alternative_first_exon	CUFF.1102	chrX	+	chrX:15699171-15706783;chrX:15693092-15706783;chrX:15693902-15706783;chrX:15699311-15706783	chrX:15693696-15706783	chrX:15693055-15693091;chrX:15693813-15693901;chrX:15699124-15699310	chrX:15693598-15693695			260;41
K	jcn_only_AA	CUFF.1114	chrX	-	chrX:85219058-85302487	chrX:85282562-85302487					93;36
K	jcn_only_AD	CUFF.1128	chrX	+	chrX:133594369-133607388	chrX:133594566-133607388		chrX:133594369-133594565	chrX:133594368-133594369		15;118
N	alternative_donor	CUFF.1098	chrX	-	chrX:9130946-9132573;chrX:9130946-9132333	chrX:9130946-9131117		chrX:9131118-9132333;chrX:9132334-9132573	chrX:9132333-9132334;chrX:9132573-9132574		33;5
K	intron_retention	CUFF.1097	chrX	-	chrX:2405744-2406828				chrX:2405743-2405744;chrX:2406828-2406829		17;85
K	jcn_only_AA	CUFF.1099	chrX	-	chrX:10417657-10422909	chrX:10417757-10422909		chrX:10417657-10417756	chrX:10417656-10417657		13;71
K	intron_retention	CUFF.1128	chrX	+	chrX:133594369-133607388				chrX:133594368-133594369;chrX:133607388-133607389		15;89
N	alternative_acceptor	CUFF.1098	chrX	-	chrX:9050777-9130837	chrX:9130355-9130837		chrX:9050777-9130354	chrX:9050776-9050777		38;1
K	cassette	CUFF.1110	chrX	+	chrX:47038895-47039278	chrX:47038895-47039082;chrX:47039181-47039278		chrX:47039083-47039180			52;41
N	alternative_donor	CUFF.1114	chrX	-	chrX:85282562-85302487	chrX:85282562-85302250		chrX:85302251-85302487	chrX:85302487-85302488		36;6
N	alternative_donor	CUFF.1098	chrX	-	chrX:9130946-9131117;chrX:9130946-9132333	chrX:9130946-9132573		chrX:9131118-9132333;chrX:9132334-9132573	chrX:9132333-9132334;chrX:9132573-9132574		19;19
N	cassette	CUFF.1095	chrX	+	chrX:1387773-1401570	chrX:1387773-1393647;chrX:1393712-1401570		chrX:1393648-1393711			137;428
K	jcn_only_AD	CUFF.1106	chrX	+	chrX:45129987-45184737	chrX:45184464-45184737					36;193
N	alternative_first_exon		chrX	-	chrX:20258724-20284681	chrX:20258724-20259710	chrX:20284682-20284958	chrX:20259711-20259808			18;12
K	intron_retention	CUFF.1136	chrX	+	chrX:153608380-153608593				chrX:153608379-153608380;chrX:153608593-153608594		1061;226
K	alternative_first_exon	CUFF.1121	chrX	-	chrX:106224708-106235517	chrX:106224708-106228325	chrX:106235518-106235603	chrX:106228326-106228473			3;18
N	jcn_only_AD	CUFF.1104,CUFF.1111	chrX	-	chrX:53569501-53570846	chrX:53569501-53570801		chrX:53570802-53570846	chrX:53570846-53570847		87;49
N	jcn_only_AA	CUFF.1095,CUFF.1102	chrX	+	chrX:1424421-1428294	chrX:1424421-1424520		chrX:1424521-1428294	chrX:1428294-1428295		612;15
K	alternative_last_exon	CUFF.1102	chrX	+	chrX:15711182-15720904;chrX:15711182-15715362	chrX:15711182-15713793	chrX:15720905-15721946;chrX:15715363-15715978	chrX:15713794-15713856			310;102
K	intron_retention	CUFF.1121	chrX	-	chrX:106184863-106185205				chrX:106184862-106184863;chrX:106185205-106185206		46;51
K	intron_retention	CUFF.1125	chrX	-	chrX:119377887-119378618				chrX:119377886-119377887;chrX:119378618-119378619		127;381
K	alternative_last_exon	CUFF.1128,CUFF.1131	chrX	+	chrX:133632715-133654511	chrX:133632715-133634059	chrX:133654512-133654642	chrX:133634060-133634698			283;33
K	alternative_last_exon	CUFF.1125	chrX	-	chrX:119355498-119378618,chrX:119374209-119378618;chrX:119271100-119378618;chrX:119312412-119378618	chrX:119377887-119378618	chrX:119270952-119271099;chrX:119312247-119312411	chrX:119374080-119377886			231;395
N	jcn_only_AA	CUFF.1104	chrX	-	chrX:20183080-20185706	chrX:20183179-20185706		chrX:20183080-20183178	chrX:20183079-20183080		29;80
N	jcn_only_AD	CUFF.1100	chrX	-	chrX:53652220-53654360	chrX:53652220-53652746					13;22
K	alternative_donor	CUFF.1121	chrX	-	chrX:106184863-106185205	chrX:106184863-106185167		chrX:106185168-106185205	chrX:106185205-106185206		46;30
N	jcn_only_AD	CUFF.1136	chrX	+	chrX:153607898-153608049	chrX:153607927-153608049		chrX:153607898-153607926	chrX:153607897-153607898		77;187
K	jcn_only_AD	CUFF.1135	chrX	+	chrX:153238312-153247300	chrX:153238338-153247300		chrX:153238312-153238337	chrX:153238311-153238312	chrX:153247301-153248646;chrX:153237778-153238311	68;93
K	intron_retention	CUFF.1098	chrX	-	chrX:9000503-9000999				chrX:9000502-9000503;chrX:9000999-9001000		110;21
N	alternative_donor	CUFF.1136	chrX	+	chrX:153607898-153608049	chrX:153607927-153608049		chrX:153607898-153607926	chrX:153607897-153607898		77;222
N	alternative_donor	CUFF.1101	chrX	-	chrX:15344169-15349337;chrX:15344169-15349995	chrX:15344169-15349711		chrX:15349338-15349711;chrX:15349712-15349995	chrX:15349711-15349712;chrX:15349995-15349996		68;155
N	cassette	CUFF.1100	chrX	-	chrX:13803928-13834962	chrX:13803928-13825768;chrX:13825889-13834962		chrX:13825769-13825888			105;62
K	alternative_last_exon	CUFF.1125	chrX	-	chrX:119355498-119378618,chrX:119374209-119378618;chrX:119312412-119378618;chrX:119377887-119378618	chrX:119271100-119378618	chrX:119312247-119312411;chrX:119374080-119377886	chrX:119270952-119271099			596;30
K	cassette	CUFF.1122	chrX	+	chrX:107369418-107374489	chrX:107369418-107372010;chrX:107372083-107374489		chrX:107372011-107372082			58;155
K	jcn_only_AA	CUFF.1097	chrX	-	chrX:2408811-2418857	chrX:2408814-2418857		chrX:2408811-2408813	chrX:2408810-2408811		4;174
K	intron_retention	CUFF.1136	chrX	+	chrX:153608728-153609112				chrX:153608727-153608728;chrX:153609112-153609113		1231;62
N	alternative_donor	CUFF.1099,CUFF.1101	chrX	-	chrX:10535644-10645504	chrX:10535644-10588329		chrX:10588330-10645504	chrX:10645504-10645505		36;1
N	intron_retention		chrX	-	chrX:53658435-53658518				chrX:53658434-53658435;chrX:53658518-53658519		7;67
N	alternative_donor	CUFF.1104	chrX	-	chrX:46382561-46387784	chrX:46382561-46387769		chrX:46387770-46387784	chrX:46387784-46387785		179;30
N	alternative_acceptor		chrX	-	chrX:46360768-46387784;chrX:46382561-46387784	chrX:46384874-46387784		chrX:46360768-46382560;chrX:46382561-46384873	chrX:46360767-46360768;chrX:46382560-46382561		21;6
K	intron_retention	CUFF.1121	chrX	-	chrX:106184863-106185167				chrX:106184862-106184863;chrX:106185167-106185168		12;44
K	alternative_first_exon	CUFF.1097,CUFF.1134	chrX	-	chrX:152988744-152988962,chrX:152988744-152989470,chrX:152988744-152989788;chrX:152988744-152989409;chrX:152988744-152989655	chrX:152988744-152989941	chrX:152989410-152989598;chrX:152989656-152989838	chrX:152989942-152990240			1103;35
K	alternative_first_exon	CUFF.1129	chrX	+	chrX:134193765-134254454	chrX:134250853-134254454	chrX:134193715-134193764	chrX:134250614-134250852			27;109
N	alternative_acceptor	CUFF.1095	chrX	+	chrX:1404814-1407411	chrX:1404814-1406066		chrX:1406067-1407411	chrX:1407411-1407412		1055;8
N	alternative_acceptor		chrX	-	chrX:46360768-46387784;chrX:46384874-46387784	chrX:46382561-46387784		chrX:46360768-46382560;chrX:46382561-46384873	chrX:46360767-46360768;chrX:46382560-46382561		22;5
K	alternative_first_exon	CUFF.1102	chrX	+	chrX:15699171-15706783;chrX:15693696-15706783;chrX:15693092-15706783;chrX:15693902-15706783	chrX:15699311-15706783	chrX:15693598-15693695;chrX:15693055-15693091;chrX:15693813-15693901	chrX:15699124-15699310			185;116
N	jcn_only_AD	CUFF.1098	chrX	-	chrX:9130946-9132573;chrX:9130946-9132333	chrX:9130946-9131117		chrX:9131118-9132333;chrX:9132334-9132573	chrX:9132333-9132334;chrX:9132573-9132574		40;15
N	alternative_acceptor	CUFF.1104	chrX	-	chrX:20190987-20193281	chrX:20190990-20193281		chrX:20190987-20190989	chrX:20190986-20190987		33;27
N	alternative_donor	CUFF.1101	chrX	-	chrX:15344169-15349337;chrX:15344169-15349711	chrX:15344169-15349995		chrX:15349338-15349711;chrX:15349712-15349995	chrX:15349711-15349712;chrX:15349995-15349996		176;47
N	intron_retention		chrX	-	chrX:46382561-46387784				chrX:46382560-46382561;chrX:46387784-46387785		179;77
K	alternative_donor	CUFF.1122	chrX	+	chrX:107335067-107369306	chrX:107335110-107369306		chrX:107335067-107335109	chrX:107335066-107335067		126;49
K	alternative_acceptor	CUFF.1106	chrX	+	chrX:45184847-45192754	chrX:45184847-45192518		chrX:45192519-45192754	chrX:45192754-45192755		51;35
K	cassette	CUFF.1103	chrX	-	chrX:19935453-19947902	chrX:19935453-19941275;chrX:19941526-19947902		chrX:19941276-19941525			65;125
K	alternative_first_exon	CUFF.1104	chrX	-	chrX:20227523-20252875	chrX:20227523-20236917	chrX:20252876-20252932	chrX:20236918-20237133			86;207
K	intron_retention	CUFF.1119	chrX	+	chrX:103357693-103357885				chrX:103357692-103357693;chrX:103357885-103357886		2276;5
N	cassette	CUFF.1132	chrX	+	chrX:148863659-148867663;chrX:148863691-148867663	chrX:148863691-148867418,chrX:148863659-148867418;chrX:148867506-148867663		chrX:148867419-148867505			141;110
N	intron_retention		chrX	-	chrX:13835315-13835376				chrX:13835314-13835315;chrX:13835376-13835377		27;76
K	intron_retention	CUFF.1134	chrX	-	chrX:152988744-152989409				chrX:152988743-152988744;chrX:152989409-152989410		1120;165
K	coord_cassette	CUFF.1095	chrX	+	chrX:1419520-1428294	chrX:1419520-1422815;chrX:1422913-1424338;chrX:1424421-1428294		chrX:1422816-1422912;chrX:1424339-1424420			421;249
N	alternative_first_exon	CUFF.1132	chrX	+	chrX:148863659-148867418,chrX:148863691-148867418	chrX:148864250-148867418	chrX:148863584-148863658	chrX:148864099-148864249			59;156
N	alternative_acceptor	CUFF.1102	chrX	+	chrX:15706982-15711085	chrX:15706982-15709260		chrX:15709261-15711085	chrX:15711085-15711086		346;20
N	jcn_only_AA	CUFF.1095	chrX	+	chrX:1404814-1407411	chrX:1404814-1406066		chrX:1406067-1407411	chrX:1407411-1407412		1055;74
N	cassette	CUFF.1095	chrX	+	chrX:1419520-1428294	chrX:1419520-1424338;chrX:1424421-1428294		chrX:1424339-1424420			421;302
K	intron_retention	CUFF.1106	chrX	+	chrX:45184847-45192754				chrX:45184846-45184847;chrX:45192754-45192755		51;77
N	alternative_donor	CUFF.1098	chrX	-	chrX:9001117-9050619	chrX:9001117-9001892		chrX:9001893-9050619	chrX:9050619-9050620		39;0
K	jcn_only_AD	CUFF.1122	chrX	+	chrX:107335067-107369306	chrX:107335110-107369306		chrX:107335067-107335109	chrX:107335066-107335067		126;63
K	alternative_first_exon	CUFF.1102	chrX	+	chrX:15699171-15706783;chrX:15693696-15706783;chrX:15693902-15706783;chrX:15699311-15706783	chrX:15693092-15706783	chrX:15693598-15693695;chrX:15693813-15693901;chrX:15699124-15699310	chrX:15693055-15693091			261;40
N	jcn_only_AD		chrX	-	chrX:9130946-9132573;chrX:9130946-9131117	chrX:9130946-9132333		chrX:9131118-9132333;chrX:9132334-9132573	chrX:9132333-9132334;chrX:9132573-9132574		34;21
N	jcn_only_AA	CUFF.1095	chrX	+	chrX:1393712-1401570;chrX:1393712-1400763	chrX:1393712-1401301		chrX:1400764-1401301;chrX:1401302-1401570	chrX:1401301-1401302;chrX:1401570-1401571		89;82
K	alternative_acceptor	CUFF.1131	chrX	+	chrX:142113879-142121813	chrX:142113879-142121810		chrX:142121811-142121813	chrX:142121813-142121814		143;224
K	intron_retention	CUFF.1114	chrX	-	chrX:85236814-85282494				chrX:85236813-85236814;chrX:85282494-85282495		10;10
K	jcn_only_AD	CUFF.1121	chrX	-	chrX:106184863-106185205	chrX:106184863-106185167		chrX:106185168-106185205	chrX:106185205-106185206		46;12
N	intron_retention		chrX	+	chrX:107381115-107393381				chrX:107381114-107381115;chrX:107393381-107393382		38;139
K	intron_retention		chrX	-	chrX:46382561-46387769				chrX:46382560-46382561;chrX:46387769-46387770		28;72
K	alternative_donor	CUFF.1122	chrX	+	chrX:107395089-107396208	chrX:107395236-107396208		chrX:107395089-107395235	chrX:107395088-107395089		204;47
N	jcn_only_AD		chrX	+	chrX:148863659-148867418	chrX:148863691-148867418		chrX:148863659-148863690	chrX:148863658-148863659		53;30
N	alternative_donor	CUFF.1104,CUFF.1111	chrX	-	chrX:53569501-53570846	chrX:53569501-53570801		chrX:53570802-53570846	chrX:53570846-53570847		87;40
K	cassette	CUFF.1118	chrX	-	chrX:100170073-100182958	chrX:100170073-100177781;chrX:100178051-100182958		chrX:100177782-100178050			71;42
K	cassette	CUFF.1122	chrX	+	chrX:107369418-107372010	chrX:107369418-107370022;chrX:107370325-107372010		chrX:107370023-107370324			159;26
K	intron_retention	CUFF.1103	chrX	-	chrX:19932387-19932468				chrX:19932386-19932387;chrX:19932468-19932469		289;134
K	alternative_last_exon	CUFF.1103	chrX	-	chrX:19948773-19955622	chrX:19954017-19955622	chrX:19947016-19948772	chrX:19953927-19954016			125;69
K	alternative_last_exon	CUFF.1121	chrX	-	chrX:106235661-106236459;chrX:106059017-106236459	chrX:106229431-106236459	chrX:106057002-106059016	chrX:106229213-106229430			69;19
N	jcn_only_AD	CUFF.1101	chrX	-	chrX:15344169-15349337;chrX:15344169-15349711	chrX:15344169-15349995		chrX:15349338-15349711;chrX:15349712-15349995	chrX:15349711-15349712;chrX:15349995-15349996		38;47
N	alternative_donor	CUFF.1096	chrX	+	chrX:1515542-1517717	chrX:1516118-1517717		chrX:1515542-1516117	chrX:1515541-1515542		269;14
K	alternative_first_exon	CUFF.1108	chrX	-	chrX:46360771-46387769	chrX:46360771-46382371	chrX:46387770-46387880	chrX:46382372-46383096			6;241
K	alternative_donor	CUFF.1110	chrX	+	chrX:47039437-47039610	chrX:47039440-47039610		chrX:47039437-47039439	chrX:47039436-47039437		79;10
K	cassette	CUFF.1123	chrX	-	chrX:114358566-114364717	chrX:114358566-114361405;chrX:114361457-114364717		chrX:114361406-114361456			40;7
K	intron_retention	CUFF.1134	chrX	-	chrX:152988744-152989941				chrX:152988743-152988744;chrX:152989941-152989942		24;156
K	jcn_only_AA	CUFF.1131	chrX	+	chrX:142113879-142121813	chrX:142113879-142121810		chrX:142121811-142121813	chrX:142121813-142121814		143;452
N	intron_retention	CUFF.1111	chrX	-	chrX:53569501-53570801				chrX:53569500-53569501;chrX:53570801-53570802		49;27
N	jcn_only_AD	CUFF.1100	chrX	-	chrX:13825889-13834962	chrX:13825889-13830989		chrX:13830990-13834962	chrX:13834962-13834963		40;87
N	alternative_acceptor	CUFF.1095	chrX	+	chrX:1393712-1401570;chrX:1393712-1400763	chrX:1393712-1401301		chrX:1400764-1401301;chrX:1401302-1401570	chrX:1401301-1401302;chrX:1401570-1401571		73;38
K	mutually_exclusive	CUFF.1098	chrX	-	chrX:8997460-8998301,chrX:8998402-9000170	chrX:8997460-8998162,chrX:8998248-9000170	chrX:8998302-8998401	chrX:8998163-8998247			88;31
N	intron_retention		chrX	+	chrX:153607898-153608049				chrX:153607897-153607898;chrX:153608049-153608050		77;167
N	jcn_only_AA		chrX	-	chrX:46360768-46387784;chrX:46382561-46387784	chrX:46384874-46387784		chrX:46360768-46382560;chrX:46382561-46384873	chrX:46360767-46360768;chrX:46382560-46382561		196;22
N	jcn_only_AA	CUFF.1114	chrX	-	chrX:85118100-85282494	chrX:85236814-85282494		chrX:85118100-85236813	chrX:85118099-85118100		11;10
N	jcn_only_AA	CUFF.1104	chrX	-	chrX:20190987-20193281	chrX:20190990-20193281		chrX:20190987-20190989	chrX:20190986-20190987		33;41
N	alternative_donor	CUFF.1100	chrX	-	chrX:13825889-13834962	chrX:13825889-13830989		chrX:13830990-13834962	chrX:13834962-13834963		40;4
K	cassette	CUFF.1101	chrX	-	chrX:15344169-15353622	chrX:15344169-15349995;chrX:15350115-15353622		chrX:15349996-15350114			23;92
N	jcn_only_AA	CUFF.1102	chrX	+	chrX:15706982-15711085	chrX:15706982-15709260		chrX:15709261-15711085	chrX:15711085-15711086		346;129
K	intron_retention	CUFF.1136	chrX	+	chrX:153607927-153608049				chrX:153607926-153607927;chrX:153608049-153608050		187;23
K	jcn_only_AD	CUFF.1110	chrX	+	chrX:47035986-47040613	chrX:47039906-47040613					19;127
N	jcn_only_AD	CUFF.1104	chrX	-	chrX:46382561-46387784	chrX:46382561-46387769		chrX:46387770-46387784	chrX:46387784-46387785		179;28
K	alternative_first_exon	CUFF.1134	chrX	-	chrX:152988744-152988962,chrX:152988744-152989470,chrX:152988744-152989788;chrX:152988744-152989409;chrX:152988744-152989941	chrX:152988744-152989655	chrX:152989410-152989598;chrX:152989942-152990240	chrX:152989656-152989838			1001;137
K	intron_retention	CUFF.1103	chrX	-	chrX:19931598-19932269				chrX:19931597-19931598;chrX:19932269-19932270		163;230
K	mutually_exclusive	CUFF.1101	chrX	-	chrX:15343275-15349711,chrX:15350115-15353622	chrX:15343275-15344035,chrX:15344169-15353622	chrX:15349712-15350114	chrX:15344036-15344168			207;25
N	alternative_acceptor	CUFF.1095	chrX	+	chrX:1393712-1401570;chrX:1393712-1401301	chrX:1393712-1400763		chrX:1400764-1401301;chrX:1401302-1401570	chrX:1401301-1401302;chrX:1401570-1401571		53;58
N	alternative_donor	CUFF.1100,CUFF.1121	chrX	-	chrX:13801641-13803740	chrX:13801641-13801897		chrX:13801898-13803740	chrX:13803740-13803741		1014;6
K	cassette	CUFF.1122	chrX	+	chrX:107381222-107393381	chrX:107381222-107381342;chrX:107381422-107393381		chrX:107381343-107381421			34;175
N	intron_retention	CUFF.1134	chrX	-	chrX:152988744-152989788				chrX:152988743-152988744;chrX:152989788-152989789		38;232
K	alternative_first_exon	CUFF.1134	chrX	-	chrX:152988744-152988962,chrX:152988744-152989470,chrX:152988744-152989788;chrX:152988744-152989941;chrX:152988744-152989655	chrX:152988744-152989409	chrX:152989942-152990240;chrX:152989656-152989838	chrX:152989410-152989598			287;851
N	jcn_only_AD	CUFF.1098	chrX	-	chrX:9130946-9131117;chrX:9130946-9132333	chrX:9130946-9132573		chrX:9131118-9132333;chrX:9132334-9132573	chrX:9132333-9132334;chrX:9132573-9132574		36;19
K	intron_retention	CUFF.1122	chrX	+	chrX:107335067-107369306				chrX:107335066-107335067;chrX:107369306-107369307		126;35
N	alternative_acceptor	CUFF.1104	chrX	-	chrX:20183080-20185706	chrX:20183179-20185706		chrX:20183080-20183178	chrX:20183079-20183080		29;51
K	jcn_only_AA	CUFF.1110	chrX	+	chrX:47035986-47040613	chrX:47035986-47038501					19;50
N	alternative_acceptor	CUFF.1114	chrX	-	chrX:85118100-85282494	chrX:85236814-85282494		chrX:85118100-85236813	chrX:85118099-85118100		11;3
N	intron_retention		chrX	+	chrX:103358265-103359942				chrX:103358264-103358265;chrX:103359942-103359943		13;1153
K	intron_retention	CUFF.1103	chrX	-	chrX:19933168-19933762				chrX:19933167-19933168;chrX:19933762-19933763		139;76
N	alternative_acceptor		chrX	-	chrX:46382561-46387784;chrX:46384874-46387784	chrX:46360768-46387784		chrX:46360768-46382560;chrX:46382561-46384873	chrX:46360767-46360768;chrX:46382560-46382561		11;16
K	alternative_donor	CUFF.1135	chrX	+	chrX:153238312-153247300	chrX:153238338-153247300		chrX:153238312-153238337	chrX:153238311-153238312	chrX:153247301-153248646;chrX:153237778-153238311	68;46
N	cassette	CUFF.1095	chrX	+	chrX:1419520-1424338	chrX:1419520-1422815;chrX:1422913-1424338		chrX:1422816-1422912			124;229
K	coord_cassette	CUFF.1122	chrX	+	chrX:107369418-107374489	chrX:107369418-107370022;chrX:107370325-107372010;chrX:107372083-107374489		chrX:107370023-107370324;chrX:107372011-107372082			58;24
N	jcn_only_AD	CUFF.1100,CUFF.1121	chrX	-	chrX:13801641-13803740	chrX:13801641-13801897		chrX:13801898-13803740	chrX:13803740-13803741		1014;29
K	alternative_last_exon	CUFF.1108	chrX	-	chrX:46360771-46387769	chrX:46382561-46387769	chrX:46357063-46360770	chrX:46382351-46382560			4;39
K	intron_retention	CUFF.1130	chrX	-	chrX:134290954-134291240				chrX:134290953-134290954;chrX:134291240-134291241		69;60
K	cassette	CUFF.1113	chrX	+	chrX:78005721-78006706	chrX:78005721-78006226;chrX:78006290-78006706		chrX:78006227-78006289			16;80
N	alternative_donor		chrX	+	chrX:148863659-148867418	chrX:148863691-148867418		chrX:148863659-148863690	chrX:148863658-148863659		53;22
K	alternative_acceptor	CUFF.1100	chrX	-	chrX:13791150-13794356	chrX:13792744-13794356		chrX:13791150-13792743	chrX:13791149-13791150		259;695
K	intron_retention	CUFF.1111	chrX	-	chrX:53569501-53570846				chrX:53569500-53569501;chrX:53570846-53570847		87;34
K	coord_cassette	CUFF.1122	chrX	+	chrX:107377389-107381033	chrX:107377389-107377568;chrX:107377642-107380320;chrX:107380401-107381033		chrX:107377569-107377641;chrX:107380321-107380400			29;178
N	jcn_only_AA		chrX	+	chrX:1393712-1400763;chrX:1393712-1401301	chrX:1393712-1401570		chrX:1400764-1401301;chrX:1401302-1401570	chrX:1401301-1401302;chrX:1401570-1401571		156;15
N	jcn_only_AD	CUFF.1096	chrX	+	chrX:1515542-1517717	chrX:1516118-1517717		chrX:1515542-1516117	chrX:1515541-1515542		269;24
K	jcn_only_AA	CUFF.1106	chrX	+	chrX:45184847-45192754	chrX:45184847-45192518		chrX:45192519-45192754	chrX:45192754-45192755		51;35
N	jcn_only_AA	CUFF.1095	chrX	+	chrX:1393712-1401570;chrX:1393712-1401301	chrX:1393712-1400763		chrX:1400764-1401301;chrX:1401302-1401570	chrX:1401301-1401302;chrX:1401570-1401571		97;74
N	intron_retention		chrX	-	chrX:85118100-85282494				chrX:85118099-85118100;chrX:85282494-85282495		11;22
N	jcn_only_AA		chrX	-	chrX:53652220-53654360	chrX:53652990-53654360					13;25
N	jcn_only_AD	CUFF.1114	chrX	-	chrX:85282562-85302487	chrX:85282562-85302250		chrX:85302251-85302487	chrX:85302487-85302488		36;15
K	alternative_first_exon	CUFF.1113	chrX	+	chrX:78003532-78010287	chrX:78006809-78010287	chrX:78003120-78003531	chrX:78006707-78006808			30;39
K	alternative_donor	CUFF.1128	chrX	+	chrX:133594369-133607388	chrX:133594566-133607388		chrX:133594369-133594565	chrX:133594368-133594369		15;112
N	intron_retention		chrX	-	chrX:119374209-119378618				chrX:119374208-119374209;chrX:119378618-119378619		22;551
N	alternative_acceptor		chrX	+	chrX:1393712-1400763;chrX:1393712-1401301	chrX:1393712-1401570		chrX:1400764-1401301;chrX:1401302-1401570	chrX:1401301-1401302;chrX:1401570-1401571		96;15
K	alternative_first_exon	CUFF.1135	chrX	+	chrX:153238312-153247300,chrX:153238338-153247300	chrX:153246075-153247300	chrX:153237778-153238311	chrX:153245976-153246074		chrX:153247301-153248646	115;86
K	alternative_first_exon	CUFF.1106	chrX	+	chrX:45042590-45184352	chrX:45182893-45184352	chrX:45042409-45042589	chrX:45182792-45182892			48;94
N	intron_retention	CUFF.1134	chrX	-	chrX:152988744-152989470				chrX:152988743-152988744;chrX:152989470-152989471		22;393
K	alternative_last_exon	CUFF.1125	chrX	-	chrX:119355498-119378618,chrX:119374209-119378618;chrX:119271100-119378618;chrX:119377887-119378618	chrX:119312412-119378618	chrX:119270952-119271099;chrX:119374080-119377886	chrX:119312247-119312411			477;149
N	jcn_only_AD	CUFF.1103,CUFF.1134	chrX	-	chrX:19948059-19953926	chrX:19948059-19953475		chrX:19953476-19953926	chrX:19953926-19953927		141;30
K	alternative_last_exon	CUFF.1102	chrX	+	chrX:15711182-15720904;chrX:15711182-15713793	chrX:15711182-15715362	chrX:15720905-15721946;chrX:15713794-15713856	chrX:15715363-15715978			278;134
N	alternative_donor		chrX	-	chrX:9130946-9132573;chrX:9130946-9131117	chrX:9130946-9132333		chrX:9131118-9132333;chrX:9132334-9132573	chrX:9132333-9132334;chrX:9132573-9132574		24;14
K	intron_retention	CUFF.1136	chrX	+	chrX:153609163-153609241				chrX:153609162-153609163;chrX:153609241-153609242		1345;186
N	jcn_only_AA	CUFF.1098	chrX	-	chrX:9050777-9130837	chrX:9130355-9130837		chrX:9050777-9130354	chrX:9050776-9050777		38;18
N	alternative_acceptor	CUFF.1095,CUFF.1102	chrX	+	chrX:1424421-1428294	chrX:1424421-1424520		chrX:1424521-1428294	chrX:1428294-1428295		612;5
N	jcn_only_AA		chrX	-	chrX:46382561-46387784;chrX:46384874-46387784	chrX:46360768-46387784		chrX:46360768-46382560;chrX:46382561-46384873	chrX:46360767-46360768;chrX:46382560-46382561		202;16
K	alternative_first_exon	CUFF.1097,CUFF.1103	chrX	-	chrX:2408814-2418857	chrX:2408814-2418351	chrX:2418858-2419071	chrX:2418352-2418450			116;21
K	intron_retention		chrX	+	chrX:1409403-1413220				chrX:1409402-1409403;chrX:1413220-1413221		997;87
N	alternative_donor	CUFF.1101	chrX	-	chrX:15344169-15349995;chrX:15344169-15349711	chrX:15344169-15349337		chrX:15349338-15349711;chrX:15349712-15349995	chrX:15349711-15349712;chrX:15349995-15349996		202;21
K	cassette	CUFF.1136	chrX	+	chrX:153607927-153608301	chrX:153607927-153608049;chrX:153608155-153608301		chrX:153608050-153608154			1156;232
N	cassette	CUFF.1095	chrX	+	chrX:1401673-1407411	chrX:1401673-1404670;chrX:1404814-1407411		chrX:1404671-1404813			76;960
N	jcn_only_AD	CUFF.1098	chrX	-	chrX:9001117-9050619	chrX:9001117-9001892		chrX:9001893-9050619	chrX:9050619-9050620		39;26
N	intron_retention		chrX	+	chrX:103357938-103358124				chrX:103357937-103357938;chrX:103358124-103358125		39;1724
N	jcn_only_AD	CUFF.1101	chrX	-	chrX:15344169-15349337;chrX:15344169-15349995	chrX:15344169-15349711		chrX:15349338-15349711;chrX:15349712-15349995	chrX:15349711-15349712;chrX:15349995-15349996		54;32
K	jcn_only_AA	CUFF.1100	chrX	-	chrX:13791150-13794356	chrX:13792744-13794356		chrX:13791150-13792743	chrX:13791149-13791150		259;709
K	jcn_only_AD	CUFF.1122	chrX	+	chrX:107395089-107396208	chrX:107395236-107396208		chrX:107395089-107395235	chrX:107395088-107395089		204;51
K	alternative_acceptor	CUFF.1097	chrX	-	chrX:2408811-2418857	chrX:2408814-2418857		chrX:2408811-2408813	chrX:2408810-2408811		4;86
N	jcn_only_AD	CUFF.1099,CUFF.1101	chrX	-	chrX:10535644-10645504	chrX:10535644-10588329		chrX:10588330-10645504	chrX:10645504-10645505		36;96
K	cassette	CUFF.1110	chrX	+	chrX:47028898-47032526	chrX:47028898-47030426;chrX:47030658-47032526		chrX:47030427-47030657			31;6
K	cassette	CUFF.1101	chrX	-	chrX:15339895-15343141	chrX:15339895-15342786;chrX:15342994-15343141		chrX:15342787-15342993			71;370
K	cassette	CUFF.1138	chrY	+	chrY:20893684-20894740	chrY:20893684-20894044;chrY:20894159-20894740		chrY:20894045-20894158		chrY:20893583-20893683;chrY:20894741-20894877	74;86
K	cassette	CUFF.1140	chrY	-	chrY:24027300-24028418	chrY:24027300-24027386;chrY:24027498-24028418		chrY:24027387-24027497			15;202
K	alternative_last_exon	CUFF.1138	chrY	+	chrY:20894878-20899940	chrY:20894878-20898228	chrY:20899941-20901182	chrY:20898229-20898379		chrY:20894741-20894877	185;65
K	cassette	CUFF.1139	chrY	+	chrY:23675924-23681035	chrY:23675924-23678942;chrY:23679121-23681035		chrY:23678943-23679120			54;28
K	alternative_first_exon	CUFF.1138	chrY	+	chrY:20883069-20893582	chrY:20891910-20893582	chrY:20882957-20883068	chrY:20891726-20891909		chrY:20893583-20893683	53;55
K	cassette	CUFF.1140	chrY	-	chrY:24032860-24037971	chrY:24032860-24034774;chrY:24034953-24037971		chrY:24034775-24034952			37;202
K	intron_retention	CUFF.713	chr22	-	chr22:30741180-30742300				chr22:30741179-30741180;chr22:30742300-30742301		38;52
K	intron_retention	CUFF.701	chr22	+	chr22:20748953-20749622				chr22:20748952-20748953;chr22:20749622-20749623		51;7
N	alternative_acceptor	CUFF.704	chr22	-	chr22:21841217-21841853	chr22:21841265-21841853		chr22:21841217-21841264	chr22:21841216-21841217		290;16
N	intron_retention		chr22	-	chr22:51018232-51018485				chr22:51018231-51018232;chr22:51018485-51018486		290;218
N	alternative_donor	CUFF.717	chr22	+	chr22:45148508-45173041	chr22:45148621-45173041		chr22:45148508-45148620	chr22:45148507-45148508		209;10
N	jcn_only_AA	CUFF.708	chr22	+	chr22:25855483-25856833;chr22:25855483-25905149	chr22:25855483-25915889		chr22:25856834-25905149;chr22:25905150-25915889	chr22:25905149-25905150;chr22:25915889-25915890	chr22:25855383-25855482	88;23
N	mutually_exclusive	CUFF.717	chr22	+	chr22:45182487-45204186,chr22:45204319-45210551	chr22:45182487-45197956,chr22:45198045-45210551	chr22:45204187-45204318	chr22:45197957-45198044			9;7
K	jcn_only_AA	CUFF.701,CUFF.717	chr22	+	chr22:45122515-45182336	chr22:45122515-45127609					234;14
K	intron_retention	CUFF.697	chr22	-	chr22:18077383-18080959				chr22:18077382-18077383;chr22:18080959-18080960		137;117
K	jcn_only_AD	CUFF.706	chr22	+	chr22:24717292-24720187	chr22:24718887-24720187		chr22:24717292-24718886	chr22:24717291-24717292	chr22:24720188-24720395;chr22:24717256-24717291	126;114
K	cassette	CUFF.697	chr22	-	chr22:18096087-18111368	chr22:18096087-18102226;chr22:18102293-18111368		chr22:18102227-18102292			25;277
N	alternative_acceptor		chr22	+	chr22:29668421-29669726;chr22:29668421-29674119	chr22:29668421-29669729		chr22:29669727-29669729;chr22:29669730-29674119	chr22:29669729-29669730;chr22:29674119-29674120		99;41
N	jcn_only_AA	CUFF.697	chr22	-	chr22:18096087-18102226	chr22:18101894-18102226		chr22:18096087-18101893	chr22:18096086-18096087		445;23
N	intron_retention		chr22	-	chr22:30735024-30736197				chr22:30735023-30735024;chr22:30736197-30736198		46;24
K	alternative_acceptor	CUFF.710	chr22	+	chr22:29668242-29668374	chr22:29668242-29668368		chr22:29668369-29668374	chr22:29668374-29668375		84;421
K	intron_retention		chr22	+	chr22:25855483-25856833				chr22:25855482-25855483;chr22:25856833-25856834	chr22:25855383-25855482;chr22:25856834-25857645	72;28
K	jcn_only_AD	CUFF.710	chr22	+	chr22:29683124-29688125	chr22:29687589-29688125					7;210
N	alternative_donor		chr22	-	chr22:51018232-51018485	chr22:51018232-51018402		chr22:51018403-51018485	chr22:51018485-51018486		290;69
K	jcn_only_AA	CUFF.715	chr22	+	chr22:37697061-37697975	chr22:37697061-37697921		chr22:37697922-37697975	chr22:37697975-37697976		119;84
K	alternative_first_exon	CUFF.722	chr22	-	chr22:51020787-51039578	chr22:51020787-51020986	chr22:51039579-51039979	chr22:51020987-51021428			114;429
K	cassette	CUFF.719	chr22	+	chr22:47188474-47189397	chr22:47188474-47188564;chr22:47188660-47189397		chr22:47188565-47188659		chr22:47188417-47188473;chr22:47189398-47189738	729;98
N	mutually_exclusive	CUFF.719	chr22	+	chr22:47189739-47274548,chr22:47274620-47287161	chr22:47189739-47193340,chr22:47193518-47287161	chr22:47274549-47274619	chr22:47193341-47193517		chr22:47189398-47189738;chr22:47287162-47287290	337;23
K	intron_retention	CUFF.703	chr22	+	chr22:21058345-21058475				chr22:21058344-21058345;chr22:21058475-21058476		16;110
N	alternative_acceptor	CUFF.715,CUFF.717	chr22	+	chr22:45173110-45182336	chr22:45173110-45181921		chr22:45181922-45182336	chr22:45182336-45182337		192;9
K	intron_retention		chr22	-	chr22:30735024-30735118				chr22:30735023-30735024;chr22:30735118-30735119		237;28
K	intron_retention	CUFF.722	chr22	-	chr22:51007511-51007764				chr22:51007510-51007511;chr22:51007764-51007765		488;145
K	intron_retention	CUFF.704	chr22	-	chr22:21832391-21832873				chr22:21832390-21832391;chr22:21832873-21832874		165;57
N	jcn_only_AA	CUFF.708	chr22	+	chr22:25855483-25856833;chr22:25855483-25915889	chr22:25855483-25905149		chr22:25856834-25905149;chr22:25905150-25915889	chr22:25905149-25905150;chr22:25915889-25915890	chr22:25855383-25855482	95;16
K	intron_retention	CUFF.713	chr22	-	chr22:30736371-30736683				chr22:30736370-30736371;chr22:30736683-30736684		97;101
K	intron_retention	CUFF.704	chr22	-	chr22:21829590-21830280				chr22:21829589-21829590;chr22:21830280-21830281		230;53
K	alternative_first_exon	CUFF.710	chr22	+	chr22:29664339-29668204	chr22:29665652-29668204	chr22:29663905-29664338	chr22:29665553-29665651			457;22
N	jcn_only_AD	CUFF.715	chr22	+	chr22:37705365-37707028	chr22:37706074-37707028		chr22:37705365-37706073	chr22:37705364-37705365		119;62
N	intron_retention		chr22	-	chr22:51015023-51015285				chr22:51015022-51015023;chr22:51015285-51015286		33;123
K	cassette	CUFF.706	chr22	+	chr22:24765289-24808615	chr22:24765289-24807555;chr22:24807673-24808615		chr22:24807556-24807672		chr22:24765186-24765288;chr22:24808616-24808675	122;17
K	cassette	CUFF.703	chr22	+	chr22:21056998-21057293	chr22:21056998-21057117;chr22:21057182-21057293		chr22:21057118-21057181			173;33
K	alternative_first_exon	CUFF.719	chr22	+	chr22:47158746-47185208	chr22:47159229-47185208	chr22:47158430-47158745	chr22:47159130-47159228			25;126
N	cassette	CUFF.719	chr22	+	chr22:47193518-47287161	chr22:47193518-47274548;chr22:47274620-47287161		chr22:47274549-47274619		chr22:47193341-47193517;chr22:47287162-47287290	24;324
N	jcn_only_AD	CUFF.717	chr22	+	chr22:45148508-45173041	chr22:45148621-45173041		chr22:45148508-45148620	chr22:45148507-45148508		209;23
K	intron_retention	CUFF.710	chr22	+	chr22:29684776-29686401				chr22:29684775-29684776;chr22:29686401-29686402		239;34
K	intron_retention	CUFF.703	chr22	+	chr22:21058329-21058475				chr22:21058328-21058329;chr22:21058475-21058476		1197;98
N	cassette	CUFF.710	chr22	+	chr22:29674206-29682911	chr22:29674206-29678378;chr22:29678547-29682911		chr22:29678379-29678546			71;582
K	cassette	CUFF.717	chr22	+	chr22:45204319-45210551	chr22:45204319-45204551;chr22:45204613-45210551		chr22:45204552-45204612			462;26
N	alternative_last_exon		chr22	+	chr22:20755049-20759666	chr22:20755049-20755566	chr22:20759667-20762844	chr22:20755567-20755662			27;54
N	alternative_acceptor	CUFF.710	chr22	+	chr22:29668421-29669729;chr22:29668421-29674119	chr22:29668421-29669726		chr22:29669727-29669729;chr22:29669730-29674119	chr22:29669729-29669730;chr22:29674119-29674120		127;13
N	jcn_only_AA	CUFF.715,CUFF.717	chr22	+	chr22:45173110-45182336	chr22:45173110-45181921		chr22:45181922-45182336	chr22:45182336-45182337		192;24
N	coord_cassette	CUFF.719	chr22	+	chr22:47158746-47189397	chr22:47158746-47185208;chr22:47185369-47188416;chr22:47188474-47189397		chr22:47185209-47185368;chr22:47188417-47188473		chr22:47158518-47158745;chr22:47189398-47189738	94;124
K	cassette	CUFF.697	chr22	-	chr22:18082862-18095577	chr22:18082862-18083857;chr22:18083948-18095577		chr22:18083858-18083947			48;176
K	alternative_first_exon	CUFF.703	chr22	+	chr22:21056595-21056873	chr22:21056749-21056873	chr22:21055137-21056594	chr22:21056595-21056748			88;75
N	jcn_only_AA	CUFF.713	chr22	-	chr22:30735169-30752718	chr22:30749062-30752718		chr22:30735169-30749061	chr22:30735168-30735169		30;476
K	intron_retention	CUFF.703	chr22	+	chr22:21057182-21057293				chr22:21057181-21057182;chr22:21057293-21057294		49;158
N	jcn_only_AA	CUFF.704	chr22	-	chr22:21828970-21829499	chr22:21829090-21829499		chr22:21828970-21829089	chr22:21828969-21828970		391;23
N	alternative_acceptor	CUFF.715	chr22	+	chr22:37695348-37696947;chr22:37695348-37696110	chr22:37695348-37696193		chr22:37696111-37696193;chr22:37696194-37696947	chr22:37696193-37696194;chr22:37696947-37696948		207;52
N	jcn_only_AD	CUFF.704	chr22	-	chr22:51015464-51015784	chr22:51015464-51015752		chr22:51015753-51015784	chr22:51015784-51015785		42;464
N	jcn_only_AD	CUFF.722	chr22	-	chr22:30735024-30736197	chr22:30735024-30735118		chr22:30735119-30736197	chr22:30736197-30736198		46;237
N	cassette	CUFF.722	chr22	-	chr22:51014765-51015285	chr22:51014765-51014964;chr22:51015067-51015285		chr22:51014965-51015066			45;258
K	jcn_only_AA	CUFF.707	chr22	-	chr22:25124342-25130050	chr22:25124369-25130050		chr22:25124342-25124368	chr22:25124341-25124342		46;181
N	jcn_only_AA	CUFF.715	chr22	+	chr22:37695348-37696947;chr22:37695348-37696110	chr22:37695348-37696193		chr22:37696111-37696193;chr22:37696194-37696947	chr22:37696193-37696194;chr22:37696947-37696948		226;103
N	jcn_only_AA	CUFF.710	chr22	+	chr22:29668421-29669729;chr22:29668421-29674119	chr22:29668421-29669726		chr22:29669727-29669729;chr22:29669730-29674119	chr22:29669729-29669730;chr22:29674119-29674120		563;148
K	intron_retention	CUFF.704	chr22	-	chr22:21829590-21830290				chr22:21829589-21829590;chr22:21830290-21830291		93;59
K	alternative_acceptor	CUFF.704	chr22	-	chr22:21832391-21832873	chr22:21832451-21832873		chr22:21832391-21832450	chr22:21832390-21832391		165;134
K	cassette	CUFF.715	chr22	+	chr22:37697061-37699294	chr22:37697061-37697975;chr22:37698073-37699294		chr22:37697976-37698072			112;119
N	alternative_acceptor	CUFF.710	chr22	+	chr22:29668421-29669729;chr22:29668421-29669726	chr22:29668421-29674119		chr22:29669727-29669729;chr22:29669730-29674119	chr22:29669729-29669730;chr22:29674119-29674120		54;86
K	cassette	CUFF.715	chr22	+	chr22:37697061-37699294	chr22:37697061-37697921;chr22:37698073-37699294		chr22:37697922-37698072			112;108
K	alternative_first_exon	CUFF.714	chr22	+	chr22:31688685-31733653	chr22:31731403-31733653	chr22:31688485-31688684	chr22:31731284-31731402			28;35
K	intron_retention		chr22	-	chr22:21830450-21830932				chr22:21830449-21830450;chr22:21830932-21830933		212;98
K	jcn_only_AA	CUFF.710	chr22	+	chr22:29668242-29668374	chr22:29668242-29668368		chr22:29668369-29668374	chr22:29668374-29668375		84;856
K	jcn_only_AA	CUFF.710	chr22	+	chr22:29694886-29695223	chr22:29694886-29695184		chr22:29695185-29695223	chr22:29695223-29695224		275;177
K	intron_retention	CUFF.710	chr22	+	chr22:29695322-29695588				chr22:29695321-29695322;chr22:29695588-29695589		304;45
N	intron_retention		chr22	+	chr22:20753981-20754921				chr22:20753980-20753981;chr22:20754921-20754922		11;19
K	cassette	CUFF.710	chr22	+	chr22:29669854-29674018	chr22:29669854-29670253;chr22:29670272-29674018		chr22:29670254-29670271			638;204
K	alternative_donor	CUFF.709	chr22	+	chr22:29469210-29490245	chr22:29469216-29490245		chr22:29469210-29469215	chr22:29469209-29469210		25;20
N	intron_retention		chr22	+	chr22:25855483-25915889				chr22:25855482-25855483;chr22:25915889-25915890	chr22:25855383-25855482	23;21
N	jcn_only_AA		chr22	+	chr22:25855483-25905149;chr22:25855483-25915889	chr22:25855483-25856833		chr22:25856834-25905149;chr22:25905150-25915889	chr22:25905149-25905150;chr22:25915889-25915890	chr22:25855383-25855482	39;72
K	intron_retention	CUFF.710	chr22	+	chr22:29684776-29687553				chr22:29684775-29684776;chr22:29687553-29687554		88;16
N	cassette	CUFF.701	chr22	+	chr22:20748953-20754921	chr22:20748953-20749622;chr22:20749709-20754921		chr22:20749623-20749708			14;50
K	cassette	CUFF.719	chr22	+	chr22:47189739-47274548	chr22:47189739-47193340;chr22:47193518-47274548		chr22:47193341-47193517		chr22:47189398-47189738;chr22:47274549-47274619	387;175
K	intron_retention	CUFF.704	chr22	-	chr22:21842671-21846282				chr22:21842670-21842671;chr22:21846282-21846283		242;162
N	alternative_acceptor		chr22	+	chr22:37695348-37696193;chr22:37695348-37696110	chr22:37695348-37696947		chr22:37696111-37696193;chr22:37696194-37696947	chr22:37696193-37696194;chr22:37696947-37696948		70;189
K	cassette	CUFF.707	chr22	-	chr22:25155957-25158364	chr22:25155957-25157845;chr22:25157929-25158364		chr22:25157846-25157928			97;13
K	intron_retention		chr22	+	chr22:21057981-21058106				chr22:21057980-21057981;chr22:21058106-21058107		433;228
N	coord_cassette	CUFF.722	chr22	-	chr22:51019090-51020677	chr22:51019090-51019848;chr22:51019983-51020177;chr22:51020292-51020677		chr22:51019849-51019982;chr22:51020178-51020291			176;690
N	jcn_only_AA	CUFF.710	chr22	+	chr22:29668421-29669729;chr22:29668421-29669726	chr22:29668421-29674119		chr22:29669727-29669729;chr22:29669730-29674119	chr22:29669729-29669730;chr22:29674119-29674120		626;86
N	cassette	CUFF.703	chr22	+	chr22:21057981-21058255	chr22:21057981-21058106;chr22:21058172-21058255		chr22:21058107-21058171			92;466
K	intron_retention	CUFF.717	chr22	+	chr22:45204319-45204551				chr22:45204318-45204319;chr22:45204551-45204552		29;35
N	intron_retention		chr22	+	chr22:25916130-25916648				chr22:25916129-25916130;chr22:25916648-25916649		25;44
N	intron_retention		chr22	+	chr22:29684745-29688488				chr22:29684744-29684745;chr22:29688488-29688489		17;90
K	cassette	CUFF.719	chr22	+	chr22:47158746-47188416	chr22:47158746-47185208;chr22:47185369-47188416		chr22:47185209-47185368		chr22:47158518-47158745;chr22:47188417-47188473	311;116
K	intron_retention	CUFF.713	chr22	-	chr22:30742509-30748939				chr22:30742508-30742509;chr22:30748939-30748940		65;18
N	jcn_only_AA	CUFF.704	chr22	-	chr22:21841217-21841853	chr22:21841265-21841853		chr22:21841217-21841264	chr22:21841216-21841217		290;25
K	intron_retention	CUFF.704	chr22	-	chr22:21832451-21832873				chr22:21832450-21832451;chr22:21832873-21832874		201;5
N	alternative_acceptor	CUFF.708	chr22	+	chr22:25855483-25856833;chr22:25855483-25905149	chr22:25855483-25915889		chr22:25856834-25905149;chr22:25905150-25915889	chr22:25905149-25905150;chr22:25915889-25915890	chr22:25855383-25855482	7;23
N	cassette	CUFF.704	chr22	-	chr22:21830450-21832078	chr22:21830450-21830932;chr22:21831031-21832078		chr22:21830933-21831030			18;90
N	intron_retention		chr22	-	chr22:51018232-51018402				chr22:51018231-51018232;chr22:51018402-51018403		19;239
N	intron_retention	CUFF.722	chr22	-	chr22:51016364-51016512				chr22:51016363-51016364;chr22:51016512-51016513		23;40
K	intron_retention	CUFF.722	chr22	-	chr22:51018260-51018402				chr22:51018259-51018260;chr22:51018402-51018403		1010;210
K	intron_retention	CUFF.722	chr22	-	chr22:51017937-51018155				chr22:51017936-51017937;chr22:51018155-51018156		1492;26
K	coord_cassette	CUFF.717	chr22	+	chr22:45198045-45210551	chr22:45198045-45204186;chr22:45204319-45204551;chr22:45204613-45210551		chr22:45204187-45204318;chr22:45204552-45204612			10;27
N	jcn_only_AA	CUFF.715,CUFF.719	chr22	+	chr22:37695348-37696193;chr22:37695348-37696947	chr22:37695348-37696110		chr22:37696111-37696193;chr22:37696194-37696947	chr22:37696193-37696194;chr22:37696947-37696948		293;36
K	intron_retention		chr22	+	chr22:20748625-20748852				chr22:20748624-20748625;chr22:20748852-20748853		4;69
N	coord_cassette	CUFF.719	chr22	+	chr22:47158746-47189397	chr22:47158746-47188416;chr22:47188474-47188564;chr22:47188660-47189397		chr22:47188417-47188473;chr22:47188565-47188659		chr22:47158518-47158745;chr22:47189398-47189738	94;102
N	alternative_acceptor	CUFF.708	chr22	+	chr22:25855483-25856833;chr22:25855483-25915889	chr22:25855483-25905149		chr22:25856834-25905149;chr22:25905150-25915889	chr22:25905149-25905150;chr22:25915889-25915890	chr22:25855383-25855482	28;2
K	alternative_acceptor	CUFF.709,CUFF.710	chr22	+	chr22:29521405-29533489	chr22:29521405-29533329		chr22:29533330-29533489	chr22:29533489-29533490		218;77
K	intron_retention	CUFF.722	chr22	-	chr22:51018701-51018786				chr22:51018700-51018701;chr22:51018786-51018787		751;569
K	alternative_last_exon	CUFF.709	chr22	+	chr22:29538089-29563031	chr22:29538089-29550325	chr22:29563032-29564420	chr22:29550326-29550834			114;54
N	jcn_only_AD	CUFF.722	chr22	-	chr22:51012145-51012763	chr22:51012145-51012236		chr22:51012237-51012763	chr22:51012763-51012764		362;91
N	intron_retention		chr22	-	chr22:30741057-30742372				chr22:30741056-30741057;chr22:30742372-30742373		2;219
K	jcn_only_AD	CUFF.704	chr22	-	chr22:21829590-21830290	chr22:21829590-21830280		chr22:21830281-21830290	chr22:21830290-21830291		93;230
N	jcn_only_AD	CUFF.701	chr22	+	chr22:20748625-20749622	chr22:20748953-20749622		chr22:20748625-20748952	chr22:20748624-20748625		17;51
N	intron_retention		chr22	-	chr22:51011352-51012053				chr22:51011351-51011352;chr22:51012053-51012054		119;298
N	intron_retention		chr22	+	chr22:20748625-20749622				chr22:20748624-20748625;chr22:20749622-20749623		17;31
N	intron_retention		chr22	+	chr22:21057981-21058255				chr22:21057980-21057981;chr22:21058255-21058256		92;223
N	alternative_acceptor	CUFF.722	chr22	-	chr22:51012145-51012763	chr22:51012351-51012763		chr22:51012145-51012350	chr22:51012144-51012145		362;31
K	alternative_acceptor	CUFF.710	chr22	+	chr22:29694886-29695223	chr22:29694886-29695184		chr22:29695185-29695223	chr22:29695223-29695224		275;108
K	intron_retention	CUFF.704	chr22	-	chr22:21831031-21832078				chr22:21831030-21831031;chr22:21832078-21832079		15;97
N	alternative_donor	CUFF.719	chr22	+	chr22:47309343-47393529	chr22:47370296-47393529		chr22:47309343-47370295	chr22:47309342-47309343	chr22:47393530-47393605	17;2
K	intron_retention	CUFF.722	chr22	-	chr22:51009722-51009803				chr22:51009721-51009722;chr22:51009803-51009804		521;108
K	intron_retention	CUFF.722	chr22	-	chr22:51013030-51014463				chr22:51013029-51013030;chr22:51014463-51014464		462;174
N	jcn_only_AD	CUFF.719	chr22	+	chr22:47309343-47393529	chr22:47370296-47393529		chr22:47309343-47370295	chr22:47309342-47309343	chr22:47393530-47393605	17;539
K	alternative_acceptor	CUFF.715	chr22	+	chr22:37697061-37697975	chr22:37697061-37697921		chr22:37697922-37697975	chr22:37697975-37697976		119;54
N	intron_retention		chr22	-	chr22:21830450-21832078				chr22:21830449-21830450;chr22:21832078-21832079		18;114
K	cassette	CUFF.707	chr22	-	chr22:25158489-25170288	chr22:25158489-25165637;chr22:25165757-25170288		chr22:25165638-25165756			110;7
N	intron_retention		chr22	-	chr22:51019090-51020677				chr22:51019089-51019090;chr22:51020677-51020678		176;162
K	intron_retention	CUFF.722	chr22	-	chr22:51020787-51020986				chr22:51020786-51020787;chr22:51020986-51020987		227;586
K	jcn_only_AD	CUFF.703	chr22	+	chr22:21058329-21058475	chr22:21058345-21058475		chr22:21058329-21058344	chr22:21058328-21058329		1197;16
N	alternative_donor	CUFF.704	chr22	-	chr22:51015464-51015784	chr22:51015464-51015752		chr22:51015753-51015784	chr22:51015784-51015785		42;268
K	intron_retention	CUFF.703	chr22	+	chr22:21058040-21058255				chr22:21058039-21058040;chr22:21058255-21058256		334;289
K	intron_retention		chr22	+	chr22:20755049-20755566				chr22:20755048-20755049;chr22:20755566-20755567		81;27
K	intron_retention	CUFF.710	chr22	+	chr22:29695271-29695588				chr22:29695270-29695271;chr22:29695588-29695589		241;43
K	intron_retention	CUFF.722	chr22	-	chr22:51015067-51015285				chr22:51015066-51015067;chr22:51015285-51015286		262;155
K	intron_retention	CUFF.699	chr22	+	chr22:19420131-19420787				chr22:19420130-19420131;chr22:19420787-19420788	chr22:19420788-19420871	341;27
K	intron_retention	CUFF.717	chr22	+	chr22:45148508-45182336				chr22:45148507-45148508;chr22:45182336-45182337		405;6
K	intron_retention	CUFF.722	chr22	-	chr22:51010738-51011303				chr22:51010737-51010738;chr22:51011303-51011304		632;66
K	intron_retention	CUFF.722	chr22	-	chr22:51020292-51020457				chr22:51020291-51020292;chr22:51020457-51020458		95;174
K	alternative_acceptor	CUFF.707	chr22	-	chr22:25124342-25130050	chr22:25124369-25130050		chr22:25124342-25124368	chr22:25124341-25124342		46;104
K	intron_retention	CUFF.703	chr22	+	chr22:21058517-21058598				chr22:21058516-21058517;chr22:21058598-21058599		1042;22
N	intron_retention	CUFF.701	chr22	+	chr22:20748953-20754921				chr22:20748952-20748953;chr22:20754921-20754922		14;17
K	cassette	CUFF.717	chr22	+	chr22:45148508-45182336	chr22:45148508-45173041;chr22:45173110-45182336		chr22:45173042-45173109			405;170
K	intron_retention	CUFF.704	chr22	-	chr22:21831054-21832078				chr22:21831053-21831054;chr22:21832078-21832079		271;74
N	alternative_acceptor	CUFF.722	chr22	-	chr22:51018232-51018402	chr22:51018260-51018402		chr22:51018232-51018259	chr22:51018231-51018232		19;603
K	intron_retention	CUFF.703	chr22	+	chr22:21058172-21058255				chr22:21058171-21058172;chr22:21058255-21058256		661;241
K	cassette	CUFF.715	chr22	+	chr22:37699444-37705252	chr22:37699444-37700212;chr22:37700328-37705252		chr22:37700213-37700327			64;44
K	jcn_only_AA	CUFF.710	chr22	+	chr22:29683124-29688125	chr22:29683124-29684594					7;529
K	intron_retention	CUFF.722	chr22	-	chr22:51019983-51020177				chr22:51019982-51019983;chr22:51020177-51020178		1002;138
K	intron_retention	CUFF.710	chr22	+	chr22:29687589-29688125				chr22:29687588-29687589;chr22:29688125-29688126		210;7
N	alternative_donor	CUFF.722	chr22	-	chr22:30735024-30736197	chr22:30735024-30735118		chr22:30735119-30736197	chr22:30736197-30736198		46;41
K	alternative_first_exon	CUFF.706	chr22	+	chr22:24698353-24709280	chr22:24700421-24709280	chr22:24698163-24698352	chr22:24700322-24700420		chr22:24709281-24709434	198;44
K	alternative_last_exon	CUFF.709,CUFF.719	chr22	+	chr22:47308085-47370185	chr22:47308085-47309229	chr22:47370186-47370295	chr22:47309230-47309352		chr22:47307970-47308084	366;81
N	jcn_only_AD		chr22	-	chr22:51018232-51018485	chr22:51018232-51018402		chr22:51018403-51018485	chr22:51018485-51018486		290;19
N	jcn_only_AA		chr22	+	chr22:29668421-29669726;chr22:29668421-29674119	chr22:29668421-29669729		chr22:29669727-29669729;chr22:29669730-29674119	chr22:29669729-29669730;chr22:29674119-29674120		235;477
N	alternative_donor	CUFF.701	chr22	+	chr22:20748625-20749622	chr22:20748953-20749622		chr22:20748625-20748952	chr22:20748624-20748625		17;96
N	alternative_donor	CUFF.715	chr22	+	chr22:37705365-37707028	chr22:37706074-37707028		chr22:37705365-37706073	chr22:37705364-37705365		119;13
K	jcn_only_AD	CUFF.713	chr22	-	chr22:30738869-30748939	chr22:30738869-30740921					677;329
K	alternative_donor	CUFF.703	chr22	+	chr22:21058329-21058475	chr22:21058345-21058475		chr22:21058329-21058344	chr22:21058328-21058329		1197;75
N	alternative_acceptor		chr22	+	chr22:25855483-25905149;chr22:25855483-25915889	chr22:25855483-25856833		chr22:25856834-25905149;chr22:25905150-25915889	chr22:25905149-25905150;chr22:25915889-25915890	chr22:25855383-25855482	25;5
K	intron_retention	CUFF.722	chr22	-	chr22:51020525-51020677				chr22:51020524-51020525;chr22:51020677-51020678		97;154
K	intron_retention	CUFF.710	chr22	+	chr22:29683124-29688125				chr22:29683123-29683124;chr22:29688125-29688126		7;44
K	intron_retention		chr22	+	chr22:45244941-45255610				chr22:45244940-45244941;chr22:45255610-45255611		506;66
N	coord_cassette	CUFF.722	chr22	-	chr22:51019090-51020677	chr22:51019090-51019848;chr22:51019983-51020177;chr22:51020292-51020457;chr22:51020525-51020677		chr22:51019849-51019982;chr22:51020178-51020291;chr22:51020458-51020524			176;271
K	alternative_donor	CUFF.706	chr22	+	chr22:24717292-24720187	chr22:24718887-24720187		chr22:24717292-24718886	chr22:24717291-24717292	chr22:24720188-24720395;chr22:24717256-24717291	126;166
K	jcn_only_AA	CUFF.704	chr22	-	chr22:21832391-21832873	chr22:21832451-21832873		chr22:21832391-21832450	chr22:21832390-21832391		165;201
K	alternative_donor	CUFF.704	chr22	-	chr22:21829590-21830290	chr22:21829590-21830280		chr22:21830281-21830290	chr22:21830290-21830291		93;142
N	jcn_only_AA		chr22	+	chr22:37695348-37696193;chr22:37695348-37696110	chr22:37695348-37696947		chr22:37696111-37696193;chr22:37696194-37696947	chr22:37696193-37696194;chr22:37696947-37696948		139;189
N	cassette	CUFF.717	chr22	+	chr22:45244941-45258154	chr22:45244941-45255610;chr22:45255715-45258154		chr22:45255611-45255714			37;441
N	intron_retention	CUFF.710	chr22	+	chr22:29684776-29687550				chr22:29684775-29684776;chr22:29687550-29687551		96;17
K	cassette	CUFF.703	chr22	+	chr22:21057411-21057920	chr22:21057411-21057755;chr22:21057813-21057920		chr22:21057756-21057812			102;682
N	jcn_only_AA	CUFF.722	chr22	-	chr22:51012145-51012763	chr22:51012351-51012763		chr22:51012145-51012350	chr22:51012144-51012145		362;76
K	cassette	CUFF.722	chr22	-	chr22:51020292-51020677	chr22:51020292-51020457;chr22:51020525-51020677		chr22:51020458-51020524			721;82
N	alternative_acceptor	CUFF.715,CUFF.719	chr22	+	chr22:37695348-37696193;chr22:37695348-37696947	chr22:37695348-37696110		chr22:37696111-37696193;chr22:37696194-37696947	chr22:37696193-37696194;chr22:37696947-37696948		241;18
K	intron_retention	CUFF.715	chr22	+	chr22:37707569-37708060				chr22:37707568-37707569;chr22:37708060-37708061		121;44
K	alternative_first_exon	CUFF.722	chr22	-	chr22:51016364-51016512;chr22:51016364-51016977	chr22:51016364-51016814	chr22:51016978-51017088	chr22:51016815-51016935			151;95
K	intron_retention	CUFF.710	chr22	+	chr22:29694886-29695223				chr22:29694885-29694886;chr22:29695223-29695224		275;69
K	jcn_only_AA	CUFF.709,CUFF.710	chr22	+	chr22:29521405-29533489	chr22:29521405-29533329		chr22:29533330-29533489	chr22:29533489-29533490		218;84
K	alternative_donor	CUFF.710	chr22	+	chr22:29695271-29695588	chr22:29695322-29695588		chr22:29695271-29695321	chr22:29695270-29695271		241;153
K	alternative_last_exon	CUFF.710,CUFF.715	chr22	+	chr22:29684776-29687550;chr22:29684776-29687553	chr22:29684776-29686401	chr22:29687554-29687588	chr22:29686402-29687545			170;208
K	cassette	CUFF.717	chr22	+	chr22:45198045-45210551	chr22:45198045-45204186;chr22:45204319-45210551		chr22:45204187-45204318			10;647
N	alternative_acceptor	CUFF.722	chr22	-	chr22:51009963-51010434	chr22:51009969-51010434		chr22:51009963-51009968	chr22:51009962-51009963		57;249
K	alternative_first_exon	CUFF.704,CUFF.713	chr22	-	chr22:21846384-21868422;chr22:21846384-21871613	chr22:21846384-21868418	chr22:21871614-21871920	chr22:21868419-21868421			440;17
N	cassette	CUFF.719	chr22	+	chr22:47158746-47189397	chr22:47158746-47188416;chr22:47188474-47189397		chr22:47188417-47188473		chr22:47158518-47158745;chr22:47189398-47189738	94;451
N	alternative_acceptor	CUFF.704	chr22	-	chr22:21828970-21829499	chr22:21829090-21829499		chr22:21828970-21829089	chr22:21828969-21828970		391;20
N	alternative_acceptor	CUFF.697	chr22	-	chr22:18096087-18102226	chr22:18101894-18102226		chr22:18096087-18101893	chr22:18096086-18096087		445;1
K	intron_retention	CUFF.710	chr22	+	chr22:29694886-29695184				chr22:29694885-29694886;chr22:29695184-29695185		177;79
N	jcn_only_AA	CUFF.722	chr22	-	chr22:51018232-51018402	chr22:51018260-51018402		chr22:51018232-51018259	chr22:51018231-51018232		19;1010
N	alternative_acceptor	CUFF.713	chr22	-	chr22:30735169-30752718	chr22:30749062-30752718		chr22:30735169-30749061	chr22:30735168-30735169		30;45
N	cassette	CUFF.701	chr22	+	chr22:20748953-20759666	chr22:20748953-20754921;chr22:20755049-20759666		chr22:20754922-20755048			58;28
N	intron_retention		chr22	+	chr22:50920193-50920265				chr22:50920192-50920193;chr22:50920265-50920266		45;7
K	jcn_only_AD	CUFF.710	chr22	+	chr22:29695271-29695588	chr22:29695322-29695588		chr22:29695271-29695321	chr22:29695270-29695271		241;304
N	cassette	CUFF.717	chr22	+	chr22:45182487-45204186	chr22:45182487-45197956;chr22:45198045-45204186		chr22:45197957-45198044			11;729
K	alternative_first_exon	CUFF.699	chr22	+	chr22:19420131-19420787	chr22:19420383-19420787	chr22:19419425-19420130	chr22:19420288-19420382		chr22:19420788-19420871	491;27
K	intron_retention	CUFF.722	chr22	-	chr22:51020292-51020677				chr22:51020291-51020292;chr22:51020677-51020678		721;164
K	jcn_only_AD	CUFF.709	chr22	+	chr22:29469210-29490245	chr22:29469216-29490245		chr22:29469210-29469215	chr22:29469209-29469210		25;40
N	jcn_only_AA	CUFF.722	chr22	-	chr22:51009963-51010434	chr22:51009969-51010434		chr22:51009963-51009968	chr22:51009962-51009963		57;505
N	alternative_donor	CUFF.722	chr22	-	chr22:51012145-51012763	chr22:51012145-51012236		chr22:51012237-51012763	chr22:51012763-51012764		362;62
K	alternative_last_exon	CUFF.713	chr22	-	chr22:30738869-30748939	chr22:30742509-30748939	chr22:30738460-30738868	chr22:30742301-30742508			419;85
K	intron_retention	CUFF.722	chr22	-	chr22:51017089-51017464				chr22:51017088-51017089;chr22:51017464-51017465		57;440
K	alternative_donor	CUFF.669	chr20	-	chr20:3171466-3172410	chr20:3171466-3171835		chr20:3171836-3172410	chr20:3172410-3172411		64;51
K	intron_retention	CUFF.681	chr20	+	chr20:33589889-33589979				chr20:33589888-33589889;chr20:33589979-33589980		930;141
N	jcn_only_AA	CUFF.679	chr20	-	chr20:31115717-31123243	chr20:31121289-31123243		chr20:31115717-31121288	chr20:31115716-31115717		124;14
N	alternative_donor	CUFF.676	chr20	+	chr20:30156028-30156922;chr20:30155610-30156922;chr20:30156084-30156922	chr20:30149544-30156922		chr20:30149544-30155609;chr20:30155610-30156027;chr20:30156028-30156083	chr20:30149543-30149544;chr20:30155609-30155610;chr20:30156027-30156028		30;37
K	alternative_donor	CUFF.676	chr20	+	chr20:30126065-30132749	chr20:30126163-30132749		chr20:30126065-30126162	chr20:30126064-30126065		289;170
N	cassette	CUFF.676	chr20	+	chr20:30132839-30137866	chr20:30132839-30136831;chr20:30136918-30137866		chr20:30136832-30136917			98;399
K	cassette	CUFF.674	chr20	-	chr20:29966195-29978225	chr20:29966195-29976125;chr20:29976163-29978225		chr20:29976126-29976162			38;29
K	jcn_only_AA	CUFF.682	chr20	-	chr20:34246905-34252800	chr20:34246937-34252800		chr20:34246905-34246936	chr20:34246904-34246905		97;37
N	alternative_donor	CUFF.679	chr20	-	chr20:31115717-31123243;chr20:31115717-31120119	chr20:31115717-31172371		chr20:31120120-31123243;chr20:31123244-31172371	chr20:31123243-31123244;chr20:31172371-31172372		2;119
N	cassette	CUFF.674	chr20	-	chr20:29965243-29978225	chr20:29965243-29966154;chr20:29966195-29978225		chr20:29966155-29966194			21;65
N	jcn_only_AD	CUFF.669	chr20	-	chr20:61991052-61992528	chr20:61991052-61992441		chr20:61992442-61992528	chr20:61992528-61992529		34;2
N	alternative_acceptor	CUFF.676	chr20	+	chr20:30135410-30136479	chr20:30135410-30136182		chr20:30136183-30136479	chr20:30136479-30136480		75;411
K	jcn_only_AD	CUFF.676	chr20	+	chr20:30126065-30132749	chr20:30126163-30132749		chr20:30126065-30126162	chr20:30126064-30126065		289;40
K	cassette	CUFF.685	chr20	-	chr20:61982380-61987326	chr20:61982380-61986847;chr20:61986948-61987326		chr20:61986848-61986947			3;105
K	cassette	CUFF.676	chr20	+	chr20:30136918-30137866	chr20:30136918-30137009;chr20:30137136-30137866		chr20:30137010-30137135			584;834
N	alternative_donor		chr20	+	chr20:30135410-30136479	chr20:30135496-30136479		chr20:30135410-30135495	chr20:30135409-30135410		75;19
K	jcn_only_AD	CUFF.675	chr20	-	chr20:30009482-30011622	chr20:30009482-30011612		chr20:30011613-30011622	chr20:30011622-30011623		59;208
N	jcn_only_AA	CUFF.679	chr20	-	chr20:31097744-31099149;chr20:31074605-31099149	chr20:31062546-31099149					138;261
N	jcn_only_AD	CUFF.676	chr20	+	chr20:30156028-30156922;chr20:30155610-30156922;chr20:30156084-30156922	chr20:30149544-30156922		chr20:30149544-30155609;chr20:30155610-30156027;chr20:30156028-30156083	chr20:30149543-30149544;chr20:30155609-30155610;chr20:30156027-30156028		245;37
N	jcn_only_AD	CUFF.679	chr20	-	chr20:31115717-31123243;chr20:31115717-31120119	chr20:31115717-31172371		chr20:31120120-31123243;chr20:31123244-31172371	chr20:31123243-31123244;chr20:31172371-31172372		146;119
K	alternative_last_exon	CUFF.669	chr20	-	chr20:3171466-3172410	chr20:3171885-3172410	chr20:3170897-3171465	chr20:3171836-3171884			89;15
K	alternative_donor	CUFF.681	chr20	+	chr20:33589330-33589750	chr20:33589396-33589750		chr20:33589330-33589395	chr20:33589329-33589330		1612;74
N	intron_retention		chr20	+	chr20:30136597-30136831				chr20:30136596-30136597;chr20:30136831-30136832		122;876
K	intron_retention	CUFF.668	chr20	+	chr20:2842711-2843248				chr20:2842710-2842711;chr20:2843248-2843249		95;10
K	intron_retention	CUFF.668	chr20	+	chr20:2843357-2843452				chr20:2843356-2843357;chr20:2843452-2843453		112;35
N	jcn_only_AA		chr20	-	chr20:31115717-31172371	chr20:31136689-31172371		chr20:31115717-31136688	chr20:31115716-31115717		119;44
K	jcn_only_AD	CUFF.668	chr20	+	chr20:2842351-2843710	chr20:2843581-2843710					27;139
K	alternative_last_exon	CUFF.680,CUFF.683	chr20	+	chr20:61569606-61572842	chr20:61569606-61569951	chr20:61572843-61572972	chr20:61569952-61570273		chr20:61569388-61569605	19;143
K	intron_retention		chr20	+	chr20:30149540-30154012				chr20:30149539-30149540;chr20:30154012-30154013		1358;74
K	intron_retention	CUFF.668	chr20	+	chr20:2842777-2843224				chr20:2842776-2842777;chr20:2843224-2843225		13;20
N	cassette	CUFF.676	chr20	+	chr20:30137925-30147413	chr20:30137925-30142548;chr20:30142633-30147413		chr20:30142549-30142632			564;873
K	jcn_only_AD	CUFF.681	chr20	+	chr20:33589330-33589750	chr20:33589396-33589750		chr20:33589330-33589395	chr20:33589329-33589330		1612;136
N	intron_retention		chr20	+	chr20:30135410-30136479				chr20:30135409-30135410;chr20:30136479-30136480		75;372
K	alternative_last_exon	CUFF.680	chr20	+	chr20:33114149-33122431	chr20:33114149-33117655	chr20:33122432-33123482	chr20:33117656-33119079			450;132
K	alternative_acceptor	CUFF.676,CUFF.681	chr20	+	chr20:33589889-33589979	chr20:33589889-33589961		chr20:33589962-33589979	chr20:33589979-33589980		930;181
N	coord_cassette	CUFF.676	chr20	+	chr20:30115386-30132749	chr20:30115386-30115724;chr20:30115854-30125981;chr20:30126065-30132749		chr20:30115725-30115853;chr20:30125982-30126064			68;430
K	alternative_donor	CUFF.682	chr20	-	chr20:34246937-34252800	chr20:34246937-34252723		chr20:34252724-34252800	chr20:34252800-34252801		37;22
N	alternative_donor	CUFF.679	chr20	-	chr20:31115717-31172371;chr20:31115717-31123243	chr20:31115717-31120119		chr20:31120120-31123243;chr20:31123244-31172371	chr20:31123243-31123244;chr20:31172371-31172372		121;0
K	jcn_only_AA	CUFF.676,CUFF.683	chr20	+	chr20:30132839-30136831	chr20:30132839-30136767		chr20:30136768-30136831	chr20:30136831-30136832		397;17
N	alternative_donor	CUFF.676	chr20	+	chr20:30149544-30156922;chr20:30156028-30156922;chr20:30156084-30156922	chr20:30155610-30156922		chr20:30149544-30155609;chr20:30155610-30156027;chr20:30156028-30156083	chr20:30149543-30149544;chr20:30155609-30155610;chr20:30156027-30156028		54;13
K	alternative_first_exon	CUFF.673	chr20	+	chr20:21284112-21306916	chr20:21284486-21306916	chr20:21283850-21284111	chr20:21284364-21284485			14;22
K	cassette	CUFF.676	chr20	+	chr20:30154099-30156922	chr20:30154099-30155880;chr20:30156028-30156922		chr20:30155881-30156027			1144;89
K	intron_retention	CUFF.681	chr20	+	chr20:33589153-33589233				chr20:33589152-33589153;chr20:33589233-33589234		365;786
N	jcn_only_AA	CUFF.679	chr20	-	chr20:31062546-31099149;chr20:31074605-31099149	chr20:31097744-31099149					370;29
N	coord_cassette	CUFF.676	chr20	+	chr20:30132839-30137866	chr20:30132839-30136767;chr20:30136918-30137009;chr20:30137136-30137866		chr20:30136768-30136917;chr20:30137010-30137135			98;591
N	jcn_only_AD		chr20	+	chr20:30135410-30136479	chr20:30135496-30136479		chr20:30135410-30135495	chr20:30135409-30135410		75;32
K	alternative_acceptor	CUFF.682	chr20	-	chr20:34246905-34252800	chr20:34246937-34252800		chr20:34246905-34246936	chr20:34246904-34246905		97;17
N	alternative_acceptor	CUFF.667	chr20	-	chr20:1517957-1532336	chr20:1517960-1532336		chr20:1517957-1517959	chr20:1517956-1517957		41;168
K	coord_cassette	CUFF.668	chr20	+	chr20:2840454-2841094	chr20:2840454-2840699;chr20:2840798-2840884;chr20:2841014-2841094		chr20:2840700-2840797;chr20:2840885-2841013			29;19
K	jcn_only_AA	CUFF.668	chr20	+	chr20:2842351-2843710	chr20:2842351-2842450					27;185
K	alternative_first_exon	CUFF.679	chr20	-	chr20:31062546-31099149	chr20:31062546-31071164	chr20:31099150-31099269	chr20:31071165-31071370			175;168
K	cassette	CUFF.670	chr20	-	chr20:14308205-14318049	chr20:14308205-14309779;chr20:14309974-14318049		chr20:14309780-14309973			14;70
K	jcn_only_AD	CUFF.669	chr20	-	chr20:3171466-3172410	chr20:3171466-3171835		chr20:3171836-3172410	chr20:3172410-3172411		64;52
K	intron_retention		chr20	+	chr20:30137925-30142548				chr20:30137924-30137925;chr20:30142548-30142549		1078;28
N	alternative_acceptor	CUFF.679	chr20	-	chr20:31115717-31123243	chr20:31121289-31123243		chr20:31115717-31121288	chr20:31115716-31115717		124;0
N	cassette	CUFF.676	chr20	+	chr20:30132839-30137866	chr20:30132839-30136767;chr20:30136918-30137866		chr20:30136768-30136917			98;440
K	cassette	CUFF.673	chr20	+	chr20:21284112-21307127	chr20:21284112-21306916;chr20:21307045-21307127		chr20:21306917-21307044			11;28
N	alternative_acceptor		chr20	+	chr20:16730120-16744966	chr20:16730120-16730411		chr20:16730412-16744966	chr20:16744966-16744967		23;19
N	jcn_only_AD	CUFF.676	chr20	+	chr20:30132839-30136831	chr20:30136597-30136831		chr20:30132839-30136596	chr20:30132838-30132839		397;122
N	cassette	CUFF.676	chr20	+	chr20:30115386-30132749	chr20:30115386-30125981;chr20:30126163-30132749		chr20:30125982-30126162			68;244
N	cassette	CUFF.676	chr20	+	chr20:30149540-30156922	chr20:30149540-30154012;chr20:30154099-30156922		chr20:30154013-30154098			100;1018
N	coord_cassette	CUFF.674	chr20	-	chr20:29965243-29978225	chr20:29965243-29966154;chr20:29966195-29976125;chr20:29976163-29978225		chr20:29966155-29966194;chr20:29976126-29976162			21;34
N	alternative_donor	CUFF.667,CUFF.675	chr20	-	chr20:1517957-1532516	chr20:1517957-1532336		chr20:1532337-1532516	chr20:1532516-1532517		345;264
K	intron_retention	CUFF.679	chr20	-	chr20:31108726-31115560				chr20:31108725-31108726;chr20:31115560-31115561		118;101
K	cassette	CUFF.676	chr20	+	chr20:30115386-30125981	chr20:30115386-30115724;chr20:30115854-30125981		chr20:30115725-30115853			292;582
N	jcn_only_AD	CUFF.676	chr20	+	chr20:30149544-30156922;chr20:30155610-30156922;chr20:30156084-30156922	chr20:30156028-30156922		chr20:30149544-30155609;chr20:30155610-30156027;chr20:30156028-30156083	chr20:30149543-30149544;chr20:30155609-30155610;chr20:30156027-30156028		261;21
K	alternative_first_exon	CUFF.681	chr20	+	chr20:33567608-33568380	chr20:33568283-33568380	chr20:33567464-33567607	chr20:33568100-33568282			115;19
K	intron_retention	CUFF.681	chr20	+	chr20:33589889-33589961				chr20:33589888-33589889;chr20:33589961-33589962		251;131
N	alternative_donor	CUFF.676	chr20	+	chr20:30149544-30156922;chr20:30156028-30156922;chr20:30155610-30156922	chr20:30156084-30156922		chr20:30149544-30155609;chr20:30155610-30156027;chr20:30156028-30156083	chr20:30149543-30149544;chr20:30155609-30155610;chr20:30156027-30156028		53;14
K	alternative_donor	CUFF.680	chr20	+	chr20:33104267-33114072	chr20:33104682-33114072		chr20:33104267-33104681	chr20:33104266-33104267		379;150
K	jcn_only_AD	CUFF.682	chr20	-	chr20:34246937-34252800	chr20:34246937-34252723		chr20:34252724-34252800	chr20:34252800-34252801		37;39
N	alternative_donor	CUFF.669	chr20	-	chr20:61991052-61992528	chr20:61991052-61992441		chr20:61992442-61992528	chr20:61992528-61992529		34;1
K	jcn_only_AD	CUFF.680	chr20	+	chr20:33104267-33114072	chr20:33104682-33114072		chr20:33104267-33104681	chr20:33104266-33104267		379;126
K	alternative_first_exon	CUFF.675,CUFF.682	chr20	-	chr20:30009482-30016345	chr20:30009482-30011622,chr20:30009482-30011612	chr20:30016346-30016438	chr20:30011623-30011736			86;175
N	jcn_only_AA	CUFF.679	chr20	-	chr20:31097744-31099149;chr20:31062546-31099149	chr20:31074605-31099149					290;109
N	jcn_only_AD		chr20	-	chr20:31115717-31172371;chr20:31115717-31120119	chr20:31115717-31123243		chr20:31120120-31123243;chr20:31123244-31172371	chr20:31123243-31123244;chr20:31172371-31172372		140;124
N	coord_cassette	CUFF.676	chr20	+	chr20:30115386-30132749	chr20:30115386-30115724;chr20:30115854-30125981;chr20:30126163-30132749		chr20:30115725-30115853;chr20:30125982-30126162			68;406
N	jcn_only_AD	CUFF.667,CUFF.675	chr20	-	chr20:1517957-1532516	chr20:1517957-1532336		chr20:1532337-1532516	chr20:1532516-1532517		345;41
K	alternative_acceptor	CUFF.676,CUFF.683	chr20	+	chr20:30132839-30136831	chr20:30132839-30136767		chr20:30136768-30136831	chr20:30136831-30136832		397;435
K	intron_retention	CUFF.676	chr20	+	chr20:30154099-30155880				chr20:30154098-30154099;chr20:30155880-30155881		151;34
K	intron_retention	CUFF.681	chr20	+	chr20:33588962-33589047				chr20:33588961-33588962;chr20:33589047-33589048		11;379
N	alternative_acceptor		chr20	-	chr20:31115717-31172371	chr20:31136689-31172371		chr20:31115717-31136688	chr20:31115716-31115717		119;0
K	alternative_donor	CUFF.675	chr20	-	chr20:30009482-30011622	chr20:30009482-30011612		chr20:30011613-30011622	chr20:30011622-30011623		59;104
N	jcn_only_AA		chr20	+	chr20:16730120-16744966	chr20:16730120-16730411		chr20:16730412-16744966	chr20:16744966-16744967		23;68
N	jcn_only_AA	CUFF.676	chr20	+	chr20:30135410-30136479	chr20:30135410-30136182		chr20:30136183-30136479	chr20:30136479-30136480		75;191
K	jcn_only_AA	CUFF.676,CUFF.681	chr20	+	chr20:33589889-33589979	chr20:33589889-33589961		chr20:33589962-33589979	chr20:33589979-33589980		930;251
N	jcn_only_AD	CUFF.676	chr20	+	chr20:30149544-30156922;chr20:30156028-30156922;chr20:30155610-30156922	chr20:30156084-30156922		chr20:30149544-30155609;chr20:30155610-30156027;chr20:30156028-30156083	chr20:30149543-30149544;chr20:30155609-30155610;chr20:30156027-30156028		201;81
N	coord_cassette	CUFF.676	chr20	+	chr20:30132839-30137866	chr20:30132839-30136831;chr20:30136918-30137009;chr20:30137136-30137866		chr20:30136832-30136917;chr20:30137010-30137135			98;620
N	cassette	CUFF.676	chr20	+	chr20:30115386-30132749	chr20:30115386-30125981;chr20:30126065-30132749		chr20:30125982-30126064			68;238
K	cassette	CUFF.676	chr20	+	chr20:30154099-30156922	chr20:30154099-30155880;chr20:30156084-30156922		chr20:30155881-30156083			1144;125
N	alternative_donor	CUFF.676	chr20	+	chr20:30132839-30136831	chr20:30136597-30136831		chr20:30132839-30136596	chr20:30132838-30132839		397;30
N	alternative_donor		chr20	-	chr20:31115717-31172371;chr20:31115717-31120119	chr20:31115717-31123243		chr20:31120120-31123243;chr20:31123244-31172371	chr20:31123243-31123244;chr20:31172371-31172372		119;2
N	alternative_donor	CUFF.676	chr20	+	chr20:30149544-30156922;chr20:30155610-30156922;chr20:30156084-30156922	chr20:30156028-30156922		chr20:30149544-30155609;chr20:30155610-30156027;chr20:30156028-30156083	chr20:30149543-30149544;chr20:30155609-30155610;chr20:30156027-30156028		64;3
K	jcn_only_AD	CUFF.680	chr20	+	chr20:33114149-33122431	chr20:33118039-33122431					354;17
K	alternative_last_exon	CUFF.679	chr20	-	chr20:31052938-31062403;chr20:31044199-31062403	chr20:31052921-31062403	chr20:31043921-31044198	chr20:31052496-31052920			229;341
N	jcn_only_AD	CUFF.676	chr20	+	chr20:30149544-30156922;chr20:30156028-30156922;chr20:30156084-30156922	chr20:30155610-30156922		chr20:30149544-30155609;chr20:30155610-30156027;chr20:30156028-30156083	chr20:30149543-30149544;chr20:30155609-30155610;chr20:30156027-30156028		139;143
K	intron_retention	CUFF.668	chr20	+	chr20:2844730-2844824				chr20:2844729-2844730;chr20:2844824-2844825		171;171
N	jcn_only_AA	CUFF.667	chr20	-	chr20:1517957-1532336	chr20:1517960-1532336		chr20:1517957-1517959	chr20:1517956-1517957		41;338
N	jcn_only_AD	CUFF.679	chr20	-	chr20:31115717-31172371;chr20:31115717-31123243	chr20:31115717-31120119		chr20:31120120-31123243;chr20:31123244-31172371	chr20:31123243-31123244;chr20:31172371-31172372		243;21
K	intron_retention	CUFF.669	chr20	-	chr20:3171885-3172410				chr20:3171884-3171885;chr20:3172410-3172411		19;15
K	intron_retention	CUFF.695	chr21	-	chr21:47557249-47558421				chr21:47557248-47557249;chr21:47558421-47558422	chr21:47557153-47557248;chr21:47558422-47558560	918;31
N	cassette	CUFF.686	chr21	+	chr21:15695909-15709500	chr21:15695909-15708400;chr21:15708579-15709500		chr21:15708401-15708578			15;133
K	alternative_last_exon	CUFF.689	chr21	-	chr21:39471433-39492400;chr21:39325309-39492400	chr21:39427076-39492400	chr21:39471371-39471432;chr21:39325124-39325308	chr21:39426222-39427075			134;158
