#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	intron_retention	CUFF.704	chr22	-	chr22:18077383-18080959				chr22:18077382-18077383;chr22:18080959-18080960		45.24
K	intron_retention	CUFF.1148	chrX	-	chrX:152988744-152989941				chrX:152988743-152988744;chrX:152989941-152989942		18.82
K	jcn_only_AD	CUFF.415	chr16	+	chr16:89793734-89795642	chr16:89793766-89795642		chr16:89793734-89793765	chr16:89793733-89793734		55.15
K	intron_retention		chr7	+	chr7:107253878-107262074				chr7:107253877-107253878;chr7:107262074-107262075		9.02
K	cassette	CUFF.639	chr2	+	chr2:160602449-160608912	chr2:160602449-160604315;chr2:160605415-160608912		chr2:160604316-160605414			51.15
N	jcn_only_AD	CUFF.336	chr15	+	chr15:74754440-74758376;chr15:74754373-74758376	chr15:74754369-74758376		chr15:74754369-74754372;chr15:74754373-74754439	chr15:74754368-74754369;chr15:74754372-74754373		18.97
N	intron_retention		chr16	-	chr16:4465854-4466459				chr16:4465853-4465854;chr16:4466459-4466460		77.42
K	intron_retention	CUFF.675	chr20	+	chr20:2843357-2843452				chr20:2843356-2843357;chr20:2843452-2843453		70.37
K	intron_retention	CUFF.53	chr1	-	chr1:156909703-156909998				chr1:156909702-156909703;chr1:156909998-156909999		11.76
K	alternative_donor	CUFF.674,CUFF.688	chr20	-	chr20:1517957-1532516	chr20:1517957-1532336		chr20:1532337-1532516	chr20:1532516-1532517		80.00
N	jcn_only_AD	CUFF.976	chr7	+	chr7:54614433-54614639;chr7:54613910-54614639	chr7:54612482-54614639		chr7:54612482-54613909;chr7:54613910-54614432	chr7:54612481-54612482;chr7:54613909-54613910		57.82
N	alternative_acceptor		chr2	+	chr2:101609990-101612257	chr2:101609990-101611861		chr2:101611862-101612257	chr2:101612257-101612258		68.89
K	jcn_only_AA	CUFF.187	chr11	+	chr11:119056220-119056633;chr11:119056220-119056557	chr11:119056220-119056630		chr11:119056558-119056630;chr11:119056631-119056633	chr11:119056630-119056631;chr11:119056633-119056634		37.96
K	intron_retention	CUFF.663	chr2	+	chr2:220096763-220096981				chr2:220096762-220096763;chr2:220096981-220096982		10.67
K	jcn_only_AA	CUFF.939	chr6	+	chr6:111306342-111310230	chr6:111306342-111310190		chr6:111310191-111310230	chr6:111310230-111310231		76.79
N	alternative_donor	CUFF.2	chr1	+	chr1:1987002-1987922	chr1:1987316-1987922		chr1:1987002-1987315	chr1:1987001-1987002		21.25
K	cassette	CUFF.939	chr6	+	chr6:111306342-111312949	chr6:111306342-111310190;chr6:111310269-111312949		chr6:111310191-111310268			81.63
N	alternative_acceptor	CUFF.743	chr3	-	chr3:33592888-33600798	chr3:33600668-33600798		chr3:33592888-33600667	chr3:33592887-33592888		4.55
K	intron_retention	CUFF.37	chr1	-	chr1:113464756-113471713				chr1:113464755-113464756;chr1:113471713-113471714		10.13
K	intron_retention	CUFF.457	chr17	+	chr17:61571021-61571282				chr17:61571020-61571021;chr17:61571282-61571283		3.99
K	intron_retention	CUFF.236	chr12	-	chr12:77257125-77259928				chr12:77257124-77257125;chr12:77259928-77259929		25.86
K	intron_retention	CUFF.765	chr3	-	chr3:107574077-107575926				chr3:107574076-107574077;chr3:107575926-107575927		14.34
K	cassette	CUFF.765	chr3	-	chr3:107574077-107575926	chr3:107574077-107574159;chr3:107574273-107575926		chr3:107574160-107574272			11.06
N	alternative_last_exon	CUFF.486	chr18	-	chr18:44483597-44500021	chr18:44486279-44500021	chr18:44483490-44483596	chr18:44485634-44486278			71.43
N	alternative_first_exon	CUFF.787	chr3	+	chr3:132764865-132948113	chr3:132911672-132948113	chr3:132764746-132764864	chr3:132911571-132911671			85.71
N	jcn_only_AD	CUFF.726	chr22	+	chr22:47309343-47393529	chr22:47370296-47393529		chr22:47309343-47370295	chr22:47309342-47309343		92.55
K	cassette	CUFF.594	chr2	-	chr2:31423492-31424999	chr2:31423492-31424727;chr2:31424865-31424999		chr2:31424728-31424864			13.51
N	alternative_acceptor	CUFF.53	chr1	-	chr1:156908306-156909339	chr1:156909078-156909339		chr1:156908306-156909077	chr1:156908305-156908306		36.92
K	cassette	CUFF.1130	chrX	+	chrX:78003532-78005670	chrX:78003532-78004459;chrX:78004728-78005670		chrX:78004460-78004727			14.81
N	jcn_only_AD		chr6	+	chr6:112558118-112600322	chr6:112598514-112600322		chr6:112558118-112598513	chr6:112558117-112558118		50.00
K	intron_retention		chr14	-	chr14:75136830-75137464				chr14:75136829-75136830;chr14:75137464-75137465	chr14:75136650-75136829;chr14:75137465-75137574	15.62
N	alternative_donor	CUFF.176	chr11	-	chr11:102960048-102962515;chr11:102960048-102962244	chr11:102960048-102962412		chr11:102962245-102962412;chr11:102962413-102962515	chr11:102962412-102962413;chr11:102962515-102962516		11.63
K	alternative_last_exon	CUFF.1117	chrX	+	chrX:15711182-15720904;chrX:15711182-15713793	chrX:15711182-15715362	chrX:15720905-15721927;chrX:15713794-15713856	chrX:15715363-15715961			51.14
N	jcn_only_AA	CUFF.685	chr20	-	chr20:31097744-31099149;chr20:31062546-31099149	chr20:31074605-31099149					28.85
N	alternative_donor	CUFF.334	chr15	-	chr15:67700814-67713672	chr15:67700814-67705840		chr15:67705841-67713672	chr15:67713672-67713673		56.25
N	jcn_only_AD		chr3	-	chr3:107567966-107568669;chr3:107567966-107575926	chr3:107567966-107572719					46.97
K	alternative_first_exon	CUFF.1109	chr9	+	chr9:139794973-139802521,chr9:139795129-139802521	chr9:139796849-139802521	chr9:139794874-139794972	chr9:139796595-139796848			17.16
N	alternative_acceptor	CUFF.858	chr4	+	chr4:120379233-120381897	chr4:120379233-120381337		chr4:120381338-120381897	chr4:120381897-120381898		50.67
K	intron_retention	CUFF.880	chr5	-	chr5:64886130-64887274				chr5:64886129-64886130;chr5:64887274-64887275		19.63
N	jcn_only_AA	CUFF.106	chr10	-	chr10:46135412-46143741;chr10:46113709-46143741	chr10:46135870-46143741					15.00
N	alternative_acceptor	CUFF.435,CUFF.464	chr17	+	chr17:66519068-66519865	chr17:66519068-66519854		chr17:66519855-66519865	chr17:66519865-66519866		1.90
N	jcn_only_AA	CUFF.793	chr3	-	chr3:141697525-141712379	chr3:141708357-141712379		chr3:141697525-141708356	chr3:141697524-141697525		9.38
K	cassette	CUFF.346	chr15	-	chr15:82981344-82982924	chr15:82981344-82982303;chr15:82982498-82982924		chr15:82982304-82982497			12.50
K	intron_retention	CUFF.415	chr16	+	chr16:89799821-89799889				chr16:89799820-89799821;chr16:89799889-89799890		29.83
N	coord_cassette	CUFF.426	chr17	-	chr17:15546131-15580489	chr17:15546131-15554404;chr17:15555261-15562115;chr17:15562191-15580489		chr17:15554405-15555260;chr17:15562116-15562190			78.21
K	intron_retention	CUFF.165	chr11	+	chr11:65479751-65479849				chr11:65479750-65479751;chr11:65479849-65479850		85.42
N	cassette	CUFF.322	chr15	-	chr15:55485032-55486493	chr15:55485032-55486350;chr15:55486382-55486493		chr15:55486351-55486381			37.50
K	intron_retention	CUFF.618	chr2	-	chr2:86398436-86400772				chr2:86398435-86398436;chr2:86400772-86400773		35.29
N	jcn_only_AA	CUFF.823	chr4	+	chr4:20570628-20591266	chr4:20570628-20574856		chr4:20574857-20591266	chr4:20591266-20591267		17.65
N	jcn_only_AD		chr5	-	chr5:64887330-64887698	chr5:64887330-64887669		chr5:64887670-64887698	chr5:64887698-64887699		93.15
N	jcn_only_AD	CUFF.802	chr3	+	chr3:186756662-186760441	chr3:186759755-186760441		chr3:186756662-186759754	chr3:186756661-186756662		10.92
K	cassette	CUFF.1154	chrY	+	chrY:23675924-23681035	chrY:23675924-23678942;chrY:23679121-23681035		chrY:23678943-23679120			50.00
N	jcn_only_AD	CUFF.722	chr22	+	chr22:37705365-37707028	chr22:37706074-37707028		chr22:37705365-37706073	chr22:37705364-37705365		72.22
K	intron_retention	CUFF.418	chr17	+	chr17:1940251-1943048				chr17:1940250-1940251;chr17:1943048-1943049		28.75
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		13.79
N	alternative_donor	CUFF.278,CUFF.289	chr14	-	chr14:92105595-92126180;chr14:92105595-92136157	chr14:92105595-92112480		chr14:92112481-92126180;chr14:92126181-92136157	chr14:92126180-92126181;chr14:92136157-92136158		0.00
K	cassette	CUFF.109	chr10	+	chr10:60037083-60047320	chr10:60037083-60042658;chr10:60042843-60047320		chr10:60042659-60042842			4.76
N	alternative_donor	CUFF.1081	chr9	-	chr9:86924630-86928273	chr9:86924630-86925326		chr9:86925327-86928273	chr9:86928273-86928274		40.00
K	intron_retention	CUFF.604	chr2	-	chr2:61729446-61749745				chr2:61729445-61729446;chr2:61749745-61749746		45.51
K	alternative_acceptor	CUFF.138	chr11	+	chr11:829541-829985	chr11:829541-829967		chr11:829968-829985	chr11:829985-829986	chr11:829360-829540;chr11:829986-830132	52.08
K	intron_retention	CUFF.942	chr6	-	chr6:114277858-114279812				chr6:114277857-114277858;chr6:114279812-114279813		4.03
K	intron_retention	CUFF.445	chr17	-	chr17:40738910-40744073				chr17:40738909-40738910;chr17:40744073-40744074		53.62
K	intron_retention		chr3	-	chr3:141712428-141713861				chr3:141712427-141712428;chr3:141713861-141713862		29.12
N	alternative_first_exon	CUFF.377	chr16	-	chr16:4445341-4447318;chr16:4445341-4455491;chr16:4445341-4466459	chr16:4445341-4466785	chr16:4455492-4455568;chr16:4466460-4466665	chr16:4466786-4466962			14.94
N	alternative_donor	CUFF.292	chr14	+	chr14:92915561-92920243;chr14:92918991-92920243	chr14:92915504-92920243		chr14:92915504-92915560;chr14:92915561-92918990	chr14:92915503-92915504;chr14:92915560-92915561		15.62
K	intron_retention	CUFF.36	chr1	+	chr1:110212194-110213935				chr1:110212193-110212194;chr1:110213935-110213936		39.13
K	intron_retention	CUFF.259	chr14	+	chr14:24567597-24567683				chr14:24567596-24567597;chr14:24567683-24567684		1.30
N	alternative_acceptor	CUFF.633	chr2	-	chr2:110920710-110922096	chr2:110920713-110922096		chr2:110920710-110920712	chr2:110920709-110920710		50.00
K	intron_retention	CUFF.180	chr11	+	chr11:117070149-117073717				chr11:117070148-117070149;chr11:117073717-117073718		85.71
K	intron_retention	CUFF.228	chr12	-	chr12:56572319-56572593				chr12:56572318-56572319;chr12:56572593-56572594		66.67
N	alternative_donor	CUFF.221	chr12	+	chr12:52403024-52404664	chr12:52404347-52404664		chr12:52403024-52404346	chr12:52403023-52403024		8.70
N	jcn_only_AA		chr19	+	chr19:17448474-17448816;chr19:17448474-17448707	chr19:17448474-17448682		chr19:17448683-17448707;chr19:17448708-17448816	chr19:17448707-17448708;chr19:17448816-17448817		34.03
K	coord_cassette	CUFF.603	chr2	+	chr2:48848430-48873591	chr2:48848430-48869540;chr2:48869597-48872171;chr2:48872257-48873591		chr2:48869541-48869596;chr2:48872172-48872256			93.62
N	intron_retention		chr11	-	chr11:8498831-8502080				chr11:8498830-8498831;chr11:8502080-8502081		8.70
N	jcn_only_AD		chr14	-	chr14:104245159-104263707	chr14:104245159-104251131					85.71
N	jcn_only_AA	CUFF.715	chr22	+	chr22:29538089-29563031	chr22:29538089-29550325		chr22:29550326-29563031	chr22:29563031-29563032		41.18
K	intron_retention	CUFF.572	chr2	-	chr2:231192-233100				chr2:231191-231192;chr2:233100-233101		17.59
N	alternative_donor		chr17	-	chr17:1616190-1617149	chr17:1616190-1616996		chr17:1616997-1617149	chr17:1617149-1617150		65.62
N	intron_retention		chr9	-	chr9:130952636-130953103				chr9:130952635-130952636;chr9:130953103-130953104		81.82
K	cassette	CUFF.765	chr3	-	chr3:107595034-107596159	chr3:107595034-107595281;chr3:107595379-107596159		chr3:107595282-107595378			43.06
K	cassette	CUFF.707	chr22	+	chr22:20749709-20754921	chr22:20749709-20753884;chr22:20753981-20754921		chr22:20753885-20753980			45.45
N	alternative_donor	CUFF.271,CUFF.278	chr14	-	chr14:75138187-75139533	chr14:75138187-75138671		chr14:75138672-75139533	chr14:75139533-75139534	chr14:75138111-75138186;chr14:75139534-75139655	2.94
K	alternative_last_exon	CUFF.310	chr15	+	chr15:40558697-40564424	chr15:40558697-40559123	chr15:40564425-40564922	chr15:40559124-40559236			28.07
N	alternative_donor	CUFF.473	chr17	-	chr17:79894070-79900171;chr17:79894070-79894623	chr17:79894070-79898625		chr17:79894624-79898625;chr17:79898626-79900171	chr17:79898625-79898626;chr17:79900171-79900172	chr17:79893999-79894069	5.26
K	alternative_acceptor	CUFF.418	chr17	+	chr17:1939386-1939822	chr17:1939386-1939722		chr17:1939723-1939822	chr17:1939822-1939823		15.00
N	intron_retention		chr10	-	chr10:73975613-73975964				chr10:73975612-73975613;chr10:73975964-73975965		76.00
N	jcn_only_AD	CUFF.231	chr12	+	chr12:57853985-57857447	chr12:57854339-57857447		chr12:57853985-57854338	chr12:57853984-57853985		83.72
N	intron_retention		chr19	+	chr19:4311877-4323568				chr19:4311876-4311877;chr19:4323568-4323569		73.61
N	jcn_only_AA	CUFF.669	chr2	+	chr2:241404164-241404272	chr2:241404164-241404251		chr2:241404252-241404272	chr2:241404272-241404273		4.64
N	alternative_acceptor		chr3	+	chr3:8775677-8819162	chr3:8775677-8787211		chr3:8787212-8819162	chr3:8819162-8819163		33.33
N	jcn_only_AD	CUFF.889	chr5	+	chr5:128862150-128863440	chr5:128862209-128863440		chr5:128862150-128862208	chr5:128862149-128862150		86.67
N	alternative_acceptor	CUFF.450	chr17	+	chr17:61561903-61562596	chr17:61561903-61562330		chr17:61562331-61562596	chr17:61562596-61562597		59.18
N	alternative_acceptor	CUFF.754	chr3	-	chr3:49463856-49466540	chr3:49463862-49466540		chr3:49463856-49463861	chr3:49463855-49463856		81.48
K	cassette	CUFF.979	chr7	+	chr7:65592728-65599266	chr7:65592728-65595730;chr7:65595830-65599266		chr7:65595731-65595829			47.83
K	alternative_first_exon	CUFF.911	chr6	-	chr6:13470863-13486242;chr6:13470863-13472212	chr6:13470863-13486869	chr6:13486243-13486491;chr6:13472213-13472325	chr6:13486870-13487974			30.00
N	alternative_donor		chr11	-	chr11:67771269-67772276	chr11:67771269-67771417		chr11:67771418-67772276	chr11:67772276-67772277		84.62
K	jcn_only_AD	CUFF.618	chr2	-	chr2:86386795-86389098	chr2:86386795-86389074		chr2:86389075-86389098	chr2:86389098-86389099		28.48
K	jcn_only_AA	CUFF.159	chr11	-	chr11:61514596-61514822	chr11:61514614-61514822		chr11:61514596-61514613	chr11:61514595-61514596		81.58
K	jcn_only_AA	CUFF.560	chr19	-	chr19:51525921-51526347	chr19:51525954-51526347		chr19:51525921-51525953	chr19:51525920-51525921		91.80
N	alternative_donor	CUFF.979	chr7	+	chr7:65579902-65592690;chr7:65591631-65592690	chr7:65579958-65592690		chr7:65579902-65579957;chr7:65579958-65591630	chr7:65579901-65579902;chr7:65579957-65579958		68.75
N	jcn_only_AA	CUFF.317	chr15	-	chr15:45470505-45492924	chr15:45491319-45492924		chr15:45470505-45491318	chr15:45470504-45470505		15.00
K	alternative_first_exon	CUFF.253,CUFF.254	chr13	-	chr13:101132618-101133373	chr13:101132618-101133233	chr13:101133374-101133501	chr13:101133234-101133330			11.29
K	intron_retention	CUFF.984	chr7	+	chr7:75045057-75045258				chr7:75045056-75045057;chr7:75045258-75045259		67.80
K	alternative_first_exon	CUFF.520,CUFF.558	chr19	-	chr19:11541841-11546510	chr19:11541841-11545593	chr19:11546511-11546683	chr19:11545594-11545925			54.08
N	intron_retention		chr3	-	chr3:27352508-27353589				chr3:27352507-27352508;chr3:27353589-27353590		40.00
K	intron_retention	CUFF.734	chr3	+	chr3:19992554-20017134				chr3:19992553-19992554;chr3:20017134-20017135		86.84
K	jcn_only_AD	CUFF.111	chr10	+	chr10:69866559-69902696	chr10:69882098-69902696					75.00
N	alternative_acceptor	CUFF.2,CUFF.8	chr1	+	chr1:1991031-2066700	chr1:1991031-2002737		chr1:2002738-2066700	chr1:2066700-2066701		2.38
N	alternative_donor	CUFF.802	chr3	+	chr3:186649184-186681572;chr3:186660216-186681572;chr3:186648928-186681572;chr3:186666727-186681572	chr3:186648624-186681572		chr3:186648624-186648927;chr3:186648928-186649183;chr3:186649184-186660215;chr3:186660216-186666726	chr3:186648623-186648624;chr3:186648927-186648928;chr3:186649183-186649184;chr3:186660215-186660216		81.29
K	coord_cassette	CUFF.3	chr1	+	chr1:10491459-10500403	chr1:10491459-10493898;chr1:10494023-10494713;chr1:10494748-10500403		chr1:10493899-10494022;chr1:10494714-10494747			60.61
K	alternative_last_exon	CUFF.85	chr1	-	chr1:247320520-247322307,chr1:247320706-247322307;chr1:247287174-247322307	chr1:247302060-247322307	chr1:247319106-247320519;chr1:247285180-247287173	chr1:247301359-247302059			14.12
N	alternative_acceptor	CUFF.325	chr15	+	chr15:57574797-57578354;chr15:57574797-57583026	chr15:57574797-57591423		chr15:57578355-57583026;chr15:57583027-57591423	chr15:57583026-57583027;chr15:57591423-57591424		31.43
K	intron_retention	CUFF.131	chr10	-	chr10:119765350-119768592				chr10:119765349-119765350;chr10:119768592-119768593		42.86
N	jcn_only_AD	CUFF.87	chr10	+	chr10:5138770-5141518	chr10:5141072-5141518					77.08
N	alternative_acceptor	CUFF.743	chr3	-	chr3:33614847-33617660	chr3:33615989-33617660		chr3:33614847-33615988	chr3:33614846-33614847		0.47
K	cassette	CUFF.1057	chr8	-	chr8:126948578-126963157	chr8:126948578-126958176;chr8:126958427-126963157		chr8:126958177-126958426			58.06
K	intron_retention	CUFF.504	chr19	+	chr19:1438580-1438805				chr19:1438579-1438580;chr19:1438805-1438806		28.33
N	coord_cassette	CUFF.843	chr4	-	chr4:83816928-83821229	chr4:83816928-83819141;chr4:83819216-83820865;chr4:83820891-83821229		chr4:83819142-83819215;chr4:83820866-83820890			99.34
N	alternative_last_exon	CUFF.140	chr11	-	chr11:2187780-2188664;chr11:2187999-2188664	chr11:2188263-2188664	chr11:2187043-2187779;chr11:2187863-2187998	chr11:2188117-2188262			94.23
K	jcn_only_AA	CUFF.61,CUFF.7	chr1	+	chr1:167301773-167343392	chr1:167301773-167334703					95.92
N	jcn_only_AA	CUFF.269	chr14	+	chr14:76249874-76259258	chr14:76249874-76259255					33.33
N	alternative_donor		chr2	-	chr2:177042550-177042742	chr2:177042550-177042730		chr2:177042731-177042742	chr2:177042742-177042743		61.11
N	jcn_only_AA		chr10	+	chr10:35416496-35437295	chr10:35416496-35426709					41.94
K	cassette	CUFF.124	chr10	+	chr10:96972698-96979647	chr10:96972698-96974608;chr10:96974733-96979647		chr10:96974609-96974732			82.35
N	jcn_only_AA	CUFF.633	chr2	-	chr2:110927576-110958997	chr2:110937262-110958997					96.92
K	alternative_first_exon	CUFF.325	chr15	+	chr15:57511789-57523349;chr15:57490024-57523349	chr15:57506595-57523349	chr15:57489971-57490023	chr15:57506194-57506594			82.11
K	alternative_acceptor	CUFF.110	chr10	-	chr10:69575888-69583071	chr10:69575892-69583071		chr10:69575888-69575891	chr10:69575887-69575888	chr10:69583072-69583150;chr10:69575798-69575887	36.84
N	jcn_only_AD	CUFF.90	chr10	+	chr10:6271144-6274857;chr10:6270182-6274857;chr10:6273278-6274857;chr10:6268329-6274857	chr10:6266177-6274857					23.30
K	intron_retention	CUFF.617	chr2	-	chr2:79362890-79363090				chr2:79362889-79362890;chr2:79363090-79363091		56.00
K	jcn_only_AA	CUFF.842	chr4	-	chr4:83536173-83542364	chr4:83536235-83542364		chr4:83536173-83536234	chr4:83536172-83536173		34.78
N	cassette	CUFF.225	chr12	+	chr12:53856352-53859715;chr12:53856352-53861004	chr12:53856352-53858543;chr12:53858637-53859715,chr12:53858637-53861004		chr12:53858544-53858636			32.30
K	alternative_first_exon	CUFF.763	chr3	-	chr3:93646252-93647545;chr3:93646252-93692517,chr3:93646252-93692406	chr3:93646252-93677354	chr3:93692518-93692910	chr3:93677355-93677451			7.97
K	alternative_acceptor	CUFF.956	chr6	-	chr6:170117997-170118883	chr6:170118003-170118883		chr6:170117997-170118002	chr6:170117996-170117997		81.82
K	alternative_acceptor	CUFF.920	chr6	+	chr6:32122961-32123544	chr6:32122961-32123464		chr6:32123465-32123544	chr6:32123544-32123545		36.67
N	cassette	CUFF.426	chr17	-	chr17:15546131-15584178;chr17:15562191-15584178	chr17:15562191-15580489,chr17:15546131-15580489;chr17:15580595-15584178		chr17:15580490-15580594			26.37
K	intron_retention	CUFF.204	chr12	-	chr12:11461376-11461582				chr12:11461375-11461376;chr12:11461582-11461583		19.10
K	intron_retention	CUFF.792	chr3	-	chr3:133914027-133921573				chr3:133914026-133914027;chr3:133921573-133921574		45.24
K	intron_retention	CUFF.161	chr11	-	chr11:62364005-62364108				chr11:62364004-62364005;chr11:62364108-62364109		11.67
K	alternative_first_exon	CUFF.10	chr1	+	chr1:22963196-22964102	chr1:22963354-22964102	chr1:22962999-22963195	chr1:22963206-22963353			81.82
K	alternative_last_exon	CUFF.1153	chrY	+	chrY:20894878-20899940	chrY:20894878-20898228	chrY:20899941-20901182	chrY:20898229-20898379			34.97
N	jcn_only_AD	CUFF.390	chr16	-	chr16:23504780-23505623	chr16:23504780-23505619		chr16:23505620-23505623	chr16:23505623-23505624	chr16:23504681-23504779;chr16:23505624-23505699	23.08
K	alternative_donor	CUFF.752,CUFF.775	chr3	-	chr3:49338125-49339870	chr3:49338125-49339816		chr3:49339817-49339870	chr3:49339870-49339871		83.87
N	jcn_only_AA		chr2	+	chr2:220095073-220096981	chr2:220095073-220096649					30.08
N	jcn_only_AD	CUFF.1052	chr8	+	chr8:107738486-107749747;chr8:107726214-107749747	chr8:107738538-107749747		chr8:107726214-107738485;chr8:107738486-107738537	chr8:107726213-107726214;chr8:107738485-107738486		13.51
N	jcn_only_AA		chr17	+	chr17:61574347-61584416	chr17:61574347-61574497		chr17:61574498-61584416	chr17:61584416-61584417		98.68
N	jcn_only_AD	CUFF.954	chr6	+	chr6:161455482-161469647	chr6:161469324-161469647		chr6:161455482-161469323	chr6:161455481-161455482	chr6:161469648-161471011;chr6:161455291-161455481	53.85
N	alternative_acceptor	CUFF.1101	chr9	-	chr9:131483760-131483929;chr9:131483810-131483929	chr9:131483782-131483929		chr9:131483760-131483781;chr9:131483782-131483809	chr9:131483759-131483760;chr9:131483781-131483782		87.95
K	alternative_last_exon	CUFF.205	chr12	+	chr12:11712317-11743183	chr12:11712317-11716634	chr12:11743184-11743402	chr12:11716635-11717337			22.73
K	intron_retention	CUFF.989	chr7	+	chr7:91718844-91722410				chr7:91718843-91718844;chr7:91722410-91722411		61.54
K	alternative_last_exon	CUFF.854	chr4	-	chr4:153128821-153146395	chr4:153143912-153146395	chr4:153128573-153128820	chr4:153143528-153143911			63.64
K	alternative_donor	CUFF.980	chr7	+	chr7:73098135-73100965	chr7:73098232-73100965		chr7:73098135-73098231	chr7:73098134-73098135		15.13
N	intron_retention	CUFF.716	chr22	+	chr22:29684776-29687550				chr22:29684775-29684776;chr22:29687550-29687551		37.50
K	jcn_only_AD	CUFF.307	chr15	+	chr15:30771397-30776704	chr15:30773111-30776704					38.89
N	jcn_only_AD	CUFF.102	chr10	+	chr10:35437420-35467816;chr10:35426808-35467816;chr10:35416122-35467816;chr10:35456732-35467816;chr10:35464634-35467816	chr10:35464928-35467816		chr10:35416122-35426807;chr10:35426808-35437419;chr10:35437420-35456731;chr10:35456732-35464633;chr10:35464634-35464927	chr10:35416121-35416122;chr10:35426807-35426808;chr10:35437419-35437420;chr10:35456731-35456732;chr10:35464633-35464634		39.24
K	coord_cassette	CUFF.837	chr4	+	chr4:77184997-77230296	chr4:77184997-77189812;chr4:77189967-77192720;chr4:77192922-77230296		chr4:77189813-77189966;chr4:77192721-77192921			87.27
N	jcn_only_AA	CUFF.364,CUFF.386	chr16	+	chr16:21756358-21763255	chr16:21756358-21758618		chr16:21758619-21763255	chr16:21763255-21763256		1.80
K	intron_retention	CUFF.202	chr12	-	chr12:7090794-7090971				chr12:7090793-7090794;chr12:7090971-7090972		19.33
N	jcn_only_AA	CUFF.402	chr16	-	chr16:67223084-67223533	chr16:67223099-67223533		chr16:67223084-67223098	chr16:67223083-67223084		12.90
N	cassette	CUFF.1110	chrX	+	chrX:1387773-1401570	chrX:1387773-1393647;chrX:1393736-1401570		chrX:1393648-1393735			80.91
K	intron_retention	CUFF.840	chr4	+	chr4:78531849-78532141				chr4:78531848-78531849;chr4:78532141-78532142		16.28
K	alternative_last_exon	CUFF.958	chr7	+	chr7:195733-208897	chr7:195733-197129	chr7:208898-209066	chr7:197130-197648			62.86
N	alternative_donor	CUFF.325	chr15	+	chr15:57384090-57458599;chr15:57426699-57458599;chr15:57401516-57458599	chr15:57422171-57458599		chr15:57384090-57401515;chr15:57401516-57422170;chr15:57422171-57426698	chr15:57384089-57384090;chr15:57401515-57401516;chr15:57422170-57422171		0.00
K	alternative_first_exon	CUFF.1118	chrX	-	chrX:19954017-19955622	chrX:19954017-19955535	chrX:19955623-19955650	chrX:19955536-19955615			10.34
K	intron_retention	CUFF.604	chr2	-	chr2:61720189-61721028				chr2:61720188-61720189;chr2:61721028-61721029		43.75
K	alternative_acceptor	CUFF.884	chr5	-	chr5:82948641-82969242	chr5:82948644-82969242		chr5:82948641-82948643	chr5:82948640-82948641		78.26
N	alternative_donor	CUFF.306	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		0.00
N	jcn_only_AD		chr10	+	chr10:35416122-35426709	chr10:35416496-35426709		chr10:35416122-35416495	chr10:35416121-35416122		27.66
K	mutually_exclusive	CUFF.1086	chr9	+	chr9:105768661-105774263,chr9:105774380-105780606	chr9:105768661-105772982,chr9:105773088-105780606	chr9:105774264-105774379	chr9:105772983-105773087			44.44
N	alternative_donor	CUFF.657	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		10.00
N	jcn_only_AA	CUFF.445	chr17	-	chr17:40738156-40739851	chr17:40738910-40739851					76.92
N	cassette	CUFF.97	chr10	-	chr10:27044671-27054146;chr10:27040713-27054146	chr10:27044671-27047990,chr10:27040713-27047990;chr10:27048165-27054146		chr10:27047991-27048164			87.50
N	alternative_donor	CUFF.456	chr17	+	chr17:60777141-60813446;chr17:60783831-60813446	chr17:60784969-60813446		chr17:60777141-60783830;chr17:60783831-60784968	chr17:60777140-60777141;chr17:60783830-60783831		1.35
N	coord_cassette	CUFF.136	chr11	-	chr11:408207-409867	chr11:408207-408694;chr11:408894-409216;chr11:409309-409867		chr11:408695-408893;chr11:409217-409308			88.30
K	jcn_only_AD	CUFF.370	chr16	+	chr16:2141610-2142889	chr16:2141616-2142889		chr16:2141610-2141615	chr16:2141609-2141610		11.04
N	coord_cassette	CUFF.426	chr17	-	chr17:15546131-15584178	chr17:15546131-15554404;chr17:15555261-15562115;chr17:15562191-15584178		chr17:15554405-15555260;chr17:15562116-15562190			54.95
N	jcn_only_AD		chr16	-	chr16:57513598-57513772;chr16:57513598-57513756	chr16:57513598-57517869					40.00
N	jcn_only_AA		chr2	+	chr2:109092307-109098165	chr2:109092307-109098152		chr2:109098153-109098165	chr2:109098165-109098166		28.57
N	coord_cassette	CUFF.18	chr1	+	chr1:32541424-32557275	chr1:32541424-32542164;chr1:32542248-32542363;chr1:32542448-32557275		chr1:32542165-32542247;chr1:32542364-32542447			21.82
N	intron_retention		chr4	-	chr4:83816001-83821229				chr4:83816000-83816001;chr4:83821229-83821230		19.15
K	cassette	CUFF.1089	chr9	+	chr9:116770835-116778974	chr9:116770835-116778392;chr9:116778453-116778974		chr9:116778393-116778452			95.45
N	jcn_only_AA	CUFF.959	chr7	-	chr7:1778839-1781844	chr7:1779172-1781844		chr7:1778839-1779171	chr7:1778838-1778839		6.80
K	jcn_only_AA	CUFF.1073	chr9	+	chr9:43861207-43884944	chr9:43861207-43875988					55.56
N	alternative_acceptor	CUFF.468	chr17	-	chr17:79258696-79263490	chr17:79262746-79263490		chr17:79258696-79262745	chr17:79258695-79258696	chr17:79263491-79263608;chr17:79258650-79258695	22.50
K	alternative_first_exon	CUFF.669	chr2	+	chr2:241396887-241398446,chr2:241381924-241398446;chr2:241394438-241398446;chr2:241397535-241398446	chr2:241392512-241398446	chr2:241394347-241394437;chr2:241397319-241397534	chr2:241392147-241392511			43.05
N	alternative_first_exon		chr3	-	chr3:27257372-27297786	chr3:27257372-27257860	chr3:27297787-27297862	chr3:27257861-27258014			90.48
N	jcn_only_AD	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;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;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		5.00
N	alternative_acceptor		chr19	+	chr19:40478152-40478368	chr19:40478152-40478275		chr19:40478276-40478368	chr19:40478368-40478369		68.18
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55714743-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		6.34
N	jcn_only_AA	CUFF.920,CUFF.922	chr6	+	chr6:33240504-33243573	chr6:33240504-33243276		chr6:33243277-33243573	chr6:33243573-33243574		4.23
K	alternative_donor	CUFF.768	chr3	+	chr3:112046542-112048192	chr3:112046554-112048192		chr3:112046542-112046553	chr3:112046541-112046542		40.91
K	alternative_last_exon	CUFF.1117	chrX	+	chrX:15711182-15713793;chrX:15711182-15715362	chrX:15711182-15720904	chrX:15713794-15713856;chrX:15715363-15715961	chrX:15720905-15721927			39.77
K	alternative_first_exon	CUFF.1109	chr9	+	chr9:139780994-139793164;chr9:139784995-139793164;chr9:139777163-139793164	chr9:139780732-139793164	chr9:139780897-139780993;chr9:139784801-139784994;chr9:139777119-139777162	chr9:139780437-139780731			47.20
K	alternative_acceptor	CUFF.439	chr17	+	chr17:33640726-33648755	chr17:33640726-33648753		chr17:33648754-33648755	chr17:33648755-33648756		40.00
N	mutually_exclusive	CUFF.374	chr16	+	chr16:3117417-3118180,chr16:3118241-3118990	chr16:3117417-3117984,chr16:3118012-3118990	chr16:3118181-3118240	chr16:3117985-3118011			86.67
N	jcn_only_AD	CUFF.581	chr2	-	chr2:4009485-4021134	chr2:4009485-4015768		chr2:4015769-4021134	chr2:4021134-4021135		31.15
N	mutually_exclusive	CUFF.259	chr14	+	chr14:24563464-24566100,chr14:24566347-24567411	chr14:24563464-24563974,chr14:24564055-24567411	chr14:24566101-24566346	chr14:24563975-24564054			27.66
N	coord_cassette	CUFF.234	chr12	+	chr12:69203073-69229608	chr12:69203073-69218142;chr12:69218211-69218334;chr12:69218432-69229608		chr12:69218143-69218210;chr12:69218335-69218431			61.45
K	intron_retention	CUFF.460	chr17	+	chr17:61908587-61908686				chr17:61908586-61908587;chr17:61908686-61908687		0.80
N	cassette	CUFF.454	chr17	-	chr17:57775340-57784731	chr17:57775340-57776231;chr17:57777238-57784731		chr17:57776232-57777237			84.78
N	intron_retention		chr22	-	chr22:21830450-21832078				chr22:21830449-21830450;chr22:21832078-21832079		94.29
N	alternative_donor	CUFF.708	chr22	+	chr22:21056595-21056873	chr22:21056749-21056873		chr22:21056595-21056748	chr22:21056594-21056595		37.50
K	alternative_last_exon	CUFF.93	chr10	-	chr10:17646047-17659081	chr10:17657964-17659081	chr10:17645929-17646046	chr10:17657398-17657963			47.83
K	intron_retention	CUFF.728	chr22	-	chr22:51019983-51020177				chr22:51019982-51019983;chr22:51020177-51020178		23.14
K	jcn_only_AA	CUFF.304	chr15	+	chr15:25207357-25222924	chr15:25207357-25213078					66.67
N	jcn_only_AD	CUFF.683	chr20	+	chr20:30132839-30136831	chr20:30136597-30136831		chr20:30132839-30136596	chr20:30132838-30132839	chr20:30136832-30136917;chr20:30132750-30132838	8.70
N	jcn_only_AA	CUFF.589	chr2	-	chr2:27708371-27712481	chr2:27709110-27712481		chr2:27708371-27709109	chr2:27708370-27708371		2.04
N	intron_retention		chr12	+	chr12:13366756-13367504				chr12:13366755-13366756;chr12:13367504-13367505		75.92
N	alternative_donor	CUFF.289	chr14	-	chr14:92105595-92112480;chr14:92105595-92136157	chr14:92105595-92126180		chr14:92112481-92126180;chr14:92126181-92136157	chr14:92126180-92126181;chr14:92136157-92136158		0.00
K	intron_retention		chr11	+	chr11:63999437-63999901				chr11:63999436-63999437;chr11:63999901-63999902		6.44
N	alternative_first_exon	CUFF.1022	chr7	+	chr7:157647568-157655236	chr7:157650241-157655236	chr7:157647139-157647567	chr7:157649982-157650240			78.95
N	alternative_donor	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;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;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		51.35
K	jcn_only_AA	CUFF.810	chr4	+	chr4:1126229-1126514	chr4:1126229-1126496		chr4:1126497-1126514	chr4:1126514-1126515		9.62
K	alternative_acceptor	CUFF.703	chr21	-	chr21:47556968-47557152	chr21:47556988-47557152		chr21:47556968-47556987	chr21:47556967-47556968		33.33
N	cassette	CUFF.703	chr21	-	chr21:47558561-47562022;chr21:47558561-47565330	chr21:47558561-47558793;chr21:47558838-47565330,chr21:47558838-47562022		chr21:47558794-47558837			51.35
K	cassette	CUFF.119	chr10	-	chr10:78709125-78713558	chr10:78709125-78711794;chr10:78711918-78713558		chr10:78711795-78711917			6.00
N	coord_cassette	CUFF.114	chr10	-	chr10:73956748-73972944	chr10:73956748-73958206;chr10:73958424-73963184;chr10:73963283-73970489;chr10:73970590-73972944		chr10:73958207-73958423;chr10:73963185-73963282;chr10:73970490-73970589			71.67
N	jcn_only_AD	CUFF.321	chr15	-	chr15:50822127-50830905	chr15:50822127-50824208		chr15:50824209-50830905	chr15:50830905-50830906		8.87
N	alternative_donor	CUFF.106	chr10	-	chr10:46135412-46143741	chr10:46135412-46135688		chr10:46135689-46143741	chr10:46143741-46143742		0.00
N	intron_retention		chr6	-	chr6:31938156-31938369				chr6:31938155-31938156;chr6:31938369-31938370		94.31
N	intron_retention		chr15	+	chr15:40568307-40569316				chr15:40568306-40568307;chr15:40569316-40569317		64.29
N	jcn_only_AA	CUFF.230	chr12	-	chr12:56705180-56708634;chr12:56705238-56708634;chr12:56705199-56708634	chr12:56706670-56708634		chr12:56705180-56705198;chr12:56705199-56705237;chr12:56705238-56706669	chr12:56705179-56705180;chr12:56705198-56705199;chr12:56705237-56705238		7.37
N	cassette	CUFF.945	chr6	-	chr6:128563748-128718710	chr6:128563748-128643183;chr6:128643456-128718710		chr6:128643184-128643455			90.31
K	intron_retention	CUFF.618	chr2	-	chr2:86397965-86400772				chr2:86397964-86397965;chr2:86400772-86400773		62.50
N	alternative_acceptor	CUFF.763	chr3	-	chr3:93646252-93692517	chr3:93647642-93692517		chr3:93646252-93647641	chr3:93646251-93646252		40.00
K	alternative_last_exon	CUFF.240	chr12	-	chr12:113633695-113645242	chr12:113638619-113645242	chr12:113633150-113633694	chr12:113637767-113638618			68.18
N	alternative_donor	CUFF.708	chr22	+	chr22:21056998-21057293	chr22:21057182-21057293		chr22:21056998-21057181	chr22:21056997-21056998		6.94
K	cassette	CUFF.897	chr5	-	chr5:141041357-141044488	chr5:141041357-141041609;chr5:141041823-141044488		chr5:141041610-141041822			44.44
N	alternative_donor	CUFF.971	chr7	-	chr7:37382368-37433424;chr7:37382368-37488277;chr7:37382368-37488462;chr7:37382368-37382655	chr7:37382368-37392635		chr7:37382656-37392635;chr7:37392636-37433424;chr7:37433425-37488277;chr7:37488278-37488462	chr7:37392635-37392636;chr7:37433424-37433425;chr7:37488277-37488278;chr7:37488462-37488463		0.00
K	alternative_last_exon	CUFF.827	chr4	-	chr4:36195270-36212011	chr4:36211037-36212011	chr4:36195200-36195269	chr4:36210898-36211036			88.89
N	coord_cassette	CUFF.628	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			93.94
K	jcn_only_AA	CUFF.946	chr6	-	chr6:133055523-133055618	chr6:133055526-133055618		chr6:133055523-133055525	chr6:133055522-133055523		14.81
N	jcn_only_AD	CUFF.526	chr19	+	chr19:16199931-16204345	chr19:16203943-16204345		chr19:16199931-16203942	chr19:16199930-16199931		1.02
N	alternative_donor	CUFF.292	chr14	+	chr14:92792323-92900255	chr14:92874779-92900255		chr14:92792323-92874778	chr14:92792322-92792323		0.00
N	alternative_donor		chr3	-	chr3:107568819-107572719	chr3:107568819-107569143		chr3:107569144-107572719	chr3:107572719-107572720		8.33
N	alternative_acceptor	CUFF.739	chr3	+	chr3:28357915-28358243;chr3:28357915-28360999	chr3:28357915-28360222		chr3:28358244-28360222;chr3:28360223-28360999	chr3:28360222-28360223;chr3:28360999-28361000		1.77
N	intron_retention		chr2	-	chr2:253116-264781				chr2:253115-253116;chr2:264781-264782		4.17
N	jcn_only_AA	CUFF.929	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		31.32
N	jcn_only_AD	CUFF.1146	chrX	+	chrX:148864250-148867418;chrX:148863659-148867418	chrX:148863691-148867418		chrX:148863659-148863690;chrX:148863691-148864249	chrX:148863658-148863659;chrX:148863690-148863691		25.81
N	jcn_only_AA	CUFF.119	chr10	-	chr10:78778858-78787580	chr10:78782695-78787580		chr10:78778858-78782694	chr10:78778857-78778858		3.53
N	jcn_only_AA	CUFF.734	chr3	+	chr3:19992554-20017092;chr3:19992554-20017134;chr3:19992554-20017078	chr3:19992554-20012039		chr3:20012040-20017078;chr3:20017079-20017092;chr3:20017093-20017134	chr3:20017078-20017079;chr3:20017092-20017093;chr3:20017134-20017135		5.00
K	jcn_only_AA	CUFF.273	chr14	+	chr14:61545646-61550272	chr14:61545646-61550267		chr14:61550268-61550272	chr14:61550272-61550273		70.73
K	intron_retention	CUFF.1016	chr7	+	chr7:150814865-150815296				chr7:150814864-150814865;chr7:150815296-150815297		17.30
N	alternative_acceptor	CUFF.578,CUFF.598	chr2	+	chr2:38177739-38201182	chr2:38177739-38178375		chr2:38178376-38201182	chr2:38201182-38201183		5.26
N	alternative_donor	CUFF.273	chr14	+	chr14:61512886-61517229	chr14:61515016-61517229		chr14:61512886-61515015	chr14:61512885-61512886		1.32
N	alternative_acceptor	CUFF.810	chr4	+	chr4:186283866-186290903	chr4:186283866-186284538		chr4:186284539-186290903	chr4:186290903-186290904		84.00
N	jcn_only_AA	CUFF.577	chr2	+	chr2:33477912-33482434	chr2:33477912-33482350		chr2:33482351-33482434	chr2:33482434-33482435		89.07
K	jcn_only_AA	CUFF.626	chr2	+	chr2:99232997-99234630	chr2:99232997-99234608		chr2:99234609-99234630	chr2:99234630-99234631		46.75
K	intron_retention	CUFF.173	chr11	-	chr11:94703261-94704140				chr11:94703260-94703261;chr11:94704140-94704141		52.56
N	jcn_only_AD		chr8	-	chr8:99057628-99057942	chr8:99057628-99057735		chr8:99057736-99057942	chr8:99057942-99057943		97.26
K	intron_retention	CUFF.166	chr11	-	chr11:67766776-67766988				chr11:67766775-67766776;chr11:67766988-67766989		30.66
K	alternative_last_exon	CUFF.882,CUFF.890	chr5	+	chr5:81608671-81637517	chr5:81608671-81613816	chr5:81637518-81637609	chr5:81613817-81614622			97.69
K	alternative_donor	CUFF.893	chr5	+	chr5:137514892-137515348	chr5:137515023-137515348		chr5:137514892-137515022	chr5:137514891-137514892		9.09
K	alternative_first_exon	CUFF.997	chr7	-	chr7:100818093-100823322	chr7:100818093-100822377	chr7:100823323-100823622	chr7:100822378-100822578			40.00
K	cassette	CUFF.741	chr3	-	chr3:33437773-33438536	chr3:33437773-33438236;chr3:33438371-33438536		chr3:33438237-33438370			78.38
N	jcn_only_AD	CUFF.240,CUFF.241	chr12	-	chr12:120148426-120149982	chr12:120148426-120148853		chr12:120148854-120149982	chr12:120149982-120149983		15.79
K	intron_retention	CUFF.809	chr4	+	chr4:657660-657902				chr4:657659-657660;chr4:657902-657903		64.96
N	jcn_only_AA	CUFF.581	chr2	-	chr2:4020665-4021134;chr2:4015879-4021134;chr2:4020693-4021134;chr2:4009485-4021134	chr2:4009394-4021134		chr2:4009394-4009484;chr2:4009485-4015878;chr2:4015879-4020664;chr2:4020665-4020692	chr2:4009393-4009394;chr2:4009484-4009485;chr2:4015878-4015879;chr2:4020664-4020665		6.67
K	alternative_first_exon	CUFF.530	chr19	+	chr19:17445932-17447628	chr19:17447537-17447628	chr19:17445654-17445931	chr19:17447428-17447536			35.29
N	coord_cassette	CUFF.377	chr16	-	chr16:4455569-4462356	chr16:4455569-4457501;chr16:4457686-4458181;chr16:4458253-4462356		chr16:4457502-4457685;chr16:4458182-4458252			95.85
N	jcn_only_AD	CUFF.316,CUFF.332	chr15	-	chr15:44878049-44881449	chr15:44878049-44880764		chr15:44880765-44881449	chr15:44881449-44881450		20.83
K	jcn_only_AA	CUFF.350	chr15	-	chr15:84873728-84898603	chr15:84874072-84898603					56.00
N	cassette	CUFF.945	chr6	-	chr6:128320050-128324341	chr6:128320050-128322340;chr6:128322353-128324341		chr6:128322341-128322352			59.21
K	intron_retention	CUFF.298	chr14	-	chr14:104204198-104205015				chr14:104204197-104204198;chr14:104205015-104205016		41.94
K	alternative_first_exon	CUFF.895	chr5	+	chr5:140027748-140028055,chr5:140027593-140028055;chr5:140026895-140028055	chr5:140027510-140028055	chr5:140026576-140026894	chr5:140027305-140027509			65.28
N	intron_retention	CUFF.460	chr17	+	chr17:61904884-61904979				chr17:61904883-61904884;chr17:61904979-61904980		54.55
K	alternative_acceptor	CUFF.102	chr10	+	chr10:35495980-35500583	chr10:35495980-35500181		chr10:35500182-35500583	chr10:35500583-35500584		46.43
N	jcn_only_AA	CUFF.325	chr15	+	chr15:57574797-57578354;chr15:57574797-57591423	chr15:57574797-57583026		chr15:57578355-57583026;chr15:57583027-57591423	chr15:57583026-57583027;chr15:57591423-57591424		9.45
N	jcn_only_AD	CUFF.603	chr2	+	chr2:48898820-49003418;chr2:48996214-49003418	chr2:48996261-49003418		chr2:48898820-48996213;chr2:48996214-48996260	chr2:48898819-48898820;chr2:48996213-48996214		13.21
N	cassette	CUFF.640	chr2	-	chr2:166714915-166727306	chr2:166714915-166721493;chr2:166721588-166727306		chr2:166721494-166721587			76.92
K	intron_retention	CUFF.183	chr11	-	chr11:118531625-118531868				chr11:118531624-118531625;chr11:118531868-118531869		16.88
N	jcn_only_AD	CUFF.490	chr18	+	chr18:56033461-56034977	chr18:56034459-56034977		chr18:56033461-56034458	chr18:56033460-56033461		5.02
N	alternative_donor		chr2	-	chr2:73227617-73228657	chr2:73227617-73228653		chr2:73228654-73228657	chr2:73228657-73228658		90.74
N	alternative_acceptor	CUFF.1081	chr9	-	chr9:86924630-86928273	chr9:86925503-86928273		chr9:86924630-86925502	chr9:86924629-86924630		57.14
K	alternative_first_exon	CUFF.575	chr2	-	chr2:287893-288552	chr2:287893-288012	chr2:288553-288926	chr2:288013-288296			32.43
N	jcn_only_AA		chr19	-	chr19:6192041-6199490;chr19:6192065-6199490	chr19:6176455-6199490					75.00
N	jcn_only_AD		chr6	-	chr6:31938925-31939705	chr6:31938925-31939096		chr6:31939097-31939705	chr6:31939705-31939706		89.73
K	intron_retention		chr16	-	chr16:30006165-30006423				chr16:30006164-30006165;chr16:30006423-30006424		42.86
K	cassette	CUFF.696	chr21	-	chr21:30963546-30971149	chr21:30963546-30968845;chr21:30968891-30971149		chr21:30968846-30968890			63.86
N	intron_retention		chr11	-	chr11:10827488-10828835				chr11:10827487-10827488;chr11:10828835-10828836		55.27
K	cassette	CUFF.132	chr10	-	chr10:123670667-123681863	chr10:123670667-123673304;chr10:123673409-123681863		chr10:123673305-123673408			74.16
K	alternative_acceptor	CUFF.61,CUFF.65	chr1	+	chr1:171123354-171130296	chr1:171123354-171130202		chr1:171130203-171130296	chr1:171130296-171130297		56.25
K	cassette	CUFF.119	chr10	-	chr10:78669855-78674693	chr10:78669855-78673814;chr10:78673896-78674693		chr10:78673815-78673895			10.53
N	alternative_acceptor	CUFF.869,CUFF.878	chr5	+	chr5:56510021-56526672	chr5:56510021-56517202		chr5:56517203-56526672	chr5:56526672-56526673	chr5:56509901-56510020;chr5:56526673-56526796	7.14
K	alternative_first_exon	CUFF.161	chr11	-	chr11:62368162-62368894	chr11:62368162-62368494	chr11:62368895-62369312	chr11:62368495-62368804			57.14
K	cassette	CUFF.943	chr6	-	chr6:116980088-116981898	chr6:116980088-116981395;chr6:116981533-116981898		chr6:116981396-116981532			30.30
N	alternative_acceptor	CUFF.838	chr4	-	chr4:77977254-77987401	chr4:77979789-77987401		chr4:77977254-77979788	chr4:77977253-77977254		58.82
K	alternative_first_exon	CUFF.595	chr2	+	chr2:33505226-33518226	chr2:33516855-33518226	chr2:33505106-33505225	chr2:33516756-33516854			2.95
N	cassette	CUFF.382	chr16	+	chr16:14031716-14038579	chr16:14031716-14037830;chr16:14037953-14038579		chr16:14037831-14037952			76.62
K	intron_retention	CUFF.601	chr2	-	chr2:46842325-46843725				chr2:46842324-46842325;chr2:46843725-46843726		41.56
K	intron_retention	CUFF.777	chr3	+	chr3:122880303-122880726				chr3:122880302-122880303;chr3:122880726-122880727		25.00
K	alternative_last_exon	CUFF.961,CUFF.976	chr7	+	chr7:54617864-54621559,chr7:54617864-54636823;chr7:54617864-54636701	chr7:54617864-54618445	chr7:54636702-54638862	chr7:54618446-54620314			53.79
K	jcn_only_AD	CUFF.1097,CUFF.1103	chr9	-	chr9:135702442-135703399	chr9:135702442-135702693					6.43
N	jcn_only_AA	CUFF.765	chr3	-	chr3:107572902-107573976;chr3:107572807-107573976	chr3:107573542-107573976		chr3:107572807-107572901;chr3:107572902-107573541	chr3:107572806-107572807;chr3:107572901-107572902		39.56
K	intron_retention	CUFF.575	chr2	-	chr2:286204-286289				chr2:286203-286204;chr2:286289-286290		3.38
N	alternative_acceptor	CUFF.768,CUFF.769	chr3	+	chr3:119196296-119198897;chr3:119196296-119198754	chr3:119196296-119197180		chr3:119197181-119198754;chr3:119198755-119198897	chr3:119198754-119198755;chr3:119198897-119198898		44.58
K	intron_retention	CUFF.904	chr5	-	chr5:178030759-178030844				chr5:178030758-178030759;chr5:178030844-178030845		52.33
N	intron_retention		chr11	+	chr11:74624828-74630577				chr11:74624827-74624828;chr11:74630577-74630578		53.85
K	intron_retention	CUFF.66	chr1	-	chr1:174128129-174128301				chr1:174128128-174128129;chr1:174128301-174128302		64.15
N	alternative_donor	CUFF.726	chr22	+	chr22:47309343-47393529	chr22:47370296-47393529		chr22:47309343-47370295	chr22:47309342-47309343		0.00
K	intron_retention	CUFF.358	chr15	+	chr15:97327061-97327382				chr15:97327060-97327061;chr15:97327382-97327383		6.90
N	jcn_only_AA	CUFF.212	chr12	+	chr12:26205930-26208211	chr12:26205930-26208168		chr12:26208169-26208211	chr12:26208211-26208212		3.82
K	alternative_last_exon	CUFF.873	chr5	+	chr5:51307437-51374717	chr5:51307437-51339451	chr5:51374718-51374824	chr5:51339452-51339771			53.85
K	intron_retention	CUFF.922	chr6	+	chr6:33243661-33243741				chr6:33243660-33243661;chr6:33243741-33243742		1.72
K	cassette	CUFF.787	chr3	+	chr3:132948196-133098595	chr3:132948196-133097185;chr3:133097401-133098595		chr3:133097186-133097400			16.67
N	jcn_only_AD		chr3	-	chr3:33686396-33700998;chr3:33686396-33700465;chr3:33686396-33686835;chr3:33686396-33686773	chr3:33686396-33686494					22.51
K	cassette	CUFF.904	chr5	-	chr5:178032384-178035376	chr5:178032384-178032825;chr5:178032867-178035376		chr5:178032826-178032866			8.70
K	alternative_first_exon	CUFF.737,CUFF.747	chr3	-	chr3:38061844-38065827;chr3:38061844-38070996	chr3:38061844-38065646	chr3:38070997-38071331	chr3:38065647-38066316			53.85
K	intron_retention	CUFF.1134	chrX	+	chrX:103357693-103357885				chrX:103357692-103357693;chrX:103357885-103357886	chrX:103357422-103357692;chrX:103357886-103357937	7.50
K	jcn_only_AA	CUFF.267	chr14	-	chr14:52486897-52495439	chr14:52494063-52495439					13.33
K	cassette	CUFF.1099	chr9	+	chr9:131013220-131016932	chr9:131013220-131015379;chr9:131015417-131016932		chr9:131015380-131015416			50.00
N	cassette	CUFF.647	chr2	-	chr2:175689247-175742567	chr2:175689247-175711607;chr2:175711686-175742567		chr2:175711608-175711685			87.60
N	alternative_acceptor	CUFF.247	chr13	+	chr13:31192194-31195900	chr13:31192194-31195209		chr13:31195210-31195900	chr13:31195900-31195901		0.00
N	jcn_only_AD	CUFF.17	chr1	+	chr1:31819588-31821675	chr1:31819666-31821675		chr1:31819588-31819665	chr1:31819587-31819588		4.05
N	cassette	CUFF.155	chr11	+	chr11:36424929-36453402	chr11:36424929-36440804;chr11:36440854-36453402		chr11:36440805-36440853			74.42
N	jcn_only_AD	CUFF.176	chr11	-	chr11:102960048-102962412;chr11:102960048-102962244	chr11:102960048-102962515		chr11:102962245-102962412;chr11:102962413-102962515	chr11:102962412-102962413;chr11:102962515-102962516		62.59
K	alternative_donor	CUFF.502	chr18	+	chr18:77875468-77890985	chr18:77875534-77890985		chr18:77875468-77875533	chr18:77875467-77875468		28.00
K	alternative_donor	CUFF.1073	chr9	+	chr9:43915898-43920248	chr9:43915980-43920248		chr9:43915898-43915979	chr9:43915897-43915898		93.02
K	intron_retention	CUFF.589	chr2	-	chr2:27668856-27669126				chr2:27668855-27668856;chr2:27669126-27669127		5.56
N	alternative_donor	CUFF.516,CUFF.537	chr19	-	chr19:33954969-33968951	chr19:33954969-33967985		chr19:33967986-33968951	chr19:33968951-33968952		2.84
K	alternative_last_exon	CUFF.61,CUFF.83	chr1	+	chr1:167365665-167367230	chr1:167365665-167365769	chr1:167367231-167367370	chr1:167365770-167366152			79.26
K	coord_cassette	CUFF.975	chr7	+	chr7:44247798-44251845	chr7:44247798-44250440;chr7:44250531-44250621;chr7:44250724-44251152;chr7:44251204-44251845		chr7:44250441-44250530;chr7:44250622-44250723;chr7:44251153-44251203			72.22
N	jcn_only_AD	CUFF.475	chr17	-	chr17:79993940-79994057;chr17:79993940-79994066	chr17:79993940-79994022		chr17:79994023-79994057;chr17:79994058-79994066	chr17:79994057-79994058;chr17:79994066-79994067		10.50
K	intron_retention	CUFF.140	chr11	-	chr11:2188747-2189095				chr11:2188746-2188747;chr11:2189095-2189096		27.27
K	alternative_last_exon	CUFF.25	chr1	-	chr1:54382790-54389576	chr1:54387441-54389576	chr1:54382247-54382789	chr1:54387141-54387440			71.60
N	cassette	CUFF.631	chr2	+	chr2:109066146-109068854	chr2:109066146-109067483;chr2:109067569-109068854		chr2:109067484-109067568			76.47
N	alternative_donor	CUFF.603	chr2	+	chr2:48898820-49003418;chr2:48996214-49003418	chr2:48996261-49003418		chr2:48898820-48996213;chr2:48996214-48996260	chr2:48898819-48898820;chr2:48996213-48996214		0.00
K	jcn_only_AA	CUFF.617	chr2	-	chr2:79364464-79365092	chr2:79364469-79365092		chr2:79364464-79364468	chr2:79364463-79364464		51.91
K	intron_retention		chr3	-	chr3:125787090-125802935				chr3:125787089-125787090;chr3:125802935-125802936		5.81
K	jcn_only_AA	CUFF.136	chr11	-	chr11:407535-407816	chr11:407569-407816		chr11:407535-407568	chr11:407534-407535		79.81
N	coord_cassette	CUFF.231	chr12	+	chr12:57854339-57858455	chr12:57854339-57857447;chr12:57857575-57857781;chr12:57857875-57858455		chr12:57857448-57857574;chr12:57857782-57857874			72.73
N	cassette	CUFF.802	chr3	+	chr3:186648624-186769036	chr3:186648624-186681572;chr3:186681715-186769036		chr3:186681573-186681714			72.90
N	jcn_only_AA		chr15	+	chr15:40545491-40549043;chr15:40545491-40555999	chr15:40545491-40556004		chr15:40549044-40555999;chr15:40556000-40556004	chr15:40555999-40556000;chr15:40556004-40556005		91.11
N	jcn_only_AA	CUFF.579,CUFF.665	chr2	+	chr2:3464108-3466628;chr2:3464108-3469367	chr2:3464108-3464417		chr2:3464418-3466628;chr2:3466629-3469367	chr2:3466628-3466629;chr2:3469367-3469368		5.98
K	cassette	CUFF.486	chr18	-	chr18:44483597-44486189	chr18:44483597-44484064;chr18:44484170-44486189		chr18:44484065-44484169			50.00
N	alternative_donor	CUFF.386	chr16	+	chr16:21737980-21739561	chr16:21738481-21739561		chr16:21737980-21738480	chr16:21737979-21737980		1.23
K	intron_retention	CUFF.193	chr11	-	chr11:124757396-124757628				chr11:124757395-124757396;chr11:124757628-124757629		8.51
K	alternative_first_exon	CUFF.836	chr4	-	chr4:77097064-77116859	chr4:77097064-77097589	chr4:77116860-77117045	chr4:77097590-77097681			9.52
K	cassette	CUFF.78	chr1	+	chr1:222819028-222823633	chr1:222819028-222822170;chr1:222822193-222823633		chr1:222822171-222822192			25.00
N	intron_retention		chr16	-	chr16:57513601-57513772				chr16:57513600-57513601;chr16:57513772-57513773		78.79
N	alternative_donor	CUFF.1033	chr8	-	chr8:56676540-56685785;chr8:56676540-56685827	chr8:56676540-56685534		chr8:56685535-56685785;chr8:56685786-56685827	chr8:56685785-56685786;chr8:56685827-56685828		4.57
K	jcn_only_AA	CUFF.193	chr11	-	chr11:124766952-124768293	chr11:124767158-124768293		chr11:124766952-124767157	chr11:124766951-124766952		55.56
N	jcn_only_AD	CUFF.473	chr17	-	chr17:79894070-79900171;chr17:79894070-79894623	chr17:79894070-79898625		chr17:79894624-79898625;chr17:79898626-79900171	chr17:79898625-79898626;chr17:79900171-79900172	chr17:79893999-79894069	2.89
K	intron_retention	CUFF.666	chr2	+	chr2:232258622-232259491				chr2:232258621-232258622;chr2:232259491-232259492		50.98
N	jcn_only_AD		chr7	-	chr7:117501371-117511643;chr7:117501371-117512157	chr7:117501371-117514054					20.00
K	alternative_donor	CUFF.272,CUFF.278	chr14	-	chr14:75140815-75142443	chr14:75140815-75142401		chr14:75142402-75142443	chr14:75142443-75142444	chr14:75140737-75140814;chr14:75142444-75142649	36.09
N	alternative_donor	CUFF.1000	chr7	+	chr7:107204192-107205032;chr7:107204505-107205032;chr7:107204655-107205032	chr7:107204693-107205032		chr7:107204192-107204504;chr7:107204505-107204654;chr7:107204655-107204692	chr7:107204191-107204192;chr7:107204504-107204505;chr7:107204654-107204655		15.79
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	chr11:118404981-118405070	50.88
N	cassette	CUFF.879	chr5	-	chr5:60198336-60214091	chr5:60198336-60199474;chr5:60199544-60214091		chr5:60199475-60199543			52.94
K	cassette	CUFF.920	chr6	+	chr6:32121414-32122363	chr6:32121414-32121775;chr6:32122172-32122363		chr6:32121776-32122171			33.80
N	alternative_donor		chr16	-	chr16:70255305-70256273	chr16:70255305-70256269		chr16:70256270-70256273	chr16:70256273-70256274		53.85
N	alternative_donor	CUFF.257	chr14	+	chr14:23389408-23392180	chr14:23390330-23392180		chr14:23389408-23390329	chr14:23389407-23389408		95.24
K	intron_retention	CUFF.436	chr17	+	chr17:29686034-29687504				chr17:29686033-29686034;chr17:29687504-29687505		3.57
N	jcn_only_AD	CUFF.752,CUFF.796	chr3	-	chr3:156262229-156266693;chr3:156262229-156266654	chr3:156262229-156266593		chr3:156266594-156266654;chr3:156266655-156266693	chr3:156266654-156266655;chr3:156266693-156266694		2.04
N	jcn_only_AA		chr7	-	chr7:37433521-37488462;chr7:37382368-37488462	chr7:37469360-37488462		chr7:37382368-37433520;chr7:37433521-37469359	chr7:37382367-37382368;chr7:37433520-37433521		50.00
N	jcn_only_AD	CUFF.671	chr2	-	chr2:242435950-242436596;chr2:242435950-242437030	chr2:242435950-242436714		chr2:242436597-242436714;chr2:242436715-242437030	chr2:242436714-242436715;chr2:242437030-242437031		2.45
K	alternative_first_exon	CUFF.37	chr1	-	chr1:113471975-113472502,chr1:113471975-113497897;chr1:113471975-113499460;chr1:113471975-113478445	chr1:113471975-113498656	chr1:113499461-113499724;chr1:113478446-113478667	chr1:113498657-113498975			24.64
N	alternative_first_exon	CUFF.385	chr16	+	chr16:19592976-19612985	chr16:19603197-19612985	chr16:19592847-19592975	chr16:19603103-19603196			85.39
K	alternative_first_exon	CUFF.1098,CUFF.1103	chr9	-	chr9:130953142-130953558,chr9:130953142-130954010,chr9:130953142-130954133;chr9:130953142-130966464	chr9:130953142-130953710	chr9:130966465-130966754	chr9:130953711-130953886			36.84
N	alternative_acceptor	CUFF.2	chr1	+	chr1:2106753-2116021	chr1:2106753-2113270		chr1:2113271-2116021	chr1:2116021-2116022		0.00
K	intron_retention	CUFF.207	chr12	+	chr12:13364523-13366412				chr12:13364522-13364523;chr12:13366412-13366413		55.10
K	intron_retention	CUFF.754	chr3	-	chr3:49460997-49461507				chr3:49460996-49460997;chr3:49461507-49461508		36.84
N	alternative_donor	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55714743-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		1.71
N	intron_retention		chr8	-	chr8:99054947-99057170				chr8:99054946-99054947;chr8:99057170-99057171		82.24
N	alternative_acceptor	CUFF.579	chr2	+	chr2:3461465-3464033	chr2:3461465-3461565		chr2:3461566-3464033	chr2:3464033-3464034		11.54
K	alternative_acceptor	CUFF.946	chr6	-	chr6:133047978-133049879	chr6:133048152-133049879		chr6:133047978-133048151	chr6:133047977-133047978		41.07
K	alternative_donor	CUFF.47	chr1	-	chr1:151158427-151162599	chr1:151158427-151162480		chr1:151162481-151162599	chr1:151162599-151162600		78.79
N	jcn_only_AA	CUFF.435,CUFF.464	chr17	+	chr17:66519068-66519865	chr17:66519068-66519854		chr17:66519855-66519865	chr17:66519865-66519866		3.13
K	jcn_only_AA	CUFF.147	chr11	-	chr11:5685404-5686885	chr11:5686626-5686885		chr11:5685404-5686625	chr11:5685403-5685404		49.07
K	cassette	CUFF.875	chr5	-	chr5:54420857-54423084	chr5:54420857-54422181;chr5:54422268-54423084		chr5:54422182-54422267			30.00
N	intron_retention	CUFF.472	chr17	-	chr17:79478653-79478788				chr17:79478652-79478653;chr17:79478788-79478789		35.71
K	intron_retention	CUFF.114	chr10	-	chr10:73975868-73975964				chr10:73975867-73975868;chr10:73975964-73975965		20.00
K	coord_cassette	CUFF.264	chr14	+	chr14:50069187-50080973	chr14:50069187-50070269;chr14:50070337-50074117;chr14:50074840-50080973		chr14:50070270-50070336;chr14:50074118-50074839			41.82
N	alternative_acceptor	CUFF.347	chr15	-	chr15:83358206-83378345	chr15:83358687-83378345		chr15:83358206-83358686	chr15:83358205-83358206		14.52
K	intron_retention	CUFF.922	chr6	+	chr6:33239900-33240404				chr6:33239899-33239900;chr6:33240404-33240405		2.79
N	coord_cassette	CUFF.322	chr15	-	chr15:55485032-55488550	chr15:55485032-55486350;chr15:55486382-55486493;chr15:55486558-55488550		chr15:55486351-55486381;chr15:55486494-55486557			8.70
K	jcn_only_AD	CUFF.241	chr12	-	chr12:120204987-120210573	chr12:120204987-120208588					28.57
N	alternative_donor	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57521042;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;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		0.00
K	cassette	CUFF.564	chr19	+	chr19:52905282-52909159	chr19:52905282-52905681;chr19:52905799-52909159		chr19:52905682-52905798			40.54
N	jcn_only_AA		chr14	-	chr14:104251252-104263707;chr14:104245159-104263707	chr14:104261001-104263707					48.72
K	intron_retention	CUFF.432	chr17	+	chr17:25972376-25972886				chr17:25972375-25972376;chr17:25972886-25972887		10.26
K	cassette	CUFF.195	chr12	-	chr12:347177-351779	chr12:347177-347336;chr12:347510-351779		chr12:347337-347509			54.12
K	cassette	CUFF.586	chr2	+	chr2:16573595-16613772	chr2:16573595-16612998;chr2:16613076-16613772		chr2:16612999-16613075			64.29
N	intron_retention		chr17	+	chr17:61905570-61906853				chr17:61905569-61905570;chr17:61906853-61906854		8.61
K	mutually_exclusive	CUFF.618	chr2	-	chr2:86393768-86398330,chr2:86398436-86400772	chr2:86393768-86397871,chr2:86397965-86400772	chr2:86398331-86398435	chr2:86397872-86397964			90.00
N	jcn_only_AA	CUFF.481	chr18	+	chr18:12014373-12021700;chr18:12014373-12028041	chr18:12014373-12017612		chr18:12017613-12021700;chr18:12021701-12028041	chr18:12021700-12021701;chr18:12028041-12028042		6.73
K	alternative_acceptor	CUFF.209	chr12	-	chr12:22611490-22612425	chr12:22611520-22612425		chr12:22611490-22611519	chr12:22611489-22611490		81.03
K	intron_retention	CUFF.769	chr3	+	chr3:119196296-119198897				chr3:119196295-119196296;chr3:119198897-119198898		92.25
K	intron_retention	CUFF.633	chr2	-	chr2:110920713-110922096				chr2:110920712-110920713;chr2:110922096-110922097		60.00
N	cassette	CUFF.374	chr16	+	chr16:3118012-3118990	chr16:3118012-3118180;chr16:3118241-3118990		chr16:3118181-3118240			67.45
N	intron_retention		chr12	+	chr12:13364475-13367969				chr12:13364474-13364475;chr12:13367969-13367970		80.46
K	jcn_only_AA	CUFF.4	chr1	+	chr1:11083387-11084358	chr1:11083387-11084120		chr1:11084121-11084358	chr1:11084358-11084359		89.66
K	intron_retention	CUFF.1092	chr9	-	chr9:123555536-123555637				chr9:123555535-123555536;chr9:123555637-123555638		26.67
N	alternative_donor	CUFF.984	chr7	+	chr7:75040010-75040937	chr7:75040858-75040937		chr7:75040010-75040857	chr7:75040009-75040010		81.82
N	alternative_donor	CUFF.663	chr2	+	chr2:220095128-220096649;chr2:220094623-220096649	chr2:220095073-220096649		chr2:220094623-220095072;chr2:220095073-220095127	chr2:220094622-220094623;chr2:220095072-220095073		21.71
N	jcn_only_AD		chr7	-	chr7:37382368-37433424;chr7:37382368-37392635;chr7:37382368-37488277;chr7:37382368-37488462	chr7:37382368-37382655		chr7:37382656-37392635;chr7:37392636-37433424;chr7:37433425-37488277;chr7:37488278-37488462	chr7:37392635-37392636;chr7:37433424-37433425;chr7:37488277-37488278;chr7:37488462-37488463		21.74
N	alternative_acceptor	CUFF.910	chr6	-	chr6:5144497-5216850;chr6:5113652-5216850;chr6:5138974-5216850	chr6:5187215-5216850		chr6:5113652-5138973;chr6:5138974-5144496;chr6:5144497-5187214	chr6:5113651-5113652;chr6:5138973-5138974;chr6:5144496-5144497		0.00
K	alternative_first_exon	CUFF.1117	chrX	+	chrX:15699171-15706783;chrX:15693092-15706783;chrX:15693902-15706783;chrX:15699311-15706783	chrX:15693696-15706783	chrX:15692971-15693091;chrX:15693813-15693901;chrX:15699124-15699310	chrX:15693624-15693695			7.27
N	jcn_only_AD	CUFF.1033	chr8	-	chr8:56676540-56685785;chr8:56676540-56685534	chr8:56676540-56685827		chr8:56685535-56685785;chr8:56685786-56685827	chr8:56685785-56685786;chr8:56685827-56685828		71.13