K	jcn_only_AD	CUFF.686	chr21	+	chr21:15685442-15688521	chr21:15685453-15688521		chr21:15685442-15685452	chr21:15685441-15685442		17;82
K	alternative_first_exon	CUFF.695	chr21	-	chr21:47558838-47565330	chr21:47558838-47562022	chr21:47565331-47565492	chr21:47562023-47562119		chr21:47558794-47558837	291;14
N	cassette	CUFF.695	chr21	-	chr21:47558561-47562022;chr21:47558561-47565330	chr21:47558561-47558793;chr21:47558838-47565330,chr21:47558838-47562022		chr21:47558794-47558837		chr21:47558422-47558560;chr21:47565331-47565492	121;337
K	jcn_only_AD	CUFF.688,CUFF.691	chr21	-	chr21:30971258-31015145	chr21:30971258-30973547				chr21:30971150-30971257	309;347
N	alternative_acceptor	CUFF.687	chr21	-	chr21:15981890-15985196	chr21:15984967-15985196		chr21:15981890-15984966	chr21:15981889-15981890	chr21:15985197-15985234;chr21:15981803-15981889	318;11
N	jcn_only_AA	CUFF.686	chr21	+	chr21:15680941-15685264	chr21:15680941-15681292		chr21:15681293-15685264	chr21:15685264-15685265		86;13
K	intron_retention	CUFF.695	chr21	-	chr21:47565493-47565731				chr21:47565492-47565493;chr21:47565731-47565732	chr21:47565331-47565492;chr21:47565732-47565861	374;46
N	jcn_only_AA	CUFF.695	chr21	-	chr21:47571895-47572820	chr21:47571920-47572820		chr21:47571895-47571919	chr21:47571894-47571895	chr21:47572821-47572944;chr21:47571806-47571894	265;27
K	jcn_only_AA	CUFF.695	chr21	-	chr21:47556968-47557152	chr21:47556988-47557152		chr21:47556968-47556987	chr21:47556967-47556968	chr21:47557153-47557248;chr21:47556893-47556967	531;276
K	alternative_acceptor	CUFF.691	chr21	-	chr21:40977930-40981509	chr21:40978275-40981509		chr21:40977930-40978274	chr21:40977929-40977930	chr21:40981510-40981592;chr21:40977428-40977929	112;92
K	alternative_last_exon	CUFF.686	chr21	+	chr21:15646479-15659870	chr21:15646479-15651916	chr21:15659871-15660018	chr21:15651917-15651978			45;393
K	alternative_donor	CUFF.686	chr21	+	chr21:15685442-15688521	chr21:15685453-15688521		chr21:15685442-15685452	chr21:15685441-15685442		17;42
K	alternative_first_exon	CUFF.692	chr21	-	chr21:43342195-43362255	chr21:43342195-43346680	chr21:43362256-43362367	chr21:43346681-43346776		chr21:43342081-43342194	162;8
K	alternative_last_exon	CUFF.689	chr21	-	chr21:39427076-39492400;chr21:39325309-39492400	chr21:39471433-39492400	chr21:39426222-39427075;chr21:39325124-39325308	chr21:39471371-39471432			241;51
K	jcn_only_AD	CUFF.695	chr21	-	chr21:47556409-47556898;chr21:47556409-47556828	chr21:47556409-47556892		chr21:47556829-47556892;chr21:47556893-47556898	chr21:47556892-47556893;chr21:47556898-47556899	chr21:47556077-47556408;chr21:47556899-47556967	382;38
K	intron_retention	CUFF.695	chr21	-	chr21:47556968-47557152				chr21:47556967-47556968;chr21:47557152-47557153	chr21:47556893-47556967;chr21:47557153-47557248	531;20
K	jcn_only_AD	CUFF.695	chr21	-	chr21:47556409-47556892;chr21:47556409-47556828	chr21:47556409-47556898		chr21:47556829-47556892;chr21:47556893-47556898	chr21:47556892-47556893;chr21:47556898-47556899	chr21:47556077-47556408;chr21:47556899-47556967	279;141
K	alternative_acceptor	CUFF.695	chr21	-	chr21:47558838-47565330	chr21:47558967-47565330		chr21:47558838-47558966	chr21:47558837-47558838	chr21:47565331-47565492;chr21:47558794-47558837	320;33
N	alternative_donor	CUFF.686	chr21	+	chr21:15680941-15685264	chr21:15681420-15685264		chr21:15680941-15681419	chr21:15680940-15680941		86;3
K	intron_retention	CUFF.686	chr21	+	chr21:15660868-15663890				chr21:15660867-15660868;chr21:15663890-15663891		199;16
N	jcn_only_AD	CUFF.692,CUFF.695	chr21	-	chr21:47566242-47570032	chr21:47566242-47566704		chr21:47566705-47570032	chr21:47570032-47570033	chr21:47566180-47566241;chr21:47570033-47570164	361;22
K	intron_retention	CUFF.686	chr21	+	chr21:15660868-15663606				chr21:15660867-15660868;chr21:15663606-15663607		384;17
N	alternative_acceptor	CUFF.686	chr21	+	chr21:15680941-15685264	chr21:15680941-15681292		chr21:15681293-15685264	chr21:15685264-15685265		86;1
K	jcn_only_AA	CUFF.695	chr21	-	chr21:47558838-47565330	chr21:47558967-47565330		chr21:47558838-47558966	chr21:47558837-47558838	chr21:47565331-47565492;chr21:47558794-47558837	320;37
K	alternative_donor	CUFF.695	chr21	-	chr21:47556409-47556898;chr21:47556409-47556828	chr21:47556409-47556892		chr21:47556829-47556892;chr21:47556893-47556898	chr21:47556892-47556893;chr21:47556898-47556899	chr21:47556077-47556408;chr21:47556899-47556967	482;51
K	alternative_donor	CUFF.695	chr21	-	chr21:47556409-47556892;chr21:47556409-47556828	chr21:47556409-47556898		chr21:47556829-47556892;chr21:47556893-47556898	chr21:47556892-47556893;chr21:47556898-47556899	chr21:47556077-47556408;chr21:47556899-47556967	392;141
N	cassette	CUFF.695	chr21	-	chr21:47558561-47565330	chr21:47558561-47558793;chr21:47558967-47565330		chr21:47558794-47558966		chr21:47558422-47558560;chr21:47565331-47565492	93;172
K	jcn_only_AA	CUFF.691	chr21	-	chr21:40977930-40981509	chr21:40978275-40981509		chr21:40977930-40978274	chr21:40977929-40977930	chr21:40981510-40981592;chr21:40977428-40977929	112;69
K	cassette	CUFF.690	chr21	+	chr21:40178045-40181958	chr21:40178045-40178374;chr21:40178733-40181958		chr21:40178375-40178732			16;51
K	alternative_acceptor	CUFF.695	chr21	-	chr21:47556968-47557152	chr21:47556988-47557152		chr21:47556968-47556987	chr21:47556967-47556968	chr21:47557153-47557248;chr21:47556893-47556967	531;143
N	alternative_donor	CUFF.686	chr21	+	chr21:15664069-15678016	chr21:15676682-15678016		chr21:15664069-15676681	chr21:15664068-15664069		72;37
K	intron_retention	CUFF.686	chr21	+	chr21:15688690-15689793				chr21:15688689-15688690;chr21:15689793-15689794		16;87
N	jcn_only_AD	CUFF.686	chr21	+	chr21:15680941-15685264	chr21:15681420-15685264		chr21:15680941-15681419	chr21:15680940-15680941		86;13
K	alternative_last_exon	CUFF.686	chr21	+	chr21:15664069-15678016	chr21:15664069-15671758	chr21:15678017-15678163	chr21:15671759-15673792			65;224
K	cassette	CUFF.688	chr21	-	chr21:30963546-30971149	chr21:30963546-30968845;chr21:30968891-30971149		chr21:30968846-30968890		chr21:30963432-30963545;chr21:30971150-30971257	227;414
N	jcn_only_AA	CUFF.687	chr21	-	chr21:15981890-15985196	chr21:15984967-15985196		chr21:15981890-15984966	chr21:15981889-15981890	chr21:15985197-15985234;chr21:15981803-15981889	318;25
K	alternative_last_exon	CUFF.691	chr21	-	chr21:40969917-40981509	chr21:40977930-40981509,chr21:40978275-40981509	chr21:40968976-40969916	chr21:40977428-40977929		chr21:40981510-40981592	41;280
N	alternative_acceptor	CUFF.695	chr21	-	chr21:47571895-47572820	chr21:47571920-47572820		chr21:47571895-47571919	chr21:47571894-47571895	chr21:47572821-47572944;chr21:47571806-47571894	265;14
K	alternative_last_exon	CUFF.686	chr21	+	chr21:15660868-15663890	chr21:15660868-15663606	chr21:15663891-15664068	chr21:15663607-15663877			191;364
K	intron_retention	CUFF.686	chr21	+	chr21:15646434-15646458				chr21:15646433-15646434;chr21:15646458-15646459		49;86
K	alternative_first_exon	CUFF.691,CUFF.695	chr21	-	chr21:40969917-40981509	chr21:40969917-40971267	chr21:40981510-40981592	chr21:40971268-40971583		chr21:40969074-40969916	18;56
K	alternative_first_exon	CUFF.686	chr21	+	chr21:15646479-15659870	chr21:15651979-15659870	chr21:15646077-15646478	chr21:15651917-15651978			49;425
N	jcn_only_AD	CUFF.686	chr21	+	chr21:15664069-15678016	chr21:15676682-15678016		chr21:15664069-15676681	chr21:15664068-15664069		72;10
K	jcn_only_AD	CUFF.688,CUFF.695	chr21	-	chr21:47556409-47556892;chr21:47556409-47556898	chr21:47556409-47556828		chr21:47556829-47556892;chr21:47556893-47556898	chr21:47556892-47556893;chr21:47556898-47556899	chr21:47556077-47556408;chr21:47556899-47556967	179;241
K	alternative_donor	CUFF.688,CUFF.695	chr21	-	chr21:47556409-47556892;chr21:47556409-47556898	chr21:47556409-47556828		chr21:47556829-47556892;chr21:47556893-47556898	chr21:47556892-47556893;chr21:47556898-47556899	chr21:47556077-47556408;chr21:47556899-47556967	192;341
N	cassette	CUFF.688	chr21	-	chr21:30909707-30927372	chr21:30909707-30910118;chr21:30910206-30927372		chr21:30910119-30910205		chr21:30909254-30909706;chr21:30927373-30927623	74;45
N	intron_retention		chr21	-	chr21:15984967-15985196				chr21:15984966-15984967;chr21:15985196-15985197	chr21:15984758-15984966;chr21:15985197-15985234	25;82
K	alternative_first_exon	CUFF.686	chr21	+	chr21:15642931-15651916	chr21:15646479-15651916	chr21:15642846-15642930	chr21:15646077-15646478			19;435
K	alternative_last_exon	CUFF.689	chr21	-	chr21:39471433-39492400;chr21:39427076-39492400	chr21:39325309-39492400	chr21:39471371-39471432;chr21:39426222-39427075	chr21:39325124-39325308			209;83
N	alternative_donor	CUFF.692,CUFF.695	chr21	-	chr21:47566242-47570032	chr21:47566242-47566704		chr21:47566705-47570032	chr21:47570032-47570033	chr21:47566180-47566241;chr21:47570033-47570164	361;3
K	intron_retention	CUFF.998	chr7	+	chr7:148982588-148984655				chr7:148982587-148982588;chr7:148984655-148984656		199;20
K	alternative_acceptor	CUFF.1000,CUFF.951	chr7	+	chr7:30791921-30793349	chr7:30791921-30793346		chr7:30793347-30793349	chr7:30793349-30793350		35;10
N	cassette	CUFF.970	chr7	-	chr7:86574363-86594219	chr7:86574363-86577042;chr7:86577239-86594219		chr7:86577043-86577238			4;321
N	alternative_donor	CUFF.953	chr7	-	chr7:37433521-37488462	chr7:37433521-37488277		chr7:37488278-37488462	chr7:37488462-37488463		208;97
N	coord_cassette	CUFF.961	chr7	+	chr7:73101231-73106925	chr7:73101231-73101328;chr7:73101426-73105245;chr7:73105343-73106925		chr7:73101329-73101425;chr7:73105246-73105342			232;505
N	jcn_only_AD	CUFF.970	chr7	-	chr7:86569432-86571333	chr7:86569432-86570667		chr7:86570668-86571333	chr7:86571333-86571334		32;19
N	alternative_acceptor		chr7	+	chr7:6630107-6631333	chr7:6630107-6631276		chr7:6631277-6631333	chr7:6631333-6631334		32;24
N	jcn_only_AA		chr7	-	chr7:156516873-156526870	chr7:156521415-156526870					158;178
K	jcn_only_AA	CUFF.970	chr7	-	chr7:86542382-86544038	chr7:86542521-86544038		chr7:86542382-86542520	chr7:86542381-86542382		26;112
N	cassette	CUFF.1000	chr7	+	chr7:150831656-150837065	chr7:150831656-150835229;chr7:150835401-150837065		chr7:150835230-150835400			9;328
K	intron_retention	CUFF.982	chr7	-	chr7:102234690-102234938				chr7:102234689-102234690;chr7:102234938-102234939		106;113
N	cassette	CUFF.952	chr7	+	chr7:34724297-34851381;chr7:34724297-34867012	chr7:34724297-34818106;chr7:34818178-34851381,chr7:34818178-34867012		chr7:34818107-34818177			95;113
K	alternative_first_exon	CUFF.1004	chr7	-	chr7:156619439-156626446;chr7:156619439-156685621	chr7:156619439-156626432	chr7:156685622-156685996	chr7:156626433-156626486			838;101
N	alternative_donor	CUFF.986	chr7	+	chr7:107254178-107258772;chr7:107256835-107258772	chr7:107253878-107258772		chr7:107253878-107254177;chr7:107254178-107256834	chr7:107253877-107253878;chr7:107254177-107254178		113;130
K	alternative_last_exon	CUFF.986	chr7	+	chr7:107253878-107254098,chr7:107253878-107256705;chr7:107253878-107269266;chr7:107253878-107255690	chr7:107253878-107262074,chr7:107253878-107258772	chr7:107269267-107269714;chr7:107255691-107256405	chr7:107262075-107262315			485;257
K	cassette	CUFF.970	chr7	-	chr7:86539318-86541387	chr7:86539318-86540937;chr7:86541012-86541387		chr7:86540938-86541011			84;135
N	intron_retention		chr7	-	chr7:75053912-75054356				chr7:75053911-75053912;chr7:75054356-75054357		109;100
N	cassette	CUFF.950	chr7	-	chr7:22357657-22396448	chr7:22357657-22395596;chr7:22396231-22396448		chr7:22395597-22396230			62;163
K	coord_cassette	CUFF.998	chr7	+	chr7:148984868-148989301	chr7:148984868-148987028;chr7:148987130-148988646;chr7:148988837-148989301		chr7:148987029-148987129;chr7:148988647-148988836			199;23
K	intron_retention	CUFF.993	chr7	-	chr7:127255150-127255454				chr7:127255149-127255150;chr7:127255454-127255455		232;85
N	intron_retention		chr7	+	chr7:75045309-75045380				chr7:75045308-75045309;chr7:75045380-75045381		102;547
N	alternative_donor	CUFF.997	chr7	+	chr7:136554166-136676933	chr7:136635828-136676933		chr7:136554166-136635827	chr7:136554165-136554166		23;5
N	jcn_only_AD	CUFF.986	chr7	+	chr7:107254178-107258772;chr7:107256835-107258772	chr7:107253878-107258772		chr7:107253878-107254177;chr7:107254178-107256834	chr7:107253877-107253878;chr7:107254177-107254178		69;130
N	alternative_acceptor	CUFF.1004,CUFF.1005	chr7	-	chr7:156469378-156471770;chr7:156469319-156471770	chr7:156471045-156471770		chr7:156469319-156469377;chr7:156469378-156471044	chr7:156469318-156469319;chr7:156469377-156469378		74;62
N	intron_retention		chr7	+	chr7:129028782-129028896				chr7:129028781-129028782;chr7:129028896-129028897		29;142
K	jcn_only_AD	CUFF.961	chr7	+	chr7:73098232-73100965	chr7:73098254-73100965		chr7:73098232-73098253	chr7:73098231-73098232		195;1781
K	coord_cassette	CUFF.960	chr7	+	chr7:65592728-65599266	chr7:65592728-65595113;chr7:65595236-65595730;chr7:65595830-65599266		chr7:65595114-65595235;chr7:65595731-65595829			293;79
K	alternative_last_exon	CUFF.971	chr7	+	chr7:91732141-91739435	chr7:91732141-91734991	chr7:91739436-91740086	chr7:91734992-91735077			48;170
N	alternative_donor		chr7	-	chr7:117501371-117512157;chr7:117501371-117514054	chr7:117501371-117511643		chr7:117511644-117512157;chr7:117512158-117514054	chr7:117512157-117512158;chr7:117514054-117514055		163;5
K	intron_retention	CUFF.961	chr7	+	chr7:73101062-73101147				chr7:73101061-73101062;chr7:73101147-73101148		2488;18
N	jcn_only_AD		chr7	-	chr7:156526952-156529186;chr7:156526952-156549086	chr7:156526952-156540617					344;42
K	intron_retention	CUFF.985	chr7	+	chr7:107215756-107216853				chr7:107215755-107215756;chr7:107216853-107216854		2589;78
N	jcn_only_AD	CUFF.986	chr7	+	chr7:107256835-107258772;chr7:107253878-107258772	chr7:107254178-107258772		chr7:107253878-107254177;chr7:107254178-107256834	chr7:107253877-107253878;chr7:107254177-107254178		170;29
K	intron_retention	CUFF.1004	chr7	-	chr7:156469319-156471770				chr7:156469318-156469319;chr7:156471770-156471771		16;50
K	alternative_first_exon	CUFF.957	chr7	+	chr7:54614433-54614639;chr7:54613910-54614639	chr7:54612482-54614639	chr7:54614318-54614432;chr7:54613811-54613909	chr7:54612315-54612481			215;251
N	jcn_only_AA	CUFF.945,CUFF.966	chr7	+	chr7:6631499-6634065	chr7:6631499-6634042		chr7:6634043-6634065	chr7:6634065-6634066		68;17
N	alternative_donor	CUFF.982	chr7	-	chr7:102251590-102252518;chr7:102251590-102257071	chr7:102251590-102256969		chr7:102252519-102256969;chr7:102256970-102257071	chr7:102256969-102256970;chr7:102257071-102257072		142;44
K	alternative_last_exon	CUFF.965	chr7	-	chr7:74881027-74977921	chr7:74973331-74977921	chr7:74880905-74881026	chr7:74973248-74973330			238;178
N	intron_retention		chr7	+	chr7:75040010-75044162				chr7:75040009-75040010;chr7:75044162-75044163		31;111
K	cassette	CUFF.994	chr7	+	chr7:128850955-128851476	chr7:128850955-128851223;chr7:128851352-128851476		chr7:128851224-128851351			19;149
K	intron_retention	CUFF.986	chr7	+	chr7:107234551-107236311				chr7:107234550-107234551;chr7:107236311-107236312		868;126
K	alternative_acceptor	CUFF.970	chr7	-	chr7:86542382-86544038	chr7:86542521-86544038		chr7:86542382-86542520	chr7:86542381-86542382		26;231
N	intron_retention		chr7	-	chr7:107569651-107569856				chr7:107569650-107569651;chr7:107569856-107569857		78;112
N	alternative_donor	CUFF.989	chr7	-	chr7:110603622-111030626;chr7:110603622-111127293	chr7:110603622-111031893		chr7:111030627-111031893;chr7:111031894-111127293	chr7:111031893-111031894;chr7:111127293-111127294		2096;0
K	cassette	CUFF.986	chr7	+	chr7:107236448-107240841	chr7:107236448-107240676;chr7:107240748-107240841		chr7:107240677-107240747			800;197
N	jcn_only_AA		chr7	+	chr7:128865281-129019481	chr7:128865281-129019478		chr7:129019479-129019481	chr7:129019481-129019482		4;4
N	alternative_donor	CUFF.953	chr7	-	chr7:36934623-37025527;chr7:36934623-37052903	chr7:36934623-37024519		chr7:37024520-37025527;chr7:37025528-37052903	chr7:37025527-37025528;chr7:37052903-37052904		358;3
N	alternative_donor	CUFF.985	chr7	+	chr7:107214329-107215632;chr7:107214267-107215632	chr7:107211712-107215632		chr7:107211712-107214266;chr7:107214267-107214328	chr7:107211711-107211712;chr7:107214266-107214267		11;2661
K	alternative_first_exon	CUFF.948	chr7	+	chr7:16793656-16815835	chr7:16815510-16815835	chr7:16793160-16793655	chr7:16815289-16815509			12;282
K	jcn_only_AA	CUFF.970	chr7	-	chr7:86541488-86542256	chr7:86541562-86542256		chr7:86541488-86541561	chr7:86541487-86541488		28;353
N	jcn_only_AD		chr7	-	chr7:156526952-156540617;chr7:156526952-156549086	chr7:156526952-156529186					367;19
K	cassette	CUFF.986	chr7	+	chr7:107224428-107236311	chr7:107224428-107234399;chr7:107234551-107236311		chr7:107234400-107234550			106;786
K	alternative_first_exon	CUFF.955	chr7	-	chr7:38937730-38969071;chr7:38937730-38971877	chr7:38937730-38948753	chr7:38971878-38972082	chr7:38948754-38948829		chr7:38937691-38937729	73;142
N	alternative_donor	CUFF.986	chr7	+	chr7:107256835-107258772;chr7:107253878-107258772	chr7:107254178-107258772		chr7:107253878-107254177;chr7:107254178-107256834	chr7:107253877-107253878;chr7:107254177-107254178		205;38
N	intron_retention		chr7	+	chr7:107204693-107205032				chr7:107204692-107204693;chr7:107205032-107205033		21;81
K	jcn_only_AD	CUFF.998	chr7	+	chr7:148982588-148984655	chr7:148982788-148984655		chr7:148982588-148982787	chr7:148982587-148982588		199;36
N	alternative_acceptor	CUFF.1004	chr7	-	chr7:156556490-156589082	chr7:156572427-156589082		chr7:156556490-156572426	chr7:156556489-156556490		630;0
K	alternative_donor	CUFF.976	chr7	+	chr7:92158239-92158789	chr7:92158498-92158789		chr7:92158239-92158497	chr7:92158238-92158239		38;44
K	cassette	CUFF.982	chr7	-	chr7:102228218-102232731	chr7:102228218-102230605;chr7:102230744-102232731		chr7:102230606-102230743			66;240
K	jcn_only_AA	CUFF.971	chr7	+	chr7:91730371-91732000	chr7:91730371-91731907		chr7:91731908-91732000	chr7:91732000-91732001		128;83
N	cassette	CUFF.953	chr7	-	chr7:37272800-37298785	chr7:37272800-37283960;chr7:37283997-37298785		chr7:37283961-37283996			47;85
K	intron_retention	CUFF.966	chr7	+	chr7:75040118-75040690				chr7:75040117-75040118;chr7:75040690-75040691		154;5
N	jcn_only_AD	CUFF.985	chr7	+	chr7:107214329-107215632;chr7:107214267-107215632	chr7:107211712-107215632		chr7:107211712-107214266;chr7:107214267-107214328	chr7:107211711-107211712;chr7:107214266-107214267		164;2661
N	jcn_only_AD		chr7	-	chr7:36901342-36934613	chr7:36901342-36909997		chr7:36909998-36934613	chr7:36934613-36934614		58;330
N	alternative_first_exon	CUFF.960	chr7	+	chr7:65579958-65610429	chr7:65599362-65610429	chr7:65579500-65579957	chr7:65599267-65599361			120;353
N	jcn_only_AA		chr7	-	chr7:156476858-156516805	chr7:156480886-156516805					146;314
K	intron_retention	CUFF.941	chr7	+	chr7:208977-286380				chr7:208976-208977;chr7:286380-286381		7;19
N	jcn_only_AA	CUFF.984	chr7	-	chr7:102462651-102553532	chr7:102524760-102553532					119;260
K	jcn_only_AD	CUFF.997	chr7	+	chr7:136553865-136554007	chr7:136553921-136554007		chr7:136553865-136553920	chr7:136553864-136553865		183;196
K	jcn_only_AD	CUFF.971	chr7	+	chr7:91732141-91739435	chr7:91737948-91739435					33;80
N	alternative_donor	CUFF.984,CUFF.989	chr7	-	chr7:110603622-111031893;chr7:110603622-111127293	chr7:110603622-111030626		chr7:111030627-111031893;chr7:111031894-111127293	chr7:111031893-111031894;chr7:111127293-111127294		2096;0
N	jcn_only_AD	CUFF.982	chr7	-	chr7:102251590-102256969;chr7:102251590-102252518	chr7:102251590-102257071		chr7:102252519-102256969;chr7:102256970-102257071	chr7:102256969-102256970;chr7:102257071-102257072		97;140
K	alternative_acceptor	CUFF.971	chr7	+	chr7:91730371-91732000	chr7:91730371-91731907		chr7:91731908-91732000	chr7:91732000-91732001		128;79
K	cassette	CUFF.992	chr7	-	chr7:117364787-117368142	chr7:117364787-117365105;chr7:117365312-117368142		chr7:117365106-117365311			87;44
K	intron_retention	CUFF.976	chr7	+	chr7:92164285-92166164				chr7:92164284-92164285;chr7:92166164-92166165		61;7
K	intron_retention	CUFF.982	chr7	-	chr7:102234690-102234893				chr7:102234689-102234690;chr7:102234893-102234894		101;153
K	alternative_donor	CUFF.997	chr7	+	chr7:136553865-136554007	chr7:136553921-136554007		chr7:136553865-136553920	chr7:136553864-136553865		183;117
N	intron_retention		chr7	+	chr7:150817233-150820880				chr7:150817232-150817233;chr7:150820880-150820881		116;219
K	mutually_exclusive	CUFF.982	chr7	-	chr7:102240836-102246304,chr7:102246435-102249207	chr7:102240836-102242770,chr7:102242853-102249207	chr7:102246305-102246434	chr7:102242771-102242852			34;37
N	jcn_only_AD	CUFF.953	chr7	-	chr7:37053041-37136223	chr7:37053041-37072951		chr7:37072952-37136223	chr7:37136223-37136224		160;174
K	intron_retention	CUFF.993	chr7	-	chr7:127251731-127251998				chr7:127251730-127251731;chr7:127251998-127251999		365;40
N	intron_retention		chr7	-	chr7:37382368-37488462				chr7:37382367-37382368;chr7:37488462-37488463		6;68
N	cassette	CUFF.966	chr7	+	chr7:75042211-75044162	chr7:75042211-75043917;chr7:75044077-75044162		chr7:75043918-75044076			51;278
K	alternative_first_exon	CUFF.957	chr7	+	chr7:54614433-54614639;chr7:54612482-54614639	chr7:54613910-54614639	chr7:54614318-54614432;chr7:54612315-54612481	chr7:54613811-54613909			406;60
N	jcn_only_AD	CUFF.982	chr7	-	chr7:102251590-102252518;chr7:102251590-102257071	chr7:102251590-102256969		chr7:102252519-102256969;chr7:102256970-102257071	chr7:102256969-102256970;chr7:102257071-102257072		174;63
K	cassette	CUFF.982	chr7	-	chr7:102223340-102224664	chr7:102223340-102223450;chr7:102223516-102224664		chr7:102223451-102223515			23;159
K	alternative_last_exon	CUFF.952	chr7	+	chr7:34888276-34888934;chr7:34888276-34917687	chr7:34888276-34889176	chr7:34917688-34918043	chr7:34889177-34889674			276;211
N	cassette	CUFF.961	chr7	+	chr7:73101426-73106925;chr7:73101231-73106925	chr7:73101231-73105245,chr7:73101426-73105245;chr7:73105343-73106925		chr7:73105246-73105342			355;515
N	jcn_only_AD	CUFF.941	chr7	+	chr7:193805-195553	chr7:195328-195553		chr7:193805-195327	chr7:193804-193805		7;37
K	intron_retention		chr7	+	chr7:73101426-73105245				chr7:73101425-73101426;chr7:73105245-73105246		347;649
K	alternative_first_exon	CUFF.954,CUFF.992	chr7	-	chr7:37954056-37966281	chr7:37954056-37955694	chr7:37966282-37966376	chr7:37955695-37956530			58;38
N	jcn_only_AA	CUFF.987	chr7	-	chr7:107572823-107575859	chr7:107572939-107575859		chr7:107572823-107572938	chr7:107572822-107572823		73;197
N	mutually_exclusive	CUFF.961	chr7	+	chr7:73101231-73105245,chr7:73105343-73106925	chr7:73101231-73101328,chr7:73101426-73106925	chr7:73105246-73105342	chr7:73101329-73101425			236;241
K	intron_retention	CUFF.982	chr7	-	chr7:102242853-102249207				chr7:102242852-102242853;chr7:102249207-102249208		27;71
K	alternative_last_exon	CUFF.949	chr7	-	chr7:19095789-19153499	chr7:19152764-19153499	chr7:19095674-19095788	chr7:19152573-19152763			54;367
K	intron_retention	CUFF.989	chr7	-	chr7:110603622-111127293				chr7:110603621-110603622;chr7:111127293-111127294		2096;85
N	intron_retention		chr7	-	chr7:36901342-36934613				chr7:36901341-36901342;chr7:36934613-36934614		58;55
N	cassette	CUFF.989	chr7	-	chr7:110303778-110603555	chr7:110303778-110526648;chr7:110526752-110603555		chr7:110526649-110526751			89;1668
N	intron_retention		chr7	+	chr7:75040010-75040690				chr7:75040009-75040010;chr7:75040690-75040691		40;93
K	alternative_last_exon	CUFF.978	chr7	+	chr7:93621479-93640352	chr7:93621479-93629608	chr7:93640353-93640522	chr7:93629609-93629684			41;42
K	alternative_first_exon	CUFF.1000	chr7	+	chr7:150813738-150813879,chr7:150783097-150813879,chr7:150784160-150813879;chr7:150809332-150813879;chr7:150783148-150813879;chr7:150812729-150813879;chr7:150784292-150813879	chr7:150787635-150813879	chr7:150809218-150809331;chr7:150782832-150783147;chr7:150811718-150812728;chr7:150784160-150784291	chr7:150787580-150787634			636;12
N	alternative_donor	CUFF.966	chr7	+	chr7:75040010-75040937	chr7:75040858-75040937		chr7:75040010-75040857	chr7:75040009-75040010		14;63
K	intron_retention		chr7	+	chr7:107220747-107221203				chr7:107220746-107220747;chr7:107221203-107221204		594;37
N	alternative_first_exon	CUFF.995	chr7	+	chr7:129017465-129019481,chr7:129015768-129019481;chr7:128865281-129019481	chr7:129008393-129019481	chr7:128864864-128865280	chr7:129007894-129008392			103;529
K	alternative_first_exon	CUFF.985	chr7	+	chr7:107204693-107205032,chr7:107204505-107205032;chr7:107204192-107205032	chr7:107204655-107205032	chr7:107203929-107204191	chr7:107204304-107204654			207;2907
N	jcn_only_AD		chr7	-	chr7:110603622-111030626;chr7:110603622-111031893	chr7:110603622-111127293		chr7:111030627-111031893;chr7:111031894-111127293	chr7:111031893-111031894;chr7:111127293-111127294		168;2096
N	alternative_acceptor	CUFF.985	chr7	+	chr7:107215756-107216853	chr7:107215756-107216810		chr7:107216811-107216853	chr7:107216853-107216854		2589;106
N	intron_retention		chr7	+	chr7:150831656-150838984				chr7:150831655-150831656;chr7:150838984-150838985		30;30
K	jcn_only_AD	CUFF.996	chr7	+	chr7:134249522-134252909	chr7:134250299-134252909		chr7:134249522-134250298	chr7:134249521-134249522		24;111
N	jcn_only_AA	CUFF.953	chr7	-	chr7:37256301-37262219	chr7:37257362-37262219		chr7:37256301-37257361	chr7:37256300-37256301		164;64
N	cassette	CUFF.970	chr7	-	chr7:86577239-86688640	chr7:86577239-86594219;chr7:86594341-86688640		chr7:86594220-86594340			6;137
N	jcn_only_AD	CUFF.985	chr7	+	chr7:107211712-107215632;chr7:107214329-107215632	chr7:107214267-107215632		chr7:107211712-107214266;chr7:107214267-107214328	chr7:107211711-107211712;chr7:107214266-107214267		2770;55
N	intron_retention		chr7	+	chr7:75040010-75040937				chr7:75040009-75040010;chr7:75040937-75040938		14;132
N	cassette	CUFF.945	chr7	+	chr7:6641772-6647590	chr7:6641772-6647167;chr7:6647229-6647590		chr7:6647168-6647228			107;334
N	alternative_acceptor	CUFF.950	chr7	-	chr7:22233074-22233532	chr7:22233396-22233532		chr7:22233074-22233395	chr7:22233073-22233074		196;108
N	alternative_donor	CUFF.985	chr7	+	chr7:107211712-107215632;chr7:107214267-107215632	chr7:107214329-107215632		chr7:107211712-107214266;chr7:107214267-107214328	chr7:107211711-107211712;chr7:107214266-107214267		2665;7
N	jcn_only_AA		chr7	-	chr7:75054992-75066792	chr7:75055736-75066792					105;247
K	intron_retention	CUFF.1004	chr7	-	chr7:156473269-156474522				chr7:156473268-156473269;chr7:156474522-156474523		28;47
K	cassette	CUFF.984	chr7	-	chr7:102668006-102669797	chr7:102668006-102669046;chr7:102669196-102669797		chr7:102669047-102669195			18;355
N	jcn_only_AD	CUFF.982	chr7	-	chr7:102251590-102256969;chr7:102251590-102257071	chr7:102251590-102252518		chr7:102252519-102256969;chr7:102256970-102257071	chr7:102256969-102256970;chr7:102257071-102257072		203;35
K	alternative_acceptor	CUFF.943	chr7	-	chr7:1778839-1781844	chr7:1779172-1781844		chr7:1778839-1779171	chr7:1778838-1778839		45;159
K	cassette	CUFF.1004	chr7	-	chr7:156626487-156629506	chr7:156626487-156627171;chr7:156627270-156629506		chr7:156627172-156627269			4418;97
N	intron_retention	CUFF.961	chr7	+	chr7:73108381-73111795				chr7:73108380-73108381;chr7:73111795-73111796		25;116
N	alternative_donor	CUFF.953	chr7	-	chr7:36934623-37052903;chr7:36934623-37024519	chr7:36934623-37025527		chr7:37024520-37025527;chr7:37025528-37052903	chr7:37025527-37025528;chr7:37052903-37052904		359;2
K	intron_retention	CUFF.993	chr7	-	chr7:127251903-127251998				chr7:127251902-127251903;chr7:127251998-127251999		46;32
K	alternative_first_exon	CUFF.957	chr7	+	chr7:54612482-54614639;chr7:54613910-54614639	chr7:54614433-54614639	chr7:54612315-54612481;chr7:54613811-54613909	chr7:54614318-54614432			311;155
N	alternative_donor	CUFF.956	chr7	+	chr7:44247798-44250621	chr7:44250531-44250621		chr7:44247798-44250530	chr7:44247797-44247798		288;84
N	cassette	CUFF.956	chr7	+	chr7:44247798-44251845	chr7:44247798-44250621;chr7:44250724-44251845		chr7:44250622-44250723			99;129
K	intron_retention	CUFF.987	chr7	-	chr7:107580804-107591670				chr7:107580803-107580804;chr7:107591670-107591671		38;59
N	jcn_only_AD	CUFF.956	chr7	+	chr7:44247798-44250621	chr7:44250531-44250621		chr7:44247798-44250530	chr7:44247797-44247798		288;52
N	alternative_donor	CUFF.941	chr7	+	chr7:193805-195553	chr7:195328-195553		chr7:193805-195327	chr7:193804-193805		7;5
N	jcn_only_AD	CUFF.953	chr7	-	chr7:36934623-37025527;chr7:36934623-37052903	chr7:36934623-37024519		chr7:37024520-37025527;chr7:37025528-37052903	chr7:37025527-37025528;chr7:37052903-37052904		467;113
N	alternative_donor	CUFF.960	chr7	+	chr7:65579958-65592690;chr7:65591631-65592690	chr7:65579902-65592690		chr7:65579902-65579957;chr7:65579958-65591630	chr7:65579901-65579902;chr7:65579957-65579958		325;227
K	jcn_only_AD	CUFF.976	chr7	+	chr7:92158239-92158789	chr7:92158498-92158789		chr7:92158239-92158497	chr7:92158238-92158239		38;46
N	intron_retention		chr7	+	chr7:107220747-107224326				chr7:107220746-107220747;chr7:107224326-107224327		137;22
N	jcn_only_AD		chr7	-	chr7:86594341-86595129	chr7:86594341-86595124		chr7:86595125-86595129	chr7:86595129-86595130		49;262
K	cassette	CUFF.960	chr7	+	chr7:65592728-65599266	chr7:65592728-65595730;chr7:65595830-65599266		chr7:65595731-65595829			293;152
K	alternative_first_exon	CUFF.1000	chr7	+	chr7:150813738-150813879,chr7:150783097-150813879,chr7:150784160-150813879;chr7:150809332-150813879;chr7:150787635-150813879;chr7:150783148-150813879;chr7:150812729-150813879	chr7:150784292-150813879	chr7:150809218-150809331;chr7:150787580-150787634;chr7:150782832-150783147;chr7:150811718-150812728	chr7:150784160-150784291			618;30
K	intron_retention	CUFF.961	chr7	+	chr7:73107745-73107953				chr7:73107744-73107745;chr7:73107953-73107954		803;24
K	intron_retention	CUFF.966	chr7	+	chr7:75044077-75044162				chr7:75044076-75044077;chr7:75044162-75044163		269;49
K	alternative_last_exon	CUFF.987	chr7	-	chr7:107580804-107591670	chr7:107583065-107591670	chr7:107580434-107580803	chr7:107582746-107583064			96;465
N	jcn_only_AA	CUFF.950	chr7	-	chr7:22206767-22232984	chr7:22231261-22232984		chr7:22206767-22231260	chr7:22206766-22206767		54;197
K	coord_cassette	CUFF.982	chr7	-	chr7:102228218-102232731	chr7:102228218-102228680;chr7:102228893-102230605;chr7:102230744-102232731		chr7:102228681-102228892;chr7:102230606-102230743			66;145
N	coord_cassette	CUFF.961	chr7	+	chr7:73106977-73111934	chr7:73106977-73107658;chr7:73107745-73107953;chr7:73108000-73111934		chr7:73107659-73107744;chr7:73107954-73107999			376;221
N	alternative_donor	CUFF.992	chr7	-	chr7:117501371-117511643;chr7:117501371-117512157	chr7:117501371-117514054		chr7:117511644-117512157;chr7:117512158-117514054	chr7:117512157-117512158;chr7:117514054-117514055		9;159
N	jcn_only_AD		chr7	-	chr7:75068503-75070231	chr7:75068503-75069883					2;146
N	alternative_acceptor		chr7	+	chr7:129015768-129019481	chr7:129015768-129019478		chr7:129019479-129019481	chr7:129019481-129019482		85;14
N	cassette	CUFF.953	chr7	-	chr7:36917723-36934458	chr7:36917723-36927164;chr7:36927278-36934458		chr7:36927165-36927277			31;272
N	intron_retention		chr7	+	chr7:107214267-107215632				chr7:107214266-107214267;chr7:107215632-107215633		55;23
N	alternative_donor	CUFF.984	chr7	-	chr7:102453979-102462486	chr7:102453979-102454780		chr7:102454781-102462486	chr7:102462486-102462487		473;4
K	alternative_last_exon	CUFF.952	chr7	+	chr7:34724297-34818106,chr7:34724297-34818073	chr7:34724297-34725362	chr7:34818107-34818177	chr7:34725363-34725829			190;109
N	cassette	CUFF.994	chr7	+	chr7:128848693-128850203	chr7:128848693-128849129;chr7:128849239-128850203		chr7:128849130-128849238			35;13
N	jcn_only_AA	CUFF.949	chr7	-	chr7:19153547-19156293	chr7:19155755-19156293		chr7:19153547-19155754	chr7:19153546-19153547		424;29
N	alternative_donor	CUFF.982	chr7	-	chr7:102251590-102256969;chr7:102251590-102257071	chr7:102251590-102252518		chr7:102252519-102256969;chr7:102256970-102257071	chr7:102256969-102256970;chr7:102257071-102257072		184;2
N	jcn_only_AD	CUFF.995	chr7	+	chr7:129019591-129028896	chr7:129028782-129028896		chr7:129019591-129028781	chr7:129019590-129019591		647;29
N	jcn_only_AA	CUFF.1004,CUFF.1005	chr7	-	chr7:156469378-156471770;chr7:156469319-156471770	chr7:156471045-156471770		chr7:156469319-156469377;chr7:156469378-156471044	chr7:156469318-156469319;chr7:156469377-156469378		121;30
N	alternative_acceptor	CUFF.1000,CUFF.995	chr7	+	chr7:129008393-129019481	chr7:129008393-129019478		chr7:129019479-129019481	chr7:129019481-129019482		356;24
K	intron_retention	CUFF.987	chr7	-	chr7:107599926-107600135				chr7:107599925-107599926;chr7:107600135-107600136		23;49
N	alternative_donor	CUFF.950	chr7	-	chr7:22206767-22232984	chr7:22206767-22231146		chr7:22231147-22232984	chr7:22232984-22232985		54;101
K	intron_retention	CUFF.987	chr7	-	chr7:107572939-107575859				chr7:107572938-107572939;chr7:107575859-107575860		197;240
N	intron_retention		chr7	+	chr7:75042211-75044162				chr7:75042210-75042211;chr7:75044162-75044163		51;24
K	alternative_first_exon	CUFF.1000	chr7	+	chr7:150813738-150813879,chr7:150783097-150813879,chr7:150784160-150813879;chr7:150809332-150813879;chr7:150787635-150813879;chr7:150812729-150813879;chr7:150784292-150813879	chr7:150783148-150813879	chr7:150809218-150809331;chr7:150787580-150787634;chr7:150811718-150812728;chr7:150784160-150784291	chr7:150782832-150783147			604;44
N	intron_retention		chr7	+	chr7:150817833-150820880				chr7:150817832-150817833;chr7:150820880-150820881		86;333
K	coord_cassette	CUFF.998	chr7	+	chr7:148984868-148987028	chr7:148984868-148985521;chr7:148986549-148986638;chr7:148986818-148987028		chr7:148985522-148986548;chr7:148986639-148986817			27;88
K	intron_retention	CUFF.985	chr7	+	chr7:107204655-107205032				chr7:107204654-107204655;chr7:107205032-107205033		3070;68
N	jcn_only_AD	CUFF.947	chr7	-	chr7:7592554-7594786	chr7:7592554-7594318		chr7:7594319-7594786	chr7:7594786-7594787		728;103
N	intron_retention	CUFF.956	chr7	+	chr7:44247798-44250440				chr7:44247797-44247798;chr7:44250440-44250441		78;83
N	cassette	CUFF.965	chr7	-	chr7:74981241-74984789	chr7:74981241-74982815;chr7:74982903-74984789		chr7:74982816-74982902			84;277
K	intron_retention	CUFF.1004	chr7	-	chr7:156589187-156619298				chr7:156589186-156589187;chr7:156619298-156619299		703;47
K	intron_retention	CUFF.1004	chr7	-	chr7:156555871-156556362				chr7:156555870-156555871;chr7:156556362-156556363		775;42
N	alternative_donor	CUFF.947	chr7	-	chr7:7592554-7594786	chr7:7592554-7594318		chr7:7594319-7594786	chr7:7594786-7594787		728;27
K	alternative_acceptor	CUFF.946,CUFF.986	chr7	+	chr7:107234551-107236313	chr7:107234551-107236311		chr7:107236312-107236313	chr7:107236313-107236314		36;505
N	intron_retention		chr7	+	chr7:107220747-107221090				chr7:107220746-107220747;chr7:107221090-107221091		39;17
N	jcn_only_AA	CUFF.985	chr7	+	chr7:107211712-107215632	chr7:107211712-107214148		chr7:107214149-107215632	chr7:107215632-107215633		2661;65
K	intron_retention	CUFF.985	chr7	+	chr7:107207632-107211589				chr7:107207631-107207632;chr7:107211589-107211590		2409;70
K	intron_retention	CUFF.1000	chr7	+	chr7:150820974-150825666				chr7:150820973-150820974;chr7:150825666-150825667		672;117
K	intron_retention	CUFF.998	chr7	+	chr7:148990584-148990841				chr7:148990583-148990584;chr7:148990841-148990842		23;290
N	cassette	CUFF.992	chr7	-	chr7:117424509-117431344	chr7:117424509-117426439;chr7:117426480-117431344		chr7:117426440-117426479			10;1
N	jcn_only_AA		chr7	+	chr7:73108381-73111795;chr7:73108381-73110735	chr7:73108381-73111934		chr7:73110736-73111795;chr7:73111796-73111934	chr7:73111795-73111796;chr7:73111934-73111935		78;393
N	intron_retention		chr7	+	chr7:73098135-73105245				chr7:73098134-73098135;chr7:73105245-73105246		23;164
K	cassette	CUFF.963	chr7	+	chr7:73275597-73279322	chr7:73275597-73275798;chr7:73275922-73279322		chr7:73275799-73275921			60;69
N	coord_cassette	CUFF.971	chr7	+	chr7:91712970-91714808	chr7:91712970-91713953;chr7:91714018-91714132;chr7:91714255-91714808		chr7:91713954-91714017;chr7:91714133-91714254			4;31
N	cassette	CUFF.952	chr7	+	chr7:34724297-34851381;chr7:34724297-34867012	chr7:34724297-34818073;chr7:34818178-34851381,chr7:34818178-34867012		chr7:34818074-34818177			95;150
N	alternative_donor		chr7	-	chr7:36934623-37025527;chr7:36934623-37024519	chr7:36934623-37052903		chr7:37024520-37025527;chr7:37025528-37052903	chr7:37025527-37025528;chr7:37052903-37052904		5;356
N	alternative_donor	CUFF.985	chr7	+	chr7:107211712-107215632;chr7:107214329-107215632	chr7:107214267-107215632		chr7:107211712-107214266;chr7:107214267-107214328	chr7:107211711-107211712;chr7:107214266-107214267		2668;4
K	alternative_last_exon	CUFF.986	chr7	+	chr7:107253878-107254098,chr7:107253878-107256705;chr7:107253878-107269266;chr7:107253878-107262074,chr7:107253878-107258772	chr7:107253878-107255690	chr7:107269267-107269714;chr7:107262075-107262315	chr7:107255691-107256405			454;288
K	cassette	CUFF.957	chr7	+	chr7:54617864-54636823	chr7:54617864-54621559;chr7:54621767-54636823		chr7:54621560-54621766			227;56
K	intron_retention	CUFF.1000	chr7	+	chr7:150814865-150815296				chr7:150814864-150814865;chr7:150815296-150815297		1369;485
N	jcn_only_AA	CUFF.961	chr7	+	chr7:73108381-73111934;chr7:73108381-73110735	chr7:73108381-73111795		chr7:73110736-73111795;chr7:73111796-73111934	chr7:73111795-73111796;chr7:73111934-73111935		445;25
N	jcn_only_AD	CUFF.960	chr7	+	chr7:65579902-65592690;chr7:65579958-65592690	chr7:65591631-65592690		chr7:65579902-65579957;chr7:65579958-65591630	chr7:65579901-65579902;chr7:65579957-65579958		585;21
K	intron_retention	CUFF.971	chr7	+	chr7:91718844-91722410				chr7:91718843-91718844;chr7:91722410-91722411		33;16
K	jcn_only_AA	CUFF.1000,CUFF.978	chr7	+	chr7:150815432-150815591	chr7:150815432-150815560		chr7:150815561-150815591	chr7:150815591-150815592		1036;157
N	alternative_acceptor	CUFF.953	chr7	-	chr7:37053041-37136223	chr7:37073018-37136223		chr7:37053041-37073017	chr7:37053040-37053041		160;2
N	alternative_donor		chr7	-	chr7:110603622-111030626;chr7:110603622-111031893	chr7:110603622-111127293		chr7:111030627-111031893;chr7:111031894-111127293	chr7:111031893-111031894;chr7:111127293-111127294		0;2096
K	cassette	CUFF.955	chr7	-	chr7:38766589-38768141	chr7:38766589-38767940;chr7:38768035-38768141		chr7:38767941-38768034		chr7:38766509-38766588;chr7:38768142-38768186	101;79
N	alternative_last_exon		chr7	+	chr7:73108000-73111934	chr7:73108000-73108321	chr7:73111935-73112024	chr7:73108322-73108881			14;552
K	intron_retention	CUFF.957	chr7	+	chr7:54617864-54636823				chr7:54617863-54617864;chr7:54636823-54636824		227;132
N	alternative_acceptor	CUFF.985	chr7	+	chr7:107207632-107211589	chr7:107207632-107208199		chr7:107208200-107211589	chr7:107211589-107211590		2409;6
K	intron_retention	CUFF.965	chr7	-	chr7:74984930-74988197				chr7:74984929-74984930;chr7:74988197-74988198		114;112
K	alternative_donor	CUFF.998	chr7	+	chr7:148982588-148984655	chr7:148982788-148984655		chr7:148982588-148982787	chr7:148982587-148982588		199;39
N	alternative_donor	CUFF.950	chr7	-	chr7:22233652-22259484	chr7:22233652-22234187		chr7:22234188-22259484	chr7:22259484-22259485		255;0
N	cassette	CUFF.1000	chr7	+	chr7:150815720-150819811	chr7:150815720-150817073;chr7:150817233-150819811		chr7:150817074-150817232			64;1154
K	cassette	CUFF.984	chr7	-	chr7:102462651-102495223	chr7:102462651-102473286;chr7:102473422-102495223		chr7:102473287-102473421			83;99
K	intron_retention	CUFF.987	chr7	-	chr7:107643417-107643555				chr7:107643416-107643417;chr7:107643555-107643556		74;14
K	intron_retention	CUFF.982	chr7	-	chr7:102236555-102240306				chr7:102236554-102236555;chr7:102240306-102240307		455;43
N	jcn_only_AD	CUFF.953	chr7	-	chr7:37433521-37488462	chr7:37433521-37488277		chr7:37488278-37488462	chr7:37488462-37488463		208;46
N	alternative_acceptor	CUFF.964	chr7	-	chr7:74607950-74608617	chr7:74607952-74608617		chr7:74607950-74607951	chr7:74607949-74607950		544;11
K	intron_retention	CUFF.986	chr7	+	chr7:107234551-107236313				chr7:107234550-107234551;chr7:107236313-107236314		36;128
N	jcn_only_AA		chr7	-	chr7:156526952-156549086	chr7:156529310-156549086					325;14
K	intron_retention	CUFF.987	chr7	-	chr7:107570065-107571800				chr7:107570064-107570065;chr7:107571800-107571801		273;189
N	jcn_only_AD	CUFF.989	chr7	-	chr7:110603622-111030626;chr7:110603622-111127293	chr7:110603622-111031893		chr7:111030627-111031893;chr7:111031894-111127293	chr7:111031893-111031894;chr7:111127293-111127294		2161;103
K	alternative_acceptor	CUFF.982	chr7	-	chr7:102236555-102240306	chr7:102236577-102240306		chr7:102236555-102236576	chr7:102236554-102236555		455;117
K	intron_retention	CUFF.982	chr7	-	chr7:102251590-102257071				chr7:102251589-102251590;chr7:102257071-102257072		140;38
N	jcn_only_AD	CUFF.953,CUFF.984	chr7	-	chr7:102572381-102603979	chr7:102572381-102573767		chr7:102573768-102603979	chr7:102603979-102603980		328;54
N	alternative_donor	CUFF.960	chr7	+	chr7:65579902-65592690;chr7:65591631-65592690	chr7:65579958-65592690		chr7:65579902-65579957;chr7:65579958-65591630	chr7:65579901-65579902;chr7:65579957-65579958		227;325
N	alternative_donor		chr7	-	chr7:86594341-86595129	chr7:86594341-86595124		chr7:86595125-86595129	chr7:86595129-86595130		49;129
N	cassette	CUFF.966	chr7	+	chr7:75044513-75045258	chr7:75044513-75044869;chr7:75045057-75045258		chr7:75044870-75045056			130;134
N	jcn_only_AA	CUFF.985	chr7	+	chr7:107207632-107211589	chr7:107207632-107208199		chr7:107208200-107211589	chr7:107211589-107211590		2409;23
K	alternative_last_exon	CUFF.941	chr7	+	chr7:195733-208897	chr7:195733-197129	chr7:208898-208976	chr7:197130-197673			31;930
N	jcn_only_AA	CUFF.1000	chr7	+	chr7:150825772-150831486	chr7:150825772-150828158		chr7:150828159-150831486	chr7:150831486-150831487		712;65
K	cassette	CUFF.981	chr7	-	chr7:100818093-100823322	chr7:100818093-100822377;chr7:100822418-100823322		chr7:100822378-100822417			41;463
N	alternative_acceptor	CUFF.949	chr7	-	chr7:19153547-19156293	chr7:19155755-19156293		chr7:19153547-19155754	chr7:19153546-19153547		424;18
N	jcn_only_AD	CUFF.952	chr7	+	chr7:34888276-34889176	chr7:34889035-34889176		chr7:34888276-34889034	chr7:34888275-34888276		153;24
N	alternative_acceptor	CUFF.985	chr7	+	chr7:107211712-107215632	chr7:107211712-107214148		chr7:107214149-107215632	chr7:107215632-107215633		2661;13
K	intron_retention		chr7	+	chr7:128848693-128849129				chr7:128848692-128848693;chr7:128849129-128849130		15;24
N	alternative_donor	CUFF.966	chr7	+	chr7:75040010-75040690	chr7:75040118-75040690		chr7:75040010-75040117	chr7:75040009-75040010		40;137
K	intron_retention		chr7	+	chr7:75042211-75043917				chr7:75042210-75042211;chr7:75043917-75043918		274;19
N	alternative_donor	CUFF.953,CUFF.984	chr7	-	chr7:102572381-102603979	chr7:102572381-102573767		chr7:102573768-102603979	chr7:102603979-102603980		328;1
K	intron_retention	CUFF.986	chr7	+	chr7:107224428-107236311				chr7:107224427-107224428;chr7:107236311-107236312		106;87
N	coord_cassette	CUFF.966	chr7	+	chr7:75040010-75044162	chr7:75040010-75040937;chr7:75041043-75042066;chr7:75042211-75043917;chr7:75044077-75044162		chr7:75040938-75041042;chr7:75042067-75042210;chr7:75043918-75044076			31;192
K	alternative_first_exon	CUFF.1000	chr7	+	chr7:150813738-150813879,chr7:150783097-150813879,chr7:150784160-150813879;chr7:150809332-150813879;chr7:150787635-150813879;chr7:150783148-150813879;chr7:150784292-150813879	chr7:150812729-150813879	chr7:150809218-150809331;chr7:150787580-150787634;chr7:150782832-150783147;chr7:150784160-150784291	chr7:150811718-150812728			421;227
N	alternative_donor	CUFF.970	chr7	-	chr7:86569432-86571333	chr7:86569432-86570667		chr7:86570668-86571333	chr7:86571333-86571334		32;14
N	jcn_only_AD	CUFF.989	chr7	-	chr7:111161506-111201906	chr7:111161506-111172573		chr7:111172574-111201906	chr7:111201906-111201907		138;146
K	intron_retention	CUFF.970	chr7	-	chr7:86541488-86542256				chr7:86541487-86541488;chr7:86542256-86542257		28;239
K	jcn_only_AA	CUFF.982	chr7	-	chr7:102236555-102240306	chr7:102236577-102240306		chr7:102236555-102236576	chr7:102236554-102236555		455;213
K	cassette	CUFF.951	chr7	+	chr7:30793555-30818047	chr7:30793555-30805960;chr7:30806178-30818047		chr7:30805961-30806177			28;47
N	cassette	CUFF.952	chr7	+	chr7:34724297-34867012;chr7:34818178-34867012	chr7:34724297-34851381,chr7:34818178-34851381;chr7:34851476-34867012		chr7:34851382-34851475			42;193
N	alternative_acceptor	CUFF.945,CUFF.966	chr7	+	chr7:6631499-6634065	chr7:6631499-6634042		chr7:6634043-6634065	chr7:6634065-6634066		68;8
K	cassette	CUFF.984	chr7	-	chr7:102473422-102517913	chr7:102473422-102495223;chr7:102495308-102517913		chr7:102495224-102495307			31;148
K	intron_retention	CUFF.1000	chr7	+	chr7:150837204-150838984				chr7:150837203-150837204;chr7:150838984-150838985		64;20
N	jcn_only_AA	CUFF.999	chr7	+	chr7:65579958-65610429	chr7:65579958-65592690					143;358
K	alternative_acceptor	CUFF.986	chr7	+	chr7:107253878-107262074	chr7:107253878-107258772		chr7:107258773-107262074	chr7:107262074-107262075		189;75
K	alternative_last_exon	CUFF.989	chr7	-	chr7:110603622-111127293	chr7:111123785-111127293	chr7:110603556-110603621	chr7:111123391-111123784			1551;39
N	alternative_donor	CUFF.995	chr7	+	chr7:129019591-129028896	chr7:129028782-129028896		chr7:129019591-129028781	chr7:129019590-129019591		647;5
N	jcn_only_AA	CUFF.989	chr7	-	chr7:111161506-111201906	chr7:111172642-111201906		chr7:111161506-111172641	chr7:111161505-111161506		138;152
N	cassette	CUFF.961	chr7	+	chr7:73101231-73105245;chr7:73101231-73106925	chr7:73101231-73101328;chr7:73101426-73105245,chr7:73101426-73106925		chr7:73101329-73101425			536;918
K	alternative_first_exon	CUFF.958,CUFF.970	chr7	-	chr7:86548627-86549023;chr7:86548627-86554843	chr7:86548627-86550078	chr7:86554844-86554972	chr7:86550079-86550212			86;24
N	jcn_only_AD		chr7	-	chr7:75054992-75066792	chr7:75054992-75055643					105;295
N	alternative_acceptor	CUFF.950	chr7	-	chr7:22206767-22232984	chr7:22231261-22232984		chr7:22206767-22231260	chr7:22206766-22206767		54;4
K	alternative_last_exon	CUFF.986	chr7	+	chr7:107253878-107254098,chr7:107253878-107256705;chr7:107253878-107262074,chr7:107253878-107258772;chr7:107253878-107255690	chr7:107253878-107269266	chr7:107262075-107262315;chr7:107255691-107256405	chr7:107269267-107269714			605;137
K	cassette	CUFF.984	chr7	-	chr7:102669866-102696090	chr7:102669866-102695534;chr7:102695626-102696090		chr7:102695535-102695625			161;157
N	alternative_acceptor	CUFF.1004,CUFF.1005	chr7	-	chr7:156471045-156471770;chr7:156469319-156471770	chr7:156469378-156471770		chr7:156469319-156469377;chr7:156469378-156471044	chr7:156469318-156469319;chr7:156469377-156469378		78;58
N	alternative_donor	CUFF.953	chr7	-	chr7:37053041-37136223	chr7:37053041-37072951		chr7:37072952-37136223	chr7:37136223-37136224		160;1
N	jcn_only_AA	CUFF.1004,CUFF.1005	chr7	-	chr7:156471045-156471770;chr7:156469319-156471770	chr7:156469378-156471770		chr7:156469319-156469377;chr7:156469378-156471044	chr7:156469318-156469319;chr7:156469377-156469378		47;105
K	intron_retention	CUFF.986	chr7	+	chr7:107221023-107221203				chr7:107221022-107221023;chr7:107221203-107221204		10;46
K	cassette	CUFF.960	chr7	+	chr7:65592728-65595730	chr7:65592728-65595113;chr7:65595236-65595730		chr7:65595114-65595235			104;76
N	intron_retention		chr7	+	chr7:107220812-107221203				chr7:107220811-107220812;chr7:107221203-107221204		39;39
K	cassette	CUFF.955	chr7	-	chr7:38835212-38836344	chr7:38835212-38836014;chr7:38836127-38836344		chr7:38836015-38836126		chr7:38835065-38835211;chr7:38836345-38836464	66;176
N	jcn_only_AD	CUFF.985	chr7	+	chr7:107211712-107215632;chr7:107214267-107215632	chr7:107214329-107215632		chr7:107211712-107214266;chr7:107214267-107214328	chr7:107211711-107211712;chr7:107214266-107214267		2715;110
N	alternative_donor	CUFF.982	chr7	-	chr7:102251590-102256969;chr7:102251590-102252518	chr7:102251590-102257071		chr7:102252519-102256969;chr7:102256970-102257071	chr7:102256969-102256970;chr7:102257071-102257072		46;140
N	coord_cassette	CUFF.1004	chr7	-	chr7:156626487-156685621	chr7:156626487-156627171;chr7:156627270-156629506;chr7:156629580-156685621		chr7:156627172-156627269;chr7:156629507-156629579			249;97
K	mutually_exclusive	CUFF.984	chr7	-	chr7:102669866-102695534,chr7:102695626-102696090	chr7:102669866-102687255,chr7:102687468-102696090	chr7:102695535-102695625	chr7:102687256-102687467			158;32
N	jcn_only_AD	CUFF.960	chr7	+	chr7:65579902-65592690;chr7:65591631-65592690	chr7:65579958-65592690		chr7:65579902-65579957;chr7:65579958-65591630	chr7:65579901-65579902;chr7:65579957-65579958		248;358
K	alternative_first_exon	CUFF.986	chr7	+	chr7:107220812-107221203,chr7:107221091-107221203;chr7:107220747-107221203	chr7:107221023-107221203	chr7:107220372-107220746	chr7:107220927-107221022			290;6
K	alternative_acceptor	CUFF.970	chr7	-	chr7:86541488-86542256	chr7:86541562-86542256		chr7:86541488-86541561	chr7:86541487-86541488		28;342
N	alternative_acceptor		chr7	+	chr7:128865281-129019481	chr7:128865281-129019478		chr7:129019479-129019481	chr7:129019481-129019482		4;2
N	jcn_only_AD	CUFF.966	chr7	+	chr7:75040010-75040690	chr7:75040118-75040690		chr7:75040010-75040117	chr7:75040009-75040010		40;154
N	jcn_only_AA	CUFF.1004	chr7	-	chr7:156556490-156589082	chr7:156572427-156589082		chr7:156556490-156572426	chr7:156556489-156556490		630;24
N	alternative_acceptor	CUFF.965	chr7	-	chr7:74953399-74982536	chr7:74981241-74982536		chr7:74953399-74981240	chr7:74953398-74953399		156;3
N	cassette	CUFF.1004	chr7	-	chr7:156626487-156685621	chr7:156626487-156629506;chr7:156629580-156685621		chr7:156629507-156629579			249;3934
K	intron_retention		chr7	+	chr7:150831656-150835229				chr7:150831655-150831656;chr7:150835229-150835230		550;65
K	cassette	CUFF.965	chr7	-	chr7:74984930-74988197	chr7:74984930-74987565;chr7:74987790-74988197		chr7:74987566-74987789			114;266
N	intron_retention		chr7	-	chr7:107572823-107575859				chr7:107572822-107572823;chr7:107575859-107575860		73;385
N	jcn_only_AA	CUFF.964	chr7	-	chr7:74607950-74608617	chr7:74607952-74608617		chr7:74607950-74607951	chr7:74607949-74607950		544;21
K	cassette	CUFF.993	chr7	-	chr7:127251731-127253075	chr7:127251731-127251998;chr7:127252055-127253075		chr7:127251999-127252054			15;347
N	alternative_donor	CUFF.953	chr7	-	chr7:37256301-37262219	chr7:37256301-37257316		chr7:37257317-37262219	chr7:37262219-37262220		164;1
K	jcn_only_AD	CUFF.982	chr7	-	chr7:102234690-102234938	chr7:102234690-102234893		chr7:102234894-102234938	chr7:102234938-102234939		106;101
N	alternative_donor	CUFF.955	chr7	-	chr7:38813845-38816278	chr7:38813845-38814788		chr7:38814789-38816278	chr7:38816278-38816279	chr7:38813715-38813844;chr7:38816279-38816376	60;33
N	alternative_acceptor	CUFF.950	chr7	-	chr7:22162140-22165221	chr7:22165040-22165221		chr7:22162140-22165039	chr7:22162139-22162140		4;6
N	jcn_only_AA	CUFF.1000,CUFF.995	chr7	+	chr7:129008393-129019481	chr7:129008393-129019478		chr7:129019479-129019481	chr7:129019481-129019482		356;48
K	cassette	CUFF.982	chr7	-	chr7:102242853-102249207	chr7:102242853-102246304;chr7:102246435-102249207		chr7:102246305-102246434			27;197
K	alternative_first_exon	CUFF.947,CUFF.970	chr7	-	chr7:7594821-7605544	chr7:7594821-7603867	chr7:7605545-7606627	chr7:7603868-7604049			44;722
N	alternative_acceptor	CUFF.953	chr7	-	chr7:37256301-37262219	chr7:37257362-37262219		chr7:37256301-37257361	chr7:37256300-37256301		164;12
K	cassette	CUFF.1010	chr7	+	chr7:157647568-157649981	chr7:157647568-157648618;chr7:157648823-157649981		chr7:157648619-157648822			150;26
K	alternative_first_exon	CUFF.960	chr7	+	chr7:65610488-65617194	chr7:65615936-65617194	chr7:65610430-65610487	chr7:65615640-65615935			563;275
K	intron_retention	CUFF.1000	chr7	+	chr7:150815432-150815560				chr7:150815431-150815432;chr7:150815560-150815561		157;140
N	cassette	CUFF.945	chr7	+	chr7:6641772-6647167	chr7:6641772-6642294;chr7:6642384-6647167		chr7:6642295-6642383			65;563
K	alternative_first_exon	CUFF.1000	chr7	+	chr7:150813738-150813879,chr7:150783097-150813879,chr7:150784160-150813879;chr7:150787635-150813879;chr7:150783148-150813879;chr7:150812729-150813879;chr7:150784292-150813879	chr7:150809332-150813879	chr7:150787580-150787634;chr7:150782832-150783147;chr7:150811718-150812728;chr7:150784160-150784291	chr7:150809218-150809331			541;107
K	alternative_acceptor	CUFF.993	chr7	-	chr7:127251040-127251588	chr7:127251261-127251588		chr7:127251040-127251260	chr7:127251039-127251040		323;127
K	alternative_donor	CUFF.982	chr7	-	chr7:102234690-102234938	chr7:102234690-102234893		chr7:102234894-102234938	chr7:102234938-102234939		106;70
K	alternative_last_exon	CUFF.1000	chr7	+	chr7:150817233-150820880;chr7:150817233-150819811	chr7:150817233-150817606	chr7:150819812-150820973	chr7:150817607-150817911			242;1399
K	alternative_first_exon	CUFF.961	chr7	+	chr7:73098135-73100965,chr7:73098331-73100965;chr7:73097714-73100965	chr7:73098232-73100965,chr7:73098254-73100965	chr7:73097263-73097713	chr7:73098097-73098231			617;1355
K	cassette	CUFF.965	chr7	-	chr7:74981241-74982815	chr7:74981241-74982536;chr7:74982650-74982815		chr7:74982537-74982649			152;366
N	jcn_only_AD		chr7	-	chr7:156526952-156540617;chr7:156526952-156529186	chr7:156526952-156549086					61;325
N	alternative_first_exon	CUFF.946	chr7	+	chr7:7197058-7273933	chr7:7222452-7273933	chr7:7196933-7197057	chr7:7222140-7222451			59;113
N	alternative_acceptor		chr7	+	chr7:150817833-150820880	chr7:150817833-150819811		chr7:150819812-150820880	chr7:150820880-150820881		86;905
N	intron_retention		chr7	+	chr7:75039744-75044162				chr7:75039743-75039744;chr7:75044162-75044163		124;22
N	jcn_only_AD	CUFF.955	chr7	-	chr7:38869929-38902144	chr7:38869929-38870815		chr7:38870816-38902144	chr7:38902144-38902145	chr7:38869854-38869928;chr7:38902145-38902222	345;31
K	alternative_last_exon	CUFF.961	chr7	+	chr7:73112025-73117708	chr7:73112025-73112161	chr7:73117709-73119590	chr7:73112162-73112636			219;909
K	alternative_acceptor	CUFF.1000,CUFF.978	chr7	+	chr7:150815432-150815591	chr7:150815432-150815560		chr7:150815561-150815591	chr7:150815591-150815592		1036;108
N	alternative_acceptor	CUFF.1000	chr7	+	chr7:150825772-150831486	chr7:150825772-150828158		chr7:150828159-150831486	chr7:150831486-150831487		712;10
K	cassette	CUFF.992	chr7	-	chr7:117385985-117396608	chr7:117385985-117386066;chr7:117386154-117396608		chr7:117386067-117386153			38;23
K	jcn_only_AA	CUFF.1000,CUFF.951	chr7	+	chr7:30791921-30793349	chr7:30791921-30793346		chr7:30793347-30793349	chr7:30793349-30793350		35;20
K	cassette	CUFF.987	chr7	-	chr7:107576102-107577537	chr7:107576102-107576723;chr7:107576819-107577537		chr7:107576724-107576818			409;46
N	jcn_only_AA		chr7	+	chr7:129015768-129019481	chr7:129015768-129019478		chr7:129019479-129019481	chr7:129019481-129019482		85;28
N	intron_retention		chr7	+	chr7:73111847-73111934				chr7:73111846-73111847;chr7:73111934-73111935		20;57
K	intron_retention		chr7	+	chr7:75039744-75039888				chr7:75039743-75039744;chr7:75039888-75039889		187;3
N	alternative_donor	CUFF.986	chr7	+	chr7:107254178-107258772;chr7:107253878-107258772	chr7:107256835-107258772		chr7:107253878-107254177;chr7:107254178-107256834	chr7:107253877-107253878;chr7:107254177-107254178		168;75
K	alternative_donor	CUFF.961	chr7	+	chr7:73098232-73100965	chr7:73098254-73100965		chr7:73098232-73098253	chr7:73098231-73098232		195;964
N	intron_retention		chr7	+	chr7:75045695-75045764				chr7:75045694-75045695;chr7:75045764-75045765		54;618
N	alternative_acceptor	CUFF.961	chr7	+	chr7:73108381-73111934;chr7:73108381-73110735	chr7:73108381-73111795		chr7:73110736-73111795;chr7:73111796-73111934	chr7:73111795-73111796;chr7:73111934-73111935		481;18
N	jcn_only_AA	CUFF.985	chr7	+	chr7:107215756-107216853	chr7:107215756-107216810		chr7:107216811-107216853	chr7:107216853-107216854		2589;165
K	cassette	CUFF.984	chr7	-	chr7:102669866-102696090	chr7:102669866-102687255;chr7:102687468-102696090		chr7:102687256-102687467			161;32
K	intron_retention	CUFF.956	chr7	+	chr7:44247798-44250621				chr7:44247797-44247798;chr7:44250621-44250622		288;88
K	intron_retention	CUFF.966	chr7	+	chr7:75040858-75040937				chr7:75040857-75040858;chr7:75040937-75040938		45;86
N	alternative_donor	CUFF.1000	chr7	+	chr7:150815720-150817073	chr7:150816342-150817073		chr7:150815720-150816341	chr7:150815719-150815720		1903;56
N	cassette	CUFF.1000	chr7	+	chr7:150831656-150838984	chr7:150831656-150837065;chr7:150837204-150838984		chr7:150837066-150837203			30;37
N	alternative_acceptor	CUFF.1004,CUFF.1005	chr7	-	chr7:156469378-156471770;chr7:156471045-156471770	chr7:156469319-156471770		chr7:156469319-156469377;chr7:156469378-156471044	chr7:156469318-156469319;chr7:156469377-156469378		120;16
K	alternative_first_exon	CUFF.984	chr7	-	chr7:102696195-102715142	chr7:102696195-102714692	chr7:102715143-102715383	chr7:102714693-102715025			213;110
N	jcn_only_AD	CUFF.955	chr7	-	chr7:38813845-38816278	chr7:38813845-38814788		chr7:38814789-38816278	chr7:38816278-38816279	chr7:38813715-38813844;chr7:38816279-38816376	60;56
N	jcn_only_AA		chr7	+	chr7:150817833-150820880	chr7:150817833-150819811		chr7:150819812-150820880	chr7:150820880-150820881		86;1086
N	jcn_only_AA	CUFF.961	chr7	+	chr7:73108381-73111795;chr7:73108381-73111934	chr7:73108381-73110735		chr7:73110736-73111795;chr7:73111796-73111934	chr7:73111795-73111796;chr7:73111934-73111935		418;53
K	alternative_first_exon	CUFF.997	chr7	+	chr7:136553740-136554007	chr7:136553865-136554007,chr7:136553921-136554007	chr7:136553416-136553739	chr7:136553742-136553864			31;246
N	cassette	CUFF.955	chr7	-	chr7:38860866-38902144	chr7:38860866-38869853;chr7:38869929-38902144		chr7:38869854-38869928		chr7:38860803-38860865;chr7:38902145-38902222	17;285
N	jcn_only_AD	CUFF.1000	chr7	+	chr7:150815720-150817073	chr7:150816342-150817073		chr7:150815720-150816341	chr7:150815719-150815720		1903;257
N	jcn_only_AD	CUFF.985	chr7	+	chr7:107207632-107211589	chr7:107208311-107211589		chr7:107207632-107208310	chr7:107207631-107207632		2409;30
N	jcn_only_AA	CUFF.970	chr7	-	chr7:86569432-86571333	chr7:86570702-86571333		chr7:86569432-86570701	chr7:86569431-86569432		32;20
K	intron_retention	CUFF.992	chr7	-	chr7:117398025-117400488				chr7:117398024-117398025;chr7:117400488-117400489		89;100
K	intron_retention	CUFF.982	chr7	-	chr7:102246435-102249207				chr7:102246434-102246435;chr7:102249207-102249208		229;40
N	alternative_donor	CUFF.952	chr7	+	chr7:34888276-34889176	chr7:34889035-34889176		chr7:34888276-34889034	chr7:34888275-34888276		153;4
K	intron_retention	CUFF.957	chr7	+	chr7:54617864-54618445				chr7:54617863-54617864;chr7:54618445-54618446		55;50
N	alternative_first_exon	CUFF.995	chr7	+	chr7:129015768-129019478,chr7:128991503-129019478;chr7:128865281-129019478	chr7:129008393-129019478	chr7:128864864-128865280	chr7:129007894-129008392			92;72
N	intron_retention		chr7	+	chr7:100771765-100771809				chr7:100771764-100771765;chr7:100771809-100771810		33;30
K	cassette	CUFF.998	chr7	+	chr7:148987130-148989301	chr7:148987130-148988646;chr7:148988837-148989301		chr7:148988647-148988836			77;27
N	intron_retention		chr7	+	chr7:107204505-107205032				chr7:107204504-107204505;chr7:107205032-107205033		43;1214
K	jcn_only_AA	CUFF.946,CUFF.986	chr7	+	chr7:107234551-107236313	chr7:107234551-107236311		chr7:107236312-107236313	chr7:107236313-107236314		36;868
K	intron_retention	CUFF.966	chr7	+	chr7:75045057-75045258				chr7:75045056-75045057;chr7:75045258-75045259		95;368
N	intron_retention	CUFF.956	chr7	+	chr7:44247798-44248005				chr7:44247797-44247798;chr7:44248005-44248006		104;155
N	jcn_only_AD	CUFF.966	chr7	+	chr7:75040010-75040937	chr7:75040858-75040937		chr7:75040010-75040857	chr7:75040009-75040010		14;45
N	jcn_only_AD	CUFF.950	chr7	-	chr7:22233652-22259484	chr7:22233652-22234187		chr7:22234188-22259484	chr7:22259484-22259485		255;31
K	intron_retention		chr7	+	chr7:73106977-73107658				chr7:73106976-73106977;chr7:73107658-73107659		776;53
N	jcn_only_AA	CUFF.950	chr7	-	chr7:22233074-22233532	chr7:22233396-22233532		chr7:22233074-22233395	chr7:22233073-22233074		196;51
K	alternative_first_exon	CUFF.992	chr7	-	chr7:117432836-117450818	chr7:117432836-117433466	chr7:117450819-117451043	chr7:117433467-117433662			258;27
N	jcn_only_AA		chr7	+	chr7:75039744-75044162	chr7:75039744-75039888					124;187
K	intron_retention	CUFF.1000	chr7	+	chr7:150815432-150815591				chr7:150815431-150815432;chr7:150815591-150815592		1036;160
K	cassette	CUFF.979	chr7	-	chr7:99032892-99057708	chr7:99032892-99039012;chr7:99039111-99057708		chr7:99039013-99039110			99;43
N	alternative_donor		chr7	-	chr7:36901342-36934613	chr7:36901342-36909997		chr7:36909998-36934613	chr7:36934613-36934614		58;3
N	jcn_only_AD	CUFF.984,CUFF.989	chr7	-	chr7:110603622-111031893;chr7:110603622-111127293	chr7:110603622-111030626		chr7:111030627-111031893;chr7:111031894-111127293	chr7:111031893-111031894;chr7:111127293-111127294		2199;65
K	alternative_first_exon	CUFF.953	chr7	-	chr7:37172840-37236705;chr7:37172840-37250990	chr7:37172840-37243713	chr7:37250991-37251122	chr7:37243714-37243905			400;14
K	cassette	CUFF.997	chr7	+	chr7:136554166-136699566	chr7:136554166-136676933;chr7:136677012-136699566		chr7:136676934-136677011			190;26
N	jcn_only_AA	CUFF.953	chr7	-	chr7:37053041-37136223	chr7:37073018-37136223		chr7:37053041-37073017	chr7:37053040-37053041		160;163
N	alternative_donor		chr7	-	chr7:111201980-111202519	chr7:111201980-111202499		chr7:111202500-111202519	chr7:111202519-111202520		223;11
K	alternative_acceptor	CUFF.952	chr7	+	chr7:34724297-34818106	chr7:34724297-34818073		chr7:34818074-34818106	chr7:34818106-34818107		77;88
K	intron_retention	CUFF.986	chr7	+	chr7:107224428-107234399				chr7:107224427-107224428;chr7:107234399-107234400		846;20
N	cassette	CUFF.971	chr7	+	chr7:91609648-91622198	chr7:91609648-91621471;chr7:91621526-91622198		chr7:91621472-91621525			65;13
K	intron_retention	CUFF.982	chr7	-	chr7:102234292-102234496				chr7:102234291-102234292;chr7:102234496-102234497		356;12
K	alternative_first_exon	CUFF.1010	chr7	+	chr7:157647568-157655236	chr7:157650241-157655236	chr7:157647125-157647567	chr7:157649982-157650240			55;109
K	jcn_only_AA	CUFF.993	chr7	-	chr7:127251731-127251998	chr7:127251903-127251998		chr7:127251731-127251902	chr7:127251730-127251731		365;46
K	alternative_donor	CUFF.996	chr7	+	chr7:134249522-134252909	chr7:134250299-134252909		chr7:134249522-134250298	chr7:134249521-134249522		24;65
K	jcn_only_AA	CUFF.986	chr7	+	chr7:107253878-107262074	chr7:107253878-107258772		chr7:107258773-107262074	chr7:107262074-107262075		189;130
N	cassette	CUFF.955	chr7	-	chr7:38908854-38948753	chr7:38908854-38937690;chr7:38937730-38948753		chr7:38937691-38937729		chr7:38908746-38908853	23;214
K	alternative_first_exon	CUFF.947,CUFF.958	chr7	-	chr7:55755618-55759006	chr7:55755618-55756605	chr7:55759007-55759193	chr7:55756606-55756994			16;46
K	intron_retention		chr7	-	chr7:36901342-36909997				chr7:36901341-36901342;chr7:36909997-36909998		330;56
N	jcn_only_AA	CUFF.1004,CUFF.1005	chr7	-	chr7:156469378-156471770;chr7:156471045-156471770	chr7:156469319-156471770		chr7:156469319-156469377;chr7:156469378-156471044	chr7:156469318-156469319;chr7:156469377-156469378		135;16
K	intron_retention	CUFF.1004	chr7	-	chr7:156472001-156473136				chr7:156472000-156472001;chr7:156473136-156473137		16;44
N	alternative_acceptor	CUFF.987	chr7	-	chr7:107572823-107575859	chr7:107572939-107575859		chr7:107572823-107572938	chr7:107572822-107572823		73;303
K	jcn_only_AA	CUFF.993	chr7	-	chr7:127251040-127251588	chr7:127251261-127251588		chr7:127251040-127251260	chr7:127251039-127251040		323;127
K	cassette	CUFF.982	chr7	-	chr7:102228218-102230605	chr7:102228218-102228680;chr7:102228893-102230605		chr7:102228681-102228892			197;169
N	jcn_only_AA	CUFF.941	chr7	+	chr7:7222452-7273933	chr7:7222452-7249057					105;204
N	mutually_exclusive	CUFF.970	chr7	-	chr7:86574363-86594219,chr7:86594341-86688640	chr7:86574363-86577042,chr7:86577239-86688640	chr7:86594220-86594340	chr7:86577043-86577238			4;7
N	jcn_only_AD	CUFF.992	chr7	-	chr7:117501371-117511643;chr7:117501371-117512157	chr7:117501371-117514054		chr7:117511644-117512157;chr7:117512158-117514054	chr7:117512157-117512158;chr7:117514054-117514055		83;159
N	jcn_only_AD	CUFF.997	chr7	+	chr7:136554166-136676933	chr7:136635828-136676933		chr7:136554166-136635827	chr7:136554165-136554166		23;10
N	jcn_only_AD	CUFF.953,CUFF.984	chr7	-	chr7:102608565-102665509	chr7:102608565-102613596		chr7:102613597-102665509	chr7:102665509-102665510		335;31
N	cassette	CUFF.956	chr7	+	chr7:44250724-44251845	chr7:44250724-44251152;chr7:44251204-44251845		chr7:44251153-44251203			27;291
N	intron_retention		chr7	+	chr7:75045049-75045258				chr7:75045048-75045049;chr7:75045258-75045259		37;371
N	jcn_only_AD	CUFF.953	chr7	-	chr7:37256301-37262219	chr7:37256301-37257316		chr7:37257317-37262219	chr7:37262219-37262220		164;42
K	mutually_exclusive	CUFF.979	chr7	-	chr7:99032892-99057708,chr7:99057817-99063751	chr7:99032892-99045574,chr7:99045812-99063751	chr7:99057709-99057816	chr7:99045575-99045811			102;85
N	alternative_acceptor		chr7	+	chr7:73108381-73111795;chr7:73108381-73110735	chr7:73108381-73111934		chr7:73110736-73111795;chr7:73111796-73111934	chr7:73111795-73111796;chr7:73111934-73111935		106;393
N	intron_retention		chr7	+	chr7:44250531-44250621				chr7:44250530-44250531;chr7:44250621-44250622		52;27
N	jcn_only_AA	CUFF.965	chr7	-	chr7:74953399-74982536	chr7:74981241-74982536		chr7:74953399-74981240	chr7:74953398-74953399		156;465
N	alternative_acceptor	CUFF.961	chr7	+	chr7:73108381-73111795;chr7:73108381-73111934	chr7:73108381-73110735		chr7:73110736-73111795;chr7:73111796-73111934	chr7:73111795-73111796;chr7:73111934-73111935		411;88
K	alternative_acceptor	CUFF.993	chr7	-	chr7:127251731-127251998	chr7:127251903-127251998		chr7:127251731-127251902	chr7:127251730-127251731		365;60
N	alternative_donor	CUFF.985	chr7	+	chr7:107207632-107211589	chr7:107208311-107211589		chr7:107207632-107208310	chr7:107207631-107207632		2409;30
K	intron_retention	CUFF.998	chr7	+	chr7:148991108-148991470				chr7:148991107-148991108;chr7:148991470-148991471		26;27
N	jcn_only_AD		chr7	-	chr7:156476858-156516805	chr7:156476858-156480723					146;24
K	coord_cassette	CUFF.945	chr7	+	chr7:6641772-6647590	chr7:6641772-6642294;chr7:6642384-6647167;chr7:6647229-6647590		chr7:6642295-6642383;chr7:6647168-6647228			107;540
K	intron_retention	CUFF.986	chr7	+	chr7:107253878-107262074				chr7:107253877-107253878;chr7:107262074-107262075		189;141
K	coord_cassette	CUFF.956	chr7	+	chr7:44247798-44251845	chr7:44247798-44250621;chr7:44250724-44251152;chr7:44251204-44251845		chr7:44250622-44250723;chr7:44251153-44251203			99;252
N	alternative_donor	CUFF.960	chr7	+	chr7:65579902-65592690;chr7:65579958-65592690	chr7:65591631-65592690		chr7:65579902-65579957;chr7:65579958-65591630	chr7:65579901-65579902;chr7:65579957-65579958		552;0
N	jcn_only_AD	CUFF.992	chr7	-	chr7:117501371-117511643;chr7:117501371-117514054	chr7:117501371-117512157		chr7:117511644-117512157;chr7:117512158-117514054	chr7:117512157-117512158;chr7:117514054-117514055		202;40
K	intron_retention	CUFF.995	chr7	+	chr7:129037166-129040130				chr7:129037165-129037166;chr7:129040130-129040131		759;39
N	cassette	CUFF.987	chr7	-	chr7:107642179-107643293	chr7:107642179-107642571;chr7:107642830-107643293		chr7:107642572-107642829			52;40
N	intron_retention		chr7	+	chr7:150831656-150837065				chr7:150831655-150831656;chr7:150837065-150837066		9;23
N	jcn_only_AA		chr7	+	chr7:6630107-6631333	chr7:6630107-6631276		chr7:6631277-6631333	chr7:6631333-6631334		32;33
N	cassette	CUFF.982	chr7	-	chr7:102249902-102257071	chr7:102249902-102251532;chr7:102251590-102257071		chr7:102251533-102251589			57;182
N	jcn_only_AD	CUFF.984	chr7	-	chr7:102453979-102462486	chr7:102453979-102454780		chr7:102454781-102462486	chr7:102462486-102462487		473;113
N	alternative_acceptor	CUFF.989	chr7	-	chr7:111161506-111201906	chr7:111172642-111201906		chr7:111161506-111172641	chr7:111161505-111161506		138;16
K	jcn_only_AA	CUFF.952	chr7	+	chr7:34724297-34818106	chr7:34724297-34818073		chr7:34818074-34818106	chr7:34818106-34818107		77;185
N	intron_retention		chr7	+	chr7:73101426-73106925				chr7:73101425-73101426;chr7:73106925-73106926		123;669
N	jcn_only_AD	CUFF.950	chr7	-	chr7:22206767-22232984	chr7:22206767-22231146		chr7:22231147-22232984	chr7:22232984-22232985		54;52
K	alternative_last_exon	CUFF.1004	chr7	-	chr7:156589187-156619298	chr7:156616618-156619298	chr7:156589083-156589186	chr7:156616528-156616617			475;10
N	cassette	CUFF.986	chr7	+	chr7:107220747-107224326	chr7:107220747-107221203;chr7:107221310-107224326		chr7:107221204-107221309			137;440
N	alternative_donor	CUFF.953,CUFF.984	chr7	-	chr7:102608565-102665509	chr7:102608565-102613596		chr7:102613597-102665509	chr7:102665509-102665510		335;0
K	jcn_only_AA	CUFF.943	chr7	-	chr7:1778839-1781844	chr7:1779172-1781844		chr7:1778839-1779171	chr7:1778838-1778839		45;151
N	jcn_only_AD		chr7	-	chr7:36934623-37025527;chr7:36934623-37024519	chr7:36934623-37052903		chr7:37024520-37025527;chr7:37025528-37052903	chr7:37025527-37025528;chr7:37052903-37052904		223;356
N	intron_retention		chr7	+	chr7:107221091-107221203				chr7:107221090-107221091;chr7:107221203-107221204		27;42
K	intron_retention	CUFF.970	chr7	-	chr7:86541562-86542256				chr7:86541561-86541562;chr7:86542256-86542257		353;19