N	jcn_only_AD		chr19	-	chr19:6047516-6148241;chr19:6047516-6049146;chr19:6047516-6057172;chr19:6047516-6072015	chr19:6047516-6110403		chr19:6049147-6057172;chr19:6057173-6072015;chr19:6072016-6110403;chr19:6110404-6148241	chr19:6057172-6057173;chr19:6072015-6072016;chr19:6110403-6110404;chr19:6148241-6148242		60.25
K	alternative_first_exon	CUFF.651	chr2	+	chr2:191334376-191334483;chr2:191302288-191334483	chr2:191307732-191334483	chr2:191334148-191334375;chr2:191300703-191302287	chr2:191307225-191307731			25.00
N	jcn_only_AA	CUFF.155,CUFF.163	chr11	+	chr11:64000087-64000175	chr11:64000087-64000172		chr11:64000173-64000175	chr11:64000175-64000176		4.59
N	alternative_donor	CUFF.352	chr15	-	chr15:44884637-44888257	chr15:44884637-44887456		chr15:44887457-44888257	chr15:44888257-44888258		60.00
K	alternative_acceptor	CUFF.514,CUFF.564	chr19	+	chr19:7075117-7075686	chr19:7075117-7075665		chr19:7075666-7075686	chr19:7075686-7075687		50.00
K	intron_retention	CUFF.622	chr2	-	chr2:88874596-88874878				chr2:88874595-88874596;chr2:88874878-88874879		51.61
K	intron_retention	CUFF.187	chr11	+	chr11:119056662-119057324				chr11:119056661-119056662;chr11:119057324-119057325		93.04
K	alternative_acceptor	CUFF.845	chr4	-	chr4:99399898-99403155	chr4:99399962-99403155		chr4:99399898-99399961	chr4:99399897-99399898		96.49
N	coord_cassette	CUFF.67	chr1	+	chr1:196913069-196927020	chr1:196913069-196918565;chr1:196918780-196919981;chr1:196920159-196927020		chr1:196918566-196918779;chr1:196919982-196920158		chr1:196912830-196913068;chr1:196927021-196927203	83.33
K	alternative_last_exon	CUFF.170	chr11	+	chr11:74622471-74630577	chr11:74622471-74624739	chr11:74630578-74631150	chr11:74624740-74624807			5.75
K	jcn_only_AD	CUFF.705	chr22	+	chr22:19420131-19420787	chr22:19420383-19420787		chr22:19420131-19420382	chr22:19420130-19420131		92.86
K	alternative_first_exon	CUFF.838	chr4	-	chr4:77979789-77996624;chr4:77979789-77985865	chr4:77979789-77987401	chr4:77996625-77997233;chr4:77985866-77986241	chr4:77987402-77987558			42.18
N	intron_retention		chr7	+	chr7:107224428-107236311				chr7:107224427-107224428;chr7:107236311-107236312		45.10
N	alternative_acceptor	CUFF.1033	chr8	-	chr8:56663717-56668802	chr8:56664106-56668802		chr8:56663717-56664105	chr8:56663716-56663717		2.01
K	intron_retention	CUFF.673	chr2	+	chr2:242606254-242607557				chr2:242606253-242606254;chr2:242607557-242607558		8.66
N	alternative_donor	CUFF.316,CUFF.332	chr15	-	chr15:44878049-44881449	chr15:44878049-44880764		chr15:44880765-44881449	chr15:44881449-44881450		5.00
N	jcn_only_AA		chr19	+	chr19:52085136-52092800	chr19:52085136-52089879		chr19:52089880-52092800	chr19:52092800-52092801		85.71
K	alternative_first_exon	CUFF.180	chr11	+	chr11:117071059-117073717;chr11:117070149-117073717,chr11:117070546-117073717	chr11:117072658-117073717	chr11:117069971-117070148	chr11:117072490-117072657			18.06
K	cassette	CUFF.52	chr1	-	chr1:156453223-156470277	chr1:156453223-156469223;chr1:156469353-156470277		chr1:156469224-156469352			33.33
K	alternative_donor	CUFF.5	chr1	+	chr1:11159872-11161857	chr1:11159968-11161857		chr1:11159872-11159967	chr1:11159871-11159872		48.57
N	jcn_only_AA	CUFF.880	chr5	-	chr5:64907709-64909924	chr5:64909683-64909924		chr5:64907709-64909682	chr5:64907708-64907709		17.39
K	alternative_first_exon	CUFF.747	chr3	-	chr3:38058211-38061678	chr3:38058211-38060460	chr3:38061679-38061843	chr3:38060461-38060560			36.36
K	jcn_only_AA	CUFF.347	chr15	-	chr15:83331986-83332311	chr15:83332048-83332311		chr15:83331986-83332047	chr15:83331985-83331986		7.81
N	jcn_only_AA	CUFF.752	chr3	-	chr3:49343322-49365118	chr3:49363279-49365118					83.33
N	jcn_only_AD		chr3	-	chr3:124996654-125042231	chr3:124996654-124997967		chr3:124997968-125042231	chr3:125042231-125042232		70.00
N	jcn_only_AA		chr18	+	chr18:55711941-56057877	chr18:55711941-55833019					81.89
K	jcn_only_AD	CUFF.215,CUFF.239	chr12	-	chr12:48258961-48272750	chr12:48258961-48272598		chr12:48272599-48272750	chr12:48272750-48272751		21.55
N	jcn_only_AD	CUFF.254	chr13	-	chr13:24460646-24463270	chr13:24460646-24462816		chr13:24462817-24463270	chr13:24463270-24463271		66.67
N	alternative_first_exon	CUFF.212	chr12	+	chr12:26205536-26208168;chr12:26148064-26208168;chr12:26205930-26208168;chr12:26174452-26208168	chr12:26164755-26208168	chr12:26147970-26148063;chr12:26205414-26205929;chr12:26174353-26174451	chr12:26164591-26164754			36.11
N	alternative_acceptor	CUFF.671	chr2	-	chr2:242435950-242437030	chr2:242436794-242437030		chr2:242435950-242436793	chr2:242435949-242435950		4.00
N	jcn_only_AD	CUFF.119,CUFF.134	chr10	-	chr10:78647274-78649208	chr10:78647274-78647552		chr10:78647553-78649208	chr10:78649208-78649209		6.93
N	mutually_exclusive	CUFF.671	chr2	-	chr2:242440212-242447420,chr2:242447551-242447857	chr2:242440212-242440892,chr2:242441124-242447857	chr2:242447421-242447550	chr2:242440893-242441123			19.44
N	alternative_donor		chr6	+	chr6:112558118-112600322	chr6:112598514-112600322		chr6:112558118-112598513	chr6:112558117-112558118		0.00
K	intron_retention	CUFF.325	chr15	+	chr15:57565461-57574642				chr15:57565460-57565461;chr15:57574642-57574643		16.85
N	cassette	CUFF.1042	chr8	-	chr8:80954904-80962679;chr8:80954904-80963761	chr8:80954904-80956401;chr8:80956444-80963761,chr8:80956444-80962679		chr8:80956402-80956443			31.43
N	cassette	CUFF.278	chr14	-	chr14:75136830-75138110	chr14:75136830-75137464;chr14:75137575-75138110		chr14:75137465-75137574		chr14:75136650-75136829;chr14:75138111-75138186	87.30
K	intron_retention		chr22	-	chr22:30735024-30735118				chr22:30735023-30735024;chr22:30735118-30735119		32.35
K	cassette	CUFF.677	chr20	-	chr20:14308205-14318049	chr20:14308205-14309779;chr20:14309974-14318049		chr20:14309780-14309973			90.00
K	alternative_last_exon	CUFF.274	chr14	-	chr14:69522329-69542061	chr14:69529229-69542061	chr14:69517499-69522328	chr14:69529063-69529228			66.67
N	alternative_donor	CUFF.102	chr10	+	chr10:35437420-35467816;chr10:35426808-35467816;chr10:35416122-35467816;chr10:35456732-35467816;chr10:35464634-35467816	chr10:35464928-35467816		chr10:35416122-35426807;chr10:35426808-35437419;chr10:35437420-35456731;chr10:35456732-35464633;chr10:35464634-35464927	chr10:35416121-35416122;chr10:35426807-35426808;chr10:35437419-35437420;chr10:35456731-35456732;chr10:35464633-35464634		6.82
N	mutually_exclusive	CUFF.316	chr15	-	chr15:44859791-44864880,chr15:44865019-44876011	chr15:44859791-44862722,chr15:44862857-44876011	chr15:44864881-44865018	chr15:44862723-44862856			58.33
K	jcn_only_AD	CUFF.920	chr6	+	chr6:32122172-32122363;chr6:32122182-32122363	chr6:32122024-32122363		chr6:32122024-32122171;chr6:32122172-32122181	chr6:32122023-32122024;chr6:32122171-32122172		9.77
K	intron_retention	CUFF.812	chr4	-	chr4:2934418-2934832				chr4:2934417-2934418;chr4:2934832-2934833		98.56
N	alternative_acceptor	CUFF.468	chr17	-	chr17:79220041-79220684	chr17:79220474-79220684		chr17:79220041-79220473	chr17:79220040-79220041		96.43
K	alternative_last_exon	CUFF.1016,CUFF.980	chr7	+	chr7:150831656-150835229,chr7:150831656-150837065,chr7:150831656-150838984;chr7:150831656-150834816	chr7:150831656-150833312	chr7:150834817-150835455	chr7:150833313-150833697			18.35
K	coord_cassette	CUFF.998	chr7	-	chr7:102228218-102232731	chr7:102228218-102228680;chr7:102228893-102230605;chr7:102230744-102232731		chr7:102228681-102228892;chr7:102230606-102230743			66.67
N	alternative_acceptor	CUFF.28	chr1	+	chr1:70820892-70832009;chr1:70820892-70832126	chr1:70820892-70831828		chr1:70831829-70832009;chr1:70832010-70832126	chr1:70832009-70832010;chr1:70832126-70832127		18.67
K	intron_retention	CUFF.532	chr19	+	chr19:18119587-18119779				chr19:18119586-18119587;chr19:18119779-18119780		9.43
K	intron_retention	CUFF.524	chr19	-	chr19:14876617-14877046				chr19:14876616-14876617;chr19:14877046-14877047		68.18
N	jcn_only_AA	CUFF.269	chr14	+	chr14:58899176-58906787;chr14:58899176-58909423	chr14:58899176-58899829		chr14:58899830-58906787;chr14:58906788-58909423	chr14:58906787-58906788;chr14:58909423-58909424		9.59
K	intron_retention		chr9	-	chr9:130941184-130941267				chr9:130941183-130941184;chr9:130941267-130941268		83.94
K	jcn_only_AD	CUFF.140,CUFF.184	chr11	-	chr11:2190926-2192926	chr11:2190926-2192914		chr11:2192915-2192926	chr11:2192926-2192927		25.00
N	mutually_exclusive	CUFF.259	chr14	+	chr14:24563644-24566100,chr14:24566347-24567411	chr14:24563644-24563974,chr14:24564055-24567411	chr14:24566101-24566346	chr14:24563975-24564054			27.66
N	jcn_only_AD	CUFF.1051	chr8	+	chr8:106456610-106573590	chr8:106541198-106573590		chr8:106456610-106541197	chr8:106456609-106456610		4.60
N	cassette	CUFF.904	chr5	-	chr5:178043950-178045556	chr5:178043950-178044344;chr5:178044436-178045556		chr5:178044345-178044435			54.84
N	alternative_acceptor	CUFF.1016,CUFF.994	chr7	+	chr7:150815432-150815591	chr7:150815432-150815560		chr7:150815561-150815591	chr7:150815591-150815592		8.92
K	alternative_donor	CUFF.954	chr6	+	chr6:161514872-161518111	chr6:161514884-161518111		chr6:161514872-161514883	chr6:161514871-161514872	chr6:161518112-161518208;chr6:161514805-161514871	83.87
K	alternative_acceptor	CUFF.278	chr14	-	chr14:75136830-75137464	chr14:75136846-75137464		chr14:75136830-75136845	chr14:75136829-75136830	chr14:75137465-75137574;chr14:75136650-75136829	16.92
N	cassette	CUFF.683	chr20	+	chr20:30115386-30132749	chr20:30115386-30125981;chr20:30126065-30132749		chr20:30125982-30126064		chr20:30115287-30115385;chr20:30132750-30132838	89.60
N	jcn_only_AD		chr7	-	chr7:117501371-117511643;chr7:117501371-117514054	chr7:117501371-117512157					35.00
K	cassette	CUFF.792	chr3	-	chr3:133894884-133901845	chr3:133894884-133896784;chr3:133896918-133901845		chr3:133896785-133896917			22.75
K	alternative_last_exon	CUFF.910	chr6	-	chr6:5240957-5260880;chr6:5109726-5260880	chr6:5216972-5260880	chr6:5102728-5109725	chr6:5216851-5216971			64.79
N	jcn_only_AD	CUFF.923	chr6	+	chr6:34452922-34494019;chr6:34482846-34494019	chr6:34434048-34494019		chr6:34434048-34452921;chr6:34452922-34482845	chr6:34434047-34434048;chr6:34452921-34452922		29.85
K	coord_cassette	CUFF.720	chr22	-	chr22:30738869-30748939	chr22:30738869-30740921;chr22:30741180-30742300;chr22:30742509-30748939		chr22:30740922-30741179;chr22:30742301-30742508			7.82
N	jcn_only_AA	CUFF.879	chr5	-	chr5:60224787-60240758	chr5:60227976-60240758		chr5:60224787-60227975	chr5:60224786-60224787		3.66
N	coord_cassette	CUFF.387	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			89.34
K	mutually_exclusive	CUFF.654	chr2	-	chr2:204326649-204341798,chr2:204341880-204354306	chr2:204326649-204334961,chr2:204335037-204354306	chr2:204341799-204341879	chr2:204334962-204335036			67.24
N	cassette	CUFF.818	chr4	-	chr4:6377659-6382723	chr4:6377659-6380133;chr4:6380300-6382723		chr4:6380134-6380299			94.51
N	cassette	CUFF.325	chr15	+	chr15:57543622-57545459	chr15:57543622-57544618;chr15:57544691-57545459		chr15:57544619-57544690			68.32
N	alternative_donor	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57515373;chr16:57513601-57521042;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;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		0.00
K	intron_retention	CUFF.564	chr19	+	chr19:52918293-52918376				chr19:52918292-52918293;chr19:52918376-52918377		16.67
N	jcn_only_AD	CUFF.936	chr6	+	chr6:90338943-90340151	chr6:90338958-90340151		chr6:90338943-90338957	chr6:90338942-90338943		39.83
K	mutually_exclusive	CUFF.1118	chrX	-	chrX:19935453-19941275,chrX:19941526-19947902	chrX:19935453-19936189,chrX:19936218-19947902	chrX:19941276-19941525	chrX:19936190-19936217			12.12
N	alternative_donor	CUFF.350	chr15	-	chr15:64658275-64665896	chr15:64658275-64665354		chr15:64665355-64665896	chr15:64665896-64665897		78.12
K	intron_retention	CUFF.812	chr4	-	chr4:2934486-2934832				chr4:2934485-2934486;chr4:2934832-2934833		65.64
K	intron_retention	CUFF.709	chr22	-	chr22:21842671-21846282				chr22:21842670-21842671;chr22:21846282-21846283		29.57
K	intron_retention	CUFF.1142	chrX	+	chrX:133594369-133607388				chrX:133594368-133594369;chrX:133607388-133607389		66.67
K	jcn_only_AD	CUFF.542	chr19	-	chr19:39924059-39924161;chr19:39924059-39924133	chr19:39924059-39924157		chr19:39924134-39924157;chr19:39924158-39924161	chr19:39924157-39924158;chr19:39924161-39924162		2.39
N	jcn_only_AD		chr1	+	chr1:167227155-167301706;chr1:167288294-167301706	chr1:167298544-167301706					12.00
N	intron_retention		chr22	+	chr22:21057981-21058106				chr22:21057980-21057981;chr22:21058106-21058107		94.19
K	cassette	CUFF.563	chr19	+	chr19:52264484-52271897	chr19:52264484-52266614;chr19:52266771-52271897		chr19:52266615-52266770			13.64
N	alternative_donor	CUFF.849	chr4	+	chr4:124571485-124573941	chr4:124571488-124573941		chr4:124571485-124571487	chr4:124571484-124571485		49.18
N	jcn_only_AD	CUFF.979	chr7	+	chr7:65579958-65592690;chr7:65591631-65592690	chr7:65579902-65592690		chr7:65579902-65579957;chr7:65579958-65591630	chr7:65579901-65579902;chr7:65579957-65579958		23.08
K	intron_retention	CUFF.1010	chr7	+	chr7:129028782-129028896				chr7:129028781-129028782;chr7:129028896-129028897		48.15
N	jcn_only_AD	CUFF.390	chr16	-	chr16:23505700-23507009;chr16:23505700-23507034	chr16:23505700-23507014		chr16:23507010-23507014;chr16:23507015-23507034	chr16:23507014-23507015;chr16:23507034-23507035	chr16:23505624-23505699;chr16:23507035-23507099	56.21
K	intron_retention		chr3	-	chr3:125741776-125745177				chr3:125741775-125741776;chr3:125745177-125745178		33.33
K	cassette	CUFF.1073	chr9	+	chr9:43885073-43890295	chr9:43885073-43887610;chr9:43887734-43890295		chr9:43887611-43887733			50.00
N	cassette	CUFF.648	chr2	-	chr2:177041421-177042438	chr2:177041421-177042059;chr2:177042223-177042438		chr2:177042060-177042222			89.21
N	jcn_only_AD	CUFF.230,CUFF.239	chr12	-	chr12:113618864-113623082	chr12:113618864-113621527		chr12:113621528-113623082	chr12:113623082-113623083		57.14
K	intron_retention	CUFF.232	chr12	+	chr12:58017882-58018282				chr12:58017881-58017882;chr12:58018282-58018283		14.67
N	jcn_only_AD	CUFF.734	chr3	+	chr3:19992554-20017092	chr3:20012210-20017092		chr3:19992554-20012209	chr3:19992553-19992554		34.48
K	jcn_only_AA	CUFF.49	chr1	-	chr1:153925112-153925280	chr1:153925127-153925280		chr1:153925112-153925126	chr1:153925111-153925112		26.32
N	alternative_donor	CUFF.340	chr15	+	chr15:77750839-77756581	chr15:77750901-77756581		chr15:77750839-77750900	chr15:77750838-77750839		3.09
N	jcn_only_AD	CUFF.289	chr14	-	chr14:92105595-92112480;chr14:92105595-92136157	chr14:92105595-92126180		chr14:92112481-92126180;chr14:92126181-92136157	chr14:92126180-92126181;chr14:92136157-92136158		6.45
K	intron_retention	CUFF.202	chr12	-	chr12:7090345-7090755				chr12:7090344-7090345;chr12:7090755-7090756		15.62
N	cassette	CUFF.333	chr15	-	chr15:66786891-66789979;chr15:66786891-66789827	chr15:66786891-66787240;chr15:66787758-66789979,chr15:66787758-66789827		chr15:66787241-66787757			84.09
K	alternative_acceptor	CUFF.1001	chr7	+	chr7:107234551-107236313	chr7:107234551-107236311		chr7:107236312-107236313	chr7:107236313-107236314		87.22
K	alternative_first_exon	CUFF.1118	chrX	-	chrX:19948059-19953926	chrX:19948059-19953475	chrX:19953927-19954016	chrX:19953476-19953759			79.35
N	alternative_donor	CUFF.984	chr7	+	chr7:75040010-75040690	chr7:75040118-75040690		chr7:75040010-75040117	chr7:75040009-75040010		82.86
K	alternative_first_exon	CUFF.114	chr10	-	chr10:73973090-73975534;chr10:73973090-73975539;chr10:73973090-73975964	chr10:73973090-73976578	chr10:73975540-73975867;chr10:73975965-73976126	chr10:73976579-73976962			25.95
N	alternative_acceptor	CUFF.919	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		6.60
K	intron_retention		chr12	-	chr12:7088742-7090165				chr12:7088741-7088742;chr12:7090165-7090166		2.55
N	intron_retention		chr11	-	chr11:10821157-10821636				chr11:10821156-10821157;chr11:10821636-10821637		85.37
N	jcn_only_AD	CUFF.847	chr4	-	chr4:83816001-83821229	chr4:83816001-83816844					28.30
K	cassette	CUFF.1086	chr9	+	chr9:105774380-105780606	chr9:105774380-105779169;chr9:105779244-105780606		chr9:105779170-105779243			26.67
K	cassette	CUFF.132	chr10	-	chr10:123659510-123670420	chr10:123659510-123661905;chr10:123662136-123670420		chr10:123661906-123662135			96.65
N	intron_retention		chr6	+	chr6:31937094-31937291				chr6:31937093-31937094;chr6:31937291-31937292		43.90
N	jcn_only_AA	CUFF.1101	chr9	-	chr9:131483810-131483929;chr9:131483782-131483929	chr9:131483760-131483929		chr9:131483760-131483781;chr9:131483782-131483809	chr9:131483759-131483760;chr9:131483781-131483782		5.49
N	cassette	CUFF.379	chr16	+	chr16:4526489-4556895	chr16:4526489-4555484;chr16:4555612-4556895		chr16:4555485-4555611			97.01
K	intron_retention	CUFF.728	chr22	-	chr22:51020787-51020986				chr22:51020786-51020787;chr22:51020986-51020987		83.52
K	intron_retention	CUFF.703	chr21	-	chr21:47565493-47565731				chr21:47565492-47565493;chr21:47565731-47565732		18.03
K	intron_retention	CUFF.1033	chr8	-	chr8:56668971-56675193				chr8:56668970-56668971;chr8:56675193-56675194		28.03
N	jcn_only_AA		chr11	+	chr11:118402587-118402960;chr11:118402587-118403124;chr11:118402587-118402811	chr11:118402587-118403004				chr11:118401663-118402586	17.33
N	jcn_only_AD	CUFF.457	chr17	+	chr17:61554705-61555291	chr17:61555152-61555291		chr17:61554705-61555151	chr17:61554704-61554705		19.66
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		0.00
K	cassette	CUFF.988	chr7	-	chr7:86539318-86541387	chr7:86539318-86540937;chr7:86541012-86541387		chr7:86540938-86541011			9.09
N	jcn_only_AA		chr3	-	chr3:124996654-125042231	chr3:125032501-125042231					11.76
N	jcn_only_AD	CUFF.310	chr15	+	chr15:40558697-40564424	chr15:40559199-40564424		chr15:40558697-40559198	chr15:40558696-40558697		25.00
N	cassette	CUFF.350	chr15	-	chr15:84871760-84873177;chr15:84871773-84873177	chr15:84871773-84872928,chr15:84871760-84872928;chr15:84873084-84873177		chr15:84872929-84873083			54.37
N	jcn_only_AD	CUFF.333	chr15	-	chr15:66787758-66789979	chr15:66787758-66789827		chr15:66789828-66789979	chr15:66789979-66789980		6.64
K	intron_retention	CUFF.765	chr3	-	chr3:107572807-107573976				chr3:107572806-107572807;chr3:107573976-107573977		90.79
K	jcn_only_AD	CUFF.1080	chr9	-	chr9:86485548-86498727	chr9:86485548-86495211					40.00
N	alternative_donor	CUFF.271	chr14	-	chr14:59946070-59950397;chr14:59946070-59950207	chr14:59946070-59950526		chr14:59950208-59950397;chr14:59950398-59950526	chr14:59950397-59950398;chr14:59950526-59950527		67.80
K	alternative_first_exon	CUFF.980	chr7	+	chr7:73098331-73100965,chr7:73098254-73100965;chr7:73097714-73100965	chr7:73098135-73100965,chr7:73098232-73100965	chr7:73097261-73097713	chr7:73098097-73098134			70.51
K	alternative_first_exon	CUFF.687	chr20	+	chr20:33567608-33568380	chr20:33568283-33568380	chr20:33567464-33567607	chr20:33567805-33568282			62.50
N	cassette	CUFF.377	chr16	-	chr16:4407261-4408367	chr16:4407261-4407968;chr16:4408105-4408367		chr16:4407969-4408104			86.96
N	cassette	CUFF.593	chr2	+	chr2:27721665-27722263	chr2:27721665-27722008;chr2:27722076-27722263		chr2:27722009-27722075			78.00
N	jcn_only_AA	CUFF.1073,CUFF.1096	chr9	+	chr9:43853617-43861002;chr9:43853617-43861005	chr9:43853617-43854068		chr9:43854069-43861002;chr9:43861003-43861005	chr9:43861002-43861003;chr9:43861005-43861006		64.71
N	jcn_only_AA	CUFF.1001	chr7	+	chr7:107236448-107240841	chr7:107236448-107240676		chr7:107240677-107240841	chr7:107240841-107240842		5.30
K	intron_retention	CUFF.285	chr14	+	chr14:77935329-77935419				chr14:77935328-77935329;chr14:77935419-77935420		61.54
N	alternative_donor	CUFF.852	chr4	-	chr4:152065203-152069073	chr4:152065203-152065371		chr4:152065372-152069073	chr4:152069073-152069074		6.90
K	alternative_acceptor	CUFF.626,CUFF.666	chr2	+	chr2:232258622-232259491	chr2:232258622-232259365		chr2:232259366-232259491	chr2:232259491-232259492		52.83
K	alternative_last_exon	CUFF.611	chr2	-	chr2:73280681-73285656,chr2:73269715-73285656,chr2:73268791-73285656;chr2:73268061-73285656	chr2:73277029-73285656	chr2:73267983-73268060	chr2:73276133-73277028			54.30
N	alternative_first_exon		chr20	-	chr20:3171466-3172410	chr20:3171466-3171835	chr20:3172411-3172467	chr20:3171836-3172230			99.36
K	cassette	CUFF.1032	chr8	-	chr8:38001905-38003480	chr8:38001905-38002739;chr8:38002834-38003480		chr8:38002740-38002833			84.31
K	cassette	CUFF.354	chr15	+	chr15:91298169-91303823	chr15:91298169-91303210;chr15:91303510-91303823		chr15:91303211-91303509			86.36
K	alternative_donor	CUFF.1014	chr7	+	chr7:148982588-148984655	chr7:148982788-148984655		chr7:148982588-148982787	chr7:148982587-148982588		22.00
N	cassette	CUFF.17	chr1	+	chr1:31769923-31791955	chr1:31769923-31782890;chr1:31783012-31791955		chr1:31782891-31783011			89.09
K	cassette	CUFF.423	chr17	+	chr17:6348725-6350782	chr17:6348725-6349414;chr17:6349508-6350782		chr17:6349415-6349507			1.02
K	alternative_first_exon	CUFF.386	chr16	+	chr16:21712349-21716489,chr16:21712391-21716489	chr16:21716359-21716489	chr16:21712209-21712348	chr16:21716216-21716358			62.75
N	jcn_only_AA		chr1	+	chr1:78546545-78560635	chr1:78546545-78558440		chr1:78558441-78560635	chr1:78560635-78560636		84.62
K	alternative_last_exon	CUFF.864,CUFF.869	chr5	+	chr5:40980012-40981493	chr5:40980012-40980088	chr5:40981494-40983041	chr5:40980089-40980538			66.67
K	alternative_donor	CUFF.44,CUFF.49	chr1	-	chr1:145926413-145927113	chr1:145926413-145927048		chr1:145927049-145927113	chr1:145927113-145927114		28.57
K	intron_retention		chr22	+	chr22:20755049-20755566				chr22:20755048-20755049;chr22:20755566-20755567		5.88
N	jcn_only_AD	CUFF.1125,CUFF.1137	chrX	-	chrX:53569501-53570846	chrX:53569501-53570801		chrX:53570802-53570846	chrX:53570846-53570847		9.18
N	jcn_only_AD		chr16	-	chr16:70255305-70256273	chr16:70255305-70256269		chr16:70256270-70256273	chr16:70256273-70256274		70.00
N	coord_cassette	CUFF.984	chr7	+	chr7:75040010-75044162	chr7:75040010-75040937;chr7:75041043-75042066;chr7:75042211-75044162		chr7:75040938-75041042;chr7:75042067-75042210			30.00
K	intron_retention	CUFF.716	chr22	+	chr22:29695322-29695588				chr22:29695321-29695322;chr22:29695588-29695589		5.04
N	intron_retention		chr14	-	chr14:104202540-104205015				chr14:104202539-104202540;chr14:104205015-104205016		77.42
K	intron_retention	CUFF.1018	chr7	-	chr7:156555871-156556362				chr7:156555870-156555871;chr7:156556362-156556363		3.68
N	jcn_only_AA	CUFF.737	chr3	-	chr3:27297863-27326092	chr3:27320465-27326092		chr3:27297863-27320464	chr3:27297862-27297863		1.80
K	jcn_only_AA	CUFF.576	chr2	-	chr2:675631-677288	chr2:676239-677288		chr2:675631-676238	chr2:675630-675631		5.49
K	alternative_first_exon	CUFF.884	chr5	-	chr5:82969369-82971106;chr5:82969369-82969951;chr5:82969369-82978143;chr5:82969369-83016607	chr5:82969369-82970344	chr5:82969952-82970139;chr5:82978144-82978427;chr5:83016608-83017432	chr5:82970345-82970701			54.72
K	intron_retention	CUFF.450	chr17	+	chr17:46990328-46993437				chr17:46990327-46990328;chr17:46993437-46993438		30.30
K	coord_cassette	CUFF.797	chr3	-	chr3:165504100-165555101	chr3:165504100-165545773;chr3:165545858-165547304;chr3:165548830-165555101		chr3:165545774-165545857;chr3:165547305-165548829			5.31
N	jcn_only_AA	CUFF.519	chr19	+	chr19:11468416-11470282;chr19:11468416-11470207	chr19:11468416-11470146		chr19:11470147-11470207;chr19:11470208-11470282	chr19:11470207-11470208;chr19:11470282-11470283		4.69
K	coord_cassette	CUFF.195	chr12	-	chr12:347177-369016	chr12:347177-351779;chr12:351921-352844;chr12:352980-369016		chr12:351780-351920;chr12:352845-352979			74.55
K	alternative_donor	CUFF.953	chr6	-	chr6:151754366-151757580	chr6:151754366-151757554		chr6:151757555-151757580	chr6:151757580-151757581		46.43
N	mutually_exclusive	CUFF.178	chr11	+	chr11:107904638-107920616,chr11:107920794-107923386	chr11:107904638-107916996,chr11:107917097-107923386	chr11:107920617-107920793	chr11:107916997-107917096			31.34
K	coord_cassette	CUFF.133	chr10	+	chr10:124157491-124172435	chr10:124157491-124159858;chr10:124159905-124166091;chr10:124166190-124172435		chr10:124159859-124159904;chr10:124166092-124166189			91.02
K	intron_retention	CUFF.671	chr2	-	chr2:242438590-242438671				chr2:242438589-242438590;chr2:242438671-242438672		3.12
K	intron_retention	CUFF.769	chr3	+	chr3:119205780-119207775				chr3:119205779-119205780;chr3:119207775-119207776		41.67
K	cassette	CUFF.239	chr12	-	chr12:113601080-113603448	chr12:113601080-113601871;chr12:113602091-113603448		chr12:113601872-113602090			27.12
N	jcn_only_AD	CUFF.352	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		12.54
N	jcn_only_AD	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;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;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		6.79
K	alternative_last_exon	CUFF.460,CUFF.464	chr17	+	chr17:66526143-66547224	chr17:66526143-66526417	chr17:66547225-66547549	chr17:66526418-66529653			76.06
N	jcn_only_AA		chr6	+	chr6:31927178-31928817	chr6:31927178-31927786					94.55
N	alternative_acceptor	CUFF.325,CUFF.354	chr15	+	chr15:57211105-57212099	chr15:57211105-57212089		chr15:57212090-57212099	chr15:57212099-57212100		92.00
N	alternative_donor		chr6	-	chr6:43483929-43484464	chr6:43483929-43484233		chr6:43484234-43484464	chr6:43484464-43484465		82.61
N	alternative_donor		chr18	+	chr18:55833094-55895061;chr18:55862966-55895061	chr18:55888990-55895061		chr18:55833094-55862965;chr18:55862966-55888989	chr18:55833093-55833094;chr18:55862965-55862966		0.00
N	alternative_acceptor	CUFF.390	chr16	-	chr16:23504843-23505623;chr16:23504780-23505623	chr16:23504909-23505623		chr16:23504780-23504842;chr16:23504843-23504908	chr16:23504779-23504780;chr16:23504842-23504843	chr16:23505624-23505699;chr16:23504681-23504779	57.57
N	jcn_only_AA	CUFF.106	chr10	-	chr10:46113709-46143741;chr10:46135870-46143741	chr10:46135412-46143741					75.00
N	jcn_only_AA	CUFF.187	chr11	+	chr11:119056338-119056630	chr11:119056338-119056557		chr11:119056558-119056630	chr11:119056630-119056631		43.75
N	jcn_only_AA	CUFF.802	chr3	+	chr3:186790736-186791946	chr3:186790736-186791192		chr3:186791193-186791946	chr3:186791946-186791947		3.61
K	alternative_first_exon	CUFF.664	chr2	+	chr2:228160033-228162389	chr2:228161243-228162389	chr2:228159985-228160032	chr2:228160919-228161242			95.45
N	jcn_only_AA	CUFF.352	chr15	-	chr15:90414779-90431752;chr15:90421533-90431752	chr15:90420657-90431752		chr15:90414779-90420656;chr15:90420657-90421532	chr15:90414778-90414779;chr15:90420656-90420657		32.02
K	cassette	CUFF.468	chr17	-	chr17:79244825-79249768	chr17:79244825-79246315;chr17:79246428-79249768		chr17:79246316-79246427		chr17:79244718-79244824;chr17:79249769-79249951	51.85
N	alternative_donor	CUFF.683	chr20	+	chr20:30132839-30136831	chr20:30136597-30136831		chr20:30132839-30136596	chr20:30132838-30132839	chr20:30136832-30136917;chr20:30132750-30132838	2.58
N	jcn_only_AD		chr17	+	chr17:61905570-61907211	chr17:61906924-61907211					93.08
K	cassette	CUFF.897	chr5	-	chr5:141034003-141035187	chr5:141034003-141034928;chr5:141034968-141035187		chr5:141034929-141034967			95.24
N	jcn_only_AA	CUFF.497	chr18	-	chr18:67563282-67623990;chr18:67614670-67623990	chr18:67614769-67623990		chr18:67563282-67614669;chr18:67614670-67614768	chr18:67563281-67563282;chr18:67614669-67614670		63.64
K	intron_retention	CUFF.149	chr11	-	chr11:6638385-6638531				chr11:6638384-6638385;chr11:6638531-6638532		72.56
N	alternative_donor	CUFF.716	chr22	+	chr22:29695271-29695588	chr22:29695322-29695588		chr22:29695271-29695321	chr22:29695270-29695271		73.75
N	jcn_only_AA	CUFF.278	chr14	-	chr14:75138187-75139533	chr14:75138724-75139533		chr14:75138187-75138723	chr14:75138186-75138187	chr14:75139534-75139655;chr14:75138111-75138186	23.26
N	cassette	CUFF.379	chr16	+	chr16:4526489-4555484	chr16:4526489-4533637;chr16:4533756-4555484		chr16:4533638-4533755			95.00
N	cassette	CUFF.316	chr15	-	chr15:44862857-44876011	chr15:44862857-44864880;chr15:44865019-44876011		chr15:44864881-44865018			55.88
K	intron_retention	CUFF.961	chr7	+	chr7:6639524-6639757				chr7:6639523-6639524;chr7:6639757-6639758		88.14
N	jcn_only_AD		chr17	+	chr17:61904875-61905497	chr17:61905284-61905497					39.67
N	alternative_donor	CUFF.639	chr2	+	chr2:160585687-160599571	chr2:160590594-160599571		chr2:160585687-160590593	chr2:160585686-160585687		0.00
N	alternative_donor	CUFF.974	chr7	-	chr7:38869929-38902144	chr7:38869929-38870815		chr7:38870816-38902144	chr7:38902144-38902145		0.00
N	alternative_donor	CUFF.743	chr3	-	chr3:33592888-33600798	chr3:33592888-33600616		chr3:33600617-33600798	chr3:33600798-33600799		4.55
K	alternative_acceptor	CUFF.138	chr11	+	chr11:826267-828259	chr11:826267-828229		chr11:828230-828259	chr11:828259-828260	chr11:826050-826266;chr11:828260-828772	36.47
K	alternative_acceptor	CUFF.806	chr3	-	chr3:194063432-194071970	chr3:194063435-194071970		chr3:194063432-194063434	chr3:194063431-194063432		28.57
N	jcn_only_AA	CUFF.640	chr2	-	chr2:166732743-166737188	chr2:166736478-166737188		chr2:166732743-166736477	chr2:166732742-166732743		41.67
N	intron_retention		chrX	-	chrX:46382561-46387769				chrX:46382560-46382561;chrX:46387769-46387770		65.52
K	cassette	CUFF.812	chr4	-	chr4:2933193-2933551	chr4:2933193-2933281;chr4:2933391-2933551		chr4:2933282-2933390			50.31