N	jcn_only_AD		chr7	-	chr7:117501371-117512157;chr7:117501371-117514054	chr7:117501371-117511643		chr7:117511644-117512157;chr7:117512158-117514054	chr7:117512157-117512158;chr7:117514054-117514055		199;43
N	coord_cassette	CUFF.966	chr7	+	chr7:75040010-75044162	chr7:75040010-75040937;chr7:75041043-75042066;chr7:75042211-75044162		chr7:75040938-75041042;chr7:75042067-75042210			31;33
N	intron_retention	CUFF.961	chr7	+	chr7:73108381-73110735				chr7:73108380-73108381;chr7:73110735-73110736		53;104
K	cassette	CUFF.998	chr7	+	chr7:148984868-148989301	chr7:148984868-148987028;chr7:148987130-148989301		chr7:148987029-148987129			199;42
K	intron_retention	CUFF.961	chr7	+	chr7:73108381-73111934				chr7:73108380-73108381;chr7:73111934-73111935		393;113
N	alternative_donor	CUFF.989	chr7	-	chr7:111161506-111201906	chr7:111161506-111172573		chr7:111172574-111201906	chr7:111201906-111201907		138;1
N	jcn_only_AD		chr7	-	chr7:111201980-111202519	chr7:111201980-111202499		chr7:111202500-111202519	chr7:111202519-111202520		223;22
N	alternative_donor	CUFF.955	chr7	-	chr7:38869929-38902144	chr7:38869929-38870815		chr7:38870816-38902144	chr7:38902144-38902145	chr7:38869854-38869928;chr7:38902145-38902222	345;0
K	alternative_last_exon	CUFF.999	chr7	+	chr7:150384176-150389402	chr7:150384176-150386576	chr7:150389403-150390825	chr7:150386577-150386888			88;369
N	jcn_only_AD		chr7	-	chr7:156516873-156526870	chr7:156516873-156518128					158;277
N	intron_retention		chr7	+	chr7:73106977-73111934				chr7:73106976-73106977;chr7:73111934-73111935		376;73
K	intron_retention	CUFF.1000	chr7	+	chr7:150835401-150837065				chr7:150835400-150835401;chr7:150837065-150837066		38;179
N	jcn_only_AD	CUFF.960	chr7	+	chr7:65579958-65592690;chr7:65591631-65592690	chr7:65579902-65592690		chr7:65579902-65579957;chr7:65579958-65591630	chr7:65579901-65579902;chr7:65579957-65579958		379;227
N	alternative_donor	CUFF.992	chr7	-	chr7:117501371-117511643;chr7:117501371-117514054	chr7:117501371-117512157		chr7:117511644-117512157;chr7:117512158-117514054	chr7:117512157-117512158;chr7:117514054-117514055		164;4
K	alternative_first_exon	CUFF.1004,CUFF.982	chr7	-	chr7:156629580-156685621	chr7:156629580-156685163	chr7:156685622-156685996	chr7:156685164-156685256			4289;87
N	cassette	CUFF.984	chr7	-	chr7:102566822-102603979	chr7:102566822-102572327;chr7:102572381-102603979		chr7:102572328-102572380			36;312
N	cassette	CUFF.953	chr7	-	chr7:37382368-37488277;chr7:37382368-37488462	chr7:37382368-37433424;chr7:37433521-37488277,chr7:37433521-37488462		chr7:37433425-37433520			89;188
N	jcn_only_AD	CUFF.953	chr7	-	chr7:36934623-37052903;chr7:36934623-37024519	chr7:36934623-37025527		chr7:37024520-37025527;chr7:37025528-37052903	chr7:37025527-37025528;chr7:37052903-37052904		469;111
N	intron_retention	CUFF.1005	chr7	-	chr7:156471045-156471770				chr7:156471044-156471045;chr7:156471770-156471771		30;71
N	alternative_acceptor	CUFF.970	chr7	-	chr7:86569432-86571333	chr7:86570702-86571333		chr7:86569432-86570701	chr7:86569431-86569432		32;2
N	jcn_only_AA	CUFF.950	chr7	-	chr7:22162140-22165221	chr7:22165040-22165221		chr7:22162140-22165039	chr7:22162139-22162140		4;24
N	intron_retention		chr7	+	chr7:6639524-6639757				chr7:6639523-6639524;chr7:6639757-6639758		27;106
N	jcn_only_AD	CUFF.986	chr7	+	chr7:107254178-107258772;chr7:107253878-107258772	chr7:107256835-107258772		chr7:107253878-107254177;chr7:107254178-107256834	chr7:107253877-107253878;chr7:107254177-107254178		159;40
N	alternative_acceptor	CUFF.928	chr6	-	chr6:128330411-128385902;chr6:128330414-128385902;chr6:128384671-128385902	chr6:128383570-128385902		chr6:128330411-128330413;chr6:128330414-128383569;chr6:128383570-128384670	chr6:128330410-128330411;chr6:128330413-128330414;chr6:128383569-128383570		620;0
N	alternative_acceptor	CUFF.913	chr6	-	chr6:43480837-43481096	chr6:43480939-43481096		chr6:43480837-43480938	chr6:43480836-43480837		32;1197
K	intron_retention	CUFF.900	chr6	+	chr6:32122024-32122363				chr6:32122023-32122024;chr6:32122363-32122364		19;172
K	intron_retention	CUFF.918	chr6	+	chr6:90323610-90326277				chr6:90323609-90323610;chr6:90326277-90326278		148;9
K	intron_retention	CUFF.898	chr6	+	chr6:31936867-31937056				chr6:31936866-31936867;chr6:31937056-31937057		1691;90
N	jcn_only_AD	CUFF.893	chr6	+	chr6:28116603-28117260	chr6:28116617-28117260		chr6:28116603-28116616	chr6:28116602-28116603		18;323
N	jcn_only_AA	CUFF.924	chr6	-	chr6:114281204-114292020;chr6:114289861-114292020;chr6:114283559-114292020	chr6:114281183-114292020		chr6:114281183-114281203;chr6:114281204-114283558;chr6:114283559-114289860	chr6:114281182-114281183;chr6:114281203-114281204;chr6:114283558-114283559		441;485
K	alternative_first_exon	CUFF.917	chr6	+	chr6:88066222-88074678	chr6:88068920-88074678	chr6:88066019-88066221	chr6:88068800-88068919			946;218
N	intron_retention		chr6	-	chr6:31939459-31939705				chr6:31939458-31939459;chr6:31939705-31939706		43;318
N	coord_cassette	CUFF.928	chr6	-	chr6:128320050-128326228	chr6:128320050-128322340;chr6:128322353-128324341;chr6:128324378-128326228		chr6:128322341-128322352;chr6:128324342-128324377			21;895
K	intron_retention	CUFF.899	chr6	-	chr6:31937802-31937885				chr6:31937801-31937802;chr6:31937885-31937886		584;24
N	alternative_donor	CUFF.927	chr6	+	chr6:126342412-126359850	chr6:126342427-126359850		chr6:126342412-126342426	chr6:126342411-126342412		44;32
K	cassette	CUFF.926	chr6	-	chr6:116973356-116979965	chr6:116973356-116977846;chr6:116978016-116979965		chr6:116977847-116978015			17;41
K	intron_retention	CUFF.898	chr6	+	chr6:31936239-31936677				chr6:31936238-31936239;chr6:31936677-31936678		830;307
N	alternative_donor	CUFF.928	chr6	-	chr6:128561296-128563665	chr6:128561296-128562367		chr6:128562368-128563665	chr6:128563665-128563666		1112;15
N	jcn_only_AA	CUFF.900	chr6	+	chr6:126307769-126314938	chr6:126307769-126314902		chr6:126314903-126314938	chr6:126314938-126314939		51;381
N	alternative_acceptor	CUFF.913	chr6	-	chr6:43483929-43484464;chr6:43483834-43484464;chr6:43483852-43484464;chr6:43483926-43484464	chr6:43483785-43484464		chr6:43483785-43483833;chr6:43483834-43483851;chr6:43483852-43483925;chr6:43483926-43483928	chr6:43483784-43483785;chr6:43483833-43483834;chr6:43483851-43483852;chr6:43483925-43483926		1513;228
N	alternative_acceptor	CUFF.913	chr6	-	chr6:43483929-43484464;chr6:43483834-43484464;chr6:43483852-43484464;chr6:43483785-43484464	chr6:43483926-43484464		chr6:43483785-43483833;chr6:43483834-43483851;chr6:43483852-43483925;chr6:43483926-43483928	chr6:43483784-43483785;chr6:43483833-43483834;chr6:43483851-43483852;chr6:43483925-43483926		421;1320
K	intron_retention	CUFF.918	chr6	+	chr6:90322090-90323510				chr6:90322089-90322090;chr6:90323510-90323511		360;129
K	alternative_donor	CUFF.898	chr6	+	chr6:31935860-31936104	chr6:31935897-31936104		chr6:31935860-31935896	chr6:31935859-31935860		164;191
N	alternative_donor	CUFF.894	chr6	+	chr6:29943295-29945430	chr6:29945281-29945430		chr6:29943295-29945280	chr6:29943294-29943295		79;2
N	jcn_only_AA	CUFF.913	chr6	-	chr6:43483929-43484464;chr6:43483834-43484464;chr6:43483852-43484464;chr6:43483785-43484464	chr6:43483926-43484464		chr6:43483785-43483833;chr6:43483834-43483851;chr6:43483852-43483925;chr6:43483926-43483928	chr6:43483784-43483785;chr6:43483833-43483834;chr6:43483851-43483852;chr6:43483925-43483926		421;1345
K	jcn_only_AD	CUFF.934	chr6	+	chr6:150206810-150240322	chr6:150217376-150240322					23;53
K	jcn_only_AD	CUFF.927	chr6	+	chr6:126307769-126314902	chr6:126307837-126314902		chr6:126307769-126307836	chr6:126307768-126307769		381;160
K	intron_retention	CUFF.913	chr6	-	chr6:43480939-43481096				chr6:43480938-43480939;chr6:43481096-43481097		1457;1019
N	jcn_only_AA	CUFF.928	chr6	-	chr6:128718834-128841403;chr6:128812995-128841403;chr6:128840287-128841403	chr6:128730478-128841403		chr6:128718834-128730477;chr6:128730478-128812994;chr6:128812995-128840286	chr6:128718833-128718834;chr6:128730477-128730478;chr6:128812994-128812995		677;105
N	alternative_donor	CUFF.914	chr6	+	chr6:46623772-46626698	chr6:46626266-46626698		chr6:46623772-46626265	chr6:46623771-46623772		87;4
N	jcn_only_AA	CUFF.928	chr6	-	chr6:128812995-128841403;chr6:128730478-128841403;chr6:128840287-128841403	chr6:128718834-128841403		chr6:128718834-128730477;chr6:128730478-128812994;chr6:128812995-128840286	chr6:128718833-128718834;chr6:128730477-128730478;chr6:128812994-128812995		171;611
N	jcn_only_AA	CUFF.924	chr6	-	chr6:114281183-114292020;chr6:114281204-114292020;chr6:114283559-114292020	chr6:114289861-114292020		chr6:114281183-114281203;chr6:114281204-114283558;chr6:114283559-114289860	chr6:114281182-114281183;chr6:114281203-114281204;chr6:114283558-114283559		651;275
K	cassette	CUFF.910	chr6	-	chr6:39859156-39864972	chr6:39859156-39859398;chr6:39859540-39864972		chr6:39859399-39859539			111;30
N	jcn_only_AA	CUFF.913	chr6	-	chr6:43483929-43484464;chr6:43483834-43484464;chr6:43483852-43484464;chr6:43483926-43484464	chr6:43483785-43484464		chr6:43483785-43483833;chr6:43483834-43483851;chr6:43483852-43483925;chr6:43483926-43483928	chr6:43483784-43483785;chr6:43483833-43483834;chr6:43483851-43483852;chr6:43483925-43483926		1538;228
K	alternative_first_exon	CUFF.892	chr6	-	chr6:13470863-13472212;chr6:13470863-13486869	chr6:13470863-13486242	chr6:13472213-13472327;chr6:13486870-13487991	chr6:13486243-13486470			82;43
K	intron_retention	CUFF.898	chr6	+	chr6:31935860-31936104				chr6:31935859-31935860;chr6:31936104-31936105		164;454
N	alternative_donor	CUFF.922	chr6	+	chr6:112375365-112375537	chr6:112375374-112375537		chr6:112375365-112375373	chr6:112375364-112375365		190;57
K	intron_retention	CUFF.898	chr6	+	chr6:31928872-31928972				chr6:31928871-31928872;chr6:31928972-31928973		51;3
K	alternative_donor	CUFF.900	chr6	+	chr6:32122024-32122363;chr6:32122182-32122363	chr6:32122172-32122363		chr6:32122024-32122171;chr6:32122172-32122181	chr6:32122023-32122024;chr6:32122171-32122172		228;46
N	alternative_acceptor	CUFF.928	chr6	-	chr6:128718834-128841403;chr6:128812995-128841403;chr6:128730478-128841403	chr6:128840287-128841403		chr6:128718834-128730477;chr6:128730478-128812994;chr6:128812995-128840286	chr6:128718833-128718834;chr6:128730477-128730478;chr6:128812994-128812995		613;0
N	jcn_only_AA	CUFF.929	chr6	-	chr6:133055523-133055618	chr6:133055526-133055618		chr6:133055523-133055525	chr6:133055522-133055523		1496;28
N	intron_retention		chr6	-	chr6:31939359-31939705				chr6:31939358-31939359;chr6:31939705-31939706		12;361
K	alternative_acceptor	CUFF.914	chr6	+	chr6:46638966-46644383	chr6:46638966-46644119		chr6:46644120-46644383	chr6:46644383-46644384		381;197
K	alternative_donor	CUFF.900	chr6	+	chr6:32122024-32122363;chr6:32122172-32122363	chr6:32122182-32122363		chr6:32122024-32122171;chr6:32122172-32122181	chr6:32122023-32122024;chr6:32122171-32122172		65;209
N	mutually_exclusive	CUFF.929	chr6	-	chr6:133046119-133049879,chr6:133050073-133055391	chr6:133046119-133047860,chr6:133048152-133055391	chr6:133049880-133050072	chr6:133047861-133048151			65;95
N	cassette	CUFF.923	chr6	+	chr6:112558118-112627530	chr6:112558118-112604255;chr6:112604370-112627530		chr6:112604256-112604369			46;75
N	alternative_last_exon	CUFF.927	chr6	+	chr6:46636531-46644383	chr6:46636531-46637871	chr6:46644384-46644480	chr6:46637872-46638013			36;527
K	jcn_only_AA	CUFF.908	chr6	-	chr6:35478788-35479956	chr6:35478803-35479956		chr6:35478788-35478802	chr6:35478787-35478788		15;86
K	alternative_acceptor	CUFF.900	chr6	+	chr6:32121414-32121972	chr6:32121414-32121775		chr6:32121776-32121972	chr6:32121972-32121973		66;158
N	jcn_only_AA		chr6	-	chr6:114281183-114289797	chr6:114283559-114289797		chr6:114281183-114283558	chr6:114281182-114281183		255;138
N	jcn_only_AA	CUFF.890	chr6	-	chr6:5144497-5216850;chr6:5138974-5216850;chr6:5187215-5216850	chr6:5113652-5216850					207;148
N	jcn_only_AA	CUFF.890	chr6	-	chr6:5144497-5216850;chr6:5113652-5216850;chr6:5187215-5216850	chr6:5138974-5216850					186;170
K	alternative_first_exon	CUFF.899,CUFF.916	chr6	-	chr6:75975055-75994117	chr6:75975055-75977356	chr6:75994118-75994740	chr6:75977357-75977464			19;29
N	cassette	CUFF.928	chr6	-	chr6:128320050-128324341	chr6:128320050-128322340;chr6:128322353-128324341		chr6:128322341-128322352			72;761
K	cassette	CUFF.928	chr6	-	chr6:128563748-128718710	chr6:128563748-128643183;chr6:128643456-128718710		chr6:128643184-128643455			74;1097
K	alternative_first_exon	CUFF.922	chr6	+	chr6:112382492-112385957	chr6:112382599-112385957	chr6:112382194-112382491	chr6:112382500-112382598			385;21
N	jcn_only_AA		chr6	+	chr6:32122961-32123544	chr6:32122961-32123464		chr6:32123465-32123544	chr6:32123544-32123545		18;352
K	intron_retention	CUFF.929	chr6	-	chr6:133055523-133055618				chr6:133055522-133055523;chr6:133055618-133055619		1496;51
N	jcn_only_AA	CUFF.913	chr6	-	chr6:43483834-43484464;chr6:43483852-43484464;chr6:43483926-43484464;chr6:43483785-43484464	chr6:43483929-43484464		chr6:43483785-43483833;chr6:43483834-43483851;chr6:43483852-43483925;chr6:43483926-43483928	chr6:43483784-43483785;chr6:43483833-43483834;chr6:43483851-43483852;chr6:43483925-43483926		1745;21
K	jcn_only_AA	CUFF.900	chr6	+	chr6:32121414-32121972	chr6:32121414-32121775		chr6:32121776-32121972	chr6:32121972-32121973		66;10
K	intron_retention	CUFF.927	chr6	+	chr6:126320760-126327987				chr6:126320759-126320760;chr6:126327987-126327988		199;15
K	intron_retention	CUFF.899	chr6	-	chr6:31939503-31939705				chr6:31939502-31939503;chr6:31939705-31939706		83;284
K	alternative_first_exon	CUFF.888	chr6	+	chr6:2988266-2989761	chr6:2988944-2989761	chr6:2988104-2988265	chr6:2988839-2988943			156;109
K	cassette	CUFF.918	chr6	+	chr6:90337416-90338830	chr6:90337416-90337965;chr6:90338061-90338830		chr6:90337966-90338060			250;103
K	intron_retention	CUFF.924	chr6	-	chr6:114270252-114270331				chr6:114270251-114270252;chr6:114270331-114270332		180;7
N	intron_retention		chr6	-	chr6:31938917-31939096				chr6:31938916-31938917;chr6:31939096-31939097		20;115
K	intron_retention	CUFF.897	chr6	+	chr6:31796040-31796081				chr6:31796039-31796040;chr6:31796081-31796082		9;11
N	alternative_acceptor	CUFF.899	chr6	-	chr6:31939503-31939705;chr6:31938925-31939705;chr6:31939359-31939705	chr6:31939459-31939705		chr6:31938925-31939358;chr6:31939359-31939458;chr6:31939459-31939502	chr6:31938924-31938925;chr6:31939358-31939359;chr6:31939458-31939459		240;94
K	alternative_first_exon	CUFF.924	chr6	-	chr6:114281183-114283530,chr6:114281183-114289797,chr6:114281183-114291418;chr6:114281183-114292020;chr6:114281183-114289493	chr6:114281183-114291643	chr6:114292021-114292449;chr6:114289494-114289592	chr6:114291644-114291903			1059;97
N	alternative_donor	CUFF.893	chr6	+	chr6:28116603-28117260	chr6:28116617-28117260		chr6:28116603-28116616	chr6:28116602-28116603		18;171
N	cassette	CUFF.900	chr6	+	chr6:32130400-32133914	chr6:32130400-32132355;chr6:32132435-32133914		chr6:32132356-32132434			19;84
K	intron_retention		chr6	-	chr6:31938925-31939096				chr6:31938924-31938925;chr6:31939096-31939097		365;113
N	alternative_acceptor	CUFF.924	chr6	-	chr6:114281183-114292020;chr6:114281204-114292020;chr6:114289861-114292020	chr6:114283559-114292020		chr6:114281183-114281203;chr6:114281204-114283558;chr6:114283559-114289860	chr6:114281182-114281183;chr6:114281203-114281204;chr6:114283558-114283559		567;1
K	cassette	CUFF.927	chr6	+	chr6:126329892-126332398	chr6:126329892-126330480;chr6:126330581-126332398		chr6:126330481-126330580			212;13
K	cassette	CUFF.937	chr6	+	chr6:161529892-161530786	chr6:161529892-161529982;chr6:161530074-161530786		chr6:161529983-161530073			259;60
N	jcn_only_AA	CUFF.913	chr6	-	chr6:43483929-43484464;chr6:43483852-43484464;chr6:43483926-43484464;chr6:43483785-43484464	chr6:43483834-43484464		chr6:43483785-43483833;chr6:43483834-43483851;chr6:43483852-43483925;chr6:43483926-43483928	chr6:43483784-43483785;chr6:43483833-43483834;chr6:43483851-43483852;chr6:43483925-43483926		1652;114
N	alternative_first_exon	CUFF.892	chr6	-	chr6:114289861-114292020	chr6:114289861-114291643	chr6:114292021-114292449	chr6:114291644-114291903			234;106
K	jcn_only_AA	CUFF.939	chr6	-	chr6:170117997-170118883	chr6:170118003-170118883		chr6:170117997-170118002	chr6:170117996-170117997		67;62
K	alternative_first_exon	CUFF.892	chr6	-	chr6:13470863-13486242;chr6:13470863-13486869	chr6:13470863-13472212	chr6:13486243-13486470;chr6:13486870-13487991	chr6:13472213-13472327			95;30
K	cassette	CUFF.933	chr6	+	chr6:145142155-145148746	chr6:145142155-145148483;chr6:145148523-145148746		chr6:145148484-145148522			96;152
N	intron_retention		chr6	-	chr6:133055526-133055618				chr6:133055525-133055526;chr6:133055618-133055619		28;51
N	jcn_only_AA	CUFF.899	chr6	-	chr6:31939503-31939705;chr6:31939459-31939705;chr6:31938925-31939705	chr6:31939359-31939705		chr6:31938925-31939358;chr6:31939359-31939458;chr6:31939459-31939502	chr6:31938924-31938925;chr6:31939358-31939359;chr6:31939458-31939459		143;12
N	jcn_only_AA	CUFF.922,CUFF.937	chr6	+	chr6:112375609-112382193	chr6:112375609-112375825		chr6:112375826-112382193	chr6:112382193-112382194		234;65
N	mutually_exclusive	CUFF.918	chr6	+	chr6:90143095-90305634,chr6:90305734-90312747	chr6:90143095-90276552,chr6:90276816-90312747	chr6:90305635-90305733	chr6:90276553-90276815			138;21
N	jcn_only_AD	CUFF.928	chr6	-	chr6:128561296-128563665	chr6:128561296-128562367		chr6:128562368-128563665	chr6:128563665-128563666		1112;108
N	alternative_acceptor	CUFF.899	chr6	-	chr6:31938530-31938688	chr6:31938603-31938688		chr6:31938530-31938602	chr6:31938529-31938530		138;184
K	intron_retention	CUFF.898	chr6	+	chr6:31936316-31936462				chr6:31936315-31936316;chr6:31936462-31936463		306;12
K	intron_retention	CUFF.937	chr6	+	chr6:161529892-161529982				chr6:161529891-161529892;chr6:161529982-161529983		56;62
K	alternative_first_exon	CUFF.918	chr6	+	chr6:90193278-90276552,chr6:90272643-90276552;chr6:90272618-90276552;chr6:90218678-90276552	chr6:90218969-90276552	chr6:90272285-90272617;chr6:90218565-90218677	chr6:90218871-90218968			418;21
K	alternative_acceptor	CUFF.905	chr6	+	chr6:33239900-33240404	chr6:33239900-33240363		chr6:33240364-33240404	chr6:33240404-33240405		231;265
K	cassette	CUFF.937	chr6	+	chr6:161455482-161469647	chr6:161455482-161469277;chr6:161469324-161469647		chr6:161469278-161469323			12;292
N	alternative_acceptor	CUFF.924	chr6	-	chr6:114281204-114292020;chr6:114289861-114292020;chr6:114283559-114292020	chr6:114281183-114292020		chr6:114281183-114281203;chr6:114281204-114283558;chr6:114283559-114289860	chr6:114281182-114281183;chr6:114281203-114281204;chr6:114283558-114283559		83;485
K	coord_cassette	CUFF.923	chr6	+	chr6:112558118-112627530	chr6:112558118-112600322;chr6:112600441-112604255;chr6:112604370-112627530		chr6:112600323-112600440;chr6:112604256-112604369			46;69
K	cassette	CUFF.922	chr6	+	chr6:112386201-112389407	chr6:112386201-112388171;chr6:112388236-112389407		chr6:112388172-112388235			260;186
N	alternative_acceptor	CUFF.928	chr6	-	chr6:128540242-128561179	chr6:128556750-128561179		chr6:128540242-128556749	chr6:128540241-128540242		1161;3
K	alternative_acceptor	CUFF.889	chr6	-	chr6:3155158-3155858	chr6:3155290-3155858		chr6:3155158-3155289	chr6:3155157-3155158		35;45
N	cassette	CUFF.929	chr6	-	chr6:133046119-133049879;chr6:133046119-133055391	chr6:133046119-133047860;chr6:133047978-133049879,chr6:133047978-133055391		chr6:133047861-133047977			254;360
N	alternative_acceptor	CUFF.899	chr6	-	chr6:31939503-31939705;chr6:31939459-31939705;chr6:31938925-31939705	chr6:31939359-31939705		chr6:31938925-31939358;chr6:31939359-31939458;chr6:31939459-31939502	chr6:31938924-31938925;chr6:31939358-31939359;chr6:31939458-31939459		308;26
K	jcn_only_AA	CUFF.914	chr6	+	chr6:46638966-46644383	chr6:46638966-46644119		chr6:46644120-46644383	chr6:46644383-46644384		381;120
K	cassette	CUFF.914	chr6	+	chr6:46630236-46636445	chr6:46630236-46632510;chr6:46632624-46636445		chr6:46632511-46632623			224;348
N	jcn_only_AD	CUFF.924	chr6	-	chr6:43483929-43484464	chr6:43483929-43484233		chr6:43484234-43484464	chr6:43484464-43484465		21;136
N	alternative_acceptor	CUFF.899	chr6	-	chr6:31939459-31939705;chr6:31938925-31939705;chr6:31939359-31939705	chr6:31939503-31939705		chr6:31938925-31939358;chr6:31939359-31939458;chr6:31939459-31939502	chr6:31938924-31938925;chr6:31939358-31939359;chr6:31939458-31939459		137;197
N	cassette	CUFF.918	chr6	+	chr6:90333777-90337301	chr6:90333777-90334257;chr6:90334411-90337301		chr6:90334258-90334410			53;219
K	cassette	CUFF.937	chr6	+	chr6:161518209-161522923	chr6:161518209-161519309;chr6:161519460-161522923		chr6:161519310-161519459			116;136
K	intron_retention	CUFF.913	chr6	-	chr6:43480613-43480806				chr6:43480612-43480613;chr6:43480806-43480807		1547;1106
K	alternative_first_exon	CUFF.918	chr6	+	chr6:90193278-90276552,chr6:90272643-90276552;chr6:90218969-90276552;chr6:90218678-90276552	chr6:90272618-90276552	chr6:90218871-90218968;chr6:90218565-90218677	chr6:90272285-90272617			170;269
K	intron_retention	CUFF.897	chr6	+	chr6:31795803-31796033				chr6:31795802-31795803;chr6:31796033-31796034		9;11
K	intron_retention	CUFF.902	chr6	+	chr6:32823983-32825781				chr6:32823982-32823983;chr6:32825781-32825782		18;39
N	cassette	CUFF.913	chr6	-	chr6:43481372-43483626	chr6:43481372-43483332;chr6:43483440-43483626		chr6:43483333-43483439			914;966
N	cassette	CUFF.921	chr6	+	chr6:111306342-111312949	chr6:111306342-111310190;chr6:111310269-111312949		chr6:111310191-111310268			4;511
N	intron_retention		chr6	+	chr6:348842-350821				chr6:348841-348842;chr6:350821-350822		196;856
N	jcn_only_AA	CUFF.913	chr6	-	chr6:43480837-43481096	chr6:43480939-43481096		chr6:43480837-43480938	chr6:43480836-43480837		32;1457
N	alternative_donor	CUFF.911,CUFF.928	chr6	-	chr6:128327201-128330274	chr6:128327201-128329190		chr6:128329191-128330274	chr6:128330274-128330275		1162;20
N	alternative_acceptor	CUFF.928	chr6	-	chr6:128383570-128385902;chr6:128330411-128385902;chr6:128384671-128385902	chr6:128330414-128385902		chr6:128330411-128330413;chr6:128330414-128383569;chr6:128383570-128384670	chr6:128330410-128330411;chr6:128330413-128330414;chr6:128383569-128383570		14;606
K	intron_retention	CUFF.918	chr6	+	chr6:90337416-90338830				chr6:90337415-90337416;chr6:90338830-90338831		250;52
K	alternative_first_exon	CUFF.918	chr6	+	chr6:90193278-90276552,chr6:90272643-90276552;chr6:90218969-90276552;chr6:90272618-90276552	chr6:90218678-90276552	chr6:90218871-90218968;chr6:90272285-90272617	chr6:90218565-90218677			335;104
N	mutually_exclusive	CUFF.929	chr6	-	chr6:133046119-133049879,chr6:133050119-133055391	chr6:133046119-133047860,chr6:133047978-133055391	chr6:133049880-133050118	chr6:133047861-133047977			86;35
K	alternative_acceptor	CUFF.929	chr6	-	chr6:133047978-133049879	chr6:133048152-133049879		chr6:133047978-133048151	chr6:133047977-133047978		276;204
K	alternative_first_exon	CUFF.932	chr6	+	chr6:144613044-144724258	chr6:144665441-144724258	chr6:144612873-144613043	chr6:144665165-144665440			56;186
N	jcn_only_AD	CUFF.914	chr6	+	chr6:46623772-46626698	chr6:46626266-46626698		chr6:46623772-46626265	chr6:46623771-46623772		87;56
K	intron_retention	CUFF.905	chr6	+	chr6:33244045-33244167				chr6:33244044-33244045;chr6:33244167-33244168		1119;79
K	intron_retention		chr6	-	chr6:43481372-43483332				chr6:43481371-43481372;chr6:43483332-43483333		1187;129
K	alternative_last_exon	CUFF.911	chr6	-	chr6:41462632-41513826	chr6:41491964-41513826	chr6:41462591-41462631	chr6:41491534-41491963			22;4008
K	intron_retention	CUFF.913	chr6	-	chr6:43481190-43481325				chr6:43481189-43481190;chr6:43481325-43481326		1315;717
N	alternative_acceptor	CUFF.899	chr6	-	chr6:31938917-31939096	chr6:31938925-31939096		chr6:31938917-31938924	chr6:31938916-31938917		20;240
K	intron_retention	CUFF.914	chr6	+	chr6:46644481-46645347				chr6:46644480-46644481;chr6:46645347-46645348		221;234
K	intron_retention	CUFF.888	chr6	+	chr6:2989968-2990102				chr6:2989967-2989968;chr6:2990102-2990103		64;333
K	jcn_only_AA	CUFF.905	chr6	+	chr6:33239900-33240404	chr6:33239900-33240363		chr6:33240364-33240404	chr6:33240404-33240405		231;418
N	alternative_acceptor	CUFF.928	chr6	-	chr6:128718834-128841403;chr6:128730478-128841403;chr6:128840287-128841403	chr6:128812995-128841403		chr6:128718834-128730477;chr6:128730478-128812994;chr6:128812995-128840286	chr6:128718833-128718834;chr6:128730477-128730478;chr6:128812994-128812995		613;0
N	jcn_only_AA	CUFF.888	chr6	+	chr6:2988266-2989761	chr6:2988266-2988661		chr6:2988662-2989761	chr6:2989761-2989762		240;11
K	alternative_first_exon	CUFF.936	chr6	-	chr6:151757690-151765600;chr6:151757690-151766442	chr6:151757690-151773150	chr6:151765601-151765760;chr6:151766443-151767020	chr6:151773151-151773351		chr6:151757555-151757689	958;129
K	alternative_last_exon	CUFF.936	chr6	-	chr6:151757690-151773150	chr6:151766961-151773150	chr6:151757276-151757689	chr6:151766443-151766960			138;714
K	intron_retention	CUFF.898	chr6	+	chr6:31929164-31929323				chr6:31929163-31929164;chr6:31929323-31929324		56;141
N	alternative_acceptor	CUFF.898,CUFF.905	chr6	+	chr6:31936316-31936462	chr6:31936316-31936399		chr6:31936400-31936462	chr6:31936462-31936463		306;24
K	intron_retention	CUFF.938	chr6	+	chr6:165241453-165243009				chr6:165241452-165241453;chr6:165243009-165243010		260;57
K	jcn_only_AD	CUFF.918	chr6	+	chr6:90338943-90340151	chr6:90338958-90340151		chr6:90338943-90338957	chr6:90338942-90338943		111;169
N	mutually_exclusive	CUFF.929	chr6	-	chr6:133046119-133049879,chr6:133050119-133055391	chr6:133046119-133047860,chr6:133048152-133055391	chr6:133049880-133050118	chr6:133047861-133048151			86;95
K	intron_retention	CUFF.918	chr6	+	chr6:90337416-90337965				chr6:90337415-90337416;chr6:90337965-90337966		14;39
K	alternative_donor	CUFF.908,CUFF.936	chr6	-	chr6:151754366-151757580	chr6:151754366-151757554		chr6:151757555-151757580	chr6:151757580-151757581	chr6:151754290-151754365;chr6:151757581-151757689	264;327
N	intron_retention	CUFF.898	chr6	+	chr6:31928872-31929117				chr6:31928871-31928872;chr6:31929117-31929118		262;16
K	alternative_first_exon	CUFF.890	chr6	-	chr6:5109726-5132951,chr6:5109726-5144371;chr6:5109726-5260880	chr6:5109726-5113304	chr6:5260881-5261270	chr6:5113305-5113651			58;253
K	intron_retention	CUFF.929	chr6	-	chr6:133050073-133055391				chr6:133050072-133050073;chr6:133055391-133055392		84;105
K	intron_retention	CUFF.898	chr6	+	chr6:31936574-31936647				chr6:31936573-31936574;chr6:31936647-31936648		300;35
K	cassette	CUFF.902	chr6	+	chr6:32823983-32825781	chr6:32823983-32825039;chr6:32825172-32825781		chr6:32825040-32825171			18;282
K	alternative_first_exon	CUFF.924	chr6	-	chr6:114281183-114283530,chr6:114281183-114289797,chr6:114281183-114291418;chr6:114281183-114291643;chr6:114281183-114292020	chr6:114281183-114289493	chr6:114291644-114291903;chr6:114292021-114292449	chr6:114289494-114289592			1124;32
N	jcn_only_AA	CUFF.928	chr6	-	chr6:128383570-128385902;chr6:128330414-128385902;chr6:128384671-128385902	chr6:128330411-128385902		chr6:128330411-128330413;chr6:128330414-128383569;chr6:128383570-128384670	chr6:128330410-128330411;chr6:128330413-128330414;chr6:128383569-128383570		1277;14
N	jcn_only_AD		chr6	-	chr6:114283559-114289797;chr6:114283559-114332294	chr6:114283559-114292020		chr6:114289798-114292020;chr6:114292021-114332294	chr6:114292020-114292021;chr6:114332294-114332295		172;15
K	cassette	CUFF.910	chr6	-	chr6:39856832-39864972	chr6:39856832-39859081;chr6:39859156-39864972		chr6:39859082-39859155			42;136
K	alternative_donor	CUFF.927	chr6	+	chr6:126307769-126314902	chr6:126307837-126314902		chr6:126307769-126307836	chr6:126307768-126307769		381;155
K	jcn_only_AD	CUFF.900	chr6	+	chr6:32122024-32122363;chr6:32122182-32122363	chr6:32122172-32122363		chr6:32122024-32122171;chr6:32122172-32122181	chr6:32122023-32122024;chr6:32122171-32122172		393;61
K	jcn_only_AD	CUFF.937	chr6	+	chr6:161514872-161518111	chr6:161514884-161518111		chr6:161514872-161514883	chr6:161514871-161514872		94;63
N	alternative_donor	CUFF.924	chr6	-	chr6:43483929-43484464	chr6:43483929-43484233		chr6:43484234-43484464	chr6:43484464-43484465		21;95
N	alternative_acceptor	CUFF.924	chr6	-	chr6:114281183-114292020;chr6:114281204-114292020;chr6:114283559-114292020	chr6:114289861-114292020		chr6:114281183-114281203;chr6:114281204-114283558;chr6:114283559-114289860	chr6:114281182-114281183;chr6:114281203-114281204;chr6:114283558-114283559		561;7
N	jcn_only_AA	CUFF.899	chr6	-	chr6:31938917-31939096	chr6:31938925-31939096		chr6:31938917-31938924	chr6:31938916-31938917		20;365
N	jcn_only_AD	CUFF.914	chr6	+	chr6:46636531-46644383	chr6:46638966-46644383					55;381
K	intron_retention	CUFF.924	chr6	-	chr6:114267313-114270142				chr6:114267312-114267313;chr6:114270142-114270143		270;26
K	cassette	CUFF.939	chr6	-	chr6:170112636-170115803	chr6:170112636-170114828;chr6:170114939-170115803		chr6:170114829-170114938			14;82
K	jcn_only_AA	CUFF.926	chr6	-	chr6:116988076-116989728	chr6:116988371-116989728		chr6:116988076-116988370	chr6:116988075-116988076		23;36
K	jcn_only_AD	CUFF.900	chr6	+	chr6:32122172-32122363;chr6:32122182-32122363	chr6:32122024-32122363		chr6:32122024-32122171;chr6:32122172-32122181	chr6:32122023-32122024;chr6:32122171-32122172		435;19
N	alternative_acceptor	CUFF.888	chr6	+	chr6:2988266-2989761	chr6:2988266-2988661		chr6:2988662-2989761	chr6:2989761-2989762		240;32
N	alternative_acceptor	CUFF.928	chr6	-	chr6:128383570-128385902;chr6:128330414-128385902;chr6:128384671-128385902	chr6:128330411-128385902		chr6:128330411-128330413;chr6:128330414-128383569;chr6:128383570-128384670	chr6:128330410-128330411;chr6:128330413-128330414;chr6:128383569-128383570		606;14
K	intron_retention	CUFF.905	chr6	+	chr6:33243435-33243573				chr6:33243434-33243435;chr6:33243573-33243574		95;30
K	cassette	CUFF.898	chr6	+	chr6:31928872-31929323	chr6:31928872-31928972;chr6:31929164-31929323		chr6:31928973-31929163			24;57
N	intron_retention		chr6	+	chr6:31937094-31937291				chr6:31937093-31937094;chr6:31937291-31937292		30;270
N	jcn_only_AA	CUFF.913	chr6	-	chr6:43481372-43483332	chr6:43483045-43483332		chr6:43481372-43483044	chr6:43481371-43481372		1187;31
K	cassette	CUFF.900	chr6	+	chr6:32121414-32122363	chr6:32121414-32121972;chr6:32122024-32122363		chr6:32121973-32122023			347;38
K	intron_retention	CUFF.924	chr6	-	chr6:114277858-114279812				chr6:114277857-114277858;chr6:114279812-114279813		593;300
N	intron_retention		chr6	-	chr6:31938530-31938688				chr6:31938529-31938530;chr6:31938688-31938689		138;317
N	jcn_only_AD	CUFF.894	chr6	+	chr6:29943295-29945430	chr6:29945281-29945430		chr6:29943295-29945280	chr6:29943294-29943295		79;28
N	intron_retention		chr6	+	chr6:46636531-46644383				chr6:46636530-46636531;chr6:46644383-46644384		55;106
K	cassette	CUFF.927	chr6	+	chr6:126329619-126332398	chr6:126329619-126329802;chr6:126329892-126332398		chr6:126329803-126329891			180;208
K	alternative_first_exon	CUFF.907	chr6	+	chr6:34452922-34494019;chr6:34482846-34494019	chr6:34434048-34494019	chr6:34452767-34452921;chr6:34482601-34482845	chr6:34433916-34434047			120;8
N	cassette	CUFF.929	chr6	-	chr6:133047978-133055391;chr6:133046119-133055391;chr6:133048152-133055391	chr6:133047978-133049879,chr6:133048152-133049879,chr6:133046119-133049879;chr6:133050073-133055391		chr6:133049880-133050072			268;396
N	alternative_acceptor	CUFF.913	chr6	-	chr6:43481372-43483332	chr6:43483045-43483332		chr6:43481372-43483044	chr6:43481371-43481372		1187;43
K	alternative_first_exon	CUFF.936	chr6	-	chr6:151757690-151766442;chr6:151757690-151773150	chr6:151757690-151765600	chr6:151766443-151767020;chr6:151773151-151773351	chr6:151765601-151765760		chr6:151757555-151757689	978;109
N	alternative_first_exon	CUFF.937	chr6	+	chr6:161488329-161491639;chr6:161413116-161491639	chr6:161471012-161491639	chr6:161412705-161413115	chr6:161469648-161471011			31;154
K	alternative_first_exon	CUFF.890,CUFF.928	chr6	-	chr6:128718834-128730438;chr6:128718834-128841403	chr6:128718834-128812876	chr6:128841404-128841843	chr6:128812877-128813025			749;272
K	cassette	CUFF.900	chr6	+	chr6:32121414-32122363	chr6:32121414-32121972;chr6:32122182-32122363		chr6:32121973-32122181			347;267
N	jcn_only_AD	CUFF.916	chr6	-	chr6:75977465-75993935	chr6:75977465-75982179		chr6:75982180-75993935	chr6:75993935-75993936		54;3
N	alternative_donor	CUFF.898	chr6	+	chr6:31937094-31937291	chr6:31937198-31937291		chr6:31937094-31937197	chr6:31937093-31937094		30;746
K	cassette	CUFF.927	chr6	+	chr6:126320760-126329537	chr6:126320760-126327987;chr6:126328101-126329537		chr6:126327988-126328100			448;174
N	alternative_acceptor	CUFF.928	chr6	-	chr6:128812995-128841403;chr6:128730478-128841403;chr6:128840287-128841403	chr6:128718834-128841403		chr6:128718834-128730477;chr6:128730478-128812994;chr6:128812995-128840286	chr6:128718833-128718834;chr6:128730477-128730478;chr6:128812994-128812995		2;611
K	alternative_last_exon	CUFF.890	chr6	-	chr6:5240957-5260880;chr6:5109726-5260880	chr6:5216972-5260880	chr6:5102732-5109725	chr6:5216851-5216971			95;274
K	alternative_first_exon	CUFF.933	chr6	+	chr6:144898425-144999541;chr6:144904737-144999541	chr6:144981412-144999541	chr6:144904254-144904736	chr6:144980921-144981411			68;73
N	jcn_only_AA	CUFF.928	chr6	-	chr6:128383570-128385902;chr6:128330411-128385902;chr6:128330414-128385902	chr6:128384671-128385902		chr6:128330411-128330413;chr6:128330414-128383569;chr6:128383570-128384670	chr6:128330410-128330411;chr6:128330413-128330414;chr6:128383569-128383570		1265;26
K	jcn_only_AD	CUFF.908,CUFF.936	chr6	-	chr6:151754366-151757580	chr6:151754366-151757554		chr6:151757555-151757580	chr6:151757580-151757581	chr6:151754290-151754365;chr6:151757581-151757689	264;180
K	intron_retention	CUFF.913	chr6	-	chr6:43480302-43480498				chr6:43480301-43480302;chr6:43480498-43480499		420;1557
N	jcn_only_AD	CUFF.887	chr6	+	chr6:291701-304627	chr6:292561-304627		chr6:291701-292560	chr6:291700-291701		78;984
N	intron_retention		chr6	-	chr6:31938925-31939705				chr6:31938924-31938925;chr6:31939705-31939706		17;212
K	alternative_last_exon	CUFF.908	chr6	-	chr6:35478788-35479956,chr6:35478803-35479956	chr6:35479584-35479956	chr6:35478638-35478787	chr6:35479425-35479583			88;71
K	intron_retention	CUFF.898	chr6	+	chr6:31930576-31930761				chr6:31930575-31930576;chr6:31930761-31930762		255;21
K	cassette	CUFF.917	chr6	+	chr6:88058625-88066018	chr6:88058625-88060111;chr6:88060220-88066018		chr6:88060112-88060219			18;688
N	alternative_acceptor		chr6	+	chr6:112604395-112627530	chr6:112604395-112604499		chr6:112604500-112627530	chr6:112627530-112627531		28;5
K	alternative_first_exon	CUFF.908	chr6	-	chr6:35478788-35479956	chr6:35478788-35479424	chr6:35479957-35480071	chr6:35479425-35479773			10;56
N	cassette	CUFF.887	chr6	+	chr6:304662-335113;chr6:292561-345853	chr6:292561-311879,chr6:304662-311879;chr6:311963-335113,chr6:311963-345853		chr6:311880-311962			519;694
N	jcn_only_AA	CUFF.899	chr6	-	chr6:31939459-31939705;chr6:31938925-31939705;chr6:31939359-31939705	chr6:31939503-31939705		chr6:31938925-31939358;chr6:31939359-31939458;chr6:31939459-31939502	chr6:31938924-31938925;chr6:31939358-31939359;chr6:31939458-31939459		72;83
K	intron_retention	CUFF.898	chr6	+	chr6:31935897-31936104				chr6:31935896-31935897;chr6:31936104-31936105		276;409
K	mutually_exclusive	CUFF.923	chr6	+	chr6:112558118-112666314,chr6:112666362-112668493	chr6:112558118-112664599,chr6:112664981-112668493	chr6:112666315-112666361	chr6:112664600-112664980			103;136
K	alternative_first_exon	CUFF.902	chr6	+	chr6:32822067-32823914;chr6:32812052-32823914	chr6:32812648-32823914	chr6:32821878-32822066;chr6:32811913-32812051	chr6:32812552-32812647			172;62
N	alternative_donor		chr6	-	chr6:114283559-114292020;chr6:114283559-114332294	chr6:114283559-114289797		chr6:114289798-114292020;chr6:114292021-114332294	chr6:114292020-114292021;chr6:114332294-114332295		35;10
N	jcn_only_AA		chr6	+	chr6:112604395-112627530	chr6:112604395-112604499		chr6:112604500-112627530	chr6:112627530-112627531		28;69
N	alternative_donor	CUFF.916	chr6	-	chr6:75977465-75993935	chr6:75977465-75982179		chr6:75982180-75993935	chr6:75993935-75993936		54;0
K	cassette	CUFF.928	chr6	-	chr6:128326390-128330274	chr6:128326390-128327170;chr6:128327201-128330274		chr6:128327171-128327200			105;1149
N	jcn_only_AA	CUFF.928	chr6	-	chr6:128330411-128385902;chr6:128330414-128385902;chr6:128384671-128385902	chr6:128383570-128385902		chr6:128330411-128330413;chr6:128330414-128383569;chr6:128383570-128384670	chr6:128330410-128330411;chr6:128330413-128330414;chr6:128383569-128383570		1262;29
N	jcn_only_AD	CUFF.898	chr6	+	chr6:31937094-31937291	chr6:31937198-31937291		chr6:31937094-31937197	chr6:31937093-31937094		30;1329
N	alternative_donor	CUFF.923	chr6	+	chr6:112558118-112600322	chr6:112598514-112600322		chr6:112558118-112598513	chr6:112558117-112558118		85;0
N	alternative_acceptor		chr6	-	chr6:114281183-114289797	chr6:114283559-114289797		chr6:114281183-114283558	chr6:114281182-114281183		255;11
N	alternative_acceptor	CUFF.928	chr6	-	chr6:128718834-128841403;chr6:128812995-128841403;chr6:128840287-128841403	chr6:128730478-128841403		chr6:128718834-128730477;chr6:128730478-128812994;chr6:128812995-128840286	chr6:128718833-128718834;chr6:128730477-128730478;chr6:128812994-128812995		611;2
N	alternative_acceptor	CUFF.924	chr6	-	chr6:114281183-114291643	chr6:114289861-114291643		chr6:114281183-114289860	chr6:114281182-114281183		100;4
K	intron_retention	CUFF.910	chr6	-	chr6:39851801-39853526				chr6:39851800-39851801;chr6:39853526-39853527		23;60
N	alternative_acceptor	CUFF.913	chr6	-	chr6:43483929-43484464;chr6:43483834-43484464;chr6:43483926-43484464;chr6:43483785-43484464	chr6:43483852-43484464		chr6:43483785-43483833;chr6:43483834-43483851;chr6:43483852-43483925;chr6:43483926-43483928	chr6:43483784-43483785;chr6:43483833-43483834;chr6:43483851-43483852;chr6:43483925-43483926		1680;61
K	alternative_acceptor	CUFF.896	chr6	-	chr6:31508312-31509726	chr6:31508442-31509726		chr6:31508312-31508441	chr6:31508311-31508312		56;24
K	jcn_only_AD	CUFF.898	chr6	+	chr6:31935860-31936104	chr6:31935897-31936104		chr6:31935860-31935896	chr6:31935859-31935860		164;276
N	intron_retention		chr6	+	chr6:112375374-112375537				chr6:112375373-112375374;chr6:112375537-112375538		37;88
N	jcn_only_AD	CUFF.933	chr6	+	chr6:145119127-145124171	chr6:145120610-145124171		chr6:145119127-145120609	chr6:145119126-145119127		259;26
N	intron_retention		chr6	-	chr6:43480837-43481096				chr6:43480836-43480837;chr6:43481096-43481097		32;1227
K	intron_retention	CUFF.900	chr6	+	chr6:32122182-32122363				chr6:32122181-32122182;chr6:32122363-32122364		373;25
K	alternative_first_exon	CUFF.924	chr6	-	chr6:114281183-114283530,chr6:114281183-114289797,chr6:114281183-114291418;chr6:114281183-114291643;chr6:114281183-114289493	chr6:114281183-114292020	chr6:114291644-114291903;chr6:114289494-114289592	chr6:114292021-114292449			744;412
N	cassette	CUFF.929	chr6	-	chr6:133047978-133055391;chr6:133046119-133055391;chr6:133048152-133055391	chr6:133047978-133049879,chr6:133048152-133049879,chr6:133046119-133049879;chr6:133050119-133055391		chr6:133049880-133050118			268;530
N	cassette	CUFF.918	chr6	+	chr6:90143095-90305634	chr6:90143095-90276552;chr6:90276816-90305634		chr6:90276553-90276815			155;463
K	intron_retention	CUFF.898	chr6	+	chr6:31928872-31929323				chr6:31928871-31928872;chr6:31929323-31929324		24;81
N	alternative_donor	CUFF.933	chr6	+	chr6:145119127-145124171	chr6:145120610-145124171		chr6:145119127-145120609	chr6:145119126-145119127		259;5
K	intron_retention	CUFF.899	chr6	-	chr6:31938256-31938382				chr6:31938255-31938256;chr6:31938382-31938383		458;80
N	jcn_only_AA	CUFF.899	chr6	-	chr6:31939503-31939705;chr6:31939459-31939705;chr6:31939359-31939705	chr6:31938925-31939705		chr6:31938925-31939358;chr6:31939359-31939458;chr6:31939459-31939502	chr6:31938924-31938925;chr6:31939358-31939359;chr6:31939458-31939459		138;17
K	intron_retention	CUFF.887	chr6	+	chr6:348275-348768				chr6:348274-348275;chr6:348768-348769		910;309
K	alternative_donor	CUFF.918	chr6	+	chr6:90338943-90340151	chr6:90338958-90340151		chr6:90338943-90338957	chr6:90338942-90338943		111;190
N	jcn_only_AD		chr6	-	chr6:114283559-114292020;chr6:114283559-114289797	chr6:114283559-114332294		chr6:114289798-114292020;chr6:114292021-114332294	chr6:114292020-114292021;chr6:114332294-114332295		153;34
K	intron_retention	CUFF.914	chr6	+	chr6:46638966-46644383				chr6:46638965-46638966;chr6:46644383-46644384		381;152
K	intron_retention	CUFF.905	chr6	+	chr6:33239900-33240404				chr6:33239899-33239900;chr6:33240404-33240405		231;101
N	jcn_only_AA	CUFF.890	chr6	-	chr6:5144497-5216850;chr6:5113652-5216850;chr6:5138974-5216850	chr6:5187215-5216850					331;25
N	cassette	CUFF.918	chr6	+	chr6:90312847-90321990	chr6:90312847-90315725;chr6:90315825-90321990		chr6:90315726-90315824			63;433
N	alternative_acceptor	CUFF.913	chr6	-	chr6:43483834-43484464;chr6:43483852-43484464;chr6:43483926-43484464;chr6:43483785-43484464	chr6:43483929-43484464		chr6:43483785-43483833;chr6:43483834-43483851;chr6:43483852-43483925;chr6:43483926-43483928	chr6:43483784-43483785;chr6:43483833-43483834;chr6:43483851-43483852;chr6:43483925-43483926		1717;24
N	jcn_only_AA	CUFF.898,CUFF.905	chr6	+	chr6:31936316-31936462	chr6:31936316-31936399		chr6:31936400-31936462	chr6:31936462-31936463		306;34
N	jcn_only_AA	CUFF.928	chr6	-	chr6:128718834-128841403;chr6:128812995-128841403;chr6:128730478-128841403	chr6:128840287-128841403		chr6:128718834-128730477;chr6:128730478-128812994;chr6:128812995-128840286	chr6:128718833-128718834;chr6:128730477-128730478;chr6:128812994-128812995		740;41
N	alternative_acceptor	CUFF.913	chr6	-	chr6:43483929-43484464;chr6:43483852-43484464;chr6:43483926-43484464;chr6:43483785-43484464	chr6:43483834-43484464		chr6:43483785-43483833;chr6:43483834-43483851;chr6:43483852-43483925;chr6:43483926-43483928	chr6:43483784-43483785;chr6:43483833-43483834;chr6:43483851-43483852;chr6:43483925-43483926		1633;108
K	alternative_first_exon	CUFF.902	chr6	+	chr6:32812648-32823914;chr6:32812052-32823914	chr6:32822067-32823914	chr6:32812552-32812647;chr6:32811913-32812051	chr6:32821878-32822066			154;80
N	jcn_only_AD		chr6	-	chr6:114283559-114292020;chr6:114283559-114332294	chr6:114283559-114289797		chr6:114289798-114292020;chr6:114292021-114332294	chr6:114292020-114292021;chr6:114332294-114332295		49;138
K	jcn_only_AA	CUFF.889	chr6	-	chr6:3155158-3155858	chr6:3155290-3155858		chr6:3155158-3155289	chr6:3155157-3155158		35;58
K	intron_retention	CUFF.900	chr6	+	chr6:32122172-32122363				chr6:32122171-32122172;chr6:32122363-32122364		61;34
K	cassette	CUFF.927	chr6	+	chr6:126317187-126319368	chr6:126317187-126319198;chr6:126319281-126319368		chr6:126319199-126319280			178;586
K	intron_retention		chr6	+	chr6:31927178-31927786				chr6:31927177-31927178;chr6:31927786-31927787		268;77
K	alternative_first_exon	CUFF.911	chr6	-	chr6:41491964-41513737,chr6:41491964-41516115;chr6:41491964-41515198	chr6:41491964-41513826	chr6:41515199-41515385	chr6:41513827-41513981			2404;2343
N	alternative_acceptor		chr6	+	chr6:32122961-32123544	chr6:32122961-32123464		chr6:32123465-32123544	chr6:32123544-32123545		18;183
K	cassette	CUFF.918	chr6	+	chr6:90326377-90327672	chr6:90326377-90326592;chr6:90326676-90327672		chr6:90326593-90326675			113;25
N	alternative_acceptor	CUFF.928	chr6	-	chr6:128383570-128385902;chr6:128330411-128385902;chr6:128330414-128385902	chr6:128384671-128385902		chr6:128330411-128330413;chr6:128330414-128383569;chr6:128383570-128384670	chr6:128330410-128330411;chr6:128330413-128330414;chr6:128383569-128383570		620;0
K	intron_retention	CUFF.924	chr6	-	chr6:114277316-114277782				chr6:114277315-114277316;chr6:114277782-114277783		497;37
N	alternative_first_exon		chr6	-	chr6:31938925-31939705	chr6:31938925-31939096	chr6:31939706-31940166	chr6:31939097-31939462			35;551
K	coord_cassette	CUFF.927	chr6	+	chr6:126329619-126332398	chr6:126329619-126329802;chr6:126329892-126330480;chr6:126330581-126332398		chr6:126329803-126329891;chr6:126330481-126330580			180;15
K	intron_retention	CUFF.933	chr6	+	chr6:145157678-145160308				chr6:145157677-145157678;chr6:145160308-145160309		125;28
K	intron_retention	CUFF.924	chr6	-	chr6:114281183-114291643				chr6:114281182-114281183;chr6:114291643-114291644		100;64
N	cassette	CUFF.923	chr6	+	chr6:112558118-112604255	chr6:112558118-112600322;chr6:112600441-112604255		chr6:112600323-112600440			67;81
N	cassette	CUFF.887	chr6	+	chr6:320365-345853;chr6:311963-345853	chr6:311963-335113,chr6:320365-335113;chr6:335164-345853		chr6:335114-335163			206;740
N	alternative_acceptor	CUFF.922,CUFF.937	chr6	+	chr6:112375609-112382193	chr6:112375609-112375825		chr6:112375826-112382193	chr6:112382193-112382194		234;8
N	jcn_only_AA	CUFF.928	chr6	-	chr6:128383570-128385902;chr6:128330411-128385902;chr6:128384671-128385902	chr6:128330414-128385902		chr6:128330411-128330413;chr6:128330414-128383569;chr6:128383570-128384670	chr6:128330410-128330411;chr6:128330413-128330414;chr6:128383569-128383570		70;1221
N	alternative_acceptor	CUFF.924	chr6	-	chr6:114281183-114292020;chr6:114289861-114292020;chr6:114283559-114292020	chr6:114281204-114292020		chr6:114281183-114281203;chr6:114281204-114283558;chr6:114283559-114289860	chr6:114281182-114281183;chr6:114281203-114281204;chr6:114283558-114283559		493;75
K	alternative_last_exon	CUFF.937	chr6	+	chr6:161471012-161491639	chr6:161471012-161488230	chr6:161491640-161491882	chr6:161488231-161488315			72;5
N	jcn_only_AD	CUFF.923	chr6	+	chr6:112558118-112600322	chr6:112598514-112600322		chr6:112558118-112598513	chr6:112558117-112558118		85;26
N	cassette	CUFF.900	chr6	+	chr6:32122555-32123544;chr6:32122555-32123464	chr6:32122555-32122806;chr6:32122961-32123544,chr6:32122961-32123464		chr6:32122807-32122960			619;309
N	cassette	CUFF.929	chr6	-	chr6:133046119-133049879;chr6:133046119-133055391	chr6:133046119-133047860;chr6:133048152-133049879,chr6:133048152-133055391		chr6:133047861-133048151			254;376
K	intron_retention	CUFF.905	chr6	+	chr6:33239900-33240363				chr6:33239899-33239900;chr6:33240363-33240364		418;48
N	jcn_only_AA	CUFF.928	chr6	-	chr6:128540242-128561179	chr6:128556750-128561179		chr6:128540242-128556749	chr6:128540241-128540242		1161;90
N	jcn_only_AA		chr6	+	chr6:31927178-31928817	chr6:31927178-31927786					15;268
N	jcn_only_AD	CUFF.921	chr6	+	chr6:111303333-111306208	chr6:111303707-111306208		chr6:111303333-111303706	chr6:111303332-111303333		403;62
K	intron_retention	CUFF.899	chr6	-	chr6:31938603-31938688				chr6:31938602-31938603;chr6:31938688-31938689		101;282
N	jcn_only_AA	CUFF.924	chr6	-	chr6:114281183-114291643	chr6:114289861-114291643		chr6:114281183-114289860	chr6:114281182-114281183		100;110
N	jcn_only_AA	CUFF.913	chr6	-	chr6:43483929-43484464;chr6:43483834-43484464;chr6:43483926-43484464;chr6:43483785-43484464	chr6:43483852-43484464		chr6:43483785-43483833;chr6:43483834-43483851;chr6:43483852-43483925;chr6:43483926-43483928	chr6:43483784-43483785;chr6:43483833-43483834;chr6:43483851-43483852;chr6:43483925-43483926		1708;58
K	jcn_only_AA	CUFF.929	chr6	-	chr6:133047978-133049879	chr6:133048152-133049879		chr6:133047978-133048151	chr6:133047977-133047978		276;217
K	intron_retention	CUFF.890	chr6	-	chr6:5104185-5108785				chr6:5104184-5104185;chr6:5108785-5108786		18;153
N	alternative_acceptor	CUFF.900	chr6	+	chr6:126307769-126314938	chr6:126307769-126314902		chr6:126314903-126314938	chr6:126314938-126314939		51;174
N	alternative_first_exon	CUFF.893	chr6	+	chr6:28109808-28112108	chr6:28110042-28112108	chr6:28109688-28109807	chr6:28109901-28110041			18;224
K	intron_retention	CUFF.902	chr6	+	chr6:32825172-32825781				chr6:32825171-32825172;chr6:32825781-32825782		357;50
K	cassette	CUFF.900	chr6	+	chr6:32121414-32122363	chr6:32121414-32121775;chr6:32122172-32122363		chr6:32121776-32122171			347;138
N	jcn_only_AA	CUFF.924	chr6	-	chr6:114281183-114292020;chr6:114289861-114292020;chr6:114283559-114292020	chr6:114281204-114292020		chr6:114281183-114281203;chr6:114281204-114283558;chr6:114283559-114289860	chr6:114281182-114281183;chr6:114281203-114281204;chr6:114283558-114283559		775;151
K	cassette	CUFF.918	chr6	+	chr6:90326377-90331640	chr6:90326377-90327672;chr6:90327751-90331640		chr6:90327673-90327750			51;92
K	alternative_first_exon	CUFF.908	chr6	-	chr6:35477090-35479424	chr6:35477090-35477410	chr6:35479425-35479773	chr6:35477411-35477527			40;28
K	intron_retention	CUFF.888	chr6	+	chr6:2988944-2989761				chr6:2988943-2988944;chr6:2989761-2989762		166;24
N	coord_cassette	CUFF.887	chr6	+	chr6:292561-345853	chr6:292561-304627;chr6:304662-311879;chr6:311963-345853		chr6:304628-304661;chr6:311880-311962			470;376
N	alternative_donor	CUFF.887	chr6	+	chr6:291701-304627	chr6:292561-304627		chr6:291701-292560	chr6:291700-291701		78;307
K	cassette	CUFF.928	chr6	-	chr6:128313855-128316606	chr6:128313855-128316393;chr6:128316412-128316606		chr6:128316394-128316411			96;186
K	alternative_acceptor	CUFF.939	chr6	-	chr6:170117997-170118883	chr6:170118003-170118883		chr6:170117997-170118002	chr6:170117996-170117997		67;30
K	intron_retention	CUFF.937	chr6	+	chr6:161494645-161501912				chr6:161494644-161494645;chr6:161501912-161501913		176;73
K	alternative_first_exon	CUFF.937	chr6	+	chr6:161413116-161455290	chr6:161443260-161455290	chr6:161412705-161413115	chr6:161443167-161443259			4;22
K	alternative_acceptor	CUFF.926	chr6	-	chr6:116988076-116989728	chr6:116988371-116989728		chr6:116988076-116988370	chr6:116988075-116988076		23;40
N	mutually_exclusive	CUFF.929	chr6	-	chr6:133046119-133049879,chr6:133050073-133055391	chr6:133046119-133047860,chr6:133047978-133055391	chr6:133049880-133050072	chr6:133047861-133047977			65;35
K	intron_retention	CUFF.929	chr6	-	chr6:133044194-133044872				chr6:133044193-133044194;chr6:133044872-133044873		821;69
K	alternative_acceptor	CUFF.908	chr6	-	chr6:35478788-35479956	chr6:35478803-35479956		chr6:35478788-35478802	chr6:35478787-35478788		15;46
K	alternative_donor	CUFF.900	chr6	+	chr6:32122172-32122363;chr6:32122182-32122363	chr6:32122024-32122363		chr6:32122024-32122171;chr6:32122172-32122181	chr6:32122023-32122024;chr6:32122171-32122172		255;19
K	intron_retention	CUFF.895	chr6	-	chr6:30711974-30712085				chr6:30711973-30711974;chr6:30712085-30712086		261;50
N	jcn_only_AD	CUFF.927	chr6	+	chr6:126342412-126359850	chr6:126342427-126359850		chr6:126342412-126342426	chr6:126342411-126342412		44;63
K	coord_cassette	CUFF.918	chr6	+	chr6:90326377-90331640	chr6:90326377-90326592;chr6:90326676-90327672;chr6:90327751-90331640		chr6:90326593-90326675;chr6:90327673-90327750			51;23
K	alternative_donor	CUFF.937	chr6	+	chr6:161514872-161518111	chr6:161514884-161518111		chr6:161514872-161514883	chr6:161514871-161514872		94;31
N	jcn_only_AD	CUFF.900	chr6	+	chr6:32125498-32130344	chr6:32125702-32130344					15;227
K	intron_retention	CUFF.922	chr6	+	chr6:112375365-112375537				chr6:112375364-112375365;chr6:112375537-112375538		190;90
N	jcn_only_AD	CUFF.911,CUFF.928	chr6	-	chr6:128327201-128330274	chr6:128327201-128329190		chr6:128329191-128330274	chr6:128330274-128330275		1162;154
K	jcn_only_AD	CUFF.900	chr6	+	chr6:32122024-32122363;chr6:32122172-32122363	chr6:32122182-32122363		chr6:32122024-32122171;chr6:32122172-32122181	chr6:32122023-32122024;chr6:32122171-32122172		80;373
N	intron_retention		chr6	-	chr6:133047978-133055391				chr6:133047977-133047978;chr6:133055391-133055392		29;106
K	intron_retention	CUFF.922	chr6	+	chr6:112382498-112385966				chr6:112382497-112382498;chr6:112385966-112385967		149;20
N	jcn_only_AA	CUFF.899	chr6	-	chr6:31939503-31939705;chr6:31938925-31939705;chr6:31939359-31939705	chr6:31939459-31939705		chr6:31938925-31939358;chr6:31939359-31939458;chr6:31939459-31939502	chr6:31938924-31938925;chr6:31939358-31939359;chr6:31939458-31939459		112;43
K	alternative_first_exon	CUFF.907	chr6	+	chr6:34434048-34494019;chr6:34482846-34494019	chr6:34452922-34494019	chr6:34433916-34434047;chr6:34482601-34482845	chr6:34452767-34452921			91;37
N	cassette	CUFF.918	chr6	+	chr6:90276816-90312747	chr6:90276816-90305634;chr6:90305734-90312747		chr6:90305635-90305733			211;420
N	cassette	CUFF.893	chr6	+	chr6:28109808-28116093	chr6:28109808-28112108;chr6:28112203-28116093		chr6:28112109-28112202			10;90
K	intron_retention	CUFF.902	chr6	+	chr6:32823983-32825039				chr6:32823982-32823983;chr6:32825039-32825040		278;39
N	jcn_only_AA	CUFF.928	chr6	-	chr6:128718834-128841403;chr6:128730478-128841403;chr6:128840287-128841403	chr6:128812995-128841403		chr6:128718834-128730477;chr6:128730478-128812994;chr6:128812995-128840286	chr6:128718833-128718834;chr6:128730477-128730478;chr6:128812994-128812995		757;24
N	intron_retention		chr6	-	chr6:31938156-31938369				chr6:31938155-31938156;chr6:31938369-31938370		45;135
N	coord_cassette	CUFF.929	chr6	-	chr6:133046119-133055391	chr6:133046119-133047860;chr6:133047978-133049879;chr6:133050119-133055391		chr6:133047861-133047977;chr6:133049880-133050118			165;296
K	intron_retention	CUFF.900	chr6	+	chr6:32123756-32125413				chr6:32123755-32123756;chr6:32125413-32125414		780;55
N	alternative_acceptor	CUFF.929	chr6	-	chr6:133055523-133055618	chr6:133055526-133055618		chr6:133055523-133055525	chr6:133055522-133055523		1496;46
K	alternative_first_exon	CUFF.936	chr6	-	chr6:151757690-151765600;chr6:151757690-151773150	chr6:151757690-151766442	chr6:151765601-151765760;chr6:151773151-151773351	chr6:151766443-151767020		chr6:151757555-151757689	238;849
N	alternative_acceptor	CUFF.899	chr6	-	chr6:31939503-31939705;chr6:31939459-31939705;chr6:31939359-31939705	chr6:31938925-31939705		chr6:31938925-31939358;chr6:31939359-31939458;chr6:31939459-31939502	chr6:31938924-31938925;chr6:31939358-31939359;chr6:31939458-31939459		317;17
N	intron_retention		chr6	-	chr6:43481372-43483343				chr6:43481371-43481372;chr6:43483343-43483344		57;162
N	alternative_donor	CUFF.921	chr6	+	chr6:111303333-111306208	chr6:111303707-111306208		chr6:111303333-111303706	chr6:111303332-111303333		403;43
K	coord_cassette	CUFF.910	chr6	-	chr6:39856832-39864972	chr6:39856832-39859081;chr6:39859156-39859398;chr6:39859540-39864972		chr6:39859082-39859155;chr6:39859399-39859539			42;35
K	intron_retention	CUFF.927	chr6	+	chr6:126319831-126320602				chr6:126319830-126319831;chr6:126320602-126320603		724;6
N	alternative_last_exon	CUFF.928	chr6	-	chr6:128320050-128322340	chr6:128321476-128322340	chr6:128319865-128320049	chr6:128321034-128321475			186;1707
K	alternative_first_exon	CUFF.927	chr6	+	chr6:126307769-126314902,chr6:126307837-126314902	chr6:126307920-126314902	chr6:126307486-126307768	chr6:126307841-126307919			418;18
N	jcn_only_AD	CUFF.898	chr6	+	chr6:31927178-31928817	chr6:31928518-31928817					15;313
K	jcn_only_AA	CUFF.896	chr6	-	chr6:31508312-31509726	chr6:31508442-31509726		chr6:31508312-31508441	chr6:31508311-31508312		56;30
N	jcn_only_AD	CUFF.922	chr6	+	chr6:112375365-112375537	chr6:112375374-112375537		chr6:112375365-112375373	chr6:112375364-112375365		190;37
K	cassette	CUFF.928	chr6	-	chr6:128320050-128326228	chr6:128320050-128324341;chr6:128324378-128326228		chr6:128324342-128324377			21;679
N	jcn_only_AA		chr6	+	chr6:161413116-161491639	chr6:161413116-161455290					30;4
N	cassette	CUFF.923	chr6	+	chr6:112558118-112668493	chr6:112558118-112664599;chr6:112664981-112668493		chr6:112664600-112664980			218;191
N	jcn_only_AA	CUFF.924	chr6	-	chr6:114281183-114292020;chr6:114281204-114292020;chr6:114289861-114292020	chr6:114283559-114292020		chr6:114281183-114281203;chr6:114281204-114283558;chr6:114283559-114289860	chr6:114281182-114281183;chr6:114281203-114281204;chr6:114283558-114283559		910;15
K	alternative_first_exon	CUFF.892	chr6	-	chr6:13470863-13486242;chr6:13470863-13472212	chr6:13470863-13486869	chr6:13486243-13486470;chr6:13472213-13472327	chr6:13486870-13487991			73;52
N	cassette	CUFF.887	chr6	+	chr6:292561-311879	chr6:292561-304627;chr6:304662-311879		chr6:304628-304661			53;808
K	alternative_first_exon	CUFF.907	chr6	+	chr6:34434048-34494019;chr6:34452922-34494019	chr6:34482846-34494019	chr6:34433916-34434047;chr6:34452767-34452921	chr6:34482601-34482845			45;83
K	intron_retention	CUFF.905	chr6	+	chr6:33243844-33243952				chr6:33243843-33243844;chr6:33243952-33243953		984;85
K	intron_retention	CUFF.927	chr6	+	chr6:126319281-126319368				chr6:126319280-126319281;chr6:126319368-126319369		642;39
K	intron_retention	CUFF.918	chr6	+	chr6:90327751-90331640				chr6:90327750-90327751;chr6:90331640-90331641		108;20
K	cassette	CUFF.905	chr6	+	chr6:33240504-33243573	chr6:33240504-33243276;chr6:33243435-33243573		chr6:33243277-33243434			538;73
N	alternative_donor		chr6	-	chr6:114283559-114292020;chr6:114283559-114289797	chr6:114283559-114332294		chr6:114289798-114292020;chr6:114292021-114332294	chr6:114292020-114292021;chr6:114332294-114332295		11;34
N	alternative_donor		chr6	-	chr6:114283559-114289797;chr6:114283559-114332294	chr6:114283559-114292020		chr6:114289798-114292020;chr6:114292021-114332294	chr6:114292020-114292021;chr6:114332294-114332295		44;1
N	alternative_last_exon		chr6	+	chr6:32125498-32130344	chr6:32125498-32125616	chr6:32130345-32130399	chr6:32125617-32126161			12;340
N	jcn_only_AA	CUFF.890	chr6	-	chr6:5113652-5216850;chr6:5138974-5216850;chr6:5187215-5216850	chr6:5144497-5216850					343;13
K	intron_retention	CUFF.898	chr6	+	chr6:31937198-31937291				chr6:31937197-31937198;chr6:31937291-31937292		1329;87
K	intron_retention	CUFF.905	chr6	+	chr6:33243661-33243741				chr6:33243660-33243661;chr6:33243741-33243742		820;291
N	jcn_only_AA	CUFF.899	chr6	-	chr6:31938530-31938688	chr6:31938603-31938688		chr6:31938530-31938602	chr6:31938529-31938530		138;101
K	cassette	CUFF.918	chr6	+	chr6:90327751-90333128	chr6:90327751-90331640;chr6:90331746-90333128		chr6:90331641-90331745			6;115
K	jcn_only_AA	CUFF.896	chr6	-	chr6:31509926-31513885	chr6:31512536-31513885					87;214
K	cassette	CUFF.926	chr6	-	chr6:116980088-116981898	chr6:116980088-116981395;chr6:116981533-116981898		chr6:116981396-116981532			38;17
N	coord_cassette	CUFF.929	chr6	-	chr6:133046119-133055391	chr6:133046119-133047860;chr6:133047978-133049879;chr6:133050073-133055391		chr6:133047861-133047977;chr6:133049880-133050072			165;247
N	jcn_only_AA	CUFF.928	chr6	-	chr6:128540242-128643183	chr6:128563748-128643183					19;1013
K	intron_retention	CUFF.899	chr6	-	chr6:31937981-31938119				chr6:31937980-31937981;chr6:31938119-31938120		550;32
K	alternative_first_exon	CUFF.902	chr6	+	chr6:32812648-32823914;chr6:32822067-32823914	chr6:32812052-32823914	chr6:32812552-32812647;chr6:32821878-32822066	chr6:32811913-32812051			142;92
K	jcn_only_AA	CUFF.908	chr6	-	chr6:35477090-35479424	chr6:35478788-35479424					57;80
N	cassette	CUFF.923	chr6	+	chr6:112558118-112668493	chr6:112558118-112666314;chr6:112666362-112668493		chr6:112666315-112666361			218;103
K	jcn_only_AD	CUFF.857	chr5	-	chr5:54410147-54415640	chr5:54410147-54415628		chr5:54415629-54415640	chr5:54415640-54415641		31;122
N	jcn_only_AD	CUFF.871	chr5	+	chr5:131630703-131647853	chr5:131631315-131647853		chr5:131630703-131631314	chr5:131630702-131630703		68;24
N	alternative_acceptor	CUFF.850	chr5	-	chr5:37309370-37310653	chr5:37309675-37310653		chr5:37309370-37309674	chr5:37309369-37309370		21;5
N	alternative_donor	CUFF.885	chr5	+	chr5:177636434-177637132	chr5:177636449-177637132		chr5:177636434-177636448	chr5:177636433-177636434		12;725
K	alternative_last_exon	CUFF.865	chr5	+	chr5:81608671-81637517	chr5:81608671-81613816	chr5:81637518-81637609	chr5:81613817-81614622			13;121
N	alternative_donor	CUFF.871	chr5	+	chr5:131658049-131662969	chr5:131660336-131662969		chr5:131658049-131660335	chr5:131658048-131658049		80;5
N	alternative_acceptor	CUFF.886	chr5	-	chr5:178032384-178035376	chr5:178032867-178035376		chr5:178032384-178032866	chr5:178032383-178032384		93;3
K	cassette	CUFF.874	chr5	+	chr5:137520887-137521649	chr5:137520887-137521200;chr5:137521400-137521649		chr5:137521201-137521399			196;83
K	intron_retention	CUFF.876	chr5	+	chr5:140027510-140028055				chr5:140027509-140027510;chr5:140028055-140028056		541;282
N	jcn_only_AA	CUFF.852	chr5	+	chr5:40936588-40937653	chr5:40936588-40937339		chr5:40937340-40937653	chr5:40937653-40937654		31;43
K	jcn_only_AA	CUFF.851	chr5	+	chr5:39521730-39524364	chr5:39521730-39524352		chr5:39524353-39524364	chr5:39524364-39524365		16;45
K	alternative_donor	CUFF.862	chr5	-	chr5:60199544-60200618	chr5:60199544-60200614		chr5:60200615-60200618	chr5:60200618-60200619		487;27
K	cassette	CUFF.886	chr5	-	chr5:178032384-178039416	chr5:178032384-178035376;chr5:178035460-178039416		chr5:178035377-178035459			68;87
N	cassette	CUFF.886	chr5	-	chr5:178045780-178050256	chr5:178045780-178046838;chr5:178046898-178050256		chr5:178046839-178046897			114;138
K	intron_retention	CUFF.859	chr5	+	chr5:54456072-54456157				chr5:54456071-54456072;chr5:54456157-54456158		368;44
K	alternative_last_exon	CUFF.869	chr5	-	chr5:127396337-127396835;chr5:127302621-127396835;chr5:127292614-127396835	chr5:127359991-127396835	chr5:127301533-127302620;chr5:127292496-127292613	chr5:127359628-127359990			257;260
K	alternative_donor	CUFF.876	chr5	+	chr5:140027510-140028055	chr5:140027593-140028055		chr5:140027510-140027592	chr5:140027509-140027510		541;724
K	intron_retention	CUFF.878	chr5	-	chr5:141041357-141041609				chr5:141041356-141041357;chr5:141041609-141041610		227;16
N	jcn_only_AA	CUFF.861	chr5	+	chr5:56510021-56526672	chr5:56510021-56517202		chr5:56517203-56526672	chr5:56526672-56526673		36;35
K	intron_retention	CUFF.875	chr5	+	chr5:139915124-139916973				chr5:139915123-139915124;chr5:139916973-139916974		96;355
K	intron_retention	CUFF.886	chr5	-	chr5:178043950-178045556				chr5:178043949-178043950;chr5:178045556-178045557		59;48
K	cassette	CUFF.857	chr5	-	chr5:54442685-54468765	chr5:54442685-54468415;chr5:54468479-54468765		chr5:54468416-54468478			151;152
N	mutually_exclusive	CUFF.859	chr5	+	chr5:54456072-54456821,chr5:54457084-54459882	chr5:54456072-54456157,chr5:54456225-54459882	chr5:54456822-54457083	chr5:54456158-54456224			47;121
N	alternative_donor		chr5	-	chr5:178050418-178057554	chr5:178050418-178053946		chr5:178053947-178057554	chr5:178057554-178057555		22;31
N	jcn_only_AA	CUFF.875	chr5	+	chr5:139815843-139818045;chr5:139815843-139818078	chr5:139815843-139818087		chr5:139818046-139818078;chr5:139818079-139818087	chr5:139818078-139818079;chr5:139818087-139818088		294;96
K	cassette	CUFF.857	chr5	-	chr5:54420857-54423084	chr5:54420857-54422181;chr5:54422268-54423084		chr5:54422182-54422267			109;56
K	cassette	CUFF.860	chr5	-	chr5:54593227-54603214	chr5:54593227-54594418;chr5:54594493-54603214		chr5:54594419-54594492			63;12
K	intron_retention	CUFF.886	chr5	-	chr5:178030936-178032303				chr5:178030935-178030936;chr5:178032303-178032304		126;76
N	jcn_only_AA	ENSG00000188242.4	chr5	-	chr5:472081-472793;chr5:466642-472793;chr5:472709-472793	chr5:471939-472793		chr5:466642-471938;chr5:471939-472080;chr5:472081-472708	chr5:466641-466642;chr5:471938-471939;chr5:472080-472081		2478;26
K	cassette	CUFF.859	chr5	+	chr5:54456225-54459882	chr5:54456225-54456821;chr5:54457084-54459882		chr5:54456822-54457083			99;132
N	cassette	CUFF.875	chr5	+	chr5:139886563-139889221	chr5:139886563-139887369;chr5:139887584-139889221		chr5:139887370-139887583			74;58
N	cassette	CUFF.886	chr5	-	chr5:178045780-178050256	chr5:178045780-178046838;chr5:178047675-178050256		chr5:178046839-178047674			114;289
N	alternative_donor	CUFF.875	chr5	+	chr5:139917820-139918503	chr5:139917847-139918503		chr5:139917820-139917846	chr5:139917819-139917820		45;434
K	intron_retention	CUFF.882	chr5	-	chr5:149781814-149782125				chr5:149781813-149781814;chr5:149782125-149782126		175;84
N	alternative_acceptor	CUFF.875	chr5	+	chr5:139876864-139884405	chr5:139876864-139877622		chr5:139877623-139884405	chr5:139884405-139884406		16;3
N	alternative_last_exon		chr5	+	chr5:139909382-139916973	chr5:139909382-139914946	chr5:139916974-139917174	chr5:139914947-139915575			157;847
K	intron_retention	CUFF.847	chr5	-	chr5:2746901-2747654				chr5:2746900-2746901;chr5:2747654-2747655		26;10
K	cassette	CUFF.878	chr5	-	chr5:141034003-141035187	chr5:141034003-141034928;chr5:141034968-141035187		chr5:141034929-141034967			304;172
K	intron_retention	CUFF.864	chr5	-	chr5:69493218-69497694				chr5:69493217-69493218;chr5:69497694-69497695	chr5:69493082-69493217;chr5:69497695-69497869	146;33
K	alternative_last_exon	CUFF.848	chr5	+	chr5:36177395-36183941	chr5:36177395-36181919	chr5:36183942-36184520	chr5:36181920-36182695			589;455
K	intron_retention	CUFF.859	chr5	+	chr5:54456072-54456947				chr5:54456071-54456072;chr5:54456947-54456948		59;81
K	coord_cassette	CUFF.882	chr5	-	chr5:149785885-149792187	chr5:149785885-149786443;chr5:149786524-149786714;chr5:149786888-149792187		chr5:149786444-149786523;chr5:149786715-149786887			416;794
K	jcn_only_AD	CUFF.862	chr5	-	chr5:60198336-60214091	chr5:60198336-60199474					274;282
N	cassette	CUFF.869	chr5	-	chr5:127412786-127418426;chr5:127396937-127418426	chr5:127412786-127417664,chr5:127396937-127417664;chr5:127417887-127418426		chr5:127417665-127417886			96;196
K	jcn_only_AD	CUFF.846,CUFF.882	chr5	-	chr5:1075606-1076252	chr5:1075606-1076005		chr5:1076006-1076252	chr5:1076252-1076253		21;77
K	jcn_only_AA	CUFF.854,CUFF.861	chr5	+	chr5:50685767-50687176	chr5:50685767-50687107		chr5:50687108-50687176	chr5:50687176-50687177		62;157
N	alternative_acceptor	CUFF.875	chr5	+	chr5:139815843-139818045;chr5:139815843-139818087	chr5:139815843-139818078		chr5:139818046-139818078;chr5:139818079-139818087	chr5:139818078-139818079;chr5:139818087-139818088		148;104
K	jcn_only_AA	CUFF.854,CUFF.875	chr5	+	chr5:139915124-139916973	chr5:139915124-139916922		chr5:139916923-139916973	chr5:139916973-139916974		96;502
K	alternative_acceptor	CUFF.851	chr5	+	chr5:39521730-39524364	chr5:39521730-39524352		chr5:39524353-39524364	chr5:39524364-39524365		16;24
N	jcn_only_AA	CUFF.856	chr5	+	chr5:52161652-52177704	chr5:52161652-52162871		chr5:52162872-52177704	chr5:52177704-52177705		77;74
K	intron_retention	CUFF.876	chr5	+	chr5:140039781-140040342				chr5:140039780-140039781;chr5:140040342-140040343		986;10
K	jcn_only_AA	CUFF.866	chr5	-	chr5:82948641-82969242	chr5:82948644-82969242		chr5:82948641-82948643	chr5:82948640-82948641		62;435
N	alternative_acceptor	CUFF.852	chr5	+	chr5:40936588-40937653	chr5:40936588-40937339		chr5:40937340-40937653	chr5:40937653-40937654		31;63
K	jcn_only_AD	CUFF.869	chr5	-	chr5:127398193-127418661	chr5:127398193-127418426		chr5:127418427-127418661	chr5:127418661-127418662		73;37
K	alternative_acceptor	CUFF.875	chr5	+	chr5:139865318-139866590	chr5:139865318-139866542		chr5:139866543-139866590	chr5:139866590-139866591		8;28
K	alternative_donor	CUFF.863	chr5	-	chr5:64906871-64907583	chr5:64906871-64907429		chr5:64907430-64907583	chr5:64907583-64907584		116;159
K	alternative_last_exon	CUFF.857	chr5	-	chr5:54429357-54436141	chr5:54433465-54436141	chr5:54429240-54429356	chr5:54433315-54433464			112;105
N	jcn_only_AD	CUFF.875	chr5	+	chr5:139909382-139916973	chr5:139915124-139916973					53;96
N	alternative_donor	CUFF.860,CUFF.886	chr5	-	chr5:54577344-54579030	chr5:54577344-54578943		chr5:54578944-54579030	chr5:54579030-54579031		31;4
K	intron_retention	CUFF.872	chr5	+	chr5:134191018-134193046				chr5:134191017-134191018;chr5:134193046-134193047		12;111
K	jcn_only_AD	CUFF.876	chr5	+	chr5:140027510-140028055	chr5:140027593-140028055		chr5:140027510-140027592	chr5:140027509-140027510		541;1329
N	alternative_acceptor	CUFF.871,CUFF.875	chr5	+	chr5:131658049-131662969	chr5:131658049-131660153		chr5:131660154-131662969	chr5:131662969-131662970		80;3
K	jcn_only_AA	CUFF.861	chr5	+	chr5:56531860-56542126	chr5:56531860-56532939					99;65
N	jcn_only_AA	ENSG00000188242.4	chr5	-	chr5:472081-472793;chr5:466642-472793;chr5:471939-472793	chr5:472709-472793		chr5:466642-471938;chr5:471939-472080;chr5:472081-472708	chr5:466641-466642;chr5:471938-471939;chr5:472080-472081		2317;187
K	jcn_only_AD	CUFF.869,CUFF.878	chr5	-	chr5:141050196-141050891	chr5:141050196-141050831		chr5:141050832-141050891	chr5:141050891-141050892		30;157
N	jcn_only_AD	CUFF.881	chr5	-	chr5:36703067-36705822	chr5:36703067-36705781		chr5:36705782-36705822	chr5:36705822-36705823		12;177
K	jcn_only_AA	CUFF.848,CUFF.880	chr5	+	chr5:145651238-145694458	chr5:145651238-145664184					12;15
N	alternative_donor	CUFF.880	chr5	+	chr5:145616996-145634505	chr5:145631439-145634505		chr5:145616996-145631438	chr5:145616995-145616996		5;0
N	cassette	CUFF.882	chr5	-	chr5:149782189-149785821;chr5:149782189-149784242	chr5:149782189-149782683;chr5:149782876-149785821,chr5:149782876-149784242		chr5:149782684-149782875			114;144
K	intron_retention	CUFF.877	chr5	+	chr5:140706205-140707336				chr5:140706204-140706205;chr5:140707336-140707337		99;9
K	alternative_donor	CUFF.869,CUFF.878	chr5	-	chr5:141050196-141050891	chr5:141050196-141050831		chr5:141050832-141050891	chr5:141050891-141050892		30;95
N	jcn_only_AA	CUFF.859,CUFF.871	chr5	+	chr5:131649462-131657876	chr5:131649462-131656557		chr5:131656558-131657876	chr5:131657876-131657877		83;29
K	intron_retention	CUFF.886	chr5	-	chr5:178049461-178050256				chr5:178049460-178049461;chr5:178050256-178050257		64;81
N	jcn_only_AD		chr5	-	chr5:64887330-64887698	chr5:64887330-64887669					24;23
K	jcn_only_AD	CUFF.872	chr5	+	chr5:134190853-134193046	chr5:134191018-134193046		chr5:134190853-134191017	chr5:134190852-134190853		77;12
K	cassette	CUFF.862	chr5	-	chr5:60199544-60214091	chr5:60199544-60200618;chr5:60200701-60214091		chr5:60200619-60200700			11;364
K	intron_retention		chr5	+	chr5:134181903-134182352				chr5:134181902-134181903;chr5:134182352-134182353		129;26
K	alternative_last_exon	CUFF.873	chr5	-	chr5:137194953-137223848	chr5:137219311-137223848	chr5:137194745-137194952	chr5:137218388-137219310			45;165
K	cassette	CUFF.869	chr5	-	chr5:127302621-127412638	chr5:127302621-127396835;chr5:127396937-127412638		chr5:127396836-127396936			36;134
K	intron_retention	CUFF.886	chr5	-	chr5:178044436-178045556				chr5:178044435-178044436;chr5:178045556-178045557		63;43
K	alternative_donor	CUFF.869	chr5	-	chr5:127398193-127418661	chr5:127398193-127418426		chr5:127418427-127418661	chr5:127418661-127418662		73;210
K	intron_retention	CUFF.861	chr5	+	chr5:56533000-56542126				chr5:56532999-56533000;chr5:56542126-56542127		38;36
K	alternative_last_exon	CUFF.867	chr5	+	chr5:121358103-121411009	chr5:121358103-121362636	chr5:121411010-121411363	chr5:121362637-121364314			48;22
N	alternative_donor	CUFF.881	chr5	-	chr5:36703067-36705822	chr5:36703067-36705781		chr5:36705782-36705822	chr5:36705822-36705823		12;101
K	intron_retention	CUFF.878	chr5	-	chr5:141052701-141052967				chr5:141052700-141052701;chr5:141052967-141052968		47;64
N	alternative_acceptor	CUFF.855,CUFF.856	chr5	+	chr5:52177854-52183646	chr5:52177854-52178711		chr5:52178712-52183646	chr5:52183646-52183647		37;2
K	jcn_only_AA	CUFF.859	chr5	+	chr5:54456225-54456879	chr5:54456225-54456821		chr5:54456822-54456879	chr5:54456879-54456880		63;34
N	alternative_acceptor	CUFF.852,CUFF.880	chr5	+	chr5:40980012-40981493	chr5:40980012-40980088		chr5:40980089-40981493	chr5:40981493-40981494		64;15
N	jcn_only_AA	CUFF.886	chr5	-	chr5:178032384-178035376	chr5:178032867-178035376		chr5:178032384-178032866	chr5:178032383-178032384		93;14
K	intron_retention	CUFF.876	chr5	+	chr5:140041799-140041886				chr5:140041798-140041799;chr5:140041886-140041887		970;14
K	cassette	CUFF.848	chr5	+	chr5:36153145-36177066;chr5:36153145-36166620	chr5:36153145-36163746;chr5:36163859-36166620,chr5:36163859-36177066		chr5:36163747-36163858			2222;627
N	jcn_only_AA	CUFF.875	chr5	+	chr5:139815843-139818045;chr5:139815843-139818087	chr5:139815843-139818078		chr5:139818046-139818078;chr5:139818079-139818087	chr5:139818078-139818079;chr5:139818087-139818088		209;181
K	alternative_acceptor	CUFF.866	chr5	-	chr5:82948641-82969242	chr5:82948644-82969242		chr5:82948641-82948643	chr5:82948640-82948641		62;216
K	cassette	CUFF.875	chr5	+	chr5:139866646-139884405	chr5:139866646-139876104;chr5:139876864-139884405		chr5:139876105-139876863			20;52
N	jcn_only_AD	CUFF.871	chr5	+	chr5:131658049-131662969	chr5:131660336-131662969		chr5:131658049-131660335	chr5:131658048-131658049		80;32
N	jcn_only_AA	CUFF.860	chr5	-	chr5:54569206-54570441	chr5:54569255-54570441		chr5:54569206-54569254	chr5:54569205-54569206		43;21
N	jcn_only_AD	CUFF.875	chr5	+	chr5:139917820-139918503	chr5:139917847-139918503		chr5:139917820-139917846	chr5:139917819-139917820		45;749
N	jcn_only_AD	CUFF.884	chr5	-	chr5:127338515-127359826	chr5:127338515-127339335					34;26
N	alternative_acceptor	CUFF.861	chr5	+	chr5:56510021-56526672	chr5:56510021-56517202		chr5:56517203-56526672	chr5:56526672-56526673		36;1
K	alternative_last_exon	CUFF.884	chr5	-	chr5:162516353-162683856	chr5:162683277-162683856	chr5:162516251-162516352	chr5:162682987-162683276			70;292
N	jcn_only_AA	CUFF.875	chr5	+	chr5:139815843-139818078;chr5:139815843-139818087	chr5:139815843-139818045		chr5:139818046-139818078;chr5:139818079-139818087	chr5:139818078-139818079;chr5:139818087-139818088		277;113
K	cassette	CUFF.878	chr5	-	chr5:141041357-141044488	chr5:141041357-141041609;chr5:141041823-141044488		chr5:141041610-141041822			45;238
K	alternative_donor	CUFF.846,CUFF.882	chr5	-	chr5:1075606-1076252	chr5:1075606-1076005		chr5:1076006-1076252	chr5:1076252-1076253		21;77
N	jcn_only_AD	CUFF.860,CUFF.886	chr5	-	chr5:54577344-54579030	chr5:54577344-54578943		chr5:54578944-54579030	chr5:54579030-54579031		31;5
K	alternative_last_exon	CUFF.884	chr5	-	chr5:162516353-162852808	chr5:162683994-162852808	chr5:162516251-162516352	chr5:162683774-162683993			30;248
K	intron_retention	CUFF.875	chr5	+	chr5:139865318-139866590				chr5:139865317-139865318;chr5:139866590-139866591		8;53
K	cassette	CUFF.886	chr5	-	chr5:178047675-178050256	chr5:178047675-178049393;chr5:178049461-178050256		chr5:178049394-178049460			173;40
N	cassette	CUFF.869	chr5	-	chr5:127396937-127417664;chr5:127396937-127418426	chr5:127396937-127412638;chr5:127412786-127418426,chr5:127412786-127417664		chr5:127412639-127412785			107;156
N	alternative_acceptor	CUFF.875	chr5	+	chr5:139815843-139818045;chr5:139815843-139818078	chr5:139815843-139818087		chr5:139818046-139818078;chr5:139818079-139818087	chr5:139818078-139818079;chr5:139818087-139818088		156;96
K	intron_retention	CUFF.886	chr5	-	chr5:178043950-178044344				chr5:178043949-178043950;chr5:178044344-178044345		50;82
N	alternative_acceptor	CUFF.859,CUFF.871	chr5	+	chr5:131649462-131657876	chr5:131649462-131656557		chr5:131656558-131657876	chr5:131657876-131657877		83;9
K	jcn_only_AD	CUFF.862,CUFF.886	chr5	-	chr5:178043950-178045556	chr5:178043950-178044344		chr5:178044345-178045556	chr5:178045556-178045557		59;50
K	alternative_first_exon	CUFF.862	chr5	-	chr5:60214216-60217880	chr5:60214216-60214338	chr5:60217881-60217982	chr5:60214339-60214468			325;242
N	intron_retention		chr5	-	chr5:64887330-64887669				chr5:64887329-64887330;chr5:64887669-64887670		23;25
K	intron_retention	CUFF.886	chr5	-	chr5:178046898-178050256				chr5:178046897-178046898;chr5:178050256-178050257		31;99
N	intron_retention		chr5	+	chr5:137514892-137515348				chr5:137514891-137514892;chr5:137515348-137515349		203;138
N	jcn_only_AA	ENSG00000188242.4	chr5	-	chr5:466642-472793;chr5:471939-472793;chr5:472709-472793	chr5:472081-472793		chr5:466642-471938;chr5:471939-472080;chr5:472081-472708	chr5:466641-466642;chr5:471938-471939;chr5:472080-472081		2474;30
N	jcn_only_AA	CUFF.875	chr5	+	chr5:139918669-139921756	chr5:139918669-139918943		chr5:139918944-139921756	chr5:139921756-139921757		46;804
K	intron_retention	CUFF.859	chr5	+	chr5:54460008-54460427				chr5:54460007-54460008;chr5:54460427-54460428		78;132
K	alternative_acceptor	CUFF.886	chr5	-	chr5:178043950-178045556	chr5:178044436-178045556		chr5:178043950-178044435	chr5:178043949-178043950		59;130
K	intron_retention	CUFF.859	chr5	+	chr5:54456225-54456879				chr5:54456224-54456225;chr5:54456879-54456880		63;48
N	alternative_donor	CUFF.871	chr5	+	chr5:131630703-131647853	chr5:131631315-131647853		chr5:131630703-131631314	chr5:131630702-131630703		68;14
K	alternative_last_exon	CUFF.855	chr5	+	chr5:51307437-51374717	chr5:51307437-51339451	chr5:51374718-51374824	chr5:51339452-51339743			93;151
K	intron_retention	CUFF.872	chr5	+	chr5:134190853-134193046				chr5:134190852-134190853;chr5:134193046-134193047		77;118
N	alternative_acceptor	CUFF.876	chr5	+	chr5:140031392-140031672	chr5:140031392-140031651		chr5:140031652-140031672	chr5:140031672-140031673		2486;22
K	cassette	CUFF.859	chr5	+	chr5:54456225-54459882	chr5:54456225-54456879;chr5:54457084-54459882		chr5:54456880-54457083			99;150
K	jcn_only_AD	CUFF.870	chr5	+	chr5:128862150-128863440	chr5:128862209-128863440		chr5:128862150-128862208	chr5:128862149-128862150		3;49
K	alternative_donor	CUFF.857	chr5	-	chr5:54410147-54415640	chr5:54410147-54415628		chr5:54415629-54415640	chr5:54415640-54415641		31;94
K	intron_retention	CUFF.876	chr5	+	chr5:140040401-140041204				chr5:140040400-140040401;chr5:140041204-140041205		843;36
K	alternative_acceptor	CUFF.859	chr5	+	chr5:54456225-54456879	chr5:54456225-54456821		chr5:54456822-54456879	chr5:54456879-54456880		63;21
N	cassette	CUFF.869	chr5	-	chr5:127396937-127418661;chr5:127396937-127418426	chr5:127396937-127398065;chr5:127398193-127418661,chr5:127398193-127418426		chr5:127398066-127398192			259;60
K	intron_retention	CUFF.886	chr5	-	chr5:178030759-178030844				chr5:178030758-178030759;chr5:178030844-178030845		137;105
K	alternative_first_exon	CUFF.862,CUFF.881	chr5	-	chr5:148756589-148783670	chr5:148756589-148758767	chr5:148783671-148783860	chr5:148758768-148758917			72;232
N	alternative_acceptor	ENSG00000188242.4	chr5	-	chr5:472081-472793;chr5:466642-472793;chr5:471939-472793	chr5:472709-472793		chr5:466642-471938;chr5:471939-472080;chr5:472081-472708	chr5:466641-466642;chr5:471938-471939;chr5:472080-472081		2268;44
N	cassette	CUFF.885	chr5	+	chr5:177636434-177637553;chr5:177636449-177637553	chr5:177636449-177637132,chr5:177636434-177637132;chr5:177637274-177637553		chr5:177637133-177637273			148;1242
K	cassette	CUFF.862	chr5	-	chr5:60186914-60194102	chr5:60186914-60187863;chr5:60189471-60194102		chr5:60187864-60189470			152;127
N	alternative_first_exon	CUFF.872	chr5	+	chr5:134182554-134190587;chr5:134181428-134190587	chr5:134181903-134190587	chr5:134181910-134182553;chr5:134181328-134181427	chr5:134181696-134181902			135;14
K	cassette	CUFF.882	chr5	-	chr5:149785885-149786714	chr5:149785885-149786443;chr5:149786524-149786714		chr5:149786444-149786523			163;835
K	alternative_first_exon	CUFF.846,CUFF.862	chr5	-	chr5:60200701-60214091	chr5:60200701-60203106	chr5:60214092-60214215	chr5:60203107-60203202			290;43
K	alternative_first_exon	CUFF.876	chr5	+	chr5:140027748-140028055;chr5:140026895-140028055	chr5:140027510-140028055,chr5:140027593-140028055	chr5:140026643-140026894	chr5:140027280-140027509			239;1232
N	cassette	CUFF.869	chr5	-	chr5:127396937-127418661;chr5:127396937-127418426	chr5:127396937-127398061;chr5:127398193-127418661,chr5:127398193-127418426		chr5:127398062-127398192			259;93
N	intron_retention		chr5	-	chr5:64886130-64887274				chr5:64886129-64886130;chr5:64887274-64887275		39;38
K	intron_retention	CUFF.875	chr5	+	chr5:139865318-139866542				chr5:139865317-139865318;chr5:139866542-139866543		24;72
N	alternative_acceptor	ENSG00000188242.4	chr5	-	chr5:466642-472793;chr5:471939-472793;chr5:472709-472793	chr5:472081-472793		chr5:466642-471938;chr5:471939-472080;chr5:472081-472708	chr5:466641-466642;chr5:471938-471939;chr5:472080-472081		2308;4
K	intron_retention	CUFF.874	chr5	+	chr5:137515023-137515348				chr5:137515022-137515023;chr5:137515348-137515349		329;55
N	alternative_last_exon		chr5	+	chr5:134181903-134190587	chr5:134181903-134182352	chr5:134190588-134195526	chr5:134182353-134182553			26;121
K	intron_retention	CUFF.875	chr5	+	chr5:139851881-139862164				chr5:139851880-139851881;chr5:139862164-139862165		20;132
K	alternative_donor	CUFF.862,CUFF.886	chr5	-	chr5:178043950-178045556	chr5:178043950-178044344		chr5:178044345-178045556	chr5:178045556-178045557		59;99
K	intron_retention		chr5	+	chr5:139918669-139918943				chr5:139918668-139918669;chr5:139918943-139918944		804;23
K	cassette	CUFF.850	chr5	-	chr5:37309370-37314299	chr5:37309370-37310653;chr5:37310846-37314299		chr5:37310654-37310845			87;25
K	alternative_first_exon	CUFF.853	chr5	+	chr5:44809666-44811110	chr5:44810095-44811110	chr5:44808942-44809665	chr5:44809929-44810094			96;20
K	alternative_last_exon	CUFF.884	chr5	-	chr5:162439295-162516250	chr5:162465480-162516250	chr5:162439271-162439294	chr5:162464975-162465479			42;181
N	intron_retention		chr5	-	chr5:64887330-64887698				chr5:64887329-64887330;chr5:64887698-64887699		24;23
K	jcn_only_AA	CUFF.861,CUFF.867	chr5	+	chr5:56543043-56545280	chr5:56543043-56545235		chr5:56545236-56545280	chr5:56545280-56545281		27;209
N	jcn_only_AA	ENSG00000188242.4	chr5	-	chr5:472081-472793;chr5:471939-472793;chr5:472709-472793	chr5:466642-472793		chr5:466642-471938;chr5:471939-472080;chr5:472081-472708	chr5:466641-466642;chr5:471938-471939;chr5:472080-472081		243;2261
K	jcn_only_AD	CUFF.862	chr5	-	chr5:60199544-60200618	chr5:60199544-60200614		chr5:60200615-60200618	chr5:60200618-60200619		487;55
K	jcn_only_AD	CUFF.863	chr5	-	chr5:64906871-64907583	chr5:64906871-64907429		chr5:64907430-64907583	chr5:64907583-64907584		116;52
N	jcn_only_AA	CUFF.875	chr5	+	chr5:139876864-139884405	chr5:139876864-139877622		chr5:139877623-139884405	chr5:139884405-139884406		16;27
K	cassette	CUFF.882	chr5	-	chr5:149785885-149792187	chr5:149785885-149786714;chr5:149786888-149792187		chr5:149786715-149786887			416;612
K	intron_retention	CUFF.882	chr5	-	chr5:149786524-149786714				chr5:149786523-149786524;chr5:149786714-149786715		1156;47
K	alternative_first_exon	CUFF.870	chr5	+	chr5:129019967-129030412	chr5:129023908-129030412	chr5:129019813-129019966	chr5:129023738-129023907			13;21
N	alternative_first_exon	CUFF.872	chr5	+	chr5:134182554-134190587;chr5:134181903-134190587	chr5:134181428-134190587	chr5:134181910-134182553;chr5:134181696-134181902	chr5:134181328-134181427			137;12
N	jcn_only_AD	CUFF.885	chr5	+	chr5:177636434-177637132	chr5:177636449-177637132		chr5:177636434-177636448	chr5:177636433-177636434		12;1345
N	alternative_acceptor	CUFF.860	chr5	-	chr5:54569206-54570441	chr5:54569255-54570441		chr5:54569206-54569254	chr5:54569205-54569206		43;11
K	alternative_last_exon	CUFF.869	chr5	-	chr5:127396337-127396835;chr5:127292614-127396835;chr5:127359991-127396835	chr5:127302621-127396835	chr5:127292496-127292613;chr5:127359628-127359990	chr5:127301533-127302620			403;114
N	jcn_only_AA	CUFF.852,CUFF.880	chr5	+	chr5:40980012-40981493	chr5:40980012-40980088		chr5:40980089-40981493	chr5:40981493-40981494		64;30
N	alternative_acceptor	ENSG00000188242.4	chr5	-	chr5:472081-472793;chr5:471939-472793;chr5:472709-472793	chr5:466642-472793		chr5:466642-471938;chr5:471939-472080;chr5:472081-472708	chr5:466641-466642;chr5:471938-471939;chr5:472080-472081		51;2261
N	alternative_first_exon	CUFF.872	chr5	+	chr5:134181428-134190587;chr5:134181903-134190587	chr5:134182554-134190587	chr5:134181328-134181427;chr5:134181696-134181902	chr5:134181910-134182553			26;123
N	jcn_only_AA	CUFF.855,CUFF.856	chr5	+	chr5:52177854-52183646	chr5:52177854-52178711		chr5:52178712-52183646	chr5:52183646-52183647		37;24
N	alternative_acceptor	ENSG00000188242.4	chr5	-	chr5:472081-472793;chr5:466642-472793;chr5:472709-472793	chr5:471939-472793		chr5:466642-471938;chr5:471939-472080;chr5:472081-472708	chr5:466641-466642;chr5:471938-471939;chr5:472080-472081		2309;3
N	jcn_only_AD	CUFF.850	chr5	-	chr5:37364487-37370922	chr5:37364487-37370767		chr5:37370768-37370922	chr5:37370922-37370923		37;148
K	alternative_acceptor	CUFF.854,CUFF.875	chr5	+	chr5:139915124-139916973	chr5:139915124-139916922		chr5:139916923-139916973	chr5:139916973-139916974		96;349
K	alternative_first_exon	CUFF.874	chr5	+	chr5:137514892-137515348;chr5:137514540-137515348	chr5:137515023-137515348	chr5:137514408-137514539	chr5:137514641-137515022			227;265
K	cassette	CUFF.862	chr5	-	chr5:60224787-60240758	chr5:60224787-60227933;chr5:60227976-60240758		chr5:60227934-60227975			288;31
K	alternative_first_exon	CUFF.870	chr5	+	chr5:128796176-128844769	chr5:128797451-128844769	chr5:128795882-128796175	chr5:128796795-128797450			27;13
K	cassette	CUFF.857	chr5	-	chr5:54415747-54420630	chr5:54415747-54416252;chr5:54416379-54420630		chr5:54416253-54416378			73;99
K	alternative_acceptor	CUFF.854,CUFF.861	chr5	+	chr5:50685767-50687176	chr5:50685767-50687107		chr5:50687108-50687176	chr5:50687176-50687177		62;102
K	alternative_last_exon	CUFF.863	chr5	-	chr5:64900873-64905069	chr5:64902995-64905069	chr5:64900738-64900872	chr5:64902648-64902994			49;291
N	alternative_donor	CUFF.850	chr5	-	chr5:37364487-37370922	chr5:37364487-37370767		chr5:37370768-37370922	chr5:37370922-37370923		37;149
K	cassette	CUFF.848	chr5	+	chr5:36166765-36170445	chr5:36166765-36168414;chr5:36168550-36170445		chr5:36168415-36168549			296;2000
K	alternative_first_exon	CUFF.847	chr5	-	chr5:2749902-2752772	chr5:2749902-2751278	chr5:2752773-2753061	chr5:2751279-2751776			29;33
K	jcn_only_AA	CUFF.886	chr5	-	chr5:178043950-178045556	chr5:178044436-178045556		chr5:178043950-178044435	chr5:178043949-178043950		59;63
K	alternative_donor	CUFF.870	chr5	+	chr5:128862150-128863440	chr5:128862209-128863440		chr5:128862150-128862208	chr5:128862149-128862150		3;36
K	jcn_only_AA	CUFF.875	chr5	+	chr5:139865318-139866590	chr5:139865318-139866542		chr5:139866543-139866590	chr5:139866590-139866591		8;24
K	jcn_only_AA	CUFF.849	chr5	-	chr5:36668814-36725215	chr5:36705954-36725215					27;176
K	intron_retention	CUFF.875	chr5	+	chr5:139915124-139916922				chr5:139915123-139915124;chr5:139916922-139916923		502;223
K	alternative_last_exon	CUFF.869	chr5	-	chr5:127396337-127396835;chr5:127302621-127396835;chr5:127359991-127396835	chr5:127292614-127396835	chr5:127301533-127302620;chr5:127359628-127359990	chr5:127292496-127292613			398;119
K	alternative_first_exon	CUFF.861	chr5	+	chr5:56531860-56542126	chr5:56533000-56542126	chr5:56531793-56531859	chr5:56532890-56532999			73;27
K	alternative_donor	CUFF.872	chr5	+	chr5:134190853-134193046	chr5:134191018-134193046		chr5:134190853-134191017	chr5:134190852-134190853		77;95
K	intron_retention	CUFF.885	chr5	+	chr5:177631742-177631815				chr5:177631741-177631742;chr5:177631815-177631816		179;1025
N	intron_retention		chr5	+	chr5:134181903-134190587				chr5:134181902-134181903;chr5:134190587-134190588		22;10
K	mutually_exclusive	CUFF.859	chr5	+	chr5:54456072-54456947,chr5:54457084-54459882	chr5:54456072-54456157,chr5:54456225-54459882	chr5:54456948-54457083	chr5:54456158-54456224			130;121
N	cassette	CUFF.861	chr5	+	chr5:56472228-56526672	chr5:56472228-56509900;chr5:56510021-56526672		chr5:56509901-56510020			18;39
N	jcn_only_AD	CUFF.878	chr5	-	chr5:149782876-149785821	chr5:149782876-149784242					30;111
N	jcn_only_AD		chr5	-	chr5:178050418-178057554	chr5:178050418-178053946		chr5:178053947-178057554	chr5:178057554-178057555		22;313
K	cassette	CUFF.863	chr5	-	chr5:64907709-64909924	chr5:64907709-64909553;chr5:64909683-64909924		chr5:64909554-64909682			190;174
K	cassette	CUFF.866	chr5	-	chr5:82969369-83016607	chr5:82969369-82971106;chr5:82971157-83016607		chr5:82971107-82971156			11;23
K	alternative_acceptor	CUFF.861,CUFF.867	chr5	+	chr5:56543043-56545280	chr5:56543043-56545235		chr5:56545236-56545280	chr5:56545280-56545281		27;168
N	jcn_only_AA	CUFF.850	chr5	-	chr5:37309370-37310653	chr5:37309675-37310653		chr5:37309370-37309674	chr5:37309369-37309370		21;10
K	intron_retention	CUFF.860	chr5	-	chr5:54566316-54566405				chr5:54566315-54566316;chr5:54566405-54566406		56;24
K	intron_retention	CUFF.852	chr5	+	chr5:40972697-40976851				chr5:40972696-40972697;chr5:40976851-40976852		106;164
N	jcn_only_AA	CUFF.871,CUFF.875	chr5	+	chr5:131658049-131662969	chr5:131658049-131660153		chr5:131660154-131662969	chr5:131662969-131662970		80;20
K	cassette	CUFF.862	chr5	-	chr5:60199544-60214091	chr5:60199544-60200614;chr5:60200701-60214091		chr5:60200615-60200700			11;185
N	alternative_acceptor	CUFF.875	chr5	+	chr5:139918669-139921756	chr5:139918669-139918943		chr5:139918944-139921756	chr5:139921756-139921757		46;316
K	cassette	CUFF.862	chr5	-	chr5:60217983-60224690	chr5:60217983-60220117;chr5:60220336-60224690		chr5:60220118-60220335			332;108
K	intron_retention	CUFF.882	chr5	-	chr5:149781568-149785821				chr5:149781567-149781568;chr5:149785821-149785822		337;163
K	cassette	CUFF.863	chr5	-	chr5:64910047-64920020	chr5:64910047-64913919;chr5:64914083-64920020		chr5:64913920-64914082			79;256
N	alternative_acceptor	CUFF.856	chr5	+	chr5:52161652-52177704	chr5:52161652-52162871		chr5:52162872-52177704	chr5:52177704-52177705		77;3
N	alternative_acceptor	CUFF.875	chr5	+	chr5:139815843-139818078;chr5:139815843-139818087	chr5:139815843-139818045		chr5:139818046-139818078;chr5:139818079-139818087	chr5:139818078-139818079;chr5:139818087-139818088		200;52
K	jcn_only_AA	CUFF.848	chr5	+	chr5:36163859-36177066	chr5:36163859-36166620					559;251
K	alternative_first_exon	CUFF.884	chr5	-	chr5:162516353-162852808	chr5:162516353-162683856	chr5:162852809-162852926	chr5:162683857-162684053			34;123
K	coord_cassette	CUFF.869	chr5	-	chr5:127396937-127418426	chr5:127396937-127412638;chr5:127412786-127417664;chr5:127417887-127418426		chr5:127412639-127412785;chr5:127417665-127417886			79;155
N	jcn_only_AA	CUFF.876	chr5	+	chr5:140031392-140031672	chr5:140031392-140031651		chr5:140031652-140031672	chr5:140031672-140031673		2486;47
K	cassette	CUFF.876	chr5	+	chr5:140028123-140031298	chr5:140028123-140028467;chr5:140028566-140031298		chr5:140028468-140028565			1243;915
N	jcn_only_AD	CUFF.880	chr5	+	chr5:145616996-145634505	chr5:145631439-145634505		chr5:145616996-145631438	chr5:145616995-145616996		5;4
K	alternative_first_exon	CUFF.854	chr5	+	chr5:50680565-50683323	chr5:50682461-50683323	chr5:50680375-50680564	chr5:50681999-50682460			101;123
N	jcn_only_AD	CUFF.828	chr4	-	chr4:83816928-83820865;chr4:83816928-83819141	chr4:83816928-83821229					110;36
K	jcn_only_AA	CUFF.827	chr4	-	chr4:83536173-83542364	chr4:83536235-83542364		chr4:83536173-83536234	chr4:83536172-83536173		27;49
N	cassette	CUFF.793	chr4	+	chr4:649796-650662	chr4:649796-650033;chr4:650082-650662		chr4:650034-650081			47;52
N	jcn_only_AA	CUFF.839	chr4	-	chr4:152100550-152108574	chr4:152102882-152108574		chr4:152100550-152102881	chr4:152100549-152100550		169;47
N	alternative_donor	CUFF.835	chr4	+	chr4:124582989-124750249	chr4:124695531-124750249		chr4:124582989-124695530	chr4:124582988-124582989		160;1
K	jcn_only_AA	CUFF.842	chr4	-	chr4:162954808-163032422	chr4:162954811-163032422		chr4:162954808-162954810	chr4:162954807-162954808		30;3
K	alternative_donor	CUFF.834	chr4	+	chr4:120434076-120449894	chr4:120434126-120449894		chr4:120434076-120434125	chr4:120434075-120434076		993;77
N	jcn_only_AD		chr4	-	chr4:77097064-77116859	chr4:77097064-77097589					33;4
N	jcn_only_AD	CUFF.828	chr4	-	chr4:83816928-83819141;chr4:83816928-83821229	chr4:83816928-83820865					104;42
K	cassette	CUFF.802	chr4	-	chr4:6087357-6114448	chr4:6087357-6107199;chr4:6107695-6114448		chr4:6107200-6107694			22;206
N	alternative_acceptor	CUFF.835	chr4	+	chr4:124750343-124846338	chr4:124750343-124784729		chr4:124784730-124846338	chr4:124846338-124846339		172;1
K	cassette	CUFF.842	chr4	-	chr4:162421287-162459317	chr4:162421287-162431549;chr4:162431577-162459317		chr4:162431550-162431576			8;39
N	alternative_acceptor	CUFF.842	chr4	-	chr4:162463846-162508606	chr4:162473730-162508606		chr4:162463846-162473729	chr4:162463845-162463846		45;1
K	intron_retention	CUFF.801	chr4	-	chr4:3948645-3949468				chr4:3948644-3948645;chr4:3949468-3949469		32;38
K	alternative_donor	CUFF.803	chr4	-	chr4:6380300-6382767	chr4:6380300-6382723		chr4:6382724-6382767	chr4:6382767-6382768		43;223
K	alternative_acceptor	CUFF.830	chr4	-	chr4:99399898-99403155	chr4:99399962-99403155		chr4:99399898-99399961	chr4:99399897-99399898		13;225
N	jcn_only_AD		chr4	-	chr4:74477547-74486155	chr4:74477547-74486004		chr4:74486005-74486155	chr4:74486155-74486156		3;149
N	intron_retention		chr4	+	chr4:120379233-120381897				chr4:120379232-120379233;chr4:120381897-120381898		42;58
K	alternative_last_exon	CUFF.822,CUFF.837	chr4	+	chr4:77184997-77230296	chr4:77184997-77189812	chr4:77230297-77232376	chr4:77189813-77189966			67;138
K	alternative_donor	CUFF.844	chr4	+	chr4:186185653-186188122	chr4:186185765-186188122		chr4:186185653-186185764	chr4:186185652-186185653		55;10
K	cassette	CUFF.813	chr4	+	chr4:37839236-37841469	chr4:37839236-37841138;chr4:37841306-37841469		chr4:37841139-37841305			10;187
K	intron_retention	CUFF.815	chr4	+	chr4:57302142-57302427				chr4:57302141-57302142;chr4:57302427-57302428		49;124
N	alternative_donor	CUFF.806	chr4	+	chr4:6925839-6969030	chr4:6956066-6969030		chr4:6925839-6956065	chr4:6925838-6925839		27;0
N	alternative_last_exon	CUFF.828	chr4	-	chr4:83819216-83821229;chr4:83820891-83821229	chr4:83816001-83821229,chr4:83816928-83821229	chr4:83818859-83819215;chr4:83820608-83820890	chr4:83814162-83816000		chr4:83821230-83821376	369;66
N	alternative_acceptor		chr4	-	chr4:152147239-152148911	chr4:152147393-152148911		chr4:152147239-152147392	chr4:152147238-152147239		1;8
N	alternative_donor	CUFF.821	chr4	-	chr4:77102255-77116859	chr4:77102255-77105809		chr4:77105810-77116859	chr4:77116859-77116860		19;0
K	intron_retention	CUFF.810	chr4	+	chr4:20618571-20622026				chr4:20618570-20618571;chr4:20622026-20622027		228;53
N	jcn_only_AD	CUFF.821	chr4	-	chr4:77102255-77116859	chr4:77102255-77105809		chr4:77105810-77116859	chr4:77116859-77116860		19;30
N	jcn_only_AD	CUFF.806	chr4	+	chr4:6925839-6969030	chr4:6956066-6969030		chr4:6925839-6956065	chr4:6925838-6925839		27;5
K	cassette	CUFF.814	chr4	-	chr4:56471517-56473603;chr4:56466743-56473603	chr4:56466743-56473464,chr4:56471517-56473464;chr4:56473516-56473603		chr4:56473465-56473515			484;235
K	jcn_only_AD	CUFF.820	chr4	-	chr4:74459311-74481607	chr4:74459311-74464356					65;152
N	jcn_only_AA	CUFF.844	chr4	+	chr4:120379233-120381897	chr4:120379233-120381337		chr4:120381338-120381897	chr4:120381897-120381898		42;41
N	jcn_only_AA	CUFF.842	chr4	-	chr4:162463846-162508606	chr4:162473730-162508606		chr4:162463846-162473729	chr4:162463845-162463846		45;46
N	alternative_acceptor		chr4	-	chr4:83816001-83821229	chr4:83816928-83821229		chr4:83816001-83816927	chr4:83816000-83816001	chr4:83821230-83821376	46;66
K	cassette	CUFF.810	chr4	+	chr4:20555592-20568884	chr4:20555592-20555930;chr4:20555964-20568884		chr4:20555931-20555963			132;192
K	alternative_last_exon	CUFF.842	chr4	-	chr4:162402322-162421167	chr4:162416633-162421167	chr4:162402172-162402321	chr4:162416195-162416632			47;139
N	cassette	CUFF.832	chr4	-	chr4:107847107-108109583	chr4:107847107-108049098;chr4:108049167-108109583		chr4:108049099-108049166			7;448
K	alternative_acceptor	CUFF.795	chr4	+	chr4:1126229-1126514	chr4:1126229-1126496		chr4:1126497-1126514	chr4:1126514-1126515		21;37
K	intron_retention	CUFF.828	chr4	-	chr4:83820891-83821229				chr4:83820890-83820891;chr4:83821229-83821230	chr4:83820866-83820890;chr4:83821230-83821376	389;25
N	jcn_only_AD	CUFF.811,CUFF.828	chr4	-	chr4:83816928-83820865;chr4:83816928-83821229	chr4:83816928-83819141					78;68
K	jcn_only_AD	CUFF.828	chr4	-	chr4:83819216-83821229	chr4:83819216-83820865				chr4:83818859-83819215	96;137
K	alternative_first_exon	CUFF.829	chr4	-	chr4:85416998-85418711	chr4:85416998-85417645	chr4:85418712-85419692	chr4:85417646-85418103			11;16
N	jcn_only_AA	CUFF.839	chr4	-	chr4:152096827-152097685	chr4:152096848-152097685		chr4:152096827-152096847	chr4:152096826-152096827		27;17
K	cassette	CUFF.802	chr4	-	chr4:6066736-6081898	chr4:6066736-6080665;chr4:6080726-6081898		chr4:6080666-6080725			20;271
N	cassette	CUFF.839	chr4	-	chr4:152065203-152069073	chr4:152065203-152065371;chr4:152065441-152069073		chr4:152065372-152065440			84;49
K	cassette	CUFF.814	chr4	-	chr4:56466743-56473464;chr4:56466743-56473603	chr4:56466743-56471441;chr4:56471517-56473603,chr4:56471517-56473464		chr4:56471442-56471516			540;259
K	jcn_only_AA	CUFF.830	chr4	-	chr4:99399898-99403155	chr4:99399962-99403155		chr4:99399898-99399961	chr4:99399897-99399898		13;348
K	jcn_only_AA	CUFF.813	chr4	+	chr4:37831754-37841479	chr4:37831754-37836239					231;276
N	jcn_only_AA	CUFF.820	chr4	-	chr4:74477547-74486155	chr4:74481654-74486155					3;89
K	intron_retention	CUFF.797	chr4	-	chr4:2933193-2933281				chr4:2933192-2933193;chr4:2933281-2933282		328;210
K	alternative_first_exon	CUFF.844	chr4	+	chr4:186209237-186231788	chr4:186217185-186231788	chr4:186209166-186209236	chr4:186216916-186217184			16;72
N	alternative_donor		chr4	-	chr4:36231268-36245312	chr4:36231268-36245230		chr4:36245231-36245312	chr4:36245312-36245313		19;295
K	alternative_first_exon	CUFF.803	chr4	-	chr4:6382822-6415629,chr4:6382822-6473290,chr4:6382822-6525169;chr4:6382822-6536997;chr4:6382822-6383503	chr4:6382822-6473886	chr4:6536998-6537104;chr4:6383504-6384852	chr4:6473887-6474220			280;147
K	intron_retention	CUFF.797	chr4	-	chr4:2932878-2932953				chr4:2932877-2932878;chr4:2932953-2932954		396;197
K	alternative_first_exon	CUFF.826	chr4	+	chr4:81105210-81112625	chr4:81106673-81112625	chr4:81105033-81105209	chr4:81106459-81106672			29;170
K	alternative_donor	CUFF.822	chr4	+	chr4:77189922-77192720	chr4:77189967-77192720		chr4:77189922-77189966	chr4:77189921-77189922		13;92
K	intron_retention	CUFF.797	chr4	-	chr4:2932681-2932787				chr4:2932680-2932681;chr4:2932787-2932788		271;152
N	alternative_acceptor		chr4	+	chr4:645878-647640	chr4:645878-646284		chr4:646285-647640	chr4:647640-647641		44;332
N	alternative_donor	CUFF.803	chr4	-	chr4:6537105-6565286	chr4:6537105-6557260		chr4:6557261-6565286	chr4:6565286-6565287		193;2
N	intron_retention		chr4	-	chr4:2934418-2934832				chr4:2934417-2934418;chr4:2934832-2934833		34;149
N	cassette	CUFF.803	chr4	-	chr4:6377659-6382723	chr4:6377659-6380133;chr4:6380300-6382723		chr4:6380134-6380299			22;461
N	alternative_acceptor	CUFF.823	chr4	-	chr4:77977254-77987401	chr4:77979789-77987401		chr4:77977254-77979788	chr4:77977253-77977254		118;112
K	jcn_only_AD	CUFF.822	chr4	+	chr4:77189922-77192720	chr4:77189967-77192720		chr4:77189922-77189966	chr4:77189921-77189922		13;136
K	alternative_first_exon	CUFF.806	chr4	+	chr4:6911679-6925099;chr4:6911233-6925099	chr4:6912329-6925099	chr4:6910872-6911232	chr4:6912151-6912328			309;71
K	intron_retention	CUFF.826	chr4	+	chr4:81118371-81118778				chr4:81118370-81118371;chr4:81118778-81118779		63;18
K	cassette	CUFF.822	chr4	+	chr4:77192922-77230296	chr4:77192922-77199221;chr4:77199378-77230296		chr4:77199222-77199377			122;13
K	cassette	CUFF.834	chr4	+	chr4:120376289-120381337	chr4:120376289-120379125;chr4:120379326-120381337		chr4:120379126-120379325			334;95
N	jcn_only_AA	CUFF.820	chr4	-	chr4:74464436-74477447	chr4:74470305-74477447		chr4:74464436-74470304	chr4:74464435-74464436		118;106
K	jcn_only_AD	CUFF.835	chr4	+	chr4:124571485-124573941	chr4:124571488-124573941		chr4:124571485-124571487	chr4:124571484-124571485		63;77
K	alternative_donor	CUFF.839	chr4	-	chr4:152096827-152097685	chr4:152096827-152097676		chr4:152097677-152097685	chr4:152097685-152097686		27;33
K	cassette	CUFF.819	chr4	-	chr4:70465113-70512647	chr4:70465113-70501408;chr4:70501541-70512647		chr4:70501409-70501540			55;30
K	cassette	CUFF.796	chr4	-	chr4:1701798-1713600	chr4:1701798-1705322;chr4:1705428-1713600		chr4:1705323-1705427			134;147
K	jcn_only_AD	CUFF.803,CUFF.828	chr4	-	chr4:83821377-83821524	chr4:83821377-83821486		chr4:83821487-83821524	chr4:83821524-83821525	chr4:83821230-83821376;chr4:83821525-83822207	37;560
N	alternative_donor	CUFF.834	chr4	+	chr4:120381976-120382871	chr4:120381983-120382871		chr4:120381976-120381982	chr4:120381975-120381976		41;155
K	alternative_first_exon	CUFF.814	chr4	-	chr4:56496628-56502710	chr4:56496628-56502247	chr4:56502711-56502958	chr4:56502248-56502524			90;438
N	alternative_donor	CUFF.834	chr4	+	chr4:120384135-120414487	chr4:120409873-120414487		chr4:120384135-120409872	chr4:120384134-120384135		252;1
K	intron_retention	CUFF.801	chr4	-	chr4:3949735-3949816				chr4:3949734-3949735;chr4:3949816-3949817		146;56
N	alternative_acceptor	CUFF.839	chr4	-	chr4:152096827-152097685	chr4:152096848-152097685		chr4:152096827-152096847	chr4:152096826-152096827		27;9
N	jcn_only_AA	CUFF.823	chr4	-	chr4:77977254-77987401	chr4:77979789-77987401		chr4:77977254-77979788	chr4:77977253-77977254		118;790
N	alternative_donor	CUFF.821,CUFF.839	chr4	-	chr4:152100550-152108574	chr4:152100550-152102840		chr4:152102841-152108574	chr4:152108574-152108575		169;1
K	alternative_last_exon	CUFF.809	chr4	+	chr4:13831472-13961612	chr4:13831472-13930973	chr4:13961613-13961710	chr4:13930974-13932852			113;94
K	intron_retention	ENSG00000215127.5	chr4	-	chr4:68927570-68927629				chr4:68927569-68927570;chr4:68927629-68927630		232;24
K	cassette	CUFF.834	chr4	+	chr4:120449945-120471533	chr4:120449945-120464907;chr4:120465001-120471533		chr4:120464908-120465000			1423;88
K	alternative_donor	CUFF.803,CUFF.828	chr4	-	chr4:83821377-83821524	chr4:83821377-83821486		chr4:83821487-83821524	chr4:83821524-83821525	chr4:83821230-83821376;chr4:83821525-83822207	37;314
K	alternative_first_exon	CUFF.844	chr4	+	chr4:186125622-186168447	chr4:186131410-186168447	chr4:186125307-186125621	chr4:186131202-186131409			14;52
K	jcn_only_AA	CUFF.819	chr4	-	chr4:70513414-70518905	chr4:70513417-70518905		chr4:70513414-70513416	chr4:70513413-70513414		146;41
N	jcn_only_AD	CUFF.815	chr4	+	chr4:57308027-57312860	chr4:57312544-57312860		chr4:57308027-57312543	chr4:57308026-57308027		141;6
K	jcn_only_AA	CUFF.837	chr4	+	chr4:130701255-130724146	chr4:130701255-130710066					12;54
N	coord_cassette	CUFF.826	chr4	+	chr4:81105210-81117505	chr4:81105210-81112625;chr4:81112724-81115266;chr4:81115394-81117505		chr4:81112626-81112723;chr4:81115267-81115393			22;126
N	jcn_only_AA	CUFF.815	chr4	+	chr4:57308027-57312860	chr4:57308027-57312522		chr4:57312523-57312860	chr4:57312860-57312861		141;4
K	cassette	CUFF.801	chr4	-	chr4:3954901-3957050	chr4:3954901-3956686;chr4:3956761-3957050		chr4:3956687-3956760			340;53
K	cassette	CUFF.797	chr4	-	chr4:2933193-2933551	chr4:2933193-2933281;chr4:2933391-2933551		chr4:2933282-2933390			165;261
N	jcn_only_AD		chr4	-	chr4:36231268-36245312	chr4:36231268-36245230		chr4:36245231-36245312	chr4:36245312-36245313		19;386
N	alternative_acceptor	CUFF.812	chr4	-	chr4:36195270-36212011	chr4:36211037-36212011		chr4:36195270-36211036	chr4:36195269-36195270		54;1
N	alternative_last_exon	CUFF.828	chr4	-	chr4:83819216-83821229;chr4:83816001-83821229,chr4:83816928-83821229	chr4:83820891-83821229	chr4:83818859-83819215;chr4:83814162-83816000	chr4:83820608-83820890		chr4:83821230-83821376	142;293
N	jcn_only_AA	CUFF.834	chr4	+	chr4:120415679-120418965	chr4:120415679-120418816		chr4:120418817-120418965	chr4:120418965-120418966		486;42
N	jcn_only_AA		chr4	-	chr4:83816001-83821229	chr4:83816928-83821229		chr4:83816001-83816927	chr4:83816000-83816001	chr4:83821230-83821376	46;36
N	cassette	CUFF.823	chr4	-	chr4:77979789-77996624	chr4:77979789-77987401;chr4:77987559-77996624		chr4:77987402-77987558			153;683
K	intron_retention	CUFF.818	chr4	-	chr4:69054335-69056965				chr4:69054334-69054335;chr4:69056965-69056966		53;140
N	jcn_only_AD	CUFF.803	chr4	-	chr4:6537105-6565286	chr4:6537105-6557260		chr4:6557261-6565286	chr4:6565286-6565287		193;23
N	alternative_acceptor	CUFF.797	chr4	-	chr4:2934905-2935293	chr4:2934937-2935293		chr4:2934905-2934936	chr4:2934904-2934905		37;170
K	alternative_first_exon	CUFF.803	chr4	-	chr4:6382822-6415629,chr4:6382822-6473290,chr4:6382822-6525169;chr4:6382822-6536997;chr4:6382822-6473886	chr4:6382822-6383503	chr4:6536998-6537104;chr4:6473887-6474220	chr4:6383504-6384852			351;76
K	jcn_only_AD	CUFF.811	chr4	-	chr4:36014454-36047600	chr4:36014454-36017007					21;83
N	jcn_only_AD	CUFF.834	chr4	+	chr4:120381976-120382871	chr4:120381983-120382871		chr4:120381976-120381982	chr4:120381975-120381976		41;315
K	cassette	CUFF.802	chr4	-	chr4:6055876-6058423	chr4:6055876-6056474;chr4:6056531-6058423		chr4:6056475-6056530			291;18
K	intron_retention	CUFF.813	chr4	+	chr4:37848733-37848822				chr4:37848732-37848733;chr4:37848822-37848823		459;157
N	jcn_only_AD	CUFF.818	chr4	-	chr4:69071816-69083623	chr4:69071816-69078079		chr4:69078080-69083623	chr4:69083623-69083624		181;19
N	jcn_only_AD	CUFF.808	chr4	-	chr4:69057035-69071752	chr4:69057035-69057124					24;32
N	alternative_acceptor	CUFF.811	chr4	-	chr4:36152667-36160351	chr4:36159173-36160351		chr4:36152667-36159172	chr4:36152666-36152667		74;2
N	cassette	CUFF.823	chr4	-	chr4:77969816-77977114	chr4:77969816-77976302;chr4:77976534-77977114		chr4:77976303-77976533			79;831
K	intron_retention	CUFF.797	chr4	-	chr4:2933193-2933551				chr4:2933192-2933193;chr4:2933551-2933552		165;214
K	cassette	CUFF.810	chr4	+	chr4:20570628-20591266	chr4:20570628-20574856;chr4:20574884-20591266		chr4:20574857-20574883			39;34
K	alternative_donor	CUFF.835	chr4	+	chr4:124571485-124573941	chr4:124571488-124573941		chr4:124571485-124571487	chr4:124571484-124571485		63;38
K	alternative_first_exon	CUFF.803	chr4	-	chr4:6382822-6415629,chr4:6382822-6473290,chr4:6382822-6525169;chr4:6382822-6473886;chr4:6382822-6383503	chr4:6382822-6536997	chr4:6473887-6474220;chr4:6383504-6384852	chr4:6536998-6537104			320;107
N	jcn_only_AD	CUFF.845	chr4	+	chr4:191012637-191013578	chr4:191013443-191013578		chr4:191012637-191013442	chr4:191012636-191012637		76;104
N	alternative_donor	CUFF.803,CUFF.842	chr4	-	chr4:162577647-162680562	chr4:162577647-162585967		chr4:162585968-162680562	chr4:162680562-162680563		43;0
K	intron_retention	CUFF.796	chr4	-	chr4:1713655-1713927				chr4:1713654-1713655;chr4:1713927-1713928		44;95
K	intron_retention	CUFF.803	chr4	-	chr4:6382822-6383503				chr4:6382821-6382822;chr4:6383503-6383504		83;57
N	alternative_donor	CUFF.818	chr4	-	chr4:69071816-69083623	chr4:69071816-69078079		chr4:69078080-69083623	chr4:69083623-69083624		181;2
K	intron_retention	CUFF.797	chr4	-	chr4:2933664-2933771				chr4:2933663-2933664;chr4:2933771-2933772		331;177
K	jcn_only_AD	CUFF.803	chr4	-	chr4:6380300-6382767	chr4:6380300-6382723		chr4:6382724-6382767	chr4:6382767-6382768		43;469
N	alternative_acceptor	CUFF.839	chr4	-	chr4:152100550-152108574	chr4:152102882-152108574		chr4:152100550-152102881	chr4:152100549-152100550		169;3
N	jcn_only_AA	CUFF.810	chr4	+	chr4:20552522-20555427	chr4:20552522-20554050		chr4:20554051-20555427	chr4:20555427-20555428		357;68
K	intron_retention	CUFF.823	chr4	-	chr4:77977477-77979659				chr4:77977476-77977477;chr4:77979659-77979660		829;180
K	cassette	CUFF.801	chr4	-	chr4:3949948-3954837	chr4:3949948-3952865;chr4:3952947-3954837		chr4:3952866-3952946			31;143
N	jcn_only_AA	CUFF.834	chr4	+	chr4:120384135-120414487	chr4:120384135-120409799		chr4:120409800-120414487	chr4:120414487-120414488		252;30
K	alternative_last_exon	CUFF.795,CUFF.844	chr4	+	chr4:186283866-186290903	chr4:186283866-186284538	chr4:186290904-186291436	chr4:186284539-186285206			58;114
K	alternative_first_exon	CUFF.810	chr4	+	chr4:20255618-20258294	chr4:20256699-20258294	chr4:20254883-20255617	chr4:20256453-20256698			4;210
K	alternative_donor	CUFF.844	chr4	+	chr4:186253868-186260532	chr4:186253914-186260532		chr4:186253868-186253913	chr4:186253867-186253868		24;61
N	jcn_only_AA	CUFF.793	chr4	+	chr4:661796-663837	chr4:661796-663834		chr4:663835-663837	chr4:663837-663838		19;104
K	jcn_only_AD	CUFF.839	chr4	-	chr4:152096827-152097685	chr4:152096827-152097676		chr4:152097677-152097685	chr4:152097685-152097686		27;12
K	alternative_first_exon	CUFF.809	chr4	+	chr4:13659479-13831403	chr4:13821896-13831403	chr4:13659371-13659478	chr4:13821667-13821895			39;145
N	alternative_acceptor	CUFF.834	chr4	+	chr4:120415679-120418965	chr4:120415679-120418816		chr4:120418817-120418965	chr4:120418965-120418966		486;29
N	alternative_donor	CUFF.806	chr4	+	chr4:6969152-6995910	chr4:6989077-6995910		chr4:6969152-6989076	chr4:6969151-6969152		29;0
N	alternative_donor	CUFF.839,CUFF.842	chr4	-	chr4:162463846-162508606	chr4:162463846-162473639		chr4:162473640-162508606	chr4:162508606-162508607		45;0
K	intron_retention	CUFF.830	chr4	-	chr4:99403327-99407888				chr4:99403326-99403327;chr4:99407888-99407889		374;49
K	intron_retention	CUFF.797	chr4	-	chr4:2934486-2934832				chr4:2934485-2934486;chr4:2934832-2934833		247;42
K	intron_retention		chr4	-	chr4:83816001-83816844				chr4:83816000-83816001;chr4:83816844-83816845		79;52
K	alternative_first_exon	CUFF.802	chr4	-	chr4:6114725-6201979	chr4:6114725-6196217	chr4:6201980-6202282	chr4:6196218-6196405			92;98
N	cassette	CUFF.793	chr4	+	chr4:660404-663834	chr4:660404-661644;chr4:661796-663834		chr4:661645-661795			140;140
N	jcn_only_AD	CUFF.806	chr4	+	chr4:6969152-6995910	chr4:6989077-6995910		chr4:6969152-6989076	chr4:6969151-6969152		29;12
N	alternative_donor	CUFF.845	chr4	+	chr4:191012637-191013578	chr4:191013443-191013578		chr4:191012637-191013442	chr4:191012636-191012637		76;546
K	alternative_first_exon	CUFF.839	chr4	-	chr4:152147239-152148911,chr4:152147239-152246392;chr4:152147239-152187237	chr4:152147239-152147319	chr4:152187238-152187467	chr4:152147320-152147667			76;81
K	intron_retention	CUFF.815	chr4	+	chr4:57302095-57302427				chr4:57302094-57302095;chr4:57302427-57302428		49;127
K	intron_retention	CUFF.797	chr4	-	chr4:2932878-2933281				chr4:2932877-2932878;chr4:2933281-2933282		12;225
K	alternative_acceptor	CUFF.797	chr4	-	chr4:2934137-2934326	chr4:2934240-2934326		chr4:2934137-2934239	chr4:2934136-2934137		14;263
N	alternative_acceptor	CUFF.793	chr4	+	chr4:661796-663837	chr4:661796-663834		chr4:663835-663837	chr4:663837-663838		19;52
K	alternative_last_exon	CUFF.840	chr4	-	chr4:153128821-153146395	chr4:153143912-153146395	chr4:153128573-153128820	chr4:153143533-153143911			52;108
K	intron_retention		chr4	-	chr4:152065203-152065371				chr4:152065202-152065203;chr4:152065371-152065372		52;36
N	jcn_only_AA	CUFF.834	chr4	+	chr4:120419059-120433505	chr4:120419059-120420715		chr4:120420716-120433505	chr4:120433505-120433506		130;20
N	alternative_donor	CUFF.815	chr4	+	chr4:57308027-57312860	chr4:57312544-57312860		chr4:57308027-57312543	chr4:57308026-57308027		141;20
K	alternative_first_exon	CUFF.808	chr4	-	chr4:11401738-11431048	chr4:11401738-11430086	chr4:11431049-11431389	chr4:11430087-11430300			37;158
K	alternative_last_exon	CUFF.838	chr4	-	chr4:142241055-142244575	chr4:142242536-142244575	chr4:142240506-142241054	chr4:142242188-142242535			34;79
K	intron_retention	CUFF.828	chr4	-	chr4:83821377-83821524				chr4:83821376-83821377;chr4:83821524-83821525	chr4:83821230-83821376;chr4:83821525-83822207	37;90
N	cassette	CUFF.793	chr4	+	chr4:647109-647640	chr4:647109-647225;chr4:647497-647640		chr4:647226-647496			41;975
N	jcn_only_AA	CUFF.835	chr4	+	chr4:124750343-124846338	chr4:124750343-124784729		chr4:124784730-124846338	chr4:124846338-124846339		172;18
K	alternative_last_exon	CUFF.797	chr4	-	chr4:2932878-2933281	chr4:2933193-2933281	chr4:2932288-2932877	chr4:2933102-2933192			16;221
N	alternative_acceptor	CUFF.834	chr4	+	chr4:120419059-120433505	chr4:120419059-120420715		chr4:120420716-120433505	chr4:120433505-120433506		130;8
K	cassette	CUFF.826	chr4	+	chr4:81115394-81117505	chr4:81115394-81117166;chr4:81117279-81117505		chr4:81117167-81117278			207;79
K	coord_cassette	CUFF.830	chr4	-	chr4:99428880-99578690	chr4:99428880-99495607;chr4:99495734-99495894;chr4:99496057-99578690		chr4:99495608-99495733;chr4:99495895-99496056			95;27
K	intron_retention	CUFF.839	chr4	-	chr4:152096827-152097685				chr4:152096826-152096827;chr4:152097685-152097686		27;29
K	cassette	CUFF.810	chr4	+	chr4:20525801-20530571	chr4:20525801-20526771;chr4:20526796-20530571		chr4:20526772-20526795			12;22
K	jcn_only_AA	CUFF.795	chr4	+	chr4:1126229-1126514	chr4:1126229-1126496		chr4:1126497-1126514	chr4:1126514-1126515		21;67
N	jcn_only_AA	CUFF.834	chr4	+	chr4:120434126-120449894	chr4:120434126-120440643		chr4:120440644-120449894	chr4:120449894-120449895		110;19
K	alternative_first_exon	CUFF.833	chr4	-	chr4:120116724-120133681	chr4:120116724-120116865	chr4:120133682-120133861	chr4:120116866-120116996			13;177
K	alternative_first_exon	CUFF.823	chr4	-	chr4:77987559-77995942;chr4:77987559-77996624	chr4:77987559-77996251	chr4:77996625-77997158	chr4:77996252-77996509			762;330
K	intron_retention	CUFF.830	chr4	-	chr4:99403327-99405549				chr4:99403326-99403327;chr4:99405549-99405550		89;36
N	intron_retention		chr4	-	chr4:99405593-99407888				chr4:99405592-99405593;chr4:99407888-99407889		29;48
N	alternative_acceptor	CUFF.820	chr4	-	chr4:74464436-74477447	chr4:74470305-74477447		chr4:74464436-74470304	chr4:74464435-74464436		118;20
K	cassette	CUFF.814	chr4	-	chr4:56471517-56475286	chr4:56471517-56473603;chr4:56473634-56475286		chr4:56473604-56473633			227;377
K	alternative_acceptor	CUFF.827	chr4	-	chr4:83536173-83542364	chr4:83536235-83542364		chr4:83536173-83536234	chr4:83536172-83536173		27;35
N	jcn_only_AA		chr4	-	chr4:152147239-152148911	chr4:152147393-152148911		chr4:152147239-152147392	chr4:152147238-152147239		1;23
N	jcn_only_AA	CUFF.797	chr4	-	chr4:2934905-2935293	chr4:2934937-2935293		chr4:2934905-2934936	chr4:2934904-2934905		37;348
N	jcn_only_AD	CUFF.821,CUFF.839	chr4	-	chr4:152100550-152108574	chr4:152100550-152102840		chr4:152102841-152108574	chr4:152108574-152108575		169;39
K	cassette	CUFF.839	chr4	-	chr4:152080505-152095821	chr4:152080505-152086740;chr4:152086849-152095821		chr4:152086741-152086848			16;70
K	intron_retention	CUFF.843	chr4	+	chr4:165675328-165675462				chr4:165675327-165675328;chr4:165675462-165675463		24;84
N	coord_cassette	CUFF.813	chr4	+	chr4:37848917-37857228	chr4:37848917-37850142;chr4:37850273-37851804;chr4:37851995-37857228		chr4:37850143-37850272;chr4:37851805-37851994			96;218
K	intron_retention	CUFF.834	chr4	+	chr4:120381398-120381885				chr4:120381397-120381398;chr4:120381885-120381886		294;32
K	alternative_acceptor	CUFF.819	chr4	-	chr4:70513414-70518905	chr4:70513417-70518905		chr4:70513414-70513416	chr4:70513413-70513414		146;44
N	jcn_only_AA	CUFF.812	chr4	-	chr4:36195270-36212011	chr4:36211037-36212011		chr4:36195270-36211036	chr4:36195269-36195270		54;97
N	jcn_only_AA		chr4	-	chr4:69057243-69078079	chr4:69071816-69078079		chr4:69057243-69071815	chr4:69057242-69057243		53;19
K	jcn_only_AA	CUFF.797	chr4	-	chr4:2934137-2934326	chr4:2934240-2934326		chr4:2934137-2934239	chr4:2934136-2934137		14;427
K	intron_retention	CUFF.838	chr4	-	chr4:142244773-142245955				chr4:142244772-142244773;chr4:142245955-142245956		30;32
N	alternative_acceptor	CUFF.797	chr4	-	chr4:2934418-2934832	chr4:2934486-2934832		chr4:2934418-2934485	chr4:2934417-2934418		34;218
N	alternative_donor		chr4	-	chr4:74477547-74486155	chr4:74477547-74486004		chr4:74486005-74486155	chr4:74486155-74486156		3;126
K	coord_cassette	CUFF.814	chr4	-	chr4:56471517-56475286	chr4:56471517-56473464;chr4:56473516-56473603;chr4:56473634-56475286		chr4:56473465-56473515;chr4:56473604-56473633			227;182
K	cassette	CUFF.820	chr4	-	chr4:74447586-74450896	chr4:74447586-74447905;chr4:74448008-74450896		chr4:74447906-74448007			143;66
K	mutually_exclusive	CUFF.814	chr4	-	chr4:56466743-56473464,chr4:56473516-56473603	chr4:56466743-56471441,chr4:56471517-56473603	chr4:56473465-56473515	chr4:56471442-56471516			145;87
N	intron_retention	CUFF.830	chr4	-	chr4:99403327-99405535				chr4:99403326-99403327;chr4:99405535-99405536		29;36
K	cassette	CUFF.822	chr4	+	chr4:77172974-77184856	chr4:77172974-77177330;chr4:77177677-77184856		chr4:77177331-77177676			185;11
N	jcn_only_AA	CUFF.818	chr4	-	chr4:69071816-69083623	chr4:69078196-69083623		chr4:69071816-69078195	chr4:69071815-69071816		181;42
K	intron_retention	CUFF.828	chr4	-	chr4:83821377-83821486				chr4:83821376-83821377;chr4:83821486-83821487	chr4:83821230-83821376;chr4:83821487-83822207	560;43
K	coord_cassette	CUFF.814	chr4	-	chr4:56466743-56473603	chr4:56466743-56471441;chr4:56471517-56473464;chr4:56473516-56473603		chr4:56471442-56471516;chr4:56473465-56473515			377;82
K	intron_retention	CUFF.793	chr4	+	chr4:657660-657902				chr4:657659-657660;chr4:657902-657903		231;69
K	alternative_first_exon	CUFF.816	chr4	+	chr4:57775206-57776795	chr4:57775754-57776795	chr4:57774983-57775205	chr4:57775526-57775753			598;128
N	jcn_only_AA	CUFF.797	chr4	-	chr4:2934418-2934832	chr4:2934486-2934832		chr4:2934418-2934485	chr4:2934417-2934418		34;247
K	cassette	CUFF.819	chr4	-	chr4:70460968-70464963	chr4:70460968-70461967;chr4:70462100-70464963		chr4:70461968-70462099			97;55
K	cassette	CUFF.844	chr4	+	chr4:186267805-186274638	chr4:186267805-186272598;chr4:186272764-186274638		chr4:186272599-186272763			79;60
K	alternative_acceptor	CUFF.842	chr4	-	chr4:162954808-163032422	chr4:162954811-163032422		chr4:162954808-162954810	chr4:162954807-162954808		30;2
K	intron_retention	CUFF.834	chr4	+	chr4:120419059-120433505				chr4:120419058-120419059;chr4:120433505-120433506		130;324
K	cassette	CUFF.810	chr4	+	chr4:20490606-20493383	chr4:20490606-20492425;chr4:20492438-20493383		chr4:20492426-20492437			2;17
K	intron_retention	CUFF.797	chr4	-	chr4:2933391-2933551				chr4:2933390-2933391;chr4:2933551-2933552		284;264
K	cassette	CUFF.830	chr4	-	chr4:99403327-99407888	chr4:99403327-99405549;chr4:99405750-99407888		chr4:99405550-99405749			374;113
N	alternative_acceptor		chr4	-	chr4:69057243-69078079	chr4:69071816-69078079		chr4:69057243-69071815	chr4:69057242-69057243		53;4
N	jcn_only_AD	CUFF.834	chr4	+	chr4:120384135-120414487	chr4:120409873-120414487		chr4:120384135-120409872	chr4:120384134-120384135		252;159
K	intron_retention	CUFF.832	chr4	-	chr4:107845362-107845701				chr4:107845361-107845362;chr4:107845701-107845702		524;17
N	jcn_only_AA		chr4	+	chr4:645878-647640	chr4:645878-646284		chr4:646285-647640	chr4:647640-647641		44;76
K	jcn_only_AA	CUFF.811	chr4	-	chr4:36014454-36047600	chr4:36020909-36047600					21;54
K	jcn_only_AD	CUFF.844	chr4	+	chr4:186253868-186260532	chr4:186253914-186260532		chr4:186253868-186253913	chr4:186253867-186253868		24;97
K	alternative_last_exon	CUFF.828	chr4	-	chr4:83816928-83820865	chr4:83819216-83820865	chr4:83814063-83816927	chr4:83818859-83819215		chr4:83820866-83820890	41;109
N	alternative_acceptor	CUFF.818	chr4	-	chr4:69071816-69083623	chr4:69078196-69083623		chr4:69071816-69078195	chr4:69071815-69071816		181;2
K	intron_retention	CUFF.834	chr4	+	chr4:120414593-120415587				chr4:120414592-120414593;chr4:120415587-120415588		348;32
N	alternative_last_exon	CUFF.821	chr4	-	chr4:77105934-77116859;chr4:77097064-77116859	chr4:77102255-77116859	chr4:77096944-77097063	chr4:77101812-77102254			71;21
K	cassette	CUFF.801	chr4	-	chr4:3949948-3952865	chr4:3949948-3951174;chr4:3951320-3952865		chr4:3951175-3951319			110;160
N	jcn_only_AD	CUFF.835	chr4	+	chr4:124582989-124750249	chr4:124695531-124750249		chr4:124582989-124695530	chr4:124582988-124582989		160;15
N	jcn_only_AA	CUFF.811	chr4	-	chr4:36152667-36160351	chr4:36159173-36160351		chr4:36152667-36159172	chr4:36152666-36152667		74;41
N	alternative_last_exon	CUFF.828	chr4	-	chr4:83816001-83821229,chr4:83816928-83821229;chr4:83820891-83821229	chr4:83819216-83821229	chr4:83814162-83816000;chr4:83820608-83820890	chr4:83818859-83819215		chr4:83821230-83821376	359;76
K	intron_retention	CUFF.839	chr4	-	chr4:152096827-152097676				chr4:152096826-152096827;chr4:152097676-152097677		12;20
N	alternative_acceptor	CUFF.844	chr4	+	chr4:120379233-120381897	chr4:120379233-120381337		chr4:120381338-120381897	chr4:120381897-120381898		42;39
K	cassette	CUFF.814	chr4	-	chr4:56475347-56496568	chr4:56475347-56482504;chr4:56482553-56496568		chr4:56482505-56482552			124;864
K	jcn_only_AD	CUFF.834	chr4	+	chr4:120434076-120449894	chr4:120434126-120449894		chr4:120434076-120434125	chr4:120434075-120434076		993;110
N	alternative_acceptor	CUFF.834	chr4	+	chr4:120384135-120414487	chr4:120384135-120409799		chr4:120409800-120414487	chr4:120414487-120414488		252;1
N	alternative_acceptor	CUFF.834	chr4	+	chr4:120434126-120449894	chr4:120434126-120440643		chr4:120440644-120449894	chr4:120449894-120449895		110;0
K	alternative_last_exon	CUFF.811	chr4	-	chr4:36059766-36075310	chr4:36069901-36075310	chr4:36059592-36059765	chr4:36067544-36069900			47;29
K	alternative_donor	CUFF.815	chr4	+	chr4:57302095-57302427	chr4:57302142-57302427		chr4:57302095-57302141	chr4:57302094-57302095		49;30
N	cassette	CUFF.801	chr4	-	chr4:3945100-3954837	chr4:3945100-3949816;chr4:3949948-3954837		chr4:3949817-3949947			80;63
N	intron_retention		chr4	-	chr4:77977254-77987401				chr4:77977253-77977254;chr4:77987401-77987402		118;26
N	alternative_acceptor	CUFF.815	chr4	+	chr4:57308027-57312860	chr4:57308027-57312522		chr4:57312523-57312860	chr4:57312860-57312861		141;1
N	jcn_only_AD	CUFF.839,CUFF.842	chr4	-	chr4:162463846-162508606	chr4:162463846-162473639		chr4:162473640-162508606	chr4:162508606-162508607		45;43
N	jcn_only_AD	CUFF.833	chr4	-	chr4:83816001-83821229	chr4:83816001-83816844					46;79
K	cassette	CUFF.813	chr4	+	chr4:37841882-37847253	chr4:37841882-37845984;chr4:37846175-37847253		chr4:37845985-37846174			152;264
N	intron_retention		chr4	-	chr4:83816001-83821229				chr4:83816000-83816001;chr4:83821229-83821230	chr4:83821230-83821376	46;45
K	mutually_exclusive	CUFF.796	chr4	-	chr4:1701798-1713600,chr4:1713718-1713856	chr4:1701798-1705322,chr4:1705428-1713856	chr4:1713601-1713717	chr4:1705323-1705427			75;47
N	coord_cassette	CUFF.801	chr4	-	chr4:3945100-3949816	chr4:3945100-3948495;chr4:3948645-3949468;chr4:3949735-3949816		chr4:3948496-3948644;chr4:3949469-3949734			24;91
K	intron_retention	CUFF.830	chr4	-	chr4:99405750-99407888				chr4:99405749-99405750;chr4:99407888-99407889		134;28
K	cassette	CUFF.806	chr4	+	chr4:7008454-7011603	chr4:7008454-7009250;chr4:7009353-7011603		chr4:7009251-7009352			62;68
N	alternative_acceptor	CUFF.810	chr4	+	chr4:20552522-20555427	chr4:20552522-20554050		chr4:20554051-20555427	chr4:20555427-20555428		357;28
K	jcn_only_AD	CUFF.844	chr4	+	chr4:186185653-186188122	chr4:186185765-186188122		chr4:186185653-186185764	chr4:186185652-186185653		55;15
K	intron_retention	CUFF.825	chr4	+	chr4:78531849-78532141				chr4:78531848-78531849;chr4:78532141-78532142		24;14
K	jcn_only_AD	CUFF.815	chr4	+	chr4:57302095-57302427	chr4:57302142-57302427		chr4:57302095-57302141	chr4:57302094-57302095		49;49
K	intron_retention	CUFF.830	chr4	-	chr4:99399898-99403155				chr4:99399897-99399898;chr4:99403155-99403156		13;94
K	alternative_last_exon	CUFF.837	chr4	+	chr4:130821810-130849722	chr4:130821810-130829788	chr4:130849723-130849966	chr4:130829789-130829858			56;8
N	jcn_only_AD	CUFF.803,CUFF.842	chr4	-	chr4:162577647-162680562	chr4:162577647-162585967		chr4:162585968-162680562	chr4:162680562-162680563		43;61
K	alternative_last_exon	CUFF.758	chr3	+	chr3:112048234-112051032	chr3:112048234-112049096	chr3:112051033-112051638	chr3:112049097-112049248			113;45
N	alternative_acceptor		chr3	+	chr3:8775677-8819162	chr3:8775677-8787211		chr3:8787212-8819162	chr3:8819162-8819163		15;52
K	cassette	CUFF.773	chr3	+	chr3:132948196-133098595	chr3:132948196-133097185;chr3:133097401-133098595		chr3:133097186-133097400			452;154
K	alternative_first_exon	CUFF.758	chr3	+	chr3:112021562-112045368	chr3:112026046-112045368	chr3:112021325-112021561	chr3:112025947-112026045			80;32
K	alternative_first_exon	CUFF.740,CUFF.770	chr3	-	chr3:45721564-45730511	chr3:45721564-45729867	chr3:45730512-45730722	chr3:45729868-45730374			44;44
N	jcn_only_AD		chr3	-	chr3:141772992-141868024	chr3:141772992-141811902		chr3:141811903-141868024	chr3:141868024-141868025		678;61
K	cassette	CUFF.788	chr3	+	chr3:186769135-186790636	chr3:186769135-186782307;chr3:186782405-186790636		chr3:186782308-186782404			284;29
N	intron_retention		chr3	-	chr3:33481418-33481825				chr3:33481417-33481418;chr3:33481825-33481826		24;9
N	jcn_only_AA	CUFF.732	chr3	-	chr3:33454320-33458249	chr3:33457593-33458249		chr3:33454320-33457592	chr3:33454319-33454320		71;32
K	alternative_first_exon	CUFF.745	chr3	+	chr3:51741184-51742863	chr3:51741671-51742863	chr3:51740993-51741183	chr3:51741372-51741670			46;81
N	jcn_only_AD	CUFF.725	chr3	+	chr3:19989014-19992297	chr3:19989356-19992297		chr3:19989014-19989355	chr3:19989013-19989014		559;22
N	alternative_acceptor	CUFF.755	chr3	-	chr3:107572902-107573976;chr3:107572807-107573976	chr3:107573542-107573976		chr3:107572807-107572901;chr3:107572902-107573541	chr3:107572806-107572807;chr3:107572901-107572902		263;6
N	jcn_only_AA	CUFF.728	chr3	+	chr3:28357915-28358243;chr3:28357915-28360222	chr3:28357915-28360999		chr3:28358244-28360222;chr3:28360223-28360999	chr3:28360222-28360223;chr3:28360999-28361000		76;501
N	jcn_only_AD	CUFF.727	chr3	-	chr3:27233734-27243000;chr3:27233734-27235551	chr3:27233734-27236027		chr3:27235552-27236027;chr3:27236028-27243000	chr3:27236027-27236028;chr3:27243000-27243001		310;28
N	mutually_exclusive	CUFF.772	chr3	-	chr3:127294109-127294591,chr3:127294653-127294782	chr3:127294109-127294245,chr3:127294349-127294782	chr3:127294592-127294652	chr3:127294246-127294348			13;43
K	intron_retention	CUFF.755	chr3	-	chr3:107574077-107575926				chr3:107574076-107574077;chr3:107575926-107575927		692;104
N	jcn_only_AD	CUFF.782	chr3	-	chr3:156261059-156262096	chr3:156261059-156262082		chr3:156262083-156262096	chr3:156262096-156262097		452;38
K	cassette	CUFF.726	chr3	-	chr3:25657078-25660144	chr3:25657078-25659908;chr3:25660001-25660144		chr3:25659909-25660000			47;417
N	jcn_only_AA	CUFF.743	chr3	-	chr3:49354912-49362134;chr3:49349088-49362134;chr3:49348171-49362134	chr3:49350047-49362134					216;13
N	alternative_acceptor	CUFF.727	chr3	-	chr3:27405336-27410715;chr3:27394411-27410715	chr3:27409054-27410715		chr3:27394411-27405335;chr3:27405336-27409053	chr3:27394410-27394411;chr3:27405335-27405336		76;0
K	intron_retention	CUFF.737	chr3	-	chr3:38051303-38051394				chr3:38051302-38051303;chr3:38051394-38051395		302;14
N	alternative_donor	CUFF.766,CUFF.772	chr3	-	chr3:125007073-125032151	chr3:125007073-125011308		chr3:125011309-125032151	chr3:125032151-125032152		80;1
N	alternative_donor	CUFF.733,CUFF.766	chr3	-	chr3:124951499-124953143	chr3:124951499-124951952		chr3:124951953-124953143	chr3:124953143-124953144		466;156
K	intron_retention	CUFF.771	chr3	+	chr3:126133023-126135158				chr3:126133022-126133023;chr3:126135158-126135159		440;54
N	cassette	CUFF.755	chr3	-	chr3:107567966-107572719	chr3:107567966-107568669;chr3:107568819-107572719		chr3:107568670-107568818			301;76
N	cassette	CUFF.772	chr3	-	chr3:127294109-127294782;chr3:127294109-127294591	chr3:127294109-127294245;chr3:127294349-127294782,chr3:127294349-127294591		chr3:127294246-127294348			159;241
N	mutually_exclusive	CUFF.755	chr3	-	chr3:107576050-107591814,chr3:107591874-107594976	chr3:107576050-107586157,chr3:107586273-107594976	chr3:107591815-107591873	chr3:107586158-107586272			377;52
K	intron_retention	CUFF.732	chr3	-	chr3:33437773-33438236				chr3:33437772-33437773;chr3:33438236-33438237		84;59
N	cassette	CUFF.773	chr3	+	chr3:132948196-133109023	chr3:132948196-133098595;chr3:133100006-133109023		chr3:133098596-133100005			42;425
N	alternative_donor	CUFF.728	chr3	+	chr3:28357915-28360999;chr3:28358351-28360999	chr3:28360371-28360999		chr3:28357915-28358350;chr3:28358351-28360370	chr3:28357914-28357915;chr3:28358350-28358351		584;261
K	intron_retention	CUFF.728	chr3	+	chr3:28357915-28360999				chr3:28357914-28357915;chr3:28360999-28361000		501;233
N	alternative_acceptor	CUFF.771	chr3	+	chr3:126135352-126137297;chr3:126135352-126137300	chr3:126135352-126135614		chr3:126135615-126137297;chr3:126137298-126137300	chr3:126137297-126137298;chr3:126137300-126137301	chr3:126137301-126137368	377;246
N	alternative_donor	CUFF.727	chr3	-	chr3:27233734-27243000;chr3:27233734-27235551	chr3:27233734-27236027		chr3:27235552-27236027;chr3:27236028-27243000	chr3:27236027-27236028;chr3:27243000-27243001		292;2
N	intron_retention		chr3	-	chr3:141697525-141713861				chr3:141697524-141697525;chr3:141713861-141713862		22;132
N	alternative_acceptor	CUFF.727	chr3	-	chr3:27394411-27410715;chr3:27409054-27410715	chr3:27405336-27410715		chr3:27394411-27405335;chr3:27405336-27409053	chr3:27394410-27394411;chr3:27405335-27405336		76;0
N	alternative_acceptor	CUFF.772	chr3	-	chr3:127299007-127313642	chr3:127310794-127313642		chr3:127299007-127310793	chr3:127299006-127299007		886;18
K	alternative_last_exon	CUFF.773	chr3	+	chr3:133100006-133109023	chr3:133100006-133105267	chr3:133109024-133109178	chr3:133105268-133105355			119;1
N	cassette	CUFF.760	chr3	-	chr3:119246689-119263396	chr3:119246689-119255983;chr3:119256266-119263396		chr3:119255984-119256265			590;132
K	alternative_first_exon	CUFF.741	chr3	-	chr3:47018271-47023421	chr3:47018271-47020963	chr3:47023422-47023598	chr3:47020964-47021101			52;107
K	intron_retention		chr3	-	chr3:127294349-127294591				chr3:127294348-127294349;chr3:127294591-127294592		162;53
N	alternative_donor	CUFF.766,CUFF.776	chr3	-	chr3:125032501-125042152;chr3:125032501-125042231	chr3:125032501-125033780		chr3:125033781-125042152;chr3:125042153-125042231	chr3:125042152-125042153;chr3:125042231-125042232		157;0
N	jcn_only_AD	CUFF.728	chr3	+	chr3:28357915-28360999;chr3:28360371-28360999	chr3:28358351-28360999		chr3:28357915-28358350;chr3:28358351-28360370	chr3:28357914-28357915;chr3:28358350-28358351		524;36
N	mutually_exclusive	CUFF.778	chr3	-	chr3:141697525-141724282,chr3:141724387-141747420	chr3:141697525-141713861,chr3:141713984-141747420	chr3:141724283-141724386	chr3:141713862-141713983			10;200
K	cassette	CUFF.773	chr3	+	chr3:132948196-133098595	chr3:132948196-133022047;chr3:133022182-133098595		chr3:133022048-133022181			452;36
K	coord_cassette	CUFF.755	chr3	-	chr3:107576050-107591814	chr3:107576050-107585498;chr3:107585601-107586157;chr3:107586273-107591814		chr3:107585499-107585600;chr3:107586158-107586272			561;29
N	intron_retention		chr3	-	chr3:125725408-125725956				chr3:125725407-125725408;chr3:125725956-125725957		122;169
K	alternative_last_exon	CUFF.773	chr3	+	chr3:132793203-132948109	chr3:132793203-132837881	chr3:132948110-132948195	chr3:132837882-132838352			16;83
K	intron_retention	CUFF.761	chr3	+	chr3:119529042-119530385				chr3:119529041-119529042;chr3:119530385-119530386		123;124
K	alternative_first_exon	CUFF.773	chr3	+	chr3:132757280-132764745	chr3:132760700-132764745	chr3:132757144-132757279	chr3:132760591-132760699			183;138
K	jcn_only_AA	CUFF.765	chr3	+	chr3:122864440-122864964	chr3:122864440-122864945		chr3:122864946-122864964	chr3:122864964-122864965		675;95
N	cassette	CUFF.778	chr3	-	chr3:141724387-141868024	chr3:141724387-141820576;chr3:141820684-141868024		chr3:141820577-141820683			173;366
K	intron_retention	CUFF.744	chr3	-	chr3:49462308-49462381				chr3:49462307-49462308;chr3:49462381-49462382		1051;19
K	cassette	CUFF.741	chr3	-	chr3:47018334-47023421	chr3:47018334-47018427;chr3:47018531-47023421		chr3:47018428-47018530			63;141
N	coord_cassette	CUFF.773	chr3	+	chr3:132948196-133109023	chr3:132948196-133097185;chr3:133097401-133098595;chr3:133100006-133109023		chr3:133097186-133097400;chr3:133098596-133100005			42;112
K	jcn_only_AA	CUFF.733	chr3	-	chr3:33626413-33633886	chr3:33633732-33633886					28;1
K	cassette	CUFF.727	chr3	-	chr3:27244049-27297786	chr3:27244049-27257222;chr3:27257372-27297786		chr3:27257223-27257371			104;120
K	cassette	CUFF.783	chr3	-	chr3:165504100-165547304	chr3:165504100-165545773;chr3:165545858-165547304		chr3:165545774-165545857			84;41
K	intron_retention	CUFF.744	chr3	-	chr3:49460997-49461507				chr3:49460996-49460997;chr3:49461507-49461508		237;1004
N	cassette	CUFF.759	chr3	+	chr3:119196296-119198754	chr3:119196296-119197180;chr3:119197322-119198754		chr3:119197181-119197321			15;109
N	jcn_only_AD	CUFF.728	chr3	+	chr3:28357915-28360999;chr3:28358351-28360999	chr3:28360371-28360999		chr3:28357915-28358350;chr3:28358351-28360370	chr3:28357914-28357915;chr3:28358350-28358351		537;23
N	jcn_only_AD		chr3	-	chr3:127313777-127317038	chr3:127313777-127314294		chr3:127314295-127317038	chr3:127317038-127317039		72;762
N	cassette	CUFF.771	chr3	+	chr3:126113822-126114784	chr3:126113822-126114167;chr3:126114273-126114784		chr3:126114168-126114272			212;122
N	coord_cassette	CUFF.788	chr3	+	chr3:186681715-186769036	chr3:186681715-186756529;chr3:186756662-186759704;chr3:186759755-186760441;chr3:186761099-186769036		chr3:186756530-186756661;chr3:186759705-186759754;chr3:186760442-186761098			27;349
K	alternative_last_exon	CUFF.745,CUFF.775	chr3	+	chr3:51747327-51749077	chr3:51747327-51747979	chr3:51749078-51750153	chr3:51747980-51748169			54;118
N	intron_retention		chr3	-	chr3:125787090-125802771				chr3:125787089-125787090;chr3:125802771-125802772		22;102
K	cassette	CUFF.753	chr3	-	chr3:93646252-93692517	chr3:93646252-93647545;chr3:93647642-93692517		chr3:93647546-93647641			7;177
N	mutually_exclusive	CUFF.778	chr3	-	chr3:141697525-141724282,chr3:141724387-141811902	chr3:141697525-141713861,chr3:141713984-141811902	chr3:141724283-141724386	chr3:141713862-141713983			10;200
K	alternative_first_exon	CUFF.782	chr3	-	chr3:156271571-156272745;chr3:156271571-156271781	chr3:156271571-156272525	chr3:156272746-156272973;chr3:156271782-156271981	chr3:156272526-156272676			214;49
N	alternative_donor	CUFF.732,CUFF.737	chr3	-	chr3:33454320-33458249	chr3:33454320-33457497		chr3:33457498-33458249	chr3:33458249-33458250		71;9
N	jcn_only_AD	CUFF.743	chr3	-	chr3:33467234-33482168	chr3:33467234-33481227		chr3:33481228-33482168	chr3:33482168-33482169		104;68
K	alternative_first_exon	CUFF.772	chr3	-	chr3:127299007-127306912,chr3:127299007-127309725,chr3:127299007-127310732;chr3:127299007-127313642	chr3:127299007-127309252	chr3:127313643-127313776	chr3:127309253-127309586			923;355
N	jcn_only_AA	CUFF.755	chr3	-	chr3:107586425-107591814	chr3:107591328-107591814		chr3:107586425-107591327	chr3:107586424-107586425		140;54
K	coord_cassette	CUFF.760	chr3	-	chr3:119246689-119263396	chr3:119246689-119248688;chr3:119248785-119255983;chr3:119256266-119263396		chr3:119248689-119248784;chr3:119255984-119256265			590;62
N	alternative_acceptor	CUFF.727	chr3	-	chr3:27297863-27326092	chr3:27320465-27326092		chr3:27297863-27320464	chr3:27297862-27297863		381;1
K	alternative_first_exon	CUFF.745	chr3	+	chr3:51743450-51746488	chr3:51745736-51746488	chr3:51742864-51743449	chr3:51745227-51745735			173;141
K	intron_retention	CUFF.728	chr3	+	chr3:28357915-28358243				chr3:28357914-28357915;chr3:28358243-28358244		54;117
N	cassette	CUFF.788	chr3	+	chr3:186756662-186769036	chr3:186756662-186760441;chr3:186761099-186769036		chr3:186760442-186761098			4;679
N	coord_cassette	CUFF.788	chr3	+	chr3:186756662-186769036	chr3:186756662-186759704;chr3:186759755-186760441;chr3:186761099-186769036		chr3:186759705-186759754;chr3:186760442-186761098			4;339
N	alternative_first_exon	CUFF.733	chr3	-	chr3:33686396-33686494;chr3:33686396-33700465;chr3:33686396-33700998	chr3:33686396-33686835,chr3:33686396-33686773	chr3:33700466-33700709;chr3:33700999-33701258	chr3:33686836-33687042			441;579
N	alternative_acceptor	CUFF.755	chr3	-	chr3:107559252-107560951	chr3:107560867-107560951		chr3:107559252-107560866	chr3:107559251-107559252		54;94
K	intron_retention	CUFF.762	chr3	-	chr3:120369713-120371438				chr3:120369712-120369713;chr3:120371438-120371439		139;32
K	intron_retention	CUFF.725	chr3	+	chr3:19992554-20017078				chr3:19992553-19992554;chr3:20017078-20017079		496;94
K	cassette	CUFF.727	chr3	-	chr3:27183074-27203951	chr3:27183074-27184935;chr3:27184966-27203951		chr3:27184936-27184965			195;16
N	alternative_donor	CUFF.759	chr3	+	chr3:119187954-119188666;chr3:119187854-119188666	chr3:119188106-119188666		chr3:119187854-119187953;chr3:119187954-119188105	chr3:119187853-119187854;chr3:119187953-119187954		390;152
N	jcn_only_AA	CUFF.778	chr3	-	chr3:141693034-141697361	chr3:141693037-141697361		chr3:141693034-141693036	chr3:141693033-141693034		303;195
K	cassette	CUFF.781	chr3	-	chr3:155520381-155523385	chr3:155520381-155521839;chr3:155521963-155523385		chr3:155521840-155521962			255;173
N	intron_retention		chr3	+	chr3:28360371-28360999				chr3:28360370-28360371;chr3:28360999-28361000		23;310
K	alternative_last_exon	CUFF.775	chr3	+	chr3:133407209-133418748;chr3:133407209-133419725	chr3:133407209-133410566	chr3:133418749-133419168;chr3:133419726-133420037	chr3:133410567-133410675			273;24
K	alternative_last_exon	CUFF.756	chr3	-	chr3:108464359-108475354	chr3:108474753-108475354	chr3:108464278-108464358	chr3:108474424-108474752			274;158
N	jcn_only_AD	CUFF.743	chr3	-	chr3:49330032-49331839	chr3:49330032-49330978		chr3:49330979-49331839	chr3:49331839-49331840		435;189
K	cassette	CUFF.741	chr3	-	chr3:46982556-47017842	chr3:46982556-47007473;chr3:47007620-47017842		chr3:47007474-47007619			423;117
K	alternative_last_exon	CUFF.773,CUFF.775	chr3	+	chr3:133419898-133472438	chr3:133419898-133426336	chr3:133472439-133472547	chr3:133426337-133426516			50;66
K	coord_cassette	CUFF.762	chr3	-	chr3:120360541-120365819	chr3:120360541-120363444;chr3:120363467-120365113;chr3:120365214-120365819		chr3:120363445-120363466;chr3:120365114-120365213			129;78
K	cassette	CUFF.744	chr3	-	chr3:49462872-49463684	chr3:49462872-49463315;chr3:49463430-49463684		chr3:49463316-49463429			38;916
K	alternative_first_exon	CUFF.785	chr3	+	chr3:178866008-178916537	chr3:178867505-178916537	chr3:178865902-178866007	chr3:178867327-178867504			139;27
K	cassette	CUFF.791	chr3	-	chr3:196214450-196229743	chr3:196214450-196215477;chr3:196215555-196229743		chr3:196215478-196215554			10;2
N	mutually_exclusive	CUFF.755	chr3	-	chr3:107586273-107591814,chr3:107591874-107596748;chr3:107586273-107594976,chr3:107595034-107596748	chr3:107586273-107596159,chr3:107596345-107596748	chr3:107591815-107591873;chr3:107594977-107595033	chr3:107596160-107596344			84;135
K	alternative_first_exon	CUFF.770	chr3	-	chr3:126071791-126076079	chr3:126071791-126072854	chr3:126076080-126076285	chr3:126072855-126073205			28;253
N	jcn_only_AA	CUFF.727	chr3	-	chr3:27405336-27410715;chr3:27409054-27410715	chr3:27394411-27410715		chr3:27394411-27405335;chr3:27405336-27409053	chr3:27394410-27394411;chr3:27405335-27405336		20;76
N	jcn_only_AD	CUFF.751	chr3	-	chr3:73453547-73482789;chr3:73453547-73610601;chr3:73453547-73651504;chr3:73453547-73523605;chr3:73453547-73618301	chr3:73453547-73605850		chr3:73482790-73523605;chr3:73523606-73605850;chr3:73605851-73610601;chr3:73610602-73618301;chr3:73618302-73651504	chr3:73523605-73523606;chr3:73605850-73605851;chr3:73610601-73610602;chr3:73618301-73618302;chr3:73651504-73651505		512;57