N	jcn_only_AA	CUFF.780	chr3	-	chr3:125032501-125042152	chr3:125033898-125042152		chr3:125032501-125033897	chr3:125032500-125032501		2.59
N	alternative_donor		chr7	-	chr7:36901342-36934613	chr7:36901342-36909997		chr7:36909998-36934613	chr7:36934613-36934614		5.88
K	intron_retention	CUFF.1112	chrX	-	chrX:2405744-2406828				chrX:2405743-2405744;chrX:2406828-2406829		78.12
N	cassette	CUFF.269	chr14	+	chr14:58925264-58927703	chr14:58925264-58926560;chr14:58926789-58927703		chr14:58926561-58926788			46.67
N	intron_retention		chr2	-	chr2:177042550-177042730				chr2:177042549-177042550;chr2:177042730-177042731		78.26
K	intron_retention		chr11	+	chr11:63999437-63999865				chr11:63999436-63999437;chr11:63999865-63999866		8.97
N	jcn_only_AD	CUFF.498	chr18	-	chr18:72914296-72920374;chr18:72914296-72920315	chr18:72914296-72917147		chr18:72917148-72920315;chr18:72920316-72920374	chr18:72920315-72920316;chr18:72920374-72920375		5.83
K	intron_retention	CUFF.894	chr5	+	chr5:139865318-139866542				chr5:139865317-139865318;chr5:139866542-139866543	chr5:139865174-139865317;chr5:139866543-139866645	60.87
K	alternative_first_exon	CUFF.15	chr1	+	chr1:28655636-28657107,chr1:28655692-28657107	chr1:28656887-28657107	chr1:28655423-28655635	chr1:28656776-28656886			24.68
N	alternative_acceptor	CUFF.579,CUFF.665	chr2	+	chr2:3464108-3466628;chr2:3464108-3469367	chr2:3464108-3464417		chr2:3464418-3466628;chr2:3466629-3469367	chr2:3466628-3466629;chr2:3469367-3469368		0.88
K	alternative_last_exon	CUFF.838	chr4	-	chr4:77979789-77996624	chr4:77987559-77996624	chr4:77979613-77979788	chr4:77987229-77987558			64.75
N	alternative_acceptor		chr16	+	chr16:3115828-3117443	chr16:3115828-3117377		chr16:3117378-3117443	chr16:3117443-3117444		96.50
K	intron_retention	CUFF.144	chr11	-	chr11:2905365-2905899				chr11:2905364-2905365;chr11:2905899-2905900		9.57
K	intron_retention	CUFF.589	chr2	-	chr2:27688750-27693794				chr2:27688749-27688750;chr2:27693794-27693795		83.33
K	alternative_first_exon	CUFF.425,CUFF.451	chr17	-	chr17:15492542-15499827	chr17:15492542-15496650	chr17:15499828-15499976	chr17:15496651-15496809			56.41
K	jcn_only_AA	CUFF.1097	chr9	-	chr9:125616861-125617462	chr9:125616895-125617462		chr9:125616861-125616894	chr9:125616860-125616861		62.22
N	intron_retention		chr16	-	chr16:57513598-57513756				chr16:57513597-57513598;chr16:57513756-57513757		83.87
K	jcn_only_AD	CUFF.20,CUFF.9	chr1	-	chr1:16909254-16918341	chr1:16909254-16910088					33.33
N	cassette	CUFF.423	chr17	+	chr17:6352728-6353681	chr17:6352728-6353347;chr17:6353393-6353681		chr17:6353348-6353392			94.44
K	alternative_first_exon	CUFF.884	chr5	-	chr5:82969369-82971106;chr5:82969369-82970344;chr5:82969369-82969951;chr5:82969369-83016607	chr5:82969369-82978143	chr5:82970345-82970701;chr5:82969952-82970139;chr5:83016608-83017432	chr5:82978144-82978427			20.75
K	cassette	CUFF.163	chr11	+	chr11:63998413-63999342	chr11:63998413-63998503;chr11:63998620-63999342		chr11:63998504-63998619			42.77
K	alternative_last_exon	CUFF.1123	chrX	-	chrX:46382561-46387784;chrX:46360768-46387784	chrX:46384874-46387784	chrX:46357085-46360767	chrX:46384734-46384873			20.00
N	alternative_acceptor	CUFF.880	chr5	-	chr5:64907709-64909924	chr5:64909683-64909924		chr5:64907709-64909682	chr5:64907708-64907709		1.30
N	jcn_only_AD		chr17	+	chr17:29706042-29708890;chr17:29707246-29708890	chr17:29706376-29708890					67.09
K	jcn_only_AA	CUFF.920	chr6	+	chr6:32122961-32123544	chr6:32122961-32123464		chr6:32123465-32123544	chr6:32123544-32123545		55.47
K	intron_retention	CUFF.951	chr6	+	chr6:145157678-145160308				chr6:145157677-145157678;chr6:145160308-145160309		41.84
K	cassette	CUFF.258	chr14	+	chr14:24459569-24473545	chr14:24459569-24470592;chr14:24470727-24473545		chr14:24470593-24470726			78.46
N	alternative_first_exon	CUFF.693	chr21	+	chr21:15646479-15659870	chr21:15651979-15659870	chr21:15646075-15646478	chr21:15651917-15651978		chr21:15659871-15660018	81.82
K	intron_retention	CUFF.647	chr2	-	chr2:175666541-175673632				chr2:175666540-175666541;chr2:175673632-175673633		13.08
N	intron_retention		chr6	+	chr6:33243435-33243573				chr6:33243434-33243435;chr6:33243573-33243574		56.52
N	jcn_only_AA	CUFF.182	chr11	+	chr11:118405071-118416833;chr11:118405071-118405221	chr11:118405071-118406222		chr11:118405222-118406222;chr11:118406223-118416833	chr11:118406222-118406223;chr11:118416833-118416834	chr11:118404981-118405070	3.11
K	cassette	CUFF.569	chr19	-	chr19:56307617-56312937	chr19:56307617-56309594;chr19:56309671-56312937		chr19:56309595-56309670			16.92
K	intron_retention		chr12	+	chr12:53861078-53861588				chr12:53861077-53861078;chr12:53861588-53861589		18.18
K	cassette	CUFF.1069	chr9	+	chr9:34989829-34993196	chr9:34989829-34990664;chr9:34990810-34993196		chr9:34990665-34990809			23.81
N	jcn_only_AA	CUFF.763	chr3	-	chr3:93646252-93692517	chr3:93647642-93692517		chr3:93646252-93647641	chr3:93646251-93646252		85.71
N	jcn_only_AA		chr8	+	chr8:7123432-7131717	chr8:7123432-7124095		chr8:7124096-7131717	chr8:7131717-7131718	chr8:7123323-7123431	72.73
N	jcn_only_AD	CUFF.389	chr16	+	chr16:22466187-22470675	chr16:22466927-22470675		chr16:22466187-22466926	chr16:22466186-22466187		6.06
N	jcn_only_AD	CUFF.201	chr12	+	chr12:4662256-4668022;chr12:4665717-4668022	chr12:4665669-4668022		chr12:4662256-4665668;chr12:4665669-4665716	chr12:4662255-4662256;chr12:4665668-4665669		40.44
N	cassette	CUFF.475	chr17	-	chr17:79994890-79995506	chr17:79994890-79995325;chr17:79995424-79995506		chr17:79995326-79995423			89.76
K	intron_retention	CUFF.944	chr6	+	chr6:126319831-126320602				chr6:126319830-126319831;chr6:126320602-126320603		3.33
N	alternative_acceptor	CUFF.754	chr3	-	chr3:49462487-49462799	chr3:49462580-49462799		chr3:49462487-49462579	chr3:49462486-49462487		27.91
K	cassette	CUFF.567	chr19	+	chr19:55087577-55098667	chr19:55087577-55098476;chr19:55098528-55098667		chr19:55098477-55098527			17.06
K	alternative_donor	CUFF.703	chr21	-	chr21:47556409-47556898;chr21:47556409-47556828	chr21:47556409-47556892		chr21:47556829-47556892;chr21:47556893-47556898	chr21:47556892-47556893;chr21:47556898-47556899		10.00
N	alternative_acceptor	CUFF.292	chr14	+	chr14:92922953-92949023	chr14:92922953-92923597		chr14:92923598-92949023	chr14:92949023-92949024		2.38
K	intron_retention	CUFF.1115	chrX	-	chrX:13791150-13794356				chrX:13791149-13791150;chrX:13794356-13794357		17.39
N	jcn_only_AD		chr15	+	chr15:24813330-24814929;chr15:24811948-24814929	chr15:24813711-24814929					33.33
K	cassette	CUFF.920	chr6	+	chr6:32122555-32123544;chr6:32122555-32123464	chr6:32122555-32122806;chr6:32122961-32123544,chr6:32122961-32123464		chr6:32122807-32122960			41.20
N	jcn_only_AD	CUFF.377	chr16	-	chr16:57509132-57509761	chr16:57509132-57509417					95.86
K	alternative_last_exon	CUFF.492	chr18	-	chr18:61064487-61067280	chr18:61066557-61067280	chr18:61063528-61064486	chr18:61066414-61066556		chr18:61067281-61067429	73.00
N	jcn_only_AD	CUFF.374	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		17.14
N	cassette	CUFF.63	chr1	-	chr1:169696667-169698326;chr1:169697069-169698326	chr1:169696667-169697198,chr1:169697069-169697198;chr1:169697388-169698326		chr1:169697199-169697387			58.06
K	jcn_only_AA	CUFF.29,CUFF.73	chr1	+	chr1:207277776-207286345	chr1:207277776-207286243		chr1:207286244-207286345	chr1:207286345-207286346		35.19
K	intron_retention	CUFF.394	chr16	+	chr16:31371785-31372383				chr16:31371784-31371785;chr16:31372383-31372384		37.50
K	alternative_first_exon	CUFF.818	chr4	-	chr4:6382822-6473290,chr4:6382822-6473886,chr4:6382822-6525169,chr4:6382822-6536997;chr4:6382822-6415629	chr4:6382822-6383503	chr4:6415630-6415758	chr4:6383504-6386011			32.58
K	alternative_acceptor	CUFF.619	chr2	-	chr2:86831602-86839281	chr2:86832542-86839281		chr2:86831602-86832541	chr2:86831601-86831602		63.49
K	jcn_only_AA	CUFF.654	chr2	-	chr2:204306137-204309590	chr2:204306804-204309590		chr2:204306137-204306803	chr2:204306136-204306137		88.36
N	jcn_only_AD	CUFF.306	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		5.13
N	alternative_acceptor	CUFF.566	chr19	+	chr19:54657578-54658995;chr19:54657578-54659046	chr19:54657578-54657680		chr19:54657681-54658995;chr19:54658996-54659046	chr19:54658995-54658996;chr19:54659046-54659047		72.16
K	jcn_only_AA	CUFF.1098	chr9	-	chr9:130943079-130947825	chr9:130943094-130947825		chr9:130943079-130943093	chr9:130943078-130943079		80.28
K	jcn_only_AA	CUFF.557	chr19	+	chr19:50308834-50308981	chr19:50308834-50308917		chr19:50308918-50308981	chr19:50308981-50308982		95.76
K	alternative_last_exon	CUFF.894	chr5	+	chr5:139909382-139916973	chr5:139909382-139914946	chr5:139916974-139917174	chr5:139914947-139915571		chr5:139907769-139909381	82.29
N	cassette	CUFF.743	chr3	-	chr3:33543261-33557514	chr3:33543261-33552049;chr3:33552257-33557514		chr3:33552050-33552256			90.82
K	cassette	CUFF.879	chr5	-	chr5:60217983-60224690	chr5:60217983-60220117;chr5:60220336-60224690		chr5:60220118-60220335			54.24
K	alternative_first_exon	CUFF.12	chr1	-	chr1:26212361-26227981	chr1:26212361-26219004	chr1:26227982-26228173	chr1:26219005-26219098			38.46
N	alternative_acceptor		chr2	-	chr2:61761039-61765626	chr2:61764723-61765626		chr2:61761039-61764722	chr2:61761038-61761039		87.88
K	cassette	CUFF.18	chr1	+	chr1:32541424-32542363	chr1:32541424-32542164;chr1:32542248-32542363		chr1:32542165-32542247			45.76
N	jcn_only_AD	CUFF.292	chr14	+	chr14:92915504-92920243;chr14:92918991-92920243	chr14:92915561-92920243		chr14:92915504-92915560;chr14:92915561-92918990	chr14:92915503-92915504;chr14:92915560-92915561		60.87
N	alternative_first_exon	CUFF.703	chr21	-	chr21:47558838-47565330	chr21:47558838-47562022	chr21:47565331-47565492	chr21:47562023-47562690			7.25
K	jcn_only_AA	CUFF.665	chr2	+	chr2:231934883-231937046	chr2:231934883-231936902		chr2:231936903-231937046	chr2:231937046-231937047		10.58
K	alternative_first_exon	CUFF.6	chr1	-	chr1:11710892-11713447;chr1:11710892-11714375	chr1:11710892-11715696	chr1:11713448-11713601;chr1:11714376-11714739	chr1:11715697-11715916			23.81
N	jcn_only_AD	CUFF.276	chr14	-	chr14:71227900-71232158;chr14:71227900-71267383	chr14:71227900-71249939		chr14:71232159-71249939;chr14:71249940-71267383	chr14:71249939-71249940;chr14:71267383-71267384		3.37
K	alternative_acceptor	CUFF.860	chr5	-	chr5:471939-472793	chr5:472081-472793		chr5:471939-472080	chr5:471938-471939		73.81
N	mutually_exclusive	CUFF.132	chr10	-	chr10:123670667-123681863,chr10:123681927-123683780	chr10:123670667-123673304,chr10:123673409-123683780	chr10:123681864-123681926	chr10:123673305-123673408			5.56
K	intron_retention	CUFF.475	chr17	-	chr17:79994185-79994259				chr17:79994184-79994185;chr17:79994259-79994260		12.33
N	alternative_donor	CUFF.29	chr1	+	chr1:78445304-78546358	chr1:78512019-78546358		chr1:78445304-78512018	chr1:78445303-78445304		0.00
K	intron_retention	CUFF.532	chr19	+	chr19:18120504-18120591				chr19:18120503-18120504;chr19:18120591-18120592		9.52
K	intron_retention	CUFF.687	chr20	+	chr20:33589889-33589979				chr20:33589888-33589889;chr20:33589979-33589980		56.25
N	jcn_only_AD		chr14	+	chr14:76201633-76211437	chr14:76203951-76211437					37.04
K	cassette	CUFF.1098	chr9	-	chr9:130931799-130932298	chr9:130931799-130931901;chr9:130931980-130932298		chr9:130931902-130931979			17.23
N	jcn_only_AA	CUFF.874	chr5	+	chr5:52161652-52177704	chr5:52161652-52162871		chr5:52162872-52177704	chr5:52177704-52177705		37.93
N	jcn_only_AA	CUFF.576	chr2	-	chr2:675631-676573	chr2:676239-676573		chr2:675631-676238	chr2:675630-675631		78.79
N	alternative_acceptor	CUFF.497	chr18	-	chr18:67614769-67623990;chr18:67563282-67623990	chr18:67614670-67623990		chr18:67563282-67614669;chr18:67614670-67614768	chr18:67563281-67563282;chr18:67614669-67614670		0.00
K	cassette	CUFF.894	chr5	+	chr5:139886563-139889221	chr5:139886563-139887369;chr5:139887584-139889221		chr5:139887370-139887583		chr5:139886420-139886562;chr5:139889222-139889397	67.86
K	intron_retention	CUFF.171	chr11	-	chr11:75522582-75524647				chr11:75522581-75522582;chr11:75524647-75524648		41.89
N	jcn_only_AD	CUFF.551	chr19	+	chr19:45261671-45261980	chr19:45261731-45261980		chr19:45261671-45261730	chr19:45261670-45261671		6.56
N	alternative_donor		chr6	-	chr6:31938925-31939705	chr6:31938925-31939096		chr6:31939097-31939705	chr6:31939705-31939706		93.75
K	cassette	CUFF.1089	chr9	+	chr9:116769720-116770756	chr9:116769720-116770623;chr9:116770660-116770756		chr9:116770624-116770659			83.05
N	jcn_only_AA		chr14	-	chr14:71227900-71249939	chr14:71232205-71249939		chr14:71227900-71232204	chr14:71227899-71227900		93.75
K	alternative_acceptor	CUFF.252	chr13	-	chr13:78470694-78473993	chr13:78472470-78473993		chr13:78470694-78472469	chr13:78470693-78470694		83.87
N	intron_retention		chr19	-	chr19:49311494-49314240				chr19:49311493-49311494;chr19:49314240-49314241		45.71
N	jcn_only_AD		chr17	-	chr17:1616350-1617149	chr17:1616350-1616996		chr17:1616997-1617149	chr17:1617149-1617150		69.68
K	alternative_last_exon	CUFF.700	chr21	-	chr21:40977930-40981509;chr21:40969917-40981509	chr21:40978275-40981509	chr21:40968976-40969916	chr21:40977430-40978274			87.22
N	cassette	CUFF.887	chr5	-	chr5:127396937-127418661;chr5:127396937-127418426	chr5:127396937-127398061;chr5:127398193-127418661,chr5:127398193-127418426		chr5:127398062-127398192			25.81
K	cassette	CUFF.1118	chrX	-	chrX:19935453-19947902	chrX:19935453-19936189;chrX:19936218-19947902		chrX:19936190-19936217			5.56
N	alternative_acceptor	CUFF.581	chr2	-	chr2:4020665-4021134;chr2:4009394-4021134;chr2:4015879-4021134;chr2:4009485-4021134	chr2:4020693-4021134		chr2:4009394-4009484;chr2:4009485-4015878;chr2:4015879-4020664;chr2:4020665-4020692	chr2:4009393-4009394;chr2:4009484-4009485;chr2:4015878-4015879;chr2:4020664-4020665		3.23
N	jcn_only_AD		chr3	-	chr3:49343322-49365118	chr3:49343322-49348052					82.09
K	intron_retention	CUFF.21	chr1	-	chr1:41486451-41486535				chr1:41486450-41486451;chr1:41486535-41486536		37.93
N	jcn_only_AD	CUFF.1070	chr9	-	chr9:35077397-35078601	chr9:35077397-35078137		chr9:35078138-35078601	chr9:35078601-35078602		50.00
N	jcn_only_AA	CUFF.450	chr17	+	chr17:61561903-61562596	chr17:61561903-61562330		chr17:61562331-61562596	chr17:61562596-61562597		57.45
N	alternative_donor	CUFF.547,CUFF.560	chr19	-	chr19:41944320-41946385;chr19:41944320-41945786	chr19:41944320-41945378		chr19:41945379-41945786;chr19:41945787-41946385	chr19:41945786-41945787;chr19:41946385-41946386		32.34
K	coord_cassette	CUFF.208	chr12	+	chr12:21229504-21294447	chr12:21229504-21279041;chr12:21279192-21284056;chr12:21284171-21294447		chr12:21279042-21279191;chr12:21284057-21284170		chr12:21229386-21229503;chr12:21294448-21294592	95.56
N	alternative_donor	CUFF.1115,CUFF.1135	chrX	-	chrX:13825889-13834962	chrX:13825889-13830989		chrX:13830990-13834962	chrX:13834962-13834963		2.22
N	jcn_only_AA	CUFF.1051	chr8	+	chr8:106456610-106573590	chr8:106456610-106463785		chr8:106463786-106573590	chr8:106573590-106573591		23.85
N	cassette	CUFF.201	chr12	+	chr12:4654479-4655474;chr12:4653071-4655474	chr12:4654479-4654947,chr12:4653071-4654947;chr12:4654999-4655474		chr12:4654948-4654998			20.00
N	jcn_only_AD	CUFF.140	chr11	-	chr11:406060-406348	chr11:406060-406141		chr11:406142-406348	chr11:406348-406349		12.00
K	jcn_only_AA	CUFF.999	chr7	-	chr7:102462651-102553532	chr7:102524760-102553532					91.79
N	alternative_acceptor	CUFF.919	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		37.50
K	alternative_acceptor	CUFF.842	chr4	-	chr4:83536173-83542364	chr4:83536235-83542364		chr4:83536173-83536234	chr4:83536172-83536173		28.57
K	intron_retention	CUFF.522	chr19	+	chr19:12918144-12918232				chr19:12918143-12918144;chr19:12918232-12918233		22.86
K	intron_retention	CUFF.929	chr6	-	chr6:43480939-43481096				chr6:43480938-43480939;chr6:43481096-43481097		69.18
K	intron_retention	CUFF.728	chr22	-	chr22:51013030-51014463				chr22:51013029-51013030;chr22:51014463-51014464		9.92
N	cassette	CUFF.490	chr18	+	chr18:56001125-56016768	chr18:56001125-56010137;chr18:56010336-56016768		chr18:56010138-56010335			84.38
K	intron_retention	CUFF.285	chr14	+	chr14:77934528-77935419				chr14:77934527-77934528;chr14:77935419-77935420		19.49
N	mutually_exclusive	CUFF.648	chr2	-	chr2:177041421-177042438,chr2:177042555-177043756	chr2:177041421-177042059,chr2:177042223-177043756	chr2:177042439-177042554	chr2:177042060-177042222			72.73
N	alternative_first_exon	CUFF.106	chr10	-	chr10:46113709-46143741;chr10:46113709-46120030	chr10:46113709-46116227	chr10:46143742-46143982;chr10:46120031-46120085	chr10:46116228-46116411			41.89
K	alternative_first_exon	CUFF.132,CUFF.93	chr10	-	chr10:17636383-17645558	chr10:17636383-17641288	chr10:17645559-17645872	chr10:17641289-17641410			81.82
N	alternative_acceptor	CUFF.703	chr21	-	chr21:47571895-47572820	chr21:47571920-47572820		chr21:47571895-47571919	chr21:47571894-47571895		2.94
K	intron_retention	CUFF.675	chr20	+	chr20:2842777-2843224				chr20:2842776-2842777;chr20:2843224-2843225		69.23
N	jcn_only_AA	CUFF.725	chr22	+	chr22:45148508-45182336	chr22:45148508-45173041		chr22:45173042-45182336	chr22:45182336-45182337		15.38
N	alternative_donor	CUFF.209	chr12	-	chr12:22627826-22631246	chr12:22627826-22630195		chr12:22630196-22631246	chr12:22631246-22631247		8.60
K	cassette	CUFF.152	chr11	-	chr11:10825966-10827453	chr11:10825966-10826459;chr11:10826563-10827453		chr11:10826460-10826562			94.62
K	intron_retention	CUFF.671	chr2	-	chr2:242439697-242440154				chr2:242439696-242439697;chr2:242440154-242440155		1.91
K	alternative_acceptor	CUFF.262	chr14	-	chr14:31358462-31358589	chr14:31358484-31358589		chr14:31358462-31358483	chr14:31358461-31358462		33.33
K	intron_retention		chr8	+	chr8:74891097-74891313				chr8:74891096-74891097;chr8:74891313-74891314		15.07
N	alternative_acceptor	CUFF.208	chr12	+	chr12:21242864-21279041	chr12:21242864-21245446		chr12:21245447-21279041	chr12:21279041-21279042	chr12:21279042-21279191	0.00
N	coord_cassette	CUFF.24	chr1	+	chr1:54360221-54371767	chr1:54360221-54368729;chr1:54368940-54370338;chr1:54370483-54371767		chr1:54368730-54368939;chr1:54370339-54370482			66.04
K	jcn_only_AD	CUFF.879,CUFF.880	chr5	-	chr5:60199544-60200618	chr5:60199544-60200614		chr5:60200615-60200618	chr5:60200618-60200619		14.74
K	coord_cassette	CUFF.467	chr17	-	chr17:76994046-77005745	chr17:76994046-76996181;chr17:76996353-77001453;chr17:77001564-77005745		chr17:76996182-76996352;chr17:77001454-77001563			67.37
K	alternative_first_exon	CUFF.526	chr19	+	chr19:16178773-16186856;chr19:16178549-16186856	chr19:16186520-16186856	chr19:16178344-16178548	chr19:16186421-16186519			25.93
K	intron_retention	CUFF.163	chr11	+	chr11:64000338-64001365				chr11:64000337-64000338;chr11:64001365-64001366		32.94
K	alternative_last_exon	CUFF.902	chr5	-	chr5:162516353-162683856	chr5:162683277-162683856	chr5:162516251-162516352	chr5:162682985-162683276			76.00
K	intron_retention	CUFF.635	chr2	+	chr2:118595561-118596782				chr2:118595560-118595561;chr2:118596782-118596783		37.50
K	intron_retention	CUFF.530	chr19	+	chr19:17449551-17449931				chr19:17449550-17449551;chr19:17449931-17449932		92.92
K	alternative_first_exon	CUFF.921	chr6	+	chr6:32812648-32823914;chr6:32812052-32823914	chr6:32822067-32823914	chr6:32811913-32812051	chr6:32821878-32822066			63.77
K	intron_retention	CUFF.152	chr11	-	chr11:10827558-10828801				chr11:10827557-10827558;chr11:10828801-10828802		54.85
K	alternative_first_exon	CUFF.1063	chr8	+	chr8:144818109-144822028	chr8:144821674-144822028	chr8:144818020-144818108	chr8:144821477-144821673			56.25
N	jcn_only_AD	CUFF.374	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		23.43
N	cassette	CUFF.325	chr15	+	chr15:57523456-57524909	chr15:57523456-57524488;chr15:57524629-57524909		chr15:57524489-57524628			90.00
N	alternative_acceptor	CUFF.475	chr17	-	chr17:79994890-79995325	chr17:79994965-79995325		chr17:79994890-79994964	chr17:79994889-79994890		48.31
K	cassette	CUFF.195	chr12	-	chr12:352980-371954	chr12:352980-369016;chr12:369224-371954		chr12:369017-369223			54.15
K	intron_retention	CUFF.1121	chrX	+	chrX:45184847-45192754				chrX:45184846-45184847;chrX:45192754-45192755		48.39
K	cassette	CUFF.132	chr10	-	chr10:123629554-123661905	chr10:123629554-123658355;chr10:123658485-123661905		chr10:123658356-123658484			36.96
K	mutually_exclusive	CUFF.121	chr10	-	chr10:80808690-80814352,chr10:80814486-80825503	chr10:80808690-80810038,chr10:80810175-80825503	chr10:80814353-80814485	chr10:80810039-80810174			80.00
N	alternative_first_exon	CUFF.310	chr15	+	chr15:40531337-40545378,chr15:40545216-40545378,chr15:40544465-40545378;chr15:40509869-40545378;chr15:40544893-40545378	chr15:40532883-40545378	chr15:40509629-40509868;chr15:40544751-40544892	chr15:40532681-40532882			46.67
K	alternative_acceptor	CUFF.160	chr11	+	chr11:61608198-61615630	chr11:61608198-61615292		chr11:61615293-61615630	chr11:61615630-61615631	chr11:61608096-61608197;chr11:61615631-61615756	38.93
N	alternative_donor	CUFF.933,CUFF.945	chr6	-	chr6:128313855-128316606;chr6:128313855-128316591	chr6:128313855-128316393		chr6:128316394-128316591;chr6:128316592-128316606	chr6:128316591-128316592;chr6:128316606-128316607		15.00
K	intron_retention		chr2	-	chr2:263373-263563				chr2:263372-263373;chr2:263563-263564		8.82
K	alternative_donor	CUFF.519	chr19	+	chr19:11474496-11474836	chr19:11474512-11474836		chr19:11474496-11474511	chr19:11474495-11474496		25.64
N	alternative_donor	CUFF.453,CUFF.475	chr17	-	chr17:56083889-56084304	chr17:56083889-56084267		chr17:56084268-56084304	chr17:56084304-56084305		20.69
N	alternative_donor	CUFF.954	chr6	+	chr6:161413116-161455290	chr6:161443260-161455290		chr6:161413116-161443259	chr6:161413115-161413116	chr6:161455291-161455481;chr6:161412759-161413115	0.00
K	coord_cassette	CUFF.900	chr5	-	chr5:149782189-149785821	chr5:149782189-149784242;chr5:149784331-149784647;chr5:149784744-149785821		chr5:149784243-149784330;chr5:149784648-149784743			66.20
N	jcn_only_AD	CUFF.663	chr2	+	chr2:220095128-220096649;chr2:220094623-220096649	chr2:220095073-220096649		chr2:220094623-220095072;chr2:220095073-220095127	chr2:220094622-220094623;chr2:220095072-220095073		22.70
N	alternative_donor	CUFF.321	chr15	-	chr15:50822127-50830905	chr15:50822127-50824208		chr15:50824209-50830905	chr15:50830905-50830906		0.00
N	jcn_only_AA		chr15	+	chr15:24811948-24813043;chr15:24811948-24813677;chr15:24811948-24813038	chr15:24811948-24814929					22.22
K	jcn_only_AD	CUFF.50	chr1	+	chr1:155180419-155181917	chr1:155181338-155181917					25.45
K	alternative_last_exon	CUFF.965	chr7	-	chr7:19095789-19153499	chr7:19152764-19153499	chr7:19095674-19095788	chr7:19152580-19152763			69.05
N	jcn_only_AA	CUFF.317	chr15	-	chr15:45464201-45464344	chr15:45464277-45464344		chr15:45464201-45464276	chr15:45464200-45464201		9.47
N	jcn_only_AD	CUFF.796	chr3	-	chr3:156261059-156262096	chr3:156261059-156262082		chr3:156262083-156262096	chr3:156262096-156262097		3.92
N	intron_retention		chr19	+	chr19:1440241-1440347				chr19:1440240-1440241;chr19:1440347-1440348		43.96
N	coord_cassette	CUFF.445	chr17	-	chr17:40738156-40761103	chr17:40738156-40739851;chr17:40739883-40744073;chr17:40744181-40761103		chr17:40739852-40739882;chr17:40744074-40744180			50.00
N	jcn_only_AD	CUFF.139,CUFF.176	chr11	-	chr11:102960048-102962412;chr11:102960048-102962515	chr11:102960048-102962244		chr11:102962245-102962412;chr11:102962413-102962515	chr11:102962412-102962413;chr11:102962515-102962516		24.46
K	alternative_last_exon	CUFF.357	chr15	+	chr15:94449519-94527014	chr15:94449519-94512822	chr15:94527015-94527477	chr15:94512823-94512924			33.33
N	cassette	CUFF.14	chr1	-	chr1:28555535-28559431	chr1:28555535-28556641;chr1:28556764-28559431		chr1:28556642-28556763			85.07
K	alternative_last_exon	CUFF.403,CUFF.407	chr16	+	chr16:70399035-70399987	chr16:70399035-70399835	chr16:70399988-70400783	chr16:70399836-70399930			3.11
N	alternative_acceptor	CUFF.566	chr19	+	chr19:10381903-10394804	chr19:10381903-10385440		chr19:10385441-10394804	chr19:10394804-10394805		50.00
N	alternative_donor	CUFF.217	chr12	-	chr12:48375613-48375889	chr12:48375613-48375727		chr12:48375728-48375889	chr12:48375889-48375890		5.88
K	alternative_acceptor	CUFF.112	chr10	+	chr10:70673036-70673146	chr10:70673036-70673105		chr10:70673106-70673146	chr10:70673146-70673147		38.71
K	intron_retention	CUFF.139	chr11	-	chr11:1775132-1775223				chr11:1775131-1775132;chr11:1775223-1775224		54.84
K	jcn_only_AA	CUFF.454	chr17	-	chr17:57756906-57784731;chr17:57777551-57784731	chr17:57777238-57784731					10.81
K	jcn_only_AA	CUFF.533	chr19	-	chr19:20236319-20243269	chr19:20236593-20243269		chr19:20236319-20236592	chr19:20236318-20236319		84.96
N	jcn_only_AD	CUFF.165	chr11	+	chr11:65486221-65486343	chr11:65486247-65486343		chr11:65486221-65486246	chr11:65486220-65486221		4.71
K	coord_cassette	CUFF.946	chr6	-	chr6:133046119-133055391	chr6:133046119-133047860;chr6:133047978-133049879;chr6:133050073-133055391		chr6:133047861-133047977;chr6:133049880-133050072			53.57
N	coord_cassette	CUFF.67	chr1	+	chr1:196913069-196927020	chr1:196913069-196918584;chr1:196918780-196919981;chr1:196920159-196927020		chr1:196918585-196918779;chr1:196919982-196920158		chr1:196912830-196913068;chr1:196927021-196927203	85.26
N	coord_cassette	CUFF.387	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			86.73
N	alternative_acceptor	CUFF.274	chr14	-	chr14:69584993-69585910	chr14:69584996-69585910		chr14:69584993-69584995	chr14:69584992-69584993		58.33
N	jcn_only_AA	CUFF.765	chr3	-	chr3:107567966-107572719;chr3:107569199-107572719	chr3:107568819-107572719		chr3:107567966-107568818;chr3:107568819-107569198	chr3:107567965-107567966;chr3:107568818-107568819		19.30
N	cassette	CUFF.259	chr14	+	chr14:24567888-24568766	chr14:24567888-24568257;chr14:24568446-24568766		chr14:24568258-24568445			98.15
K	cassette	CUFF.54	chr1	-	chr1:158444458-158464191	chr1:158444458-158449694;chr1:158451593-158464191		chr1:158449695-158451592			24.27
N	intron_retention	CUFF.377	chr16	-	chr16:4411471-4411749				chr16:4411470-4411471;chr16:4411749-4411750		77.61
N	jcn_only_AA	CUFF.171	chr11	-	chr11:75514771-75522468;chr11:75514563-75522468	chr11:75520420-75522468		chr11:75514563-75514770;chr11:75514771-75520419	chr11:75514562-75514563;chr11:75514770-75514771		13.10
K	intron_retention	CUFF.114	chr10	-	chr10:73964264-73970489				chr10:73964263-73964264;chr10:73970489-73970490		18.18
K	jcn_only_AA	CUFF.920	chr6	+	chr6:32121414-32121972	chr6:32121414-32121775		chr6:32121776-32121972	chr6:32121972-32121973		30.77
K	alternative_first_exon	CUFF.1091	chr9	+	chr9:117350201-117354831	chr9:117350399-117354831	chr9:117350026-117350200	chr9:117350279-117350398			9.76
N	intron_retention		chr16	-	chr16:4412133-4445289				chr16:4412132-4412133;chr16:4445289-4445290		80.00
N	jcn_only_AD	CUFF.136	chr11	-	chr11:410028-417293;chr11:410028-414822	chr11:410028-417324		chr11:414823-417293;chr11:417294-417324	chr11:417293-417294;chr11:417324-417325		2.62
N	jcn_only_AA	CUFF.877	chr5	-	chr5:54569206-54570441	chr5:54569255-54570441		chr5:54569206-54569254	chr5:54569205-54569206		28.95
K	intron_retention	CUFF.165	chr11	+	chr11:65482382-65484137				chr11:65482381-65482382;chr11:65484137-65484138		7.29
K	alternative_first_exon	CUFF.963,CUFF.977	chr7	-	chr7:55755618-55759006	chr7:55755618-55756605	chr7:55759007-55759193	chr7:55756606-55756994			13.33
N	alternative_acceptor	CUFF.919	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		34.03
K	intron_retention		chr11	-	chr11:119291097-119291578				chr11:119291096-119291097;chr11:119291578-119291579		10.08
K	intron_retention	CUFF.812	chr4	-	chr4:2933193-2933281				chr4:2933192-2933193;chr4:2933281-2933282		60.14
K	cassette	CUFF.654	chr2	-	chr2:204326649-204341798;chr2:204326649-204354306	chr2:204326649-204334961;chr2:204335037-204354306,chr2:204335037-204341798		chr2:204334962-204335036			55.66
N	alternative_acceptor	CUFF.856	chr4	-	chr4:162463846-162508606	chr4:162473730-162508606		chr4:162463846-162473729	chr4:162463845-162463846		0.93
K	alternative_first_exon	CUFF.1078,CUFF.1085	chr9	-	chr9:71160753-71161474	chr9:71160753-71160844	chr9:71161475-71161597	chr9:71160845-71161032			62.50
N	alternative_acceptor		chr10	-	chr10:78637649-78644746	chr10:78637652-78644746		chr10:78637649-78637651	chr10:78637648-78637649		25.00
K	alternative_acceptor	CUFF.1008	chr7	-	chr7:127251731-127251998	chr7:127251903-127251998		chr7:127251731-127251902	chr7:127251730-127251731		24.14
N	alternative_donor	CUFF.347	chr15	-	chr15:83358206-83378345;chr15:83358206-83358514;chr15:83358206-83377523	chr15:83358206-83366608		chr15:83358515-83366608;chr15:83366609-83377523;chr15:83377524-83378345	chr15:83366608-83366609;chr15:83377523-83377524;chr15:83378345-83378346		0.00
N	jcn_only_AD	CUFF.457	chr17	+	chr17:61562428-61562596;chr17:61561903-61562596	chr17:61562331-61562596		chr17:61561903-61562330;chr17:61562331-61562427	chr17:61561902-61561903;chr17:61562330-61562331		23.81
N	jcn_only_AD	CUFF.663	chr2	+	chr2:220094681-220094949;chr2:220094623-220094949	chr2:220094703-220094949		chr2:220094623-220094680;chr2:220094681-220094702	chr2:220094622-220094623;chr2:220094680-220094681		2.44
K	intron_retention	CUFF.526	chr19	+	chr19:16198908-16199854				chr19:16198907-16198908;chr19:16199854-16199855		8.11