K	jcn_only_AA	CUFF.762	chr3	-	chr3:120352176-120357301	chr3:120352438-120357301		chr3:120352176-120352437	chr3:120352175-120352176		244;51
N	alternative_acceptor	CUFF.755	chr3	-	chr3:107586425-107591814	chr3:107591328-107591814		chr3:107586425-107591327	chr3:107586424-107586425		140;2
K	alternative_first_exon	CUFF.765	chr3	+	chr3:122786054-122808014	chr3:122786423-122808014	chr3:122785822-122786053	chr3:122786144-122786422			45;25
K	alternative_first_exon	CUFF.769,CUFF.782	chr3	-	chr3:156271571-156272525;chr3:156271571-156271781	chr3:156271571-156272745	chr3:156272526-156272676;chr3:156271782-156271981	chr3:156272746-156272973			178;85
N	alternative_acceptor	CUFF.744	chr3	-	chr3:49462487-49462799	chr3:49462580-49462799		chr3:49462487-49462579	chr3:49462486-49462487		937;63
N	alternative_first_exon	CUFF.733	chr3	-	chr3:33686396-33686494;chr3:33686396-33686835,chr3:33686396-33686773;chr3:33686396-33700998	chr3:33686396-33700465	chr3:33686836-33687042;chr3:33700999-33701258	chr3:33700466-33700709			686;334
N	jcn_only_AD	CUFF.751	chr3	-	chr3:73453547-73482789;chr3:73453547-73610601;chr3:73453547-73523605;chr3:73453547-73605850;chr3:73453547-73618301	chr3:73453547-73651504		chr3:73482790-73523605;chr3:73523606-73605850;chr3:73605851-73610601;chr3:73610602-73618301;chr3:73618302-73651504	chr3:73523605-73523606;chr3:73605850-73605851;chr3:73610601-73610602;chr3:73618301-73618302;chr3:73651504-73651505		564;5
N	cassette	CUFF.769	chr3	-	chr3:125752522-125786789	chr3:125752522-125769785;chr3:125769894-125786789		chr3:125769786-125769893			1580;3518
N	alternative_donor	CUFF.727,CUFF.772	chr3	-	chr3:27233734-27243000;chr3:27233734-27236027	chr3:27233734-27235551		chr3:27235552-27236027;chr3:27236028-27243000	chr3:27236027-27236028;chr3:27243000-27243001		293;1
K	jcn_only_AD	CUFF.758	chr3	+	chr3:112046542-112048192	chr3:112046554-112048192		chr3:112046542-112046553	chr3:112046541-112046542		74;59
N	intron_retention	CUFF.747	chr3	-	chr3:57582951-57583058				chr3:57582950-57582951;chr3:57583058-57583059		38;462
N	alternative_first_exon	CUFF.733	chr3	-	chr3:33686396-33686494;chr3:33686396-33700465;chr3:33686396-33686835,chr3:33686396-33686773	chr3:33686396-33700998	chr3:33700466-33700709;chr3:33686836-33687042	chr3:33700999-33701258			978;42
K	intron_retention	CUFF.737	chr3	-	chr3:38050128-38050532				chr3:38050127-38050128;chr3:38050532-38050533		336;101
N	alternative_donor	CUFF.766	chr3	-	chr3:125032501-125042152;chr3:125032501-125033780	chr3:125032501-125042231		chr3:125033781-125042152;chr3:125042153-125042231	chr3:125042152-125042153;chr3:125042231-125042232		110;47
N	jcn_only_AA	CUFF.727	chr3	-	chr3:27405336-27410715;chr3:27394411-27410715	chr3:27409054-27410715		chr3:27394411-27405335;chr3:27405336-27409053	chr3:27394410-27394411;chr3:27405335-27405336		80;16
K	cassette	CUFF.733	chr3	-	chr3:33602464-33612218	chr3:33602464-33612181;chr3:33612185-33612218		chr3:33612182-33612184			38;2
N	mutually_exclusive	CUFF.755	chr3	-	chr3:107586273-107591814,chr3:107591874-107596748;chr3:107586273-107596159,chr3:107596345-107596748	chr3:107586273-107594976,chr3:107595034-107596748	chr3:107591815-107591873;chr3:107596160-107596344	chr3:107594977-107595033			177;42
K	intron_retention	CUFF.743	chr3	-	chr3:49349088-49362134				chr3:49349087-49349088;chr3:49362134-49362135		146;117
K	jcn_only_AD	CUFF.759	chr3	+	chr3:119205780-119207775	chr3:119205884-119207775		chr3:119205780-119205883	chr3:119205779-119205780		23;92
K	intron_retention	CUFF.723	chr3	+	chr3:8787560-8787655				chr3:8787559-8787560;chr3:8787655-8787656		570;76
N	coord_cassette	CUFF.788	chr3	+	chr3:186648624-186769036	chr3:186648624-186660135;chr3:186660216-186681572;chr3:186681715-186756529;chr3:186756662-186769036		chr3:186660136-186660215;chr3:186681573-186681714;chr3:186756530-186756661			207;60
N	mutually_exclusive	CUFF.769	chr3	-	chr3:125752522-125786789,chr3:125787090-125820271	chr3:125752522-125769785,chr3:125769894-125820271	chr3:125786790-125787089	chr3:125769786-125769893			249;237
K	intron_retention	CUFF.780	chr3	-	chr3:149051187-149051299				chr3:149051186-149051187;chr3:149051299-149051300		235;21
N	alternative_donor	CUFF.751	chr3	-	chr3:73453547-73482789;chr3:73453547-73610601;chr3:73453547-73523605;chr3:73453547-73605850;chr3:73453547-73618301	chr3:73453547-73651504		chr3:73482790-73523605;chr3:73523606-73605850;chr3:73605851-73610601;chr3:73610602-73618301;chr3:73618302-73651504	chr3:73523605-73523606;chr3:73605850-73605851;chr3:73610601-73610602;chr3:73618301-73618302;chr3:73651504-73651505		1;5
K	intron_retention	CUFF.759	chr3	+	chr3:119205780-119207775				chr3:119205779-119205780;chr3:119207775-119207776		23;46
K	coord_cassette	CUFF.762	chr3	-	chr3:120360541-120365819	chr3:120360541-120363165;chr3:120363291-120365113;chr3:120365214-120365819		chr3:120363166-120363290;chr3:120365114-120365213			129;67
K	cassette	CUFF.733	chr3	-	chr3:33592888-33600798	chr3:33592888-33600616;chr3:33600668-33600798		chr3:33600617-33600667			54;60
K	cassette	CUFF.732	chr3	-	chr3:33437773-33438536	chr3:33437773-33438236;chr3:33438371-33438536		chr3:33438237-33438370			55;80
K	intron_retention	CUFF.733	chr3	-	chr3:33612185-33612218				chr3:33612184-33612185;chr3:33612218-33612219		2;69
K	intron_retention	CUFF.762	chr3	-	chr3:120360541-120365819				chr3:120360540-120360541;chr3:120365819-120365820		129;80
N	alternative_acceptor	CUFF.728	chr3	+	chr3:28357915-28358243;chr3:28357915-28360222	chr3:28357915-28360999		chr3:28358244-28360222;chr3:28360223-28360999	chr3:28360222-28360223;chr3:28360999-28361000		448;501
N	jcn_only_AD	CUFF.766	chr3	-	chr3:125032501-125042152;chr3:125032501-125033780	chr3:125032501-125042231		chr3:125033781-125042152;chr3:125042153-125042231	chr3:125042152-125042153;chr3:125042231-125042232		213;47
K	intron_retention	CUFF.776	chr3	-	chr3:133896918-133901845				chr3:133896917-133896918;chr3:133901845-133901846		106;100
N	cassette	CUFF.743	chr3	-	chr3:49336069-49339816	chr3:49336069-49337899;chr3:49338125-49339816		chr3:49337900-49338124			54;467
K	jcn_only_AD	CUFF.775	chr3	+	chr3:133407209-133419725	chr3:133418468-133419725					145;38
N	jcn_only_AD	CUFF.766,CUFF.772	chr3	-	chr3:125007073-125032151	chr3:125007073-125011308		chr3:125011309-125032151	chr3:125032151-125032152		80;48
N	coord_cassette	CUFF.778	chr3	-	chr3:141697525-141747420	chr3:141697525-141712379;chr3:141712428-141713861;chr3:141713984-141747420		chr3:141712380-141712427;chr3:141713862-141713983			46;142
K	intron_retention	CUFF.737	chr3	-	chr3:38049859-38049948				chr3:38049858-38049859;chr3:38049948-38049949		493;28
K	intron_retention		chr3	-	chr3:141712428-141713861				chr3:141712427-141712428;chr3:141713861-141713862		580;133
N	cassette	CUFF.755	chr3	-	chr3:107586273-107596159;chr3:107591874-107596748	chr3:107586273-107594976,chr3:107591874-107594976;chr3:107595034-107596159,chr3:107595034-107596748		chr3:107594977-107595033			187;394
N	alternative_donor	CUFF.747	chr3	-	chr3:57582951-57583365	chr3:57582951-57583058		chr3:57583059-57583365	chr3:57583365-57583366		46;50
N	jcn_only_AD		chr3	-	chr3:71777775-71778224;chr3:71777775-71803794;chr3:71777775-71803365	chr3:71777775-71802613					753;14
K	alternative_first_exon	CUFF.768	chr3	+	chr3:125635563-125637706	chr3:125635661-125637706	chr3:125635463-125635562	chr3:125635563-125635660			672;52
K	cassette	CUFF.755	chr3	-	chr3:107576050-107586157	chr3:107576050-107585498;chr3:107585601-107586157		chr3:107585499-107585600			506;33
N	alternative_acceptor	CUFF.747	chr3	-	chr3:57569760-57570110;chr3:57569788-57570110	chr3:57569735-57570110		chr3:57569735-57569759;chr3:57569760-57569787	chr3:57569734-57569735;chr3:57569759-57569760		162;65
N	intron_retention		chr3	-	chr3:125787090-125802896				chr3:125787089-125787090;chr3:125802896-125802897		39;75
N	cassette	CUFF.788	chr3	+	chr3:186681715-186769036	chr3:186681715-186756529;chr3:186756662-186769036		chr3:186756530-186756661			27;380
N	intron_retention		chr3	+	chr3:51749200-51750033				chr3:51749199-51749200;chr3:51750033-51750034		18;154
K	cassette	CUFF.783	chr3	-	chr3:165504100-165555101	chr3:165504100-165547304;chr3:165548830-165555101		chr3:165547305-165548829			447;166
N	jcn_only_AA	CUFF.766	chr3	-	chr3:124996654-125042231	chr3:125032501-125042231					631;47
N	jcn_only_AD	CUFF.733	chr3	-	chr3:33552257-33557514	chr3:33552257-33556071		chr3:33556072-33557514	chr3:33557514-33557515		112;34
N	alternative_donor	CUFF.776,CUFF.778	chr3	-	chr3:141820684-141868024	chr3:141820684-141844990		chr3:141844991-141868024	chr3:141868024-141868025		801;3
N	alternative_donor	CUFF.751	chr3	-	chr3:73453547-73482789;chr3:73453547-73610601;chr3:73453547-73651504;chr3:73453547-73523605;chr3:73453547-73618301	chr3:73453547-73605850		chr3:73482790-73523605;chr3:73523606-73605850;chr3:73605851-73610601;chr3:73610602-73618301;chr3:73618302-73651504	chr3:73523605-73523606;chr3:73605850-73605851;chr3:73610601-73610602;chr3:73618301-73618302;chr3:73651504-73651505		6;0
N	alternative_acceptor	CUFF.776	chr3	-	chr3:133910819-133913925	chr3:133910828-133913925		chr3:133910819-133910827	chr3:133910818-133910819		37;27
N	cassette	CUFF.732	chr3	-	chr3:33444397-33450727	chr3:33444397-33450181;chr3:33450290-33450727		chr3:33450182-33450289			62;95
N	jcn_only_AD		chr3	-	chr3:71777775-71778224;chr3:71777775-71802613;chr3:71777775-71803365	chr3:71777775-71803794					743;24
N	alternative_donor	CUFF.740	chr3	-	chr3:73453547-73610601;chr3:73453547-73651504;chr3:73453547-73523605;chr3:73453547-73605850;chr3:73453547-73618301	chr3:73453547-73482789		chr3:73482790-73523605;chr3:73523606-73605850;chr3:73605851-73610601;chr3:73610602-73618301;chr3:73618302-73651504	chr3:73523605-73523606;chr3:73605850-73605851;chr3:73610601-73610602;chr3:73618301-73618302;chr3:73651504-73651505		5;1
N	alternative_acceptor	CUFF.727	chr3	-	chr3:27405336-27410715;chr3:27409054-27410715	chr3:27394411-27410715		chr3:27394411-27405335;chr3:27405336-27409053	chr3:27394410-27394411;chr3:27405335-27405336		0;76
K	alternative_first_exon	CUFF.745	chr3	+	chr3:51741184-51749077;chr3:51748138-51749077	chr3:51747327-51749077	chr3:51740993-51741183;chr3:51747980-51748137	chr3:51746489-51747326			117;43
N	jcn_only_AA	CUFF.755	chr3	-	chr3:107572902-107573976;chr3:107572807-107573976	chr3:107573542-107573976		chr3:107572807-107572901;chr3:107572902-107573541	chr3:107572806-107572807;chr3:107572901-107572902		332;22
K	cassette	CUFF.784	chr3	-	chr3:173628660-173632679	chr3:173628660-173630335;chr3:173630408-173632679		chr3:173630336-173630407			31;24
K	cassette	CUFF.781	chr3	-	chr3:155485459-155520320	chr3:155485459-155493489;chr3:155493638-155520320		chr3:155493490-155493637			642;493
K	intron_retention	CUFF.727	chr3	-	chr3:27352508-27353589				chr3:27352507-27352508;chr3:27353589-27353590		16;48
N	cassette	CUFF.768	chr3	+	chr3:125639749-125647337	chr3:125639749-125643808;chr3:125643959-125647337		chr3:125643809-125643958			9;712
K	coord_cassette	CUFF.783	chr3	-	chr3:165504100-165555101	chr3:165504100-165545773;chr3:165545858-165547304;chr3:165548830-165555101		chr3:165545774-165545857;chr3:165547305-165548829			447;58
K	cassette	CUFF.773	chr3	+	chr3:132764865-132948109	chr3:132764865-132793158;chr3:132793203-132948109		chr3:132793159-132793202			258;33
K	alternative_acceptor	CUFF.765	chr3	+	chr3:122864440-122864964	chr3:122864440-122864945		chr3:122864946-122864964	chr3:122864964-122864965		675;50
N	alternative_acceptor	CUFF.762	chr3	-	chr3:120371494-120389273	chr3:120371499-120389273		chr3:120371494-120371498	chr3:120371493-120371494		71;65
N	alternative_donor	CUFF.743	chr3	-	chr3:49330032-49331839	chr3:49330032-49330978		chr3:49330979-49331839	chr3:49331839-49331840		435;46
N	jcn_only_AD		chr3	-	chr3:49343322-49365118	chr3:49343322-49348052					69;491
N	alternative_last_exon		chr3	+	chr3:28283304-28357823	chr3:28283304-28304781	chr3:28357824-28361253	chr3:28304782-28304871			66;84
N	intron_retention	CUFF.728	chr3	+	chr3:28357915-28360222				chr3:28357914-28357915;chr3:28360222-28360223		21;187
N	intron_retention		chr3	-	chr3:38049655-38049725				chr3:38049654-38049655;chr3:38049725-38049726		412;45
N	mutually_exclusive	CUFF.755	chr3	-	chr3:107586273-107594976,chr3:107595034-107596748;chr3:107586273-107596159,chr3:107596345-107596748	chr3:107586273-107591814,chr3:107591874-107596748	chr3:107594977-107595033;chr3:107596160-107596344	chr3:107591815-107591873			177;42
K	alternative_last_exon	CUFF.765,CUFF.788	chr3	+	chr3:186790736-186791946	chr3:186790736-186791192	chr3:186791947-186792121	chr3:186791193-186791287			276;12
K	jcn_only_AA	CUFF.790	chr3	-	chr3:194063432-194071970	chr3:194063435-194071970		chr3:194063432-194063434	chr3:194063431-194063432		59;20
K	alternative_donor	CUFF.759	chr3	+	chr3:119205780-119207775	chr3:119205884-119207775		chr3:119205780-119205883	chr3:119205779-119205780		23;71
N	alternative_acceptor	CUFF.766	chr3	-	chr3:125032501-125042152	chr3:125033898-125042152		chr3:125032501-125033897	chr3:125032500-125032501		199;1
K	intron_retention		chr3	-	chr3:125787090-125802935				chr3:125787089-125787090;chr3:125802935-125802936		1723;73
N	jcn_only_AA	CUFF.755	chr3	-	chr3:107572902-107573976;chr3:107573542-107573976	chr3:107572807-107573976		chr3:107572807-107572901;chr3:107572902-107573541	chr3:107572806-107572807;chr3:107572901-107572902		319;35
K	intron_retention	CUFF.769	chr3	-	chr3:125743749-125745177				chr3:125743748-125743749;chr3:125745177-125745178		1284;1284
K	intron_retention	CUFF.741	chr3	-	chr3:46964854-46965096				chr3:46964853-46964854;chr3:46965096-46965097		518;164
K	cassette	CUFF.766	chr3	-	chr3:125050083-125093945	chr3:125050083-125057665;chr3:125057756-125093945		chr3:125057666-125057755			390;17
K	alternative_first_exon	CUFF.761	chr3	+	chr3:119501148-119526075	chr3:119501700-119526075	chr3:119499331-119501147	chr3:119501549-119501699			115;58
K	intron_retention	CUFF.788	chr3	+	chr3:186769135-186790636				chr3:186769134-186769135;chr3:186790636-186790637		284;74
N	alternative_acceptor	CUFF.743	chr3	-	chr3:49349088-49355741	chr3:49354912-49355741		chr3:49349088-49354911	chr3:49349087-49349088		129;69
N	alternative_donor	CUFF.782	chr3	-	chr3:156262229-156266593;chr3:156262229-156266693	chr3:156262229-156266654		chr3:156266594-156266654;chr3:156266655-156266693	chr3:156266654-156266655;chr3:156266693-156266694		439;14
N	cassette	CUFF.755	chr3	-	chr3:107595034-107596748	chr3:107595034-107596159;chr3:107596345-107596748		chr3:107596160-107596344			312;185
K	intron_retention	CUFF.732	chr3	-	chr3:33454320-33458249				chr3:33454319-33454320;chr3:33458249-33458250		71;19
N	jcn_only_AA	CUFF.743	chr3	-	chr3:49354912-49362134;chr3:49348171-49362134;chr3:49350047-49362134	chr3:49349088-49362134					83;146
K	alternative_first_exon	CUFF.727	chr3	-	chr3:27394411-27405177,chr3:27394411-27409013;chr3:27394411-27410715	chr3:27394411-27410521	chr3:27410716-27411048	chr3:27410522-27410715			82;44
K	intron_retention	CUFF.737	chr3	-	chr3:38050923-38051143				chr3:38050922-38050923;chr3:38051143-38051144		299;55
N	cassette	CUFF.768	chr3	+	chr3:125635563-125639667	chr3:125635563-125637706;chr3:125637770-125639667		chr3:125637707-125637769			7;769
N	alternative_donor	CUFF.751	chr3	-	chr3:73453547-73482789;chr3:73453547-73610601;chr3:73453547-73651504;chr3:73453547-73605850;chr3:73453547-73618301	chr3:73453547-73523605		chr3:73482790-73523605;chr3:73523606-73605850;chr3:73605851-73610601;chr3:73610602-73618301;chr3:73618302-73651504	chr3:73523605-73523606;chr3:73605850-73605851;chr3:73610601-73610602;chr3:73618301-73618302;chr3:73651504-73651505		6;0
N	alternative_donor		chr3	-	chr3:127313777-127317038	chr3:127313777-127314294		chr3:127314295-127317038	chr3:127317038-127317039		72;207
K	alternative_first_exon	CUFF.728	chr3	+	chr3:28283393-28304781;chr3:28283304-28304781	chr3:28295257-28304781	chr3:28283075-28283303	chr3:28295158-28295256			165;51
K	jcn_only_AD	CUFF.741,CUFF.743	chr3	-	chr3:49338125-49339870	chr3:49338125-49339816		chr3:49339817-49339870	chr3:49339870-49339871		11;495
K	jcn_only_AD	CUFF.748	chr3	+	chr3:68055888-68466429	chr3:68300062-68466429					91;153
K	alternative_first_exon	CUFF.746	chr3	-	chr3:52258329-52263676	chr3:52258329-52259542	chr3:52263677-52263798	chr3:52259543-52260179			31;7
N	jcn_only_AD	CUFF.782	chr3	-	chr3:156262229-156266593;chr3:156262229-156266654	chr3:156262229-156266693		chr3:156266594-156266654;chr3:156266655-156266693	chr3:156266654-156266655;chr3:156266693-156266694		105;376
K	jcn_only_AA	CUFF.745	chr3	+	chr3:51741184-51749077	chr3:51741184-51742863					51;69
K	cassette	CUFF.762	chr3	-	chr3:120394711-120400943	chr3:120394711-120396750;chr3:120396839-120400943		chr3:120396751-120396838			266;76
K	intron_retention	CUFF.769	chr3	-	chr3:125741776-125745235				chr3:125741775-125741776;chr3:125745235-125745236		381;1606
N	alternative_donor	CUFF.759	chr3	+	chr3:119188106-119188666;chr3:119187954-119188666	chr3:119187854-119188666		chr3:119187854-119187953;chr3:119187954-119188105	chr3:119187853-119187854;chr3:119187953-119187954		306;236
K	intron_retention	CUFF.788	chr3	+	chr3:186790736-186791946				chr3:186790735-186790736;chr3:186791946-186791947		307;22
K	alternative_first_exon	CUFF.752	chr3	+	chr3:75492798-75500360	chr3:75496448-75500360	chr3:75492659-75492797	chr3:75496223-75496447			16;483
K	jcn_only_AA	CUFF.761	chr3	+	chr3:119530574-119531643	chr3:119530574-119531532		chr3:119531533-119531643	chr3:119531643-119531644		34;141
K	intron_retention	CUFF.732	chr3	-	chr3:33431861-33434054				chr3:33431860-33431861;chr3:33434054-33434055		102;11
N	alternative_donor	CUFF.751	chr3	-	chr3:73453547-73482789;chr3:73453547-73610601;chr3:73453547-73651504;chr3:73453547-73523605;chr3:73453547-73605850	chr3:73453547-73618301		chr3:73482790-73523605;chr3:73523606-73605850;chr3:73605851-73610601;chr3:73610602-73618301;chr3:73618302-73651504	chr3:73523605-73523606;chr3:73605850-73605851;chr3:73610601-73610602;chr3:73618301-73618302;chr3:73651504-73651505		6;0
N	alternative_first_exon		chr3	-	chr3:49354912-49362134	chr3:49354912-49355741	chr3:49362135-49362196	chr3:49355742-49356253			48;28
N	alternative_donor	CUFF.751	chr3	-	chr3:73450161-73453298	chr3:73450161-73450919		chr3:73450920-73453298	chr3:73453298-73453299		493;7
K	alternative_first_exon	CUFF.745	chr3	+	chr3:51741184-51749077;chr3:51747327-51749077	chr3:51748138-51749077	chr3:51740993-51741183;chr3:51746489-51747326	chr3:51747980-51748137			78;82
N	alternative_donor	CUFF.733	chr3	-	chr3:33552257-33557514	chr3:33552257-33556071		chr3:33556072-33557514	chr3:33557514-33557515		112;3
N	jcn_only_AD	CUFF.759	chr3	+	chr3:119188106-119188666;chr3:119187954-119188666	chr3:119187854-119188666		chr3:119187854-119187953;chr3:119187954-119188105	chr3:119187853-119187854;chr3:119187953-119187954		405;236
N	alternative_donor	CUFF.751	chr3	-	chr3:73453547-73482789;chr3:73453547-73651504;chr3:73453547-73523605;chr3:73453547-73605850;chr3:73453547-73618301	chr3:73453547-73610601		chr3:73482790-73523605;chr3:73523606-73605850;chr3:73605851-73610601;chr3:73610602-73618301;chr3:73618302-73651504	chr3:73523605-73523606;chr3:73605850-73605851;chr3:73610601-73610602;chr3:73618301-73618302;chr3:73651504-73651505		6;0
N	alternative_acceptor	CUFF.778	chr3	-	chr3:141697525-141712379	chr3:141708357-141712379		chr3:141697525-141708356	chr3:141697524-141697525		497;10
N	cassette	CUFF.760	chr3	-	chr3:119246689-119255983	chr3:119246689-119248688;chr3:119248785-119255983		chr3:119248689-119248784			77;53
K	intron_retention	CUFF.754	chr3	+	chr3:97662415-97663677				chr3:97662414-97662415;chr3:97663677-97663678		46;47
K	intron_retention	CUFF.765	chr3	+	chr3:122863677-122864368				chr3:122863676-122863677;chr3:122864368-122864369		386;7
K	intron_retention	CUFF.751	chr3	-	chr3:73432957-73433799				chr3:73432956-73432957;chr3:73433799-73433800		24;589
N	cassette	CUFF.772	chr3	-	chr3:127294109-127294782;chr3:127294349-127294782	chr3:127294109-127294591,chr3:127294349-127294591;chr3:127294653-127294782		chr3:127294592-127294652			179;151
N	alternative_acceptor	CUFF.728	chr3	+	chr3:28357915-28360222;chr3:28357915-28360999	chr3:28357915-28358243		chr3:28358244-28360222;chr3:28360223-28360999	chr3:28360222-28360223;chr3:28360999-28361000		625;324
N	intron_retention		chr3	-	chr3:125775357-125786789				chr3:125775356-125775357;chr3:125786789-125786790		106;16
N	alternative_donor	CUFF.782	chr3	-	chr3:156261059-156262096	chr3:156261059-156262082		chr3:156262083-156262096	chr3:156262096-156262097		452;31
N	alternative_acceptor	CUFF.772	chr3	-	chr3:127299007-127309252	chr3:127307004-127309252		chr3:127299007-127307003	chr3:127299006-127299007		355;7
K	jcn_only_AA	CUFF.776	chr3	-	chr3:133794058-133894452	chr3:133878218-133894452					45;502
K	alternative_last_exon	CUFF.771	chr3	+	chr3:126139073-126142167	chr3:126139073-126139472	chr3:126142168-126142219	chr3:126139473-126139765		chr3:126138946-126139072	353;284
N	jcn_only_AA	CUFF.766	chr3	-	chr3:125032501-125042152	chr3:125033898-125042152		chr3:125032501-125033897	chr3:125032500-125032501		199;11
K	cassette	CUFF.738	chr3	+	chr3:38315867-38316479	chr3:38315867-38316094;chr3:38316250-38316479		chr3:38316095-38316249			54;13
N	cassette	CUFF.755	chr3	-	chr3:107568819-107572719	chr3:107568819-107569143;chr3:107569199-107572719		chr3:107569144-107569198			47;56
N	cassette	CUFF.778	chr3	-	chr3:141697525-141747420;chr3:141713984-141811902;chr3:141713984-141747420	chr3:141697525-141724282,chr3:141713984-141724282;chr3:141724387-141747420,chr3:141724387-141811902		chr3:141724283-141724386			384;733
N	alternative_donor	CUFF.743,CUFF.755	chr3	-	chr3:107572902-107573976	chr3:107572902-107573500		chr3:107573501-107573976	chr3:107573976-107573977		297;114
K	intron_retention	CUFF.766	chr3	-	chr3:124951499-124953143				chr3:124951498-124951499;chr3:124953143-124953144		466;104
K	intron_retention	CUFF.732	chr3	-	chr3:33438371-33438536				chr3:33438370-33438371;chr3:33438536-33438537		82;78
N	intron_retention		chr3	-	chr3:57569735-57582800				chr3:57569734-57569735;chr3:57582800-57582801		49;51
N	jcn_only_AD	CUFF.782	chr3	-	chr3:156262229-156266593;chr3:156262229-156266693	chr3:156262229-156266654		chr3:156266594-156266654;chr3:156266655-156266693	chr3:156266654-156266655;chr3:156266693-156266694		465;15
K	cassette	CUFF.733	chr3	-	chr3:33543261-33557514	chr3:33543261-33552049;chr3:33552257-33557514		chr3:33552050-33552256			81;129
N	jcn_only_AA	CUFF.747	chr3	-	chr3:57569788-57570110;chr3:57569735-57570110	chr3:57569760-57570110		chr3:57569735-57569759;chr3:57569760-57569787	chr3:57569734-57569735;chr3:57569759-57569760		87;272
K	alternative_last_exon	CUFF.775	chr3	+	chr3:133407209-133419725;chr3:133407209-133410566	chr3:133407209-133418748	chr3:133419726-133420037;chr3:133410567-133410675	chr3:133418749-133419168			142;155
N	jcn_only_AD		chr3	-	chr3:27233734-27236027;chr3:27233734-27235551	chr3:27233734-27243000		chr3:27235552-27236027;chr3:27236028-27243000	chr3:27236027-27236028;chr3:27243000-27243001		46;291
N	jcn_only_AD	CUFF.727	chr3	-	chr3:71777775-71803794;chr3:71777775-71802613;chr3:71777775-71803365	chr3:71777775-71778224					53;714
N	jcn_only_AA	CUFF.755	chr3	-	chr3:107573542-107573976;chr3:107572807-107573976	chr3:107572902-107573976		chr3:107572807-107572901;chr3:107572902-107573541	chr3:107572806-107572807;chr3:107572901-107572902		57;297
N	cassette	CUFF.769	chr3	-	chr3:125769894-125820271	chr3:125769894-125786789;chr3:125787090-125820271		chr3:125786790-125787089			297;3887
N	alternative_donor	CUFF.782	chr3	-	chr3:156262229-156266593;chr3:156262229-156266654	chr3:156262229-156266693		chr3:156266594-156266654;chr3:156266655-156266693	chr3:156266654-156266655;chr3:156266693-156266694		77;376
K	cassette	CUFF.755	chr3	-	chr3:107576050-107591814	chr3:107576050-107586157;chr3:107586425-107591814		chr3:107586158-107586424			561;360
K	cassette	CUFF.733	chr3	-	chr3:33617768-33623312	chr3:33617768-33618693;chr3:33618757-33623312		chr3:33618694-33618756			25;271
K	alternative_acceptor	CUFF.761	chr3	+	chr3:119530574-119531643	chr3:119530574-119531532		chr3:119531533-119531643	chr3:119531643-119531644		34;115
K	intron_retention	CUFF.732	chr3	-	chr3:33441775-33442453				chr3:33441774-33441775;chr3:33442453-33442454		138;41
K	jcn_only_AA	CUFF.744	chr3	-	chr3:49463856-49466540	chr3:49463862-49466540		chr3:49463856-49463861	chr3:49463855-49463856		67;972
N	alternative_acceptor	CUFF.747	chr3	-	chr3:57569788-57570110;chr3:57569735-57570110	chr3:57569760-57570110		chr3:57569735-57569759;chr3:57569760-57569787	chr3:57569734-57569735;chr3:57569759-57569760		76;151
K	intron_retention	CUFF.759	chr3	+	chr3:119196296-119197180				chr3:119196295-119196296;chr3:119197180-119197181		78;81
K	cassette	CUFF.725	chr3	+	chr3:19992554-20017092	chr3:19992554-20012039;chr3:20012210-20017092		chr3:20012040-20012209			132;45
N	alternative_donor	CUFF.728	chr3	+	chr3:28357915-28360999;chr3:28360371-28360999	chr3:28358351-28360999		chr3:28357915-28358350;chr3:28358351-28360370	chr3:28357914-28357915;chr3:28358350-28358351		762;83
K	alternative_donor	CUFF.758	chr3	+	chr3:112046542-112048192	chr3:112046554-112048192		chr3:112046542-112046553	chr3:112046541-112046542		74;28
N	jcn_only_AA	CUFF.743	chr3	-	chr3:49349088-49355741	chr3:49354912-49355741		chr3:49349088-49354911	chr3:49349087-49349088		129;19
K	alternative_first_exon	CUFF.737	chr3	-	chr3:38058211-38061678	chr3:38058211-38060460	chr3:38061679-38061843	chr3:38060461-38060557			239;24
N	jcn_only_AA	CUFF.728	chr3	+	chr3:28357915-28360222;chr3:28357915-28360999	chr3:28357915-28358243		chr3:28358244-28360222;chr3:28360223-28360999	chr3:28360222-28360223;chr3:28360999-28361000		522;54
K	alternative_donor	CUFF.741,CUFF.743	chr3	-	chr3:49338125-49339870	chr3:49338125-49339816		chr3:49339817-49339870	chr3:49339870-49339871		11;326
N	alternative_acceptor	CUFF.755	chr3	-	chr3:107572902-107573976;chr3:107573542-107573976	chr3:107572807-107573976		chr3:107572807-107572901;chr3:107572902-107573541	chr3:107572806-107572807;chr3:107572901-107572902		234;35
N	alternative_first_exon	CUFF.773	chr3	+	chr3:132764865-132948113	chr3:132911672-132948113	chr3:132764746-132764864	chr3:132911573-132911671			13;47
K	alternative_first_exon	CUFF.743,CUFF.746	chr3	-	chr3:49348171-49362134	chr3:49348171-49348946	chr3:49362135-49362196	chr3:49348947-49350339			4;263
N	jcn_only_AA		chr3	+	chr3:8775677-8819162	chr3:8775677-8787211		chr3:8787212-8819162	chr3:8819162-8819163		15;565
N	jcn_only_AA		chr3	+	chr3:126135352-126137300;chr3:126135352-126135614	chr3:126135352-126137297		chr3:126135615-126137297;chr3:126137298-126137300	chr3:126137297-126137298;chr3:126137300-126137301	chr3:126137301-126137368	65;278
K	alternative_first_exon	CUFF.771	chr3	+	chr3:126152048-126153018	chr3:126152318-126153018	chr3:126151912-126152047	chr3:126152202-126152317		chr3:126153019-126153224	381;139
N	jcn_only_AA	CUFF.744	chr3	-	chr3:49462487-49462799	chr3:49462580-49462799		chr3:49462487-49462579	chr3:49462486-49462487		937;40
N	mutually_exclusive	CUFF.747	chr3	-	chr3:57563115-57570110,chr3:57570192-57582800	chr3:57563115-57569624,chr3:57569735-57582800	chr3:57570111-57570191	chr3:57569625-57569734			58;86
N	jcn_only_AA	CUFF.778	chr3	-	chr3:141697525-141712379	chr3:141708357-141712379		chr3:141697525-141708356	chr3:141697524-141697525		497;128
N	alternative_acceptor		chr3	+	chr3:28333446-28357823	chr3:28333446-28334226		chr3:28334227-28357823	chr3:28357823-28357824		18;4
K	alternative_first_exon	CUFF.782	chr3	-	chr3:156266793-156271443	chr3:156266793-156269186	chr3:156271444-156271570	chr3:156269187-156269284			260;26
N	jcn_only_AA	CUFF.772	chr3	-	chr3:127299007-127313642	chr3:127310794-127313642		chr3:127299007-127310793	chr3:127299006-127299007		886;57
K	cassette	CUFF.765	chr3	+	chr3:122843191-122864368	chr3:122843191-122849326;chr3:122849464-122864368		chr3:122849327-122849463			31;39
K	alternative_first_exon	CUFF.754	chr3	+	chr3:97643256-97652537;chr3:97634581-97652537	chr3:97652352-97652537	chr3:97642975-97643255;chr3:97634454-97634580	chr3:97652346-97652351			123;26
K	alternative_last_exon	CUFF.765	chr3	+	chr3:122880303-122928045	chr3:122880303-122880726	chr3:122928046-122928246	chr3:122880727-122881022			176;98
K	cassette	CUFF.747	chr3	-	chr3:57563115-57570110	chr3:57563115-57569624;chr3:57569760-57570110		chr3:57569625-57569759			63;268
K	intron_retention	CUFF.755	chr3	-	chr3:107572807-107573976				chr3:107572806-107572807;chr3:107573976-107573977		35;393
K	intron_retention	CUFF.732	chr3	-	chr3:33481349-33481950				chr3:33481348-33481349;chr3:33481950-33481951		18;31
K	intron_retention	CUFF.765	chr3	+	chr3:122880303-122880726				chr3:122880302-122880303;chr3:122880726-122880727		71;15
K	intron_retention	CUFF.759	chr3	+	chr3:119196296-119198897				chr3:119196295-119196296;chr3:119198897-119198898		227;104
K	jcn_only_AD	CUFF.756,CUFF.766	chr3	-	chr3:124996654-125042231	chr3:124996654-124997967					631;126
N	jcn_only_AD	CUFF.766,CUFF.776	chr3	-	chr3:125032501-125042152;chr3:125032501-125042231	chr3:125032501-125033780		chr3:125033781-125042152;chr3:125042153-125042231	chr3:125042152-125042153;chr3:125042231-125042232		246;14
K	cassette	CUFF.781	chr3	-	chr3:155520381-155523927	chr3:155520381-155523385;chr3:155523513-155523927		chr3:155523386-155523512			846;230
K	alternative_first_exon	CUFF.745	chr3	+	chr3:51748138-51749077;chr3:51747327-51749077	chr3:51741184-51749077	chr3:51747980-51748137;chr3:51746489-51747326	chr3:51740993-51741183			125;35
N	jcn_only_AD	CUFF.733,CUFF.766	chr3	-	chr3:124951499-124953143	chr3:124951499-124951952		chr3:124951953-124953143	chr3:124953143-124953144		466;49
N	alternative_donor	CUFF.728	chr3	+	chr3:28360371-28360999;chr3:28358351-28360999	chr3:28357915-28360999		chr3:28357915-28358350;chr3:28358351-28360370	chr3:28357914-28357915;chr3:28358350-28358351		344;501
K	alternative_acceptor	CUFF.733	chr3	-	chr3:33673864-33686248	chr3:33673867-33686248		chr3:33673864-33673866	chr3:33673863-33673864		907;112
N	intron_retention		chr3	-	chr3:141713984-141719093				chr3:141713983-141713984;chr3:141719093-141719094		56;19
K	alternative_first_exon	CUFF.754	chr3	+	chr3:97652352-97652537;chr3:97634581-97652537	chr3:97643256-97652537	chr3:97652346-97652351;chr3:97634454-97634580	chr3:97642975-97643255			37;112
K	cassette	CUFF.783	chr3	-	chr3:165491295-165503932	chr3:165491295-165495504;chr3:165495584-165503932		chr3:165495505-165495583			421;50
N	jcn_only_AD	CUFF.751	chr3	-	chr3:73450161-73453298	chr3:73450161-73450919		chr3:73450920-73453298	chr3:73453298-73453299		493;60
K	alternative_first_exon	CUFF.782	chr3	-	chr3:156271571-156272745;chr3:156271571-156272525	chr3:156271571-156271781	chr3:156272746-156272973;chr3:156272526-156272676	chr3:156271782-156271981			134;129
N	alternative_first_exon	CUFF.728	chr3	+	chr3:28339842-28357823,chr3:28333446-28357823,chr3:28336018-28357823;chr3:28283304-28357823	chr3:28304872-28357823	chr3:28283075-28283303	chr3:28304541-28304871			153;293
N	jcn_only_AD	CUFF.751	chr3	-	chr3:73453547-73482789;chr3:73453547-73610601;chr3:73453547-73651504;chr3:73453547-73605850;chr3:73453547-73618301	chr3:73453547-73523605		chr3:73482790-73523605;chr3:73523606-73605850;chr3:73605851-73610601;chr3:73610602-73618301;chr3:73618302-73651504	chr3:73523605-73523606;chr3:73605850-73605851;chr3:73610601-73610602;chr3:73618301-73618302;chr3:73651504-73651505		548;21
N	jcn_only_AD		chr3	-	chr3:71777775-71778224;chr3:71777775-71803794;chr3:71777775-71802613	chr3:71777775-71803365					752;15
N	intron_retention		chr3	-	chr3:141713984-141811902				chr3:141713983-141713984;chr3:141811902-141811903		304;113
K	alternative_last_exon	CUFF.769	chr3	-	chr3:125741776-125745177	chr3:125743749-125745177	chr3:125741629-125741775	chr3:125743550-125743748			319;1324
N	cassette	CUFF.743	chr3	-	chr3:49315885-49318176	chr3:49315885-49316246;chr3:49316336-49318176		chr3:49316247-49316335			17;483
N	alternative_acceptor	CUFF.778	chr3	-	chr3:141693034-141697361	chr3:141693037-141697361		chr3:141693034-141693036	chr3:141693033-141693034		303;97
N	cassette	CUFF.747	chr3	-	chr3:57569735-57582800;chr3:57563115-57582800	chr3:57569735-57570110,chr3:57563115-57570110;chr3:57570192-57582800		chr3:57570111-57570191			93;264
N	cassette	CUFF.788	chr3	+	chr3:186648624-186769036	chr3:186648624-186681572;chr3:186681715-186769036		chr3:186681573-186681714			207;364
N	jcn_only_AA	CUFF.771	chr3	+	chr3:126135352-126137297;chr3:126135352-126135614	chr3:126135352-126137300		chr3:126135615-126137297;chr3:126137298-126137300	chr3:126137297-126137298;chr3:126137300-126137301	chr3:126137301-126137368	303;40
N	jcn_only_AD	CUFF.743,CUFF.782	chr3	-	chr3:156262229-156266693;chr3:156262229-156266654	chr3:156262229-156266593		chr3:156266594-156266654;chr3:156266655-156266693	chr3:156266654-156266655;chr3:156266693-156266694		391;89
N	alternative_donor	CUFF.725	chr3	+	chr3:19989014-19992297	chr3:19989356-19992297		chr3:19989014-19989355	chr3:19989013-19989014		559;22
N	intron_retention		chr3	+	chr3:28283304-28357823				chr3:28283303-28283304;chr3:28357823-28357824		82;50
N	jcn_only_AA	CUFF.728	chr3	+	chr3:28357915-28358243;chr3:28357915-28360999	chr3:28357915-28360222		chr3:28358244-28360222;chr3:28360223-28360999	chr3:28360222-28360223;chr3:28360999-28361000		555;21
N	jcn_only_AA	CUFF.727	chr3	-	chr3:27329235-27332752	chr3:27332246-27332752					111;26
N	alternative_donor		chr3	-	chr3:141772992-141868024	chr3:141772992-141811902		chr3:141811903-141868024	chr3:141868024-141868025		678;1
N	alternative_donor	CUFF.759	chr3	+	chr3:119188106-119188666;chr3:119187854-119188666	chr3:119187954-119188666		chr3:119187854-119187953;chr3:119187954-119188105	chr3:119187853-119187854;chr3:119187953-119187954		388;154
K	jcn_only_AD	CUFF.733	chr3	-	chr3:33686396-33686835	chr3:33686396-33686773		chr3:33686774-33686835	chr3:33686835-33686836		286;252
N	alternative_acceptor	CUFF.732	chr3	-	chr3:33454320-33458249	chr3:33457593-33458249		chr3:33454320-33457592	chr3:33454319-33454320		71;2
K	intron_retention	CUFF.741	chr3	-	chr3:46963630-46963725				chr3:46963629-46963630;chr3:46963725-46963726		330;180
K	cassette	CUFF.762	chr3	-	chr3:120352438-120360435;chr3:120352176-120360435	chr3:120352438-120357301,chr3:120352176-120357301;chr3:120357429-120360435		chr3:120357302-120357428			355;251
N	cassette	CUFF.778	chr3	-	chr3:141712428-141724282;chr3:141697525-141747420;chr3:141697525-141724282	chr3:141697525-141713861,chr3:141712428-141713861;chr3:141713984-141724282,chr3:141713984-141747420		chr3:141713862-141713983			739;628
N	alternative_donor	CUFF.743	chr3	-	chr3:33467234-33482168	chr3:33467234-33481227		chr3:33481228-33482168	chr3:33482168-33482169		104;34
N	cassette	CUFF.762	chr3	-	chr3:120389380-120394638	chr3:120389380-120393747;chr3:120393837-120394638		chr3:120393748-120393836			34;267
N	jcn_only_AA	CUFF.755	chr3	-	chr3:107559252-107560951	chr3:107560867-107560951		chr3:107559252-107560866	chr3:107559251-107559252		54;51
K	alternative_first_exon	CUFF.754	chr3	+	chr3:97643256-97652537;chr3:97652352-97652537	chr3:97634581-97652537	chr3:97642975-97643255;chr3:97652346-97652351	chr3:97634454-97634580			138;11
N	alternative_acceptor	CUFF.747	chr3	-	chr3:57569760-57570110;chr3:57569735-57570110	chr3:57569788-57570110		chr3:57569735-57569759;chr3:57569760-57569787	chr3:57569734-57569735;chr3:57569759-57569760		216;11
N	jcn_only_AD		chr3	-	chr3:125032501-125033780;chr3:125032501-125042231	chr3:125032501-125042152		chr3:125033781-125042152;chr3:125042153-125042231	chr3:125042152-125042153;chr3:125042231-125042232		61;199
K	intron_retention	CUFF.741	chr3	-	chr3:46965159-46966945				chr3:46965158-46965159;chr3:46966945-46966946		686;294
N	intron_retention		chr3	-	chr3:141724387-141811902				chr3:141724386-141724387;chr3:141811902-141811903		204;105
N	jcn_only_AA	CUFF.776	chr3	-	chr3:133910819-133913925	chr3:133910828-133913925		chr3:133910819-133910827	chr3:133910818-133910819		37;43
N	jcn_only_AA	CUFF.747	chr3	-	chr3:57569760-57570110;chr3:57569788-57570110	chr3:57569735-57570110		chr3:57569735-57569759;chr3:57569760-57569787	chr3:57569734-57569735;chr3:57569759-57569760		294;65
N	intron_retention		chr3	-	chr3:49462580-49462799				chr3:49462579-49462580;chr3:49462799-49462800		40;115
N	alternative_last_exon	CUFF.727	chr3	-	chr3:27183074-27204191	chr3:27204093-27204191	chr3:27182973-27183073	chr3:27203672-27204092			49;274
K	alternative_first_exon	CUFF.743	chr3	-	chr3:49349088-49351303;chr3:49349088-49362134	chr3:49349088-49355741	chr3:49362135-49362196	chr3:49355742-49356253			137;183
K	alternative_acceptor	CUFF.744	chr3	-	chr3:49463856-49466540	chr3:49463862-49466540		chr3:49463856-49463861	chr3:49463855-49463856		67;501
N	intron_retention		chr3	-	chr3:49350047-49362134				chr3:49350046-49350047;chr3:49362134-49362135		13;111
N	jcn_only_AA	CUFF.772	chr3	-	chr3:127299007-127309252	chr3:127307004-127309252		chr3:127299007-127307003	chr3:127299006-127299007		355;184
N	jcn_only_AA	CUFF.743	chr3	-	chr3:49343322-49365118	chr3:49363279-49365118					69;394
K	alternative_first_exon	CUFF.727	chr3	-	chr3:27257372-27297786	chr3:27257372-27257860	chr3:27297787-27297862	chr3:27257861-27258037			19;156
N	jcn_only_AD	CUFF.740	chr3	-	chr3:73453547-73610601;chr3:73453547-73651504;chr3:73453547-73523605;chr3:73453547-73605850;chr3:73453547-73618301	chr3:73453547-73482789		chr3:73482790-73523605;chr3:73523606-73605850;chr3:73605851-73610601;chr3:73610602-73618301;chr3:73618302-73651504	chr3:73523605-73523606;chr3:73605850-73605851;chr3:73610601-73610602;chr3:73618301-73618302;chr3:73651504-73651505		131;438
N	alternative_acceptor	CUFF.755	chr3	-	chr3:107573542-107573976;chr3:107572807-107573976	chr3:107572902-107573976		chr3:107572807-107572901;chr3:107572902-107573541	chr3:107572806-107572807;chr3:107572901-107572902		41;228
K	intron_retention		chr3	-	chr3:141697525-141712379				chr3:141697524-141697525;chr3:141712379-141712380		497;19
N	jcn_only_AA	CUFF.771	chr3	+	chr3:126135352-126137297;chr3:126135352-126137300	chr3:126135352-126135614		chr3:126135615-126137297;chr3:126137298-126137300	chr3:126137297-126137298;chr3:126137300-126137301	chr3:126137301-126137368	318;26
N	intron_retention	CUFF.766	chr3	-	chr3:124951499-124951952				chr3:124951498-124951499;chr3:124951952-124951953		49;166
K	intron_retention	CUFF.732	chr3	-	chr3:33437773-33438536				chr3:33437772-33437773;chr3:33438536-33438537		55;52
K	intron_retention	CUFF.769	chr3	-	chr3:125741776-125745177				chr3:125741775-125741776;chr3:125745177-125745178		373;1306
K	alternative_last_exon	CUFF.733	chr3	-	chr3:33638227-33644443	chr3:33644082-33644443	chr3:33638203-33638226	chr3:33643807-33644081			16;405
N	cassette	CUFF.766	chr3	-	chr3:125042289-125093945	chr3:125042289-125050001;chr3:125050083-125093945		chr3:125050002-125050082			14;496
N	cassette	CUFF.771	chr3	+	chr3:126114893-126126014	chr3:126114893-126115332;chr3:126115523-126126014		chr3:126115333-126115522			400;149
K	intron_retention	CUFF.725	chr3	+	chr3:19992554-20017134				chr3:19992553-19992554;chr3:20017134-20017135		15;244
K	intron_retention	CUFF.724	chr3	+	chr3:13976988-13977417				chr3:13976987-13976988;chr3:13977417-13977418		242;11
N	jcn_only_AA		chr3	-	chr3:127299007-127309725	chr3:127309436-127309725		chr3:127299007-127309435	chr3:127299006-127299007		20;52
N	coord_cassette	CUFF.772	chr3	-	chr3:127294109-127294782	chr3:127294109-127294245;chr3:127294349-127294591;chr3:127294653-127294782		chr3:127294246-127294348;chr3:127294592-127294652			144;172
N	jcn_only_AD	CUFF.743,CUFF.755	chr3	-	chr3:107572902-107573976	chr3:107572902-107573500		chr3:107573501-107573976	chr3:107573976-107573977		297;26
N	jcn_only_AD	CUFF.747	chr3	-	chr3:57582951-57583365	chr3:57582951-57583058		chr3:57583059-57583365	chr3:57583365-57583366		46;38
N	alternative_acceptor	CUFF.771	chr3	+	chr3:126135352-126137297;chr3:126135352-126135614	chr3:126135352-126137300		chr3:126135615-126137297;chr3:126137298-126137300	chr3:126137297-126137298;chr3:126137300-126137301	chr3:126137301-126137368	583;40
K	jcn_only_AD	CUFF.769	chr3	-	chr3:125741776-125745235	chr3:125741776-125745177		chr3:125745178-125745235	chr3:125745235-125745236		381;373
N	alternative_acceptor		chr3	+	chr3:126135352-126137300;chr3:126135352-126135614	chr3:126135352-126137297		chr3:126135615-126137297;chr3:126137298-126137300	chr3:126137297-126137298;chr3:126137300-126137301	chr3:126137301-126137368	286;337
K	intron_retention	CUFF.724	chr3	+	chr3:13978186-13978482				chr3:13978185-13978186;chr3:13978482-13978483		313;11
K	alternative_first_exon	CUFF.756	chr3	-	chr3:108475436-108475905	chr3:108475436-108475666	chr3:108475906-108476329	chr3:108475667-108475862			171;276
N	jcn_only_AA	CUFF.747	chr3	-	chr3:57569760-57570110;chr3:57569735-57570110	chr3:57569788-57570110		chr3:57569735-57569759;chr3:57569760-57569787	chr3:57569734-57569735;chr3:57569759-57569760		338;22
K	cassette	CUFF.755	chr3	-	chr3:107576050-107591814	chr3:107576050-107586157;chr3:107586273-107591814		chr3:107586158-107586272			561;335
K	alternative_first_exon	CUFF.727,CUFF.737	chr3	-	chr3:38061844-38065827;chr3:38061844-38070996	chr3:38061844-38065646	chr3:38070997-38071348	chr3:38065647-38066262			191;257
N	jcn_only_AD	CUFF.776,CUFF.778	chr3	-	chr3:141820684-141868024	chr3:141820684-141844990		chr3:141844991-141868024	chr3:141868024-141868025		801;141
K	coord_cassette	CUFF.755	chr3	-	chr3:107567966-107572719	chr3:107567966-107568669;chr3:107568819-107569143;chr3:107569199-107572719		chr3:107568670-107568818;chr3:107569144-107569198			301;56
K	intron_retention	CUFF.789	chr3	-	chr3:193560545-193560866				chr3:193560544-193560545;chr3:193560866-193560867		81;21
K	alternative_first_exon	CUFF.743,CUFF.782	chr3	-	chr3:49373030-49377916	chr3:49373030-49377356	chr3:49377917-49378243	chr3:49377357-49377554			161;183
K	jcn_only_AD	CUFF.768	chr3	+	chr3:125639749-125643808	chr3:125642984-125643808					162;1051
N	coord_cassette	CUFF.778	chr3	-	chr3:141697525-141724282	chr3:141697525-141712379;chr3:141712428-141713861;chr3:141713984-141724282		chr3:141712380-141712427;chr3:141713862-141713983			679;470
N	jcn_only_AA	CUFF.727	chr3	-	chr3:27297863-27326092	chr3:27320465-27326092		chr3:27297863-27320464	chr3:27297862-27297863		381;25
N	jcn_only_AA	CUFF.743	chr3	-	chr3:49349088-49362134;chr3:49348171-49362134;chr3:49350047-49362134	chr3:49354912-49362134					165;64
N	intron_retention		chr3	+	chr3:28358351-28360999				chr3:28358350-28358351;chr3:28360999-28361000		36;240
K	intron_retention	CUFF.745	chr3	+	chr3:51748138-51749077				chr3:51748137-51748138;chr3:51749077-51749078		68;23
N	alternative_donor		chr3	-	chr3:27233734-27236027;chr3:27233734-27235551	chr3:27233734-27243000		chr3:27235552-27236027;chr3:27236028-27243000	chr3:27236027-27236028;chr3:27243000-27243001		3;291
K	intron_retention	CUFF.739	chr3	+	chr3:38519784-38519865				chr3:38519783-38519784;chr3:38519865-38519866		11;242
K	jcn_only_AA	CUFF.776	chr3	-	chr3:133894884-133901845	chr3:133896918-133901845					223;106
N	jcn_only_AD	CUFF.759	chr3	+	chr3:119187954-119188666;chr3:119187854-119188666	chr3:119188106-119188666		chr3:119187854-119187953;chr3:119187954-119188105	chr3:119187853-119187854;chr3:119187953-119187954		429;213
K	jcn_only_AA	CUFF.733	chr3	-	chr3:33673864-33686248	chr3:33673867-33686248		chr3:33673864-33673866	chr3:33673863-33673864		907;225
K	cassette	CUFF.733	chr3	-	chr3:33614847-33617660	chr3:33614847-33615964;chr3:33615989-33617660		chr3:33615965-33615988			149;427
N	jcn_only_AD	CUFF.751	chr3	-	chr3:73453547-73482789;chr3:73453547-73610601;chr3:73453547-73651504;chr3:73453547-73523605;chr3:73453547-73605850	chr3:73453547-73618301		chr3:73482790-73523605;chr3:73523606-73605850;chr3:73605851-73610601;chr3:73610602-73618301;chr3:73618302-73651504	chr3:73523605-73523606;chr3:73605850-73605851;chr3:73610601-73610602;chr3:73618301-73618302;chr3:73651504-73651505		537;32
K	intron_retention		chr3	+	chr3:28283304-28304781				chr3:28283303-28283304;chr3:28304781-28304782		124;61
K	alternative_first_exon	CUFF.769	chr3	-	chr3:125787090-125789043,chr3:125787090-125791995,chr3:125787090-125802718,chr3:125787090-125802771,chr3:125787090-125802896;chr3:125787090-125802935	chr3:125787090-125797816	chr3:125802936-125803147	chr3:125797817-125797913			1662;29
N	jcn_only_AA	CUFF.743	chr3	-	chr3:49354912-49362134;chr3:49349088-49362134;chr3:49350047-49362134	chr3:49348171-49362134					223;6
N	intron_retention		chr3	-	chr3:125725472-125725559				chr3:125725471-125725472;chr3:125725559-125725560		15;146
N	jcn_only_AD	CUFF.759	chr3	+	chr3:119188106-119188666;chr3:119187854-119188666	chr3:119187954-119188666		chr3:119187854-119187953;chr3:119187954-119188105	chr3:119187853-119187854;chr3:119187953-119187954		449;193
N	cassette	CUFF.747	chr3	-	chr3:57563115-57570110;chr3:57563115-57582800	chr3:57563115-57569624;chr3:57569735-57570110,chr3:57569735-57582800		chr3:57569625-57569734			107;199
N	jcn_only_AA		chr3	-	chr3:73453547-73651504	chr3:73457412-73651504		chr3:73453547-73457411	chr3:73453546-73453547		5;31
N	coord_cassette	CUFF.766	chr3	-	chr3:125042289-125093945	chr3:125042289-125050001;chr3:125050083-125057665;chr3:125057756-125093945		chr3:125050002-125050082;chr3:125057666-125057755			14;21
N	alternative_acceptor	CUFF.732	chr3	-	chr3:33451080-33453072	chr3:33451094-33453072		chr3:33451080-33451093	chr3:33451079-33451080		41;61
K	alternative_donor	CUFF.733	chr3	-	chr3:33686396-33686835	chr3:33686396-33686773		chr3:33686774-33686835	chr3:33686835-33686836		286;153
N	intron_retention		chr3	-	chr3:107560867-107560951				chr3:107560866-107560867;chr3:107560951-107560952		51;151
K	intron_retention	CUFF.725	chr3	+	chr3:19992554-20017092				chr3:19992553-19992554;chr3:20017092-20017093		132;116
N	alternative_acceptor		chr3	-	chr3:73453547-73651504	chr3:73457412-73651504		chr3:73453547-73457411	chr3:73453546-73453547		5;10
N	coord_cassette	CUFF.750	chr3	-	chr3:71743093-71759562	chr3:71743093-71745610;chr3:71745672-71748764;chr3:71748860-71759562		chr3:71745611-71745671;chr3:71748765-71748859			30;872
N	jcn_only_AD	CUFF.727,CUFF.772	chr3	-	chr3:27233734-27243000;chr3:27233734-27236027	chr3:27233734-27235551		chr3:27235552-27236027;chr3:27236028-27243000	chr3:27236027-27236028;chr3:27243000-27243001		319;18
N	intron_retention		chr3	-	chr3:38051545-38051621				chr3:38051544-38051545;chr3:38051621-38051622		192;97
N	mutually_exclusive	CUFF.778	chr3	-	chr3:141712428-141724282,chr3:141724387-141811902	chr3:141712428-141713861,chr3:141713984-141811902	chr3:141724283-141724386	chr3:141713862-141713983			10;200
N	intron_retention	CUFF.755	chr3	-	chr3:107574077-107574159				chr3:107574076-107574077;chr3:107574159-107574160		170;40
N	jcn_only_AA	CUFF.733	chr3	-	chr3:33686396-33700998	chr3:33700502-33700998					48;31
N	jcn_only_AD	CUFF.732,CUFF.737	chr3	-	chr3:33454320-33458249	chr3:33454320-33457497		chr3:33457498-33458249	chr3:33458249-33458250		71;16
K	alternative_first_exon	CUFF.727,CUFF.776	chr3	-	chr3:133894884-133901845	chr3:133894884-133896784	chr3:133901846-133902003	chr3:133896785-133899850			129;229
K	intron_retention	CUFF.776	chr3	-	chr3:133914027-133921573				chr3:133914026-133914027;chr3:133921573-133921574		37;26
K	cassette	CUFF.788	chr3	+	chr3:186648624-186681572	chr3:186648624-186660135;chr3:186660216-186681572		chr3:186660136-186660215			658;125
N	jcn_only_AA	CUFF.732	chr3	-	chr3:33451080-33453072	chr3:33451094-33453072		chr3:33451080-33451093	chr3:33451079-33451080		41;116
K	coord_cassette	CUFF.755	chr3	-	chr3:107576050-107591814	chr3:107576050-107585498;chr3:107585601-107586157;chr3:107586425-107591814		chr3:107585499-107585600;chr3:107586158-107586424			561;28
N	cassette	CUFF.743	chr3	-	chr3:49365250-49377356	chr3:49365250-49372901;chr3:49373030-49377356		chr3:49372902-49373029			61;267
K	cassette	CUFF.755	chr3	-	chr3:107574077-107575926	chr3:107574077-107574854;chr3:107575172-107575926		chr3:107574855-107575171			692;236
K	intron_retention	CUFF.741	chr3	-	chr3:46963803-46964818				chr3:46963802-46963803;chr3:46964818-46964819		374;191
N	alternative_donor		chr3	-	chr3:125032501-125033780;chr3:125032501-125042231	chr3:125032501-125042152		chr3:125033781-125042152;chr3:125042153-125042231	chr3:125042152-125042153;chr3:125042231-125042232		47;110
N	cassette	CUFF.769	chr3	-	chr3:125745323-125769740	chr3:125745323-125752449;chr3:125752522-125769740		chr3:125752450-125752521			41;2026
N	jcn_only_AA	CUFF.727	chr3	-	chr3:27394411-27410715;chr3:27409054-27410715	chr3:27405336-27410715		chr3:27394411-27405335;chr3:27405336-27409053	chr3:27394410-27394411;chr3:27405335-27405336		91;4
N	jcn_only_AD	CUFF.728	chr3	+	chr3:28360371-28360999;chr3:28358351-28360999	chr3:28357915-28360999		chr3:28357915-28358350;chr3:28358351-28360370	chr3:28357914-28357915;chr3:28358350-28358351		59;501
N	alternative_acceptor	CUFF.728	chr3	+	chr3:28357915-28358243;chr3:28357915-28360999	chr3:28357915-28360222		chr3:28358244-28360222;chr3:28360223-28360999	chr3:28360222-28360223;chr3:28360999-28361000		825;124
K	coord_cassette	CUFF.781	chr3	-	chr3:155520381-155523927	chr3:155520381-155521839;chr3:155521963-155523385;chr3:155523513-155523927		chr3:155521840-155521962;chr3:155523386-155523512			846;143
N	alternative_acceptor		chr3	-	chr3:127299007-127309725	chr3:127309436-127309725		chr3:127299007-127309435	chr3:127299006-127299007		20;10
K	intron_retention	CUFF.744	chr3	-	chr3:49462487-49462799				chr3:49462486-49462487;chr3:49462799-49462800		937;136
K	intron_retention	CUFF.732	chr3	-	chr3:33453180-33454213				chr3:33453179-33453180;chr3:33454213-33454214		149;21
N	cassette	CUFF.778	chr3	-	chr3:141697525-141724282;chr3:141697525-141713861	chr3:141697525-141712379;chr3:141712428-141724282,chr3:141712428-141713861		chr3:141712380-141712427			701;483
K	alternative_donor	CUFF.769	chr3	-	chr3:125741776-125745235	chr3:125741776-125745177		chr3:125745178-125745235	chr3:125745235-125745236		381;1533
N	intron_retention		chr3	-	chr3:127294349-127294782				chr3:127294348-127294349;chr3:127294782-127294783		35;134
K	alternative_last_exon	CUFF.745,CUFF.752	chr3	+	chr3:75500554-75505767	chr3:75500554-75501682	chr3:75505768-75506637	chr3:75501683-75501902			36;686
K	intron_retention	CUFF.759	chr3	+	chr3:119207835-119209397				chr3:119207834-119207835;chr3:119209397-119209398		124;9
K	intron_retention	CUFF.762	chr3	-	chr3:120365214-120365819				chr3:120365213-120365214;chr3:120365819-120365820		174;19
N	jcn_only_AD	CUFF.751	chr3	-	chr3:73453547-73482789;chr3:73453547-73651504;chr3:73453547-73523605;chr3:73453547-73605850;chr3:73453547-73618301	chr3:73453547-73610601		chr3:73482790-73523605;chr3:73523606-73605850;chr3:73605851-73610601;chr3:73610602-73618301;chr3:73618302-73651504	chr3:73523605-73523606;chr3:73605850-73605851;chr3:73610601-73610602;chr3:73618301-73618302;chr3:73651504-73651505		555;14
N	jcn_only_AA	CUFF.762	chr3	-	chr3:120371494-120389273	chr3:120371499-120389273		chr3:120371494-120371498	chr3:120371493-120371494		71;131
K	alternative_acceptor	CUFF.762	chr3	-	chr3:120352176-120357301	chr3:120352438-120357301		chr3:120352176-120352437	chr3:120352175-120352176		244;151
N	alternative_donor	CUFF.743,CUFF.782	chr3	-	chr3:156262229-156266693;chr3:156262229-156266654	chr3:156262229-156266593		chr3:156266594-156266654;chr3:156266655-156266693	chr3:156266654-156266655;chr3:156266693-156266694		390;63
K	alternative_acceptor	CUFF.790	chr3	-	chr3:194063432-194071970	chr3:194063435-194071970		chr3:194063432-194063434	chr3:194063431-194063432		59;10
N	jcn_only_AA		chr3	+	chr3:28333446-28357823	chr3:28333446-28334226		chr3:28334227-28357823	chr3:28357823-28357824		18;19
K	cassette	CUFF.788	chr3	+	chr3:186756662-186760441	chr3:186756662-186759704;chr3:186759755-186760441		chr3:186759705-186759754			745;486
K	alternative_last_exon	CUFF.773,CUFF.775	chr3	+	chr3:133407209-133418748;chr3:133407209-133410566	chr3:133407209-133419725	chr3:133418749-133419168;chr3:133410567-133410675	chr3:133419726-133420037			179;118
N	alternative_first_exon	CUFF.769	chr3	-	chr3:27329235-27332752	chr3:27329235-27332107	chr3:27332753-27333077	chr3:27332108-27332266			81;218
K	intron_retention	CUFF.733	chr3	-	chr3:33644082-33644443				chr3:33644081-33644082;chr3:33644443-33644444		293;85
K	alternative_donor	CUFF.582	chr2	-	chr2:25190163-25194424	chr2:25190163-25194284		chr2:25194285-25194424	chr2:25194424-25194425		171;281
N	alternative_donor	CUFF.665	chr2	+	chr2:242610821-242611605;chr2:242610841-242611605	chr2:242610857-242611605		chr2:242610821-242610840;chr2:242610841-242610856	chr2:242610820-242610821;chr2:242610840-242610841		308;249
N	intron_retention		chr2	-	chr2:86397965-86400772				chr2:86397964-86397965;chr2:86400772-86400773		12;116
N	alternative_donor	CUFF.601	chr2	-	chr2:69870407-69901154;chr2:69870407-69870706;chr2:69870407-69870923	chr2:69870407-69870874		chr2:69870707-69870874;chr2:69870875-69870923;chr2:69870924-69901154	chr2:69870874-69870875;chr2:69870923-69870924;chr2:69901154-69901155		32;1
N	alternative_acceptor	CUFF.637	chr2	-	chr2:175216454-175243650;chr2:175234743-175243650	chr2:175223265-175243650		chr2:175216454-175223264;chr2:175223265-175234742	chr2:175216453-175216454;chr2:175223264-175223265		19;47
K	alternative_first_exon	CUFF.572,CUFF.647	chr2	-	chr2:676239-677288	chr2:676239-676573	chr2:677289-677522	chr2:676574-676858			14;95
N	jcn_only_AA		chr2	+	chr2:220095128-220096981	chr2:220095128-220096649					96;232
K	alternative_acceptor	CUFF.571	chr2	-	chr2:280150-283110	chr2:280153-283110		chr2:280150-280152	chr2:280149-280150		1317;200
N	jcn_only_AD	CUFF.591	chr2	+	chr2:38156080-38156404;chr2:38152569-38156404	chr2:38150511-38156404		chr2:38150511-38152568;chr2:38152569-38156079	chr2:38150510-38150511;chr2:38152568-38152569		272;29
N	jcn_only_AD		chr2	-	chr2:73227617-73228657	chr2:73227617-73228653		chr2:73228654-73228657	chr2:73228657-73228658		375;360
K	alternative_acceptor	CUFF.620	chr2	+	chr2:109102365-109102966	chr2:109102365-109102890		chr2:109102891-109102966	chr2:109102966-109102967		14;703
K	intron_retention	CUFF.612	chr2	-	chr2:88874596-88874878				chr2:88874595-88874596;chr2:88874878-88874879		43;143
N	alternative_acceptor	CUFF.599	chr2	-	chr2:68358578-68361833	chr2:68359138-68361833		chr2:68358578-68359137	chr2:68358577-68358578		254;98
N	alternative_donor	CUFF.654	chr2	+	chr2:220095073-220096649;chr2:220094623-220096649	chr2:220095128-220096649		chr2:220094623-220095072;chr2:220095073-220095127	chr2:220094622-220094623;chr2:220095072-220095073		170;124
N	cassette	CUFF.664	chr2	-	chr2:242440212-242447420	chr2:242440212-242440942;chr2:242441124-242447420		chr2:242440943-242441123			125;701
N	alternative_acceptor		chr2	+	chr2:231934883-231937046	chr2:231934883-231936902		chr2:231936903-231937046	chr2:231937046-231937047		133;189
K	intron_retention	CUFF.664	chr2	-	chr2:242432956-242434257				chr2:242432955-242432956;chr2:242434257-242434258		65;54
N	alternative_acceptor	CUFF.588	chr2	+	chr2:33477912-33482434;chr2:33477912-33482350	chr2:33477912-33482509		chr2:33482351-33482434;chr2:33482435-33482509	chr2:33482434-33482435;chr2:33482509-33482510		113;40
N	alternative_donor	CUFF.583	chr2	-	chr2:27708371-27712481	chr2:27708371-27709025		chr2:27709026-27712481	chr2:27712481-27712482		854;1
N	jcn_only_AA	CUFF.662	chr2	+	chr2:241404164-241404272	chr2:241404164-241404251		chr2:241404252-241404272	chr2:241404272-241404273		325;20
N	alternative_donor	CUFF.595	chr2	+	chr2:48898820-49003418;chr2:48996261-49003418	chr2:48996214-49003418		chr2:48898820-48996213;chr2:48996214-48996260	chr2:48898819-48898820;chr2:48996213-48996214		180;0
N	jcn_only_AD	CUFF.619	chr2	+	chr2:101565943-101584742	chr2:101582229-101584742					21;126
N	jcn_only_AD	CUFF.588	chr2	+	chr2:33335819-33359859	chr2:33359573-33359859		chr2:33335819-33359572	chr2:33335818-33335819		2;25
K	cassette	CUFF.605	chr2	-	chr2:73247394-73250316	chr2:73247394-73249650;chr2:73249706-73250316		chr2:73249651-73249705			554;436
K	intron_retention	CUFF.665	chr2	+	chr2:242577140-242590424				chr2:242577139-242577140;chr2:242590424-242590425		1585;29
K	alternative_acceptor	CUFF.610	chr2	-	chr2:86397965-86398330	chr2:86397968-86398330		chr2:86397965-86397967	chr2:86397964-86397965		47;477
K	cassette	CUFF.630	chr2	+	chr2:160602449-160608912	chr2:160602449-160604315;chr2:160605415-160608912		chr2:160604316-160605414			135;108
N	jcn_only_AA	CUFF.637	chr2	-	chr2:175223265-175243650;chr2:175216454-175243650	chr2:175234743-175243650		chr2:175216454-175223264;chr2:175223265-175234742	chr2:175216453-175216454;chr2:175223264-175223265		71;13
N	alternative_acceptor	CUFF.653	chr2	+	chr2:219457431-219458250;chr2:219457431-219458830	chr2:219457431-219458891		chr2:219458251-219458830;chr2:219458831-219458891	chr2:219458830-219458831;chr2:219458891-219458892		103;246
N	jcn_only_AA	CUFF.596	chr2	-	chr2:61761039-61764696	chr2:61761814-61764696		chr2:61761039-61761813	chr2:61761038-61761039		77;71
N	alternative_acceptor	CUFF.620	chr2	+	chr2:109068923-109085435	chr2:109068923-109079043		chr2:109079044-109085435	chr2:109085435-109085436		289;6
N	alternative_donor	CUFF.649	chr2	+	chr2:207630472-207631367;chr2:207630243-207631367;chr2:207630487-207631367	chr2:207630379-207631367		chr2:207630243-207630378;chr2:207630379-207630471;chr2:207630472-207630486	chr2:207630242-207630243;chr2:207630378-207630379;chr2:207630471-207630472		81;21
N	jcn_only_AA		chr2	+	chr2:680152-696540	chr2:680152-681255		chr2:681256-696540	chr2:696540-696541		54;77
N	cassette	CUFF.605	chr2	-	chr2:73195663-73215386	chr2:73195663-73198698;chr2:73198815-73215386		chr2:73198699-73198814			21;472
K	intron_retention	CUFF.660	chr2	-	chr2:235404481-235404655				chr2:235404480-235404481;chr2:235404655-235404656		69;39
N	alternative_acceptor	CUFF.664	chr2	-	chr2:242440493-242440892;chr2:242440263-242440892	chr2:242440335-242440892		chr2:242440263-242440334;chr2:242440335-242440492	chr2:242440262-242440263;chr2:242440334-242440335		271;41
N	alternative_donor	CUFF.665	chr2	+	chr2:242610857-242611605;chr2:242610841-242611605	chr2:242610821-242611605		chr2:242610821-242610840;chr2:242610841-242610856	chr2:242610820-242610821;chr2:242610840-242610841		321;236
K	intron_retention	CUFF.664	chr2	-	chr2:242438590-242438671				chr2:242438589-242438590;chr2:242438671-242438672		1028;66
N	jcn_only_AD	CUFF.654	chr2	+	chr2:220094623-220094949;chr2:220094703-220094949	chr2:220094681-220094949		chr2:220094623-220094680;chr2:220094681-220094702	chr2:220094622-220094623;chr2:220094680-220094681		444;24
N	jcn_only_AD	CUFF.649	chr2	+	chr2:207630472-207631367;chr2:207630379-207631367;chr2:207630487-207631367	chr2:207630243-207631367		chr2:207630243-207630378;chr2:207630379-207630471;chr2:207630472-207630486	chr2:207630242-207630243;chr2:207630378-207630379;chr2:207630471-207630472		123;35
K	intron_retention	CUFF.620	chr2	+	chr2:109089356-109091990				chr2:109089355-109089356;chr2:109091990-109091991		8;140
N	alternative_acceptor	CUFF.637	chr2	-	chr2:175223265-175243650;chr2:175234743-175243650	chr2:175216454-175243650		chr2:175216454-175223264;chr2:175223265-175234742	chr2:175216453-175216454;chr2:175223264-175223265		51;15
N	alternative_acceptor	CUFF.574,CUFF.588	chr2	+	chr2:1251216-1263141	chr2:1251216-1260176		chr2:1260177-1263141	chr2:1263141-1263142		278;8
N	alternative_donor	CUFF.595	chr2	+	chr2:48898820-49003418;chr2:48996214-49003418	chr2:48996261-49003418		chr2:48898820-48996213;chr2:48996214-48996260	chr2:48898819-48898820;chr2:48996213-48996214		180;0
N	alternative_acceptor	CUFF.574	chr2	+	chr2:1243549-1251098	chr2:1243549-1246509		chr2:1246510-1251098	chr2:1251098-1251099		291;6
N	mutually_exclusive	CUFF.647	chr2	-	chr2:204326649-204341798,chr2:204341880-204354306	chr2:204326649-204334961,chr2:204335037-204354306	chr2:204341799-204341879	chr2:204334962-204335036			135;32
N	alternative_donor	CUFF.654	chr2	+	chr2:220094623-220094949;chr2:220094703-220094949	chr2:220094681-220094949		chr2:220094623-220094680;chr2:220094681-220094702	chr2:220094622-220094623;chr2:220094680-220094681		438;18
N	coord_cassette	CUFF.605	chr2	-	chr2:73188378-73215386	chr2:73188378-73194365;chr2:73194453-73195576;chr2:73195663-73215386		chr2:73194366-73194452;chr2:73195577-73195662			48;70
N	intron_retention		chr2	-	chr2:110882901-110883213				chr2:110882900-110882901;chr2:110883213-110883214		29;44
K	alternative_acceptor	CUFF.652	chr2	+	chr2:219222458-219222759	chr2:219222458-219222708		chr2:219222709-219222759	chr2:219222759-219222760		367;50
N	coord_cassette	CUFF.619	chr2	+	chr2:101598840-101609808	chr2:101598840-101604540;chr2:101604739-101606717;chr2:101606909-101607241;chr2:101607335-101609808		chr2:101604541-101604738;chr2:101606718-101606908;chr2:101607242-101607334			35;285
N	alternative_donor	CUFF.574	chr2	+	chr2:1320148-1371114	chr2:1357637-1371114		chr2:1320148-1357636	chr2:1320147-1320148		388;0
N	alternative_donor	CUFF.594,CUFF.650	chr2	-	chr2:46842325-46844108	chr2:46842325-46843725		chr2:46843726-46844108	chr2:46844108-46844109		723;54
K	intron_retention	CUFF.638	chr2	-	chr2:175869809-175869933				chr2:175869808-175869809;chr2:175869933-175869934		120;85
N	jcn_only_AD	CUFF.654	chr2	+	chr2:220094681-220094949;chr2:220094623-220094949	chr2:220094703-220094949		chr2:220094623-220094680;chr2:220094681-220094702	chr2:220094622-220094623;chr2:220094680-220094681		406;62
K	intron_retention	CUFF.620	chr2	+	chr2:109111942-109113425				chr2:109111941-109111942;chr2:109113425-109113426		23;6
K	intron_retention	CUFF.662	chr2	+	chr2:241402930-241404032				chr2:241402929-241402930;chr2:241404032-241404033		280;33
K	alternative_first_exon	CUFF.641,CUFF.647	chr2	-	chr2:204360077-204399833	chr2:204360077-204398087	chr2:204399834-204400152	chr2:204398088-204398186			443;65
N	mutually_exclusive	CUFF.664	chr2	-	chr2:242440212-242447420,chr2:242447551-242447857	chr2:242440212-242440892,chr2:242441124-242447857	chr2:242447421-242447550	chr2:242440893-242441123			89;36
K	intron_retention	CUFF.575	chr2	+	chr2:3464108-3469367				chr2:3464107-3464108;chr2:3469367-3469368		761;97
N	cassette	CUFF.567	chr2	-	chr2:262787-264781;chr2:253116-264083;chr2:253116-264781	chr2:262787-263210,chr2:253116-263210;chr2:263373-264781,chr2:263373-264083		chr2:263211-263372			643;276
K	alternative_first_exon	CUFF.593	chr2	-	chr2:42180449-42181155	chr2:42180449-42180866	chr2:42181156-42181482	chr2:42180867-42180943			30;9
K	alternative_first_exon	CUFF.587	chr2	-	chr2:31428366-31449393	chr2:31428366-31440321	chr2:31449394-31449517	chr2:31440322-31440493			2;41
N	alternative_donor	CUFF.595	chr2	+	chr2:48996261-49003418;chr2:48996214-49003418	chr2:48898820-49003418		chr2:48898820-48996213;chr2:48996214-48996260	chr2:48898819-48898820;chr2:48996213-48996214		0;180
K	intron_retention	CUFF.649	chr2	+	chr2:207653628-207655295				chr2:207653627-207653628;chr2:207655295-207655296		266;13
N	jcn_only_AD	CUFF.595	chr2	+	chr2:48996261-49003418;chr2:48996214-49003418	chr2:48898820-49003418		chr2:48898820-48996213;chr2:48996214-48996260	chr2:48898819-48898820;chr2:48996213-48996214		106;180
N	coord_cassette	CUFF.567	chr2	-	chr2:253116-264781	chr2:253116-263210;chr2:263373-263563;chr2:263763-264781		chr2:263211-263372;chr2:263564-263762			181;368
N	intron_retention		chr2	+	chr2:3469467-3482616				chr2:3469466-3469467;chr2:3482616-3482617		101;38
K	intron_retention	CUFF.579	chr2	-	chr2:11593849-11597304				chr2:11593848-11593849;chr2:11597304-11597305		6;207
N	alternative_acceptor	CUFF.638	chr2	-	chr2:175689247-175711607	chr2:175702065-175711607		chr2:175689247-175702064	chr2:175689246-175689247		566;2
K	intron_retention	CUFF.664	chr2	-	chr2:242435950-242437030				chr2:242435949-242435950;chr2:242437030-242437031		726;28
N	jcn_only_AD	CUFF.575	chr2	+	chr2:3464108-3469367	chr2:3466843-3469367		chr2:3464108-3466842	chr2:3464107-3464108		761;98
K	cassette	CUFF.642	chr2	-	chr2:177497854-177502189	chr2:177497854-177498092;chr2:177498469-177502189		chr2:177498093-177498468			44;597
N	jcn_only_AA	CUFF.631	chr2	-	chr2:166732743-166737188	chr2:166736478-166737188		chr2:166732743-166736477	chr2:166732742-166732743		73;38
N	alternative_donor	CUFF.664	chr2	-	chr2:242435950-242436714;chr2:242435950-242437030	chr2:242435950-242436596		chr2:242436597-242436714;chr2:242436715-242437030	chr2:242436714-242436715;chr2:242437030-242437031		743;57
N	cassette	CUFF.664	chr2	-	chr2:242440212-242447420	chr2:242440212-242440892;chr2:242441215-242447420		chr2:242440893-242441214			125;832
K	cassette	CUFF.580	chr2	+	chr2:16573595-16613772	chr2:16573595-16612998;chr2:16613076-16613772		chr2:16612999-16613075			1088;109
N	cassette	CUFF.664	chr2	-	chr2:242439697-242447420	chr2:242439697-242440154;chr2:242440212-242447420		chr2:242440155-242440211			153;695
K	alternative_first_exon	CUFF.583,CUFF.624	chr2	-	chr2:27676381-27676848	chr2:27676381-27676496	chr2:27676849-27677029	chr2:27676497-27676726			53;1645
N	alternative_acceptor	CUFF.586	chr2	+	chr2:27724097-27726380	chr2:27724097-27724556		chr2:27724557-27726380	chr2:27726380-27726381		231;7
K	intron_retention		chr2	-	chr2:110920713-110922096				chr2:110920712-110920713;chr2:110922096-110922097		6;21
N	alternative_acceptor	CUFF.637	chr2	-	chr2:175223265-175243650;chr2:175216454-175243650	chr2:175234743-175243650		chr2:175216454-175223264;chr2:175223265-175234742	chr2:175216453-175216454;chr2:175223264-175223265		62;4
N	alternative_acceptor	CUFF.635,CUFF.657	chr2	+	chr2:171400499-171508137	chr2:171400499-171503418		chr2:171503419-171508137	chr2:171508137-171508138		85;0
K	alternative_last_exon	CUFF.647	chr2	-	chr2:204306137-204309590;chr2:204259813-204309590	chr2:204306804-204309590	chr2:204258971-204259812	chr2:204304069-204306803			78;170
K	cassette	CUFF.657	chr2	+	chr2:232026224-232029913	chr2:232026224-232028348;chr2:232028442-232029913		chr2:232028349-232028441			422;113
N	intron_retention	CUFF.594	chr2	-	chr2:46842325-46843725				chr2:46842324-46842325;chr2:46843725-46843726		36;6
N	alternative_donor	CUFF.630	chr2	+	chr2:160615847-160619390	chr2:160615870-160619390		chr2:160615847-160615869	chr2:160615846-160615847		191;14
N	cassette	CUFF.567	chr2	-	chr2:253116-263210;chr2:253116-262630	chr2:253116-260084;chr2:260703-262630,chr2:260703-263210		chr2:260085-260702			227;722
N	jcn_only_AD		chr2	-	chr2:287893-288552	chr2:287893-288012		chr2:288013-288552	chr2:288552-288553		22;79
N	jcn_only_AD	CUFF.595	chr2	+	chr2:48898820-49003418;chr2:48996214-49003418	chr2:48996261-49003418		chr2:48898820-48996213;chr2:48996214-48996260	chr2:48898819-48898820;chr2:48996213-48996214		219;68
N	alternative_donor	CUFF.620	chr2	+	chr2:109068923-109085435	chr2:109079142-109085435		chr2:109068923-109079141	chr2:109068922-109068923		289;6
N	jcn_only_AA	CUFF.567	chr2	-	chr2:253116-260084	chr2:256691-260084		chr2:253116-256690	chr2:253115-253116		69;22
K	intron_retention	CUFF.664	chr2	-	chr2:242438830-242439587				chr2:242438829-242438830;chr2:242439587-242439588		1365;278
N	intron_retention		chr2	+	chr2:242590527-242592926				chr2:242590526-242590527;chr2:242592926-242592927		27;61
K	intron_retention	CUFF.616	chr2	+	chr2:99225475-99226105				chr2:99225474-99225475;chr2:99226105-99226106		21;11
N	cassette	CUFF.574	chr2	+	chr2:1204917-1243509	chr2:1204917-1241659;chr2:1241790-1243509		chr2:1241660-1241789			76;227
K	intron_retention	CUFF.654	chr2	+	chr2:220099011-220099547				chr2:220099010-220099011;chr2:220099547-220099548		76;224
K	intron_retention	CUFF.654	chr2	+	chr2:220096763-220096981				chr2:220096762-220096763;chr2:220096981-220096982		758;44
K	intron_retention	CUFF.609	chr2	-	chr2:79362890-79363090				chr2:79362889-79362890;chr2:79363090-79363091		139;116
K	alternative_first_exon	CUFF.575	chr2	+	chr2:3392442-3405547	chr2:3393551-3405547	chr2:3391391-3392441	chr2:3393377-3393550			196;403
N	jcn_only_AD	CUFF.636	chr2	-	chr2:174072387-174136238	chr2:174072387-174074374		chr2:174074375-174136238	chr2:174136238-174136239		461;53
N	alternative_acceptor	CUFF.636	chr2	-	chr2:174057785-174072274	chr2:174063553-174072274		chr2:174057785-174063552	chr2:174057784-174057785		587;20
N	cassette	CUFF.631	chr2	-	chr2:166714915-166727306	chr2:166714915-166719453;chr2:166719576-166727306		chr2:166719454-166719575			78;215
K	cassette	CUFF.635	chr2	+	chr2:171356319-171371430	chr2:171356319-171358294;chr2:171358376-171371430		chr2:171358295-171358375			14;58
N	jcn_only_AA	CUFF.644,CUFF.653	chr2	+	chr2:191362446-191364740	chr2:191362446-191364557		chr2:191364558-191364740	chr2:191364740-191364741		1166;11
N	alternative_acceptor	CUFF.638	chr2	-	chr2:175689247-175742567	chr2:175740594-175742567		chr2:175689247-175740593	chr2:175689246-175689247		55;3
N	jcn_only_AA	CUFF.573,CUFF.588	chr2	+	chr2:33477912-33482434;chr2:33477912-33482509	chr2:33477912-33482350		chr2:33482351-33482434;chr2:33482435-33482509	chr2:33482434-33482435;chr2:33482509-33482510		130;77
K	intron_retention	CUFF.596	chr2	-	chr2:61722749-61724013				chr2:61722748-61722749;chr2:61724013-61724014		89;15
N	jcn_only_AA	CUFF.637	chr2	-	chr2:175223265-175243650;chr2:175234743-175243650	chr2:175216454-175243650		chr2:175216454-175223264;chr2:175223265-175234742	chr2:175216453-175216454;chr2:175223264-175223265		69;15
N	intron_retention		chr2	-	chr2:61752469-61752626				chr2:61752468-61752469;chr2:61752626-61752627		2;285
K	intron_retention	CUFF.654	chr2	+	chr2:220100035-220100195				chr2:220100034-220100035;chr2:220100195-220100196		124;158
K	intron_retention	CUFF.567	chr2	-	chr2:218109-218745				chr2:218108-218109;chr2:218745-218746		27;679
K	intron_retention	CUFF.649	chr2	+	chr2:207655411-207656406				chr2:207655410-207655411;chr2:207656406-207656407		215;58
N	alternative_donor	CUFF.644	chr2	+	chr2:191362446-191364740	chr2:191364583-191364740		chr2:191362446-191364582	chr2:191362445-191362446		1166;10
N	cassette	CUFF.647	chr2	-	chr2:204326649-204341798;chr2:204326649-204354306	chr2:204326649-204334961;chr2:204335037-204354306,chr2:204335037-204341798		chr2:204334962-204335036			216;177
N	alternative_last_exon	CUFF.654	chr2	+	chr2:220094623-220096649;chr2:220094623-220094949	chr2:220094623-220097211	chr2:220096650-220096762;chr2:220094950-220095127	chr2:220097212-220097743			359;101
N	intron_retention		chr2	-	chr2:253116-264083				chr2:253115-253116;chr2:264083-264084		284;36
N	jcn_only_AA	CUFF.624	chr2	-	chr2:110920710-110922264	chr2:110920713-110922264		chr2:110920710-110920712	chr2:110920709-110920710		278;25
N	alternative_donor	CUFF.619	chr2	+	chr2:101549464-101554214	chr2:101550623-101554214		chr2:101549464-101550622	chr2:101549463-101549464		5600;5
K	intron_retention	CUFF.624	chr2	-	chr2:110881641-110883213				chr2:110881640-110881641;chr2:110883213-110883214		425;44
K	alternative_first_exon	CUFF.638,CUFF.650	chr2	-	chr2:208030431-208031480;chr2:208030431-208031717	chr2:208030431-208030636	chr2:208031718-208032084	chr2:208030637-208030919			158;73
K	jcn_only_AA	CUFF.647	chr2	-	chr2:204354810-204355936	chr2:204354813-204355936		chr2:204354810-204354812	chr2:204354809-204354810		20;457
K	intron_retention	CUFF.624	chr2	-	chr2:110883259-110886762				chr2:110883258-110883259;chr2:110886762-110886763		577;18
N	jcn_only_AD		chr2	-	chr2:177042550-177042742	chr2:177042550-177042730					44;43
K	jcn_only_AA	CUFF.571	chr2	-	chr2:280150-283110	chr2:280153-283110		chr2:280150-280152	chr2:280149-280150		1317;404
N	intron_retention		chr2	-	chr2:204306137-204309590				chr2:204306136-204306137;chr2:204309590-204309591		23;114
K	alternative_first_exon	CUFF.588	chr2	+	chr2:33505226-33518226	chr2:33516855-33518226	chr2:33505106-33505225	chr2:33516521-33516854			134;110
K	alternative_first_exon	CUFF.656	chr2	+	chr2:228160033-228162389	chr2:228161243-228162389	chr2:228159985-228160032	chr2:228160925-228161242			1;22
N	jcn_only_AD	CUFF.665	chr2	+	chr2:242610857-242611605;chr2:242610841-242611605	chr2:242610821-242611605		chr2:242610821-242610840;chr2:242610841-242610856	chr2:242610820-242610821;chr2:242610840-242610841		79;236
N	cassette	CUFF.588	chr2	+	chr2:33505226-33525517	chr2:33505226-33518226;chr2:33518350-33525517		chr2:33518227-33518349			177;188
K	intron_retention		chr2	-	chr2:175711686-175712040				chr2:175711685-175711686;chr2:175712040-175712041		100;67
N	alternative_donor	CUFF.649	chr2	+	chr2:207630379-207631367;chr2:207630243-207631367;chr2:207630487-207631367	chr2:207630472-207631367		chr2:207630243-207630378;chr2:207630379-207630471;chr2:207630472-207630486	chr2:207630242-207630243;chr2:207630378-207630379;chr2:207630471-207630472		90;12
N	alternative_donor		chr2	-	chr2:242435950-242436714;chr2:242435950-242436596	chr2:242435950-242437030		chr2:242436597-242436714;chr2:242436715-242437030	chr2:242436714-242436715;chr2:242437030-242437031		74;726
K	intron_retention	CUFF.586	chr2	+	chr2:27730179-27730547				chr2:27730178-27730179;chr2:27730547-27730548		321;194
N	coord_cassette	CUFF.665	chr2	+	chr2:242590527-242592926	chr2:242590527-242590678;chr2:242590751-242591298;chr2:242591390-242592926		chr2:242590679-242590750;chr2:242591299-242591389			27;676
N	alternative_donor	CUFF.567	chr2	-	chr2:230045-231022	chr2:230045-230546		chr2:230547-231022	chr2:231022-231023		1226;355
K	jcn_only_AD	CUFF.571,CUFF.624	chr2	-	chr2:110927576-110958997	chr2:110927576-110935999					163;83
N	cassette	CUFF.586	chr2	+	chr2:27721665-27722263	chr2:27721665-27722008;chr2:27722076-27722263		chr2:27722009-27722075			259;87
K	intron_retention	CUFF.610	chr2	-	chr2:86398505-86400772				chr2:86398504-86398505;chr2:86400772-86400773		653;143
N	jcn_only_AD	CUFF.594,CUFF.650	chr2	-	chr2:46842325-46844108	chr2:46842325-46843725		chr2:46843726-46844108	chr2:46844108-46844109		723;36
N	cassette	CUFF.630	chr2	+	chr2:160619505-160623794	chr2:160619505-160621136;chr2:160621186-160623794		chr2:160621137-160621185			196;78
N	jcn_only_AD	CUFF.605,CUFF.624	chr2	-	chr2:73198815-73215386	chr2:73198815-73208137		chr2:73208138-73215386	chr2:73215386-73215387		479;114
K	intron_retention	CUFF.594	chr2	-	chr2:46842325-46844108				chr2:46842324-46842325;chr2:46844108-46844109		723;28
N	intron_retention		chr2	-	chr2:177042223-177042742				chr2:177042222-177042223;chr2:177042742-177042743		90;67
K	intron_retention	CUFF.575	chr2	+	chr2:3469480-3482616				chr2:3469479-3469480;chr2:3482616-3482617		66;36
N	alternative_donor	CUFF.654	chr2	+	chr2:220094681-220094949;chr2:220094703-220094949	chr2:220094623-220094949		chr2:220094623-220094680;chr2:220094681-220094702	chr2:220094622-220094623;chr2:220094680-220094681		74;382
K	intron_retention	CUFF.611	chr2	-	chr2:86849951-86850938				chr2:86849950-86849951;chr2:86850938-86850939		105;55
K	intron_retention	CUFF.665	chr2	+	chr2:242608101-242610140				chr2:242608100-242608101;chr2:242610140-242610141		563;47
K	coord_cassette	CUFF.638	chr2	-	chr2:175742857-175816891	chr2:175742857-175779785;chr2:175779900-175783261;chr2:175783294-175809615;chr2:175809672-175816891		chr2:175779786-175779899;chr2:175783262-175783293;chr2:175809616-175809671			76;88
K	alternative_first_exon	CUFF.610	chr2	-	chr2:86408496-86422460	chr2:86408496-86422044	chr2:86422461-86422970	chr2:86422045-86422140			509;21
N	jcn_only_AA	CUFF.582	chr2	-	chr2:25174424-25179911	chr2:25176505-25179911		chr2:25174424-25176504	chr2:25174423-25174424		166;49
K	intron_retention	CUFF.596	chr2	-	chr2:61711241-61712902				chr2:61711240-61711241;chr2:61712902-61712903		281;70
K	alternative_last_exon	CUFF.591	chr2	+	chr2:38231360-38239745;chr2:38231360-38294124	chr2:38231360-38244328	chr2:38294125-38294384	chr2:38244329-38244977			600;1396
K	intron_retention	CUFF.638	chr2	-	chr2:175666541-175673632				chr2:175666540-175666541;chr2:175673632-175673633		287;110
K	intron_retention	CUFF.665	chr2	+	chr2:242592785-242592926				chr2:242592784-242592785;chr2:242592926-242592927		649;44
K	intron_retention	CUFF.665	chr2	+	chr2:242598603-242606059				chr2:242598602-242598603;chr2:242606059-242606060		421;216
N	intron_retention	CUFF.664	chr2	-	chr2:242435950-242436714				chr2:242435949-242435950;chr2:242436714-242436715		13;49
K	alternative_last_exon	CUFF.586	chr2	+	chr2:27731119-27741654	chr2:27731119-27732393	chr2:27741655-27741804	chr2:27732394-27732708			222;82
K	alternative_first_exon	CUFF.575	chr2	+	chr2:3383611-3391390	chr2:3383648-3391390	chr2:3383362-3383610	chr2:3383611-3383647			50;51
N	alternative_donor	CUFF.588	chr2	+	chr2:33487889-33488360	chr2:33487892-33488360		chr2:33487889-33487891	chr2:33487888-33487889		160;30
K	intron_retention	CUFF.619	chr2	+	chr2:101587537-101591264				chr2:101587536-101587537;chr2:101591264-101591265		157;38
K	intron_retention	CUFF.652	chr2	+	chr2:219222458-219222708				chr2:219222457-219222458;chr2:219222708-219222709		72;111
N	alternative_acceptor		chr2	+	chr2:101609990-101612257	chr2:101609990-101611861		chr2:101611862-101612257	chr2:101612257-101612258		108;280
K	coord_cassette	CUFF.596	chr2	-	chr2:61727030-61749745	chr2:61727030-61729130;chr2:61729176-61729383;chr2:61729446-61749745		chr2:61729131-61729175;chr2:61729384-61729445			2019;479
N	alternative_donor	CUFF.664	chr2	-	chr2:242435950-242436596;chr2:242435950-242437030	chr2:242435950-242436714		chr2:242436597-242436714;chr2:242436715-242437030	chr2:242436714-242436715;chr2:242437030-242437031		783;17
K	coord_cassette	CUFF.647	chr2	-	chr2:204326649-204354306	chr2:204326649-204334961;chr2:204335037-204341798;chr2:204341880-204354306		chr2:204334962-204335036;chr2:204341799-204341879			43;131
K	alternative_first_exon	CUFF.632	chr2	+	chr2:169659184-169668076	chr2:169667936-169668076	chr2:169658891-169659183	chr2:169667837-169667935			235;14
K	intron_retention		chr2	-	chr2:175711686-175742567				chr2:175711685-175711686;chr2:175742567-175742568		77;71
N	jcn_only_AD	CUFF.649	chr2	+	chr2:207630472-207631367;chr2:207630379-207631367;chr2:207630243-207631367	chr2:207630487-207631367		chr2:207630243-207630378;chr2:207630379-207630471;chr2:207630472-207630486	chr2:207630242-207630243;chr2:207630378-207630379;chr2:207630471-207630472		94;64
K	alternative_donor	CUFF.650	chr2	-	chr2:207953306-207988497;chr2:207953306-207989067	chr2:207953306-207988699		chr2:207988498-207988699;chr2:207988700-207989067	chr2:207988699-207988700;chr2:207989067-207989068		446;45
N	alternative_donor		chr2	-	chr2:287893-288552	chr2:287893-288012		chr2:288013-288552	chr2:288552-288553		22;51
N	mutually_exclusive	CUFF.567	chr2	-	chr2:234273-243502,chr2:243563-247537	chr2:234273-242797,chr2:242872-247537	chr2:243503-243562	chr2:242798-242871			51;93
N	jcn_only_AD	CUFF.596	chr2	-	chr2:61749819-61753554	chr2:61749819-61752404		chr2:61752405-61753554	chr2:61753554-61753555		3545;311
K	alternative_first_exon	CUFF.651	chr2	-	chr2:211085527-211089910	chr2:211085527-211089038	chr2:211089911-211090215	chr2:211089039-211089660			61;873
K	intron_retention	CUFF.662	chr2	+	chr2:241402000-241402763				chr2:241401999-241402000;chr2:241402763-241402764		295;89
K	alternative_acceptor	CUFF.620	chr2	+	chr2:109092307-109098165	chr2:109092307-109098152		chr2:109098153-109098165	chr2:109098165-109098166		195;341
K	intron_retention	CUFF.614	chr2	+	chr2:96192968-96194965				chr2:96192967-96192968;chr2:96194965-96194966		6;80
N	coord_cassette	CUFF.630	chr2	+	chr2:160569118-160585519	chr2:160569118-160571067;chr2:160571110-160572191;chr2:160572278-160585519		chr2:160571068-160571109;chr2:160572192-160572277			19;11
N	alternative_donor	CUFF.635	chr2	+	chr2:171400499-171508137	chr2:171503450-171508137		chr2:171400499-171503449	chr2:171400498-171400499		85;0
K	intron_retention	CUFF.659	chr2	+	chr2:232258622-232259491				chr2:232258621-232258622;chr2:232259491-232259492		97;157
K	intron_retention		chr2	+	chr2:220095128-220096649				chr2:220095127-220095128;chr2:220096649-220096650		232;173
N	jcn_only_AD	CUFF.599	chr2	-	chr2:68374700-68384505;chr2:68374700-68384058	chr2:68374700-68384392		chr2:68384059-68384392;chr2:68384393-68384505	chr2:68384392-68384393;chr2:68384505-68384506		417;277
K	intron_retention	CUFF.664	chr2	-	chr2:242438200-242438403				chr2:242438199-242438200;chr2:242438403-242438404		844;99
K	alternative_first_exon	CUFF.595	chr2	+	chr2:48757128-48807725	chr2:48796226-48807725	chr2:48757064-48757127	chr2:48796127-48796225			66;10
N	jcn_only_AA	CUFF.653	chr2	+	chr2:219457431-219458250;chr2:219457431-219458891	chr2:219457431-219458830		chr2:219458251-219458830;chr2:219458831-219458891	chr2:219458830-219458831;chr2:219458891-219458892		296;103
N	alternative_donor	CUFF.635	chr2	+	chr2:171034800-171055717	chr2:171036692-171055717		chr2:171034800-171036691	chr2:171034799-171034800		11;1
K	intron_retention	CUFF.632	chr2	+	chr2:169712721-169713199				chr2:169712720-169712721;chr2:169713199-169713200		113;7
N	jcn_only_AD	CUFF.599	chr2	-	chr2:68374700-68384392;chr2:68374700-68384058	chr2:68374700-68384505		chr2:68384059-68384392;chr2:68384393-68384505	chr2:68384392-68384393;chr2:68384505-68384506		324;370
N	cassette	CUFF.638	chr2	-	chr2:175711686-175779785	chr2:175711686-175742567;chr2:175742857-175779785		chr2:175742568-175742856			79;162
K	jcn_only_AA	CUFF.664	chr2	-	chr2:242441124-242447420	chr2:242441215-242447420		chr2:242441124-242441214	chr2:242441123-242441124		569;80
N	cassette	CUFF.579	chr2	-	chr2:11593925-11605897	chr2:11593925-11597304;chr2:11597360-11605897		chr2:11597305-11597359			38;264
N	jcn_only_AA	CUFF.588	chr2	+	chr2:33477912-33482434;chr2:33477912-33482350	chr2:33477912-33482509		chr2:33482351-33482434;chr2:33482435-33482509	chr2:33482434-33482435;chr2:33482509-33482510		166;40
N	alternative_donor	CUFF.582,CUFF.651	chr2	-	chr2:25174424-25179911	chr2:25174424-25176418		chr2:25176419-25179911	chr2:25179911-25179912		166;2
N	cassette	CUFF.665	chr2	+	chr2:242594063-242598522;chr2:242594063-242606059	chr2:242594063-242594685;chr2:242594759-242598522,chr2:242594759-242606059		chr2:242594686-242594758			107;768
K	alternative_last_exon	CUFF.575,CUFF.657	chr2	+	chr2:3464108-3466628;chr2:3464108-3469367	chr2:3464108-3464417	chr2:3469368-3469479	chr2:3464418-3464794			564;754
K	intron_retention	CUFF.654	chr2	+	chr2:220100818-220101043				chr2:220100817-220100818;chr2:220101043-220101044		304;29
N	jcn_only_AA	CUFF.596	chr2	-	chr2:61761039-61765626	chr2:61764723-61765626		chr2:61761039-61764722	chr2:61761038-61761039		27;27
K	intron_retention	CUFF.657	chr2	+	chr2:232028442-232029913				chr2:232028441-232028442;chr2:232029913-232029914		222;25
N	cassette	CUFF.630	chr2	+	chr2:160569173-160585519	chr2:160569173-160572191;chr2:160572278-160585519		chr2:160572192-160572277			10;78
K	jcn_only_AD	CUFF.650	chr2	-	chr2:207953306-207989067;chr2:207953306-207988699	chr2:207953306-207988497		chr2:207988498-207988699;chr2:207988700-207989067	chr2:207988699-207988700;chr2:207989067-207989068		345;82
K	alternative_acceptor	CUFF.664	chr2	-	chr2:242441124-242447420	chr2:242441215-242447420		chr2:242441124-242441214	chr2:242441123-242441124		569;115
K	cassette	CUFF.581	chr2	-	chr2:23598556-23599654	chr2:23598556-23599108;chr2:23599201-23599654		chr2:23599109-23599200			84;222
N	jcn_only_AA	CUFF.583	chr2	-	chr2:27703994-27706155	chr2:27704128-27706155		chr2:27703994-27704127	chr2:27703993-27703994		120;669
K	jcn_only_AD	CUFF.593,CUFF.624	chr2	-	chr2:110920710-110922264	chr2:110920710-110922096		chr2:110922097-110922264	chr2:110922264-110922265		278;11
N	coord_cassette	CUFF.579	chr2	-	chr2:11593925-11605897	chr2:11593925-11597304;chr2:11597360-11598406;chr2:11598478-11605897		chr2:11597305-11597359;chr2:11598407-11598477			38;172
K	intron_retention	CUFF.583	chr2	-	chr2:27699594-27700083				chr2:27699593-27699594;chr2:27700083-27700084		815;132
N	jcn_only_AD		chr2	+	chr2:101609990-101612257	chr2:101611043-101612257		chr2:101609990-101611042	chr2:101609989-101609990		108;18
K	intron_retention	CUFF.654	chr2	+	chr2:220097406-220097800				chr2:220097405-220097406;chr2:220097800-220097801		689;283
K	intron_retention		chr2	+	chr2:242590527-242590678				chr2:242590526-242590527;chr2:242590678-242590679		1429;55
N	alternative_acceptor	CUFF.644,CUFF.653	chr2	+	chr2:191362446-191364740	chr2:191362446-191364557		chr2:191364558-191364740	chr2:191364740-191364741		1166;4
N	alternative_donor	CUFF.654	chr2	+	chr2:220094681-220094949;chr2:220094623-220094949	chr2:220094703-220094949		chr2:220094623-220094680;chr2:220094681-220094702	chr2:220094622-220094623;chr2:220094680-220094681		400;56
K	intron_retention	CUFF.583	chr2	-	chr2:27706805-27707093				chr2:27706804-27706805;chr2:27707093-27707094		777;36
N	jcn_only_AD	CUFF.654	chr2	+	chr2:220095128-220096649;chr2:220095073-220096649	chr2:220094623-220096649		chr2:220094623-220095072;chr2:220095073-220095127	chr2:220094622-220094623;chr2:220095072-220095073		417;68
N	alternative_acceptor	CUFF.664	chr2	-	chr2:242435950-242437030	chr2:242436794-242437030		chr2:242435950-242436793	chr2:242435949-242435950		726;14
K	alternative_first_exon	CUFF.596,CUFF.610	chr2	-	chr2:61761039-61761557,chr2:61761039-61761692,chr2:61761039-61763336,chr2:61761039-61763844,chr2:61761039-61764153;chr2:61761039-61765626	chr2:61761039-61764696	chr2:61765627-61765851	chr2:61764697-61765418			448;33
N	mutually_exclusive	CUFF.641	chr2	-	chr2:177041421-177042438,chr2:177042585-177043756	chr2:177041421-177042059,chr2:177042223-177043756	chr2:177042439-177042584	chr2:177042060-177042222			71;110
K	jcn_only_AA	CUFF.610	chr2	-	chr2:86397965-86398330	chr2:86397968-86398330		chr2:86397965-86397967	chr2:86397964-86397965		47;949
N	intron_retention		chr2	-	chr2:253116-263983				chr2:253115-253116;chr2:263983-263984		141;27
N	jcn_only_AD	CUFF.654	chr2	+	chr2:220095128-220096649;chr2:220094623-220096649	chr2:220095073-220096649		chr2:220094623-220095072;chr2:220095073-220095127	chr2:220094622-220094623;chr2:220095072-220095073		299;185
N	jcn_only_AD	CUFF.649	chr2	+	chr2:207630472-207631367;chr2:207630243-207631367;chr2:207630487-207631367	chr2:207630379-207631367		chr2:207630243-207630378;chr2:207630379-207630471;chr2:207630472-207630486	chr2:207630242-207630243;chr2:207630378-207630379;chr2:207630471-207630472		117;41
N	jcn_only_AD	CUFF.649	chr2	+	chr2:207630379-207631367;chr2:207630243-207631367;chr2:207630487-207631367	chr2:207630472-207631367		chr2:207630243-207630378;chr2:207630379-207630471;chr2:207630472-207630486	chr2:207630242-207630243;chr2:207630378-207630379;chr2:207630471-207630472		140;18
K	alternative_first_exon	CUFF.582	chr2	-	chr2:25190163-25194686	chr2:25190163-25194424,chr2:25190163-25194284	chr2:25194687-25194963	chr2:25194425-25194556			105;321
K	cassette	CUFF.629	chr2	+	chr2:153497429-153504309	chr2:153497429-153499932;chr2:153500059-153504309		chr2:153499933-153500058			200;166
N	intron_retention		chr2	+	chr2:3469467-3481462				chr2:3469466-3469467;chr2:3481462-3481463		41;30
K	jcn_only_AA	CUFF.611	chr2	-	chr2:86831602-86839281	chr2:86832542-86839281		chr2:86831602-86832541	chr2:86831601-86831602		54;104
K	alternative_last_exon	CUFF.632	chr2	+	chr2:169711971-169713199	chr2:169711971-169712395	chr2:169713200-169713288	chr2:169712396-169712494			446;69
K	cassette	CUFF.619	chr2	+	chr2:101565943-101580519	chr2:101565943-101579216;chr2:101579296-101580519		chr2:101579217-101579295			157;4073
K	jcn_only_AA	CUFF.609	chr2	-	chr2:79364464-79365092	chr2:79364469-79365092		chr2:79364464-79364468	chr2:79364463-79364464		893;238
K	alternative_first_exon	CUFF.616	chr2	+	chr2:99232810-99234630	chr2:99232997-99234630	chr2:99232634-99232809	chr2:99232821-99232996			12;145
N	alternative_donor	CUFF.575	chr2	+	chr2:3464108-3469367	chr2:3466843-3469367		chr2:3464108-3466842	chr2:3464107-3464108		761;127
N	jcn_only_AD	CUFF.620	chr2	+	chr2:109065737-109066088	chr2:109065746-109066088		chr2:109065737-109065745	chr2:109065736-109065737		389;123
N	jcn_only_AD	CUFF.620	chr2	+	chr2:109085541-109086106	chr2:109085789-109086106		chr2:109085541-109085788	chr2:109085540-109085541		190;103
K	intron_retention	CUFF.609	chr2	-	chr2:79365203-79365497				chr2:79365202-79365203;chr2:79365497-79365498		2661;82
N	alternative_donor	CUFF.612	chr2	-	chr2:88892924-88894986	chr2:88892924-88893430		chr2:88893431-88894986	chr2:88894986-88894987		97;9
N	alternative_donor	CUFF.620	chr2	+	chr2:109066146-109067483	chr2:109066451-109067483		chr2:109066146-109066450	chr2:109066145-109066146		80;104
N	jcn_only_AA		chr2	+	chr2:101609990-101612257	chr2:101609990-101611861		chr2:101611862-101612257	chr2:101612257-101612258		108;301
N	jcn_only_AD		chr2	-	chr2:242435950-242436714;chr2:242435950-242436596	chr2:242435950-242437030		chr2:242436597-242436714;chr2:242436715-242437030	chr2:242436714-242436715;chr2:242437030-242437031		54;726
K	intron_retention	CUFF.659	chr2	+	chr2:232258622-232259365				chr2:232258621-232258622;chr2:232259365-232259366		116;64
K	cassette	CUFF.588	chr2	+	chr2:33540337-33572433	chr2:33540337-33567904;chr2:33568031-33572433		chr2:33567905-33568030			203;371
N	jcn_only_AA	CUFF.636	chr2	-	chr2:174072387-174136238	chr2:174080565-174136238		chr2:174072387-174080564	chr2:174072386-174072387		461;26
N	intron_retention		chr2	-	chr2:253116-262630				chr2:253115-253116;chr2:262630-262631		214;26
N	cassette	CUFF.594	chr2	-	chr2:46839484-46842075	chr2:46839484-46840832;chr2:46840925-46842075		chr2:46840833-46840924			60;494
N	alternative_acceptor	CUFF.596	chr2	-	chr2:61761039-61764696	chr2:61761814-61764696		chr2:61761039-61761813	chr2:61761038-61761039		77;116
N	alternative_acceptor		chr2	+	chr2:680152-696540	chr2:680152-681255		chr2:681256-696540	chr2:696540-696541		54;22
K	intron_retention	CUFF.609	chr2	-	chr2:79364054-79364349				chr2:79364053-79364054;chr2:79364349-79364350		349;1237
K	jcn_only_AA	CUFF.620	chr2	+	chr2:109092307-109098165	chr2:109092307-109098152		chr2:109098153-109098165	chr2:109098165-109098166		195;9
N	alternative_donor		chr2	-	chr2:73227617-73228657	chr2:73227617-73228653		chr2:73228654-73228657	chr2:73228657-73228658		375;184
N	jcn_only_AD	CUFF.624	chr2	-	chr2:110881641-110883213	chr2:110881641-110882795		chr2:110882796-110883213	chr2:110883213-110883214		425;21
K	cassette	CUFF.581	chr2	-	chr2:23599798-23604091	chr2:23599798-23602994;chr2:23603113-23604091		chr2:23602995-23603112			84;180
N	coord_cassette	CUFF.579	chr2	-	chr2:11587901-11593707	chr2:11587901-11590137;chr2:11590253-11591776;chr2:11591933-11593707		chr2:11590138-11590252;chr2:11591777-11591932			16;380
N	cassette	CUFF.665	chr2	+	chr2:242590751-242592926;chr2:242591390-242592926	chr2:242590751-242592721,chr2:242591390-242592721;chr2:242592785-242592926		chr2:242592722-242592784			1586;488
K	intron_retention	CUFF.616	chr2	+	chr2:99225190-99226218				chr2:99225189-99225190;chr2:99226218-99226219		29;30
K	intron_retention	CUFF.571	chr2	-	chr2:286204-286289				chr2:286203-286204;chr2:286289-286290		1261;66
N	intron_retention		chr2	-	chr2:177042550-177042742				chr2:177042549-177042550;chr2:177042742-177042743		44;142
N	jcn_only_AA		chr2	-	chr2:242439697-242448637	chr2:242441124-242448637					85;115
N	intron_retention		chr2	+	chr2:219461022-219461057				chr2:219461021-219461022;chr2:219461057-219461058		119;33
K	coord_cassette	CUFF.567	chr2	-	chr2:234273-247537	chr2:234273-242797;chr2:242872-243502;chr2:243563-247537		chr2:242798-242871;chr2:243503-243562			1211;39
N	mutually_exclusive	CUFF.610	chr2	-	chr2:86393768-86398330,chr2:86398505-86400772	chr2:86393768-86397871,chr2:86397965-86400772	chr2:86398331-86398504	chr2:86397872-86397964			25;90
K	intron_retention	CUFF.665	chr2	+	chr2:242606254-242607557				chr2:242606253-242606254;chr2:242607557-242607558		490;40
K	intron_retention	CUFF.652	chr2	+	chr2:219221911-219222256				chr2:219221910-219221911;chr2:219222256-219222257		226;97
K	cassette	CUFF.575	chr2	+	chr2:3447663-3461391	chr2:3447663-3460920;chr2:3461001-3461391		chr2:3460921-3461000			1388;34
N	alternative_acceptor	CUFF.583	chr2	-	chr2:27703994-27706155	chr2:27704128-27706155		chr2:27703994-27704127	chr2:27703993-27703994		120;536
N	alternative_acceptor	CUFF.588	chr2	+	chr2:33477912-33482509;chr2:33477912-33482350	chr2:33477912-33482434		chr2:33482351-33482434;chr2:33482435-33482509	chr2:33482434-33482435;chr2:33482509-33482510		92;61
K	intron_retention	CUFF.591	chr2	+	chr2:38244379-38244720				chr2:38244378-38244379;chr2:38244720-38244721		65;723
N	coord_cassette	CUFF.579	chr2	-	chr2:11593925-11605897	chr2:11593925-11595467;chr2:11595601-11597304;chr2:11597360-11605897		chr2:11595468-11595600;chr2:11597305-11597359			38;213
K	cassette	CUFF.605	chr2	-	chr2:73268061-73285656	chr2:73268061-73269616;chr2:73269715-73285656		chr2:73269617-73269714			605;28
N	mutually_exclusive	CUFF.610	chr2	-	chr2:86393768-86398330,chr2:86398469-86400772	chr2:86393768-86397871,chr2:86397965-86400772	chr2:86398331-86398468	chr2:86397872-86397964			17;90
N	alternative_acceptor	CUFF.628,CUFF.653	chr2	+	chr2:219457431-219458891;chr2:219457431-219458830	chr2:219457431-219458250		chr2:219458251-219458830;chr2:219458831-219458891	chr2:219458830-219458831;chr2:219458891-219458892		310;39
N	jcn_only_AA	CUFF.638	chr2	-	chr2:175816931-175869933	chr2:175869809-175869933					9;120
K	intron_retention	CUFF.596	chr2	-	chr2:61729446-61749745				chr2:61729445-61729446;chr2:61749745-61749746		710;130
K	alternative_first_exon	CUFF.571	chr2	-	chr2:286344-287162;chr2:286344-286869	chr2:286344-287582	chr2:287163-287387;chr2:286870-286968	chr2:287583-287892			974;282
N	coord_cassette	CUFF.567	chr2	-	chr2:262787-264781	chr2:262787-263210;chr2:263373-263563;chr2:263763-264781		chr2:263211-263372;chr2:263564-263762			177;392
N	jcn_only_AD	CUFF.665	chr2	+	chr2:242610821-242611605;chr2:242610841-242611605	chr2:242610857-242611605		chr2:242610821-242610840;chr2:242610841-242610856	chr2:242610820-242610821;chr2:242610840-242610841		258;57
N	cassette	CUFF.665	chr2	+	chr2:242590751-242592926;chr2:242590751-242592721	chr2:242590751-242591298;chr2:242591390-242592926,chr2:242591390-242592721		chr2:242591299-242591389			924;837
N	cassette	CUFF.620	chr2	+	chr2:109066146-109068854	chr2:109066146-109067483;chr2:109067569-109068854		chr2:109067484-109067568			243;104
N	alternative_donor		chr2	-	chr2:175816931-175869933	chr2:175816931-175869621		chr2:175869622-175869933	chr2:175869933-175869934		9;215
K	alternative_last_exon	CUFF.591,CUFF.628	chr2	+	chr2:139326797-139331421	chr2:139326797-139328337	chr2:139331422-139332028	chr2:139328338-139328738			78;153
N	cassette	CUFF.664	chr2	-	chr2:242440212-242447420	chr2:242440212-242440892;chr2:242441124-242447420		chr2:242440893-242441123			125;1107
N	jcn_only_AA	CUFF.620	chr2	+	chr2:109068923-109085435	chr2:109068923-109079043		chr2:109079044-109085435	chr2:109085435-109085436		289;218
N	jcn_only_AD	CUFF.601	chr2	-	chr2:69870407-69901154;chr2:69870407-69870706;chr2:69870407-69870923	chr2:69870407-69870874		chr2:69870707-69870874;chr2:69870875-69870923;chr2:69870924-69901154	chr2:69870874-69870875;chr2:69870923-69870924;chr2:69901154-69901155		238;88
K	intron_retention	CUFF.596	chr2	-	chr2:61709675-61710091				chr2:61709674-61709675;chr2:61710091-61710092		309;24
N	alternative_donor	CUFF.596	chr2	-	chr2:61749819-61753554	chr2:61749819-61752404		chr2:61752405-61753554	chr2:61753554-61753555		3545;345
K	jcn_only_AD	CUFF.650	chr2	-	chr2:207953306-207988497;chr2:207953306-207988699	chr2:207953306-207989067		chr2:207988498-207988699;chr2:207988700-207989067	chr2:207988699-207988700;chr2:207989067-207989068		107;320
K	coord_cassette	CUFF.595	chr2	+	chr2:48848430-48873591	chr2:48848430-48869540;chr2:48869597-48872171;chr2:48872257-48873591		chr2:48869541-48869596;chr2:48872172-48872256			7;192
K	coord_cassette	CUFF.644	chr2	+	chr2:191273230-191300702	chr2:191273230-191280017;chr2:191280140-191298052;chr2:191298119-191300702		chr2:191280018-191280139;chr2:191298053-191298118			59;38
N	alternative_donor	CUFF.619	chr2	+	chr2:101541757-101549371	chr2:101541763-101549371		chr2:101541757-101541762	chr2:101541756-101541757		3176;24
N	jcn_only_AD	CUFF.591	chr2	+	chr2:38231360-38244328	chr2:38239793-38244328		chr2:38231360-38239792	chr2:38231359-38231360		1140;101
K	mutually_exclusive	CUFF.575	chr2	+	chr2:3469467-3481465,chr2:3481567-3482616	chr2:3469467-3470024,chr2:3470165-3482616	chr2:3481466-3481566	chr2:3470025-3470164			275;244
N	intron_retention		chr2	+	chr2:101609990-101612257				chr2:101609989-101609990;chr2:101612257-101612258		108;58
N	intron_retention		chr2	-	chr2:263373-264083				chr2:263372-263373;chr2:264083-264084		37;20
K	intron_retention	CUFF.624	chr2	-	chr2:110920710-110922096				chr2:110920709-110920710;chr2:110922096-110922097		11;20
K	cassette	CUFF.632	chr2	+	chr2:169659184-169681143	chr2:169659184-169668076;chr2:169668163-169681143		chr2:169668077-169668162			378;228
N	jcn_only_AA	CUFF.635,CUFF.657	chr2	+	chr2:171400499-171508137	chr2:171400499-171503418		chr2:171503419-171508137	chr2:171508137-171508138		85;13
K	cassette	CUFF.574	chr2	+	chr2:1094097-1133307	chr2:1094097-1099090;chr2:1099129-1133307		chr2:1099091-1099128			172;227
K	alternative_last_exon	CUFF.616	chr2	+	chr2:99232810-99234630	chr2:99232810-99232894	chr2:99234631-99235077	chr2:99232895-99232996			27;106
N	jcn_only_AA	CUFF.664	chr2	-	chr2:242440335-242440892;chr2:242440263-242440892	chr2:242440493-242440892		chr2:242440263-242440334;chr2:242440335-242440492	chr2:242440262-242440263;chr2:242440334-242440335		257;49
K	intron_retention		chr2	+	chr2:160599765-160602280				chr2:160599764-160599765;chr2:160602280-160602281		38;65
N	alternative_donor	CUFF.610	chr2	-	chr2:110920713-110922264	chr2:110920713-110922096		chr2:110922097-110922264	chr2:110922264-110922265		25;19
N	cassette	CUFF.567	chr2	-	chr2:262787-264781;chr2:253116-264781	chr2:262787-263210,chr2:253116-263210;chr2:263369-264781		chr2:263211-263368			359;240
N	alternative_last_exon	CUFF.654	chr2	+	chr2:220094623-220096649;chr2:220094623-220097211	chr2:220094623-220094949	chr2:220096650-220096762;chr2:220097212-220097743	chr2:220094950-220095127			151;309
K	intron_retention	CUFF.577	chr2	-	chr2:4007365-4007505				chr2:4007364-4007365;chr2:4007505-4007506		253;102
N	alternative_acceptor	CUFF.591	chr2	+	chr2:38156873-38201182	chr2:38156873-38177653		chr2:38177654-38201182	chr2:38201182-38201183		316;27
K	cassette	CUFF.567	chr2	-	chr2:231192-234159	chr2:231192-233100;chr2:233230-234159		chr2:233101-233229			1023;648
K	intron_retention	CUFF.613	chr2	+	chr2:88928251-88930917				chr2:88928250-88928251;chr2:88930917-88930918		35;45
K	alternative_donor	CUFF.650	chr2	-	chr2:207953306-207989067;chr2:207953306-207988699	chr2:207953306-207988497		chr2:207988498-207988699;chr2:207988700-207989067	chr2:207988699-207988700;chr2:207989067-207989068		365;126
N	alternative_donor	CUFF.649	chr2	+	chr2:207630472-207631367;chr2:207630379-207631367;chr2:207630243-207631367	chr2:207630487-207631367		chr2:207630243-207630378;chr2:207630379-207630471;chr2:207630472-207630486	chr2:207630242-207630243;chr2:207630378-207630379;chr2:207630471-207630472		68;34
K	intron_retention	CUFF.583	chr2	-	chr2:27680844-27680992				chr2:27680843-27680844;chr2:27680992-27680993		2579;7
K	jcn_only_AD	CUFF.582	chr2	-	chr2:25190163-25194424	chr2:25190163-25194284		chr2:25194285-25194424	chr2:25194424-25194425		171;303
N	alternative_acceptor	CUFF.605	chr2	-	chr2:73172229-73188259	chr2:73184233-73188259		chr2:73172229-73184232	chr2:73172228-73172229		197;1
N	jcn_only_AA	CUFF.635	chr2	+	chr2:171376051-171399415	chr2:171376051-171381014		chr2:171381015-171399415	chr2:171399415-171399416		71;14
K	intron_retention	CUFF.654	chr2	+	chr2:220100308-220100429				chr2:220100307-220100308;chr2:220100429-220100430		182;160
N	jcn_only_AD	CUFF.654	chr2	+	chr2:220094681-220094949;chr2:220094703-220094949	chr2:220094623-220094949		chr2:220094623-220094680;chr2:220094681-220094702	chr2:220094622-220094623;chr2:220094680-220094681		86;382
K	jcn_only_AA	CUFF.624	chr2	-	chr2:110927576-110958997	chr2:110937262-110958997					163;477
N	alternative_acceptor	CUFF.624	chr2	-	chr2:110881641-110883213	chr2:110882901-110883213		chr2:110881641-110882900	chr2:110881640-110881641		425;48
K	jcn_only_AD	CUFF.610	chr2	-	chr2:86386795-86389098	chr2:86386795-86389074		chr2:86389075-86389098	chr2:86389098-86389099		1065;105
N	jcn_only_AD	CUFF.610	chr2	-	chr2:110920713-110922264	chr2:110920713-110922096		chr2:110922097-110922264	chr2:110922264-110922265		25;6
K	intron_retention	CUFF.572	chr2	-	chr2:676239-676573				chr2:676238-676239;chr2:676573-676574		109;23
N	alternative_donor	CUFF.588	chr2	+	chr2:33335819-33359859	chr2:33359573-33359859		chr2:33335819-33359572	chr2:33335818-33335819		2;0
N	jcn_only_AD	CUFF.620	chr2	+	chr2:109066146-109067483	chr2:109066451-109067483		chr2:109066146-109066450	chr2:109066145-109066146		80;109
N	alternative_donor		chr2	-	chr2:61764723-61765626	chr2:61764723-61765272		chr2:61765273-61765626	chr2:61765626-61765627		27;13
N	alternative_acceptor	CUFF.635	chr2	+	chr2:171376051-171399415	chr2:171376051-171381014		chr2:171381015-171399415	chr2:171399415-171399416		71;0
K	jcn_only_AA	CUFF.624	chr2	-	chr2:110920710-110922096	chr2:110920713-110922096		chr2:110920710-110920712	chr2:110920709-110920710		11;6
N	alternative_donor	CUFF.599	chr2	-	chr2:68374700-68384392;chr2:68374700-68384058	chr2:68374700-68384505		chr2:68384059-68384392;chr2:68384393-68384505	chr2:68384392-68384393;chr2:68384505-68384506		236;370
N	jcn_only_AD	CUFF.591	chr2	+	chr2:38152569-38156404;chr2:38150511-38156404	chr2:38156080-38156404		chr2:38150511-38152568;chr2:38152569-38156079	chr2:38150510-38150511;chr2:38152568-38152569		268;32
K	jcn_only_AA	CUFF.634	chr2	-	chr2:169783801-169787174	chr2:169783873-169787174		chr2:169783801-169783872	chr2:169783800-169783801	chr2:169787175-169787372;chr2:169783666-169783800	78;11
K	intron_retention	CUFF.632	chr2	+	chr2:169711971-169713199				chr2:169711970-169711971;chr2:169713199-169713200		657;15
K	alternative_first_exon	CUFF.574	chr2	+	chr2:1158976-1161233;chr2:1133496-1161233	chr2:1159412-1161233	chr2:1133454-1133495	chr2:1159313-1159411			686;35
N	alternative_acceptor	CUFF.631	chr2	-	chr2:166732743-166737188	chr2:166736478-166737188		chr2:166732743-166736477	chr2:166732742-166732743		73;7
K	jcn_only_AD	CUFF.627	chr2	+	chr2:133070569-133074681	chr2:133070573-133074681		chr2:133070569-133070572	chr2:133070568-133070569		53;11
K	cassette	CUFF.582	chr2	-	chr2:25180844-25186273	chr2:25180844-25181415;chr2:25181471-25186273		chr2:25181416-25181470			474;87
K	intron_retention	CUFF.572	chr2	-	chr2:675631-675757				chr2:675630-675631;chr2:675757-675758		105;86
K	intron_retention	CUFF.605	chr2	-	chr2:73215478-73226077				chr2:73215477-73215478;chr2:73226077-73226078		327;175
N	alternative_donor	CUFF.630	chr2	+	chr2:160585687-160599571	chr2:160590594-160599571		chr2:160585687-160590593	chr2:160585686-160585687		164;2
N	jcn_only_AD	CUFF.595	chr2	+	chr2:48898820-49003418;chr2:48996261-49003418	chr2:48996214-49003418		chr2:48898820-48996213;chr2:48996214-48996260	chr2:48898819-48898820;chr2:48996213-48996214		247;39
N	intron_retention		chr2	-	chr2:46839484-46842075				chr2:46839483-46839484;chr2:46842075-46842076		60;11
K	intron_retention	CUFF.664	chr2	-	chr2:242437765-242438053				chr2:242437764-242437765;chr2:242438053-242438054		436;95
K	cassette	CUFF.653	chr2	+	chr2:219449445-219452308	chr2:219449445-219452027;chr2:219452124-219452308		chr2:219452028-219452123			93;30
N	jcn_only_AA	CUFF.637	chr2	-	chr2:175216454-175243650;chr2:175234743-175243650	chr2:175223265-175243650		chr2:175216454-175223264;chr2:175223265-175234742	chr2:175216453-175216454;chr2:175223264-175223265		28;56
N	jcn_only_AA		chr2	+	chr2:3482705-3488490	chr2:3482705-3482989		chr2:3482990-3488490	chr2:3488490-3488491		12;466
N	alternative_donor	CUFF.574	chr2	+	chr2:1094097-1099090	chr2:1098397-1099090		chr2:1094097-1098396	chr2:1094096-1094097		209;8
N	jcn_only_AD	CUFF.664	chr2	-	chr2:242435950-242436596;chr2:242435950-242437030	chr2:242435950-242436714		chr2:242436597-242436714;chr2:242436715-242437030	chr2:242436714-242436715;chr2:242437030-242437031		768;13
N	cassette	CUFF.665	chr2	+	chr2:242590527-242592926	chr2:242590527-242590678;chr2:242590751-242592926		chr2:242590679-242590750			27;823
K	cassette	CUFF.610	chr2	-	chr2:86393768-86398330	chr2:86393768-86397871;chr2:86397965-86398330		chr2:86397872-86397964			32;431
N	alternative_donor	CUFF.601,CUFF.612	chr2	-	chr2:69870407-69901154;chr2:69870407-69870923;chr2:69870407-69870874	chr2:69870407-69870706		chr2:69870707-69870874;chr2:69870875-69870923;chr2:69870924-69901154	chr2:69870874-69870875;chr2:69870923-69870924;chr2:69901154-69901155		30;3
N	jcn_only_AD	CUFF.583	chr2	-	chr2:27708371-27712481	chr2:27708371-27709025		chr2:27709026-27712481	chr2:27712481-27712482		854;19
K	intron_retention	CUFF.624	chr2	-	chr2:110920710-110922264				chr2:110920709-110920710;chr2:110922264-110922265		278;21
N	alternative_donor	CUFF.599	chr2	-	chr2:68374700-68384505;chr2:68374700-68384058	chr2:68374700-68384392		chr2:68384059-68384392;chr2:68384393-68384505	chr2:68384392-68384393;chr2:68384505-68384506		421;185
N	intron_retention	CUFF.624	chr2	-	chr2:110881641-110882795				chr2:110881640-110881641;chr2:110882795-110882796		21;29
N	jcn_only_AD	CUFF.588	chr2	+	chr2:33487889-33488360	chr2:33487892-33488360		chr2:33487889-33487891	chr2:33487888-33487889		160;60
N	alternative_donor	CUFF.624	chr2	-	chr2:110881641-110883213	chr2:110881641-110882795		chr2:110882796-110883213	chr2:110883213-110883214		425;111
N	jcn_only_AA	CUFF.583	chr2	-	chr2:27668317-27668611	chr2:27668497-27668611		chr2:27668317-27668496	chr2:27668316-27668317		1064;150
K	intron_retention	CUFF.596	chr2	-	chr2:61719884-61720049				chr2:61719883-61719884;chr2:61720049-61720050		151;145
N	alternative_acceptor	CUFF.582	chr2	-	chr2:25174424-25179911	chr2:25176505-25179911		chr2:25174424-25176504	chr2:25174423-25174424		166;4
K	intron_retention	CUFF.596	chr2	-	chr2:61725928-61725999				chr2:61725927-61725928;chr2:61725999-61726000		2860;21
N	alternative_donor	CUFF.591	chr2	+	chr2:38156080-38156404;chr2:38152569-38156404	chr2:38150511-38156404		chr2:38150511-38152568;chr2:38152569-38156079	chr2:38150510-38150511;chr2:38152568-38152569		34;29
N	jcn_only_AD	CUFF.635	chr2	+	chr2:171376051-171399415	chr2:171381137-171399415		chr2:171376051-171381136	chr2:171376050-171376051		71;16
N	alternative_acceptor	CUFF.646	chr2	+	chr2:200472851-200493786	chr2:200472851-200489254		chr2:200489255-200493786	chr2:200493786-200493787		252;1
K	alternative_acceptor	CUFF.611	chr2	-	chr2:86831602-86839281	chr2:86832542-86839281		chr2:86831602-86832541	chr2:86831601-86831602		54;170
K	intron_retention	CUFF.573	chr2	+	chr2:677474-680043				chr2:677473-677474;chr2:680043-680044		136;5
N	jcn_only_AD	CUFF.665	chr2	+	chr2:242610857-242611605;chr2:242610821-242611605	chr2:242610841-242611605		chr2:242610821-242610840;chr2:242610841-242610856	chr2:242610820-242610821;chr2:242610840-242610841		293;22
N	cassette	CUFF.567	chr2	-	chr2:263373-264781	chr2:263373-263563;chr2:263763-264781		chr2:263564-263762			66;585
N	alternative_acceptor	CUFF.620	chr2	+	chr2:109089356-109091990	chr2:109089356-109091244		chr2:109091245-109091990	chr2:109091990-109091991		8;69
N	intron_retention		chr2	+	chr2:220094703-220094949				chr2:220094702-220094703;chr2:220094949-220094950		62;120
K	cassette	CUFF.605	chr2	-	chr2:73188378-73195576	chr2:73188378-73194365;chr2:73194453-73195576		chr2:73194366-73194452			271;193
N	jcn_only_AA	CUFF.599	chr2	-	chr2:68358578-68361833	chr2:68359138-68361833		chr2:68358578-68359137	chr2:68358577-68358578		254;157
N	jcn_only_AD	CUFF.574	chr2	+	chr2:1079342-1204788	chr2:1168870-1204788					72;480
N	alternative_donor		chr2	+	chr2:101609990-101612257	chr2:101611043-101612257		chr2:101609990-101611042	chr2:101609989-101609990		108;9
N	cassette	CUFF.646	chr2	+	chr2:200496619-200512396	chr2:200496619-200511776;chr2:200511903-200512396		chr2:200511777-200511902			18;108
N	intron_retention		chr2	-	chr2:61764723-61765272				chr2:61764722-61764723;chr2:61765272-61765273		23;19
K	alternative_last_exon	CUFF.657	chr2	+	chr2:231951896-232003449	chr2:231951896-231973277	chr2:232003450-232003564	chr2:231973278-231973882			309;140
N	intron_retention		chr2	+	chr2:220095128-220096981				chr2:220095127-220095128;chr2:220096981-220096982		96;45
N	jcn_only_AD	CUFF.591	chr2	+	chr2:38224658-38231133	chr2:38230170-38231133		chr2:38224658-38230169	chr2:38224657-38224658		1309;229
N	jcn_only_AD	CUFF.630	chr2	+	chr2:160615847-160619390	chr2:160615870-160619390		chr2:160615847-160615869	chr2:160615846-160615847		191;26
K	intron_retention	CUFF.610	chr2	-	chr2:86398436-86400772				chr2:86398435-86398436;chr2:86400772-86400773		73;391
K	alternative_first_exon	CUFF.644	chr2	+	chr2:191307732-191334483;chr2:191302288-191334483	chr2:191334376-191334483	chr2:191300703-191302287	chr2:191334201-191334375			460;63
K	cassette	CUFF.632	chr2	+	chr2:169668163-169684667	chr2:169668163-169681143;chr2:169681228-169684667		chr2:169681144-169681227			157;225
K	intron_retention		chr2	-	chr2:242441124-242447919				chr2:242441123-242441124;chr2:242447919-242447920		472;230
N	alternative_donor	CUFF.620	chr2	+	chr2:109065737-109066088	chr2:109065746-109066088		chr2:109065737-109065745	chr2:109065736-109065737		389;63
N	alternative_donor	CUFF.583	chr2	-	chr2:27693963-27695116	chr2:27693963-27694099		chr2:27694100-27695116	chr2:27695116-27695117		743;88
N	alternative_acceptor	CUFF.596	chr2	-	chr2:61761039-61765626	chr2:61764723-61765626		chr2:61761039-61764722	chr2:61761038-61761039		27;44
N	cassette	CUFF.610	chr2	-	chr2:86397965-86400772	chr2:86397965-86398330;chr2:86398469-86400772		chr2:86398331-86398468			12;174
N	alternative_donor	CUFF.582,CUFF.637	chr2	-	chr2:175216454-175243650	chr2:175216454-175234714		chr2:175234715-175243650	chr2:175243650-175243651		15;16
N	jcn_only_AD	CUFF.643	chr2	+	chr2:186662254-186678271	chr2:186673861-186678271					23;42
N	alternative_donor	CUFF.665	chr2	+	chr2:242610857-242611605;chr2:242610821-242611605	chr2:242610841-242611605		chr2:242610821-242610840;chr2:242610841-242610856	chr2:242610820-242610821;chr2:242610840-242610841		485;72
N	jcn_only_AA	CUFF.575,CUFF.620	chr2	+	chr2:109085541-109086106	chr2:109085541-109085755		chr2:109085756-109086106	chr2:109086106-109086107		190;275
N	cassette	CUFF.656	chr2	+	chr2:228172636-228173919	chr2:228172636-228173614;chr2:228173793-228173919		chr2:228173615-228173792			9;3
K	cassette	CUFF.665	chr2	+	chr2:242577140-242590424	chr2:242577140-242577675;chr2:242577786-242590424		chr2:242577676-242577785			1585;68
K	intron_retention	CUFF.575	chr2	+	chr2:3481567-3482616				chr2:3481566-3481567;chr2:3482616-3482617		532;38
N	coord_cassette	CUFF.665	chr2	+	chr2:242590527-242592926	chr2:242590527-242590678;chr2:242590751-242591298;chr2:242591390-242592721;chr2:242592785-242592926		chr2:242590679-242590750;chr2:242591299-242591389;chr2:242592722-242592784			27;195
N	mutually_exclusive	CUFF.630	chr2	+	chr2:160599765-160604315,chr2:160605415-160608912	chr2:160599765-160602280,chr2:160602449-160608912	chr2:160604316-160605414	chr2:160602281-160602448			59;102
N	jcn_only_AA	CUFF.638	chr2	-	chr2:175689247-175742567	chr2:175740594-175742567		chr2:175689247-175740593	chr2:175689246-175689247		55;35
N	jcn_only_AD	CUFF.612	chr2	-	chr2:88892924-88894986	chr2:88892924-88893430		chr2:88893431-88894986	chr2:88894986-88894987		97;33
K	intron_retention		chr2	-	chr2:253116-260084				chr2:253115-253116;chr2:260084-260085		69;153
K	alternative_acceptor	CUFF.616	chr2	+	chr2:99232997-99234630	chr2:99232997-99234608		chr2:99234609-99234630	chr2:99234630-99234631		193;42
N	intron_retention	CUFF.596	chr2	-	chr2:61761039-61761692				chr2:61761038-61761039;chr2:61761692-61761693		55;148
K	alternative_first_exon	CUFF.632	chr2	+	chr2:169711971-169713199	chr2:169712721-169713199	chr2:169711862-169711970	chr2:169712553-169712720			452;118
N	alternative_acceptor	CUFF.664	chr2	-	chr2:242440335-242440892;chr2:242440263-242440892	chr2:242440493-242440892		chr2:242440263-242440334;chr2:242440335-242440492	chr2:242440262-242440263;chr2:242440334-242440335		264;48
K	intron_retention	CUFF.614	chr2	+	chr2:96195104-96195818				chr2:96195103-96195104;chr2:96195818-96195819		7;5
K	alternative_last_exon	CUFF.624	chr2	-	chr2:110936125-110937200	chr2:110936513-110937200	chr2:110936000-110936124	chr2:110936240-110936512			102;437
N	intron_retention	CUFF.596	chr2	-	chr2:61761039-61764153				chr2:61761038-61761039;chr2:61764153-61764154		231;151
N	mutually_exclusive	CUFF.664	chr2	-	chr2:242440212-242447420,chr2:242447551-242447857	chr2:242440212-242440942,chr2:242441124-242447857	chr2:242447421-242447550	chr2:242440943-242441123			89;23
K	cassette	CUFF.577	chr2	-	chr2:4008147-4021134	chr2:4008147-4009359;chr2:4009485-4021134		chr2:4009360-4009484			10;199
N	jcn_only_AA	CUFF.635	chr2	+	chr2:171191961-171225731	chr2:171191961-171225717		chr2:171225718-171225731	chr2:171225731-171225732		196;2
K	cassette	CUFF.650	chr2	-	chr2:207989129-208030190	chr2:207989129-208013705;chr2:208013925-208030190		chr2:208013706-208013924			372;48
K	cassette	CUFF.632	chr2	+	chr2:169699628-169707593	chr2:169699628-169707345;chr2:169707517-169707593		chr2:169707346-169707516			624;35
K	alternative_first_exon	CUFF.605	chr2	-	chr2:73215478-73226077	chr2:73215478-73221974	chr2:73226078-73226143	chr2:73221975-73222138			242;194
N	alternative_acceptor	CUFF.567	chr2	-	chr2:219002-229965	chr2:224921-229965		chr2:219002-224920	chr2:219001-219002		793;39
N	cassette	CUFF.579	chr2	-	chr2:11587901-11593707	chr2:11587901-11591327;chr2:11591933-11593707		chr2:11591328-11591932			16;651
N	intron_retention		chr2	+	chr2:220095073-220096649				chr2:220095072-220095073;chr2:220096649-220096650		185;231
K	cassette	CUFF.575	chr2	+	chr2:3405665-3425651	chr2:3405665-3425470;chr2:3425558-3425651		chr2:3425471-3425557			318;195
N	jcn_only_AD	CUFF.574	chr2	+	chr2:1320148-1371114	chr2:1357637-1371114		chr2:1320148-1357636	chr2:1320147-1320148		388;28
K	intron_retention	CUFF.664	chr2	-	chr2:242440335-242440892				chr2:242440334-242440335;chr2:242440892-242440893		35;109
N	mutually_exclusive	CUFF.610	chr2	-	chr2:86393768-86398330,chr2:86398436-86400772	chr2:86393768-86397871,chr2:86397965-86400772	chr2:86398331-86398435	chr2:86397872-86397964			15;90
N	jcn_only_AA	CUFF.575	chr2	+	chr2:3461465-3464033	chr2:3461465-3461565		chr2:3461566-3464033	chr2:3464033-3464034		1401;33
K	cassette	CUFF.583	chr2	-	chr2:27668317-27668795	chr2:27668317-27668611;chr2:27668711-27668795		chr2:27668612-27668710			48;968
N	intron_retention		chr2	-	chr2:177042550-177042730				chr2:177042549-177042550;chr2:177042730-177042731		43;135
N	alternative_donor	CUFF.636	chr2	-	chr2:174072387-174136238	chr2:174072387-174074374		chr2:174074375-174136238	chr2:174136238-174136239		461;1
K	alternative_acceptor	CUFF.624	chr2	-	chr2:110920710-110922096	chr2:110920713-110922096		chr2:110920710-110920712	chr2:110920709-110920710		11;15
N	coord_cassette	CUFF.635	chr2	+	chr2:171300557-171371430	chr2:171300557-171319877;chr2:171319956-171323015;chr2:171323222-171355101;chr2:171355214-171356155;chr2:171356319-171371430		chr2:171319878-171319955;chr2:171323016-171323221;chr2:171355102-171355213;chr2:171356156-171356318			4;55
N	alternative_acceptor	CUFF.567	chr2	-	chr2:253116-260084	chr2:256691-260084		chr2:253116-256690	chr2:253115-253116		69;29
K	cassette	CUFF.579	chr2	-	chr2:11593925-11597304	chr2:11593925-11595467;chr2:11595601-11597304		chr2:11595468-11595600			276;223
N	alternative_donor	CUFF.620	chr2	+	chr2:109085541-109086106	chr2:109085789-109086106		chr2:109085541-109085788	chr2:109085540-109085541		190;34
K	cassette	CUFF.624	chr2	-	chr2:110959072-110962476	chr2:110959072-110959949;chr2:110960057-110962476		chr2:110959950-110960056			416;248
K	alternative_donor	CUFF.627	chr2	+	chr2:133070569-133074681	chr2:133070573-133074681		chr2:133070569-133070572	chr2:133070568-133070569		53;5
N	alternative_acceptor	CUFF.636	chr2	-	chr2:174072387-174136238	chr2:174080565-174136238		chr2:174072387-174080564	chr2:174072386-174072387		461;5
N	mutually_exclusive	CUFF.664	chr2	-	chr2:242440212-242447420,chr2:242447551-242447919	chr2:242440212-242440942,chr2:242441124-242447919	chr2:242447421-242447550	chr2:242440943-242441123			89;23
K	cassette	CUFF.591	chr2	+	chr2:38177739-38201182	chr2:38177739-38178375;chr2:38179345-38201182		chr2:38178376-38179344			529;335
N	intron_retention		chr2	-	chr2:175711686-175779785				chr2:175711685-175711686;chr2:175779785-175779786		79;70
K	cassette	CUFF.611	chr2	-	chr2:86839398-86847452	chr2:86839398-86842277;chr2:86842381-86847452		chr2:86842278-86842380			89;47
N	intron_retention		chr2	-	chr2:4007227-4007505				chr2:4007226-4007227;chr2:4007505-4007506		21;196
K	alternative_acceptor	CUFF.588	chr2	+	chr2:33572578-33585669	chr2:33572578-33585663		chr2:33585664-33585669	chr2:33585669-33585670		71;142
N	alternative_acceptor	CUFF.583	chr2	-	chr2:27670502-27670678	chr2:27670525-27670678		chr2:27670502-27670524	chr2:27670501-27670502		189;38
N	cassette	CUFF.664	chr2	-	chr2:242441124-242447857;chr2:242441124-242447919	chr2:242441124-242447420;chr2:242447551-242447857,chr2:242447551-242447919		chr2:242447421-242447550			503;507
N	jcn_only_AD	CUFF.567	chr2	-	chr2:219002-229965	chr2:219002-224863		chr2:224864-229965	chr2:229965-229966		793;486
K	intron_retention	CUFF.652	chr2	+	chr2:219225383-219231746				chr2:219225382-219225383;chr2:219231746-219231747		81;74
N	intron_retention	CUFF.664	chr2	-	chr2:242447551-242447732				chr2:242447550-242447551;chr2:242447732-242447733		56;161
N	cassette	CUFF.645	chr2	-	chr2:197298183-197458231	chr2:197298183-197357967;chr2:197358100-197458231		chr2:197357968-197358099			69;132
N	jcn_only_AA	CUFF.646	chr2	+	chr2:200472851-200493786	chr2:200472851-200489254		chr2:200489255-200493786	chr2:200493786-200493787		252;29
N	intron_retention		chr2	+	chr2:241405787-241405862				chr2:241405786-241405787;chr2:241405862-241405863		42;194
K	cassette	CUFF.653	chr2	+	chr2:219433702-219445283	chr2:219433702-219438717;chr2:219438957-219445283		chr2:219438718-219438956			182;146
N	alternative_acceptor		chr2	+	chr2:3482705-3488490	chr2:3482705-3482989		chr2:3482990-3488490	chr2:3488490-3488491		12;75
K	alternative_acceptor	CUFF.634	chr2	-	chr2:169783801-169787174	chr2:169783873-169787174		chr2:169783801-169783872	chr2:169783800-169783801	chr2:169787175-169787372;chr2:169783666-169783800	78;8
K	intron_retention	CUFF.651	chr2	-	chr2:211081236-211082688				chr2:211081235-211081236;chr2:211082688-211082689		10;29
K	jcn_only_AA	CUFF.652	chr2	+	chr2:219222458-219222759	chr2:219222458-219222708		chr2:219222709-219222759	chr2:219222759-219222760		367;72
N	alternative_donor	CUFF.605,CUFF.624	chr2	-	chr2:73198815-73215386	chr2:73198815-73208137		chr2:73208138-73215386	chr2:73215386-73215387		479;7
N	jcn_only_AA	CUFF.635	chr2	+	chr2:171264355-171300476	chr2:171264355-171268210		chr2:171268211-171300476	chr2:171300476-171300477		87;78
K	intron_retention	CUFF.610	chr2	-	chr2:86398469-86400772				chr2:86398468-86398469;chr2:86400772-86400773		79;265
K	alternative_first_exon	CUFF.662	chr2	+	chr2:241392512-241398446,chr2:241394438-241398446,chr2:241381924-241398446,chr2:241397535-241398446;chr2:241375502-241398446	chr2:241396887-241398446	chr2:241375088-241375501	chr2:241396785-241396886			269;146
N	jcn_only_AD	CUFF.567	chr2	-	chr2:230045-231022	chr2:230045-230546		chr2:230547-231022	chr2:231022-231023		1226;64
N	jcn_only_AD	CUFF.583	chr2	-	chr2:27693963-27695116	chr2:27693963-27694099		chr2:27694100-27695116	chr2:27695116-27695117		743;38
N	alternative_donor	CUFF.649	chr2	+	chr2:207630472-207631367;chr2:207630379-207631367;chr2:207630487-207631367	chr2:207630243-207631367		chr2:207630243-207630378;chr2:207630379-207630471;chr2:207630472-207630486	chr2:207630242-207630243;chr2:207630378-207630379;chr2:207630471-207630472		67;35
K	intron_retention	CUFF.575	chr2	+	chr2:3447663-3460920				chr2:3447662-3447663;chr2:3460920-3460921		14;24
N	cassette	CUFF.638	chr2	-	chr2:175742857-175816891	chr2:175742857-175779785;chr2:175779900-175816891		chr2:175779786-175779899			76;91
K	alternative_first_exon	CUFF.612,CUFF.664	chr2	-	chr2:88895182-88913241	chr2:88895182-88895268	chr2:88913242-88913371	chr2:88895269-88895462			11;56
N	jcn_only_AA	CUFF.653	chr2	+	chr2:219457431-219458250;chr2:219457431-219458830	chr2:219457431-219458891		chr2:219458251-219458830;chr2:219458831-219458891	chr2:219458830-219458831;chr2:219458891-219458892		153;246
N	jcn_only_AD	CUFF.582,CUFF.651	chr2	-	chr2:25174424-25179911	chr2:25174424-25176418		chr2:25176419-25179911	chr2:25179911-25179912		166;43
N	cassette	CUFF.575	chr2	+	chr2:3469467-3482616	chr2:3469467-3481465;chr2:3481567-3482616		chr2:3481466-3481566			101;339
K	cassette	CUFF.594	chr2	-	chr2:46808731-46819613	chr2:46808731-46815213;chr2:46815319-46819613		chr2:46815214-46815318			77;535
K	intron_retention	CUFF.572	chr2	-	chr2:675631-677288				chr2:675630-675631;chr2:677288-677289		15;83
N	cassette	CUFF.605	chr2	-	chr2:73188378-73215386	chr2:73188378-73195576;chr2:73195663-73215386		chr2:73195577-73195662			48;119
N	jcn_only_AD	CUFF.601,CUFF.612	chr2	-	chr2:69870407-69901154;chr2:69870407-69870923;chr2:69870407-69870874	chr2:69870407-69870706		chr2:69870707-69870874;chr2:69870875-69870923;chr2:69870924-69901154	chr2:69870874-69870875;chr2:69870923-69870924;chr2:69901154-69901155		140;186
K	cassette	CUFF.629	chr2	+	chr2:153476233-153481951	chr2:153476233-153479050;chr2:153479072-153481951		chr2:153479051-153479071			96;72
K	intron_retention	CUFF.583	chr2	-	chr2:27668856-27669126				chr2:27668855-27668856;chr2:27669126-27669127		312;240
N	jcn_only_AD	CUFF.601	chr2	-	chr2:69870407-69901154;chr2:69870407-69870706;chr2:69870407-69870874	chr2:69870407-69870923		chr2:69870707-69870874;chr2:69870875-69870923;chr2:69870924-69901154	chr2:69870874-69870875;chr2:69870923-69870924;chr2:69901154-69901155		303;23
N	alternative_acceptor	CUFF.624	chr2	-	chr2:110920710-110922264	chr2:110920713-110922264		chr2:110920710-110920712	chr2:110920709-110920710		278;24
N	jcn_only_AD	CUFF.635	chr2	+	chr2:171400499-171508137	chr2:171503450-171508137		chr2:171400499-171503449	chr2:171400498-171400499		85;15
N	alternative_acceptor	CUFF.653	chr2	+	chr2:219457431-219458250;chr2:219457431-219458891	chr2:219457431-219458830		chr2:219458251-219458830;chr2:219458831-219458891	chr2:219458830-219458831;chr2:219458891-219458892		285;64
K	cassette	CUFF.610	chr2	-	chr2:86393768-86398330	chr2:86393768-86397871;chr2:86397968-86398330		chr2:86397872-86397967			32;788
N	cassette	CUFF.641	chr2	-	chr2:177041421-177042438	chr2:177041421-177042059;chr2:177042223-177042438		chr2:177042060-177042222			123;599
K	intron_retention	CUFF.626	chr2	+	chr2:118595561-118596782				chr2:118595560-118595561;chr2:118596782-118596783		37;26
N	intron_retention		chr2	-	chr2:242436794-242437030				chr2:242436793-242436794;chr2:242437030-242437031		56;52
N	jcn_only_AD	CUFF.591	chr2	+	chr2:38156080-38156404;chr2:38150511-38156404	chr2:38152569-38156404		chr2:38150511-38152568;chr2:38152569-38156079	chr2:38150510-38150511;chr2:38152568-38152569		61;239
N	cassette	CUFF.567	chr2	-	chr2:234273-247537;chr2:234273-243502	chr2:234273-242797;chr2:242872-243502,chr2:242872-247537		chr2:242798-242871			1272;152
K	alternative_first_exon	CUFF.605	chr2	-	chr2:73285726-73286222,chr2:73285726-73298168,chr2:73285726-73298732,chr2:73285726-73302708;chr2:73285726-73297588	chr2:73285726-73286136	chr2:73297589-73298430	chr2:73286137-73286318			796;172
N	jcn_only_AD	CUFF.644	chr2	+	chr2:191362446-191364740	chr2:191364583-191364740		chr2:191362446-191364582	chr2:191362445-191362446		1166;10
K	intron_retention		chr2	-	chr2:242439697-242440154				chr2:242439696-242439697;chr2:242440154-242440155		1477;89
K	intron_retention	CUFF.586	chr2	+	chr2:27729447-27729654				chr2:27729446-27729447;chr2:27729654-27729655		281;39
K	alternative_first_exon	CUFF.571	chr2	-	chr2:286344-287162;chr2:286344-287582	chr2:286344-286869	chr2:287163-287387;chr2:287583-287892	chr2:286870-286968			1052;204
K	intron_retention	CUFF.616	chr2	+	chr2:99232810-99232894				chr2:99232809-99232810;chr2:99232894-99232895		156;65
N	alternative_donor	CUFF.587,CUFF.596	chr2	-	chr2:31412345-31414264	chr2:31412345-31412532		chr2:31412533-31414264	chr2:31414264-31414265		69;1
N	jcn_only_AA	CUFF.652	chr2	+	chr2:220095073-220096981	chr2:220095073-220096649					115;185
N	jcn_only_AA	CUFF.664	chr2	-	chr2:242440493-242440892;chr2:242440263-242440892	chr2:242440335-242440892		chr2:242440263-242440334;chr2:242440335-242440492	chr2:242440262-242440263;chr2:242440334-242440335		272;35
N	jcn_only_AD	CUFF.601	chr2	-	chr2:69870407-69870706;chr2:69870407-69870923;chr2:69870407-69870874	chr2:69870407-69901154		chr2:69870707-69870874;chr2:69870875-69870923;chr2:69870924-69901154	chr2:69870874-69870875;chr2:69870923-69870924;chr2:69901154-69901155		296;29
N	alternative_acceptor	CUFF.583	chr2	-	chr2:27708371-27712481	chr2:27709110-27712481		chr2:27708371-27709109	chr2:27708370-27708371		854;3
K	coord_cassette	CUFF.574	chr2	+	chr2:1168870-1215567	chr2:1168870-1204788;chr2:1204917-1206142;chr2:1206366-1215567		chr2:1204789-1204916;chr2:1206143-1206365			195;151
K	cassette	CUFF.577	chr2	-	chr2:4006532-4007505	chr2:4006532-4007153;chr2:4007365-4007505		chr2:4007154-4007364			8;252
K	alternative_acceptor	CUFF.634	chr2	-	chr2:169826726-169828356	chr2:169826867-169828356		chr2:169826726-169826866	chr2:169826725-169826726	chr2:169828357-169828560;chr2:169826555-169826725	3;68
N	jcn_only_AD	CUFF.638	chr2	-	chr2:175809672-175816891	chr2:175809672-175809897		chr2:175809898-175816891	chr2:175816891-175816892		106;28
N	alternative_donor	CUFF.599	chr2	-	chr2:68374700-68384392;chr2:68374700-68384505	chr2:68374700-68384058		chr2:68384059-68384392;chr2:68384393-68384505	chr2:68384392-68384393;chr2:68384505-68384506		555;51
K	jcn_only_AA	CUFF.634	chr2	-	chr2:169826726-169828356	chr2:169826867-169828356		chr2:169826726-169826866	chr2:169826725-169826726	chr2:169828357-169828560;chr2:169826555-169826725	3;39
K	intron_retention	CUFF.665	chr2	+	chr2:242610841-242611605				chr2:242610840-242610841;chr2:242611605-242611606		22;279
N	cassette	CUFF.610	chr2	-	chr2:86397965-86400772	chr2:86397965-86398330;chr2:86398436-86400772		chr2:86398331-86398435			12;69
N	intron_retention		chr2	+	chr2:220094681-220094949				chr2:220094680-220094681;chr2:220094949-220094950		24;117
N	cassette	CUFF.572	chr2	-	chr2:675631-677288;chr2:675631-676573	chr2:675631-675757;chr2:676239-677288,chr2:676239-676573		chr2:675758-676238			45;159
N	alternative_donor	CUFF.601	chr2	-	chr2:69870407-69870706;chr2:69870407-69870923;chr2:69870407-69870874	chr2:69870407-69901154		chr2:69870707-69870874;chr2:69870875-69870923;chr2:69870924-69901154	chr2:69870874-69870875;chr2:69870923-69870924;chr2:69901154-69901155		4;29
N	jcn_only_AD	CUFF.646	chr2	+	chr2:200472851-200493786	chr2:200489320-200493786		chr2:200472851-200489319	chr2:200472850-200472851		252;29
N	alternative_donor	CUFF.591	chr2	+	chr2:38152569-38156404;chr2:38150511-38156404	chr2:38156080-38156404		chr2:38150511-38152568;chr2:38152569-38156079	chr2:38150510-38150511;chr2:38152568-38152569		59;4
N	alternative_donor	CUFF.654	chr2	+	chr2:220095128-220096649;chr2:220095073-220096649	chr2:220094623-220096649		chr2:220094623-220095072;chr2:220095073-220095127	chr2:220094622-220094623;chr2:220095072-220095073		226;68
K	alternative_last_exon	CUFF.574,CUFF.575	chr2	+	chr2:1133496-1161233	chr2:1133496-1156117	chr2:1161234-1161321	chr2:1156118-1157357			332;62
K	intron_retention	CUFF.652	chr2	+	chr2:219222458-219222759				chr2:219222457-219222458;chr2:219222759-219222760		367;100
K	jcn_only_AA	CUFF.583	chr2	-	chr2:27676381-27676848	chr2:27676607-27676848					54;140
K	intron_retention	CUFF.654	chr2	+	chr2:220094623-220094949				chr2:220094622-220094623;chr2:220094949-220094950		382;103
N	intron_retention		chr2	+	chr2:231934883-231937046				chr2:231934882-231934883;chr2:231937046-231937047		133;95
K	alternative_first_exon	CUFF.571	chr2	-	chr2:286344-286869;chr2:286344-287582	chr2:286344-287162	chr2:286870-286968;chr2:287583-287892	chr2:287163-287387			486;770
K	alternative_last_exon	CUFF.577	chr2	-	chr2:4006532-4007153	chr2:4006986-4007153	chr2:4005150-4006531	chr2:4006802-4006985			93;151
N	jcn_only_AA	CUFF.588	chr2	+	chr2:33477912-33482509;chr2:33477912-33482350	chr2:33477912-33482434		chr2:33482351-33482434;chr2:33482435-33482509	chr2:33482434-33482435;chr2:33482509-33482510		117;90
N	jcn_only_AA	CUFF.664	chr2	-	chr2:242435950-242437030	chr2:242436794-242437030		chr2:242435950-242436793	chr2:242435949-242435950		726;56
N	mutually_exclusive	CUFF.638	chr2	-	chr2:175711686-175779785,chr2:175779900-175816891	chr2:175711686-175742567,chr2:175742857-175816891	chr2:175779786-175779899	chr2:175742568-175742856			70;87
N	alternative_acceptor	CUFF.575	chr2	+	chr2:3461465-3464033	chr2:3461465-3461565		chr2:3461566-3464033	chr2:3464033-3464034		1401;19
K	alternative_first_exon	CUFF.654	chr2	+	chr2:220094623-220097211	chr2:220097085-220097211	chr2:220094386-220094622	chr2:220096982-220097084			98;843
N	alternative_donor	CUFF.635	chr2	+	chr2:171376051-171399415	chr2:171381137-171399415		chr2:171376051-171381136	chr2:171376050-171376051		71;6
N	intron_retention		chr2	-	chr2:166727531-166731188				chr2:166727530-166727531;chr2:166731188-166731189		57;71
N	jcn_only_AD	CUFF.587,CUFF.596	chr2	-	chr2:31412345-31414264	chr2:31412345-31412532		chr2:31412533-31414264	chr2:31414264-31414265		69;10
K	intron_retention	CUFF.616	chr2	+	chr2:99232810-99234630				chr2:99232809-99232810;chr2:99234630-99234631		13;13
K	intron_retention	CUFF.637	chr2	-	chr2:175216454-175243650				chr2:175216453-175216454;chr2:175243650-175243651		15;448
K	jcn_only_AA	CUFF.616,CUFF.659	chr2	+	chr2:232258622-232259491	chr2:232258622-232259365		chr2:232259366-232259491	chr2:232259491-232259492		97;116
K	intron_retention	CUFF.654	chr2	+	chr2:220097914-220098007				chr2:220097913-220097914;chr2:220098007-220098008		444;122
K	intron_retention	CUFF.653	chr2	+	chr2:219457431-219458891				chr2:219457430-219457431;chr2:219458891-219458892		246;74
N	intron_retention		chr2	-	chr2:242440263-242440892				chr2:242440262-242440263;chr2:242440892-242440893		223;161
N	jcn_only_AA	CUFF.636	chr2	-	chr2:174057785-174072274	chr2:174063553-174072274		chr2:174057785-174063552	chr2:174057784-174057785		587;41
K	alternative_first_exon	CUFF.641	chr2	-	chr2:177043827-177053146	chr2:177043827-177052792	chr2:177053147-177053356	chr2:177052793-177053005			120;78
N	jcn_only_AA	CUFF.624	chr2	-	chr2:110881641-110883213	chr2:110882901-110883213		chr2:110881641-110882900	chr2:110881640-110881641		425;29
K	intron_retention	CUFF.652	chr2	+	chr2:219231824-219232152				chr2:219231823-219231824;chr2:219232152-219232153		450;121
K	jcn_only_AA	CUFF.620	chr2	+	chr2:109102365-109102966	chr2:109102365-109102890		chr2:109102891-109102966	chr2:109102966-109102967		14;984
N	jcn_only_AA		chr2	+	chr2:231934883-231937046	chr2:231934883-231936902		chr2:231936903-231937046	chr2:231937046-231937047		133;230
N	alternative_donor	CUFF.591	chr2	+	chr2:38224658-38231133	chr2:38230170-38231133		chr2:38224658-38230169	chr2:38224657-38224658		1309;39
K	alternative_donor	CUFF.593,CUFF.624	chr2	-	chr2:110920710-110922264	chr2:110920710-110922096		chr2:110922097-110922264	chr2:110922264-110922265		278;21
N	intron_retention		chr2	-	chr2:110920713-110922264				chr2:110920712-110920713;chr2:110922264-110922265		25;21
N	cassette	CUFF.575	chr2	+	chr2:3469467-3482616	chr2:3469467-3470024;chr2:3470165-3482616		chr2:3470025-3470164			101;243
K	intron_retention	CUFF.632	chr2	+	chr2:169711971-169712395				chr2:169711970-169711971;chr2:169712395-169712396		105;16
K	intron_retention	CUFF.654	chr2	+	chr2:220098156-220098436				chr2:220098155-220098156;chr2:220098436-220098437		285;201
N	jcn_only_AD		chr2	-	chr2:88913372-88926484	chr2:88913372-88924263		chr2:88924264-88926484	chr2:88926484-88926485		6;3
N	jcn_only_AD	CUFF.654	chr2	+	chr2:220095073-220096649;chr2:220094623-220096649	chr2:220095128-220096649		chr2:220094623-220095072;chr2:220095073-220095127	chr2:220094622-220094623;chr2:220095072-220095073		253;232
N	cassette	CUFF.605	chr2	-	chr2:73172229-73195576	chr2:73172229-73188259;chr2:73188378-73195576		chr2:73188260-73188377			143;218
N	alternative_donor		chr2	-	chr2:88913372-88926484	chr2:88913372-88924263		chr2:88924264-88926484	chr2:88926484-88926485		6;0
K	intron_retention	CUFF.665	chr2	+	chr2:242594759-242606059				chr2:242594758-242594759;chr2:242606059-242606060		13;80
N	jcn_only_AA	CUFF.628,CUFF.653	chr2	+	chr2:219457431-219458891;chr2:219457431-219458830	chr2:219457431-219458250		chr2:219458251-219458830;chr2:219458831-219458891	chr2:219458830-219458831;chr2:219458891-219458892		349;49
N	jcn_only_AA	CUFF.574	chr2	+	chr2:1243549-1251098	chr2:1243549-1246509		chr2:1246510-1251098	chr2:1251098-1251099		291;77
N	alternative_acceptor	CUFF.635	chr2	+	chr2:171264355-171300476	chr2:171264355-171268210		chr2:171268211-171300476	chr2:171300476-171300477		87;4
K	alternative_first_exon	CUFF.619	chr2	+	chr2:101436877-101521194	chr2:101437662-101521194	chr2:101436614-101436876	chr2:101437407-101437661			24;118
N	intron_retention	CUFF.567	chr2	-	chr2:260703-262630				chr2:260702-260703;chr2:262630-262631		10;39
N	intron_retention		chr2	-	chr2:177042223-177042730				chr2:177042222-177042223;chr2:177042730-177042731		35;60
N	jcn_only_AD	CUFF.619	chr2	+	chr2:101549464-101554214	chr2:101550623-101554214		chr2:101549464-101550622	chr2:101549463-101549464		5600;32
N	intron_retention		chr2	-	chr2:260898-262630				chr2:260897-260898;chr2:262630-262631		55;16
N	jcn_only_AD		chr2	-	chr2:61764723-61765626	chr2:61764723-61765272		chr2:61765273-61765626	chr2:61765626-61765627		27;23
K	intron_retention	CUFF.567	chr2	-	chr2:231192-233100				chr2:231191-231192;chr2:233100-233101		643;115
N	jcn_only_AA	CUFF.583	chr2	-	chr2:27670502-27670678	chr2:27670525-27670678		chr2:27670502-27670524	chr2:27670501-27670502		189;68
N	alternative_acceptor	CUFF.662	chr2	+	chr2:241404164-241404272	chr2:241404164-241404251		chr2:241404252-241404272	chr2:241404272-241404273		325;11
N	mutually_exclusive	CUFF.665	chr2	+	chr2:242594063-242598522,chr2:242598603-242606059	chr2:242594063-242594685,chr2:242594759-242606059	chr2:242598523-242598602	chr2:242594686-242594758			47;13
K	cassette	CUFF.587	chr2	-	chr2:31423492-31424999	chr2:31423492-31424727;chr2:31424865-31424999		chr2:31424728-31424864			9;38
K	intron_retention	CUFF.596	chr2	-	chr2:61720189-61721028				chr2:61720188-61720189;chr2:61721028-61721029		140;107
K	intron_retention		chr2	-	chr2:242440212-242440892				chr2:242440211-242440212;chr2:242440892-242440893		918;181
N	cassette	CUFF.610	chr2	-	chr2:86397965-86400772	chr2:86397965-86398330;chr2:86398505-86400772		chr2:86398331-86398504			12;459
N	alternative_donor	CUFF.591	chr2	+	chr2:38231360-38244328	chr2:38239793-38244328		chr2:38231360-38239792	chr2:38231359-38231360		1140;3
N	cassette	CUFF.567	chr2	-	chr2:242872-247537;chr2:234273-247537	chr2:242872-243502,chr2:234273-243502;chr2:243563-247537		chr2:243503-243562			1316;162
K	cassette	CUFF.577	chr2	-	chr2:4009485-4021134	chr2:4009485-4015768;chr2:4015879-4021134		chr2:4015769-4015878			99;71
K	alternative_donor	CUFF.610	chr2	-	chr2:86386795-86389098	chr2:86386795-86389074		chr2:86389075-86389098	chr2:86389098-86389099		1065;60
N	jcn_only_AA	CUFF.638	chr2	-	chr2:175689247-175711607	chr2:175702065-175711607		chr2:175689247-175702064	chr2:175689246-175689247		566;43
N	jcn_only_AA	CUFF.574,CUFF.588	chr2	+	chr2:1251216-1263141	chr2:1251216-1260176		chr2:1260177-1263141	chr2:1263141-1263142		278;40
N	jcn_only_AA	CUFF.620	chr2	+	chr2:109089356-109091990	chr2:109089356-109091244		chr2:109091245-109091990	chr2:109091990-109091991		8;47
K	intron_retention	CUFF.665	chr2	+	chr2:242591390-242592926				chr2:242591389-242591390;chr2:242592926-242592927		1054;44
N	alternative_donor	CUFF.591	chr2	+	chr2:38156080-38156404;chr2:38150511-38156404	chr2:38152569-38156404		chr2:38150511-38152568;chr2:38152569-38156079	chr2:38150510-38150511;chr2:38152568-38152569		33;30
N	intron_retention	CUFF.572	chr2	-	chr2:675631-676573				chr2:675630-675631;chr2:676573-676574		29;56
N	jcn_only_AA		chr2	+	chr2:3469467-3481462	chr2:3469467-3471200					41;18
N	cassette	CUFF.605	chr2	-	chr2:73268061-73297588	chr2:73268061-73285656;chr2:73285726-73297588		chr2:73285657-73285725			62;314
N	intron_retention		chr2	+	chr2:242610857-242611605				chr2:242610856-242610857;chr2:242611605-242611606		57;261
K	alternative_acceptor	CUFF.609	chr2	-	chr2:79364464-79365092	chr2:79364469-79365092		chr2:79364464-79364468	chr2:79364463-79364464		893;117
N	jcn_only_AD	CUFF.599	chr2	-	chr2:68374700-68384392;chr2:68374700-68384505	chr2:68374700-68384058		chr2:68384059-68384392;chr2:68384393-68384505	chr2:68384392-68384393;chr2:68384505-68384506		647;47
N	intron_retention		chr2	+	chr2:242610821-242611605				chr2:242610820-242610821;chr2:242611605-242611606		236;297
K	alternative_first_exon	CUFF.574	chr2	+	chr2:1263214-1271136	chr2:1266722-1271136	chr2:1263142-1263213	chr2:1266624-1266721			217;40
K	intron_retention		chr2	-	chr2:263373-263563				chr2:263372-263373;chr2:263563-263564		685;11
N	alternative_acceptor	CUFF.573,CUFF.588	chr2	+	chr2:33477912-33482434;chr2:33477912-33482509	chr2:33477912-33482350		chr2:33482351-33482434;chr2:33482435-33482509	chr2:33482434-33482435;chr2:33482509-33482510		101;52
N	alternative_donor	CUFF.567	chr2	-	chr2:219002-229965	chr2:219002-224863		chr2:224864-229965	chr2:229965-229966		793;19
K	cassette	CUFF.579	chr2	-	chr2:11597360-11605897	chr2:11597360-11598406;chr2:11598478-11605897		chr2:11598407-11598477			329;182
K	cassette	CUFF.653	chr2	+	chr2:219445464-219447693	chr2:219445464-219445717;chr2:219445838-219447693		chr2:219445718-219445837			136;58
N	jcn_only_AA	CUFF.586	chr2	+	chr2:27724097-27726380	chr2:27724097-27724556		chr2:27724557-27726380	chr2:27726380-27726381		231;32
K	intron_retention		chr2	+	chr2:3469467-3481465				chr2:3469466-3469467;chr2:3481465-3481466		318;30
N	jcn_only_AD	CUFF.664	chr2	-	chr2:242435950-242436714;chr2:242435950-242437030	chr2:242435950-242436596		chr2:242436597-242436714;chr2:242436715-242437030	chr2:242436714-242436715;chr2:242437030-242437031		739;41
N	cassette	CUFF.647	chr2	-	chr2:204335037-204354306;chr2:204326649-204354306	chr2:204326649-204341798,chr2:204335037-204341798;chr2:204341880-204354306		chr2:204341799-204341879			81;270
N	alternative_first_exon	CUFF.654	chr2	+	chr2:220095073-220096981;chr2:220095128-220096981	chr2:220096763-220096981	chr2:220094386-220095127	chr2:220096500-220096762			190;541
N	alternative_donor	CUFF.601	chr2	-	chr2:69870407-69901154;chr2:69870407-69870706;chr2:69870407-69870874	chr2:69870407-69870923		chr2:69870707-69870874;chr2:69870875-69870923;chr2:69870924-69901154	chr2:69870874-69870875;chr2:69870923-69870924;chr2:69901154-69901155		33;0
K	cassette	CUFF.664	chr2	-	chr2:242437103-242438053	chr2:242437103-242437649;chr2:242437765-242438053		chr2:242437650-242437764			253;427
N	coord_cassette	CUFF.665	chr2	+	chr2:242590751-242592926	chr2:242590751-242591298;chr2:242591390-242592721;chr2:242592785-242592926		chr2:242591299-242591389;chr2:242592722-242592784			532;78