K	jcn_only_AA	CUFF.812	chr4	-	chr4:2934418-2934832	chr4:2934486-2934832		chr4:2934418-2934485	chr4:2934417-2934418		96.55
N	jcn_only_AD	CUFF.490	chr18	+	chr18:56001125-56008909	chr18:56008402-56008909		chr18:56001125-56008401	chr18:56001124-56001125		96.43
K	jcn_only_AA	CUFF.916	chr6	-	chr6:31509926-31513885	chr6:31512536-31513885					72.62
N	alternative_donor		chr18	+	chr18:56001125-56008269	chr18:56002770-56008269		chr18:56001125-56002769	chr18:56001124-56001125		44.68
K	alternative_donor	CUFF.402,CUFF.406	chr16	-	chr16:67221741-67222806	chr16:67221741-67222623		chr16:67222624-67222806	chr16:67222806-67222807		47.83
N	cassette	CUFF.726	chr22	+	chr22:47158746-47189397	chr22:47158746-47188416;chr22:47188474-47189397		chr22:47188417-47188473			95.79
K	alternative_acceptor	CUFF.189	chr11	-	chr11:119290142-119290760	chr11:119290231-119290760		chr11:119290142-119290230	chr11:119290141-119290142		44.83
K	alternative_first_exon	CUFF.669	chr2	+	chr2:241396887-241398446,chr2:241381924-241398446;chr2:241392512-241398446;chr2:241394438-241398446	chr2:241397535-241398446	chr2:241392147-241392511;chr2:241394347-241394437	chr2:241397319-241397534			47.02
K	alternative_donor	CUFF.138	chr11	+	chr11:827319-828259	chr11:827460-828259		chr11:827319-827459	chr11:827318-827319	chr11:828260-828772;chr11:827215-827318	83.72
K	intron_retention	CUFF.828	chr4	+	chr4:37848733-37848822				chr4:37848732-37848733;chr4:37848822-37848823		10.87
N	jcn_only_AA	CUFF.1101	chr9	-	chr9:131483760-131483929;chr9:131483782-131483929	chr9:131483810-131483929		chr9:131483760-131483781;chr9:131483782-131483809	chr9:131483759-131483760;chr9:131483781-131483782		2.14
K	alternative_acceptor	CUFF.257	chr14	+	chr14:23390330-23392180	chr14:23390330-23392177		chr14:23392178-23392180	chr14:23392180-23392181		78.12
N	jcn_only_AA	CUFF.350	chr15	-	chr15:84871760-84872928;chr15:84872839-84872928	chr15:84871773-84872928		chr15:84871760-84871772;chr15:84871773-84872838	chr15:84871759-84871760;chr15:84871772-84871773		69.35
K	intron_retention	CUFF.1014	chr7	+	chr7:148991108-148991470				chr7:148991107-148991108;chr7:148991470-148991471		72.97
K	intron_retention	CUFF.530	chr19	+	chr19:17447844-17448816				chr19:17447843-17447844;chr19:17448816-17448817		34.81
K	cassette	CUFF.1055	chr8	-	chr8:120772979-120774654	chr8:120772979-120773847;chr8:120774013-120774654		chr8:120773848-120774012			27.66
K	alternative_donor	CUFF.450	chr17	+	chr17:46990328-46993437	chr17:46990384-46993437		chr17:46990328-46990383	chr17:46990327-46990328		43.90
K	cassette	CUFF.651	chr2	+	chr2:191362446-191364740	chr2:191362446-191364557;chr2:191364583-191364740		chr2:191364558-191364582			12.96
N	alternative_acceptor	CUFF.457	chr17	+	chr17:61555460-61556171;chr17:61555460-61556367	chr17:61555460-61557129		chr17:61556172-61556367;chr17:61556368-61557129	chr17:61556367-61556368;chr17:61557129-61557130		8.70
K	cassette	CUFF.57	chr1	-	chr1:160991278-161008669	chr1:160991278-160992539;chr1:160992618-161008669		chr1:160992540-160992617			95.74
N	cassette	CUFF.67	chr1	+	chr1:196913069-196927020	chr1:196913069-196919981;chr1:196920159-196927020		chr1:196919982-196920158		chr1:196912830-196913068;chr1:196927021-196927203	85.71
K	jcn_only_AA	CUFF.223	chr12	-	chr12:52993087-52994810	chr12:52993194-52994810		chr12:52993087-52993193	chr12:52993086-52993087		79.41
N	alternative_donor	CUFF.489,CUFF.492	chr18	-	chr18:47329224-47340051;chr18:47329224-47339094;chr18:47329224-47340186;chr18:47329224-47339838;chr18:47329224-47340101	chr18:47329224-47337765		chr18:47337766-47339094;chr18:47339095-47339838;chr18:47339839-47340051;chr18:47340052-47340101;chr18:47340102-47340186	chr18:47339094-47339095;chr18:47339838-47339839;chr18:47340051-47340052;chr18:47340101-47340102;chr18:47340186-47340187		2.30
N	intron_retention		chr17	+	chr17:80417949-80426639				chr17:80417948-80417949;chr17:80426639-80426640		18.18
K	jcn_only_AD	CUFF.539	chr19	+	chr19:35642377-35642535	chr19:35642386-35642535		chr19:35642377-35642385	chr19:35642376-35642377		77.78
K	intron_retention	CUFF.535	chr19	-	chr19:21636082-21636351				chr19:21636081-21636082;chr19:21636351-21636352		26.67
N	jcn_only_AD	CUFF.818,CUFF.856	chr4	-	chr4:162577647-162680562	chr4:162577647-162585967		chr4:162585968-162680562	chr4:162680562-162680563		27.59
K	jcn_only_AA	CUFF.848	chr4	+	chr4:120415679-120418965	chr4:120415679-120418816		chr4:120418817-120418965	chr4:120418965-120418966		67.66
N	intron_retention		chr7	+	chr7:75040010-75040937				chr7:75040009-75040010;chr7:75040937-75040938		82.61
N	alternative_donor	CUFF.322,CUFF.352	chr15	-	chr15:90432373-90437112	chr15:90432373-90437108		chr15:90437109-90437112	chr15:90437112-90437113		3.03
K	cassette	CUFF.147	chr11	-	chr11:5687312-5699433	chr11:5687312-5688918;chr11:5688942-5699433		chr11:5688919-5688941			38.51
N	jcn_only_AD		chr17	-	chr17:1616190-1617149	chr17:1616190-1616996		chr17:1616997-1617149	chr17:1617149-1617150		32.72
K	intron_retention	CUFF.741	chr3	-	chr3:33441775-33442453				chr3:33441774-33441775;chr3:33442453-33442454		10.00
K	alternative_acceptor	CUFF.402	chr16	-	chr16:67223587-67223873	chr16:67223671-67223873		chr16:67223587-67223670	chr16:67223586-67223587		25.53
K	cassette	CUFF.1096	chr9	+	chr9:125054120-125084818	chr9:125054120-125075505;chr9:125075666-125084818		chr9:125075506-125075665			51.89
K	alternative_first_exon	CUFF.177,CUFF.188	chr11	-	chr11:119230945-119243416;chr11:119230945-119252182	chr11:119230945-119234558	chr11:119252183-119252421	chr11:119234559-119234988			77.27
N	alternative_acceptor	CUFF.910	chr6	-	chr6:5113652-5216850;chr6:5138974-5216850;chr6:5187215-5216850	chr6:5144497-5216850		chr6:5113652-5138973;chr6:5138974-5144496;chr6:5144497-5187214	chr6:5113651-5113652;chr6:5138973-5138974;chr6:5144496-5144497		0.00
K	coord_cassette	CUFF.900	chr5	-	chr5:149785885-149792187	chr5:149785885-149786443;chr5:149786524-149786714;chr5:149786888-149792187		chr5:149786444-149786523;chr5:149786715-149786887			85.28
N	alternative_donor	CUFF.671	chr2	-	chr2:242435950-242436596;chr2:242435950-242437030	chr2:242435950-242436714		chr2:242436597-242436714;chr2:242436715-242437030	chr2:242436714-242436715;chr2:242437030-242437031		3.55
N	alternative_acceptor	CUFF.475	chr17	-	chr17:79994185-79994259	chr17:79994199-79994259		chr17:79994185-79994198	chr17:79994184-79994185		8.72
K	cassette	CUFF.665	chr2	+	chr2:231927036-231931619	chr2:231927036-231927219;chr2:231927390-231931619		chr2:231927220-231927389			55.17
N	alternative_acceptor	CUFF.504	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		68.78
N	intron_retention		chr11	+	chr11:118402587-118402811				chr11:118402586-118402587;chr11:118402811-118402812	chr11:118401663-118402586	61.54
K	cassette	CUFF.207	chr12	+	chr12:13349807-13364402	chr12:13349807-13352111;chr12:13352468-13364402		chr12:13352112-13352467			58.12
K	jcn_only_AA	CUFF.931,CUFF.944	chr6	+	chr6:46636531-46644383	chr6:46636531-46637871					72.00
N	alternative_acceptor	CUFF.880	chr5	-	chr5:64900873-64905069	chr5:64902995-64905069		chr5:64900873-64902994	chr5:64900872-64900873		10.81
K	alternative_donor	CUFF.912	chr6	+	chr6:28116603-28117260	chr6:28116617-28117260		chr6:28116603-28116616	chr6:28116602-28116603		76.47
K	intron_retention	CUFF.663	chr2	+	chr2:220097406-220097800				chr2:220097405-220097406;chr2:220097800-220097801		24.23
K	intron_retention	CUFF.377	chr16	-	chr16:4466602-4466785				chr16:4466601-4466602;chr16:4466785-4466786		55.41
K	intron_retention	CUFF.1010	chr7	+	chr7:129037166-129040130				chr7:129037165-129037166;chr7:129040130-129040131		11.35
K	jcn_only_AA	CUFF.878,CUFF.885	chr5	+	chr5:56543043-56545280	chr5:56543043-56545235		chr5:56545236-56545280	chr5:56545280-56545281	chr5:56542902-56543042;chr5:56545281-56545403	67.24
N	alternative_acceptor	CUFF.535	chr19	-	chr19:21637275-21639262	chr19:21638407-21639262		chr19:21637275-21638406	chr19:21637274-21637275		4.55
N	alternative_donor	CUFF.838	chr4	-	chr4:74459311-74481607	chr4:74459311-74464356		chr4:74464357-74481607	chr4:74481607-74481608		66.67
N	jcn_only_AA	CUFF.481	chr18	+	chr18:11999187-12009881	chr18:11999187-12008331		chr18:12008332-12009881	chr18:12009881-12009882		2.87
K	intron_retention		chr12	-	chr12:7086688-7086759				chr12:7086687-7086688;chr12:7086759-7086760		69.57
N	coord_cassette	CUFF.572	chr2	-	chr2:262787-264781	chr2:262787-263210;chr2:263373-263563;chr2:263763-264781		chr2:263211-263372;chr2:263564-263762			58.82
K	intron_retention	CUFF.550	chr19	+	chr19:44771115-44777457				chr19:44771114-44771115;chr19:44777457-44777458		42.31
N	cassette	CUFF.478	chr18	+	chr18:166820-180235;chr18:163454-180235	chr18:163454-178932,chr18:166820-178932;chr18:179038-180235		chr18:178933-179037			66.67
K	cassette	CUFF.384	chr16	-	chr16:15180116-15185171	chr16:15180116-15180221;chr16:15180312-15185171		chr16:15180222-15180311			86.96
K	alternative_last_exon	CUFF.550	chr19	+	chr19:44771115-44777457;chr19:44771115-44777051	chr19:44771115-44771532	chr19:44777458-44779568;chr19:44777052-44777453	chr19:44771533-44772456			45.28
K	alternative_donor	CUFF.144	chr11	-	chr11:2905365-2906431	chr11:2905365-2905899		chr11:2905900-2906431	chr11:2906431-2906432		93.69
N	jcn_only_AA		chr19	+	chr19:54648069-54649330;chr19:54648069-54649277	chr19:54648069-54649333		chr19:54649278-54649330;chr19:54649331-54649333	chr19:54649330-54649331;chr19:54649333-54649334		59.46
N	alternative_acceptor		chr14	-	chr14:59939809-59941445	chr14:59941245-59941445		chr14:59939809-59941244	chr14:59939808-59939809		33.33
N	alternative_first_exon	CUFF.891	chr5	+	chr5:134182554-134190587;chr5:134181428-134190587	chr5:134181903-134190587	chr5:134182156-134182553;chr5:134181338-134181427	chr5:134181764-134181902			4.17
N	jcn_only_AD	CUFF.473	chr17	-	chr17:79894070-79898625;chr17:79894070-79894623	chr17:79894070-79900171		chr17:79894624-79898625;chr17:79898626-79900171	chr17:79898625-79898626;chr17:79900171-79900172	chr17:79893999-79894069	2.48
K	alternative_first_exon	CUFF.533	chr19	-	chr19:20243397-20349096;chr19:20243397-20261169	chr19:20243397-20351308	chr19:20349097-20349344;chr19:20261170-20261357	chr19:20351309-20351446			21.43
N	alternative_acceptor	CUFF.954	chr6	+	chr6:161455482-161469647	chr6:161455482-161469277		chr6:161469278-161469647	chr6:161469647-161469648	chr6:161455291-161455481;chr6:161469648-161471011	25.00
N	coord_cassette	CUFF.234	chr12	+	chr12:69214155-69222550	chr12:69214155-69218142;chr12:69218211-69218334;chr12:69218432-69222550		chr12:69218143-69218210;chr12:69218335-69218431			95.76
N	mutually_exclusive	CUFF.501	chr18	+	chr18:77478017-77496354,chr18:77496522-77513651	chr18:77478017-77488906,chr18:77489070-77513651	chr18:77496355-77496521	chr18:77488907-77489069			50.00
K	intron_retention	CUFF.176	chr11	-	chr11:102937103-102937187				chr11:102937102-102937103;chr11:102937187-102937188		17.98
N	alternative_donor	CUFF.490	chr18	+	chr18:55713251-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55816802-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		0.00
K	cassette	CUFF.230	chr12	-	chr12:56708751-56709604	chr12:56708751-56708913;chr12:56709027-56709604		chr12:56708914-56709026			71.57
K	intron_retention	CUFF.728	chr22	-	chr22:51020292-51020677				chr22:51020291-51020292;chr22:51020677-51020678		18.28
N	alternative_donor	CUFF.802	chr3	+	chr3:186649184-186681572;chr3:186648624-186681572;chr3:186648928-186681572;chr3:186666727-186681572	chr3:186660216-186681572		chr3:186648624-186648927;chr3:186648928-186649183;chr3:186649184-186660215;chr3:186660216-186666726	chr3:186648623-186648624;chr3:186648927-186648928;chr3:186649183-186649184;chr3:186660215-186660216		0.00
N	alternative_donor		chr19	-	chr19:41944320-41946385;chr19:41944320-41945378	chr19:41944320-41945786		chr19:41945379-41945786;chr19:41945787-41946385	chr19:41945786-41945787;chr19:41946385-41946386		42.24
N	alternative_donor	CUFF.68	chr1	+	chr1:200870288-200876961	chr1:200875624-200876961		chr1:200870288-200875623	chr1:200870287-200870288		20.00
K	intron_retention	CUFF.138	chr11	+	chr11:829184-829359				chr11:829183-829184;chr11:829359-829360	chr11:828852-829183;chr11:829360-829540	50.53
N	intron_retention		chr12	+	chr12:53861078-53862560				chr12:53861077-53861078;chr12:53862560-53862561		16.77
N	jcn_only_AD	CUFF.417	chr17	-	chr17:79263609-79269221	chr17:79263609-79268622		chr17:79268623-79269221	chr17:79269221-79269222	chr17:79263491-79263608	71.21
N	alternative_last_exon	CUFF.140	chr11	-	chr11:2188263-2188664;chr11:2187780-2188664	chr11:2187999-2188664	chr11:2188117-2188262;chr11:2187043-2187779	chr11:2187863-2187998			2.88
N	jcn_only_AD		chr3	-	chr3:71777775-71778224;chr3:71777775-71803365	chr3:71777775-71803794					25.35
N	jcn_only_AD	CUFF.979	chr7	+	chr7:65579902-65592690;chr7:65579958-65592690	chr7:65591631-65592690		chr7:65579902-65579957;chr7:65579958-65591630	chr7:65579901-65579902;chr7:65579957-65579958		9.23
K	jcn_only_AD	CUFF.676,CUFF.691	chr20	-	chr20:61991052-61992528	chr20:61991052-61992441		chr20:61992442-61992528	chr20:61992528-61992529		50.00
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55895140-55912658;chr18:55865102-55912658;chr18:55895121-55912658;chr18:55862966-55912658;chr18:55888990-55912658	chr18:55833094-55912658		chr18:55833094-55862965;chr18:55862966-55865101;chr18:55865102-55888989;chr18:55888990-55895120;chr18:55895121-55895139	chr18:55833093-55833094;chr18:55862965-55862966;chr18:55865101-55865102;chr18:55888989-55888990;chr18:55895120-55895121		42.64
K	cassette	CUFF.587	chr2	-	chr2:23599798-23604091	chr2:23599798-23602994;chr2:23603113-23604091		chr2:23602995-23603112			86.84
N	alternative_donor	CUFF.1051	chr8	+	chr8:106646586-106800945	chr8:106703164-106800945		chr8:106646586-106703163	chr8:106646585-106646586		0.00
N	alternative_first_exon	CUFF.150,CUFF.166	chr11	-	chr11:8502162-8587256;chr11:8502162-8615629	chr11:8502162-8615290	chr11:8615630-8615928	chr11:8615291-8615545			12.04
N	jcn_only_AD	CUFF.945	chr6	-	chr6:128561296-128563665	chr6:128561296-128562367		chr6:128562368-128563665	chr6:128563665-128563666		45.05
K	alternative_first_exon	CUFF.531	chr19	+	chr19:17581517-17598268	chr19:17598145-17598268	chr19:17581228-17581516	chr19:17597372-17598144			88.24
N	cassette	CUFF.97	chr10	-	chr10:27044671-27054146;chr10:27040713-27054146	chr10:27044671-27047990,chr10:27040713-27047990;chr10:27048168-27054146		chr10:27047991-27048167			88.57
K	intron_retention	CUFF.589	chr2	-	chr2:27670790-27671781				chr2:27670789-27670790;chr2:27671781-27671782		83.85
N	alternative_acceptor	CUFF.67	chr1	+	chr1:196913069-196918584;chr1:196913069-196918746	chr1:196913069-196918565		chr1:196918566-196918584;chr1:196918585-196918746	chr1:196918584-196918585;chr1:196918746-196918747	chr1:196912830-196913068;chr1:196918747-196918779	23.88
N	intron_retention		chr16	+	chr16:19584564-19590373				chr16:19584563-19584564;chr16:19590373-19590374		75.00
K	cassette	CUFF.151	chr11	-	chr11:8948722-8950923	chr11:8948722-8949049;chr11:8949230-8950923		chr11:8949050-8949229			72.63
N	cassette	CUFF.259	chr14	+	chr14:24563464-24566100;chr14:24563644-24566100	chr14:24563464-24563974,chr14:24563644-24563974;chr14:24564055-24566100		chr14:24563975-24564054			86.63
K	alternative_acceptor	CUFF.147	chr11	-	chr11:5685404-5686885	chr11:5686626-5686885		chr11:5685404-5686625	chr11:5685403-5685404		61.81
N	alternative_acceptor	CUFF.350	chr15	-	chr15:84871760-84872928;chr15:84872839-84872928	chr15:84871773-84872928		chr15:84871760-84871772;chr15:84871773-84872838	chr15:84871759-84871760;chr15:84871772-84871773		63.89
K	intron_retention	CUFF.516	chr19	-	chr19:10207250-10213243				chr19:10207249-10207250;chr19:10213243-10213244		18.18
N	jcn_only_AD	CUFF.940	chr6	+	chr6:112382492-112385957	chr6:112382599-112385957		chr6:112382492-112382598	chr6:112382491-112382492		4.69
K	jcn_only_AD	CUFF.419,CUFF.467	chr17	-	chr17:5436305-5436623	chr17:5436305-5436611		chr17:5436612-5436623	chr17:5436623-5436624		2.70
N	jcn_only_AD	CUFF.802	chr3	+	chr3:186649184-186681572;chr3:186660216-186681572;chr3:186648928-186681572;chr3:186666727-186681572	chr3:186648624-186681572		chr3:186648624-186648927;chr3:186648928-186649183;chr3:186649184-186660215;chr3:186660216-186666726	chr3:186648623-186648624;chr3:186648927-186648928;chr3:186649183-186649184;chr3:186660215-186660216		51.01
N	jcn_only_AD	CUFF.325	chr15	+	chr15:57535749-57543547	chr15:57540280-57543547		chr15:57535749-57540279	chr15:57535748-57535749		45.56
N	jcn_only_AA	CUFF.519	chr19	+	chr19:11468416-11470146;chr19:11468416-11470282	chr19:11468416-11470207		chr19:11470147-11470207;chr19:11470208-11470282	chr19:11470207-11470208;chr19:11470282-11470283		57.81
N	cassette	CUFF.905	chr6	+	chr6:304662-335113;chr6:292561-345853	chr6:292561-311879,chr6:304662-311879;chr6:311963-335113,chr6:311963-345853		chr6:311880-311962			64.65
N	alternative_donor		chr16	-	chr16:23507100-23530907	chr16:23507100-23521641		chr16:23521642-23530907	chr16:23530907-23530908	chr16:23507015-23507099	59.26
N	jcn_only_AD	CUFF.152	chr11	-	chr11:10828929-10829080;chr11:10828929-10829720	chr11:10828929-10829291		chr11:10829081-10829291;chr11:10829292-10829720	chr11:10829291-10829292;chr11:10829720-10829721		68.18
N	jcn_only_AD	CUFF.966	chr7	-	chr7:22233652-22259484	chr7:22233652-22234187		chr7:22234188-22259484	chr7:22259484-22259485		6.45
K	intron_retention	CUFF.894	chr5	+	chr5:139851881-139862164				chr5:139851880-139851881;chr5:139862164-139862165	chr5:139851824-139851880;chr5:139862165-139862252	61.54
K	alternative_acceptor	CUFF.36	chr1	+	chr1:110211994-110212257	chr1:110211994-110212092		chr1:110212093-110212257	chr1:110212257-110212258		87.85
K	mutually_exclusive	CUFF.559	chr19	-	chr19:51483744-51485582,chr19:51485714-51487106	chr19:51483744-51485022,chr19:51485171-51487106	chr19:51485583-51485713	chr19:51485023-51485170			11.11
N	alternative_acceptor	CUFF.402	chr16	-	chr16:67223084-67223533	chr16:67223099-67223533		chr16:67223084-67223098	chr16:67223083-67223084		8.99
N	alternative_donor	CUFF.693	chr21	+	chr21:15680941-15685264	chr21:15681420-15685264		chr21:15680941-15681419	chr21:15680940-15680941	chr21:15685265-15685452;chr21:15680874-15680940	9.09
K	alternative_first_exon	CUFF.467	chr17	-	chr17:77001564-77005745	chr17:77001564-77004144	chr17:77005746-77006037	chr17:77004145-77004230			15.79
N	alternative_donor		chr18	-	chr18:72914296-72917147;chr18:72914296-72920374	chr18:72914296-72920315		chr18:72917148-72920315;chr18:72920316-72920374	chr18:72920315-72920316;chr18:72920374-72920375		87.10
K	jcn_only_AD	CUFF.998	chr7	-	chr7:102234690-102234938	chr7:102234690-102234893		chr7:102234894-102234938	chr7:102234938-102234939		38.89
N	alternative_acceptor	CUFF.268,CUFF.270	chr14	+	chr14:55494190-55498606	chr14:55494190-55498580		chr14:55498581-55498606	chr14:55498606-55498607		8.82
N	jcn_only_AD	CUFF.347	chr15	-	chr15:83358206-83378345;chr15:83358206-83358514;chr15:83358206-83377523	chr15:83358206-83366608		chr15:83358515-83366608;chr15:83366609-83377523;chr15:83377524-83378345	chr15:83366608-83366609;chr15:83377523-83377524;chr15:83378345-83378346		8.98
K	jcn_only_AD	CUFF.418	chr17	+	chr17:1945170-1945898	chr17:1945526-1945898		chr17:1945170-1945525	chr17:1945169-1945170		22.27
N	alternative_acceptor		chr7	-	chr7:37469360-37488462;chr7:37382368-37488462	chr7:37433521-37488462		chr7:37382368-37433520;chr7:37433521-37469359	chr7:37382367-37382368;chr7:37433520-37433521		0.00
K	intron_retention		chr17	-	chr17:40738156-40738782				chr17:40738155-40738156;chr17:40738782-40738783		6.30
K	alternative_first_exon	CUFF.1052	chr8	+	chr8:107531368-107691437;chr8:107593480-107691437;chr8:107630412-107691437	chr8:107670314-107691437	chr8:107531171-107531367;chr8:107593125-107593479;chr8:107630316-107630411	chr8:107670221-107670313			5.41
N	alternative_donor	CUFF.974	chr7	-	chr7:38813845-38816278	chr7:38813845-38814788		chr7:38814789-38816278	chr7:38816278-38816279		7.69
N	cassette	CUFF.864	chr5	+	chr5:36153145-36177066;chr5:36153145-36166620	chr5:36153145-36163746;chr5:36163859-36166620,chr5:36163859-36177066		chr5:36163747-36163858		chr5:36152873-36153144;chr5:36177067-36177118	35.44
N	alternative_donor	CUFF.820	chr4	+	chr4:6911233-6925099;chr4:6911679-6925099	chr4:6912329-6925099		chr4:6911233-6911678;chr4:6911679-6912328	chr4:6911232-6911233;chr4:6911678-6911679		3.37
K	alternative_first_exon	CUFF.269	chr14	+	chr14:58894532-58896080;chr14:58894576-58896080	chr14:58895182-58896080	chr14:58894356-58894575	chr14:58894956-58895181			6.06
N	alternative_acceptor	CUFF.101	chr10	-	chr10:35351991-35360126	chr10:35353045-35360126		chr10:35351991-35353044	chr10:35351990-35351991		14.52
K	cassette	CUFF.584	chr2	-	chr2:11597360-11605897	chr2:11597360-11598406;chr2:11598478-11605897		chr2:11598407-11598477			14.46
K	intron_retention		chr11	+	chr11:63999437-63999981				chr11:63999436-63999437;chr11:63999981-63999982		90.35
N	cassette	CUFF.945	chr6	-	chr6:128327201-128330274	chr6:128327201-128329190;chr6:128329233-128330274		chr6:128329191-128329232			29.58
K	jcn_only_AD	CUFF.390,CUFF.406	chr16	-	chr16:70254784-70255156	chr16:70254784-70255152		chr16:70255153-70255156	chr16:70255156-70255157		50.82
N	cassette	CUFF.752	chr3	-	chr3:49365250-49377356	chr3:49365250-49372901;chr3:49373030-49377356		chr3:49372902-49373029			41.25
N	jcn_only_AD		chr14	-	chr14:71227900-71249939;chr14:71227900-71232158	chr14:71227900-71267383		chr14:71232159-71249939;chr14:71249940-71267383	chr14:71249939-71249940;chr14:71267383-71267384		26.14
K	intron_retention	CUFF.611	chr2	-	chr2:73215478-73226077				chr2:73215477-73215478;chr2:73226077-73226078		9.05
N	intron_retention		chrX	-	chrX:119374209-119378618				chrX:119374208-119374209;chrX:119378618-119378619		83.87
K	alternative_last_exon	CUFF.1083	chr9	-	chr9:99973770-100000704	chr9:100000368-100000704	chr9:99973655-99973769	chr9:99999967-100000367			64.71
N	alternative_donor	CUFF.572	chr2	-	chr2:110920710-110922264	chr2:110920710-110922096		chr2:110922097-110922264	chr2:110922264-110922265		18.18
N	jcn_only_AD	CUFF.456	chr17	+	chr17:60777141-60813446;chr17:60783831-60813446	chr17:60784969-60813446		chr17:60777141-60783830;chr17:60783831-60784968	chr17:60777140-60777141;chr17:60783830-60783831		5.95
N	jcn_only_AA	CUFF.28	chr1	+	chr1:70820892-70832009;chr1:70820892-70832126	chr1:70820892-70831828		chr1:70831829-70832009;chr1:70832010-70832126	chr1:70832009-70832010;chr1:70832126-70832127		30.43
N	jcn_only_AD		chr5	-	chr5:64906871-64907583	chr5:64906871-64907429		chr5:64907430-64907583	chr5:64907583-64907584		90.24
K	cassette	CUFF.998	chr7	-	chr7:102228218-102232731	chr7:102228218-102230605;chr7:102230744-102232731		chr7:102230606-102230743			70.37
K	cassette	CUFF.320	chr15	-	chr15:47672793-47687757	chr15:47672793-47685518;chr15:47685683-47687757		chr15:47685519-47685682			40.00
K	alternative_first_exon	CUFF.747,CUFF.766	chr3	-	chr3:108475436-108475905	chr3:108475436-108475666	chr3:108475906-108476312	chr3:108475667-108475862			62.50
K	alternative_first_exon	CUFF.796	chr3	-	chr3:156271571-156272745;chr3:156271571-156271781	chr3:156271571-156272525	chr3:156272746-156272973;chr3:156271782-156271977	chr3:156272526-156272688			28.26
K	alternative_donor	CUFF.330	chr15	+	chr15:64445539-64445850	chr15:64445586-64445850		chr15:64445539-64445585	chr15:64445538-64445539		19.35
N	alternative_donor	CUFF.1098,CUFF.1101	chr9	-	chr9:131484854-131486272	chr9:131484854-131486230		chr9:131486231-131486272	chr9:131486272-131486273		3.05
K	intron_retention	CUFF.4	chr1	+	chr1:11083387-11084120				chr1:11083386-11083387;chr1:11084120-11084121		34.45
N	jcn_only_AD	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57521007;chr16:57513601-57514206	chr16:57513601-57513756		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		4.63
K	jcn_only_AA	CUFF.1008	chr7	-	chr7:127251040-127251588	chr7:127251261-127251588		chr7:127251040-127251260	chr7:127251039-127251040		79.49
K	alternative_last_exon	CUFF.737	chr3	-	chr3:27183074-27204191	chr3:27204093-27204191	chr3:27182973-27183073	chr3:27203665-27204092			73.27
N	jcn_only_AA	CUFF.350	chr15	-	chr15:84871760-84872928;chr15:84871773-84872928	chr15:84872839-84872928		chr15:84871760-84871772;chr15:84871773-84872838	chr15:84871759-84871760;chr15:84871772-84871773		14.52
N	intron_retention	CUFF.1101	chr9	-	chr9:131484854-131486230				chr9:131484853-131484854;chr9:131486230-131486231		88.89
K	alternative_acceptor	CUFF.1016	chr7	+	chr7:150817833-150820880	chr7:150817833-150819811		chr7:150819812-150820880	chr7:150820880-150820881		94.02
N	jcn_only_AD	CUFF.708	chr22	+	chr22:21058040-21058255;chr22:21057981-21058255	chr22:21058172-21058255		chr22:21057981-21058039;chr22:21058040-21058171	chr22:21057980-21057981;chr22:21058039-21058040		1.60
N	alternative_donor	CUFF.923	chr6	+	chr6:34434048-34494019;chr6:34482846-34494019	chr6:34452922-34494019		chr6:34434048-34452921;chr6:34452922-34482845	chr6:34434047-34434048;chr6:34452921-34452922		0.00
K	jcn_only_AD	CUFF.726	chr22	+	chr22:47188660-47189397	chr22:47188702-47189397		chr22:47188660-47188701	chr22:47188659-47188660		59.76
N	jcn_only_AA		chr7	+	chr7:150384176-150389402	chr7:150384176-150386576		chr7:150386577-150389402	chr7:150389402-150389403		73.68
K	cassette	CUFF.110	chr10	-	chr10:69571422-69583071	chr10:69571422-69575797;chr10:69575888-69583071		chr10:69575798-69575887		chr10:69571282-69571421;chr10:69583072-69583150	28.33
K	jcn_only_AA	CUFF.1018	chr7	-	chr7:156516873-156526870	chr7:156521415-156526870					47.48
N	coord_cassette	CUFF.150	chr11	-	chr11:8486370-8615629	chr11:8486370-8494709;chr11:8494824-8496227;chr11:8496364-8588797;chr11:8588841-8615629		chr11:8494710-8494823;chr11:8496228-8496363;chr11:8588798-8588840			92.86
K	cassette	CUFF.403	chr16	+	chr16:67233660-67234094	chr16:67233660-67233853;chr16:67233905-67234094		chr16:67233854-67233904			94.81
K	alternative_first_exon	CUFF.575	chr2	-	chr2:286344-287162;chr2:286344-287582	chr2:286344-286869	chr2:287583-287892	chr2:286870-286962			6.76
N	alternative_donor	CUFF.95	chr10	-	chr10:76287751-76290264	chr10:76287751-76289050		chr10:76289051-76290264	chr10:76290264-76290265		41.67
N	jcn_only_AA	CUFF.1119	chrX	-	chrX:20252933-20285156	chrX:20258788-20285156		chrX:20252933-20258787	chrX:20252932-20252933		5.26
K	alternative_first_exon	CUFF.448	chr17	-	chr17:42339005-42340003	chr17:42339005-42339394	chr17:42340004-42340094	chr17:42339395-42339515			70.53
K	cassette	CUFF.87	chr10	+	chr10:5123094-5138601	chr10:5123094-5123873;chr10:5124078-5138601		chr10:5123874-5124077			76.12
N	alternative_acceptor	CUFF.631	chr2	+	chr2:109068923-109085435	chr2:109068923-109079043		chr2:109079044-109085435	chr2:109085435-109085436		0.00
N	jcn_only_AD	CUFF.90	chr10	+	chr10:6271144-6274857;chr10:6266177-6274857;chr10:6270182-6274857;chr10:6273278-6274857	chr10:6268329-6274857					31.07
N	intron_retention		chr11	+	chr11:118403177-118404571				chr11:118403176-118403177;chr11:118404571-118404572	chr11:118402865-118403176;chr11:118404572-118404602	72.92
N	jcn_only_AA	CUFF.998	chr7	-	chr7:102236555-102240306	chr7:102236577-102240306		chr7:102236555-102236576	chr7:102236554-102236555		65.62
N	intron_retention		chr16	+	chr16:3115496-3115621				chr16:3115495-3115496;chr16:3115621-3115622		93.24
K	alternative_first_exon	CUFF.90	chr10	+	chr10:6188460-6255585;chr10:6186977-6255585	chr10:6245300-6255585	chr10:6186867-6186976	chr10:6244739-6245299			96.12
K	jcn_only_AA	CUFF.550,CUFF.564	chr19	+	chr19:52901158-52901706	chr19:52901158-52901619		chr19:52901620-52901706	chr19:52901706-52901707		82.86
K	jcn_only_AA	CUFF.909	chr6	-	chr6:3155158-3155858	chr6:3155290-3155858		chr6:3155158-3155289	chr6:3155157-3155158		91.30
N	jcn_only_AD	CUFF.498	chr18	-	chr18:72914296-72917147;chr18:72914296-72920315	chr18:72914296-72920374		chr18:72917148-72920315;chr18:72920316-72920374	chr18:72920315-72920316;chr18:72920374-72920375		5.88
N	jcn_only_AD	CUFF.325	chr15	+	chr15:57213297-57565227	chr15:57555473-57565227					96.85
K	alternative_first_exon	CUFF.971	chr7	-	chr7:37172840-37250990;chr7:37172840-37236705	chr7:37172840-37243713	chr7:37250991-37251122;chr7:37236706-37236877	chr7:37243714-37243905			12.20
K	alternative_last_exon	CUFF.319	chr15	+	chr15:45768751-45804570;chr15:45768751-45789310	chr15:45768751-45769966	chr15:45804571-45804647;chr15:45789311-45789564	chr15:45769967-45770054			2.82
N	jcn_only_AD	CUFF.716	chr22	+	chr22:29695271-29695588	chr22:29695322-29695588		chr22:29695271-29695321	chr22:29695270-29695271		86.27
K	intron_retention	CUFF.395	chr16	+	chr16:56368770-56370642				chr16:56368769-56368770;chr16:56370642-56370643		78.26
N	jcn_only_AD	CUFF.780	chr3	-	chr3:125032501-125042152;chr3:125032501-125033780	chr3:125032501-125042231		chr3:125033781-125042152;chr3:125042153-125042231	chr3:125042152-125042153;chr3:125042231-125042232		1.68
N	intron_retention	CUFF.152	chr11	-	chr11:10828929-10829080				chr11:10828928-10828929;chr11:10829080-10829081		75.00
N	mutually_exclusive	CUFF.182	chr11	+	chr11:118402587-118403631,chr11:118403923-118404134	chr11:118402587-118402864,chr11:118403177-118404134	chr11:118403632-118403922	chr11:118402865-118403176		chr11:118401663-118402586	61.54
N	jcn_only_AA	CUFF.593	chr2	+	chr2:27724097-27726380	chr2:27724097-27724556		chr2:27724557-27726380	chr2:27726380-27726381		25.64
K	intron_retention	CUFF.728	chr22	-	chr22:51010738-51011303				chr22:51010737-51010738;chr22:51011303-51011304		27.72