N	jcn_only_AD	CUFF.635	chr2	+	chr2:171034800-171055717	chr2:171036692-171055717		chr2:171034800-171036691	chr2:171034799-171034800		11;11
K	jcn_only_AA	CUFF.616	chr2	+	chr2:99232997-99234630	chr2:99232997-99234608		chr2:99234609-99234630	chr2:99234630-99234631		193;77
K	intron_retention	CUFF.578	chr2	+	chr2:9244290-9244564				chr2:9244289-9244290;chr2:9244564-9244565		153;657
K	alternative_last_exon	CUFF.595	chr2	+	chr2:48898820-49003418	chr2:48898820-48906473	chr2:49003419-49003753	chr2:48906474-48906742			259;217
N	alternative_acceptor	CUFF.575,CUFF.620	chr2	+	chr2:109085541-109086106	chr2:109085541-109085755		chr2:109085756-109086106	chr2:109086106-109086107		190;187
K	alternative_acceptor	CUFF.616,CUFF.659	chr2	+	chr2:232258622-232259491	chr2:232258622-232259365		chr2:232259366-232259491	chr2:232259491-232259492		97;156
N	coord_cassette	CUFF.605	chr2	-	chr2:73188378-73215386	chr2:73188378-73195576;chr2:73195663-73198698;chr2:73198815-73215386		chr2:73195577-73195662;chr2:73198699-73198814			48;334
N	jcn_only_AD	CUFF.620	chr2	+	chr2:109068923-109085435	chr2:109079142-109085435		chr2:109068923-109079141	chr2:109068922-109068923		289;364
N	coord_cassette	CUFF.605	chr2	-	chr2:73172229-73195576	chr2:73172229-73188259;chr2:73188378-73194365;chr2:73194453-73195576		chr2:73188260-73188377;chr2:73194366-73194452			143;156
N	coord_cassette	CUFF.638	chr2	-	chr2:175779900-175816891	chr2:175779900-175783261;chr2:175783294-175809615;chr2:175809672-175816891		chr2:175783262-175783293;chr2:175809616-175809671			94;93
K	intron_retention	CUFF.609	chr2	-	chr2:79363203-79363915				chr2:79363202-79363203;chr2:79363915-79363916		199;110
K	alternative_acceptor	CUFF.647	chr2	-	chr2:204354810-204355936	chr2:204354813-204355936		chr2:204354810-204354812	chr2:204354809-204354810		20;227
K	intron_retention	CUFF.664	chr2	-	chr2:242447551-242447919				chr2:242447550-242447551;chr2:242447919-242447920		332;205
K	intron_retention	CUFF.594	chr2	-	chr2:46840925-46842075				chr2:46840924-46840925;chr2:46842075-46842076		688;20
K	alternative_first_exon	CUFF.575	chr2	+	chr2:3461465-3464033	chr2:3462233-3464033	chr2:3461392-3461464	chr2:3462134-3462232			1009;23
K	alternative_last_exon	CUFF.583	chr2	-	chr2:27672964-27676250	chr2:27676138-27676250	chr2:27672865-27672963	chr2:27675907-27676137			146;2360
N	cassette	CUFF.657	chr2	+	chr2:231927036-231931619	chr2:231927036-231927219;chr2:231927390-231931619		chr2:231927220-231927389			11;232
K	intron_retention	CUFF.665	chr2	+	chr2:242607637-242607954				chr2:242607636-242607637;chr2:242607954-242607955		553;19
N	alternative_acceptor	CUFF.664	chr2	-	chr2:242440335-242440892;chr2:242440493-242440892	chr2:242440263-242440892		chr2:242440263-242440334;chr2:242440335-242440492	chr2:242440262-242440263;chr2:242440334-242440335		89;223
N	jcn_only_AD		chr2	-	chr2:175816931-175869933	chr2:175816931-175869621		chr2:175869622-175869933	chr2:175869933-175869934		9;304
N	alternative_acceptor	CUFF.635	chr2	+	chr2:171191961-171225731	chr2:171191961-171225717		chr2:171225718-171225731	chr2:171225731-171225732		196;1
K	intron_retention	CUFF.572	chr2	-	chr2:676239-677288				chr2:676238-676239;chr2:677288-677289		6;49
N	intron_retention		chr2	+	chr2:242594063-242606059				chr2:242594062-242594063;chr2:242606059-242606060		29;408
K	cassette	CUFF.577	chr2	-	chr2:4008147-4021134	chr2:4008147-4009359;chr2:4009394-4021134		chr2:4009360-4009393			10;238
N	jcn_only_AD	CUFF.574	chr2	+	chr2:1094097-1099090	chr2:1098397-1099090		chr2:1094097-1098396	chr2:1094096-1094097		209;69
N	jcn_only_AD	CUFF.619	chr2	+	chr2:101541757-101549371	chr2:101541763-101549371		chr2:101541757-101541762	chr2:101541756-101541757		3176;48
N	intron_retention		chr2	-	chr2:207989129-208031863				chr2:207989128-207989129;chr2:208031863-208031864		27;51
K	jcn_only_AA	CUFF.588	chr2	+	chr2:33572578-33585669	chr2:33572578-33585663		chr2:33585664-33585669	chr2:33585669-33585670		71;288
N	alternative_donor	CUFF.646	chr2	+	chr2:200472851-200493786	chr2:200489320-200493786		chr2:200472851-200489319	chr2:200472850-200472851		252;0
N	jcn_only_AA	CUFF.664	chr2	-	chr2:242440335-242440892;chr2:242440493-242440892	chr2:242440263-242440892		chr2:242440263-242440334;chr2:242440335-242440492	chr2:242440262-242440263;chr2:242440334-242440335		84;223
K	intron_retention		chr2	-	chr2:242440212-242440942				chr2:242440211-242440212;chr2:242440942-242440943		180;480
K	coord_cassette	CUFF.652	chr2	+	chr2:219225383-219231746	chr2:219225383-219227457;chr2:219227626-219229350;chr2:219229476-219231746		chr2:219227458-219227625;chr2:219229351-219229475			81;305
K	alternative_first_exon	CUFF.638	chr2	-	chr2:175711686-175740515;chr2:175711686-175712446	chr2:175711686-175712040	chr2:175712447-175712545	chr2:175712041-175712311			102;77
N	jcn_only_AD	CUFF.630	chr2	+	chr2:160585687-160599571	chr2:160590594-160599571		chr2:160585687-160590593	chr2:160585686-160585687		164;19
N	alternative_acceptor	CUFF.583	chr2	-	chr2:27668317-27668611	chr2:27668497-27668611		chr2:27668317-27668496	chr2:27668316-27668317		1064;51
N	intron_retention		chr2	-	chr2:253116-256206				chr2:253115-253116;chr2:256206-256207		35;45
K	intron_retention	CUFF.583	chr2	-	chr2:27670790-27671781				chr2:27670789-27670790;chr2:27671781-27671782		125;69
N	jcn_only_AA	CUFF.605	chr2	-	chr2:73172229-73188259	chr2:73184233-73188259		chr2:73172229-73184232	chr2:73172228-73172229		197;82
K	intron_retention	CUFF.583	chr2	-	chr2:27688750-27693794				chr2:27688749-27688750;chr2:27693794-27693795		11;407
K	cassette	CUFF.641	chr2	-	chr2:177042223-177053146	chr2:177042223-177043756;chr2:177043827-177053146		chr2:177043757-177043826			246;98
K	intron_retention	CUFF.619	chr2	+	chr2:101604739-101606717				chr2:101604738-101604739;chr2:101606717-101606718		316;9
K	jcn_only_AD	CUFF.650	chr2	-	chr2:207953306-207988497;chr2:207953306-207989067	chr2:207953306-207988699		chr2:207988498-207988699;chr2:207988700-207989067	chr2:207988699-207988700;chr2:207989067-207989068		402;26
N	intron_retention		chr2	+	chr2:220095073-220096981				chr2:220095072-220095073;chr2:220096981-220096982		115;103
K	intron_retention	CUFF.596	chr2	-	chr2:61726049-61726847				chr2:61726048-61726049;chr2:61726847-61726848		3234;141
N	jcn_only_AA	CUFF.583	chr2	-	chr2:27708371-27712481	chr2:27709110-27712481		chr2:27708371-27709109	chr2:27708370-27708371		854;15
K	alternative_donor	CUFF.650	chr2	-	chr2:207953306-207988497;chr2:207953306-207988699	chr2:207953306-207989067		chr2:207988498-207988699;chr2:207988700-207989067	chr2:207988699-207988700;chr2:207989067-207989068		171;320
N	alternative_donor	CUFF.654	chr2	+	chr2:220095128-220096649;chr2:220094623-220096649	chr2:220095073-220096649		chr2:220094623-220095072;chr2:220095073-220095127	chr2:220094622-220094623;chr2:220095072-220095073		192;102
N	jcn_only_AA	CUFF.591	chr2	+	chr2:38156873-38201182	chr2:38156873-38177653		chr2:38177654-38201182	chr2:38201182-38201183		316;47
N	alternative_last_exon	CUFF.654	chr2	+	chr2:220094623-220097211;chr2:220094623-220094949	chr2:220094623-220096649	chr2:220097212-220097743;chr2:220094950-220095127	chr2:220096650-220096762			410;50
N	jcn_only_AD	CUFF.582,CUFF.637	chr2	-	chr2:175216454-175243650	chr2:175216454-175234714		chr2:175234715-175243650	chr2:175243650-175243651		15;16
N	intron_retention	CUFF.654	chr2	+	chr2:220094623-220096649				chr2:220094622-220094623;chr2:220096649-220096650		68;189
N	jcn_only_AA	CUFF.567	chr2	-	chr2:219002-229965	chr2:224921-229965		chr2:219002-224920	chr2:219001-219002		793;558
K	intron_retention	CUFF.657	chr2	+	chr2:231927390-231931619				chr2:231927389-231927390;chr2:231931619-231931620		193;37
K	alternative_first_exon	CUFF.580	chr2	+	chr2:16535569-16573520	chr2:16536536-16573520	chr2:16535524-16535568	chr2:16536437-16536535			1156;101
K	alternative_first_exon	CUFF.661	chr2	+	chr2:237476485-237489082	chr2:237478568-237489082	chr2:237476336-237476484	chr2:237478227-237478567			38;77
N	alternative_donor	CUFF.638	chr2	-	chr2:175809672-175816891	chr2:175809672-175809897		chr2:175809898-175816891	chr2:175816891-175816892		106;1
K	cassette	CUFF.638	chr2	-	chr2:175677211-175689161	chr2:175677211-175686456;chr2:175686508-175689161		chr2:175686457-175686507			484;152
N	mutually_exclusive	CUFF.664	chr2	-	chr2:242440212-242447420,chr2:242447551-242447919	chr2:242440212-242440892,chr2:242441124-242447919	chr2:242447421-242447550	chr2:242440893-242441123			89;36
K	cassette	CUFF.60	chr1	+	chr1:167272812-167301706	chr1:167272812-167288250;chr1:167288294-167301706		chr1:167288251-167288293			107;38
N	alternative_donor		chr1	+	chr1:245246991-245285221	chr1:245270600-245285221		chr1:245246991-245270599	chr1:245246990-245246991		70;1
K	alternative_last_exon	CUFF.3	chr1	+	chr1:10500471-10511433	chr1:10500471-10502321	chr1:10511434-10512309	chr1:10502322-10502945			122;350
K	jcn_only_AD	CUFF.5	chr1	+	chr1:11159872-11161857	chr1:11159968-11161857		chr1:11159872-11159967	chr1:11159871-11159872		77;579
K	jcn_only_AA	CUFF.73	chr1	-	chr1:213173726-213178374	chr1:213174255-213178374					123;146
K	alternative_donor	CUFF.49	chr1	+	chr1:155180207-155180338	chr1:155180227-155180338		chr1:155180207-155180226	chr1:155180206-155180207		155;71
N	alternative_acceptor	CUFF.9	chr1	-	chr1:16928339-16935002;chr1:16921509-16935002	chr1:16934187-16935002		chr1:16921509-16928338;chr1:16928339-16934186	chr1:16921508-16921509;chr1:16928338-16928339		22;47
N	jcn_only_AD	CUFF.55	chr1	+	chr1:160137203-160141040	chr1:160137220-160141040		chr1:160137203-160137219	chr1:160137202-160137203		11;11
K	alternative_last_exon	CUFF.80	chr1	-	chr1:247302060-247322307;chr1:247287174-247322307	chr1:247320520-247322307,chr1:247320706-247322307	chr1:247301348-247302059;chr1:247285277-247287173	chr1:247319442-247320519			217;153
K	mutually_exclusive	CUFF.60	chr1	+	chr1:167190196-167272710,chr1:167272812-167301706	chr1:167190196-167210643,chr1:167210848-167301706	chr1:167272711-167272811	chr1:167210644-167210847			123;113
K	cassette	CUFF.18	chr1	+	chr1:31783012-31791955	chr1:31783012-31791013;chr1:31791084-31791955		chr1:31791014-31791083			437;51
K	alternative_first_exon	CUFF.75	chr1	+	chr1:224363650-224377278;chr1:224371534-224377278	chr1:224371121-224377278	chr1:224363372-224363649;chr1:224371366-224371533	chr1:224370879-224371120			101;68
K	intron_retention		chr1	+	chr1:245246991-245250061				chr1:245246990-245246991;chr1:245250061-245250062		77;32
N	jcn_only_AD		chr1	-	chr1:106132408-106145898;chr1:106132408-106143891;chr1:106132408-106143252	chr1:106132408-106146784		chr1:106143253-106143891;chr1:106143892-106145898;chr1:106145899-106146784	chr1:106143891-106143892;chr1:106145898-106145899;chr1:106146784-106146785		197;101
K	intron_retention	CUFF.20	chr1	-	chr1:32827653-32829675				chr1:32827652-32827653;chr1:32829675-32829676		48;59
K	alternative_donor	CUFF.59	chr1	+	chr1:166808842-166810191	chr1:166809007-166810191		chr1:166808842-166809006	chr1:166808841-166808842		35;34
N	alternative_donor	CUFF.34	chr1	-	chr1:106132408-106146784;chr1:106132408-106143891;chr1:106132408-106143252	chr1:106132408-106145898		chr1:106143253-106143891;chr1:106143892-106145898;chr1:106145899-106146784	chr1:106143891-106143892;chr1:106145898-106145899;chr1:106146784-106146785		274;67
K	intron_retention		chr1	+	chr1:245133746-245165422				chr1:245133745-245133746;chr1:245165422-245165423		64;195
N	intron_retention		chr1	+	chr1:222802037-222838940				chr1:222802036-222802037;chr1:222838940-222838941		18;60
N	jcn_only_AD	CUFF.55	chr1	+	chr1:160146353-160147308	chr1:160146393-160147308		chr1:160146353-160146392	chr1:160146352-160146353		15;50
N	alternative_first_exon	CUFF.47	chr1	-	chr1:153927643-153930536;chr1:153927643-153930820	chr1:153927643-153930621	chr1:153930537-153930619;chr1:153930821-153931091	chr1:153930622-153930741			83;129
N	cassette	CUFF.25	chr1	+	chr1:54360029-54370338	chr1:54360029-54360111;chr1:54360221-54370338		chr1:54360112-54360220			18;631
K	intron_retention	CUFF.10	chr1	+	chr1:22963196-22964102				chr1:22963195-22963196;chr1:22964102-22964103		285;37
K	cassette	CUFF.2	chr1	+	chr1:2075781-2077465	chr1:2075781-2076827;chr1:2076951-2077465		chr1:2076828-2076950			1266;323
N	alternative_donor	CUFF.54,CUFF.6	chr1	-	chr1:158581180-158582606	chr1:158581180-158581575		chr1:158581576-158582606	chr1:158582606-158582607		11;139
N	alternative_donor	CUFF.74	chr1	+	chr1:222806592-222818895	chr1:222817929-222818895		chr1:222806592-222817928	chr1:222806591-222806592		42;10
K	alternative_first_exon	CUFF.6	chr1	-	chr1:11710892-11715696;chr1:11710892-11713447	chr1:11710892-11714375	chr1:11715697-11715938;chr1:11713448-11713650	chr1:11714376-11714739			395;66
N	jcn_only_AD	CUFF.66	chr1	+	chr1:200877016-200877857	chr1:200877678-200877857		chr1:200877016-200877677	chr1:200877015-200877016		260;101
K	intron_retention		chr1	+	chr1:54360029-54360111				chr1:54360028-54360029;chr1:54360111-54360112		442;364
N	cassette	CUFF.39	chr1	-	chr1:114424620-114429870;chr1:114423763-114429870	chr1:114423763-114429158,chr1:114424620-114429158;chr1:114429281-114429870		chr1:114429159-114429280			121;105
K	alternative_first_exon	CUFF.10	chr1	+	chr1:22963196-22964102	chr1:22963354-22964102	chr1:22962999-22963195	chr1:22963196-22963353			308;330
K	cassette	CUFF.79	chr1	+	chr1:245222761-245245384	chr1:245222761-245238875;chr1:245238914-245245384		chr1:245238876-245238913			542;646
N	jcn_only_AA		chr1	-	chr1:106132408-106145898	chr1:106144008-106145898		chr1:106132408-106144007	chr1:106132407-106132408		98;44
K	cassette	CUFF.61	chr1	-	chr1:169439425-169454800	chr1:169439425-169446392;chr1:169446996-169454800		chr1:169446393-169446995			6;139
K	intron_retention	CUFF.41	chr1	+	chr1:145580611-145581181				chr1:145580610-145580611;chr1:145581181-145581182		73;36
K	cassette	CUFF.65	chr1	+	chr1:196913069-196927020	chr1:196913069-196919981;chr1:196920159-196927020		chr1:196919982-196920158			166;170
K	alternative_first_exon	CUFF.6	chr1	-	chr1:11710892-11715696;chr1:11710892-11714375	chr1:11710892-11713447	chr1:11715697-11715938;chr1:11714376-11714739	chr1:11713448-11713650			226;235
N	alternative_donor	CUFF.60	chr1	+	chr1:167301773-167334703	chr1:167326759-167334703		chr1:167301773-167326758	chr1:167301772-167301773		321;1
K	alternative_first_exon	CUFF.16	chr1	+	chr1:28655636-28657107,chr1:28655692-28657107	chr1:28656887-28657107	chr1:28655425-28655635	chr1:28656740-28656886			355;375
N	intron_retention		chr1	-	chr1:153924081-153930874				chr1:153924080-153924081;chr1:153930874-153930875		22;85
K	jcn_only_AD	CUFF.2	chr1	+	chr1:1987002-1987922	chr1:1987316-1987922		chr1:1987002-1987315	chr1:1987001-1987002		344;73
K	jcn_only_AA	CUFF.80	chr1	-	chr1:247320520-247322307	chr1:247320706-247322307		chr1:247320520-247320705	chr1:247320519-247320520		110;47
K	alternative_first_exon	CUFF.22	chr1	-	chr1:41486451-41487287	chr1:41486451-41486535	chr1:41487288-41487387	chr1:41486536-41486605			9;193
N	jcn_only_AD	CUFF.46	chr1	+	chr1:153389040-153390541	chr1:153389755-153390541		chr1:153389040-153389754	chr1:153389039-153389040		11;34
N	alternative_acceptor	CUFF.40	chr1	-	chr1:120529706-120539619	chr1:120539370-120539619		chr1:120529706-120539369	chr1:120529705-120529706		10;9
K	cassette	CUFF.60	chr1	+	chr1:167353189-167358824	chr1:167353189-167356417;chr1:167356485-167358824		chr1:167356418-167356484			241;105
K	coord_cassette	CUFF.3	chr1	+	chr1:10491459-10500403	chr1:10491459-10493898;chr1:10494023-10494713;chr1:10494748-10500403		chr1:10493899-10494022;chr1:10494714-10494747			115;127
K	cassette	CUFF.56	chr1	-	chr1:160991278-161008669	chr1:160991278-160992539;chr1:160992618-161008669		chr1:160992540-160992617			21;26
K	jcn_only_AD	CUFF.59	chr1	+	chr1:166808842-166810191	chr1:166809007-166810191		chr1:166808842-166809006	chr1:166808841-166808842		35;46
N	coord_cassette	CUFF.19	chr1	+	chr1:32541424-32557275	chr1:32541424-32542164;chr1:32542248-32542363;chr1:32542448-32542764;chr1:32542920-32557275		chr1:32542165-32542247;chr1:32542364-32542447;chr1:32542765-32542919			15;179
K	alternative_last_exon	CUFF.63,CUFF.74	chr1	+	chr1:222837491-222838650	chr1:222837491-222838224	chr1:222838651-222841354	chr1:222838225-222838610			157;57
N	jcn_only_AD	CUFF.2	chr1	+	chr1:2101044-2103493	chr1:2103085-2103493		chr1:2101044-2103084	chr1:2101043-2101044		494;35
N	coord_cassette	CUFF.19	chr1	+	chr1:32541424-32557275	chr1:32541424-32542363;chr1:32542448-32542764;chr1:32542920-32557275		chr1:32542364-32542447;chr1:32542765-32542919			15;278
K	intron_retention	CUFF.47	chr1	-	chr1:153925127-153925280				chr1:153925126-153925127;chr1:153925280-153925281		133;19
K	alternative_donor	CUFF.2	chr1	+	chr1:1987002-1987922	chr1:1987316-1987922		chr1:1987002-1987315	chr1:1987001-1987002		344;286
K	cassette	CUFF.43	chr1	+	chr1:147563999-147566014	chr1:147563999-147564303;chr1:147564350-147566014		chr1:147564304-147564349			20;47
K	cassette	CUFF.59	chr1	+	chr1:166810326-166818174	chr1:166810326-166816730;chr1:166816830-166818174		chr1:166816731-166816829			41;29
N	coord_cassette	CUFF.2	chr1	+	chr1:2075781-2080310	chr1:2075781-2076827;chr1:2076951-2077465;chr1:2077548-2080310		chr1:2076828-2076950;chr1:2077466-2077547			41;295
K	alternative_donor	CUFF.18	chr1	+	chr1:31769944-31782890;chr1:31770061-31782890	chr1:31769923-31782890		chr1:31769923-31769943;chr1:31769944-31770060	chr1:31769922-31769923;chr1:31769943-31769944		276;142
K	jcn_only_AD	CUFF.22,CUFF.42	chr1	-	chr1:41486606-41487294	chr1:41486606-41487201		chr1:41487202-41487294	chr1:41487294-41487295		64;115
K	alternative_last_exon	CUFF.36	chr1	+	chr1:110214206-110217368;chr1:110214206-110215824;chr1:110214206-110224430	chr1:110214206-110251102	chr1:110215825-110216230;chr1:110224431-110224456	chr1:110251103-110252171			1233;26
K	coord_cassette	CUFF.51	chr1	-	chr1:156438813-156446803	chr1:156438813-156444899;chr1:156445030-156446285;chr1:156446307-156446803		chr1:156444900-156445029;chr1:156446286-156446306			53;57
K	cassette	CUFF.60	chr1	+	chr1:167353189-167365522	chr1:167353189-167358824;chr1:167358999-167365522		chr1:167358825-167358998			48;221
N	alternative_donor	CUFF.51	chr1	-	chr1:156453223-156470277	chr1:156453223-156469223		chr1:156469224-156470277	chr1:156470277-156470278		69;5
N	alternative_acceptor	CUFF.24	chr1	-	chr1:53878941-53883199	chr1:53881197-53883199		chr1:53878941-53881196	chr1:53878940-53878941		61;6
K	alternative_last_exon	CUFF.36	chr1	+	chr1:110214206-110217368;chr1:110214206-110215824;chr1:110214206-110251102	chr1:110214206-110224430	chr1:110215825-110216230;chr1:110251103-110252171	chr1:110224431-110224456			756;503
N	alternative_donor	CUFF.18	chr1	+	chr1:31819588-31821675	chr1:31819666-31821675		chr1:31819588-31819665	chr1:31819587-31819588		447;14
K	intron_retention	CUFF.47	chr1	-	chr1:153924923-153925046				chr1:153924922-153924923;chr1:153925046-153925047		206;43
K	alternative_last_exon	CUFF.80	chr1	-	chr1:247320520-247322307,chr1:247320706-247322307;chr1:247302060-247322307	chr1:247287174-247322307	chr1:247319442-247320519;chr1:247301348-247302059	chr1:247285277-247287173			356;14
N	jcn_only_AA	CUFF.58	chr1	-	chr1:161970129-161976086	chr1:161970132-161976086		chr1:161970129-161970131	chr1:161970128-161970129		9;121
N	cassette	CUFF.2	chr1	+	chr1:1987002-1990979	chr1:1987002-1987922;chr1:1988013-1990979		chr1:1987923-1988012			123;327
N	jcn_only_AD	CUFF.21	chr1	-	chr1:16909254-16918341	chr1:16909254-16910088					13;2
K	alternative_donor	CUFF.18	chr1	+	chr1:31769944-31782890;chr1:31769923-31782890	chr1:31770061-31782890		chr1:31769923-31769943;chr1:31769944-31770060	chr1:31769922-31769923;chr1:31769943-31769944		178;240
N	alternative_acceptor		chr1	+	chr1:160137220-160141040	chr1:160137220-160139462		chr1:160139463-160141040	chr1:160141040-160141041		11;11
N	alternative_donor	CUFF.2	chr1	+	chr1:1982141-1986879	chr1:1982452-1986879		chr1:1982141-1982451	chr1:1982140-1982141		374;18
K	alternative_last_exon	CUFF.3	chr1	+	chr1:10494748-10511433	chr1:10494748-10500403	chr1:10511434-10512309	chr1:10500404-10500470			66;154
K	cassette	CUFF.75	chr1	+	chr1:224378022-224380033	chr1:224378022-224378793;chr1:224378859-224380033		chr1:224378794-224378858			179;22
K	intron_retention	CUFF.74	chr1	+	chr1:222835675-222837339				chr1:222835674-222835675;chr1:222837339-222837340		76;138
K	alternative_acceptor	CUFF.21	chr1	-	chr1:33647023-33647594	chr1:33647096-33647594		chr1:33647023-33647095	chr1:33647022-33647023		54;50
K	alternative_last_exon	CUFF.60,CUFF.79	chr1	+	chr1:167365665-167367230	chr1:167365665-167365769	chr1:167367231-167367370	chr1:167365770-167366003			117;23
K	cassette	CUFF.60	chr1	+	chr1:167190196-167301706;chr1:167190196-167272710	chr1:167190196-167210643;chr1:167210848-167301706,chr1:167210848-167272710		chr1:167210644-167210847			240;146
N	alternative_donor	CUFF.34	chr1	-	chr1:106132408-106146784;chr1:106132408-106145898;chr1:106132408-106143252	chr1:106132408-106143891		chr1:106143253-106143891;chr1:106143892-106145898;chr1:106145899-106146784	chr1:106143891-106143892;chr1:106145898-106145899;chr1:106146784-106146785		245;96
N	cassette	CUFF.62	chr1	-	chr1:169696667-169697198;chr1:169696667-169698326	chr1:169696667-169696879;chr1:169697069-169698326,chr1:169697069-169697198		chr1:169696880-169697068			121;116
N	alternative_donor	CUFF.2	chr1	+	chr1:2101044-2103493	chr1:2103085-2103493		chr1:2101044-2103084	chr1:2101043-2101044		494;3
K	intron_retention	CUFF.24	chr1	-	chr1:53904722-53905099				chr1:53904721-53904722;chr1:53905099-53905100		88;181
N	jcn_only_AA		chr1	+	chr1:160137220-160141040	chr1:160137220-160139462		chr1:160139463-160141040	chr1:160141040-160141041		11;5
N	jcn_only_AD	CUFF.25	chr1	+	chr1:54356968-54359986	chr1:54357950-54359986		chr1:54356968-54357949	chr1:54356967-54356968		152;30
K	intron_retention	CUFF.41	chr1	+	chr1:145584837-145585355				chr1:145584836-145584837;chr1:145585355-145585356		128;11
N	jcn_only_AA	CUFF.40	chr1	-	chr1:120529706-120539619	chr1:120539370-120539619		chr1:120529706-120539369	chr1:120529705-120529706		10;5
K	jcn_only_AD	CUFF.49	chr1	+	chr1:155180419-155181917	chr1:155181338-155181917					346;26
K	cassette	CUFF.41	chr1	+	chr1:145575405-145578061	chr1:145575405-145577651;chr1:145577754-145578061		chr1:145577652-145577753			52;497
K	intron_retention	CUFF.20	chr1	-	chr1:32827478-32827558				chr1:32827477-32827478;chr1:32827558-32827559		90;80
K	intron_retention	CUFF.73	chr1	-	chr1:213186761-213188567				chr1:213186760-213186761;chr1:213188567-213188568		70;14
K	jcn_only_AD	CUFF.66	chr1	+	chr1:200870288-200876961	chr1:200875624-200876961					260;187
K	intron_retention	CUFF.20	chr1	-	chr1:32827137-32827330				chr1:32827136-32827137;chr1:32827330-32827331		96;35
K	cassette	CUFF.69	chr1	+	chr1:207287631-207288760	chr1:207287631-207288020;chr1:207288117-207288760		chr1:207288021-207288116			56;18
N	alternative_acceptor	CUFF.58	chr1	-	chr1:161953126-161953385	chr1:161953196-161953385		chr1:161953126-161953195	chr1:161953125-161953126		409;24
N	jcn_only_AA	CUFF.60	chr1	+	chr1:167345393-167353093	chr1:167345393-167345789		chr1:167345790-167353093	chr1:167353093-167353094		336;76
N	jcn_only_AD	CUFF.34	chr1	-	chr1:106132408-106146784;chr1:106132408-106145898;chr1:106132408-106143252	chr1:106132408-106143891		chr1:106143253-106143891;chr1:106143892-106145898;chr1:106145899-106146784	chr1:106143891-106143892;chr1:106145898-106145899;chr1:106146784-106146785		248;50
N	jcn_only_AD	CUFF.11,CUFF.62	chr1	-	chr1:169697069-169698326	chr1:169697069-169697198		chr1:169697199-169698326	chr1:169698326-169698327		93;16
K	alternative_first_exon	CUFF.73	chr1	-	chr1:213173726-213178374	chr1:213173726-213174127	chr1:213178375-213178796	chr1:213174128-213175613			244;169
K	jcn_only_AA	CUFF.45	chr1	-	chr1:151149508-151150476	chr1:151149541-151150476		chr1:151149508-151149540	chr1:151149507-151149508		195;20
K	intron_retention	CUFF.49	chr1	+	chr1:155180419-155182175				chr1:155180418-155180419;chr1:155182175-155182176		58;20
N	jcn_only_AD	CUFF.2	chr1	+	chr1:2106753-2116021	chr1:2113354-2116021		chr1:2106753-2113353	chr1:2106752-2106753		488;61
K	alternative_first_exon	CUFF.75	chr1	+	chr1:224371121-224377278;chr1:224371534-224377278	chr1:224363650-224377278	chr1:224370879-224371120;chr1:224371366-224371533	chr1:224363372-224363649			90;79
K	intron_retention		chr1	+	chr1:245133746-245180543				chr1:245133745-245133746;chr1:245180543-245180544		1095;111
K	alternative_first_exon	CUFF.21,CUFF.34	chr1	-	chr1:33631168-33646625	chr1:33631168-33642008	chr1:33646626-33647267	chr1:33642009-33642188			105;53
N	alternative_donor	CUFF.80	chr1	-	chr1:247287174-247322307	chr1:247287174-247302017		chr1:247302018-247322307	chr1:247322307-247322308		11;9
K	cassette	CUFF.4	chr1	+	chr1:11074023-11076900	chr1:11074023-11076179;chr1:11076312-11076900		chr1:11076180-11076311			514;43
K	cassette	CUFF.44	chr1	+	chr1:150249041-150253245	chr1:150249041-150252053;chr1:150252153-150253245		chr1:150252054-150252152			354;175
N	jcn_only_AD	CUFF.60	chr1	+	chr1:167345393-167353093	chr1:167345825-167353093		chr1:167345393-167345824	chr1:167345392-167345393		336;85
K	alternative_acceptor	CUFF.80	chr1	-	chr1:247320520-247322307	chr1:247320706-247322307		chr1:247320520-247320705	chr1:247320519-247320520		110;36
K	alternative_first_exon	CUFF.19	chr1	+	chr1:32538700-32540551;chr1:32539474-32540551;chr1:32538653-32540551	chr1:32538054-32540551	chr1:32539378-32539473;chr1:32538440-32538652	chr1:32537632-32538053			366;35
K	cassette	CUFF.47	chr1	-	chr1:153921861-153924493	chr1:153921861-153923735;chr1:153924143-153924493		chr1:153923736-153924142			55;257
K	coord_cassette	CUFF.60	chr1	+	chr1:167190196-167301706	chr1:167190196-167272710;chr1:167272812-167288250;chr1:167288294-167301706		chr1:167272711-167272811;chr1:167288251-167288293			13;40
K	intron_retention	CUFF.78	chr1	+	chr1:230391091-230398318				chr1:230391090-230391091;chr1:230398318-230398319		160;64
N	alternative_donor	CUFF.11,CUFF.62	chr1	-	chr1:169697069-169698326	chr1:169697069-169697198		chr1:169697199-169698326	chr1:169698326-169698327		93;8
N	alternative_acceptor		chr1	+	chr1:32540679-32541267	chr1:32540679-32541203		chr1:32541204-32541267	chr1:32541267-32541268		95;312
K	intron_retention	CUFF.4	chr1	+	chr1:11082299-11083249				chr1:11082298-11082299;chr1:11083249-11083250		64;84
K	jcn_only_AA	CUFF.60,CUFF.63	chr1	+	chr1:171123354-171130296	chr1:171123354-171130202		chr1:171130203-171130296	chr1:171130296-171130297		18;331
N	jcn_only_AD	CUFF.52	chr1	-	chr1:156933387-156937778	chr1:156933387-156933483		chr1:156933484-156937778	chr1:156937778-156937779		3;32
K	coord_cassette	CUFF.59	chr1	+	chr1:166810326-166818174	chr1:166810326-166815848;chr1:166815976-166816730;chr1:166816830-166818174		chr1:166815849-166815975;chr1:166816731-166816829			41;28
N	jcn_only_AA	CUFF.38	chr1	-	chr1:113471975-113497897	chr1:113472657-113497897		chr1:113471975-113472656	chr1:113471974-113471975		51;4
N	cassette	CUFF.18	chr1	+	chr1:31769923-31791955	chr1:31769923-31782890;chr1:31783012-31791955		chr1:31782891-31783011			23;262
N	intron_retention		chr1	+	chr1:200883724-200884202				chr1:200883723-200883724;chr1:200884202-200884203		41;41
K	cassette	CUFF.33	chr1	-	chr1:103975719-104068017	chr1:103975719-104011963;chr1:104012013-104068017		chr1:104011964-104012012			79;91
N	intron_retention		chr1	+	chr1:110211106-110211546				chr1:110211105-110211106;chr1:110211546-110211547		144;44
K	jcn_only_AD	CUFF.16	chr1	+	chr1:28655636-28657107	chr1:28655692-28657107		chr1:28655636-28655691	chr1:28655635-28655636		25;414
N	coord_cassette	CUFF.25	chr1	+	chr1:54360221-54371767	chr1:54360221-54368729;chr1:54368940-54370338;chr1:54370483-54371767		chr1:54368730-54368939;chr1:54370339-54370482			115;127
N	cassette	CUFF.25	chr1	+	chr1:54360221-54375603;chr1:54360221-54371767	chr1:54360221-54370338;chr1:54370483-54371767,chr1:54370483-54375603		chr1:54370339-54370482			189;967
N	jcn_only_AD	CUFF.52	chr1	-	chr1:156908306-156909339	chr1:156908306-156908940		chr1:156908941-156909339	chr1:156909339-156909340		79;44
K	cassette	CUFF.73	chr1	-	chr1:213181809-213188954	chr1:213181809-213186434;chr1:213186761-213188954		chr1:213186435-213186760			99;78
N	cassette	CUFF.19	chr1	+	chr1:32542448-32557275;chr1:32541424-32557275	chr1:32542448-32542764,chr1:32541424-32542764;chr1:32542920-32557275		chr1:32542765-32542919			57;366
K	alternative_last_exon	CUFF.79	chr1	+	chr1:245246991-245250034,chr1:245246991-245285221;chr1:245246991-245250546;chr1:245246991-245254795;chr1:245246991-245250061	chr1:245246991-245254328	chr1:245250547-245251236;chr1:245254796-245255091;chr1:245250062-245250160	chr1:245254329-245254794			1582;45
K	intron_retention	CUFF.4	chr1	+	chr1:11085266-11085607				chr1:11085265-11085266;chr1:11085607-11085608		171;73
K	intron_retention	CUFF.38	chr1	-	chr1:113464756-113471713				chr1:113464755-113464756;chr1:113471713-113471714		683;49
N	jcn_only_AA	CUFF.47	chr1	-	chr1:153925846-153930820	chr1:153927643-153930820					90;61
N	alternative_donor	CUFF.30	chr1	+	chr1:78445304-78546358	chr1:78512019-78546358		chr1:78445304-78512018	chr1:78445303-78445304		196;0
K	intron_retention	CUFF.47	chr1	-	chr1:153924143-153924493				chr1:153924142-153924143;chr1:153924493-153924494		146;28
K	cassette	CUFF.19	chr1	+	chr1:32541424-32542363	chr1:32541424-32542164;chr1:32542248-32542363		chr1:32542165-32542247			289;49
K	alternative_last_exon	CUFF.79	chr1	+	chr1:245246991-245250034,chr1:245246991-245285221;chr1:245246991-245254328;chr1:245246991-245250546;chr1:245246991-245250061	chr1:245246991-245254795	chr1:245254329-245254794;chr1:245250547-245251236;chr1:245250062-245250160	chr1:245254796-245255091			1574;53
K	alternative_last_exon	CUFF.72	chr1	+	chr1:211570174-211599552	chr1:211570174-211570197	chr1:211599553-211599625	chr1:211570198-211570296			186;23
N	jcn_only_AD	CUFF.34	chr1	-	chr1:106132408-106146784;chr1:106132408-106145898;chr1:106132408-106143891	chr1:106132408-106143252		chr1:106143253-106143891;chr1:106143892-106145898;chr1:106145899-106146784	chr1:106143891-106143892;chr1:106145898-106145899;chr1:106146784-106146785		249;49
N	alternative_donor	CUFF.55	chr1	+	chr1:160137203-160141040	chr1:160137220-160141040		chr1:160137203-160137219	chr1:160137202-160137203		11;5
K	alternative_donor	CUFF.5	chr1	+	chr1:11159872-11161857	chr1:11159968-11161857		chr1:11159872-11159967	chr1:11159871-11159872		77;355
K	intron_retention	CUFF.54	chr1	-	chr1:158584097-158585005				chr1:158584096-158584097;chr1:158585005-158585006		253;63
N	jcn_only_AA		chr1	+	chr1:32540679-32541267	chr1:32540679-32541203		chr1:32541204-32541267	chr1:32541267-32541268		95;410
K	alternative_first_exon	CUFF.1	chr1	+	chr1:1656203-1667255	chr1:1664284-1667255	chr1:1655853-1656202	chr1:1663966-1664283			248;178
K	intron_retention	CUFF.36	chr1	+	chr1:110211123-110211546				chr1:110211122-110211123;chr1:110211546-110211547		781;54
K	jcn_only_AA	CUFF.47	chr1	-	chr1:153925112-153925280	chr1:153925127-153925280		chr1:153925112-153925126	chr1:153925111-153925112		64;133
K	intron_retention	CUFF.6	chr1	-	chr1:11709932-11710001				chr1:11709931-11709932;chr1:11710001-11710002		105;84
K	alternative_first_exon	CUFF.38	chr1	-	chr1:113471975-113472502,chr1:113471975-113499460;chr1:113471975-113498656;chr1:113471975-113497897	chr1:113471975-113478445	chr1:113498657-113498975;chr1:113497898-113498656	chr1:113478446-113478696			188;576
K	alternative_acceptor	CUFF.45	chr1	-	chr1:151149508-151150476	chr1:151149541-151150476		chr1:151149508-151149540	chr1:151149507-151149508		195;11
N	alternative_acceptor	CUFF.52	chr1	-	chr1:156908306-156909339	chr1:156909078-156909339		chr1:156908306-156909077	chr1:156908305-156908306		79;19
N	mutually_exclusive	CUFF.25	chr1	+	chr1:54360221-54371767,chr1:54371968-54375603	chr1:54360221-54370338,chr1:54370483-54375603	chr1:54371768-54371967	chr1:54370339-54370482			112;118
N	mutually_exclusive	CUFF.39	chr1	-	chr1:114423763-114429158,chr1:114429281-114429870	chr1:114423763-114424394,chr1:114424620-114429870	chr1:114429159-114429280	chr1:114424395-114424619			34;84
K	alternative_donor	CUFF.4	chr1	+	chr1:11082299-11083249	chr1:11082308-11083249		chr1:11082299-11082307	chr1:11082298-11082299		64;184
N	intron_retention		chr1	-	chr1:156909078-156909339				chr1:156909077-156909078;chr1:156909339-156909340		21;7
K	alternative_acceptor	CUFF.30,CUFF.69	chr1	+	chr1:207277776-207286345	chr1:207277776-207286243		chr1:207286244-207286345	chr1:207286345-207286346		51;12
N	alternative_acceptor	CUFF.60	chr1	+	chr1:167345393-167353093	chr1:167345393-167345789		chr1:167345790-167353093	chr1:167353093-167353094		336;19
N	jcn_only_AA	CUFF.29	chr1	+	chr1:70820791-70832126	chr1:70820791-70831828		chr1:70831829-70832126	chr1:70832126-70832127		346;51
K	alternative_last_exon	CUFF.77	chr1	+	chr1:227597586-227617105	chr1:227597586-227613456	chr1:227617106-227618736	chr1:227613457-227613857			23;816
N	coord_cassette	CUFF.19	chr1	+	chr1:32541424-32542764	chr1:32541424-32542164;chr1:32542248-32542363;chr1:32542448-32542764		chr1:32542165-32542247;chr1:32542364-32542447			50;47
K	cassette	CUFF.64	chr1	-	chr1:174084788-174124764	chr1:174084788-174091221;chr1:174091331-174124764		chr1:174091222-174091330			281;30
N	coord_cassette	CUFF.4	chr1	+	chr1:11074023-11078789	chr1:11074023-11075580;chr1:11075704-11076900;chr1:11077065-11078789		chr1:11075581-11075703;chr1:11076901-11077064			16;76
K	cassette	CUFF.22	chr1	-	chr1:41481901-41483306	chr1:41481901-41482905;chr1:41483050-41483306		chr1:41482906-41483049			65;290
N	jcn_only_AD	CUFF.2	chr1	+	chr1:1982141-1986879	chr1:1982452-1986879		chr1:1982141-1982451	chr1:1982140-1982141		374;27
K	alternative_first_exon	CUFF.68	chr1	-	chr1:205593020-205600759	chr1:205593020-205594759	chr1:205600760-205601169	chr1:205594760-205594858		chr1:205592804-205593019	45;54
K	alternative_acceptor	CUFF.8	chr1	+	chr1:16382019-16382172	chr1:16382019-16382169		chr1:16382170-16382172	chr1:16382172-16382173		213;9
K	alternative_last_exon	CUFF.36,CUFF.60	chr1	+	chr1:110224457-110244273	chr1:110224457-110225828	chr1:110244274-110245163	chr1:110225829-110226290			650;293
K	alternative_first_exon	CUFF.67	chr1	-	chr1:202894336-202897608	chr1:202894336-202896216	chr1:202897609-202897861	chr1:202896217-202896390		chr1:202894096-202894335	80;10
N	alternative_donor	CUFF.55	chr1	+	chr1:160146353-160147308	chr1:160146393-160147308		chr1:160146353-160146392	chr1:160146352-160146353		15;32
N	alternative_first_exon	CUFF.47	chr1	-	chr1:153927643-153930820;chr1:153927643-153930621	chr1:153927643-153930536	chr1:153930821-153931091;chr1:153930622-153930741	chr1:153930537-153930619			193;19
K	alternative_donor	CUFF.22,CUFF.42	chr1	-	chr1:41486606-41487294	chr1:41486606-41487201		chr1:41487202-41487294	chr1:41487294-41487295		64;130
K	cassette	CUFF.9	chr1	-	chr1:16894526-16899636	chr1:16894526-16895567;chr1:16895732-16899636		chr1:16895568-16895731			25;185
K	cassette	CUFF.59	chr1	+	chr1:166810326-166816730	chr1:166810326-166815848;chr1:166815976-166816730		chr1:166815849-166815975			20;31
K	alternative_last_exon	CUFF.36	chr1	+	chr1:110214206-110217368;chr1:110214206-110224430;chr1:110214206-110251102	chr1:110214206-110215824	chr1:110224431-110224456;chr1:110251103-110252171	chr1:110215825-110216230			590;669
K	intron_retention	CUFF.49	chr1	+	chr1:155180686-155181182				chr1:155180685-155180686;chr1:155181182-155181183		31;34
K	intron_retention	CUFF.75	chr1	+	chr1:224380221-224380597				chr1:224380220-224380221;chr1:224380597-224380598		82;15
N	jcn_only_AA	CUFF.24	chr1	-	chr1:53878941-53883199	chr1:53881197-53883199		chr1:53878941-53881196	chr1:53878940-53878941		61;57
K	intron_retention	CUFF.47	chr1	-	chr1:153925112-153925280				chr1:153925111-153925112;chr1:153925280-153925281		64;16
K	alternative_first_exon	CUFF.19	chr1	+	chr1:32538700-32540551;chr1:32539474-32540551;chr1:32538054-32540551	chr1:32538653-32540551	chr1:32539378-32539473;chr1:32537632-32538053	chr1:32538440-32538652			67;334
N	alternative_donor	CUFF.2	chr1	+	chr1:2106753-2116021	chr1:2113354-2116021		chr1:2106753-2113353	chr1:2106752-2106753		488;2
N	jcn_only_AA	CUFF.36	chr1	+	chr1:110212194-110213935	chr1:110212194-110213908		chr1:110213909-110213935	chr1:110213935-110213936		119;1051
N	jcn_only_AD	CUFF.34	chr1	-	chr1:106132408-106146784;chr1:106132408-106143891;chr1:106132408-106143252	chr1:106132408-106145898		chr1:106143253-106143891;chr1:106143892-106145898;chr1:106145899-106146784	chr1:106143891-106143892;chr1:106145898-106145899;chr1:106146784-106146785		200;98
K	alternative_first_exon	CUFF.22,CUFF.73	chr1	-	chr1:213186761-213188954	chr1:213186761-213188567	chr1:213188955-213189263	chr1:213188568-213188875			4;84
N	alternative_acceptor	CUFF.36,CUFF.55	chr1	+	chr1:160151822-160156065	chr1:160151822-160152481		chr1:160152482-160156065	chr1:160156065-160156066		755;15
K	alternative_acceptor	CUFF.20	chr1	-	chr1:32827137-32827330	chr1:32827166-32827330		chr1:32827137-32827165	chr1:32827136-32827137		96;68
K	intron_retention	CUFF.52	chr1	-	chr1:156914990-156915836				chr1:156914989-156914990;chr1:156915836-156915837		39;38
N	intron_retention		chr1	+	chr1:54359960-54360083				chr1:54359959-54359960;chr1:54360083-54360084		26;674
K	alternative_last_exon	CUFF.11	chr1	-	chr1:25554727-25558594	chr1:25555615-25558594	chr1:25554609-25554726	chr1:25555419-25555614			33;297
K	coord_cassette	CUFF.60	chr1	+	chr1:167353189-167365522	chr1:167353189-167356417;chr1:167356485-167358824;chr1:167358999-167365522		chr1:167356418-167356484;chr1:167358825-167358998			48;81
K	intron_retention	CUFF.22	chr1	-	chr1:41486606-41487201				chr1:41486605-41486606;chr1:41487201-41487202		115;51
K	alternative_first_exon	CUFF.65	chr1	+	chr1:196789033-196918584	chr1:196913069-196918584	chr1:196788898-196789032	chr1:196912828-196913068			34;43
K	jcn_only_AD	CUFF.18	chr1	+	chr1:31769944-31782890;chr1:31770061-31782890	chr1:31769923-31782890		chr1:31769923-31769943;chr1:31769944-31770060	chr1:31769922-31769923;chr1:31769943-31769944		291;142
K	alternative_first_exon	CUFF.19	chr1	+	chr1:32538700-32540551;chr1:32538653-32540551;chr1:32538054-32540551	chr1:32539474-32540551	chr1:32538440-32538652;chr1:32537632-32538053	chr1:32539378-32539473			393;8
N	alternative_acceptor		chr1	+	chr1:110211994-110212257	chr1:110211994-110212092		chr1:110212093-110212257	chr1:110212257-110212258		29;575
N	coord_cassette	CUFF.18	chr1	+	chr1:31769923-31791955	chr1:31769923-31782890;chr1:31783012-31791013;chr1:31791084-31791955		chr1:31782891-31783011;chr1:31791014-31791083			23;43
N	alternative_donor	CUFF.80	chr1	-	chr1:247302060-247322307	chr1:247302060-247313159		chr1:247313160-247322307	chr1:247322307-247322308		156;20
K	alternative_acceptor	CUFF.80	chr1	-	chr1:247323116-247335149	chr1:247323170-247335149		chr1:247323116-247323169	chr1:247323115-247323116		135;56
K	intron_retention	CUFF.64	chr1	-	chr1:174128129-174128301				chr1:174128128-174128129;chr1:174128301-174128302		84;126
K	coord_cassette	CUFF.60	chr1	+	chr1:167210848-167301706	chr1:167210848-167272710;chr1:167272812-167288250;chr1:167288294-167301706		chr1:167272711-167272811;chr1:167288251-167288293			146;33
K	cassette	CUFF.53	chr1	-	chr1:158444458-158464191	chr1:158444458-158449694;chr1:158451593-158464191		chr1:158449695-158451592			138;158
N	alternative_first_exon	CUFF.73	chr1	-	chr1:156939836-156946774	chr1:156939836-156941488	chr1:156946775-156946846	chr1:156941489-156941710			2;165
K	jcn_only_AD	CUFF.36	chr1	+	chr1:110212194-110213908	chr1:110212857-110213908					1051;16
N	cassette	CUFF.29	chr1	+	chr1:70820892-70832126	chr1:70820892-70832009;chr1:70832012-70832126		chr1:70832010-70832011			69;94
N	alternative_donor	CUFF.52	chr1	-	chr1:156908306-156909339	chr1:156908306-156908940		chr1:156908941-156909339	chr1:156909339-156909340		79;24
K	intron_retention	CUFF.2	chr1	+	chr1:2087532-2100956				chr1:2087531-2087532;chr1:2100956-2100957		435;63
N	jcn_only_AD	CUFF.24	chr1	-	chr1:53878941-53883199	chr1:53878941-53881072		chr1:53881073-53883199	chr1:53883199-53883200		61;121
N	cassette	CUFF.62	chr1	-	chr1:169698815-169700975	chr1:169698815-169699572;chr1:169699759-169700975		chr1:169699573-169699758			65;135
K	intron_retention	CUFF.53	chr1	-	chr1:158464345-158464444				chr1:158464344-158464345;chr1:158464444-158464445		152;72
N	alternative_acceptor		chr1	-	chr1:106132408-106145898	chr1:106144008-106145898		chr1:106132408-106144007	chr1:106132407-106132408		98;4
K	alternative_first_exon	CUFF.24	chr1	-	chr1:53904722-53905447	chr1:53904722-53905099	chr1:53905448-53905791	chr1:53905100-53905321			61;169
N	alternative_acceptor		chr1	+	chr1:200860531-200867519	chr1:200860531-200867434		chr1:200867435-200867519	chr1:200867519-200867520		89;72
K	cassette	CUFF.49	chr1	+	chr1:155180419-155182175	chr1:155180419-155181917;chr1:155182011-155182175		chr1:155181918-155182010			58;297
K	jcn_only_AA	CUFF.4	chr1	+	chr1:11083387-11084358	chr1:11083387-11084120		chr1:11084121-11084358	chr1:11084358-11084359		368;255
K	alternative_acceptor	CUFF.60,CUFF.77	chr1	+	chr1:167382352-167385285	chr1:167382352-167384736		chr1:167384737-167385285	chr1:167385285-167385286		90;39
K	cassette	CUFF.19	chr1	+	chr1:32560573-32566042	chr1:32560573-32561260;chr1:32561364-32566042		chr1:32561261-32561363			384;12
K	coord_cassette	CUFF.65	chr1	+	chr1:196913069-196927020	chr1:196913069-196918584;chr1:196918780-196919981;chr1:196920159-196927020		chr1:196918585-196918779;chr1:196919982-196920158			166;127
K	intron_retention	CUFF.66	chr1	+	chr1:200883188-200883601				chr1:200883187-200883188;chr1:200883601-200883602		42;30
K	jcn_only_AA	CUFF.60,CUFF.77	chr1	+	chr1:167382352-167385285	chr1:167382352-167384736		chr1:167384737-167385285	chr1:167385285-167385286		90;27
K	jcn_only_AD	CUFF.18	chr1	+	chr1:31769944-31782890;chr1:31769923-31782890	chr1:31770061-31782890		chr1:31769923-31769943;chr1:31769944-31770060	chr1:31769922-31769923;chr1:31769943-31769944		177;256
N	alternative_acceptor	CUFF.58	chr1	-	chr1:161970129-161976086	chr1:161970132-161976086		chr1:161970129-161970131	chr1:161970128-161970129		9;60
K	intron_retention	CUFF.12	chr1	-	chr1:26228174-26230131				chr1:26228173-26228174;chr1:26230131-26230132		572;233
K	intron_retention	CUFF.22	chr1	-	chr1:41486451-41486535				chr1:41486450-41486451;chr1:41486535-41486536		265;68
K	intron_retention	CUFF.36	chr1	+	chr1:110212686-110212796				chr1:110212685-110212686;chr1:110212796-110212797		15;25
K	jcn_only_AA	CUFF.60	chr1	+	chr1:167301773-167343392	chr1:167301773-167334703					114;321
N	mutually_exclusive	CUFF.79	chr1	+	chr1:245133746-245180543,chr1:245180629-245222687	chr1:245133746-245165422,chr1:245165535-245222687	chr1:245180544-245180628	chr1:245165423-245165534			836;12
K	cassette	CUFF.51	chr1	-	chr1:156445030-156446803	chr1:156445030-156446285;chr1:156446307-156446803		chr1:156446286-156446306			18;58
N	jcn_only_AA		chr1	+	chr1:110211994-110212257	chr1:110211994-110212092		chr1:110212093-110212257	chr1:110212257-110212258		29;1551
K	jcn_only_AD	CUFF.45	chr1	-	chr1:151158427-151162599	chr1:151158427-151162480		chr1:151162481-151162599	chr1:151162599-151162600		107;79
K	alternative_first_exon	CUFF.11,CUFF.64	chr1	-	chr1:25554727-25558594	chr1:25554727-25555488	chr1:25558595-25559077	chr1:25555489-25555614			37;116
K	cassette	CUFF.4	chr1	+	chr1:11074023-11076900	chr1:11074023-11075580;chr1:11075704-11076900		chr1:11075581-11075703			514;82
K	alternative_first_exon	CUFF.45	chr1	-	chr1:151158427-151167754	chr1:151158427-151162599,chr1:151158427-151162480	chr1:151167755-151167888	chr1:151162600-151162664			26;138
K	alternative_last_exon	CUFF.26	chr1	-	chr1:54382790-54389576	chr1:54387441-54389576	chr1:54382247-54382789	chr1:54387140-54387440			54;142
K	alternative_acceptor	CUFF.4	chr1	+	chr1:11083387-11084358	chr1:11083387-11084120		chr1:11084121-11084358	chr1:11084358-11084359		368;334
K	alternative_last_exon	CUFF.80	chr1	-	chr1:247320520-247322307,chr1:247320706-247322307;chr1:247287174-247322307	chr1:247302060-247322307	chr1:247319442-247320519;chr1:247285277-247287173	chr1:247301348-247302059			167;203
K	intron_retention	CUFF.41	chr1	+	chr1:145578480-145578636				chr1:145578479-145578480;chr1:145578636-145578637		128;127
N	alternative_first_exon		chr1	-	chr1:120548212-120611947	chr1:120548212-120572528	chr1:120611948-120612240	chr1:120572529-120572610			10;29
N	alternative_first_exon	CUFF.78	chr1	+	chr1:230193826-230313963	chr1:230203154-230313963	chr1:230193439-230193825	chr1:230202941-230203153			125;2
N	alternative_acceptor	CUFF.38	chr1	-	chr1:113471975-113497897	chr1:113472657-113497897		chr1:113471975-113472656	chr1:113471974-113471975		51;2
N	coord_cassette	CUFF.25	chr1	+	chr1:54360221-54375603	chr1:54360221-54368729;chr1:54368940-54370338;chr1:54370483-54375603		chr1:54368730-54368939;chr1:54370339-54370482			74;127
N	jcn_only_AA		chr1	+	chr1:200860531-200867519	chr1:200860531-200867434		chr1:200867435-200867519	chr1:200867519-200867520		89;38
N	jcn_only_AD	CUFF.22	chr1	-	chr1:213184801-213188954	chr1:213184801-213188490		chr1:213188491-213188954	chr1:213188954-213188955		34;36
K	intron_retention	CUFF.22	chr1	-	chr1:41486606-41487294				chr1:41486605-41486606;chr1:41487294-41487295		64;131
N	alternative_donor		chr1	+	chr1:70820791-70831828	chr1:70820892-70831828		chr1:70820791-70820891	chr1:70820790-70820791		51;82
K	alternative_first_exon	CUFF.66	chr1	+	chr1:200860830-200867434;chr1:200860531-200867434	chr1:200864216-200867434	chr1:200860088-200860530	chr1:200863872-200864215			51;267
K	alternative_last_exon	CUFF.79	chr1	+	chr1:245246991-245250034,chr1:245246991-245285221;chr1:245246991-245254328;chr1:245246991-245254795;chr1:245246991-245250061	chr1:245246991-245250546	chr1:245254329-245254794;chr1:245254796-245255091;chr1:245250062-245250160	chr1:245250547-245251236			260;1367
K	intron_retention	CUFF.79	chr1	+	chr1:245133101-245180543				chr1:245133100-245133101;chr1:245180543-245180544		22;135
K	alternative_donor	CUFF.45	chr1	-	chr1:151158427-151162599	chr1:151158427-151162480		chr1:151162481-151162599	chr1:151162599-151162600		107;75
K	intron_retention	CUFF.47	chr1	-	chr1:153927466-153927540				chr1:153927465-153927466;chr1:153927540-153927541		141;71
K	alternative_first_exon	CUFF.72	chr1	+	chr1:211556268-211564957	chr1:211564013-211564957	chr1:211556145-211556267	chr1:211563906-211564012			200;33
N	alternative_first_exon	CUFF.47	chr1	-	chr1:153927643-153930536;chr1:153927643-153930621	chr1:153927643-153930820	chr1:153930537-153930619;chr1:153930622-153930741	chr1:153930821-153931091			148;64
K	intron_retention	CUFF.58	chr1	-	chr1:161953126-161953385				chr1:161953125-161953126;chr1:161953385-161953386		409;123
N	jcn_only_AA		chr1	+	chr1:78546545-78560635	chr1:78546545-78558440		chr1:78558441-78560635	chr1:78560635-78560636		5;235
K	intron_retention	CUFF.66	chr1	+	chr1:200882752-200882988				chr1:200882751-200882752;chr1:200882988-200882989		54;176
N	intron_retention		chr1	+	chr1:2100557-2100956				chr1:2100556-2100557;chr1:2100956-2100957		20;22
K	jcn_only_AA	CUFF.80	chr1	-	chr1:247323116-247335149	chr1:247323170-247335149		chr1:247323116-247323169	chr1:247323115-247323116		135;66
N	jcn_only_AA	CUFF.9	chr1	-	chr1:16928339-16935002;chr1:16921509-16935002	chr1:16934187-16935002		chr1:16921509-16928338;chr1:16928339-16934186	chr1:16921508-16921509;chr1:16928338-16928339		24;50
K	alternative_first_exon	CUFF.38	chr1	-	chr1:113471975-113472502,chr1:113471975-113499460;chr1:113471975-113497897;chr1:113471975-113478445	chr1:113471975-113498656	chr1:113497898-113498656;chr1:113478446-113478696	chr1:113498657-113498975			681;83
K	alternative_last_exon	CUFF.12	chr1	-	chr1:26212361-26227981	chr1:26227579-26227981	chr1:26210574-26212360	chr1:26226511-26227578			26;641
K	intron_retention	CUFF.26	chr1	-	chr1:54394114-54395711				chr1:54394113-54394114;chr1:54395711-54395712		295;86
K	alternative_last_exon	CUFF.79	chr1	+	chr1:245246991-245250034,chr1:245246991-245285221;chr1:245246991-245254328;chr1:245246991-245250546;chr1:245246991-245254795	chr1:245246991-245250061	chr1:245254329-245254794;chr1:245250547-245251236;chr1:245254796-245255091	chr1:245250062-245250160			1577;50
N	intron_retention		chr1	+	chr1:110211994-110212257				chr1:110211993-110211994;chr1:110212257-110212258		29;47
K	alternative_first_exon	CUFF.4	chr1	+	chr1:11072486-11073772	chr1:11072801-11073772	chr1:11072320-11072485	chr1:11072675-11072800			156;137
K	alternative_acceptor	CUFF.60,CUFF.63	chr1	+	chr1:171123354-171130296	chr1:171123354-171130202		chr1:171130203-171130296	chr1:171130296-171130297		18;256
N	alternative_donor	CUFF.36	chr1	+	chr1:110211106-110211546	chr1:110211123-110211546		chr1:110211106-110211122	chr1:110211105-110211106		144;401
K	alternative_first_exon	CUFF.64	chr1	-	chr1:174124836-174129054	chr1:174124836-174128024	chr1:174129055-174129235	chr1:174128025-174128496			30;331
K	intron_retention	CUFF.22	chr1	-	chr1:41486451-41487287				chr1:41486450-41486451;chr1:41487287-41487288		11;130
K	alternative_first_exon	CUFF.76	chr1	-	chr1:224396714-224400456	chr1:224396714-224397942	chr1:224400457-224401076	chr1:224397943-224398114			355;153
N	cassette	CUFF.78	chr1	+	chr1:230203154-230338882	chr1:230203154-230313963;chr1:230314058-230338882		chr1:230313964-230314057			24;44
N	alternative_acceptor	CUFF.51	chr1	-	chr1:156453223-156470277	chr1:156469353-156470277		chr1:156453223-156469352	chr1:156453222-156453223		69;0
K	alternative_last_exon	CUFF.8	chr1	+	chr1:16382254-16383732	chr1:16382254-16382916	chr1:16383733-16383902	chr1:16382917-16383003			137;119
K	alternative_last_exon	CUFF.66	chr1	+	chr1:200877016-200877857	chr1:200877016-200877243	chr1:200877858-200878068	chr1:200877244-200877372			256;168
K	cassette	CUFF.67	chr1	-	chr1:202861788-202863311	chr1:202861788-202862366;chr1:202862554-202863311		chr1:202862367-202862553		chr1:202860131-202861787;chr1:202863312-202863410	7;55
K	intron_retention	CUFF.54	chr1	-	chr1:158587847-158589011				chr1:158587846-158587847;chr1:158589011-158589012		5;60
N	alternative_donor	CUFF.46	chr1	+	chr1:153389040-153390541	chr1:153389755-153390541		chr1:153389040-153389754	chr1:153389039-153389040		11;7
K	alternative_last_exon	CUFF.33	chr1	-	chr1:103960847-103971908	chr1:103961438-103971908	chr1:103960701-103960846	chr1:103961289-103961437			59;88
K	alternative_first_exon	CUFF.6	chr1	-	chr1:11710892-11713447;chr1:11710892-11714375	chr1:11710892-11715696	chr1:11713448-11713650;chr1:11714376-11714739	chr1:11715697-11715938			301;160
N	alternative_acceptor	CUFF.36	chr1	+	chr1:110212194-110213935	chr1:110212194-110213908		chr1:110213909-110213935	chr1:110213935-110213936		119;496
K	alternative_last_exon	CUFF.31	chr1	-	chr1:85718386-85724206	chr1:85723155-85724206	chr1:85715639-85718385	chr1:85723031-85723154			316;294
N	cassette	CUFF.60	chr1	+	chr1:167341274-167345265	chr1:167341274-167343344;chr1:167343534-167345265		chr1:167343345-167343533			5;336
N	coord_cassette	CUFF.74	chr1	+	chr1:222824246-222826349	chr1:222824246-222825318;chr1:222825391-222825569;chr1:222825675-222826349		chr1:222825319-222825390;chr1:222825570-222825674			20;150
N	intron_retention		chr1	+	chr1:2005369-2066700				chr1:2005368-2005369;chr1:2066700-2066701		77;14
N	jcn_only_AA	CUFF.2	chr1	+	chr1:2101044-2103493	chr1:2101044-2102991		chr1:2102992-2103493	chr1:2103493-2103494		494;42
K	intron_retention	CUFF.52	chr1	-	chr1:156908306-156909339				chr1:156908305-156908306;chr1:156909339-156909340		79;9
N	jcn_only_AD	CUFF.80	chr1	-	chr1:247287174-247322307	chr1:247287174-247302017		chr1:247302018-247322307	chr1:247322307-247322308		11;13
K	jcn_only_AD	CUFF.18	chr1	+	chr1:31769923-31782890;chr1:31770061-31782890	chr1:31769944-31782890		chr1:31769923-31769943;chr1:31769944-31770060	chr1:31769922-31769923;chr1:31769943-31769944		398;35
N	alternative_donor	CUFF.47	chr1	-	chr1:207990760-207995548	chr1:207990760-207992306		chr1:207992307-207995548	chr1:207995548-207995549		14;3
K	alternative_last_exon	CUFF.34	chr1	-	chr1:106143382-106146784;chr1:106132408-106146784	chr1:106146181-106146784	chr1:106132302-106132407	chr1:106144679-106146180			136;449
K	alternative_acceptor	CUFF.47	chr1	-	chr1:153925112-153925280	chr1:153925127-153925280		chr1:153925112-153925126	chr1:153925111-153925112		64;72
K	jcn_only_AA	CUFF.30,CUFF.69	chr1	+	chr1:207277776-207286345	chr1:207277776-207286243		chr1:207286244-207286345	chr1:207286345-207286346		51;15
K	intron_retention	CUFF.59	chr1	+	chr1:166819661-166821821				chr1:166819660-166819661;chr1:166821821-166821822		68;15
N	intron_retention		chr1	-	chr1:161953196-161953385				chr1:161953195-161953196;chr1:161953385-161953386		22;168
N	coord_cassette	CUFF.4	chr1	+	chr1:11074023-11078789	chr1:11074023-11076179;chr1:11076312-11076900;chr1:11077065-11078789		chr1:11076180-11076311;chr1:11076901-11077064			16;38
K	cassette	CUFF.29	chr1	+	chr1:70832221-70833299	chr1:70832221-70832615;chr1:70832668-70833299		chr1:70832616-70832667			414;71
N	alternative_donor	CUFF.52	chr1	-	chr1:156933387-156937778	chr1:156933387-156933483		chr1:156933484-156937778	chr1:156937778-156937779		3;15
N	intron_retention		chr1	+	chr1:110212194-110213935				chr1:110212193-110212194;chr1:110213935-110213936		119;26
N	alternative_acceptor	CUFF.9	chr1	-	chr1:16928339-16935002;chr1:16934187-16935002	chr1:16921509-16935002		chr1:16921509-16928338;chr1:16928339-16934186	chr1:16921508-16921509;chr1:16928338-16928339		50;19
K	intron_retention	CUFF.54	chr1	-	chr1:158590257-158592772				chr1:158590256-158590257;chr1:158592772-158592773		4;65
K	jcn_only_AA	CUFF.22	chr1	-	chr1:41483652-41485897	chr1:41483829-41485897		chr1:41483652-41483828	chr1:41483651-41483652		90;273
K	intron_retention	CUFF.52	chr1	-	chr1:156909703-156909998				chr1:156909702-156909703;chr1:156909998-156909999		60;5
N	intron_retention		chr1	-	chr1:27425496-27425702				chr1:27425495-27425496;chr1:27425702-27425703		128;270
K	intron_retention	CUFF.13	chr1	-	chr1:27429804-27432375				chr1:27429803-27429804;chr1:27432375-27432376		132;15
N	jcn_only_AD		chr1	+	chr1:245246991-245285221	chr1:245270600-245285221		chr1:245246991-245270599	chr1:245246990-245246991		70;48
N	cassette	CUFF.34	chr1	-	chr1:106148712-106161480	chr1:106148712-106155521;chr1:106155567-106161480		chr1:106155522-106155566			35;938
K	cassette	CUFF.65	chr1	+	chr1:196913069-196919981	chr1:196913069-196918584;chr1:196918780-196919981		chr1:196918585-196918779			78;143
N	cassette	CUFF.15	chr1	-	chr1:28555535-28559431	chr1:28555535-28556641;chr1:28556764-28559431		chr1:28556642-28556763			84;109
N	jcn_only_AA	CUFF.9	chr1	-	chr1:16928339-16935002;chr1:16934187-16935002	chr1:16921509-16935002		chr1:16921509-16928338;chr1:16928339-16934186	chr1:16921508-16921509;chr1:16928338-16928339		55;19
K	jcn_only_AA	CUFF.21	chr1	-	chr1:33647023-33647594	chr1:33647096-33647594		chr1:33647023-33647095	chr1:33647022-33647023		54;68
K	intron_retention	CUFF.49	chr1	+	chr1:155182359-155182484				chr1:155182358-155182359;chr1:155182484-155182485		442;125
N	intron_retention		chr1	+	chr1:145580323-145580504				chr1:145580322-145580323;chr1:145580504-145580505		75;93
N	alternative_donor	CUFF.2	chr1	+	chr1:2087532-2100956	chr1:2100557-2100956		chr1:2087532-2100556	chr1:2087531-2087532		435;5
K	alternative_first_exon	CUFF.75	chr1	+	chr1:224371121-224377278;chr1:224363650-224377278	chr1:224371534-224377278	chr1:224370879-224371120;chr1:224363372-224363649	chr1:224371366-224371533			147;22
N	cassette	CUFF.74	chr1	+	chr1:222819028-222823633	chr1:222819028-222822170;chr1:222822193-222823633		chr1:222822171-222822192			282;37
K	alternative_first_exon	CUFF.47	chr1	-	chr1:153925846-153930820	chr1:153925846-153926013	chr1:153930821-153931091	chr1:153926014-153926082			95;134
N	jcn_only_AD	CUFF.18	chr1	+	chr1:31819588-31821675	chr1:31819666-31821675		chr1:31819588-31819665	chr1:31819587-31819588		447;19
K	jcn_only_AD	CUFF.42,CUFF.47	chr1	-	chr1:145926413-145927113	chr1:145926413-145927048		chr1:145927049-145927113	chr1:145927113-145927114		62;44
N	jcn_only_AD	CUFF.60	chr1	+	chr1:167301773-167334703	chr1:167326759-167334703		chr1:167301773-167326758	chr1:167301772-167301773		321;79
K	intron_retention	CUFF.45	chr1	-	chr1:151158097-151158273				chr1:151158096-151158097;chr1:151158273-151158274		213;19
N	jcn_only_AA	CUFF.52	chr1	-	chr1:156908306-156909339	chr1:156909078-156909339		chr1:156908306-156909077	chr1:156908305-156908306		79;21
K	intron_retention	CUFF.11	chr1	-	chr1:25558703-25558934				chr1:25558702-25558703;chr1:25558934-25558935		217;172
K	alternative_first_exon	CUFF.38	chr1	-	chr1:113471975-113472502,chr1:113471975-113499460;chr1:113471975-113498656;chr1:113471975-113478445	chr1:113471975-113497897	chr1:113498657-113498975;chr1:113478446-113478696	chr1:113497898-113498656			688;76
K	cassette	CUFF.47	chr1	-	chr1:153921121-153921590	chr1:153921121-153921309;chr1:153921377-153921590		chr1:153921310-153921376			185;82
K	jcn_only_AA	CUFF.20	chr1	-	chr1:32827137-32827330	chr1:32827166-32827330		chr1:32827137-32827165	chr1:32827136-32827137		96;129
N	mutually_exclusive	CUFF.51	chr1	-	chr1:156449589-156450625,chr1:156450764-156452228	chr1:156449589-156450434,chr1:156450570-156452228	chr1:156450626-156450763	chr1:156450435-156450569			10;12
K	cassette	CUFF.25	chr1	+	chr1:54360221-54370338	chr1:54360221-54368729;chr1:54368940-54370338		chr1:54368730-54368939			1045;147
K	cassette	CUFF.60	chr1	+	chr1:167190196-167301706;chr1:167210848-167301706	chr1:167190196-167272710,chr1:167210848-167272710;chr1:167272812-167301706		chr1:167272711-167272811			159;150
K	intron_retention	CUFF.41	chr1	+	chr1:145578296-145578400				chr1:145578295-145578296;chr1:145578400-145578401		41;523
K	intron_retention	CUFF.2	chr1	+	chr1:1991031-2066700				chr1:1991030-1991031;chr1:2066700-2066701		262;18
N	mutually_exclusive	CUFF.19	chr1	+	chr1:32541424-32542764,chr1:32542920-32557275	chr1:32541424-32542363,chr1:32542448-32557275	chr1:32542765-32542919	chr1:32542364-32542447			47;33
N	alternative_acceptor	CUFF.2	chr1	+	chr1:2106753-2116021	chr1:2106753-2113270		chr1:2113271-2116021	chr1:2116021-2116022		488;4
N	coord_cassette	CUFF.19	chr1	+	chr1:32541424-32557275	chr1:32541424-32542164;chr1:32542248-32542363;chr1:32542448-32557275		chr1:32542165-32542247;chr1:32542364-32542447			15;36
K	intron_retention	CUFF.49	chr1	+	chr1:155181338-155181917				chr1:155181337-155181338;chr1:155181917-155181918		26;46
K	cassette	CUFF.74	chr1	+	chr1:222835675-222837339	chr1:222835675-222836229;chr1:222836374-222837339		chr1:222836230-222836373			76;1711
N	cassette	CUFF.36	chr1	+	chr1:110214005-110217368	chr1:110214005-110214094;chr1:110214206-110217368		chr1:110214095-110214205			19;508
N	jcn_only_AD	CUFF.54,CUFF.6	chr1	-	chr1:158581180-158582606	chr1:158581180-158581575		chr1:158581576-158582606	chr1:158582606-158582607		11;230
K	alternative_donor	CUFF.18	chr1	+	chr1:31769923-31782890;chr1:31770061-31782890	chr1:31769944-31782890		chr1:31769923-31769943;chr1:31769944-31770060	chr1:31769922-31769923;chr1:31769943-31769944		382;36
N	alternative_acceptor	CUFF.9	chr1	-	chr1:16934187-16935002;chr1:16921509-16935002	chr1:16928339-16935002		chr1:16921509-16928338;chr1:16928339-16934186	chr1:16921508-16921509;chr1:16928338-16928339		66;3
N	alternative_donor	CUFF.34	chr1	-	chr1:106132408-106146784;chr1:106132408-106145898;chr1:106132408-106143891	chr1:106132408-106143252		chr1:106143253-106143891;chr1:106143892-106145898;chr1:106145899-106146784	chr1:106143891-106143892;chr1:106145898-106145899;chr1:106146784-106146785		264;77
N	jcn_only_AD	CUFF.12,CUFF.52	chr1	-	chr1:156918291-156921364	chr1:156918291-156918364		chr1:156918365-156921364	chr1:156921364-156921365		19;7
K	intron_retention	CUFF.4	chr1	+	chr1:11082308-11083249				chr1:11082307-11082308;chr1:11083249-11083250		321;78
K	alternative_last_exon	CUFF.2	chr1	+	chr1:1991031-2066700	chr1:1991031-2002737	chr1:2066701-2066786	chr1:2002738-2003062			180;406
N	alternative_donor	CUFF.24	chr1	-	chr1:53878941-53883199	chr1:53878941-53881072		chr1:53881073-53883199	chr1:53883199-53883200		61;11
N	cassette	CUFF.79	chr1	+	chr1:245133746-245222687;chr1:245165535-245222687	chr1:245133746-245180543,chr1:245165535-245180543;chr1:245180629-245222687		chr1:245180544-245180628			121;1377
N	alternative_acceptor	CUFF.2	chr1	+	chr1:2101044-2103493	chr1:2101044-2102991		chr1:2102992-2103493	chr1:2103493-2103494		494;9
N	jcn_only_AD	CUFF.51	chr1	-	chr1:156453223-156470277	chr1:156453223-156469223		chr1:156469224-156470277	chr1:156470277-156470278		69;30
N	jcn_only_AD	CUFF.74	chr1	+	chr1:222806592-222818895	chr1:222817929-222818895		chr1:222806592-222817928	chr1:222806591-222806592		42;214
N	jcn_only_AA	CUFF.51	chr1	-	chr1:156453223-156470277	chr1:156469353-156470277		chr1:156453223-156469352	chr1:156453222-156453223		69;37
N	alternative_donor	CUFF.22	chr1	-	chr1:213184801-213188954	chr1:213184801-213188490		chr1:213188491-213188954	chr1:213188954-213188955		34;45
K	intron_retention		chr1	-	chr1:114423763-114424394				chr1:114423762-114423763;chr1:114424394-114424395		151;32
K	cassette	CUFF.13	chr1	-	chr1:27436269-27480473	chr1:27436269-27440316;chr1:27440778-27480473		chr1:27440317-27440777			19;195
N	alternative_acceptor		chr1	+	chr1:78546545-78560635	chr1:78546545-78558440		chr1:78558441-78560635	chr1:78560635-78560636		5;25
N	intron_retention		chr1	-	chr1:106148712-106161480				chr1:106148711-106148712;chr1:106161480-106161481		35;94
N	cassette	CUFF.4	chr1	+	chr1:11074023-11078789	chr1:11074023-11076900;chr1:11077065-11078789		chr1:11076901-11077064			16;497
N	jcn_only_AA	CUFF.9	chr1	-	chr1:16934187-16935002;chr1:16921509-16935002	chr1:16928339-16935002		chr1:16921509-16928338;chr1:16928339-16934186	chr1:16921508-16921509;chr1:16928338-16928339		69;5
N	jcn_only_AD	CUFF.80	chr1	-	chr1:247302060-247322307	chr1:247302060-247313159		chr1:247313160-247322307	chr1:247322307-247322308		156;21
K	intron_retention	CUFF.4	chr1	+	chr1:11083387-11084120				chr1:11083386-11083387;chr1:11084120-11084121		255;102
K	intron_retention	CUFF.4	chr1	+	chr1:11083387-11084358				chr1:11083386-11083387;chr1:11084358-11084359		368;158
K	intron_retention	CUFF.4	chr1	+	chr1:11084393-11085166				chr1:11084392-11084393;chr1:11085166-11085167		273;115
K	jcn_only_AA	CUFF.8	chr1	+	chr1:16382019-16382172	chr1:16382019-16382169		chr1:16382170-16382172	chr1:16382172-16382173		213;18
N	jcn_only_AA	CUFF.58	chr1	-	chr1:161953126-161953385	chr1:161953196-161953385		chr1:161953126-161953195	chr1:161953125-161953126		409;22
K	alternative_first_exon	CUFF.3	chr1	+	chr1:10490626-10493898	chr1:10491459-10493898	chr1:10490061-10490625	chr1:10490859-10491458			71;160
N	alternative_donor	CUFF.60	chr1	+	chr1:167345393-167353093	chr1:167345825-167353093		chr1:167345393-167345824	chr1:167345392-167345393		336;20
K	intron_retention	CUFF.49	chr1	+	chr1:155180419-155181917				chr1:155180418-155180419;chr1:155181917-155181918		346;39
K	intron_retention		chr1	+	chr1:110211994-110212092				chr1:110211993-110211994;chr1:110212092-110212093		1551;46
K	cassette	CUFF.57	chr1	-	chr1:161042676-161043509	chr1:161042676-161043014;chr1:161043090-161043509		chr1:161043015-161043089			292;12
K	alternative_acceptor	CUFF.22	chr1	-	chr1:41483652-41485897	chr1:41483829-41485897		chr1:41483652-41483828	chr1:41483651-41483652		90;250
N	jcn_only_AD	CUFF.36	chr1	+	chr1:110211106-110211546	chr1:110211123-110211546		chr1:110211106-110211122	chr1:110211105-110211106		144;781
N	intron_retention		chr1	+	chr1:200860531-200867519				chr1:200860530-200860531;chr1:200867519-200867520		89;76
K	cassette	CUFF.31	chr1	-	chr1:85724406-85725040	chr1:85724406-85724617;chr1:85724745-85725040		chr1:85724618-85724744			311;259
N	alternative_donor	CUFF.25	chr1	+	chr1:54356968-54359986	chr1:54357950-54359986		chr1:54356968-54357949	chr1:54356967-54356968		152;7
K	alternative_donor	CUFF.42,CUFF.47	chr1	-	chr1:145926413-145927113	chr1:145926413-145927048		chr1:145927049-145927113	chr1:145927113-145927114		62;31
N	alternative_acceptor	CUFF.2	chr1	+	chr1:2005369-2066700	chr1:2005369-2029785		chr1:2029786-2066700	chr1:2066700-2066701		77;5
N	cassette	CUFF.19	chr1	+	chr1:32541424-32557275;chr1:32541424-32542764	chr1:32541424-32542363;chr1:32542448-32542764,chr1:32542448-32557275		chr1:32542364-32542447			65;275
N	jcn_only_AD	CUFF.2	chr1	+	chr1:2087532-2100956	chr1:2100557-2100956		chr1:2087532-2100556	chr1:2087531-2087532		435;20
N	intron_retention		chr1	+	chr1:160146353-160147308				chr1:160146352-160146353;chr1:160147308-160147309		15;311
K	coord_cassette	CUFF.60	chr1	+	chr1:167190196-167301706	chr1:167190196-167210643;chr1:167210848-167272710;chr1:167272812-167301706		chr1:167210644-167210847;chr1:167272711-167272811			13;26
K	intron_retention		chr1	+	chr1:245246991-245254795				chr1:245246990-245246991;chr1:245254795-245254796		17;40
N	jcn_only_AD	CUFF.30	chr1	+	chr1:78445304-78546358	chr1:78512019-78546358		chr1:78445304-78512018	chr1:78445303-78445304		196;5
K	alternative_last_exon	CUFF.24	chr1	-	chr1:53883339-53905447	chr1:53904722-53905447	chr1:53883200-53883338	chr1:53902613-53904721			67;183
K	cassette	CUFF.23	chr1	+	chr1:47139892-47152344	chr1:47139892-47147852;chr1:47147937-47152344		chr1:47147853-47147936			289;20
N	jcn_only_AD	CUFF.47	chr1	-	chr1:207990760-207995548	chr1:207990760-207992306		chr1:207992307-207995548	chr1:207995548-207995549		14;28
K	intron_retention	CUFF.16	chr1	+	chr1:28661598-28662304				chr1:28661597-28661598;chr1:28662304-28662305		138;489
K	cassette	CUFF.7	chr1	+	chr1:15753781-15755088	chr1:15753781-15754393;chr1:15754506-15755088		chr1:15754394-15754505			20;29
K	alternative_first_exon	CUFF.2	chr1	+	chr1:2066526-2066700,chr1:2006573-2066700,chr1:2043257-2066700,chr1:2005369-2066700,chr1:2013900-2066700,chr1:2036335-2066700,chr1:2029995-2066700,chr1:2006207-2066700,chr1:2006819-2066700,chr1:2005715-2066700,chr1:2047750-2066700;chr1:1991031-2066700	chr1:2065440-2066700	chr1:1990980-1991030	chr1:2065276-2065439			1429;45
K	cassette	CUFF.78	chr1	+	chr1:230385018-230390963	chr1:230385018-230386202;chr1:230386307-230390963		chr1:230386203-230386306			34;91
K	intron_retention	CUFF.47	chr1	-	chr1:153925311-153925741				chr1:153925310-153925311;chr1:153925741-153925742		215;10
N	jcn_only_AA	CUFF.2	chr1	+	chr1:2106753-2116021	chr1:2106753-2113270		chr1:2113271-2116021	chr1:2116021-2116022		488;63
K	jcn_only_AD	CUFF.49	chr1	+	chr1:155180207-155180338	chr1:155180227-155180338		chr1:155180207-155180226	chr1:155180206-155180207		155;150
K	alternative_last_exon	CUFF.1	chr1	+	chr1:1656203-1667255	chr1:1656203-1661684	chr1:1667256-1667412	chr1:1661685-1663411			228;146
K	jcn_only_AD	CUFF.4	chr1	+	chr1:11082299-11083249	chr1:11082308-11083249		chr1:11082299-11082307	chr1:11082298-11082299		64;321
N	alternative_donor	CUFF.12,CUFF.52	chr1	-	chr1:156918291-156921364	chr1:156918291-156918364		chr1:156918365-156921364	chr1:156921364-156921365		19;2
N	jcn_only_AA	CUFF.2	chr1	+	chr1:2005369-2066700	chr1:2005369-2029785		chr1:2029786-2066700	chr1:2066700-2066701		77;53
N	alternative_acceptor	CUFF.29	chr1	+	chr1:70820791-70832126	chr1:70820791-70831828		chr1:70831829-70832126	chr1:70832126-70832127		346;36
N	intron_retention	CUFF.52	chr1	-	chr1:156908306-156908940				chr1:156908305-156908306;chr1:156908940-156908941		44;9
K	alternative_first_exon	CUFF.12	chr1	-	chr1:26231230-26231539,chr1:26231230-26231634,chr1:26231230-26232342;chr1:26231230-26233278	chr1:26231230-26232879	chr1:26233279-26233561	chr1:26232880-26232993			356;142
K	alternative_first_exon	CUFF.12	chr1	-	chr1:26212361-26227981	chr1:26212361-26219004	chr1:26227982-26230304	chr1:26219005-26219098			19;15
N	jcn_only_AD		chr1	+	chr1:70820791-70831828	chr1:70820892-70831828		chr1:70820791-70820891	chr1:70820790-70820791		51;39
K	cassette	CUFF.51	chr1	-	chr1:156438813-156446803	chr1:156438813-156444899;chr1:156445030-156446803		chr1:156444900-156445029			53;52
K	intron_retention		chr1	+	chr1:110212194-110213908				chr1:110212193-110212194;chr1:110213908-110213909		1051;27
K	alternative_donor	CUFF.16	chr1	+	chr1:28655636-28657107	chr1:28655692-28657107		chr1:28655636-28655691	chr1:28655635-28655636		25;358
N	jcn_only_AA	CUFF.36,CUFF.55	chr1	+	chr1:160151822-160156065	chr1:160151822-160152481		chr1:160152482-160156065	chr1:160156065-160156066		755;80
N	alternative_donor	CUFF.66	chr1	+	chr1:200877016-200877857	chr1:200877678-200877857		chr1:200877016-200877677	chr1:200877015-200877016		260;32
N	alternative_donor		chr1	-	chr1:106132408-106145898;chr1:106132408-106143891;chr1:106132408-106143252	chr1:106132408-106146784		chr1:106143253-106143891;chr1:106143892-106145898;chr1:106145899-106146784	chr1:106143891-106143892;chr1:106145898-106145899;chr1:106146784-106146785		240;101
N	cassette	CUFF.2	chr1	+	chr1:2075781-2080310	chr1:2075781-2077465;chr1:2077548-2080310		chr1:2077466-2077547			41;1157
K	jcn_only_AD	CUFF.1059	chr9	+	chr9:43915898-43920248	chr9:43915980-43920248		chr9:43915898-43915979	chr9:43915897-43915898		45;44
N	alternative_donor	CUFF.1059	chr9	+	chr9:43907538-43908435	chr9:43908211-43908435		chr9:43907538-43908210	chr9:43907537-43907538		72;89
N	intron_retention		chr9	-	chr9:130941184-130941522				chr9:130941183-130941184;chr9:130941522-130941523		33;1070
K	cassette	CUFF.1085	chr9	+	chr9:131013220-131016932	chr9:131013220-131015379;chr9:131015417-131016932		chr9:131015380-131015416			241;295
K	intron_retention	CUFF.1093	chr9	+	chr9:139744590-139744957				chr9:139744589-139744590;chr9:139744957-139744958		506;40
K	alternative_first_exon	CUFF.1085	chr9	+	chr9:131002276-131004510	chr9:131003327-131004510	chr9:131002264-131002275	chr9:131003207-131003326			530;78
K	jcn_only_AD	CUFF.1066	chr9	-	chr9:86485548-86498727	chr9:86485548-86495211					9;11