N	alternative_donor	CUFF.21,CUFF.44	chr1	-	chr1:41486606-41487294	chr1:41486606-41487201		chr1:41487202-41487294	chr1:41487294-41487295		80.00
K	intron_retention	CUFF.641	chr2	+	chr2:169711971-169712395				chr2:169711970-169711971;chr2:169712395-169712396		22.73
K	alternative_first_exon	CUFF.68	chr1	+	chr1:200877016-200877857	chr1:200877678-200877857	chr1:200876962-200877015	chr1:200877526-200877677			96.59
K	alternative_acceptor	CUFF.1114	chrX	-	chrX:10417657-10422909	chrX:10417757-10422909		chrX:10417657-10417756	chrX:10417656-10417657		79.31
K	intron_retention	CUFF.526	chr19	+	chr19:16178549-16186856				chr19:16178548-16178549;chr19:16186856-16186857		30.26
K	alternative_first_exon	CUFF.971	chr7	-	chr7:37172840-37243713;chr7:37172840-37236705	chr7:37172840-37250990	chr7:37243714-37243905;chr7:37236706-37236877	chr7:37250991-37251122			47.56
N	intron_retention		chr5	+	chr5:140041799-140041886				chr5:140041798-140041799;chr5:140041886-140041887		50.00
N	intron_retention		chr7	-	chr7:37382368-37488462				chr7:37382367-37382368;chr7:37488462-37488463		77.78
N	jcn_only_AA	CUFF.708	chr22	+	chr22:21056998-21057293	chr22:21056998-21057117		chr22:21057118-21057293	chr22:21057293-21057294		7.59
N	alternative_donor	CUFF.802	chr3	+	chr3:186769135-186790636	chr3:186782405-186790636		chr3:186769135-186782404	chr3:186769134-186769135		1.11
N	mutually_exclusive	CUFF.202	chr12	-	chr12:7088742-7090755,chr12:7090794-7090971	chr12:7088742-7090165,chr12:7090345-7090971	chr12:7090756-7090793	chr12:7090166-7090344			99.12
K	intron_retention	CUFF.741	chr3	-	chr3:33438371-33438536				chr3:33438370-33438371;chr3:33438536-33438537		31.82
K	alternative_last_exon	CUFF.36,CUFF.61	chr1	+	chr1:110224457-110244273	chr1:110224457-110225828	chr1:110244274-110245162	chr1:110225829-110226716			75.00
N	jcn_only_AD	CUFF.155	chr11	+	chr11:36322621-36415395;chr11:36398255-36415395	chr11:36383732-36415395		chr11:36322621-36383731;chr11:36383732-36398254	chr11:36322620-36322621;chr11:36383731-36383732		2.55
K	alternative_donor	CUFF.504	chr19	+	chr19:1438428-1438805	chr19:1438580-1438805		chr19:1438428-1438579	chr19:1438427-1438428		41.63
N	jcn_only_AD	CUFF.475	chr17	-	chr17:79993940-79994066;chr17:79993940-79994022	chr17:79993940-79994057		chr17:79994023-79994057;chr17:79994058-79994066	chr17:79994057-79994058;chr17:79994066-79994067		2.92
N	intron_retention		chr2	-	chr2:61761039-61764153				chr2:61761038-61761039;chr2:61764153-61764154		72.57
K	alternative_first_exon	CUFF.256	chr13	+	chr13:103498705-103504467	chr13:103501545-103504467	chr13:103497194-103498704	chr13:103501468-103501544			50.00
N	intron_retention	CUFF.1016	chr7	+	chr7:150815432-150815560				chr7:150815431-150815432;chr7:150815560-150815561		80.33
K	alternative_last_exon	CUFF.475	chr17	-	chr17:79993122-79994066	chr17:79993940-79994066	chr17:79992913-79993121	chr17:79993668-79993939			73.47
N	mutually_exclusive	CUFF.374	chr16	+	chr16:3117417-3117984,chr16:3118012-3118180	chr16:3117417-3117554,chr16:3117615-3118180	chr16:3117985-3118011	chr16:3117555-3117614			11.06
K	alternative_last_exon	CUFF.483	chr18	+	chr18:14808579-14822603	chr18:14808579-14808670	chr18:14822604-14822676	chr18:14808671-14808823			84.62
K	intron_retention		chr17	-	chr17:76993727-76993921				chr17:76993726-76993727;chr17:76993921-76993922		27.40
N	coord_cassette	CUFF.1110	chrX	+	chrX:1419520-1428294	chrX:1419520-1422815;chrX:1422913-1424338;chrX:1424421-1428294		chrX:1422816-1422912;chrX:1424339-1424420			96.99
N	jcn_only_AD	CUFF.1131	chrX	-	chrX:85282562-85302487	chrX:85282562-85302250		chrX:85302251-85302487	chrX:85302487-85302488		7.89
N	jcn_only_AA	CUFF.809	chr4	+	chr4:661796-663837	chr4:661796-663834		chr4:663835-663837	chr4:663837-663838		82.61
N	intron_retention		chr1	+	chr1:145580323-145580504				chr1:145580322-145580323;chr1:145580504-145580505		82.14
K	intron_retention	CUFF.21	chr1	-	chr1:41486451-41487287				chr1:41486450-41486451;chr1:41487287-41487288		45.45
N	jcn_only_AA	CUFF.980	chr7	+	chr7:73108381-73111934;chr7:73108381-73110735	chr7:73108381-73111795		chr7:73110736-73111795;chr7:73111796-73111934	chr7:73111795-73111796;chr7:73111934-73111935		6.10
K	jcn_only_AA	CUFF.184	chr11	-	chr11:118919916-118920267	chr11:118920083-118920267		chr11:118919916-118920082	chr11:118919915-118919916		81.82
K	intron_retention	CUFF.922	chr6	+	chr6:33243844-33243952				chr6:33243843-33243844;chr6:33243952-33243953		12.67
K	intron_retention	CUFF.633	chr2	-	chr2:110881641-110882795				chr2:110881640-110881641;chr2:110882795-110882796		62.50
K	alternative_last_exon	CUFF.176	chr11	-	chr11:102933144-102936997	chr11:102935107-102936997	chr11:102932709-102933143	chr11:102934921-102935106			91.67
N	jcn_only_AD		chr4	+	chr4:120434076-120449894	chr4:120434126-120449894		chr4:120434076-120434125	chr4:120434075-120434076		64.52
K	alternative_first_exon	CUFF.101,CUFF.106	chr10	-	chr10:35360268-35379357;chr10:35360268-35363119;chr10:35360268-35378823	chr10:35360268-35379106	chr10:35363120-35363275;chr10:35378824-35378973	chr10:35379107-35379332			7.37
N	jcn_only_AA	CUFF.475	chr17	-	chr17:79994890-79995325	chr17:79994965-79995325		chr17:79994890-79994964	chr17:79994889-79994890		45.63
N	jcn_only_AA	CUFF.902	chr5	-	chr5:162439295-162516250	chr5:162465480-162516250		chr5:162439295-162465479	chr5:162439294-162439295		14.49
K	intron_retention	CUFF.1068	chr9	-	chr9:34709425-34709496				chr9:34709424-34709425;chr9:34709496-34709497		64.52
N	alternative_donor	CUFF.673	chr2	+	chr2:242610857-242611605;chr2:242610821-242611605	chr2:242610841-242611605		chr2:242610821-242610840;chr2:242610841-242610856	chr2:242610820-242610821;chr2:242610840-242610841		11.76
K	intron_retention	CUFF.1054	chr8	+	chr8:118541049-118542961				chr8:118541048-118541049;chr8:118542961-118542962		87.18
K	coord_cassette	CUFF.647	chr2	-	chr2:175711686-175779785	chr2:175711686-175740515;chr2:175740594-175742567;chr2:175742857-175779785		chr2:175740516-175740593;chr2:175742568-175742856			41.30
K	intron_retention	CUFF.626	chr2	+	chr2:99225190-99226218				chr2:99225189-99225190;chr2:99226218-99226219		80.00
N	alternative_acceptor	CUFF.65,CUFF.78	chr1	+	chr1:222837491-222838650	chr1:222837491-222838224		chr1:222838225-222838650	chr1:222838650-222838651		11.76
K	alternative_first_exon	CUFF.226	chr12	+	chr12:54388801-54396213	chr12:54394511-54396213	chr12:54388679-54388800	chr12:54393844-54394510			78.95
N	alternative_acceptor	CUFF.119	chr10	-	chr10:78644776-78647048;chr10:78637652-78647048	chr10:78637649-78647048		chr10:78637649-78637651;chr10:78637652-78644775	chr10:78637648-78637649;chr10:78637651-78637652		20.00
N	jcn_only_AA	CUFF.457	chr17	+	chr17:61555460-61557129;chr17:61555460-61556171	chr17:61555460-61556367		chr17:61556172-61556367;chr17:61556368-61557129	chr17:61556367-61556368;chr17:61557129-61557130		85.25
N	jcn_only_AD	CUFF.208	chr12	+	chr12:21011506-21174394	chr12:21172315-21174394		chr12:21011506-21172314	chr12:21011505-21011506		27.78
K	alternative_donor	CUFF.262	chr14	-	chr14:31355533-31358348	chr14:31355533-31358325		chr14:31358326-31358348	chr14:31358348-31358349		25.53
N	mutually_exclusive	CUFF.265	chr14	+	chr14:50247494-50249259,chr14:50249313-50249547	chr14:50247494-50249087,chr14:50249176-50249547	chr14:50249260-50249312	chr14:50249088-50249175			78.85
K	cassette	CUFF.3	chr1	+	chr1:10494748-10511433	chr1:10494748-10500403;chr1:10500471-10511433		chr1:10500404-10500470			79.17
N	intron_retention		chr20	+	chr20:30135410-30136479				chr20:30135409-30135410;chr20:30136479-30136480		55.17
N	intron_retention		chr11	-	chr11:119291046-119291578				chr11:119291045-119291046;chr11:119291578-119291579		92.45
N	coord_cassette	CUFF.102	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			87.32
N	alternative_acceptor	CUFF.193	chr11	-	chr11:124766952-124767621;chr11:124767158-124767621	chr11:124767529-124767621		chr11:124766952-124767157;chr11:124767158-124767528	chr11:124766951-124766952;chr11:124767157-124767158		20.37
N	jcn_only_AA	CUFF.193	chr11	-	chr11:124766952-124767621;chr11:124767529-124767621	chr11:124767158-124767621		chr11:124766952-124767157;chr11:124767158-124767528	chr11:124766951-124766952;chr11:124767157-124767158		60.00
K	intron_retention	CUFF.424	chr17	-	chr17:8648039-8648146				chr17:8648038-8648039;chr17:8648146-8648147		42.86
K	alternative_acceptor	CUFF.425	chr17	-	chr17:15498141-15499827	chr17:15498205-15499827		chr17:15498141-15498204	chr17:15498140-15498141		33.33
K	intron_retention	CUFF.915	chr6	-	chr6:30711974-30712085				chr6:30711973-30711974;chr6:30712085-30712086		28.00
N	jcn_only_AA		chr17	+	chr17:61907310-61907630	chr17:61907310-61907492					81.82
N	alternative_acceptor	CUFF.87	chr10	+	chr10:35484143-35495822	chr10:35484143-35490378		chr10:35490379-35495822	chr10:35495822-35495823		6.67
N	cassette	CUFF.303	chr15	+	chr15:24820151-24832713	chr15:24820151-24825373;chr15:24825478-24832713		chr15:24825374-24825477			86.26
K	intron_retention	CUFF.300	chr14	-	chr14:106208297-106208401				chr14:106208296-106208297;chr14:106208401-106208402		11.59
K	intron_retention	CUFF.166	chr11	-	chr11:67766846-67766988				chr11:67766845-67766846;chr11:67766988-67766989		63.16
N	intron_retention		chr13	+	chr13:21141925-21142023				chr13:21141924-21141925;chr13:21142023-21142024		93.75
N	alternative_donor		chr22	+	chr22:45148508-45173041	chr22:45148621-45173041		chr22:45148508-45148620	chr22:45148507-45148508		50.00
K	intron_retention	CUFF.418	chr17	+	chr17:1943669-1943798				chr17:1943668-1943669;chr17:1943798-1943799		52.94
K	intron_retention	CUFF.292	chr14	+	chr14:92915504-92920243				chr14:92915503-92915504;chr14:92920243-92920244		64.29
K	intron_retention	CUFF.576	chr2	-	chr2:675631-677288				chr2:675630-675631;chr2:677288-677289		24.56
K	alternative_first_exon	CUFF.830	chr4	+	chr4:57302095-57302427	chr4:57302142-57302427	chr4:57301907-57302094	chr4:57302099-57302141			47.37
N	cassette	CUFF.325	chr15	+	chr15:57213297-57383986	chr15:57213297-57355947;chr15:57356022-57383986		chr15:57355948-57356021			80.00
K	intron_retention	CUFF.542	chr19	-	chr19:39924402-39926297				chr19:39924401-39924402;chr19:39926297-39926298		19.01
K	alternative_first_exon	CUFF.648,CUFF.654	chr2	-	chr2:204360077-204399833	chr2:204360077-204398087	chr2:204399834-204400152	chr2:204398088-204398214			58.58
K	intron_retention	CUFF.747	chr3	-	chr3:38050128-38050532				chr3:38050127-38050128;chr3:38050532-38050533		30.43
K	intron_retention	CUFF.457	chr17	+	chr17:61562331-61562596				chr17:61562330-61562331;chr17:61562596-61562597		54.95
K	cassette	CUFF.1102	chr9	+	chr9:133320383-133327610	chr9:133320383-133325658;chr9:133325721-133327610		chr9:133325659-133325720			72.73
N	jcn_only_AD	CUFF.188	chr11	-	chr11:6637735-6638589	chr11:6637735-6637891		chr11:6637892-6638589	chr11:6638589-6638590		11.44
K	intron_retention	CUFF.147	chr11	-	chr11:5685404-5686398				chr11:5685403-5685404;chr11:5686398-5686399		83.33
K	intron_retention	CUFF.1125	chrX	-	chrX:53563629-53564516				chrX:53563628-53563629;chrX:53564516-53564517		90.27
K	intron_retention	CUFF.112	chr10	+	chr10:70673036-70673146				chr10:70673035-70673036;chr10:70673146-70673147		26.92
K	alternative_acceptor	CUFF.643	chr2	-	chr2:169826726-169828356	chr2:169826867-169828356		chr2:169826726-169826866	chr2:169826725-169826726	chr2:169828357-169828560;chr2:169826555-169826725	61.54
K	alternative_first_exon	CUFF.18	chr1	+	chr1:32539474-32540551;chr1:32538054-32540551	chr1:32538653-32540551,chr1:32538700-32540551	chr1:32537632-32538053	chr1:32538432-32538652			91.00
N	intron_retention		chr17	+	chr17:6348663-6350782				chr17:6348662-6348663;chr17:6350782-6350783		72.55
K	alternative_acceptor	CUFF.716	chr22	+	chr22:29668242-29668374	chr22:29668242-29668368		chr22:29668369-29668374	chr22:29668374-29668375		94.01
N	alternative_acceptor	CUFF.777	chr3	+	chr3:122864440-122864964	chr3:122864440-122864945		chr3:122864946-122864964	chr3:122864964-122864965		50.00
N	jcn_only_AD	CUFF.1098	chr9	-	chr9:130941184-130941522;chr9:130941184-130941267	chr9:130941184-130941351		chr9:130941268-130941351;chr9:130941352-130941522	chr9:130941351-130941352;chr9:130941522-130941523		58.02
N	jcn_only_AA	CUFF.929	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		38.93
N	cassette	CUFF.648	chr2	-	chr2:177042223-177053146	chr2:177042223-177043756;chr2:177043827-177053146		chr2:177043757-177043826			86.84
N	mutually_exclusive	CUFF.758	chr3	-	chr3:57563115-57570110,chr3:57570192-57582800	chr3:57563115-57569624,chr3:57569735-57582800	chr3:57570111-57570191	chr3:57569625-57569734			52.94
N	intron_retention		chr16	-	chr16:57507408-57507524				chr16:57507407-57507408;chr16:57507524-57507525		33.33
K	jcn_only_AA	CUFF.162	chr11	+	chr11:63669803-63670075	chr11:63669803-63670072		chr11:63670073-63670075	chr11:63670075-63670076		45.00
N	jcn_only_AA	CUFF.848	chr4	+	chr4:120434126-120449894	chr4:120434126-120440643		chr4:120440644-120449894	chr4:120449894-120449895		56.52
N	jcn_only_AD	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;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;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		2.50
K	coord_cassette	CUFF.524	chr19	-	chr19:14862484-14867049	chr19:14862484-14863140;chr19:14863339-14865765;chr19:14865940-14866465;chr19:14866690-14867049		chr19:14863141-14863338;chr19:14865766-14865939;chr19:14866466-14866689			67.90
N	intron_retention		chr11	+	chr11:118402587-118403124				chr11:118402586-118402587;chr11:118403124-118403125	chr11:118401663-118402586;chr11:118403125-118403176	96.00
K	alternative_first_exon	CUFF.988	chr7	-	chr7:86594341-86595124;chr7:86594341-86688640	chr7:86594341-86595129	chr7:86688641-86689015	chr7:86595130-86595357			47.83
K	intron_retention	CUFF.557	chr19	+	chr19:50309199-50309375				chr19:50309198-50309199;chr19:50309375-50309376		60.91
K	alternative_last_exon	CUFF.297	chr14	-	chr14:103236793-103240977	chr14:103237911-103240977	chr14:103236377-103236792	chr14:103237380-103237910			81.97
K	mutually_exclusive	CUFF.114	chr10	-	chr10:73857209-73862607,chr10:73862726-73887839	chr10:73857209-73862091,chr10:73862171-73887839	chr10:73862608-73862725	chr10:73862092-73862170			8.20
K	jcn_only_AA	CUFF.354	chr15	+	chr15:91298169-91303376	chr15:91298169-91303210		chr15:91303211-91303376	chr15:91303376-91303377		75.00
K	alternative_acceptor	CUFF.125,CUFF.90	chr10	+	chr10:98092354-98095650	chr10:98092354-98095647		chr10:98095648-98095650	chr10:98095650-98095651		62.50
N	jcn_only_AD		chr18	+	chr18:55833094-55895061;chr18:55888990-55895061	chr18:55862966-55895061		chr18:55833094-55862965;chr18:55862966-55888989	chr18:55833093-55833094;chr18:55862965-55862966		11.54
K	intron_retention	CUFF.504	chr19	+	chr19:1438428-1438805				chr19:1438427-1438428;chr19:1438805-1438806		35.85
K	intron_retention	CUFF.877	chr5	-	chr5:54566316-54566405				chr5:54566315-54566316;chr5:54566405-54566406		17.14
K	jcn_only_AA	CUFF.134	chr10	-	chr10:127541212-127548171	chr10:127542773-127548171					86.36
K	jcn_only_AD	CUFF.239	chr12	-	chr12:113617811-113618785	chr12:113617811-113618733		chr12:113618734-113618785	chr12:113618785-113618786		63.16
K	intron_retention	CUFF.589	chr2	-	chr2:27699594-27700083				chr2:27699593-27699594;chr2:27700083-27700084		14.93
N	alternative_donor	CUFF.53	chr1	-	chr1:156933387-156937778	chr1:156933387-156933483		chr1:156933484-156937778	chr1:156937778-156937779		55.56
K	coord_cassette	CUFF.979	chr7	+	chr7:65592728-65599266	chr7:65592728-65595113;chr7:65595236-65595730;chr7:65595830-65599266		chr7:65595114-65595235;chr7:65595731-65595829			20.00
K	intron_retention	CUFF.137	chr11	-	chr11:555504-555733				chr11:555503-555504;chr11:555733-555734		38.18
K	intron_retention	CUFF.532	chr19	+	chr19:18119038-18119262				chr19:18119037-18119038;chr19:18119262-18119263		66.67
N	jcn_only_AD	CUFF.386	chr16	+	chr16:21693147-21696550	chr16:21695874-21696550		chr16:21693147-21695873	chr16:21693146-21693147		77.78
K	alternative_last_exon	CUFF.152	chr11	-	chr11:10819429-10823840	chr11:10823757-10823840	chr11:10818502-10819428	chr11:10823558-10823756			38.52
N	intron_retention		chr16	+	chr16:3119111-3119281				chr16:3119110-3119111;chr16:3119281-3119282		79.77
N	alternative_acceptor	CUFF.910	chr6	-	chr6:5144497-5216850;chr6:5113652-5216850;chr6:5187215-5216850	chr6:5138974-5216850		chr6:5113652-5138973;chr6:5138974-5144496;chr6:5144497-5187214	chr6:5113651-5113652;chr6:5138973-5138974;chr6:5144496-5144497		0.00
N	alternative_donor	CUFF.579	chr2	+	chr2:3405665-3425651	chr2:3425558-3425651		chr2:3405665-3425557	chr2:3405664-3405665		0.00
K	alternative_acceptor	CUFF.85	chr1	-	chr1:247320520-247322307	chr1:247320706-247322307		chr1:247320520-247320705	chr1:247320519-247320520		41.30
N	jcn_only_AD		chr3	-	chr3:73453547-73482789;chr3:73453547-73651504;chr3:73453547-73523605;chr3:73453547-73605850;chr3:73453547-73618301	chr3:73453547-73610601					6.38
N	jcn_only_AA	CUFF.101	chr10	-	chr10:35351991-35360126	chr10:35353045-35360126		chr10:35351991-35353044	chr10:35351990-35351991		25.87
K	jcn_only_AD	CUFF.644	chr2	+	chr2:171400499-171508137	chr2:171503450-171508137					2.70
N	alternative_donor	CUFF.686	chr20	+	chr20:33114149-33122431	chr20:33118039-33122431		chr20:33114149-33118038	chr20:33114148-33114149		10.53
K	alternative_acceptor	CUFF.939	chr6	+	chr6:111306342-111310230	chr6:111306342-111310190		chr6:111310191-111310230	chr6:111310230-111310231		59.38
N	alternative_donor	CUFF.551	chr19	+	chr19:45261671-45261980	chr19:45261731-45261980		chr19:45261671-45261730	chr19:45261670-45261671		12.31
N	alternative_donor	CUFF.489	chr18	-	chr18:47329224-47337765;chr18:47329224-47340051;chr18:47329224-47339094;chr18:47329224-47339838;chr18:47329224-47340101	chr18:47329224-47340186		chr18:47337766-47339094;chr18:47339095-47339838;chr18:47339839-47340051;chr18:47340052-47340101;chr18:47340102-47340186	chr18:47339094-47339095;chr18:47339838-47339839;chr18:47340051-47340052;chr18:47340101-47340102;chr18:47340186-47340187		8.05
K	cassette	CUFF.1042	chr8	-	chr8:80963864-80965516	chr8:80963864-80964840;chr8:80964911-80965516		chr8:80964841-80964910			19.78
N	jcn_only_AD	CUFF.187	chr11	+	chr11:119056875-119057187	chr11:119056951-119057187		chr11:119056875-119056950	chr11:119056874-119056875		7.59
K	alternative_last_exon	CUFF.324	chr15	-	chr15:55742566-55783320	chr15:55759360-55783320	chr15:55742420-55742565	chr15:55759077-55759359			84.62
N	intron_retention		chr12	+	chr12:69237045-69237520				chr12:69237044-69237045;chr12:69237520-69237521		88.00
K	alternative_first_exon	CUFF.560	chr19	-	chr19:51528923-51530712;chr19:51528923-51529011;chr19:51528923-51531199	chr19:51528923-51529793	chr19:51530713-51530984;chr19:51529012-51529110;chr19:51531200-51531383	chr19:51529794-51530493			31.18
N	alternative_donor	CUFF.1026	chr8	+	chr8:17434266-17434644	chr8:17434270-17434644		chr8:17434266-17434269	chr8:17434265-17434266		15.79
K	cassette	CUFF.201	chr12	+	chr12:4662314-4668022	chr12:4662314-4665518;chr12:4665717-4668022		chr12:4665519-4665716			77.02
K	alternative_first_exon	CUFF.273	chr14	+	chr14:61448962-61449225,chr14:61448406-61449225;chr14:61448101-61449225	chr14:61448410-61449225	chr14:61447788-61448100	chr14:61448408-61448409			7.84
N	jcn_only_AD	CUFF.509	chr19	-	chr19:6047516-6049146;chr19:6047516-6110403;chr19:6047516-6057172;chr19:6047516-6072015	chr19:6047516-6148241		chr19:6049147-6057172;chr19:6057173-6072015;chr19:6072016-6110403;chr19:6110404-6148241	chr19:6057172-6057173;chr19:6072015-6072016;chr19:6110403-6110404;chr19:6148241-6148242		7.45
N	cassette	CUFF.234	chr12	+	chr12:69207409-69222550;chr12:69214155-69222550	chr12:69207409-69218142,chr12:69214155-69218142;chr12:69218211-69222550		chr12:69218143-69218210			90.48
K	alternative_acceptor	CUFF.414	chr16	-	chr16:87807148-87811473	chr16:87807196-87811473		chr16:87807148-87807195	chr16:87807147-87807148		40.00
K	alternative_acceptor	CUFF.159	chr11	-	chr11:61514596-61514822	chr11:61514614-61514822		chr11:61514596-61514613	chr11:61514595-61514596		70.83
N	alternative_first_exon	CUFF.490	chr18	+	chr18:55711941-56057877	chr18:56056425-56057877	chr18:55711599-55711940	chr18:56056317-56056424			94.74
N	jcn_only_AA		chr3	-	chr3:33617768-33623312	chr3:33618757-33623312					20.69
K	intron_retention	CUFF.450	chr17	+	chr17:46993550-46998521				chr17:46993549-46993550;chr17:46998521-46998522		7.55
N	alternative_donor	CUFF.603	chr2	+	chr2:48898820-49003418;chr2:48996261-49003418	chr2:48996214-49003418		chr2:48898820-48996213;chr2:48996214-48996260	chr2:48898819-48898820;chr2:48996213-48996214		0.00
K	jcn_only_AA	CUFF.187	chr11	+	chr11:119056220-119056633;chr11:119056220-119056630	chr11:119056220-119056557		chr11:119056558-119056630;chr11:119056631-119056633	chr11:119056630-119056631;chr11:119056633-119056634		6.12
N	alternative_donor	CUFF.1001	chr7	+	chr7:107236448-107240841	chr7:107240748-107240841		chr7:107236448-107240747	chr7:107236447-107236448		0.17
K	alternative_first_exon	CUFF.893	chr5	+	chr5:137514540-137515348	chr5:137514892-137515348,chr5:137515023-137515348	chr5:137514408-137514539	chr5:137514654-137514891			91.43
K	alternative_first_exon	CUFF.675	chr20	+	chr20:2842351-2843710	chr20:2843581-2843710	chr20:2842261-2842350	chr20:2843041-2843580			76.32
K	cassette	CUFF.162	chr11	+	chr11:63670631-63672257	chr11:63670631-63671457;chr11:63671620-63672257		chr11:63671458-63671619			22.89
K	intron_retention	CUFF.564	chr19	+	chr19:52905282-52909159				chr19:52905281-52905282;chr19:52909159-52909160		7.04
N	jcn_only_AA		chr17	+	chr17:61904875-61905210;chr17:61904875-61905188;chr17:61904875-61905478;chr17:61904875-61905497	chr17:61904875-61905033					3.76
K	intron_retention	CUFF.1016	chr7	+	chr7:150815432-150815591				chr7:150815431-150815432;chr7:150815591-150815592		21.77
K	cassette	CUFF.292	chr14	+	chr14:92958585-92959819	chr14:92958585-92959170;chr14:92959269-92959819		chr14:92959171-92959268			3.92
K	intron_retention	CUFF.955	chr6	+	chr6:165241453-165243009				chr6:165241452-165241453;chr6:165243009-165243010	chr6:165241156-165241452;chr6:165243010-165245208	25.00
N	cassette	CUFF.787	chr3	+	chr3:132764865-132948109	chr3:132764865-132793158;chr3:132793203-132948109		chr3:132793159-132793202			48.89
N	alternative_donor	CUFF.1002,CUFF.999	chr7	-	chr7:107642179-107643293	chr7:107642179-107642571		chr7:107642572-107643293	chr7:107643293-107643294		20.37
N	alternative_acceptor	CUFF.28	chr1	+	chr1:70820892-70831828;chr1:70820892-70832126	chr1:70820892-70832009		chr1:70831829-70832009;chr1:70832010-70832126	chr1:70832009-70832010;chr1:70832126-70832127		2.67
K	alternative_first_exon	CUFF.143	chr11	+	chr11:2466715-2542708	chr11:2483208-2542708	chr11:2466171-2466714	chr11:2483038-2483207			62.07
N	jcn_only_AD	CUFF.195,CUFF.224	chr12	-	chr12:53471046-53473094	chr12:53471046-53471844		chr12:53471845-53473094	chr12:53473094-53473095		5.41
K	cassette	CUFF.995	chr7	-	chr7:99032892-99057708	chr7:99032892-99039012;chr7:99039111-99057708		chr7:99039013-99039110			92.00
N	jcn_only_AA	CUFF.1066	chr9	-	chr9:15185405-15186941	chr9:15185527-15186941		chr9:15185405-15185526	chr9:15185404-15185405		6.06
K	intron_retention		chr2	-	chr2:253116-260084				chr2:253115-253116;chr2:260084-260085		54.93
N	jcn_only_AA		chr18	+	chr18:77875534-77905317	chr18:77875534-77890985		chr18:77890986-77905317	chr18:77905317-77905318		83.33
N	alternative_acceptor	CUFF.579,CUFF.631	chr2	+	chr2:109085541-109086106	chr2:109085541-109085755		chr2:109085756-109086106	chr2:109086106-109086107		15.38
N	alternative_acceptor	CUFF.572	chr2	-	chr2:262751-263210	chr2:262787-263210		chr2:262751-262786	chr2:262750-262751		30.43
K	cassette	CUFF.175	chr11	+	chr11:101852696-101863508	chr11:101852696-101857562;chr11:101857773-101863508		chr11:101857563-101857772			40.35
N	alternative_donor	CUFF.923	chr6	+	chr6:34452922-34494019;chr6:34482846-34494019	chr6:34434048-34494019		chr6:34434048-34452921;chr6:34452922-34482845	chr6:34434047-34434048;chr6:34452921-34452922		100.00
N	jcn_only_AA	CUFF.87	chr10	+	chr10:35484143-35495822	chr10:35484143-35490378		chr10:35490379-35495822	chr10:35495822-35495823		76.67
N	alternative_donor	CUFF.386	chr16	+	chr16:21716614-21721208	chr16:21716766-21721208		chr16:21716614-21716765	chr16:21716613-21716614		15.00
K	alternative_last_exon	CUFF.373	chr16	+	chr16:2653729-2663960	chr16:2653729-2660462	chr16:2663961-2664162	chr16:2660463-2661053			6.82
K	intron_retention	CUFF.115	chr10	-	chr10:74094376-74095591				chr10:74094375-74094376;chr10:74095591-74095592		91.43
N	alternative_donor	CUFF.165	chr11	+	chr11:65480527-65480818	chr11:65480530-65480818		chr11:65480527-65480529	chr11:65480526-65480527		86.27
K	alternative_donor	CUFF.475	chr17	-	chr17:79994185-79994289	chr17:79994185-79994259		chr17:79994260-79994289	chr17:79994289-79994290		74.37
K	jcn_only_AD	CUFF.244	chr13	+	chr13:21205242-21228014	chr13:21219098-21228014					12.68
N	alternative_donor	CUFF.102	chr10	+	chr10:35464928-35467816;chr10:35437420-35467816;chr10:35426808-35467816;chr10:35456732-35467816;chr10:35464634-35467816	chr10:35416122-35467816		chr10:35416122-35426807;chr10:35426808-35437419;chr10:35437420-35456731;chr10:35456732-35464633;chr10:35464634-35464927	chr10:35416121-35416122;chr10:35426807-35426808;chr10:35437419-35437420;chr10:35456731-35456732;chr10:35464633-35464634		86.36
K	alternative_first_exon	CUFF.786	chr3	-	chr3:127299007-127306912,chr3:127299007-127310732;chr3:127299007-127313642;chr3:127299007-127309725	chr3:127299007-127309252	chr3:127313643-127313776;chr3:127309726-127309965	chr3:127309253-127309667			47.31
K	alternative_last_exon	CUFF.547	chr19	-	chr19:41938968-41939441;chr19:41938314-41939441	chr19:41939340-41939441	chr19:41937223-41938313	chr19:41938319-41939339			64.02
N	alternative_donor	CUFF.1098	chr9	-	chr9:130929444-130931330;chr9:130929444-130931354	chr9:130929444-130929817		chr9:130929818-130931330;chr9:130931331-130931354	chr9:130931330-130931331;chr9:130931354-130931355		21.43
N	alternative_donor	CUFF.589,CUFF.609	chr2	-	chr2:27693963-27695116	chr2:27693963-27694099		chr2:27694100-27695116	chr2:27695116-27695117		89.80
N	cassette	CUFF.493	chr18	+	chr18:61379928-61387246	chr18:61379928-61383268;chr18:61383387-61387246		chr18:61383269-61383386			93.48
K	intron_retention		chr11	+	chr11:118401950-118402492				chr11:118401949-118401950;chr11:118402492-118402493	chr11:118401663-118401949;chr11:118402493-118402586	69.23
K	intron_retention	CUFF.954	chr6	+	chr6:161529892-161529982				chr6:161529891-161529892;chr6:161529982-161529983	chr6:161529775-161529891	77.42
K	intron_retention	CUFF.157	chr11	+	chr11:57310654-57310731				chr11:57310653-57310654;chr11:57310731-57310732		72.00
K	jcn_only_AA	CUFF.1073	chr9	+	chr9:43907538-43908435	chr9:43907538-43908111		chr9:43908112-43908435	chr9:43908435-43908436		20.00
N	alternative_donor	CUFF.504	chr19	+	chr19:1440241-1440347	chr19:1440253-1440347		chr19:1440241-1440252	chr19:1440240-1440241		78.93
K	jcn_only_AD	CUFF.406	chr16	-	chr16:70265062-70265339	chr16:70265062-70265225		chr16:70265226-70265339	chr16:70265339-70265340		27.69
N	alternative_acceptor	CUFF.350	chr15	-	chr15:84871773-84872928;chr15:84872839-84872928	chr15:84871760-84872928		chr15:84871760-84871772;chr15:84871773-84872838	chr15:84871759-84871760;chr15:84871772-84871773		27.78
N	intron_retention		chr16	-	chr16:4445341-4466785				chr16:4445340-4445341;chr16:4466785-4466786		45.45
N	alternative_last_exon		chr3	+	chr3:132793203-132948109	chr3:132793203-132837881	chr3:132948110-132948195	chr3:132837882-132838228			90.74
N	jcn_only_AA		chr12	+	chr12:26148064-26208211	chr12:26148064-26208168		chr12:26208169-26208211	chr12:26208211-26208212		35.14
N	alternative_donor	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57521007		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		16.22
K	intron_retention	CUFF.389	chr16	+	chr16:22494549-22494716				chr16:22494548-22494549;chr16:22494716-22494717		37.50
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		21.21
K	jcn_only_AD	CUFF.891	chr5	+	chr5:134190853-134193046	chr5:134191018-134193046		chr5:134190853-134191017	chr5:134190852-134190853		22.22
N	cassette	CUFF.1124	chrX	+	chrX:47028898-47032526	chrX:47028898-47030426;chrX:47030658-47032526		chrX:47030427-47030657			41.67
N	cassette	CUFF.184	chr11	-	chr11:118919599-118920267	chr11:118919599-118919729;chr11:118920083-118920267		chr11:118919730-118920082			90.95
K	jcn_only_AD	CUFF.647,CUFF.659	chr2	-	chr2:175816931-175869933	chr2:175816931-175869621		chr2:175869622-175869933	chr2:175869933-175869934		90.48
N	coord_cassette	CUFF.905	chr6	+	chr6:292561-345853	chr6:292561-304627;chr6:304662-311879;chr6:311963-345853		chr6:304628-304661;chr6:311880-311962			68.92
K	alternative_acceptor	CUFF.352	chr15	-	chr15:90432369-90437112	chr15:90432373-90437112		chr15:90432369-90432372	chr15:90432368-90432369		84.59
N	alternative_acceptor		chr15	+	chr15:57574797-57583026;chr15:57574797-57591423	chr15:57574797-57578354		chr15:57578355-57583026;chr15:57583027-57591423	chr15:57583026-57583027;chr15:57591423-57591424		68.57
K	cassette	CUFF.400	chr16	-	chr16:63565209-63651596	chr16:63565209-63566720;chr16:63566836-63651596		chr16:63566721-63566835			34.48
N	alternative_acceptor	CUFF.1004	chr7	-	chr7:110603622-111127293	chr7:111123785-111127293		chr7:110603622-111123784	chr7:110603621-110603622		0.00
N	alternative_acceptor	CUFF.18	chr1	+	chr1:32560573-32566042	chr1:32560573-32561260		chr1:32561261-32566042	chr1:32566042-32566043		0.00
N	alternative_first_exon	CUFF.207	chr12	+	chr12:13349807-13366614	chr12:13366510-13366614	chr12:13349561-13349806	chr12:13366313-13366509			93.07
K	alternative_acceptor	CUFF.259,CUFF.280	chr14	+	chr14:24572465-24573050	chr14:24572465-24572718		chr14:24572719-24573050	chr14:24573050-24573051		94.85
K	cassette	CUFF.904	chr5	-	chr5:178045780-178050256	chr5:178045780-178046838;chr5:178046898-178050256		chr5:178046839-178046897			4.20
N	alternative_acceptor	CUFF.230	chr12	-	chr12:56705180-56708634;chr12:56705238-56708634;chr12:56705199-56708634	chr12:56706670-56708634		chr12:56705180-56705198;chr12:56705199-56705237;chr12:56705238-56706669	chr12:56705179-56705180;chr12:56705198-56705199;chr12:56705237-56705238		10.94
N	cassette	CUFF.974	chr7	-	chr7:38860866-38902144	chr7:38860866-38869853;chr7:38869929-38902144		chr7:38869854-38869928			95.18
N	alternative_donor	CUFF.457	chr17	+	chr17:61568730-61571282;chr17:61571021-61571282	chr17:61567390-61571282		chr17:61567390-61568729;chr17:61568730-61571020	chr17:61567389-61567390;chr17:61568729-61568730		6.25
K	alternative_acceptor	CUFF.272	chr14	-	chr14:60018141-60027836	chr14:60018155-60027836		chr14:60018141-60018154	chr14:60018140-60018141		65.00
N	alternative_donor	CUFF.918	chr6	+	chr6:31937094-31937291	chr6:31937198-31937291		chr6:31937094-31937197	chr6:31937093-31937094		52.58
N	alternative_acceptor	CUFF.1073	chr9	+	chr9:43853617-43854068;chr9:43853617-43861005	chr9:43853617-43861002		chr9:43854069-43861002;chr9:43861003-43861005	chr9:43861002-43861003;chr9:43861005-43861006		27.27
K	alternative_acceptor	CUFF.299	chr14	+	chr14:105054647-105054958	chr14:105054647-105054914		chr14:105054915-105054958	chr14:105054958-105054959		30.00
N	alternative_first_exon	CUFF.389	chr16	+	chr16:22448814-22466022	chr16:22462980-22466022	chr16:22448329-22448813	chr16:22462874-22462979			90.00
K	cassette	CUFF.52	chr1	-	chr1:156449589-156452228	chr1:156449589-156450625;chr1:156450764-156452228		chr1:156450626-156450763			88.24
K	jcn_only_AA	CUFF.1016	chr7	+	chr7:150817833-150820880	chr7:150817833-150819811		chr7:150819812-150820880	chr7:150820880-150820881		80.56
K	jcn_only_AD	CUFF.566	chr19	+	chr19:54656737-54657451	chr19:54656820-54657451		chr19:54656737-54656819	chr19:54656736-54656737		74.78
K	alternative_acceptor	CUFF.944	chr6	+	chr6:126307769-126314938	chr6:126307769-126314902		chr6:126314903-126314938	chr6:126314938-126314939		28.57
N	intron_retention	CUFF.201	chr12	+	chr12:4662314-4665596				chr12:4662313-4662314;chr12:4665596-4665597		91.04
K	alternative_acceptor	CUFF.685	chr20	-	chr20:31052921-31062403	chr20:31052938-31062403		chr20:31052921-31052937	chr20:31052920-31052921		9.52
K	jcn_only_AD	CUFF.403	chr16	+	chr16:67233486-67233586	chr16:67233497-67233586		chr16:67233486-67233496	chr16:67233485-67233486		50.41
N	alternative_acceptor	CUFF.872,CUFF.894	chr5	+	chr5:139915124-139916973	chr5:139915124-139916922		chr5:139916923-139916973	chr5:139916973-139916974	chr5:139914947-139915123;chr5:139916974-139917174	19.40
K	alternative_acceptor	CUFF.741	chr3	-	chr3:33451080-33453072	chr3:33451094-33453072		chr3:33451080-33451093	chr3:33451079-33451080		94.31
N	cassette	CUFF.572	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			32.00
K	alternative_acceptor	CUFF.688	chr20	-	chr20:34246905-34252800	chr20:34246937-34252800		chr20:34246905-34246936	chr20:34246904-34246905		46.67
N	coord_cassette	CUFF.467	chr17	-	chr17:76993727-77005745	chr17:76993727-76993921;chr17:76994046-76994229;chr17:76994369-77005745		chr17:76993922-76994045;chr17:76994230-76994368			92.11
K	jcn_only_AA	CUFF.741	chr3	-	chr3:33451080-33453072	chr3:33451094-33453072		chr3:33451080-33451093	chr3:33451079-33451080		96.92
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		91.76
K	cassette	CUFF.708	chr22	+	chr22:21057411-21057920	chr22:21057411-21057755;chr22:21057813-21057920		chr22:21057756-21057812			52.40
K	alternative_acceptor	CUFF.665	chr2	+	chr2:231934883-231937046	chr2:231934883-231936902		chr2:231936903-231937046	chr2:231937046-231937047		7.92
K	cassette	CUFF.775	chr3	-	chr3:120394711-120400943	chr3:120394711-120396750;chr3:120396839-120400943		chr3:120396751-120396838			5.09
K	alternative_last_exon	CUFF.686	chr20	+	chr20:33114149-33122431	chr20:33114149-33117655	chr20:33122432-33122599	chr20:33117656-33119104			58.05
K	cassette	CUFF.395	chr16	+	chr16:56226529-56309842	chr16:56226529-56268924;chr16:56269297-56309842		chr16:56268925-56269296			76.47
N	coord_cassette	CUFF.201	chr12	+	chr12:4653071-4657257	chr12:4653071-4654947;chr12:4654999-4655474;chr12:4655585-4657257		chr12:4654948-4654998;chr12:4655475-4655584			56.82
N	intron_retention		chr11	-	chr11:410028-417324				chr11:410027-410028;chr11:417324-417325		47.37
N	alternative_donor	CUFF.918	chr6	+	chr6:31935860-31936104	chr6:31935897-31936104		chr6:31935860-31935896	chr6:31935859-31935860		27.10
N	alternative_acceptor		chr22	+	chr22:21057981-21058255	chr22:21057981-21058106		chr22:21058107-21058255	chr22:21058255-21058256		31.67
N	cassette	CUFF.589	chr2	-	chr2:27668317-27668795	chr2:27668317-27668611;chr2:27668711-27668795		chr2:27668612-27668710			68.57
N	alternative_acceptor	CUFF.1002	chr7	-	chr7:107572823-107575859	chr7:107572939-107575859		chr7:107572823-107572938	chr7:107572822-107572823		81.82
K	alternative_donor	CUFF.243	chr12	-	chr12:133181171-133181291	chr12:133181171-133181286		chr12:133181287-133181291	chr12:133181291-133181292		3.45
K	alternative_acceptor	CUFF.136	chr11	-	chr11:407535-407816	chr11:407569-407816		chr11:407535-407568	chr11:407534-407535		70.28
N	alternative_donor	CUFF.1066	chr9	-	chr9:15188131-15189701	chr9:15188131-15189571		chr9:15189572-15189701	chr9:15189701-15189702		43.59
K	intron_retention	CUFF.792	chr3	-	chr3:133896918-133901845				chr3:133896917-133896918;chr3:133901845-133901846		23.88
N	intron_retention		chr3	-	chr3:49349088-49362134				chr3:49349087-49349088;chr3:49362134-49362135		92.00
N	jcn_only_AD	CUFF.396	chr16	-	chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57514241		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		1.79
K	alternative_last_exon	CUFF.435	chr17	+	chr17:29490395-29508439	chr17:29490395-29496908	chr17:29508440-29508507	chr17:29496909-29497074			76.56
N	intron_retention		chr6	-	chr6:31938917-31939096				chr6:31938916-31938917;chr6:31939096-31939097		84.18
K	coord_cassette	CUFF.584	chr2	-	chr2:11593925-11605897	chr2:11593925-11595467;chr2:11595601-11597304;chr2:11597360-11605897		chr2:11595468-11595600;chr2:11597305-11597359			38.04
K	jcn_only_AA	CUFF.195	chr12	-	chr12:333283-333566	chr12:333296-333566		chr12:333283-333295	chr12:333282-333283		71.01
N	alternative_donor	CUFF.579	chr2	+	chr2:3453249-3461391;chr2:3447663-3461391	chr2:3461001-3461391		chr2:3447663-3453248;chr2:3453249-3461000	chr2:3447662-3447663;chr2:3453248-3453249		0.54
K	cassette	CUFF.223	chr12	-	chr12:52992897-52994810	chr12:52992897-52993054;chr12:52993194-52994810		chr12:52993055-52993193			48.15
K	jcn_only_AD	CUFF.180	chr11	+	chr11:117073889-117074022	chr11:117073910-117074022		chr11:117073889-117073909	chr11:117073888-117073889		66.92
N	jcn_only_AA		chr14	-	chr14:104230817-104245081;chr14:104225643-104245081	chr14:104224089-104245081					54.55
N	jcn_only_AA		chr16	+	chr16:3115828-3117443	chr16:3115828-3117377		chr16:3117378-3117443	chr16:3117443-3117444		98.29
N	coord_cassette	CUFF.589	chr2	-	chr2:27668317-27668795	chr2:27668317-27668419;chr2:27668497-27668611;chr2:27668711-27668795		chr2:27668420-27668496;chr2:27668612-27668710			75.77
K	cassette	CUFF.79	chr1	+	chr1:224378022-224380033	chr1:224378022-224378793;chr1:224378859-224380033		chr1:224378794-224378858			69.34
K	intron_retention	CUFF.1001	chr7	+	chr7:107221091-107221203				chr7:107221090-107221091;chr7:107221203-107221204		76.00
N	alternative_acceptor	CUFF.929	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		20.80
N	alternative_donor	CUFF.820	chr4	+	chr4:6912329-6925099;chr4:6911679-6925099	chr4:6911233-6925099		chr4:6911233-6911678;chr4:6911679-6912328	chr4:6911232-6911233;chr4:6911678-6911679		96.63
K	cassette	CUFF.174	chr11	+	chr11:94707233-94730187	chr11:94707233-94708817;chr11:94708913-94730187		chr11:94708818-94708912			20.00
N	jcn_only_AA	CUFF.65,CUFF.78	chr1	+	chr1:222837491-222838650	chr1:222837491-222838224		chr1:222838225-222838650	chr1:222838650-222838651		18.18
K	cassette	CUFF.567	chr19	+	chr19:55084903-55085542	chr19:55084903-55085297;chr19:55085380-55085542		chr19:55085298-55085379			69.05
K	cassette	CUFF.781	chr3	+	chr3:125639749-125647337	chr3:125639749-125643808;chr3:125643959-125647337		chr3:125643809-125643958			95.12
K	alternative_first_exon	CUFF.910	chr6	-	chr6:5109726-5132951,chr6:5109726-5144371;chr6:5109726-5260880	chr6:5109726-5113304	chr6:5260881-5261258	chr6:5113305-5113651			63.27
N	alternative_last_exon	CUFF.188	chr11	-	chr11:119230945-119252182	chr11:119244232-119252182	chr11:119230894-119230944	chr11:119243570-119244231			41.67
K	alternative_first_exon	CUFF.755	chr3	+	chr3:51743450-51746488	chr3:51745736-51746488	chr3:51742864-51743449	chr3:51745196-51745735			91.31
N	alternative_donor	CUFF.17	chr1	+	chr1:31819588-31821675	chr1:31819666-31821675		chr1:31819588-31819665	chr1:31819587-31819588		4.05
N	intron_retention		chr6	-	chr6:31938925-31939705				chr6:31938924-31938925;chr6:31939705-31939706		90.21
K	cassette	CUFF.114	chr10	-	chr10:73963283-73970489	chr10:73963283-73964179;chr10:73964264-73970489		chr10:73964180-73964263			14.93
N	jcn_only_AA	CUFF.775	chr3	-	chr3:120371494-120389273	chr3:120371499-120389273		chr3:120371494-120371498	chr3:120371493-120371494		87.91
K	jcn_only_AA	CUFF.85	chr1	-	chr1:247320520-247322307	chr1:247320706-247322307		chr1:247320520-247320705	chr1:247320519-247320520		48.08
K	jcn_only_AA	CUFF.47	chr1	-	chr1:151149508-151150476	chr1:151149541-151150476		chr1:151149508-151149540	chr1:151149507-151149508		29.69
N	alternative_donor	CUFF.490	chr18	+	chr18:55895140-55912658;chr18:55833094-55912658;chr18:55865102-55912658;chr18:55895121-55912658;chr18:55888990-55912658	chr18:55862966-55912658		chr18:55833094-55862965;chr18:55862966-55865101;chr18:55865102-55888989;chr18:55888990-55895120;chr18:55895121-55895139	chr18:55833093-55833094;chr18:55862965-55862966;chr18:55865101-55865102;chr18:55888989-55888990;chr18:55895120-55895121		0.00
N	cassette	CUFF.132	chr10	-	chr10:123673409-123687358	chr10:123673409-123683780;chr10:123683845-123687358		chr10:123683781-123683844			76.19
N	coord_cassette	CUFF.234	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			64.44
K	intron_retention	CUFF.1040	chr8	+	chr8:75262708-75263532				chr8:75262707-75262708;chr8:75263532-75263533		85.14
K	coord_cassette	CUFF.1014	chr7	+	chr7:148984868-148989301	chr7:148984868-148987028;chr7:148987130-148988646;chr7:148988837-148989301		chr7:148987029-148987129;chr7:148988647-148988836			67.65
K	intron_retention		chr8	-	chr8:99057628-99057735				chr8:99057627-99057628;chr8:99057735-99057736		5.96
K	cassette	CUFF.654	chr2	-	chr2:204335037-204354306;chr2:204326649-204354306	chr2:204326649-204341798,chr2:204335037-204341798;chr2:204341880-204354306		chr2:204341799-204341879			35.78
N	alternative_donor	CUFF.751	chr3	-	chr3:46982556-47007473;chr3:46982556-47017842	chr3:46982556-47018126		chr3:47007474-47017842;chr3:47017843-47018126	chr3:47017842-47017843;chr3:47018126-47018127		50.00
K	intron_retention	CUFF.1136	chrX	+	chrX:107335067-107369306				chrX:107335066-107335067;chrX:107369306-107369307		4.48
K	jcn_only_AD	CUFF.5	chr1	+	chr1:11159872-11161857	chr1:11159968-11161857		chr1:11159872-11159967	chr1:11159871-11159872		60.00
N	alternative_donor	CUFF.1136	chrX	+	chrX:107395089-107396208	chrX:107395236-107396208		chrX:107395089-107395235	chrX:107395088-107395089		4.98
K	cassette	CUFF.751	chr3	-	chr3:47018334-47023421	chr3:47018334-47018427;chr3:47018531-47023421		chr3:47018428-47018530			11.11
K	cassette	CUFF.1014	chr7	+	chr7:148987130-148989301	chr7:148987130-148988646;chr7:148988837-148989301		chr7:148988647-148988836			47.46
K	alternative_first_exon	CUFF.2	chr1	+	chr1:2006573-2066700,chr1:2043257-2066700,chr1:2005369-2066700,chr1:2013900-2066700,chr1:2036335-2066700,chr1:2029995-2066700,chr1:2065440-2066700,chr1:2006819-2066700,chr1:2005715-2066700,chr1:2047750-2066700;chr1:1991031-2066700;chr1:2006207-2066700	chr1:2066526-2066700	chr1:1990980-1991030;chr1:2006119-2006206	chr1:2066291-2066525			26.93
N	alternative_acceptor	CUFF.519	chr19	+	chr19:17611686-17615263	chr19:17611686-17612081		chr19:17612082-17615263	chr19:17615263-17615264		3.45
N	jcn_only_AD		chr14	-	chr14:104263856-104313344;chr14:104263856-104313635;chr14:104263856-104313111	chr14:104263856-104306415					13.95
K	jcn_only_AA	CUFF.1061	chr8	+	chr8:144351691-144356873;chr8:144351691-144354565	chr8:144351691-144356889					53.85
K	intron_retention		chr8	+	chr8:144356973-144358066				chr8:144356972-144356973;chr8:144358066-144358067		17.53
K	jcn_only_AA	CUFF.1114	chrX	-	chrX:10417657-10422909	chrX:10417757-10422909		chrX:10417657-10417756	chrX:10417656-10417657		82.86
K	cassette	CUFF.485	chr18	-	chr18:44284628-44336340	chr18:44284628-44301324;chr18:44301433-44336340		chr18:44301325-44301432			97.60
K	coord_cassette	CUFF.61	chr1	+	chr1:167353189-167365522	chr1:167353189-167356417;chr1:167356485-167358824;chr1:167358999-167365522		chr1:167356418-167356484;chr1:167358825-167358998			98.04
N	jcn_only_AD	CUFF.155	chr11	+	chr11:36459027-36472758	chr11:36467991-36472758		chr11:36459027-36467990	chr11:36459026-36459027		52.00
N	alternative_donor	CUFF.374	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		13.33
K	cassette	CUFF.983	chr7	-	chr7:74984930-74988197	chr7:74984930-74987565;chr7:74987790-74988197		chr7:74987566-74987789			25.00
N	alternative_acceptor		chr2	+	chr2:1243549-1251098	chr2:1243549-1246509		chr2:1246510-1251098	chr2:1251098-1251099		0.00
K	coord_cassette	CUFF.644	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			89.66
N	intron_retention	CUFF.504	chr19	+	chr19:1438892-1439604				chr19:1438891-1438892;chr19:1439604-1439605		38.24
K	alternative_first_exon	CUFF.1117	chrX	+	chrX:15699171-15706783;chrX:15693696-15706783;chrX:15693092-15706783;chrX:15693902-15706783	chrX:15699311-15706783	chrX:15693624-15693695;chrX:15692971-15693091;chrX:15693813-15693901	chrX:15699124-15699310			20.00
K	alternative_first_exon	CUFF.558	chr19	-	chr19:50548045-50554138	chr19:50548045-50551215	chr19:50554139-50554319	chr19:50551216-50551342			35.29
K	alternative_last_exon	CUFF.920,CUFF.944	chr6	+	chr6:126317187-126319368	chr6:126317187-126319198	chr6:126319369-126319461	chr6:126319199-126319357			94.00
N	jcn_only_AD	CUFF.945	chr6	-	chr6:128313855-128316393;chr6:128313855-128316606	chr6:128313855-128316591		chr6:128316394-128316591;chr6:128316592-128316606	chr6:128316591-128316592;chr6:128316606-128316607		1.67
N	cassette	CUFF.436	chr17	+	chr17:29576138-29585361	chr17:29576138-29584704;chr17:29584745-29585361		chr17:29584705-29584744			83.87
K	intron_retention	CUFF.182	chr11	+	chr11:118403923-118404571				chr11:118403922-118403923;chr11:118404571-118404572	chr11:118403632-118403922;chr11:118404572-118404602	6.56
N	jcn_only_AD	CUFF.97	chr10	-	chr10:27112235-27149675	chr10:27112235-27128661		chr10:27128662-27149675	chr10:27149675-27149676		4.88
K	intron_retention	CUFF.929	chr6	-	chr6:43481190-43481325				chr6:43481189-43481190;chr6:43481325-43481326		3.43
N	cassette	CUFF.595	chr2	+	chr2:33505226-33525517	chr2:33505226-33518226;chr2:33518350-33525517		chr2:33518227-33518349			93.56
N	jcn_only_AA	CUFF.726	chr22	+	chr22:47308085-47370185	chr22:47308085-47309229		chr22:47309230-47370185	chr22:47370185-47370186		12.75
N	jcn_only_AD	CUFF.316	chr15	-	chr15:44907765-44912387	chr15:44907765-44912322		chr15:44912323-44912387	chr15:44912387-44912388		52.17
K	alternative_first_exon	CUFF.483	chr18	+	chr18:14728514-14797659	chr18:14796415-14797659	chr18:14728198-14728513	chr18:14796342-14796414			25.49
K	cassette	CUFF.218	chr12	-	chr12:49334972-49351092	chr12:49334972-49349880;chr12:49349981-49351092		chr12:49349881-49349980			52.31
N	alternative_donor	CUFF.390,CUFF.406	chr16	-	chr16:23505700-23507034;chr16:23505700-23507014	chr16:23505700-23507009		chr16:23507010-23507014;chr16:23507015-23507034	chr16:23507014-23507015;chr16:23507034-23507035	chr16:23505624-23505699;chr16:23507035-23507099	32.58
N	alternative_donor	CUFF.1007,CUFF.999	chr7	-	chr7:117432836-117450818	chr7:117432836-117433466		chr7:117433467-117450818	chr7:117450818-117450819		0.00
K	jcn_only_AA	CUFF.988	chr7	-	chr7:86541488-86542256	chr7:86541562-86542256		chr7:86541488-86541561	chr7:86541487-86541488		91.37
K	alternative_last_exon	CUFF.535	chr19	-	chr19:21632180-21636351	chr19:21636082-21636351	chr19:21631832-21632179	chr19:21635760-21636081			26.45
N	alternative_donor		chr22	+	chr22:37697061-37699294	chr22:37698073-37699294		chr22:37697061-37698072	chr22:37697060-37697061		25.00
N	cassette	CUFF.752	chr3	-	chr3:49315885-49318176	chr3:49315885-49316246;chr3:49316336-49318176		chr3:49316247-49316335			85.71
K	intron_retention	CUFF.377	chr16	-	chr16:4408485-4409296				chr16:4408484-4408485;chr16:4409296-4409297		23.12
N	intron_retention		chr5	+	chr5:140040401-140041204				chr5:140040400-140040401;chr5:140041204-140041205		53.12
K	alternative_first_exon	CUFF.500	chr18	-	chr18:76737430-76738785,chr18:76737430-76738462	chr18:76737430-76737554	chr18:76738786-76738843	chr18:76737555-76737882			22.95
N	alternative_acceptor	CUFF.693	chr21	+	chr21:15680941-15685264	chr21:15680941-15681292		chr21:15681293-15685264	chr21:15685264-15685265	chr21:15680874-15680940;chr21:15685265-15685452	0.00
N	alternative_donor	CUFF.1097,CUFF.1098	chr9	-	chr9:130941184-130941522;chr9:130941184-130941351	chr9:130941184-130941267		chr9:130941268-130941351;chr9:130941352-130941522	chr9:130941351-130941352;chr9:130941522-130941523		34.59
K	alternative_acceptor	CUFF.85	chr1	-	chr1:247323116-247335149	chr1:247323170-247335149		chr1:247323116-247323169	chr1:247323115-247323116		12.50
N	jcn_only_AA		chr14	+	chr14:61512886-61514868;chr14:61512886-61514965	chr14:61512886-61517229		chr14:61514869-61514965;chr14:61514966-61517229	chr14:61514965-61514966;chr14:61517229-61517230		87.21
N	jcn_only_AA	CUFF.106	chr10	-	chr10:46135412-46143741;chr10:46135870-46143741	chr10:46113709-46143741					10.17
N	jcn_only_AA	CUFF.28	chr1	+	chr1:70820892-70831828;chr1:70820892-70832126	chr1:70820892-70832009		chr1:70831829-70832009;chr1:70832010-70832126	chr1:70832009-70832010;chr1:70832126-70832127		6.52
N	jcn_only_AD		chr14	-	chr14:104263856-104313344;chr14:104263856-104313111;chr14:104263856-104306415	chr14:104263856-104313635					56.47
N	cassette	CUFF.887	chr5	-	chr5:127412786-127418426;chr5:127396937-127418426	chr5:127412786-127417664,chr5:127396937-127417664;chr5:127417887-127418426		chr5:127417665-127417886			20.22
K	intron_retention	CUFF.224	chr12	-	chr12:53459059-53459485				chr12:53459058-53459059;chr12:53459485-53459486		90.48
K	jcn_only_AA	CUFF.138	chr11	+	chr11:826267-828259	chr11:826267-828229		chr11:828230-828259	chr11:828259-828260	chr11:826050-826266;chr11:828260-828772	49.06
K	alternative_first_exon	CUFF.79	chr1	+	chr1:224363650-224377278;chr1:224371534-224377278	chr1:224371121-224377278	chr1:224363458-224363649;chr1:224371312-224371533	chr1:224370860-224371120			33.77
K	alternative_first_exon	CUFF.189	chr11	-	chr11:119291640-119292320;chr11:119291640-119293822	chr11:119291640-119295607	chr11:119292321-119292419;chr11:119293823-119294855	chr11:119295608-119295794			31.94
N	jcn_only_AA	CUFF.2,CUFF.8	chr1	+	chr1:1991031-2066700	chr1:1991031-2002737		chr1:2002738-2066700	chr1:2066700-2066701		35.94
K	alternative_first_exon	CUFF.1150	chrX	+	chrX:153238312-153247300,chrX:153238338-153247300	chrX:153246075-153247300	chrX:153237778-153238311	chrX:153245982-153246074		chrX:153247301-153248646	62.75
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55895140-55912658;chr18:55833094-55912658;chr18:55865102-55912658;chr18:55895121-55912658;chr18:55888990-55912658	chr18:55862966-55912658		chr18:55833094-55862965;chr18:55862966-55865101;chr18:55865102-55888989;chr18:55888990-55895120;chr18:55895121-55895139	chr18:55833093-55833094;chr18:55862965-55862966;chr18:55865101-55865102;chr18:55888989-55888990;chr18:55895120-55895121		1.16
K	intron_retention	CUFF.4	chr1	+	chr1:11083387-11084358				chr1:11083386-11083387;chr1:11084358-11084359		85.48
N	alternative_acceptor	CUFF.581	chr2	-	chr2:4020665-4021134;chr2:4015879-4021134;chr2:4020693-4021134;chr2:4009485-4021134	chr2:4009394-4021134		chr2:4009394-4009484;chr2:4009485-4015878;chr2:4015879-4020664;chr2:4020665-4020692	chr2:4009393-4009394;chr2:4009484-4009485;chr2:4015878-4015879;chr2:4020664-4020665		22.58
N	cassette	CUFF.572	chr2	-	chr2:234273-247537;chr2:234273-243502	chr2:234273-242797;chr2:242872-243502,chr2:242872-247537		chr2:242798-242871			22.11
N	intron_retention	CUFF.980	chr7	+	chr7:73108381-73110735				chr7:73108380-73108381;chr7:73110735-73110736		41.18
K	intron_retention	CUFF.564	chr19	+	chr19:52901158-52901706				chr19:52901157-52901158;chr19:52901706-52901707		84.21
K	intron_retention	CUFF.426	chr17	-	chr17:15584268-15586167				chr17:15584267-15584268;chr17:15586167-15586168		7.87
N	alternative_first_exon	CUFF.478	chr18	+	chr18:158715-162982	chr18:159022-162982	chr18:158304-158714	chr18:158810-159021			83.33
N	cassette	CUFF.2	chr1	+	chr1:2075781-2080310	chr1:2075781-2077465;chr1:2077548-2080310		chr1:2077466-2077547			89.32
N	jcn_only_AA		chr19	+	chr19:40478152-40478368	chr19:40478152-40478275		chr19:40478276-40478368	chr19:40478368-40478369		65.00
N	jcn_only_AA	CUFF.560	chr19	-	chr19:51528923-51529793	chr19:51528955-51529793		chr19:51528923-51528954	chr19:51528922-51528923		6.12
K	alternative_first_exon	CUFF.133	chr10	+	chr10:124151889-124152696;chr10:124134364-124152696	chr10:124134323-124152696	chr10:124151819-124151888;chr10:124134325-124134363	chr10:124134212-124134322			6.36
K	cassette	CUFF.581	chr2	-	chr2:4008147-4021134	chr2:4008147-4009359;chr2:4009394-4021134		chr2:4009360-4009393			97.53
K	intron_retention	CUFF.316	chr15	-	chr15:44876134-44876362				chr15:44876133-44876134;chr15:44876362-44876363		82.46
K	alternative_first_exon	CUFF.302	chr15	-	chr15:23114293-23115116	chr15:23114293-23114585	chr15:23115117-23115256	chr15:23114586-23114702			84.59
N	jcn_only_AD	CUFF.849	chr4	+	chr4:124582989-124750249	chr4:124695531-124750249		chr4:124582989-124695530	chr4:124582988-124582989		2.78
K	alternative_donor	CUFF.180	chr11	+	chr11:117073889-117074022	chr11:117073910-117074022		chr11:117073889-117073909	chr11:117073888-117073889		53.60
K	intron_retention		chr16	+	chr16:3117615-3117984				chr16:3117614-3117615;chr16:3117984-3117985		5.61
K	alternative_first_exon	CUFF.950	chr6	+	chr6:144613044-144724258	chr6:144665441-144724258	chr6:144612873-144613043	chr6:144665149-144665440			71.43
N	cassette	CUFF.150	chr11	-	chr11:8496364-8615290;chr11:8496614-8615290	chr11:8496614-8502080,chr11:8496364-8502080;chr11:8502162-8615290		chr11:8502081-8502161			84.72
K	alternative_donor	CUFF.566	chr19	+	chr19:54656737-54657451	chr19:54656820-54657451		chr19:54656737-54656819	chr19:54656736-54656737		63.29
N	alternative_acceptor	CUFF.119	chr10	-	chr10:78778858-78787580	chr10:78782695-78787580		chr10:78778858-78782694	chr10:78778857-78778858		0.00
K	jcn_only_AA	CUFF.497	chr18	-	chr18:67509632-67562936	chr18:67540483-67562936					68.92
N	alternative_acceptor	CUFF.579	chr2	+	chr2:3464108-3464417;chr2:3464108-3469367	chr2:3464108-3466628		chr2:3464418-3466628;chr2:3466629-3469367	chr2:3466628-3466629;chr2:3469367-3469368		0.44
K	intron_retention	CUFF.382	chr16	+	chr16:14024748-14026013				chr16:14024747-14024748;chr16:14026013-14026014		11.32
N	jcn_only_AD	CUFF.1069	chr9	+	chr9:34991414-34993196	chr9:34992984-34993196		chr9:34991414-34992983	chr9:34991413-34991414		8.82
N	alternative_donor	CUFF.306	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		5.41
N	jcn_only_AA	CUFF.475	chr17	-	chr17:79994185-79994259	chr17:79994199-79994259		chr17:79994185-79994198	chr17:79994184-79994185		5.69
N	jcn_only_AD	CUFF.1081	chr9	-	chr9:86924630-86928273	chr9:86924630-86925326		chr9:86925327-86928273	chr9:86928273-86928274		80.00
K	intron_retention	CUFF.165	chr11	+	chr11:65484454-65486060				chr11:65484453-65484454;chr11:65486060-65486061		3.31
N	jcn_only_AD	CUFF.61	chr1	+	chr1:167345393-167353093	chr1:167345825-167353093		chr1:167345393-167345824	chr1:167345392-167345393		7.75
N	jcn_only_AD	CUFF.221	chr12	+	chr12:52403024-52404664	chr12:52404347-52404664		chr12:52403024-52404346	chr12:52403023-52403024		48.78
K	intron_retention		chr7	+	chr7:107220747-107221203				chr7:107220746-107220747;chr7:107221203-107221204		11.78
N	jcn_only_AD	CUFF.971,CUFF.999	chr7	-	chr7:102608565-102665509	chr7:102608565-102613596		chr7:102613597-102665509	chr7:102665509-102665510		3.70
N	alternative_acceptor		chr11	-	chr11:10821304-10821790	chr11:10821716-10821790		chr11:10821304-10821715	chr11:10821303-10821304		46.30
N	alternative_donor	CUFF.215,CUFF.230	chr12	-	chr12:56709027-56709604;chr12:56709027-56709690	chr12:56709027-56709500		chr12:56709501-56709604;chr12:56709605-56709690	chr12:56709604-56709605;chr12:56709690-56709691		8.97
K	coord_cassette	CUFF.765	chr3	-	chr3:107595034-107596748	chr3:107595034-107595281;chr3:107595379-107596159;chr3:107596345-107596748		chr3:107595282-107595378;chr3:107596160-107596344			37.37
N	jcn_only_AA	CUFF.566	chr19	+	chr19:54657578-54657680;chr19:54657578-54658995	chr19:54657578-54659046		chr19:54657681-54658995;chr19:54658996-54659046	chr19:54658995-54658996;chr19:54659046-54659047		68.09
N	jcn_only_AA	CUFF.754	chr3	-	chr3:49462487-49462799	chr3:49462580-49462799		chr3:49462487-49462579	chr3:49462486-49462487		27.91
N	alternative_acceptor	CUFF.453	chr17	-	chr17:56081080-56082283	chr17:56081363-56082283		chr17:56081080-56081362	chr17:56081079-56081080		3.18
K	alternative_acceptor	CUFF.228	chr12	-	chr12:56578877-56579938	chr12:56578896-56579938		chr12:56578877-56578895	chr12:56578876-56578877		31.82
N	alternative_acceptor	CUFF.497	chr18	-	chr18:67563282-67623990;chr18:67614670-67623990	chr18:67614769-67623990		chr18:67563282-67614669;chr18:67614670-67614768	chr18:67563281-67563282;chr18:67614669-67614670		0.00
K	alternative_first_exon	CUFF.337	chr15	-	chr15:75762341-75766029	chr15:75762341-75763020	chr15:75766030-75766108	chr15:75763021-75763320			83.33
N	alternative_donor	CUFF.195,CUFF.224	chr12	-	chr12:53471046-53473094	chr12:53471046-53471844		chr12:53471845-53473094	chr12:53473094-53473095		0.00
K	intron_retention	CUFF.917	chr6	+	chr6:31796040-31796081				chr6:31796039-31796040;chr6:31796081-31796082		31.25
N	coord_cassette	CUFF.385	chr16	+	chr16:19621738-19637498	chr16:19621738-19627435;chr16:19627514-19628007;chr16:19628131-19637498		chr16:19627436-19627513;chr16:19628008-19628130			96.32
N	alternative_acceptor	CUFF.1101	chr9	-	chr9:131483760-131483929;chr9:131483782-131483929	chr9:131483810-131483929		chr9:131483760-131483781;chr9:131483782-131483809	chr9:131483759-131483760;chr9:131483781-131483782		1.20
N	alternative_first_exon	CUFF.755	chr3	+	chr3:51748138-51749077;chr3:51747327-51749077	chr3:51741184-51749077	chr3:51747980-51748137;chr3:51746489-51747326	chr3:51741086-51741183			1.68
N	alternative_acceptor	CUFF.137	chr11	-	chr11:558980-560682	chr11:559499-560682		chr11:558980-559498	chr11:558979-558980		15.15
N	coord_cassette	CUFF.485	chr18	-	chr18:44284628-44338957	chr18:44284628-44301324;chr18:44301433-44310168;chr18:44310325-44311643;chr18:44311807-44338957		chr18:44301325-44301432;chr18:44310169-44310324;chr18:44311644-44311806			87.88
N	alternative_donor	CUFF.347	chr15	-	chr15:83358206-83366608;chr15:83358206-83378345;chr15:83358206-83358514	chr15:83358206-83377523		chr15:83358515-83366608;chr15:83366609-83377523;chr15:83377524-83378345	chr15:83366608-83366609;chr15:83377523-83377524;chr15:83378345-83378346		0.62
K	intron_retention	CUFF.1032	chr8	-	chr8:38005878-38006158				chr8:38005877-38005878;chr8:38006158-38006159		13.64
K	alternative_first_exon	CUFF.964	chr7	+	chr7:16793656-16815835	chr7:16815510-16815835	chr7:16793160-16793655	chr7:16815298-16815509			84.21
N	alternative_donor	CUFF.456	chr17	+	chr17:60784969-60813446;chr17:60783831-60813446	chr17:60777141-60813446		chr17:60777141-60783830;chr17:60783831-60784968	chr17:60777140-60777141;chr17:60783830-60783831		97.30
N	jcn_only_AD		chr10	+	chr10:35437420-35467799	chr10:35464634-35467799					65.00
N	coord_cassette	CUFF.234	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			87.18
N	alternative_donor	CUFF.588,CUFF.647	chr2	-	chr2:175677211-175689161	chr2:175677211-175686456		chr2:175686457-175689161	chr2:175689161-175689162		0.82
K	jcn_only_AD	CUFF.44,CUFF.49	chr1	-	chr1:145926413-145927113	chr1:145926413-145927048		chr1:145927049-145927113	chr1:145927113-145927114		37.50
N	mutually_exclusive	CUFF.225	chr12	+	chr12:53856352-53859715,chr12:53859758-53861004	chr12:53856352-53858543,chr12:53858637-53861004	chr12:53859716-53859757	chr12:53858544-53858636			4.03
N	alternative_first_exon	CUFF.284	chr14	-	chr14:75127644-75130601	chr14:75127644-75130214	chr14:75130602-75130777	chr14:75130215-75130525		chr14:75127595-75127643	89.16
N	jcn_only_AD	CUFF.564	chr19	+	chr19:52909897-52918191	chr19:52917622-52918191					20.00