N	jcn_only_AD	CUFF.1059	chr9	+	chr9:43885073-43890295	chr9:43887734-43890295		chr9:43885073-43887733	chr9:43885072-43885073		69;268
N	alternative_donor	CUFF.1094	chr9	+	chr9:139795129-139802521;chr9:139796849-139802521	chr9:139794973-139802521		chr9:139794973-139795128;chr9:139795129-139796848	chr9:139794972-139794973;chr9:139795128-139795129		30;471
K	cassette	CUFF.1079	chr9	-	chr9:123538505-123550046	chr9:123538505-123540628;chr9:123540824-123550046		chr9:123540629-123540823		chr9:123538371-123538504	91;178
K	alternative_donor	CUFF.1078	chr9	+	chr9:117350201-117354831	chr9:117350399-117354831		chr9:117350201-117350398	chr9:117350200-117350201		88;114
N	alternative_first_exon		chr9	-	chr9:125652825-125667388	chr9:125652825-125655187	chr9:125667389-125667713	chr9:125655188-125655305			16;201
N	jcn_only_AD	CUFF.1084	chr9	-	chr9:130929444-130929817;chr9:130929444-130931354	chr9:130929444-130931330		chr9:130929818-130931330;chr9:130931331-130931354	chr9:130931330-130931331;chr9:130931354-130931355		383;929
K	intron_retention	CUFF.1084	chr9	-	chr9:130940770-130940987				chr9:130940769-130940770;chr9:130940987-130940988		353;28
N	cassette	CUFF.1087	chr9	+	chr9:133333977-133342111	chr9:133333977-133339497;chr9:133339555-133342111		chr9:133339498-133339554			112;604
N	coord_cassette	CUFF.1084	chr9	-	chr9:130948056-130952966	chr9:130948056-130950141;chr9:130950214-130952607;chr9:130952724-130952966		chr9:130950142-130950213;chr9:130952608-130952723			56;634
K	cassette	CUFF.1087	chr9	+	chr9:133320383-133327610	chr9:133320383-133325658;chr9:133325721-133327610		chr9:133325659-133325720			59;551
N	alternative_donor		chr9	-	chr9:125612102-125613378	chr9:125612102-125613359		chr9:125613360-125613378	chr9:125613378-125613379		23;113
N	alternative_acceptor	CUFF.1088	chr9	-	chr9:135742341-135750501	chr9:135749827-135750501		chr9:135742341-135749826	chr9:135742340-135742341		20;0
K	intron_retention	CUFF.1084	chr9	-	chr9:130929160-130929373				chr9:130929159-130929160;chr9:130929373-130929374		1436;188
N	jcn_only_AA	CUFF.1088	chr9	-	chr9:135742341-135750501	chr9:135749827-135750501		chr9:135742341-135749826	chr9:135742340-135742341		20;9
K	intron_retention	CUFF.1086	chr9	-	chr9:131483782-131483929				chr9:131483781-131483782;chr9:131483929-131483930		139;114
K	alternative_acceptor	CUFF.1055,CUFF.1093	chr9	+	chr9:139744590-139744957	chr9:139744590-139744954		chr9:139744955-139744957	chr9:139744957-139744958		506;34
N	intron_retention		chr9	+	chr9:125027825-125033142				chr9:125027824-125027825;chr9:125033142-125033143		57;58
N	alternative_donor	CUFF.1083,CUFF.1088	chr9	-	chr9:135702442-135703399	chr9:135702442-135702693		chr9:135702694-135703399	chr9:135703399-135703400		37;5
N	alternative_acceptor	CUFF.1076	chr9	+	chr9:116791253-116793083;chr9:116791253-116794927	chr9:116791253-116794924		chr9:116793084-116794924;chr9:116794925-116794927	chr9:116794924-116794925;chr9:116794927-116794928		272;17
K	alternative_last_exon	CUFF.1059	chr9	+	chr9:43818185-43822517	chr9:43818185-43819609	chr9:43822518-43822779	chr9:43819610-43821458			79;341
K	alternative_acceptor	CUFF.1079	chr9	-	chr9:123550465-123555426	chr9:123550557-123555426		chr9:123550465-123550556	chr9:123550464-123550465		18;207
N	jcn_only_AA	CUFF.1059,CUFF.1082	chr9	+	chr9:43853617-43861002;chr9:43853617-43861005	chr9:43853617-43854068		chr9:43854069-43861002;chr9:43861003-43861005	chr9:43861002-43861003;chr9:43861005-43861006		102;43
K	alternative_first_exon	CUFF.1084,CUFF.1086	chr9	-	chr9:131484854-131486272	chr9:131484854-131486230	chr9:131486273-131486498	chr9:131486231-131486271			335;29
K	cassette	CUFF.1069	chr9	+	chr9:95588861-95599058	chr9:95588861-95591219;chr9:95591446-95599058		chr9:95591220-95591445			22;137
N	alternative_donor	CUFF.1087	chr9	+	chr9:133346903-133352257	chr9:133351777-133352257		chr9:133346903-133351776	chr9:133346902-133346903		859;3
K	cassette	CUFF.1082	chr9	+	chr9:125033355-125047447	chr9:125033355-125042721;chr9:125042878-125047447		chr9:125042722-125042877			24;959
N	jcn_only_AD	CUFF.1084	chr9	-	chr9:130929444-130931330;chr9:130929444-130931354	chr9:130929444-130929817		chr9:130929818-130931330;chr9:130931331-130931354	chr9:130931330-130931331;chr9:130931354-130931355		1260;52
K	intron_retention	CUFF.1052	chr9	-	chr9:15185405-15186941				chr9:15185404-15185405;chr9:15186941-15186942		302;126
K	cassette	CUFF.1052	chr9	-	chr9:15214248-15225914	chr9:15214248-15224337;chr9:15224504-15225914		chr9:15224338-15224503			425;136
N	jcn_only_AD		chr9	+	chr9:34991414-34993196	chr9:34992984-34993196					55;15
K	cassette	CUFF.1066	chr9	-	chr9:86514720-86523366	chr9:86514720-86517974;chr9:86518934-86523366		chr9:86517975-86518933			56;21
K	intron_retention	CUFF.1085	chr9	+	chr9:131010215-131010861				chr9:131010214-131010215;chr9:131010861-131010862		454;78
N	alternative_donor	CUFF.1084	chr9	-	chr9:130929444-130931330;chr9:130929444-130931354	chr9:130929444-130929817		chr9:130929818-130931330;chr9:130931331-130931354	chr9:130931330-130931331;chr9:130931354-130931355		854;33
N	alternative_acceptor	CUFF.1076	chr9	+	chr9:116791253-116794924;chr9:116791253-116794927	chr9:116791253-116793083		chr9:116793084-116794924;chr9:116794925-116794927	chr9:116794924-116794925;chr9:116794927-116794928		285;4
N	cassette	CUFF.1084	chr9	-	chr9:130950214-130952966;chr9:130948056-130952966	chr9:130948056-130952607,chr9:130950214-130952607;chr9:130952724-130952966		chr9:130952608-130952723			72;633
K	intron_retention	CUFF.1084	chr9	-	chr9:130948014-130953002				chr9:130948013-130948014;chr9:130953002-130953003		1339;345
N	alternative_acceptor	CUFF.1082	chr9	+	chr9:125027218-125027740;chr9:125027218-125033231	chr9:125027218-125033142		chr9:125027741-125033142;chr9:125033143-125033231	chr9:125033142-125033143;chr9:125033231-125033232		486;306
N	intron_retention	CUFF.1084	chr9	-	chr9:130929444-130929817				chr9:130929443-130929444;chr9:130929817-130929818		52;51
K	intron_retention	CUFF.1051	chr9	+	chr9:12192-12292				chr9:12191-12192;chr9:12292-12293		152;40
K	alternative_last_exon	CUFF.1088	chr9	-	chr9:135730313-135739051	chr9:135736985-135739051	chr9:135730244-135730312	chr9:135736685-135736984			34;471
N	jcn_only_AA	CUFF.1082	chr9	+	chr9:125027218-125027740;chr9:125027218-125033231	chr9:125027218-125033142		chr9:125027741-125033142;chr9:125033143-125033231	chr9:125033142-125033143;chr9:125033231-125033232		572;422
K	alternative_last_exon	CUFF.1079	chr9	-	chr9:123515590-123533625	chr9:123527126-123533625	chr9:123514157-123515589	chr9:123526360-123527125		chr9:123533626-123533795	76;148
K	alternative_acceptor	CUFF.1086	chr9	-	chr9:131483760-131483929;chr9:131483782-131483929	chr9:131483810-131483929		chr9:131483760-131483781;chr9:131483782-131483809	chr9:131483759-131483760;chr9:131483781-131483782		106;128
N	alternative_acceptor	CUFF.1082	chr9	+	chr9:125027218-125027740;chr9:125027218-125033142	chr9:125027218-125033231		chr9:125027741-125033142;chr9:125033143-125033231	chr9:125033142-125033143;chr9:125033231-125033232		318;474
N	jcn_only_AD		chr9	-	chr9:130929444-130929817;chr9:130929444-130931330	chr9:130929444-130931354		chr9:130929818-130931330;chr9:130931331-130931354	chr9:130931330-130931331;chr9:130931354-130931355		981;331
K	alternative_donor	CUFF.1079,CUFF.1084	chr9	-	chr9:123550557-123555426	chr9:123550557-123555164		chr9:123555165-123555426	chr9:123555426-123555427		207;83
N	intron_retention		chr9	+	chr9:34991414-34993196				chr9:34991413-34991414;chr9:34993196-34993197		55;36
K	intron_retention	CUFF.1084	chr9	-	chr9:130943094-130947825				chr9:130943093-130943094;chr9:130947825-130947826		2453;13
N	jcn_only_AD	CUFF.1056	chr9	-	chr9:35077397-35078601	chr9:35077397-35078137		chr9:35078138-35078601	chr9:35078601-35078602	chr9:35078602-35078733	51;211
K	mutually_exclusive	CUFF.1085	chr9	+	chr9:130985140-130988313,chr9:130988453-130996299	chr9:130985140-130986529,chr9:130986669-130996299	chr9:130988314-130988452	chr9:130986530-130986668			148;258
K	coord_cassette	CUFF.1082	chr9	+	chr9:125047567-125054027	chr9:125047567-125048058;chr9:125048226-125048317;chr9:125048446-125054027		chr9:125048059-125048225;chr9:125048318-125048445			550;155
N	alternative_first_exon	CUFF.1059	chr9	+	chr9:43908524-43915825	chr9:43915591-43915825	chr9:43907404-43908523	chr9:43914374-43915590			19;111
N	jcn_only_AA	CUFF.1052	chr9	-	chr9:15214248-15249915	chr9:15249686-15249915		chr9:15214248-15249685	chr9:15214247-15214248		61;72
K	intron_retention		chr9	-	chr9:130943079-130947825				chr9:130943078-130943079;chr9:130947825-130947826		214;23
K	jcn_only_AD	CUFF.1078	chr9	+	chr9:117350201-117354831	chr9:117350399-117354831		chr9:117350201-117350398	chr9:117350200-117350201		88;132
N	alternative_donor	CUFF.1084	chr9	-	chr9:130941184-130941267;chr9:130941184-130941351	chr9:130941184-130941522		chr9:130941268-130941351;chr9:130941352-130941522	chr9:130941351-130941352;chr9:130941522-130941523		1409;33
K	cassette	CUFF.1058	chr9	+	chr9:35396935-35397631	chr9:35396935-35397163;chr9:35397308-35397631		chr9:35397164-35397307			12;176
N	cassette	CUFF.1074	chr9	-	chr9:107651477-107690215	chr9:107651477-107665894;chr9:107666053-107690215		chr9:107665895-107666052			23;13
N	jcn_only_AA	CUFF.1059	chr9	+	chr9:43853617-43861002;chr9:43853617-43854068	chr9:43853617-43861005		chr9:43854069-43861002;chr9:43861003-43861005	chr9:43861002-43861003;chr9:43861005-43861006		105;39
N	cassette	CUFF.1088	chr9	-	chr9:135742341-135753558	chr9:135742341-135750501;chr9:135750587-135753558		chr9:135750502-135750586			13;21
K	alternative_first_exon	CUFF.1087	chr9	+	chr9:133355188-133355771	chr9:133355287-133355771	chr9:133355103-133355187	chr9:133355188-133355286			608;199
K	alternative_first_exon	CUFF.1094	chr9	+	chr9:139780732-139793164;chr9:139780994-139793164;chr9:139784995-139793164	chr9:139777163-139793164	chr9:139780487-139780731;chr9:139780901-139780993;chr9:139784801-139784994	chr9:139777119-139777162			222;124
K	intron_retention	CUFF.1086	chr9	-	chr9:131485019-131486272				chr9:131485018-131485019;chr9:131486272-131486273		147;15
K	jcn_only_AA	CUFF.1083	chr9	-	chr9:125616861-125617462	chr9:125616895-125617462		chr9:125616861-125616894	chr9:125616860-125616861		73;229
K	intron_retention	CUFF.1055	chr9	+	chr9:34990810-34993196				chr9:34990809-34990810;chr9:34993196-34993197		53;31
K	jcn_only_AD	CUFF.1079,CUFF.1084	chr9	-	chr9:123550557-123555426	chr9:123550557-123555164		chr9:123555165-123555426	chr9:123555426-123555427		207;83
K	mutually_exclusive	CUFF.1055	chr9	+	chr9:34989829-34990664,chr9:34990810-34993196	chr9:34989829-34990344,chr9:34990609-34993196	chr9:34990665-34990809	chr9:34990345-34990608			38;161
N	jcn_only_AD	CUFF.1094	chr9	+	chr9:139795129-139802521;chr9:139796849-139802521	chr9:139794973-139802521		chr9:139794973-139795128;chr9:139795129-139796848	chr9:139794972-139794973;chr9:139795128-139795129		29;471
K	intron_retention	CUFF.1055	chr9	+	chr9:34990609-34993196				chr9:34990608-34990609;chr9:34993196-34993197		211;34
K	alternative_last_exon	CUFF.1056	chr9	-	chr9:35077397-35078601	chr9:35078341-35078601	chr9:35077261-35077396	chr9:35077909-35078340		chr9:35078602-35078733	42;484
K	intron_retention		chr9	-	chr9:130953142-130953710				chr9:130953141-130953142;chr9:130953710-130953711		2111;59
K	jcn_only_AA	CUFF.1086	chr9	-	chr9:131484854-131486272	chr9:131485019-131486272		chr9:131484854-131485018	chr9:131484853-131484854		311;147
K	cassette	CUFF.1058	chr9	+	chr9:35259048-35295692	chr9:35259048-35291065;chr9:35291102-35295692		chr9:35291066-35291101			20;16
K	intron_retention	CUFF.1079	chr9	-	chr9:123550465-123555426				chr9:123550464-123550465;chr9:123555426-123555427		18;179
K	alternative_last_exon	CUFF.1052	chr9	-	chr9:15185405-15186941	chr9:15185527-15186941	chr9:15185278-15185404	chr9:15185429-15185526			237;10
K	intron_retention		chr9	+	chr9:43908524-43915359				chr9:43908523-43908524;chr9:43915359-43915360		64;48
K	alternative_last_exon	CUFF.1070	chr9	-	chr9:99973770-100000704	chr9:100000368-100000704	chr9:99973655-99973769	chr9:100000271-100000367			360;22
K	intron_retention	CUFF.1086	chr9	-	chr9:131484854-131486272				chr9:131484853-131484854;chr9:131486272-131486273		311;126
K	alternative_last_exon	CUFF.1081	chr9	-	chr9:124895254-124910390	chr9:124906658-124910390	chr9:124894745-124895253	chr9:124906561-124906657			316;15
N	cassette	CUFF.1052	chr9	-	chr9:15192694-15203820	chr9:15192694-15199858;chr9:15199924-15203820		chr9:15199859-15199923			167;358
N	cassette	CUFF.1059	chr9	+	chr9:43861207-43884944	chr9:43861207-43875988;chr9:43876146-43884944		chr9:43875989-43876145			40;40
K	intron_retention	CUFF.1086	chr9	-	chr9:131483760-131483929				chr9:131483759-131483760;chr9:131483929-131483930		20;148
N	jcn_only_AA	CUFF.1082	chr9	+	chr9:125027218-125027740;chr9:125027218-125033142	chr9:125027218-125033231		chr9:125027741-125033142;chr9:125033143-125033231	chr9:125033142-125033143;chr9:125033231-125033232		520;474
K	alternative_last_exon	CUFF.1066	chr9	-	chr9:86506417-86514575	chr9:86513864-86514575	chr9:86506210-86506416	chr9:86513516-86513863			21;74
N	alternative_acceptor	CUFF.1059	chr9	+	chr9:43907538-43908435	chr9:43907538-43908111		chr9:43908112-43908435	chr9:43908435-43908436		72;89
N	jcn_only_AD	CUFF.1083,CUFF.1084	chr9	-	chr9:130941184-130941522;chr9:130941184-130941351	chr9:130941184-130941267		chr9:130941268-130941351;chr9:130941352-130941522	chr9:130941351-130941352;chr9:130941522-130941523		75;109
N	jcn_only_AD	CUFF.1058	chr9	+	chr9:35162303-35228011	chr9:35227931-35228011		chr9:35162303-35227930	chr9:35162302-35162303		11;32
N	alternative_acceptor	CUFF.1076	chr9	+	chr9:116795009-116798579	chr9:116795009-116797470		chr9:116797471-116798579	chr9:116798579-116798580		13;1
N	jcn_only_AA	CUFF.1052	chr9	-	chr9:15250009-15267911;chr9:15211396-15267911	chr9:15226011-15267911					45;423
N	jcn_only_AA	CUFF.1059,CUFF.1069	chr9	+	chr9:43908524-43915825;chr9:43908524-43915359	chr9:43908524-43909283					120;203
K	intron_retention	CUFF.1054	chr9	-	chr9:34709425-34709496				chr9:34709424-34709425;chr9:34709496-34709497		24;61
N	intron_retention	CUFF.1059	chr9	+	chr9:43907538-43908111				chr9:43907537-43907538;chr9:43908111-43908112		102;52
N	jcn_only_AA	CUFF.1076	chr9	+	chr9:116791253-116794924;chr9:116791253-116794927	chr9:116791253-116793083		chr9:116793084-116794924;chr9:116794925-116794927	chr9:116794924-116794925;chr9:116794927-116794928		303;31
N	alternative_donor	CUFF.1083,CUFF.1084	chr9	-	chr9:130941184-130941522;chr9:130941184-130941351	chr9:130941184-130941267		chr9:130941268-130941351;chr9:130941352-130941522	chr9:130941351-130941352;chr9:130941522-130941523		395;1047
K	cassette	CUFF.1058	chr9	+	chr9:35400441-35403163	chr9:35400441-35401947;chr9:35402005-35403163		chr9:35401948-35402004			56;223
N	intron_retention	CUFF.1061	chr9	-	chr9:46686830-46687372				chr9:46686829-46686830;chr9:46687372-46687373		36;13
N	alternative_acceptor	CUFF.1059	chr9	+	chr9:43885073-43890295	chr9:43885073-43887610		chr9:43887611-43890295	chr9:43890295-43890296		69;11
N	jcn_only_AA		chr9	+	chr9:43853617-43854068;chr9:43853617-43861005	chr9:43853617-43861002		chr9:43854069-43861002;chr9:43861003-43861005	chr9:43861002-43861003;chr9:43861005-43861006		82;63
K	jcn_only_AA	CUFF.1086	chr9	-	chr9:131483760-131483929;chr9:131483782-131483929	chr9:131483810-131483929		chr9:131483760-131483781;chr9:131483782-131483809	chr9:131483759-131483760;chr9:131483781-131483782		159;276
K	alternative_acceptor	CUFF.1086	chr9	-	chr9:131483810-131483929;chr9:131483782-131483929	chr9:131483760-131483929		chr9:131483760-131483781;chr9:131483782-131483809	chr9:131483759-131483760;chr9:131483781-131483782		214;20
N	jcn_only_AA	CUFF.1052	chr9	-	chr9:15226011-15267911;chr9:15211396-15267911	chr9:15250009-15267911					434;35
K	cassette	CUFF.1084	chr9	-	chr9:130931799-130932298	chr9:130931799-130931901;chr9:130931980-130932298		chr9:130931902-130931979			595;35
N	alternative_acceptor	CUFF.1052	chr9	-	chr9:15214248-15249915	chr9:15249686-15249915		chr9:15214248-15249685	chr9:15214247-15214248		61;4
K	jcn_only_AA	CUFF.1076	chr9	+	chr9:116779065-116791189	chr9:116779065-116791012		chr9:116791013-116791189	chr9:116791189-116791190		240;64
K	cassette	CUFF.1093	chr9	+	chr9:139744590-139745206	chr9:139744590-139744957;chr9:139745013-139745206		chr9:139744958-139745012			727;481
K	alternative_first_exon	CUFF.1052	chr9	-	chr9:15226011-15267911	chr9:15226011-15232229	chr9:15267912-15267946	chr9:15232230-15232460			357;156
N	mutually_exclusive	CUFF.1084	chr9	-	chr9:130948056-130952607,chr9:130952724-130952966	chr9:130948056-130950141,chr9:130950214-130952966	chr9:130952608-130952723	chr9:130950142-130950213			36;15
N	jcn_only_AA	CUFF.1083	chr9	-	chr9:125652825-125667388	chr9:125659856-125667388					18;207
K	jcn_only_AA	CUFF.1086	chr9	-	chr9:131483760-131483929;chr9:131483810-131483929	chr9:131483782-131483929		chr9:131483760-131483781;chr9:131483782-131483809	chr9:131483759-131483760;chr9:131483781-131483782		296;139
K	intron_retention	CUFF.1079	chr9	-	chr9:123555536-123555637				chr9:123555535-123555536;chr9:123555637-123555638		84;107
N	jcn_only_AD		chr9	-	chr9:125612102-125613378	chr9:125612102-125613359		chr9:125613360-125613378	chr9:125613378-125613379		23;209
K	intron_retention	CUFF.1056	chr9	-	chr9:35074430-35076518				chr9:35074429-35074430;chr9:35076518-35076519	chr9:35074368-35074429;chr9:35076519-35076601	268;49
K	alternative_acceptor	CUFF.1086	chr9	-	chr9:131483760-131483929;chr9:131483810-131483929	chr9:131483782-131483929		chr9:131483760-131483781;chr9:131483782-131483809	chr9:131483759-131483760;chr9:131483781-131483782		148;86
K	mutually_exclusive	CUFF.1073	chr9	+	chr9:105768661-105774263,chr9:105774380-105780606	chr9:105768661-105772982,chr9:105773088-105780606	chr9:105774264-105774379	chr9:105772983-105773087			49;28
K	alternative_last_exon	CUFF.1083	chr9	-	chr9:125627937-125639749	chr9:125637648-125639749	chr9:125627628-125627936	chr9:125635981-125637647			210;269
N	jcn_only_AA	CUFF.1059	chr9	+	chr9:43885073-43890295	chr9:43885073-43887610		chr9:43887611-43890295	chr9:43890295-43890296		69;153
K	intron_retention	CUFF.1083	chr9	-	chr9:125613716-125616230				chr9:125613715-125613716;chr9:125616230-125616231		176;90
K	intron_retention	CUFF.1059	chr9	+	chr9:43907538-43908435				chr9:43907537-43907538;chr9:43908435-43908436		72;48
N	alternative_donor	CUFF.1084	chr9	-	chr9:130941184-130941522;chr9:130941184-130941267	chr9:130941184-130941351		chr9:130941268-130941351;chr9:130941352-130941522	chr9:130941351-130941352;chr9:130941522-130941523		1080;362
K	cassette	CUFF.1093	chr9	+	chr9:139744590-139745206	chr9:139744590-139744954;chr9:139745013-139745206		chr9:139744955-139745012			727;276
N	jcn_only_AD	CUFF.1079	chr9	-	chr9:123555536-123555637	chr9:123555536-123555631		chr9:123555632-123555637	chr9:123555637-123555638		84;92
N	jcn_only_AD	CUFF.1083,CUFF.1088	chr9	-	chr9:135702442-135703399	chr9:135702442-135702693		chr9:135702694-135703399	chr9:135703399-135703400		37;12
N	jcn_only_AA	CUFF.1059	chr9	+	chr9:43907538-43908435	chr9:43907538-43908111		chr9:43908112-43908435	chr9:43908435-43908436		72;102
K	alternative_last_exon	CUFF.1069,CUFF.1093	chr9	+	chr9:95600023-95646187	chr9:95600023-95600538	chr9:95646188-95646282	chr9:95600539-95600831			21;70
K	alternative_first_exon	CUFF.1082	chr9	+	chr9:125027218-125033231	chr9:125028060-125033231	chr9:125026792-125027217	chr9:125027962-125028059			240;17
K	alternative_first_exon	CUFF.1072	chr9	-	chr9:104293842-104295734	chr9:104293842-104294958	chr9:104295735-104295914	chr9:104294959-104295045			123;4
K	jcn_only_AA	CUFF.1055,CUFF.1093	chr9	+	chr9:139744590-139744957	chr9:139744590-139744954		chr9:139744955-139744957	chr9:139744957-139744958		506;39
K	intron_retention	CUFF.1086	chr9	-	chr9:131483548-131483703				chr9:131483547-131483548;chr9:131483703-131483704		49;230
N	alternative_acceptor	CUFF.1059	chr9	+	chr9:43853617-43861002;chr9:43853617-43854068	chr9:43853617-43861005		chr9:43854069-43861002;chr9:43861003-43861005	chr9:43861002-43861003;chr9:43861005-43861006		37;39
K	cassette	CUFF.1089	chr9	+	chr9:137772768-137775147	chr9:137772768-137774371;chr9:137774486-137775147		chr9:137774372-137774485			11;25
K	cassette	CUFF.1076	chr9	+	chr9:116769720-116770756	chr9:116769720-116770623;chr9:116770660-116770756		chr9:116770624-116770659			210;58
N	intron_retention		chr9	+	chr9:43908524-43909283				chr9:43908523-43908524;chr9:43909283-43909284		203;68
K	intron_retention	CUFF.1056	chr9	-	chr9:35079239-35079437				chr9:35079238-35079239;chr9:35079437-35079438	chr9:35079148-35079238;chr9:35079438-35080108	295;1214
K	alternative_first_exon	CUFF.1082	chr9	+	chr9:125027825-125033142;chr9:125027218-125033142	chr9:125028060-125033142	chr9:125026792-125027217	chr9:125027962-125028059			271;15
K	alternative_donor	CUFF.1059	chr9	+	chr9:43915898-43920248	chr9:43915980-43920248		chr9:43915898-43915979	chr9:43915897-43915898		45;52
N	jcn_only_AD	CUFF.1061,CUFF.1066	chr9	-	chr9:46686830-46687553	chr9:46686830-46687372		chr9:46687373-46687553	chr9:46687553-46687554		423;36
K	intron_retention	CUFF.1082	chr9	+	chr9:125047567-125048058				chr9:125047566-125047567;chr9:125048058-125048059		245;76
N	jcn_only_AA		chr9	+	chr9:43908524-43915825;chr9:43908524-43909283	chr9:43908524-43915359					259;64
K	intron_retention	CUFF.1084	chr9	-	chr9:130929444-130931354				chr9:130929443-130929444;chr9:130931354-130931355		331;140
N	alternative_acceptor	CUFF.1076	chr9	+	chr9:116791253-116793083;chr9:116791253-116794924	chr9:116791253-116794927		chr9:116793084-116794924;chr9:116794925-116794927	chr9:116794924-116794925;chr9:116794927-116794928		21;268
N	alternative_donor	CUFF.1094	chr9	+	chr9:139794973-139802521;chr9:139796849-139802521	chr9:139795129-139802521		chr9:139794973-139795128;chr9:139795129-139796848	chr9:139794972-139794973;chr9:139795128-139795129		484;17
K	alternative_first_exon	CUFF.1094	chr9	+	chr9:139780994-139793164;chr9:139784995-139793164;chr9:139777163-139793164	chr9:139780732-139793164	chr9:139780901-139780993;chr9:139784801-139784994;chr9:139777119-139777162	chr9:139780487-139780731			236;110
N	alternative_donor	CUFF.1061,CUFF.1066	chr9	-	chr9:46686830-46687553	chr9:46686830-46687372		chr9:46687373-46687553	chr9:46687553-46687554		423;21
N	alternative_acceptor	CUFF.1082	chr9	+	chr9:125027218-125033142;chr9:125027218-125033231	chr9:125027218-125027740		chr9:125027741-125033142;chr9:125033143-125033231	chr9:125033142-125033143;chr9:125033231-125033232		780;12
N	intron_retention	CUFF.1084	chr9	-	chr9:130929444-130931330				chr9:130929443-130929444;chr9:130931330-130931331		929;61
K	cassette	CUFF.1076	chr9	+	chr9:116770835-116778974	chr9:116770835-116778392;chr9:116778453-116778974		chr9:116778393-116778452			11;248
K	jcn_only_AA	CUFF.1079	chr9	-	chr9:123550465-123555426	chr9:123550557-123555426		chr9:123550465-123550556	chr9:123550464-123550465		18;207
N	jcn_only_AD	CUFF.1079	chr9	-	chr9:15211396-15267911	chr9:15211396-15214136					11;611
K	jcn_only_AA	CUFF.1055	chr9	+	chr9:34993442-34996391	chr9:34993442-34996261		chr9:34996262-34996391	chr9:34996391-34996392		44;421
K	intron_retention		chr9	-	chr9:130941184-130941351				chr9:130941183-130941184;chr9:130941351-130941352		42;998
N	alternative_donor	CUFF.1084	chr9	-	chr9:130929444-130929817;chr9:130929444-130931354	chr9:130929444-130931330		chr9:130929818-130931330;chr9:130931331-130931354	chr9:130931330-130931331;chr9:130931354-130931355		364;523
N	alternative_donor	CUFF.1058	chr9	+	chr9:35162303-35228011	chr9:35227931-35228011		chr9:35162303-35227930	chr9:35162302-35162303		11;0
N	alternative_acceptor		chr9	+	chr9:43853617-43854068;chr9:43853617-43861005	chr9:43853617-43861002		chr9:43854069-43861002;chr9:43861003-43861005	chr9:43861002-43861003;chr9:43861005-43861006		45;31
N	alternative_donor		chr9	-	chr9:130929444-130929817;chr9:130929444-130931330	chr9:130929444-130931354		chr9:130929818-130931330;chr9:130931331-130931354	chr9:130931330-130931331;chr9:130931354-130931355		556;331
K	intron_retention	CUFF.1061	chr9	-	chr9:46686830-46687553				chr9:46686829-46686830;chr9:46687553-46687554		423;12
K	alternative_first_exon	CUFF.1094	chr9	+	chr9:139780732-139793164;chr9:139784995-139793164;chr9:139777163-139793164	chr9:139780994-139793164	chr9:139780487-139780731;chr9:139784801-139784994;chr9:139777119-139777162	chr9:139780901-139780993			316;30
K	intron_retention	CUFF.1061	chr9	-	chr9:46687684-46687798				chr9:46687683-46687684;chr9:46687798-46687799		54;343
K	alternative_acceptor	CUFF.1082	chr9	+	chr9:125028060-125033231	chr9:125028060-125033142		chr9:125033143-125033231	chr9:125033231-125033232		27;176
K	jcn_only_AD	CUFF.1052,CUFF.1071	chr9	-	chr9:104188921-104192090	chr9:104188921-104189763					20;37
K	intron_retention	CUFF.1056	chr9	-	chr9:35075080-35075275				chr9:35075079-35075080;chr9:35075275-35075276		107;30
K	cassette	CUFF.1072	chr9	-	chr9:104239452-104249230	chr9:104239452-104242952;chr9:104243008-104249230		chr9:104242953-104243007			4;3
N	alternative_donor	CUFF.1059	chr9	+	chr9:43885073-43890295	chr9:43887734-43890295		chr9:43885073-43887733	chr9:43885072-43885073		69;20
N	cassette	CUFF.1082	chr9	+	chr9:125047567-125048317	chr9:125047567-125048058;chr9:125048226-125048317		chr9:125048059-125048225			92;193
K	alternative_acceptor	CUFF.1086	chr9	-	chr9:131484854-131486272	chr9:131485019-131486272		chr9:131484854-131485018	chr9:131484853-131484854		311;172
K	jcn_only_AA	CUFF.1082	chr9	+	chr9:125028060-125033231	chr9:125028060-125033142		chr9:125033143-125033231	chr9:125033231-125033232		27;23
N	cassette	CUFF.1084	chr9	-	chr9:130948056-130952607;chr9:130948056-130952966	chr9:130948056-130950141;chr9:130950214-130952607,chr9:130950214-130952966		chr9:130950142-130950213			109;798
K	intron_retention	CUFF.1087	chr9	+	chr9:133320383-133327610				chr9:133320382-133320383;chr9:133327610-133327611		59;38
N	intron_retention		chr9	-	chr9:130952636-130953103				chr9:130952635-130952636;chr9:130953103-130953104		114;436
K	alternative_first_exon	CUFF.1084	chr9	-	chr9:130953142-130953558,chr9:130953142-130954133,chr9:130953142-130966464;chr9:130953142-130954010	chr9:130953142-130953710	chr9:130954011-130954133	chr9:130953711-130953912			176;1343
K	intron_retention	CUFF.1056	chr9	-	chr9:35079533-35079727				chr9:35079532-35079533;chr9:35079727-35079728	chr9:35079148-35079532;chr9:35079728-35080108	163;504
N	jcn_only_AA	CUFF.1052	chr9	-	chr9:15250009-15267911;chr9:15226011-15267911	chr9:15211396-15267911					457;11
K	intron_retention	CUFF.1086	chr9	-	chr9:131484854-131486230				chr9:131484853-131484854;chr9:131486230-131486231		35;118
K	intron_retention	CUFF.1087	chr9	+	chr9:133346903-133352257				chr9:133346902-133346903;chr9:133352257-133352258		859;33
N	cassette	CUFF.1084	chr9	-	chr9:130943079-130952607	chr9:130943079-130947825;chr9:130948056-130952607		chr9:130947826-130948055			21;1158
K	cassette	CUFF.1060	chr9	-	chr9:46661549-46662447	chr9:46661549-46661770;chr9:46661861-46662447		chr9:46661771-46661860			73;25
K	alternative_acceptor	CUFF.1055	chr9	+	chr9:34993442-34996391	chr9:34993442-34996261		chr9:34996262-34996391	chr9:34996391-34996392		44;346
N	alternative_donor	CUFF.1079	chr9	-	chr9:123555536-123555637	chr9:123555536-123555631		chr9:123555632-123555637	chr9:123555637-123555638		84;91
N	jcn_only_AA	CUFF.1082	chr9	+	chr9:125027218-125033142;chr9:125027218-125033231	chr9:125027218-125027740		chr9:125027741-125033142;chr9:125033143-125033231	chr9:125033142-125033143;chr9:125033231-125033232		896;98
K	jcn_only_AA	CUFF.1084	chr9	-	chr9:130943079-130947825	chr9:130943094-130947825		chr9:130943079-130943093	chr9:130943078-130943079		214;2453
K	alternative_acceptor	CUFF.1076	chr9	+	chr9:116779065-116791189	chr9:116779065-116791012		chr9:116791013-116791189	chr9:116791189-116791190		240;58
N	jcn_only_AD	CUFF.1084	chr9	-	chr9:130941184-130941522;chr9:130941184-130941267	chr9:130941184-130941351		chr9:130941268-130941351;chr9:130941352-130941522	chr9:130941351-130941352;chr9:130941522-130941523		142;42
N	coord_cassette	CUFF.1066	chr9	-	chr9:86474287-86495211	chr9:86474287-86482598;chr9:86482776-86485433;chr9:86485548-86495211		chr9:86482599-86482775;chr9:86485434-86485547			16;12
K	cassette	CUFF.1090	chr9	+	chr9:138480579-138482636	chr9:138480579-138481256;chr9:138481331-138482636		chr9:138481257-138481330			127;92
N	alternative_donor	CUFF.1094	chr9	+	chr9:139795129-139802521;chr9:139794973-139802521	chr9:139796849-139802521		chr9:139794973-139795128;chr9:139795129-139796848	chr9:139794972-139794973;chr9:139795128-139795129		488;13
N	cassette	CUFF.1094	chr9	+	chr9:139815668-139818303	chr9:139815668-139816833;chr9:139816946-139818303		chr9:139816834-139816945			85;109
K	cassette	CUFF.1076	chr9	+	chr9:116750861-116764275	chr9:116750861-116760538;chr9:116760635-116764275		chr9:116760539-116760634			257;8
K	alternative_last_exon	CUFF.1085	chr9	+	chr9:131015417-131016932	chr9:131015417-131016287	chr9:131016933-131017626	chr9:131016288-131016441			500;51
N	jcn_only_AD	CUFF.1076	chr9	+	chr9:116795009-116798579	chr9:116797516-116798579		chr9:116795009-116797515	chr9:116795008-116795009		13;14
K	intron_retention	CUFF.1094	chr9	+	chr9:139794973-139802521				chr9:139794972-139794973;chr9:139802521-139802522		471;48
K	alternative_first_exon	CUFF.1094	chr9	+	chr9:139780732-139793164;chr9:139780994-139793164;chr9:139777163-139793164	chr9:139784995-139793164	chr9:139780487-139780731;chr9:139780901-139780993;chr9:139777119-139777162	chr9:139784801-139784994			264;82
N	intron_retention		chr9	+	chr9:34992984-34993196				chr9:34992983-34992984;chr9:34993196-34993197		15;53
K	intron_retention	CUFF.1083	chr9	-	chr9:125627821-125627902				chr9:125627820-125627821;chr9:125627902-125627903		144;59
K	intron_retention	CUFF.1093	chr9	+	chr9:139744590-139744954				chr9:139744589-139744590;chr9:139744954-139744955		39;41
K	cassette	CUFF.1073	chr9	+	chr9:105774380-105780606	chr9:105774380-105779169;chr9:105779244-105780606		chr9:105779170-105779243			105;11
N	jcn_only_AD	CUFF.1087	chr9	+	chr9:133346903-133352257	chr9:133351777-133352257		chr9:133346903-133351776	chr9:133346902-133346903		859;27
K	intron_retention		chr9	-	chr9:130941184-130941267				chr9:130941183-130941184;chr9:130941267-130941268		109;460
N	alternative_donor	CUFF.1056	chr9	-	chr9:35077397-35078601	chr9:35077397-35078137		chr9:35078138-35078601	chr9:35078601-35078602	chr9:35078602-35078733	51;451
N	jcn_only_AD	CUFF.1084	chr9	-	chr9:130941184-130941267;chr9:130941184-130941351	chr9:130941184-130941522		chr9:130941268-130941351;chr9:130941352-130941522	chr9:130941351-130941352;chr9:130941522-130941523		151;33
N	jcn_only_AD	CUFF.1059	chr9	+	chr9:43907538-43908435	chr9:43908211-43908435		chr9:43907538-43908210	chr9:43907537-43907538		72;184
K	cassette	CUFF.1085	chr9	+	chr9:131008783-131009653	chr9:131008783-131009215;chr9:131009403-131009653		chr9:131009216-131009402			544;84
K	intron_retention	CUFF.1059	chr9	+	chr9:43876146-43884944				chr9:43876145-43876146;chr9:43884944-43884945		19;74
K	alternative_first_exon	CUFF.1064,CUFF.1072	chr9	-	chr9:71160753-71161474	chr9:71160753-71160844	chr9:71161475-71161598	chr9:71160845-71161032			33;33
N	jcn_only_AD	CUFF.1094	chr9	+	chr9:139795129-139802521;chr9:139794973-139802521	chr9:139796849-139802521		chr9:139794973-139795128;chr9:139795129-139796848	chr9:139794972-139794973;chr9:139795128-139795129		482;18
N	jcn_only_AA	CUFF.1059	chr9	+	chr9:43908524-43909283;chr9:43908524-43915359	chr9:43908524-43915825					268;55
K	alternative_last_exon	CUFF.1069	chr9	+	chr9:95591446-95599058	chr9:95591446-95591955	chr9:95599059-95600022	chr9:95591956-95592140			78;127
K	jcn_only_AD	CUFF.1052	chr9	-	chr9:15188131-15189701	chr9:15188131-15189571					44;451
N	jcn_only_AA	CUFF.1076	chr9	+	chr9:116791253-116793083;chr9:116791253-116794927	chr9:116791253-116794924		chr9:116793084-116794924;chr9:116794925-116794927	chr9:116794924-116794925;chr9:116794927-116794928		299;35
N	intron_retention		chr9	-	chr9:130953142-130954133				chr9:130953141-130953142;chr9:130954133-130954134		8;47
N	cassette	CUFF.1082	chr9	+	chr9:125047567-125054027	chr9:125047567-125048317;chr9:125048446-125054027		chr9:125048318-125048445			550;130
N	intron_retention	CUFF.1079	chr9	-	chr9:123555536-123555631				chr9:123555535-123555536;chr9:123555631-123555632		92;111
K	alternative_acceptor	CUFF.1083	chr9	-	chr9:125616861-125617462	chr9:125616895-125617462		chr9:125616861-125616894	chr9:125616860-125616861		73;107
K	cassette	CUFF.1055	chr9	+	chr9:34989829-34993196	chr9:34989829-34990664;chr9:34990810-34993196		chr9:34990665-34990809			154;38
K	jcn_only_AA	CUFF.1086	chr9	-	chr9:131483810-131483929;chr9:131483782-131483929	chr9:131483760-131483929		chr9:131483760-131483781;chr9:131483782-131483809	chr9:131483759-131483760;chr9:131483781-131483782		415;20
N	alternative_donor	CUFF.1076	chr9	+	chr9:116795009-116798579	chr9:116797516-116798579		chr9:116795009-116797515	chr9:116795008-116795009		13;14
N	jcn_only_AA	CUFF.1076	chr9	+	chr9:116791253-116793083;chr9:116791253-116794924	chr9:116791253-116794927		chr9:116793084-116794924;chr9:116794925-116794927	chr9:116794924-116794925;chr9:116794927-116794928		66;268
N	cassette	CUFF.1082	chr9	+	chr9:125054120-125084818	chr9:125054120-125075505;chr9:125075666-125084818		chr9:125075506-125075665			84;621
N	intron_retention		chr9	+	chr9:43908211-43908435				chr9:43908210-43908211;chr9:43908435-43908436		184;64
K	alternative_acceptor	CUFF.1084	chr9	-	chr9:130943079-130947825	chr9:130943094-130947825		chr9:130943079-130943093	chr9:130943078-130943079		214;1196
N	alternative_acceptor	CUFF.1059,CUFF.1082	chr9	+	chr9:43853617-43861002;chr9:43853617-43861005	chr9:43853617-43854068		chr9:43854069-43861002;chr9:43861003-43861005	chr9:43861002-43861003;chr9:43861005-43861006		70;6
N	coord_cassette	CUFF.1059	chr9	+	chr9:43828222-43853496	chr9:43828222-43844143;chr9:43844316-43849744;chr9:43849852-43853496		chr9:43844144-43844315;chr9:43849745-43849851			32;37
N	jcn_only_AD	CUFF.1094	chr9	+	chr9:139794973-139802521;chr9:139796849-139802521	chr9:139795129-139802521		chr9:139794973-139795128;chr9:139795129-139796848	chr9:139794972-139794973;chr9:139795128-139795129		489;11
N	jcn_only_AA	CUFF.1076	chr9	+	chr9:116795009-116798579	chr9:116795009-116797470		chr9:116797471-116798579	chr9:116798579-116798580		13;12
K	intron_retention	CUFF.1093	chr9	+	chr9:139743233-139743562				chr9:139743232-139743233;chr9:139743562-139743563		127;175
N	intron_retention		chr8	+	chr8:144356973-144358172				chr8:144356972-144356973;chr8:144358172-144358173		31;397
N	alternative_acceptor	CUFF.1028	chr8	-	chr8:80976829-80992549	chr8:80979593-80992549		chr8:80976829-80979592	chr8:80976828-80976829		509;20
K	intron_retention	CUFF.1019	chr8	-	chr8:30643506-30657232				chr8:30643505-30643506;chr8:30657232-30657233		204;127
N	coord_cassette	CUFF.1039	chr8	+	chr8:107726214-107752570	chr8:107726214-107749747;chr8:107749829-107751685;chr8:107751812-107752570		chr8:107749748-107749828;chr8:107751686-107751811			54;115
N	alternative_first_exon	CUFF.1040	chr8	+	chr8:118541049-118552121	chr8:118543067-118552121	chr8:118540890-118541048	chr8:118542531-118543066			38;72
K	alternative_last_exon	CUFF.1028	chr8	-	chr8:80915416-80954854	chr8:80950471-80954854	chr8:80915234-80915415	chr8:80948241-80950470			186;772
K	jcn_only_AA	CUFF.1017,CUFF.1034	chr8	+	chr8:98817693-98827555	chr8:98817693-98827531		chr8:98827532-98827555	chr8:98827555-98827556		117;49
N	intron_retention		chr8	-	chr8:80965666-81083659				chr8:80965665-80965666;chr8:81083659-81083660		22;39
K	alternative_donor	CUFF.1028	chr8	-	chr8:80956444-80962679	chr8:80956444-80962580		chr8:80962581-80962679	chr8:80962679-80962680		338;174
K	cassette	CUFF.1028	chr8	-	chr8:80963864-80965516	chr8:80963864-80964840;chr8:80964911-80965516		chr8:80964841-80964910			839;310
N	intron_retention	CUFF.1028	chr8	-	chr8:80976829-81083659				chr8:80976828-80976829;chr8:81083659-81083660		53;42
K	alternative_first_exon	CUFF.1020	chr8	-	chr8:38006273-38008272	chr8:38006273-38006593	chr8:38008273-38008864	chr8:38006594-38006688			54;51
N	alternative_acceptor	CUFF.1022	chr8	-	chr8:56657681-56663522;chr8:56637819-56663522;chr8:56656180-56663522	chr8:56652778-56663522		chr8:56637819-56652777;chr8:56652778-56656179;chr8:56656180-56657680	chr8:56637818-56637819;chr8:56652777-56652778;chr8:56656179-56656180		1575;3
K	intron_retention	CUFF.1020	chr8	-	chr8:38005846-38006158				chr8:38005845-38005846;chr8:38006158-38006159		144;34
N	alternative_acceptor	CUFF.1024	chr8	+	chr8:71564988-71572379	chr8:71564988-71565929		chr8:71565930-71572379	chr8:71572379-71572380		53;8
N	jcn_only_AD		chr8	-	chr8:99055004-99057574;chr8:99055004-99057054	chr8:99055004-99057170					96;195
N	alternative_donor		chr8	-	chr8:56652778-56657619;chr8:56652778-56656039	chr8:56652778-56663522		chr8:56656040-56657619;chr8:56657620-56663522	chr8:56657619-56657620;chr8:56663522-56663523		28;51
N	jcn_only_AA	CUFF.1047	chr8	+	chr8:144351691-144356873;chr8:144351691-144356889	chr8:144351691-144354565					580;122
N	alternative_acceptor	CUFF.1035	chr8	-	chr8:99054947-99057170;chr8:99055004-99057170	chr8:99037967-99057170		chr8:99037967-99054946;chr8:99054947-99055003	chr8:99037966-99037967;chr8:99054946-99054947		11;21
K	alternative_last_exon	CUFF.1049	chr8	+	chr8:144822119-144826029	chr8:144822119-144823921	chr8:144826030-144828507	chr8:144823922-144824403			58;86
N	mutually_exclusive	CUFF.1028	chr8	-	chr8:80954904-80962679,chr8:80962707-80963761	chr8:80954904-80956401,chr8:80956444-80963761	chr8:80962680-80962706	chr8:80956402-80956443			83;17
K	intron_retention	CUFF.1015	chr8	-	chr8:22012145-22012904				chr8:22012144-22012145;chr8:22012904-22012905		190;26
K	alternative_donor	CUFF.1012	chr8	+	chr8:7123432-7124095	chr8:7123438-7124095		chr8:7123432-7123437	chr8:7123431-7123432	chr8:7124096-7125058;chr8:7123323-7123431	36;11
N	jcn_only_AA	CUFF.1038	chr8	+	chr8:106456610-106573590	chr8:106456610-106463785		chr8:106463786-106573590	chr8:106573590-106573591		170;31
K	intron_retention	CUFF.1016	chr8	-	chr8:23177566-23179642				chr8:23177565-23177566;chr8:23179642-23179643		244;51
K	alternative_acceptor	CUFF.1017,CUFF.1034	chr8	+	chr8:98817693-98827555	chr8:98817693-98827531		chr8:98827532-98827555	chr8:98827555-98827556		117;23
K	alternative_last_exon	CUFF.1047	chr8	+	chr8:144356973-144357147,chr8:144356973-144358172;chr8:144356973-144358066	chr8:144356973-144357364	chr8:144358067-144359200	chr8:144357365-144357996			567;532
N	alternative_acceptor		chr8	+	chr8:71564130-71564769	chr8:71564130-71564745		chr8:71564746-71564769	chr8:71564769-71564770		94;28
K	alternative_last_exon	CUFF.1039	chr8	+	chr8:107593480-107691437	chr8:107593480-107617009	chr8:107691438-107691520	chr8:107617010-107617498			248;242
K	jcn_only_AA	CUFF.1015	chr8	-	chr8:22012977-22013849	chr8:22013023-22013849		chr8:22012977-22013022	chr8:22012976-22012977		57;104
K	intron_retention	CUFF.1039	chr8	+	chr8:107715319-107718609				chr8:107715318-107715319;chr8:107718609-107718610		155;47
K	intron_retention		chr8	-	chr8:99057628-99057735				chr8:99057627-99057628;chr8:99057735-99057736		890;28
N	jcn_only_AA	CUFF.1022	chr8	-	chr8:56652778-56663522;chr8:56637819-56663522;chr8:56656180-56663522	chr8:56657681-56663522		chr8:56637819-56652777;chr8:56652778-56656179;chr8:56656180-56657680	chr8:56637818-56637819;chr8:56652777-56652778;chr8:56656179-56656180		1765;556
K	intron_retention		chr8	+	chr8:74891097-74891313				chr8:74891096-74891097;chr8:74891313-74891314		587;157
N	jcn_only_AD		chr8	-	chr8:99057628-99057942	chr8:99057628-99057735		chr8:99057736-99057942	chr8:99057942-99057943		58;890
K	cassette	CUFF.1044	chr8	-	chr8:126948578-126963157	chr8:126948578-126958176;chr8:126958427-126963157		chr8:126958177-126958426			25;237
K	intron_retention	CUFF.1037	chr8	+	chr8:103572801-103572988				chr8:103572800-103572801;chr8:103572988-103572989		283;54
N	jcn_only_AA	CUFF.1022	chr8	-	chr8:56657681-56663522;chr8:56652778-56663522;chr8:56637819-56663522	chr8:56656180-56663522		chr8:56637819-56652777;chr8:56652778-56656179;chr8:56656180-56657680	chr8:56637818-56637819;chr8:56652777-56652778;chr8:56656179-56656180		2153;169
K	cassette	CUFF.1041	chr8	-	chr8:120807872-120809901	chr8:120807872-120809229;chr8:120809344-120809901		chr8:120809230-120809343			447;3
N	cassette	CUFF.1022	chr8	-	chr8:56668971-56676494	chr8:56668971-56675193;chr8:56675588-56676494		chr8:56675194-56675587			66;850
N	jcn_only_AD	CUFF.1041	chr8	-	chr8:120772979-120774654	chr8:120772979-120773847		chr8:120773848-120774654	chr8:120774654-120774655		121;44
K	jcn_only_AD	CUFF.1044	chr8	-	chr8:126958427-126963429	chr8:126958427-126963157		chr8:126963158-126963429	chr8:126963429-126963430		44;209
N	alternative_acceptor	CUFF.1016	chr8	-	chr8:23189522-23190913;chr8:23186100-23190913	chr8:23186079-23190913		chr8:23186079-23186099;chr8:23186100-23189521	chr8:23186078-23186079;chr8:23186099-23186100		83;128
N	jcn_only_AD		chr8	-	chr8:22012977-22014508	chr8:22012977-22013849		chr8:22013850-22014508	chr8:22014508-22014509		82;57
N	intron_retention		chr8	-	chr8:56663717-56675193				chr8:56663716-56663717;chr8:56675193-56675194		103;411
K	coord_cassette	CUFF.1038	chr8	+	chr8:106801153-106810951	chr8:106801153-106807983;chr8:106808126-106808996;chr8:106809135-106810951		chr8:106807984-106808125;chr8:106808997-106809134			27;21
N	jcn_only_AD		chr8	-	chr8:56675588-56676195	chr8:56675588-56675980					56;124
N	alternative_acceptor		chr8	+	chr8:71543526-71558279	chr8:71543526-71544669		chr8:71544670-71558279	chr8:71558279-71558280		55;21
N	jcn_only_AD	CUFF.1041	chr8	-	chr8:120756634-120758944	chr8:120756634-120757120		chr8:120757121-120758944	chr8:120758944-120758945		12;70
K	alternative_last_exon	CUFF.1027	chr8	+	chr8:75275289-75400912	chr8:75275289-75276219	chr8:75400913-75401206	chr8:75276220-75277069			204;520
K	intron_retention		chr8	-	chr8:80965666-80976712				chr8:80965665-80965666;chr8:80976712-80976713		1026;66
N	alternative_donor	CUFF.1026	chr8	+	chr8:74891097-74893389;chr8:74891111-74893389	chr8:74891407-74893389		chr8:74891097-74891110;chr8:74891111-74891406	chr8:74891096-74891097;chr8:74891110-74891111		39;212
N	jcn_only_AD		chr8	-	chr8:56676540-56685785;chr8:56676540-56685534	chr8:56676540-56685827		chr8:56685535-56685785;chr8:56685786-56685827	chr8:56685785-56685786;chr8:56685827-56685828		282;357
N	jcn_only_AA		chr8	-	chr8:80965666-81083659;chr8:80976829-81083659	chr8:81032120-81083659					76;142
N	jcn_only_AA	CUFF.1046	chr8	+	chr8:143922642-143995378	chr8:143922642-143927810		chr8:143927811-143995378	chr8:143995378-143995379		380;51
N	jcn_only_AD		chr8	-	chr8:56656180-56663522	chr8:56656180-56657619		chr8:56657620-56663522	chr8:56663522-56663523		169;115
K	jcn_only_AD	CUFF.1028	chr8	-	chr8:80956444-80962679	chr8:80956444-80962580		chr8:80962581-80962679	chr8:80962679-80962680		338;336
N	intron_retention		chr8	-	chr8:99055004-99057054				chr8:99055003-99055004;chr8:99057054-99057055		33;365
N	cassette	CUFF.1039	chr8	+	chr8:107726214-107751685;chr8:107738538-107751685	chr8:107726214-107749747,chr8:107738538-107749747;chr8:107749829-107751685		chr8:107749748-107749828			71;91
N	cassette	CUFF.1022	chr8	-	chr8:56663717-56675193	chr8:56663717-56668802;chr8:56668971-56675193		chr8:56668803-56668970			103;696
N	alternative_donor	CUFF.1038	chr8	+	chr8:106456610-106573590	chr8:106541198-106573590		chr8:106456610-106541197	chr8:106456609-106456610		170;0
N	jcn_only_AD	CUFF.1026	chr8	+	chr8:74891407-74893389;chr8:74891111-74893389	chr8:74891097-74893389		chr8:74891097-74891110;chr8:74891111-74891406	chr8:74891096-74891097;chr8:74891110-74891111		252;10
K	intron_retention		chr8	+	chr8:118541049-118542961				chr8:118541048-118541049;chr8:118542961-118542962		32;70
N	jcn_only_AA	CUFF.1028	chr8	-	chr8:81090515-81130703;chr8:80976829-81130703	chr8:81095374-81130703		chr8:80976829-81090514;chr8:81090515-81095373	chr8:80976828-80976829;chr8:81090514-81090515		50;144
N	alternative_acceptor	CUFF.1038	chr8	+	chr8:106456610-106573590	chr8:106456610-106463785		chr8:106463786-106573590	chr8:106573590-106573591		170;0
N	alternative_donor	CUFF.1026	chr8	+	chr8:74891407-74893389;chr8:74891111-74893389	chr8:74891097-74893389		chr8:74891097-74891110;chr8:74891111-74891406	chr8:74891096-74891097;chr8:74891110-74891111		241;10
K	alternative_acceptor	CUFF.1020	chr8	-	chr8:38001905-38003480	chr8:38002834-38003480		chr8:38001905-38002833	chr8:38001904-38001905		156;64
K	intron_retention	CUFF.1015	chr8	-	chr8:22011727-22012072				chr8:22011726-22011727;chr8:22012072-22012073		203;20
N	intron_retention		chr8	-	chr8:56668971-56685827				chr8:56668970-56668971;chr8:56685827-56685828		139;108
N	jcn_only_AD		chr8	-	chr8:56652778-56663522;chr8:56652778-56657619	chr8:56652778-56656039		chr8:56656040-56657619;chr8:56657620-56663522	chr8:56657619-56657620;chr8:56663522-56663523		183;226
N	alternative_donor	CUFF.1026	chr8	+	chr8:74884857-74888064	chr8:74885229-74888064		chr8:74884857-74885228	chr8:74884856-74884857		364;27
N	alternative_donor	CUFF.1039	chr8	+	chr8:107691521-107695426	chr8:107694774-107695426		chr8:107691521-107694773	chr8:107691520-107691521		451;5
N	alternative_donor	CUFF.1041	chr8	-	chr8:120772979-120774654	chr8:120772979-120773847		chr8:120773848-120774654	chr8:120774654-120774655		121;10
K	alternative_first_exon	CUFF.1028	chr8	-	chr8:80976829-81032049,chr8:80976829-81070671,chr8:80976829-81083255,chr8:80976829-81083659;chr8:80976829-81083441;chr8:80976829-80992549	chr8:80976829-81130703	chr8:81083442-81083634;chr8:80992550-80993129	chr8:81130704-81130774			834;23
N	alternative_acceptor	CUFF.1026	chr8	+	chr8:74888197-74890990	chr8:74888197-74888539		chr8:74888540-74890990	chr8:74890990-74890991		580;28
N	alternative_donor	CUFF.1041	chr8	-	chr8:120756634-120758944	chr8:120756634-120757120		chr8:120757121-120758944	chr8:120758944-120758945		12;9
K	alternative_first_exon	CUFF.1013,CUFF.1019	chr8	-	chr8:10584177-10683661	chr8:10584177-10587705	chr8:10683662-10683754	chr8:10587706-10588022			11;184
N	jcn_only_AD	CUFF.1038	chr8	+	chr8:106646586-106800945	chr8:106703164-106800945		chr8:106646586-106703163	chr8:106646585-106646586		99;5
K	intron_retention	CUFF.1028	chr8	-	chr8:80954904-80962679				chr8:80954903-80954904;chr8:80962679-80962680		60;61
N	jcn_only_AA	CUFF.1016	chr8	-	chr8:23225948-23282563	chr8:23261587-23282563		chr8:23225948-23261586	chr8:23225947-23225948		59;86
K	alternative_first_exon	CUFF.1030	chr8	+	chr8:82192910-82195600	chr8:82193549-82195600	chr8:82192598-82192909	chr8:82193452-82193548			267;16
N	alternative_acceptor	CUFF.1022	chr8	-	chr8:56657681-56663522;chr8:56652778-56663522;chr8:56637819-56663522	chr8:56656180-56663522		chr8:56637819-56652777;chr8:56652778-56656179;chr8:56656180-56657680	chr8:56637818-56637819;chr8:56652777-56652778;chr8:56656179-56656180		1571;7
K	alternative_donor	CUFF.1044	chr8	-	chr8:126958427-126963429	chr8:126958427-126963157		chr8:126963158-126963429	chr8:126963429-126963430		44;167
K	intron_retention	CUFF.1035	chr8	-	chr8:99057317-99057574				chr8:99057316-99057317;chr8:99057574-99057575		848;33
N	alternative_donor		chr8	-	chr8:56656180-56663522	chr8:56656180-56657619		chr8:56657620-56663522	chr8:56663522-56663523		169;18
K	jcn_only_AA	CUFF.1020	chr8	-	chr8:38001905-38003480	chr8:38002834-38003480		chr8:38001905-38002833	chr8:38001904-38001905		156;29
N	alternative_acceptor	CUFF.1035	chr8	-	chr8:99055004-99057574	chr8:99057317-99057574		chr8:99055004-99057316	chr8:99055003-99055004		63;454
K	jcn_only_AD	CUFF.1014	chr8	+	chr8:17434266-17434644	chr8:17434270-17434644		chr8:17434266-17434269	chr8:17434265-17434266		31;128
N	intron_retention		chr8	-	chr8:30657165-30670301				chr8:30657164-30657165;chr8:30670301-30670302		60;302
K	intron_retention	CUFF.1016	chr8	-	chr8:23198717-23217602				chr8:23198716-23198717;chr8:23217602-23217603		7;49
K	cassette	CUFF.1032	chr8	+	chr8:92086140-92090583	chr8:92086140-92088819;chr8:92088960-92090583		chr8:92088820-92088959			13;115
N	alternative_acceptor	CUFF.1016	chr8	-	chr8:23189522-23190913;chr8:23186079-23190913	chr8:23186100-23190913		chr8:23186079-23186099;chr8:23186100-23189521	chr8:23186078-23186079;chr8:23186099-23186100		151;60
N	jcn_only_AA	CUFF.1024	chr8	+	chr8:71564988-71572379	chr8:71564988-71565929		chr8:71565930-71572379	chr8:71572379-71572380		53;83
N	jcn_only_AA	CUFF.1035	chr8	-	chr8:99054947-99057170;chr8:99037967-99057170	chr8:99055004-99057170		chr8:99037967-99054946;chr8:99054947-99055003	chr8:99037966-99037967;chr8:99054946-99054947		196;195
N	jcn_only_AA		chr8	-	chr8:81032120-81083659;chr8:80965666-81083659	chr8:80976829-81083659					164;53
N	jcn_only_AD	CUFF.1022	chr8	-	chr8:56676540-56685827;chr8:56676540-56685534	chr8:56676540-56685785		chr8:56685535-56685785;chr8:56685786-56685827	chr8:56685785-56685786;chr8:56685827-56685828		462;178
N	jcn_only_AA	CUFF.1028	chr8	-	chr8:80976829-80992549	chr8:80979593-80992549		chr8:80976829-80979592	chr8:80976828-80976829		509;49
N	jcn_only_AA	CUFF.1016	chr8	-	chr8:23186100-23190913;chr8:23186079-23190913	chr8:23189522-23190913		chr8:23186079-23186099;chr8:23186100-23189521	chr8:23186078-23186079;chr8:23186099-23186100		231;37
K	cassette	CUFF.1027	chr8	+	chr8:75262814-75272371	chr8:75262814-75263508;chr8:75263557-75272371		chr8:75263509-75263556			42;134
K	intron_retention	CUFF.1020	chr8	-	chr8:38005878-38006158				chr8:38005877-38005878;chr8:38006158-38006159		53;24
K	cassette	CUFF.1038	chr8	+	chr8:106370866-106431371	chr8:106370866-106427102;chr8:106427235-106431371		chr8:106427103-106427234			16;62
N	alternative_donor	CUFF.1028	chr8	-	chr8:80965666-81083659	chr8:80965666-80976712		chr8:80976713-81083659	chr8:81083659-81083660		22;3
N	jcn_only_AD	CUFF.1026	chr8	+	chr8:74891097-74893389;chr8:74891111-74893389	chr8:74891407-74893389		chr8:74891097-74891110;chr8:74891111-74891406	chr8:74891096-74891097;chr8:74891110-74891111		42;219
K	jcn_only_AA	CUFF.1018	chr8	-	chr8:29535521-29583671	chr8:29582536-29583671					114;51
N	cassette	CUFF.1016	chr8	-	chr8:23186079-23198504	chr8:23186079-23190913;chr8:23191137-23198504		chr8:23190914-23191136			34;118
N	alternative_acceptor	CUFF.1035	chr8	-	chr8:99055004-99057170;chr8:99037967-99057170	chr8:99054947-99057170		chr8:99037967-99054946;chr8:99054947-99055003	chr8:99037966-99037967;chr8:99054946-99054947		27;5
N	intron_retention		chr8	-	chr8:99054947-99057170				chr8:99054946-99054947;chr8:99057170-99057171		174;377
N	alternative_acceptor	CUFF.1034,CUFF.1048	chr8	+	chr8:144373938-144375141	chr8:144373938-144374312		chr8:144374313-144375141	chr8:144375141-144375142		144;6
K	alternative_acceptor	CUFF.1020	chr8	-	chr8:38005846-38006158	chr8:38005878-38006158		chr8:38005846-38005877	chr8:38005845-38005846		144;44
N	jcn_only_AA		chr8	+	chr8:71564130-71564769	chr8:71564130-71564745		chr8:71564746-71564769	chr8:71564769-71564770		94;53
K	alternative_first_exon	CUFF.1019,CUFF.1020	chr8	-	chr8:30657272-30667505;chr8:30657272-30669835	chr8:30657272-30671402	chr8:30667506-30667832;chr8:30669836-30670159	chr8:30671403-30671929			580;504
K	alternative_acceptor	CUFF.1015	chr8	-	chr8:22012977-22013849	chr8:22013023-22013849		chr8:22012977-22013022	chr8:22012976-22012977		57;56
N	cassette	CUFF.1022	chr8	-	chr8:56668971-56685827	chr8:56668971-56676494;chr8:56676540-56685827		chr8:56676495-56676539			139;189
N	alternative_donor	CUFF.1026	chr8	+	chr8:74891097-74893389;chr8:74891407-74893389	chr8:74891111-74893389		chr8:74891097-74891110;chr8:74891111-74891406	chr8:74891096-74891097;chr8:74891110-74891111		222;29
K	alternative_first_exon	CUFF.1026	chr8	+	chr8:74888197-74890990	chr8:74888727-74890990	chr8:74888065-74888196	chr8:74888404-74888726			455;537
K	intron_retention		chr8	+	chr8:144356973-144358066				chr8:144356972-144356973;chr8:144358066-144358067		336;269
K	jcn_only_AA	CUFF.1020	chr8	-	chr8:38005846-38006158	chr8:38005878-38006158		chr8:38005846-38005877	chr8:38005845-38005846		144;53
N	intron_retention		chr8	+	chr8:144356973-144357147				chr8:144356972-144356973;chr8:144357147-144357148		53;439
N	jcn_only_AA	CUFF.1041	chr8	-	chr8:120772979-120774654	chr8:120774013-120774654		chr8:120772979-120774012	chr8:120772978-120772979		121;23
K	alternative_last_exon	CUFF.1012	chr8	+	chr8:7123432-7131717	chr8:7123432-7124095	chr8:7131718-7132778	chr8:7124096-7125155		chr8:7123323-7123431	51;69
K	alternative_first_exon	CUFF.1019	chr8	-	chr8:30657272-30671402;chr8:30657272-30669835	chr8:30657272-30667505	chr8:30671403-30671929;chr8:30669836-30670159	chr8:30667506-30667832			725;359
N	jcn_only_AD	CUFF.1039	chr8	+	chr8:107371865-107531170	chr8:107460277-107531170		chr8:107371865-107460276	chr8:107371864-107371865		33;12
N	jcn_only_AD	CUFF.1038	chr8	+	chr8:106456610-106573590	chr8:106541198-106573590		chr8:106456610-106541197	chr8:106456609-106456610		170;4
N	jcn_only_AD	CUFF.1028	chr8	-	chr8:80965666-81083659	chr8:80965666-80976712		chr8:80976713-81083659	chr8:81083659-81083660		22;1026
N	jcn_only_AA	CUFF.1024	chr8	+	chr8:144349655-144356873	chr8:144349655-144351529					30;316
N	jcn_only_AD	CUFF.1041	chr8	-	chr8:120774849-120790258	chr8:120774849-120779242		chr8:120779243-120790258	chr8:120790258-120790259		7;47
N	jcn_only_AA		chr8	-	chr8:81032120-81083659;chr8:80976829-81083659	chr8:80965666-81083659					195;22
N	cassette	CUFF.1028	chr8	-	chr8:80956444-80963761	chr8:80956444-80962580;chr8:80962707-80963761		chr8:80962581-80962706			19;450
K	intron_retention	CUFF.1020	chr8	-	chr8:38002834-38003480				chr8:38002833-38002834;chr8:38003480-38003481		29;32
K	intron_retention	CUFF.1019	chr8	-	chr8:30648832-30651432				chr8:30648831-30648832;chr8:30651432-30651433		108;176
N	cassette	CUFF.1027	chr8	+	chr8:75263702-75274118	chr8:75263702-75272371;chr8:75272546-75274118		chr8:75272372-75272545			100;273
N	jcn_only_AA	CUFF.1041	chr8	-	chr8:120756634-120758944	chr8:120757277-120758944		chr8:120756634-120757276	chr8:120756633-120756634		12;68
N	jcn_only_AA	CUFF.1028	chr8	-	chr8:80976829-81130703;chr8:81095374-81130703	chr8:81090515-81130703		chr8:80976829-81090514;chr8:81090515-81095373	chr8:80976828-80976829;chr8:81090514-81090515		176;18
K	alternative_first_exon	CUFF.1019	chr8	-	chr8:30657272-30667505;chr8:30657272-30671402	chr8:30657272-30669835	chr8:30667506-30667832;chr8:30671403-30671929	chr8:30669836-30670159			863;221
N	jcn_only_AA	CUFF.1016	chr8	-	chr8:23189522-23190913;chr8:23186100-23190913	chr8:23186079-23190913		chr8:23186079-23186099;chr8:23186100-23189521	chr8:23186078-23186079;chr8:23186099-23186100		139;128
N	jcn_only_AA	CUFF.1047	chr8	+	chr8:144351691-144356873;chr8:144351691-144354565	chr8:144351691-144356889					693;10
N	jcn_only_AA	CUFF.1035	chr8	-	chr8:99055004-99057574	chr8:99057317-99057574		chr8:99055004-99057316	chr8:99055003-99055004		63;848
K	intron_retention	CUFF.1028	chr8	-	chr8:80954904-80956401				chr8:80954903-80954904;chr8:80956401-80956402		655;22
K	alternative_first_exon	CUFF.1039	chr8	+	chr8:107670314-107691437,chr8:107670414-107691437,chr8:107630412-107691437;chr8:107531368-107691437	chr8:107593480-107691437	chr8:107531171-107531367	chr8:107593128-107593479			150;333
N	jcn_only_AA	CUFF.1016	chr8	-	chr8:23189522-23190913;chr8:23186079-23190913	chr8:23186100-23190913		chr8:23186079-23186099;chr8:23186100-23189521	chr8:23186078-23186079;chr8:23186099-23186100		165;103
N	intron_retention	CUFF.1022	chr8	-	chr8:56675588-56676195				chr8:56675587-56675588;chr8:56676195-56676196		56;58
K	intron_retention	CUFF.1026	chr8	+	chr8:74888727-74890990				chr8:74888726-74888727;chr8:74890990-74890991		562;33
N	intron_retention		chr8	-	chr8:99055004-99057574				chr8:99055003-99055004;chr8:99057574-99057575		63;109
K	alternative_last_exon	CUFF.1017	chr8	+	chr8:27517057-27534085	chr8:27517057-27528416	chr8:27534086-27534293	chr8:27528417-27530631		chr8:27516013-27517056	12;32
N	cassette	CUFF.1028	chr8	-	chr8:80954904-80962679;chr8:80954904-80963761	chr8:80954904-80956401;chr8:80956444-80963761,chr8:80956444-80962679		chr8:80956402-80956443			626;455
N	jcn_only_AA	CUFF.1026	chr8	+	chr8:74888197-74890990	chr8:74888197-74888539		chr8:74888540-74890990	chr8:74890990-74890991		580;24
N	cassette	CUFF.1015	chr8	-	chr8:22011553-22012072	chr8:22011553-22011654;chr8:22011727-22012072		chr8:22011655-22011726			3;200
K	intron_retention	CUFF.1020	chr8	-	chr8:38001905-38002739				chr8:38001904-38001905;chr8:38002739-38002740		27;39
K	alternative_donor	CUFF.1014	chr8	+	chr8:17434266-17434644	chr8:17434270-17434644		chr8:17434266-17434269	chr8:17434265-17434266		31;63
N	cassette	CUFF.1028	chr8	-	chr8:80956444-80963761;chr8:80954904-80963761;chr8:80954904-80963486	chr8:80954904-80962679,chr8:80956444-80962679;chr8:80962707-80963486,chr8:80962707-80963761		chr8:80962680-80962706			676;551
N	alternative_acceptor	CUFF.1022	chr8	-	chr8:56652778-56663522;chr8:56637819-56663522;chr8:56656180-56663522	chr8:56657681-56663522		chr8:56637819-56652777;chr8:56652778-56656179;chr8:56656180-56657680	chr8:56637818-56637819;chr8:56652777-56652778;chr8:56656179-56656180		1556;22
K	intron_retention	CUFF.1028	chr8	-	chr8:80954904-80963761				chr8:80954903-80954904;chr8:80963761-80963762		566;47
K	alternative_first_exon	CUFF.1045	chr8	-	chr8:133851626-133856470	chr8:133851626-133854636	chr8:133856471-133856543	chr8:133854637-133855377			81;150
N	alternative_acceptor	CUFF.1028	chr8	-	chr8:81090515-81130703;chr8:80976829-81130703	chr8:81095374-81130703		chr8:80976829-81090514;chr8:81090515-81095373	chr8:80976828-80976829;chr8:81090514-81090515		32;4
N	jcn_only_AD	CUFF.1018,CUFF.1022	chr8	-	chr8:56676540-56685785;chr8:56676540-56685827	chr8:56676540-56685534		chr8:56685535-56685785;chr8:56685786-56685827	chr8:56685785-56685786;chr8:56685827-56685828		536;104
K	intron_retention	CUFF.1020	chr8	-	chr8:38001905-38003480				chr8:38001904-38001905;chr8:38003480-38003481		156;34
N	alternative_donor	CUFF.1039	chr8	+	chr8:107371865-107531170	chr8:107460277-107531170		chr8:107371865-107460276	chr8:107371864-107371865		33;0
N	jcn_only_AD		chr8	-	chr8:99055004-99057170;chr8:99055004-99057054	chr8:99055004-99057574					228;63
N	alternative_acceptor	CUFF.1041	chr8	-	chr8:120756634-120758944	chr8:120757277-120758944		chr8:120756634-120757276	chr8:120756633-120756634		12;72
N	alternative_last_exon		chr8	+	chr8:118541049-118552121	chr8:118541049-118542961	chr8:118552122-118552600	chr8:118542962-118543066			18;23
N	alternative_donor	CUFF.1022	chr8	-	chr8:56676540-56685827;chr8:56676540-56685534	chr8:56676540-56685785		chr8:56685535-56685785;chr8:56685786-56685827	chr8:56685785-56685786;chr8:56685827-56685828		431;110
N	jcn_only_AA	CUFF.1035	chr8	-	chr8:99054947-99057170;chr8:99055004-99057170	chr8:99037967-99057170		chr8:99037967-99054946;chr8:99054947-99055003	chr8:99037966-99037967;chr8:99054946-99054947		369;21
K	jcn_only_AD	CUFF.1020	chr8	-	chr8:38001905-38003480	chr8:38001905-38002739		chr8:38002740-38003480	chr8:38003480-38003481		156;27
K	intron_retention	CUFF.1038	chr8	+	chr8:106646586-106800945				chr8:106646585-106646586;chr8:106800945-106800946		99;11
N	alternative_donor		chr8	-	chr8:56676540-56685785;chr8:56676540-56685534	chr8:56676540-56685827		chr8:56685535-56685785;chr8:56685786-56685827	chr8:56685785-56685786;chr8:56685827-56685828		184;357
N	jcn_only_AD	CUFF.1039	chr8	+	chr8:107691521-107695426	chr8:107694774-107695426		chr8:107691521-107694773	chr8:107691520-107691521		451;70
K	intron_retention	CUFF.1027	chr8	+	chr8:75262708-75263532				chr8:75262707-75262708;chr8:75263532-75263533		19;160
N	alternative_donor		chr8	-	chr8:22012977-22014508	chr8:22012977-22013849		chr8:22013850-22014508	chr8:22014508-22014509		82;118
N	alternative_donor	CUFF.1041	chr8	-	chr8:120774849-120790258	chr8:120774849-120779242		chr8:120779243-120790258	chr8:120790258-120790259		7;2
K	alternative_first_exon	CUFF.1023	chr8	-	chr8:69218834-69243541	chr8:69218834-69224378	chr8:69243542-69243726	chr8:69224379-69224493			50;22
N	alternative_acceptor	CUFF.1041	chr8	-	chr8:120772979-120774654	chr8:120774013-120774654		chr8:120772979-120774012	chr8:120772978-120772979		121;5
N	alternative_last_exon	CUFF.1047	chr8	+	chr8:74891097-74893389	chr8:74891097-74891313	chr8:74893390-74895117	chr8:74891314-74891369			5;452
N	alternative_acceptor	CUFF.1016	chr8	-	chr8:23225948-23282563	chr8:23261587-23282563		chr8:23225948-23261586	chr8:23225947-23225948		59;1
N	intron_retention		chr8	-	chr8:56657681-56663522				chr8:56657680-56657681;chr8:56663522-56663523		556;79
N	alternative_donor	CUFF.1018,CUFF.1022	chr8	-	chr8:56676540-56685785;chr8:56676540-56685827	chr8:56676540-56685534		chr8:56685535-56685785;chr8:56685786-56685827	chr8:56685785-56685786;chr8:56685827-56685828		467;74
K	alternative_acceptor	CUFF.1011	chr8	-	chr8:2452792-2453715	chr8:2452795-2453715		chr8:2452792-2452794	chr8:2452791-2452792		16;13
N	jcn_only_AA	CUFF.1034,CUFF.1048	chr8	+	chr8:144373938-144375141	chr8:144373938-144374312		chr8:144374313-144375141	chr8:144375141-144375142		144;26
N	jcn_only_AA		chr8	-	chr8:56652778-56657619	chr8:56656180-56657619					132;115
K	jcn_only_AD	CUFF.1012	chr8	+	chr8:7123432-7124095	chr8:7123438-7124095		chr8:7123432-7123437	chr8:7123431-7123432	chr8:7124096-7125058;chr8:7123323-7123431	36;22
N	alternative_donor	CUFF.1038	chr8	+	chr8:106646586-106800945	chr8:106703164-106800945		chr8:106646586-106703163	chr8:106646585-106646586		99;0
N	alternative_acceptor	CUFF.1046	chr8	+	chr8:143922642-143995378	chr8:143922642-143927810		chr8:143927811-143995378	chr8:143995378-143995379		380;1
N	coord_cassette	CUFF.1028	chr8	-	chr8:80954904-80963486	chr8:80954904-80956401;chr8:80956444-80962580;chr8:80962707-80963486		chr8:80956402-80956443;chr8:80962581-80962706			91;99
N	alternative_donor		chr8	-	chr8:99057628-99057942	chr8:99057628-99057735		chr8:99057736-99057942	chr8:99057942-99057943		58;323
K	alternative_first_exon	CUFF.1028	chr8	-	chr8:80976829-81032049,chr8:80976829-81070671,chr8:80976829-81083255,chr8:80976829-81083659;chr8:80976829-80992549;chr8:80976829-81130703	chr8:80976829-81083441	chr8:80992550-80993129;chr8:81130704-81130774	chr8:81083442-81083634			808;49
K	coord_cassette	CUFF.1028	chr8	-	chr8:80954904-80963761	chr8:80954904-80956401;chr8:80956444-80962580;chr8:80962707-80963761		chr8:80956402-80956443;chr8:80962581-80962706			566;384
N	alternative_donor		chr8	-	chr8:56652778-56663522;chr8:56652778-56657619	chr8:56652778-56656039		chr8:56656040-56657619;chr8:56657620-56663522	chr8:56657619-56657620;chr8:56663522-56663523		61;18
K	jcn_only_AA	CUFF.1024,CUFF.1039	chr8	+	chr8:71521069-71564047	chr8:71521069-71543339					129;403
K	alternative_first_exon	CUFF.1048	chr8	+	chr8:144374455-144375141,chr8:144373781-144375141;chr8:144373029-144375141	chr8:144373938-144375141	chr8:144372915-144373028	chr8:144373070-144373937			142;141
K	alternative_first_exon	CUFF.1015,CUFF.1033	chr8	-	chr8:96081464-96085156	chr8:96081464-96084944	chr8:96085157-96085486	chr8:96084945-96085148			37;8
N	alternative_acceptor	CUFF.1035	chr8	-	chr8:99054947-99057170;chr8:99037967-99057170	chr8:99055004-99057170		chr8:99037967-99054946;chr8:99054947-99055003	chr8:99037966-99037967;chr8:99054946-99054947		26;6
N	alternative_donor		chr8	-	chr8:56652778-56663522;chr8:56652778-56656039	chr8:56652778-56657619		chr8:56656040-56657619;chr8:56657620-56663522	chr8:56657619-56657620;chr8:56663522-56663523		69;10
N	intron_retention		chr8	-	chr8:81090189-81095252				chr8:81090188-81090189;chr8:81095252-81095253		21;53
N	jcn_only_AD		chr8	-	chr8:56652778-56657619;chr8:56652778-56656039	chr8:56652778-56663522		chr8:56656040-56657619;chr8:56657620-56663522	chr8:56657619-56657620;chr8:56663522-56663523		358;51
N	jcn_only_AA	CUFF.1047	chr8	+	chr8:144351691-144354565;chr8:144351691-144356889	chr8:144351691-144356873					132;570
N	jcn_only_AD		chr8	-	chr8:99055004-99057170;chr8:99055004-99057574	chr8:99055004-99057054					257;33
K	intron_retention	CUFF.1028	chr8	-	chr8:80963864-80965516				chr8:80963863-80963864;chr8:80965516-80965517		839;108
N	alternative_acceptor	CUFF.1022	chr8	-	chr8:56657681-56663522;chr8:56652778-56663522;chr8:56656180-56663522	chr8:56637819-56663522		chr8:56637819-56652777;chr8:56652778-56656179;chr8:56656180-56657680	chr8:56637818-56637819;chr8:56652777-56652778;chr8:56656179-56656180		32;1546
N	jcn_only_AA	CUFF.1028	chr8	-	chr8:81090515-81130703;chr8:81095374-81130703	chr8:80976829-81130703		chr8:80976829-81090514;chr8:81090515-81095373	chr8:80976828-80976829;chr8:81090514-81090515		162;32
N	jcn_only_AA	CUFF.1035	chr8	-	chr8:99055004-99057170;chr8:99037967-99057170	chr8:99054947-99057170		chr8:99037967-99054946;chr8:99054947-99055003	chr8:99037966-99037967;chr8:99054946-99054947		216;174
K	jcn_only_AA	CUFF.1043	chr8	+	chr8:124629084-124646553	chr8:124629084-124637926					66;54
N	jcn_only_AD	CUFF.1046	chr8	+	chr8:143915706-143921831	chr8:143916285-143921831		chr8:143915706-143916284	chr8:143915705-143915706		326;34
K	alternative_first_exon	CUFF.1028	chr8	-	chr8:80976829-81032049,chr8:80976829-81070671,chr8:80976829-81083255,chr8:80976829-81083659;chr8:80976829-81083441;chr8:80976829-81130703	chr8:80976829-80992549	chr8:81083442-81083634;chr8:81130704-81130774	chr8:80992550-80993129			270;587
N	jcn_only_AD	CUFF.1026	chr8	+	chr8:74891097-74893389;chr8:74891407-74893389	chr8:74891111-74893389		chr8:74891097-74891110;chr8:74891111-74891406	chr8:74891096-74891097;chr8:74891110-74891111		229;32
N	alternative_acceptor	CUFF.1028	chr8	-	chr8:80976829-81130703;chr8:81095374-81130703	chr8:81090515-81130703		chr8:80976829-81090514;chr8:81090515-81095373	chr8:80976828-80976829;chr8:81090514-81090515		36;0
K	jcn_only_AA	CUFF.1011	chr8	-	chr8:2452792-2453715	chr8:2452795-2453715		chr8:2452792-2452794	chr8:2452791-2452792		16;27
N	jcn_only_AA		chr8	+	chr8:71543526-71558279	chr8:71543526-71544669		chr8:71544670-71558279	chr8:71558279-71558280		55;271
N	alternative_first_exon	CUFF.1047	chr8	+	chr8:144349655-144356873	chr8:144351691-144356873	chr8:144349511-144349654	chr8:144351468-144351690			19;589
N	jcn_only_AD		chr8	-	chr8:56652778-56663522;chr8:56652778-56656039	chr8:56652778-56657619		chr8:56656040-56657619;chr8:56657620-56663522	chr8:56657619-56657620;chr8:56663522-56663523		276;132
K	cassette	CUFF.1048	chr8	+	chr8:144375236-144377909	chr8:144375236-144377548;chr8:144377641-144377909		chr8:144377549-144377640			200;44
N	jcn_only_AA	CUFF.1022	chr8	-	chr8:56657681-56663522;chr8:56637819-56663522;chr8:56656180-56663522	chr8:56652778-56663522		chr8:56637819-56652777;chr8:56652778-56656179;chr8:56656180-56657680	chr8:56637818-56637819;chr8:56652777-56652778;chr8:56656179-56656180		2271;51
K	cassette	CUFF.1016	chr8	-	chr8:23225948-23261466	chr8:23225948-23228155;chr8:23228276-23261466		chr8:23228156-23228275			178;100
N	jcn_only_AD	CUFF.1026	chr8	+	chr8:74884857-74888064	chr8:74885229-74888064		chr8:74884857-74885228	chr8:74884856-74884857		364;16
K	alternative_first_exon	CUFF.1019,CUFF.1028	chr8	-	chr8:30643824-30648712	chr8:30643824-30643947	chr8:30648713-30648831	chr8:30643948-30644046			648;441
K	intron_retention		chr8	-	chr8:56668971-56675193				chr8:56668970-56668971;chr8:56675193-56675194		561;137
K	alternative_donor	CUFF.1020	chr8	-	chr8:38001905-38003480	chr8:38001905-38002739		chr8:38002740-38003480	chr8:38003480-38003481		156;45
N	jcn_only_AA	CUFF.1022	chr8	-	chr8:56657681-56663522;chr8:56652778-56663522;chr8:56656180-56663522	chr8:56637819-56663522		chr8:56637819-56652777;chr8:56652778-56656179;chr8:56656180-56657680	chr8:56637818-56637819;chr8:56652777-56652778;chr8:56656179-56656180		775;1546
K	intron_retention	CUFF.1028	chr8	-	chr8:80976829-81083441				chr8:80976828-80976829;chr8:81083441-81083442		34;42
K	alternative_first_exon	CUFF.1018	chr8	-	chr8:29583940-29605530	chr8:29583940-29592686	chr8:29605531-29605704	chr8:29592687-29592739			40;88
N	cassette	CUFF.1039	chr8	+	chr8:107726214-107752570	chr8:107726214-107751685;chr8:107751812-107752570		chr8:107751686-107751811			54;167
K	alternative_first_exon	CUFF.1049	chr8	+	chr8:144818109-144822028	chr8:144821674-144822028	chr8:144818020-144818108	chr8:144821488-144821673			9;52
N	alternative_acceptor	CUFF.1028	chr8	-	chr8:81090515-81130703;chr8:81095374-81130703	chr8:80976829-81130703		chr8:80976829-81090514;chr8:81090515-81095373	chr8:80976828-80976829;chr8:81090514-81090515		4;32
N	mutually_exclusive	CUFF.1022	chr8	-	chr8:56663717-56675193,chr8:56675588-56676494	chr8:56663717-56668802,chr8:56668971-56676494	chr8:56675194-56675587	chr8:56668803-56668970			143;72
N	alternative_donor	CUFF.1046	chr8	+	chr8:143915706-143921831	chr8:143916285-143921831		chr8:143915706-143916284	chr8:143915705-143915706		326;9
K	intron_retention		chr8	-	chr8:56663717-56668802				chr8:56663716-56663717;chr8:56668802-56668803		641;367
K	intron_retention		chr8	+	chr8:144356973-144357364				chr8:144356972-144356973;chr8:144357364-144357365		129;482
N	alternative_acceptor	CUFF.1016	chr8	-	chr8:23186100-23190913;chr8:23186079-23190913	chr8:23189522-23190913		chr8:23186079-23186099;chr8:23186100-23189521	chr8:23186078-23186079;chr8:23186099-23186100		188;23
N	intron_retention		chr8	-	chr8:99055004-99057170				chr8:99055003-99055004;chr8:99057170-99057171		195;414
N	alternative_first_exon	CUFF.1039	chr8	+	chr8:107738538-107749747;chr8:107726214-107749747	chr8:107738486-107749747	chr8:107726051-107726213	chr8:107738317-107738485			53;117
K	alternative_last_exon	CUFF.1014	chr8	+	chr8:17491723-17501079	chr8:17491723-17500121	chr8:17501080-17501679	chr8:17500122-17500642			75;303