N	jcn_only_AD	CUFF.879	chr5	-	chr5:60224787-60240758	chr5:60224787-60227933		chr5:60227934-60240758	chr5:60240758-60240759		4.82
N	intron_retention		chr2	+	chr2:101609990-101612257				chr2:101609989-101609990;chr2:101612257-101612258		44.00
K	intron_retention	CUFF.475	chr17	-	chr17:79994965-79995325				chr17:79994964-79994965;chr17:79995325-79995326		24.19
K	intron_retention		chr16	+	chr16:19592976-19603111				chr16:19592975-19592976;chr16:19603111-19603112		50.00
N	intron_retention		chr15	-	chr15:83355772-83357487				chr15:83355771-83355772;chr15:83357487-83357488		87.65
N	jcn_only_AA		chr19	+	chr19:17448474-17448682;chr19:17448474-17448707	chr19:17448474-17448816		chr19:17448683-17448707;chr19:17448708-17448816	chr19:17448707-17448708;chr19:17448816-17448817		40.69
K	intron_retention	CUFF.464	chr17	+	chr17:66511261-66511534				chr17:66511260-66511261;chr17:66511534-66511535		44.44
N	intron_retention	CUFF.739	chr3	+	chr3:28357915-28360222				chr3:28357914-28357915;chr3:28360222-28360223		96.25
N	jcn_only_AD	CUFF.276,CUFF.286	chr14	-	chr14:71200060-71201102	chr14:71200060-71200473		chr14:71200474-71201102	chr14:71201102-71201103		78.26
K	intron_retention	CUFF.228	chr12	-	chr12:56578877-56579938				chr12:56578876-56578877;chr12:56579938-56579939		22.41
K	intron_retention	CUFF.363	chr16	+	chr16:105883-106320				chr16:105882-105883;chr16:106320-106321		53.85
K	alternative_last_exon	CUFF.644	chr2	+	chr2:171264355-171300476	chr2:171264355-171268210	chr2:171300477-171300556	chr2:171268211-171269020			59.78
N	alternative_acceptor	CUFF.849	chr4	+	chr4:124750343-124846338	chr4:124750343-124784729		chr4:124784730-124846338	chr4:124846338-124846339		0.00
N	jcn_only_AA	CUFF.68	chr1	+	chr1:200877016-200877857	chr1:200877016-200877243		chr1:200877244-200877857	chr1:200877857-200877858		55.56
N	alternative_first_exon		chr1	-	chr1:153927643-153930621;chr1:153927643-153930820	chr1:153927643-153930536	chr1:153930821-153931091	chr1:153930537-153930678			66.67
K	jcn_only_AD	CUFF.15	chr1	+	chr1:28655636-28657107	chr1:28655692-28657107		chr1:28655636-28655691	chr1:28655635-28655636		96.55
K	cassette	CUFF.954	chr6	+	chr6:161518209-161522923	chr6:161518209-161519309;chr6:161519460-161522923		chr6:161519310-161519459		chr6:161518112-161518208;chr6:161522924-161523024	66.67
K	alternative_first_exon	CUFF.177	chr11	-	chr11:104915386-104972134	chr11:104915386-104916017,chr11:104915386-104915917	chr11:104972135-104972210	chr11:104916018-104916179			68.42
N	alternative_donor	CUFF.292	chr14	+	chr14:92915504-92920243;chr14:92918991-92920243	chr14:92915561-92920243		chr14:92915504-92915560;chr14:92915561-92918990	chr14:92915503-92915504;chr14:92915560-92915561		50.00
K	cassette	CUFF.662	chr2	+	chr2:219433702-219445283	chr2:219433702-219438717;chr2:219438957-219445283		chr2:219438718-219438956			28.04
K	cassette	CUFF.244	chr13	+	chr13:21157159-21165105	chr13:21157159-21163949;chr13:21164007-21165105		chr13:21163950-21164006			83.33
N	coord_cassette	CUFF.426	chr17	-	chr17:15546131-15584178	chr17:15546131-15562115;chr17:15562191-15580489;chr17:15580595-15580888;chr17:15580997-15584178		chr17:15562116-15562190;chr17:15580490-15580594;chr17:15580889-15580996			50.00
K	alternative_first_exon	CUFF.244	chr13	+	chr13:21141396-21148518	chr13:21142137-21148518	chr13:21140573-21141395	chr13:21141809-21142136			92.42
N	jcn_only_AA		chr7	-	chr7:37382368-37488277	chr7:37433521-37488277		chr7:37382368-37433520	chr7:37382367-37382368		50.00
N	cassette	CUFF.432	chr17	+	chr17:25958331-25967597	chr17:25958331-25965288;chr17:25965381-25967597		chr17:25965289-25965380			89.26
K	jcn_only_AD	CUFF.1039	chr8	+	chr8:74884857-74888064	chr8:74885229-74888064		chr8:74884857-74885228	chr8:74884856-74884857		34.09
N	alternative_last_exon	CUFF.207	chr12	+	chr12:1742072-1754959	chr12:1742072-1748849	chr12:1754960-1756508	chr12:1748850-1749142			77.24
N	jcn_only_AA		chr22	+	chr22:37697061-37699294;chr22:37697061-37697975	chr22:37697061-37697921		chr22:37697922-37697975;chr22:37697976-37699294	chr22:37697975-37697976;chr22:37699294-37699295		90.53
N	alternative_acceptor	CUFF.390	chr16	-	chr16:23504780-23505623;chr16:23504909-23505623	chr16:23504843-23505623		chr16:23504780-23504842;chr16:23504843-23504908	chr16:23504779-23504780;chr16:23504842-23504843	chr16:23505624-23505699;chr16:23504681-23504779	25.99
N	intron_retention		chr11	+	chr11:63670605-63671569				chr11:63670604-63670605;chr11:63671569-63671570		79.41
N	jcn_only_AD		chr15	+	chr15:24793618-24811235	chr15:24803469-24811235					21.43
N	jcn_only_AA	CUFF.298	chr14	-	chr14:104202540-104205015	chr14:104204198-104205015		chr14:104202540-104204197	chr14:104202539-104202540		88.52
K	alternative_donor	CUFF.253	chr13	-	chr13:97642064-97644761	chr13:97642064-97644675		chr13:97644676-97644761	chr13:97644761-97644762		87.95
N	jcn_only_AD	CUFF.728	chr22	-	chr22:51016364-51016977;chr22:51016364-51016814	chr22:51016364-51016512		chr22:51016513-51016814;chr22:51016815-51016977	chr22:51016814-51016815;chr22:51016977-51016978		2.83
N	jcn_only_AA		chr6	-	chr6:114281183-114291643	chr6:114289861-114291643		chr6:114281183-114289860	chr6:114281182-114281183		58.56
N	alternative_donor	CUFF.212	chr12	+	chr12:26112082-26147969	chr12:26126821-26147969		chr12:26112082-26126820	chr12:26112081-26112082		0.00
N	intron_retention		chr2	-	chr2:253116-256206				chr2:253115-253116;chr2:256206-256207		81.82
N	jcn_only_AD	CUFF.802	chr3	+	chr3:186649184-186681572;chr3:186660216-186681572;chr3:186648624-186681572;chr3:186666727-186681572	chr3:186648928-186681572		chr3:186648624-186648927;chr3:186648928-186649183;chr3:186649184-186660215;chr3:186660216-186666726	chr3:186648623-186648624;chr3:186648927-186648928;chr3:186649183-186649184;chr3:186660215-186660216		34.82
N	jcn_only_AA		chr16	-	chr16:57513598-57513756	chr16:57513601-57513756		chr16:57513598-57513600	chr16:57513597-57513598		72.22
K	intron_retention	CUFF.36	chr1	+	chr1:110211106-110211546				chr1:110211105-110211106;chr1:110211546-110211547		52.63
N	cassette	CUFF.234	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			59.44
N	intron_retention		chr22	+	chr22:21057182-21057293				chr22:21057181-21057182;chr22:21057293-21057294		78.23
N	intron_retention		chr7	-	chr7:75053912-75054356				chr7:75053911-75053912;chr7:75054356-75054357		16.13
N	cassette	CUFF.532	chr19	+	chr19:18118181-18119519	chr19:18118181-18118398;chr19:18118652-18119519		chr19:18118399-18118651			54.55
K	alternative_acceptor	CUFF.758	chr3	-	chr3:57569760-57570110;chr3:57569788-57570110	chr3:57569735-57570110		chr3:57569735-57569759;chr3:57569760-57569787	chr3:57569734-57569735;chr3:57569759-57569760		70.73
N	intron_retention		chr7	+	chr7:150831656-150838984				chr7:150831655-150831656;chr7:150838984-150838985		17.65
N	jcn_only_AD	CUFF.386	chr16	+	chr16:21737980-21739561	chr16:21738481-21739561		chr16:21737980-21738480	chr16:21737979-21737980		3.61
N	alternative_donor	CUFF.310	chr15	+	chr15:40532297-40532799;chr15:40532004-40532799;chr15:40531337-40532799	chr15:40509869-40532799		chr15:40509869-40531336;chr15:40531337-40532003;chr15:40532004-40532296	chr15:40509868-40509869;chr15:40531336-40531337;chr15:40532003-40532004		100.00
K	intron_retention	CUFF.751	chr3	-	chr3:46965159-46966945				chr3:46965158-46965159;chr3:46966945-46966946		9.23
K	intron_retention	CUFF.1118	chrX	-	chrX:19933168-19933762				chrX:19933167-19933168;chrX:19933762-19933763		54.55
K	intron_retention	CUFF.53	chr1	-	chr1:156908306-156909339				chr1:156908305-156908306;chr1:156909339-156909340		18.00
N	alternative_acceptor	CUFF.802	chr3	+	chr3:186756662-186760441	chr3:186756662-186759704		chr3:186759705-186760441	chr3:186760441-186760442		2.09
K	cassette	CUFF.998	chr7	-	chr7:102223340-102224664	chr7:102223340-102223450;chr7:102223516-102224664		chr7:102223451-102223515			72.00
K	cassette	CUFF.363	chr16	+	chr16:105883-106538	chr16:105883-106320;chr16:106421-106538		chr16:106321-106420			17.65
K	cassette	CUFF.63	chr1	-	chr1:169698815-169700975	chr1:169698815-169699572;chr1:169699759-169700975		chr1:169699573-169699758			94.12
K	alternative_donor	CUFF.322,CUFF.331	chr15	-	chr15:55483246-55484917	chr15:55483246-55484600		chr15:55484601-55484917	chr15:55484917-55484918		32.29
K	intron_retention	CUFF.475	chr17	-	chr17:79994325-79994419				chr17:79994324-79994325;chr17:79994419-79994420		30.27
N	intron_retention		chr8	-	chr8:81090189-81095252				chr8:81090188-81090189;chr8:81095252-81095253		40.00
K	jcn_only_AA	CUFF.125,CUFF.90	chr10	+	chr10:98092354-98095650	chr10:98092354-98095647		chr10:98095648-98095650	chr10:98095650-98095651		76.92
K	intron_retention	CUFF.387	chr16	+	chr16:21973838-21974081				chr16:21973837-21973838;chr16:21974081-21974082		3.24
K	cassette	CUFF.780	chr3	-	chr3:125050083-125093945	chr3:125050083-125057665;chr3:125057756-125093945		chr3:125057666-125057755			72.00
K	alternative_last_exon	CUFF.714	chr22	+	chr22:25855483-25915889;chr22:25855483-25905149	chr22:25855483-25856833	chr22:25915890-25916129;chr22:25905150-25905309	chr22:25856834-25857720			30.30
N	alternative_acceptor	CUFF.497	chr18	-	chr18:67614769-67623990;chr18:67614670-67623990	chr18:67563282-67623990		chr18:67563282-67614669;chr18:67614670-67614768	chr18:67563281-67563282;chr18:67614669-67614670		100.00
K	alternative_first_exon	CUFF.114	chr10	-	chr10:73973090-73975534;chr10:73973090-73976578;chr10:73973090-73975964	chr10:73973090-73975539	chr10:73976579-73976962;chr10:73975965-73976126	chr10:73975540-73975867			36.64
N	jcn_only_AA		chr18	+	chr18:55713021-55833023	chr18:55713021-55833019		chr18:55833020-55833023	chr18:55833023-55833024		54.55
K	alternative_first_exon	CUFF.700	chr21	-	chr21:40969917-40981509	chr21:40969917-40971267	chr21:40981510-40981592	chr21:40971268-40971583			83.33
K	coord_cassette	CUFF.379	chr16	+	chr16:4546029-4555484	chr16:4546029-4546146;chr16:4546268-4552744;chr16:4552961-4555484		chr16:4546147-4546267;chr16:4552745-4552960			88.18
N	jcn_only_AD	CUFF.628	chr2	+	chr2:101565943-101580519	chr2:101579296-101580519		chr2:101565943-101579295	chr2:101565942-101565943		35.05
N	jcn_only_AA	CUFF.652	chr2	-	chr2:197298183-197458231	chr2:197358100-197458231		chr2:197298183-197358099	chr2:197298182-197298183		35.14
K	jcn_only_AA	CUFF.679	chr20	+	chr20:16730120-16744966	chr20:16730120-16730411					45.16
K	alternative_acceptor	CUFF.1027	chr8	-	chr8:22012977-22013849	chr8:22013023-22013849		chr8:22012977-22013022	chr8:22012976-22012977		82.35
N	alternative_donor	CUFF.136	chr11	-	chr11:410028-417324;chr11:410028-414822	chr11:410028-417293		chr11:414823-417293;chr11:417294-417324	chr11:417293-417294;chr11:417324-417325		17.98
N	alternative_first_exon	CUFF.725	chr22	+	chr22:45181982-45182336,chr22:45173110-45182336;chr22:45148508-45182336;chr22:45162070-45182336;chr22:45122515-45182336	chr22:45131043-45182336	chr22:45148371-45148507;chr22:45161745-45162069;chr22:45122457-45122514	chr22:45130907-45131042			8.33
K	jcn_only_AA	CUFF.189	chr11	-	chr11:119290142-119290760	chr11:119290231-119290760		chr11:119290142-119290230	chr11:119290141-119290142		49.74
N	alternative_acceptor		chr15	+	chr15:77756730-77759524	chr15:77756730-77759436		chr15:77759437-77759524	chr15:77759524-77759525		82.32
K	alternative_acceptor	CUFF.524	chr19	-	chr19:14866657-14867049	chr19:14866690-14867049		chr19:14866657-14866689	chr19:14866656-14866657		55.56
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		58.30
N	cassette	CUFF.426	chr17	-	chr17:15532513-15539349	chr17:15532513-15534932;chr17:15535029-15539349		chr17:15534933-15535028			89.58
N	alternative_acceptor	CUFF.716	chr22	+	chr22:29668421-29669729;chr22:29668421-29669726	chr22:29668421-29674119		chr22:29669727-29669729;chr22:29669730-29674119	chr22:29669729-29669730;chr22:29674119-29674120		31.03
N	coord_cassette	CUFF.2	chr1	+	chr1:2075781-2080310	chr1:2075781-2076776;chr1:2076951-2077465;chr1:2077548-2080310		chr1:2076777-2076950;chr1:2077466-2077547			72.73
K	intron_retention	CUFF.187	chr11	+	chr11:119059577-119059713				chr11:119059576-119059577;chr11:119059713-119059714		8.15
K	alternative_first_exon	CUFF.979	chr7	+	chr7:65610488-65617194	chr7:65615936-65617194	chr7:65610430-65610487	chr7:65615682-65615935			26.56
K	alternative_acceptor	CUFF.354	chr15	+	chr15:91298169-91303376	chr15:91298169-91303210		chr15:91303211-91303376	chr15:91303376-91303377		72.22
N	jcn_only_AD	CUFF.673	chr2	+	chr2:242610857-242611605;chr2:242610841-242611605	chr2:242610821-242611605		chr2:242610821-242610840;chr2:242610841-242610856	chr2:242610820-242610821;chr2:242610840-242610841		92.31
N	cassette	CUFF.377	chr16	-	chr16:4462432-4466459	chr16:4462432-4463308;chr16:4463406-4466459		chr16:4463309-4463405			84.81
N	alternative_first_exon	CUFF.310	chr15	+	chr15:40531337-40545378,chr15:40545216-40545378,chr15:40544465-40545378;chr15:40532883-40545378;chr15:40544893-40545378	chr15:40509869-40545378	chr15:40532681-40532882;chr15:40544751-40544892	chr15:40509629-40509868			3.08
N	jcn_only_AA	CUFF.856	chr4	-	chr4:162463846-162508606	chr4:162473730-162508606		chr4:162463846-162473729	chr4:162463845-162463846		27.21
K	jcn_only_AA	CUFF.961,CUFF.984	chr7	+	chr7:6631499-6634065	chr7:6631499-6634042		chr7:6634043-6634065	chr7:6634065-6634066		54.76
K	alternative_first_exon	CUFF.285	chr14	+	chr14:77924326-77925958	chr14:77924613-77925958	chr14:77924137-77924325	chr14:77924326-77924612			97.72
K	cassette	CUFF.797	chr3	-	chr3:165504100-165555101	chr3:165504100-165547304;chr3:165548830-165555101		chr3:165547305-165548829			20.15
N	alternative_first_exon	CUFF.82	chr1	+	chr1:230203154-230338882	chr1:230314058-230338882	chr1:230202936-230203153	chr1:230313964-230314057			55.56
K	intron_retention	CUFF.904	chr5	-	chr5:178030936-178032303				chr5:178030935-178030936;chr5:178032303-178032304		46.84
K	alternative_acceptor	CUFF.556	chr19	-	chr19:49335990-49337532	chr19:49336010-49337532		chr19:49335990-49336009	chr19:49335989-49335990		3.85
K	cassette	CUFF.864	chr5	+	chr5:36166765-36170445	chr5:36166765-36168414;chr5:36168550-36170445		chr5:36168415-36168549		chr5:36166621-36166764;chr5:36170446-36170544	24.76
K	alternative_last_exon	CUFF.1060	chr8	+	chr8:143922642-143995378	chr8:143922642-143927810	chr8:143995379-143995461	chr8:143927811-143928359			92.75
N	alternative_donor	CUFF.323	chr15	+	chr15:55700985-55710420	chr15:55709958-55710420		chr15:55700985-55709957	chr15:55700984-55700985		4.65
N	intron_retention		chr3	-	chr3:49462580-49462799				chr3:49462579-49462580;chr3:49462799-49462800		55.56
N	alternative_acceptor	CUFF.1082	chr9	+	chr9:95591446-95599058	chr9:95591446-95591955		chr9:95591956-95599058	chr9:95599058-95599059		0.00
N	jcn_only_AA	CUFF.572	chr2	-	chr2:253116-260084	chr2:256691-260084		chr2:253116-256690	chr2:253115-253116		13.51
K	intron_retention	CUFF.481	chr18	+	chr18:12028151-12028840				chr18:12028150-12028151;chr18:12028840-12028841		34.48
K	alternative_acceptor	CUFF.618	chr2	-	chr2:86397965-86398330	chr2:86397968-86398330		chr2:86397965-86397967	chr2:86397964-86397965		71.43
N	cassette	CUFF.259	chr14	+	chr14:24572100-24572718	chr14:24572100-24572368;chr14:24572465-24572718		chr14:24572369-24572464			78.31
N	jcn_only_AA	CUFF.566	chr19	+	chr19:54648069-54649277;chr19:54648069-54649333	chr19:54648069-54649330		chr19:54649278-54649330;chr19:54649331-54649333	chr19:54649330-54649331;chr19:54649333-54649334		33.33
N	jcn_only_AD	CUFF.769	chr3	+	chr3:119188106-119188666;chr3:119187854-119188666	chr3:119187954-119188666		chr3:119187854-119187953;chr3:119187954-119188105	chr3:119187853-119187854;chr3:119187953-119187954		39.66
N	jcn_only_AA	CUFF.385	chr16	+	chr16:19592976-19612985;chr16:19592976-19603111	chr16:19592976-19598714					25.00
K	jcn_only_AA	CUFF.868	chr5	+	chr5:39521730-39524364	chr5:39521730-39524352		chr5:39524353-39524364	chr5:39524364-39524365		49.28
N	jcn_only_AA	CUFF.310	chr15	+	chr15:40545491-40556004;chr15:40545491-40555999	chr15:40545491-40549043		chr15:40549044-40555999;chr15:40556000-40556004	chr15:40555999-40556000;chr15:40556004-40556005		5.15
N	alternative_donor	CUFF.867	chr5	-	chr5:37309370-37310653	chr5:37309370-37309505		chr5:37309506-37310653	chr5:37310653-37310654		0.00
N	jcn_only_AA	CUFF.581	chr2	-	chr2:4020665-4021134;chr2:4009394-4021134;chr2:4015879-4021134;chr2:4009485-4021134	chr2:4020693-4021134		chr2:4009394-4009484;chr2:4009485-4015878;chr2:4015879-4020664;chr2:4020665-4020692	chr2:4009393-4009394;chr2:4009484-4009485;chr2:4015878-4015879;chr2:4020664-4020665		12.80
K	intron_retention	CUFF.980	chr7	+	chr7:73106977-73107658				chr7:73106976-73106977;chr7:73107658-73107659		9.30
K	alternative_donor	CUFF.887,CUFF.897	chr5	-	chr5:141050196-141050891	chr5:141050196-141050831		chr5:141050832-141050891	chr5:141050891-141050892		21.43
K	jcn_only_AA	CUFF.250	chr13	+	chr13:52028466-52034807	chr13:52028466-52034620		chr13:52034621-52034807	chr13:52034807-52034808		42.86
N	intron_retention		chr17	-	chr17:15531376-15532187				chr17:15531375-15531376;chr17:15532187-15532188		89.89
K	jcn_only_AD	CUFF.601,CUFF.658	chr2	-	chr2:46842325-46844108	chr2:46842325-46843725		chr2:46843726-46844108	chr2:46844108-46844109		56.25
K	jcn_only_AD	CUFF.628	chr2	+	chr2:101541757-101549371	chr2:101541763-101549371		chr2:101541757-101541762	chr2:101541756-101541757		23.95
K	cassette	CUFF.4	chr1	+	chr1:11074023-11078789	chr1:11074023-11076900;chr1:11077065-11078789		chr1:11076901-11077064			90.83
N	jcn_only_AD	CUFF.751	chr3	-	chr3:46982556-47007473;chr3:46982556-47018126	chr3:46982556-47017842		chr3:47007474-47017842;chr3:47017843-47018126	chr3:47017842-47017843;chr3:47018126-47018127		43.48
K	alternative_first_exon	CUFF.332	chr15	-	chr15:66645294-66678944;chr15:66645294-66678987,chr15:66645294-66678757	chr15:66645294-66648976	chr15:66678988-66679165	chr15:66648977-66649054			40.32
N	jcn_only_AD	CUFF.509	chr19	-	chr19:6047516-6148241;chr19:6047516-6049146;chr19:6047516-6110403;chr19:6047516-6072015	chr19:6047516-6057172		chr19:6049147-6057172;chr19:6057173-6072015;chr19:6072016-6110403;chr19:6110404-6148241	chr19:6057172-6057173;chr19:6072015-6072016;chr19:6110403-6110404;chr19:6148241-6148242		7.45
N	cassette	CUFF.257	chr14	+	chr14:23390330-23393509	chr14:23390330-23392287;chr14:23392414-23393509		chr14:23392288-23392413			87.01
K	cassette	CUFF.90	chr10	+	chr10:6263491-6264817	chr10:6263491-6263603;chr10:6263709-6264817		chr10:6263604-6263708			78.82
K	coord_cassette	CUFF.208	chr12	+	chr12:21229504-21294447	chr12:21229504-21279051;chr12:21279192-21284056;chr12:21284171-21294447		chr12:21279052-21279191;chr12:21284057-21284170		chr12:21229386-21229503;chr12:21294448-21294592	94.90
K	jcn_only_AA	CUFF.758	chr3	-	chr3:57569788-57570110;chr3:57569735-57570110	chr3:57569760-57570110		chr3:57569735-57569759;chr3:57569760-57569787	chr3:57569734-57569735;chr3:57569759-57569760		5.71
K	alternative_first_exon	CUFF.501	chr18	+	chr18:77440262-77455224	chr18:77441518-77455224	chr18:77439801-77440261	chr18:77441436-77441517			93.10
K	alternative_donor	CUFF.564	chr19	+	chr19:52901154-52901619	chr19:52901158-52901619		chr19:52901154-52901157	chr19:52901153-52901154		28.33
K	cassette	CUFF.324	chr15	-	chr15:55722978-55727102	chr15:55722978-55724694;chr15:55724801-55727102		chr15:55724695-55724800			53.47
K	intron_retention	CUFF.530	chr19	+	chr19:17449836-17449931				chr19:17449835-17449836;chr19:17449931-17449932		46.95
N	alternative_donor	CUFF.751	chr3	-	chr3:46982556-47007473;chr3:46982556-47018126	chr3:46982556-47017842		chr3:47007474-47017842;chr3:47017843-47018126	chr3:47017842-47017843;chr3:47018126-47018127		47.81
K	cassette	CUFF.407	chr16	+	chr16:70380952-70389387	chr16:70380952-70384459;chr16:70384509-70389387		chr16:70384460-70384508			96.90
N	intron_retention	CUFF.929	chr6	-	chr6:43481372-43483343				chr6:43481371-43481372;chr6:43483343-43483344		68.97
K	cassette	CUFF.1136	chrX	+	chrX:107369418-107374489	chrX:107369418-107372010;chrX:107372083-107374489		chrX:107372011-107372082			40.65
K	intron_retention	CUFF.946	chr6	-	chr6:133050073-133055391				chr6:133050072-133050073;chr6:133055391-133055392		40.74
N	intron_retention		chr11	-	chr11:10822635-10823595				chr11:10822634-10822635;chr11:10823595-10823596		68.75
K	intron_retention	CUFF.579	chr2	+	chr2:3481567-3482616				chr2:3481566-3481567;chr2:3482616-3482617		4.41
N	jcn_only_AA		chr4	+	chr4:647109-647640	chr4:647109-647225		chr4:647226-647640	chr4:647640-647641		24.49
N	intron_retention		chr16	-	chr16:4438624-4457652				chr16:4438623-4438624;chr16:4457652-4457653		79.10
N	alternative_acceptor	CUFF.802	chr3	+	chr3:186769135-186790636	chr3:186769135-186782307		chr3:186782308-186790636	chr3:186790636-186790637		0.00
N	jcn_only_AD		chr3	-	chr3:33686396-33700998;chr3:33686396-33700465;chr3:33686396-33686773;chr3:33686396-33686494	chr3:33686396-33686835					32.10
N	jcn_only_AD	CUFF.1146	chrX	+	chrX:148864250-148867418;chrX:148863691-148867418	chrX:148863659-148867418		chrX:148863659-148863690;chrX:148863691-148864249	chrX:148863658-148863659;chrX:148863690-148863691		46.67
K	alternative_first_exon	CUFF.154,CUFF.161	chr11	-	chr11:62366112-62367637	chr11:62366112-62366689	chr11:62367638-62367858	chr11:62366690-62366752			2.94
K	intron_retention	CUFF.522	chr19	+	chr19:12917894-12918019				chr19:12917893-12917894;chr19:12918019-12918020		11.11
N	jcn_only_AA	CUFF.363	chr16	+	chr16:89789592-89789686	chr16:89789592-89789667		chr16:89789668-89789686	chr16:89789686-89789687		91.95
N	alternative_acceptor	CUFF.874	chr5	+	chr5:52177854-52183646	chr5:52177854-52178711		chr5:52178712-52183646	chr5:52183646-52183647		0.00
K	intron_retention		chr2	-	chr2:260703-262630				chr2:260702-260703;chr2:262630-262631		90.91
K	intron_retention	CUFF.816	chr4	-	chr4:3949735-3949816				chr4:3949734-3949735;chr4:3949816-3949817		22.66
N	cassette	CUFF.640	chr2	-	chr2:166714915-166727306	chr2:166714915-166719453;chr2:166719576-166727306		chr2:166719454-166719575			76.92
K	jcn_only_AA	CUFF.894	chr5	+	chr5:139865318-139866590	chr5:139865318-139866542		chr5:139866543-139866590	chr5:139866590-139866591	chr5:139865174-139865317;chr5:139866591-139866645	69.23
K	alternative_last_exon	CUFF.835	chr4	-	chr4:74464436-74477447	chr4:74470305-74477447	chr4:74464357-74464435	chr4:74469698-74470304			97.55
N	jcn_only_AA		chr22	+	chr22:29521405-29533489	chr22:29521405-29533329		chr22:29533330-29533489	chr22:29533489-29533490		75.00
K	cassette	CUFF.834	chr4	-	chr4:70460968-70464963	chr4:70460968-70461967;chr4:70462100-70464963		chr4:70461968-70462099			30.30
N	alternative_acceptor	CUFF.685	chr20	-	chr20:31115717-31123243	chr20:31121289-31123243		chr20:31115717-31121288	chr20:31115716-31115717		0.00
K	intron_retention	CUFF.140	chr11	-	chr11:2190926-2192926				chr11:2190925-2190926;chr11:2192926-2192927		12.73
N	cassette	CUFF.473	chr17	-	chr17:79891253-79892528;chr17:79891253-79892801	chr17:79891253-79892201;chr17:79892366-79892528,chr17:79892366-79892801		chr17:79892202-79892365		chr17:79891183-79891252;chr17:79892802-79893023	84.25
N	jcn_only_AA	CUFF.628	chr2	+	chr2:101565943-101579216;chr2:101565943-101584742	chr2:101565943-101580519					29.58
K	alternative_last_exon	CUFF.755,CUFF.790	chr3	+	chr3:51747327-51749077	chr3:51747327-51747979	chr3:51749078-51750153	chr3:51747980-51749058			84.27
N	intron_retention		chr17	-	chr17:1616350-1617149				chr17:1616349-1616350;chr17:1617149-1617150		75.32
N	jcn_only_AD	CUFF.867	chr5	-	chr5:37309370-37310653	chr5:37309370-37309505		chr5:37309506-37310653	chr5:37310653-37310654		14.29
K	intron_retention	CUFF.891	chr5	+	chr5:134190853-134193046				chr5:134190852-134190853;chr5:134193046-134193047		84.78
K	cassette	CUFF.67	chr1	+	chr1:196913069-196919981	chr1:196913069-196918565;chr1:196918780-196919981		chr1:196918566-196918779		chr1:196912830-196913068;chr1:196919982-196920158	70.97
N	alternative_acceptor	CUFF.589	chr2	-	chr2:27672964-27676250	chr2:27676138-27676250		chr2:27672964-27676137	chr2:27672963-27672964		1.80
K	intron_retention	CUFF.152	chr11	-	chr11:10825598-10825683				chr11:10825597-10825598;chr11:10825683-10825684		30.68
K	cassette	CUFF.237	chr12	-	chr12:102796345-102813286	chr12:102796345-102811732;chr12:102811782-102813286		chr12:102811733-102811781			11.83
N	jcn_only_AD		chr19	-	chr19:6176455-6199490	chr19:6176455-6199486					39.45
K	cassette	CUFF.177	chr11	-	chr11:104912447-104915118	chr11:104912447-104914209;chr11:104914273-104915118		chr11:104914210-104914272			41.03
K	cassette	CUFF.748	chr3	+	chr3:38315867-38316479	chr3:38315867-38316094;chr3:38316250-38316479		chr3:38316095-38316249			20.00
K	cassette	CUFF.946	chr6	-	chr6:133050119-133055391	chr6:133050119-133052513;chr6:133052667-133055391		chr6:133052514-133052666			59.62
K	alternative_first_exon	CUFF.578	chr2	+	chr2:1320148-1371114	chr2:1357637-1371114	chr2:1320037-1320147	chr2:1357413-1357636			57.63
N	intron_retention	CUFF.473	chr17	-	chr17:79894738-79894845				chr17:79894737-79894738;chr17:79894845-79894846	chr17:79894624-79894737	90.24
K	intron_retention	CUFF.741	chr3	-	chr3:33453180-33454213				chr3:33453179-33453180;chr3:33454213-33454214		2.02
N	alternative_donor		chr18	+	chr18:55833094-55895061;chr18:55888990-55895061	chr18:55862966-55895061		chr18:55833094-55862965;chr18:55862966-55888989	chr18:55833093-55833094;chr18:55862965-55862966		0.00
K	alternative_acceptor	CUFF.693	chr21	+	chr21:15660868-15663890	chr21:15660868-15663606		chr21:15663607-15663890	chr21:15663890-15663891	chr21:15660725-15660867;chr21:15663891-15664068	35.71
N	alternative_acceptor	CUFF.589	chr2	-	chr2:27670502-27670678	chr2:27670525-27670678		chr2:27670502-27670524	chr2:27670501-27670502		2.09
N	alternative_acceptor	CUFF.581	chr2	-	chr2:4020665-4021134;chr2:4009394-4021134;chr2:4020693-4021134;chr2:4009485-4021134	chr2:4015879-4021134		chr2:4009394-4009484;chr2:4009485-4015878;chr2:4015879-4020664;chr2:4020665-4020692	chr2:4009393-4009394;chr2:4009484-4009485;chr2:4015878-4015879;chr2:4020664-4020665		1.61
K	intron_retention	CUFF.440	chr17	-	chr17:34499761-34500203				chr17:34499760-34499761;chr17:34500203-34500204		9.86
K	intron_retention	CUFF.751	chr3	-	chr3:46963803-46964818				chr3:46963802-46963803;chr3:46964818-46964819		25.42
N	cassette	CUFF.322	chr15	-	chr15:55485032-55488550	chr15:55485032-55486493;chr15:55486558-55488550		chr15:55486494-55486557			12.50
K	intron_retention	CUFF.406	chr16	-	chr16:70253699-70253814				chr16:70253698-70253699;chr16:70253814-70253815		68.09
N	alternative_donor	CUFF.928	chr6	-	chr6:41491964-41513826	chr6:41491964-41513737		chr6:41513738-41513826	chr6:41513826-41513827		90.91
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55833094-55912658;chr18:55865102-55912658;chr18:55895121-55912658;chr18:55862966-55912658;chr18:55888990-55912658	chr18:55895140-55912658		chr18:55833094-55862965;chr18:55862966-55865101;chr18:55865102-55888989;chr18:55888990-55895120;chr18:55895121-55895139	chr18:55833093-55833094;chr18:55862965-55862966;chr18:55865101-55865102;chr18:55888989-55888990;chr18:55895120-55895121		10.08
K	jcn_only_AD	CUFF.1018	chr7	-	chr7:156476858-156516805	chr7:156476858-156480723					79.31
K	jcn_only_AA	CUFF.21	chr1	-	chr1:41483652-41485897	chr1:41483829-41485897		chr1:41483652-41483828	chr1:41483651-41483652		92.73
N	jcn_only_AD	CUFF.578	chr2	+	chr2:1094097-1099090	chr2:1098397-1099090		chr2:1094097-1098396	chr2:1094096-1094097		11.43
K	jcn_only_AD	CUFF.36	chr1	+	chr1:110211106-110211546	chr1:110211123-110211546		chr1:110211106-110211122	chr1:110211105-110211106		95.38
K	alternative_acceptor	CUFF.654	chr2	-	chr2:204306137-204309590	chr2:204306804-204309590		chr2:204306137-204306803	chr2:204306136-204306137		86.92
N	jcn_only_AD	CUFF.918	chr6	+	chr6:31927178-31928817	chr6:31928518-31928817					94.34
N	alternative_donor	CUFF.352	chr15	-	chr15:90414779-90420537;chr15:90414779-90431752	chr15:90414779-90421496		chr15:90420538-90421496;chr15:90421497-90431752	chr15:90421496-90421497;chr15:90431752-90431753		1.02
K	intron_retention	CUFF.893	chr5	+	chr5:137514892-137515348				chr5:137514891-137514892;chr5:137515348-137515349		10.45
K	cassette	CUFF.934	chr6	+	chr6:88058625-88066018	chr6:88058625-88060111;chr6:88060220-88066018		chr6:88060112-88060219			72.73
N	alternative_donor	CUFF.187	chr11	+	chr11:119056220-119056557	chr11:119056338-119056557		chr11:119056220-119056337	chr11:119056219-119056220		51.61
N	alternative_donor	CUFF.598	chr2	+	chr2:38150511-38156404	chr2:38152569-38156404		chr2:38150511-38152568	chr2:38150510-38150511		12.50
N	alternative_acceptor	CUFF.269	chr14	+	chr14:58899176-58899829;chr14:58899176-58909423	chr14:58899176-58906787		chr14:58899830-58906787;chr14:58906788-58909423	chr14:58906787-58906788;chr14:58909423-58909424		6.25
N	cassette	CUFF.887	chr5	-	chr5:127396937-127417664;chr5:127396937-127418426	chr5:127396937-127412638;chr5:127412786-127418426,chr5:127412786-127417664		chr5:127412639-127412785			39.73
K	intron_retention	CUFF.661	chr2	+	chr2:219222458-219222759				chr2:219222457-219222458;chr2:219222759-219222760		52.38
K	alternative_first_exon	CUFF.418	chr17	+	chr17:1937137-1939263	chr17:1938315-1939263	chr17:1937073-1937136	chr17:1938133-1938314			38.78
K	cassette	CUFF.795	chr3	-	chr3:155520381-155523385	chr3:155520381-155521839;chr3:155521963-155523385		chr3:155521840-155521962			67.92
K	alternative_last_exon	CUFF.824	chr4	-	chr4:36059766-36075310	chr4:36069901-36075310	chr4:36059592-36059765	chr4:36067533-36069900			53.85
N	jcn_only_AD	CUFF.143	chr11	+	chr11:2798263-2799205	chr11:2799044-2799205		chr11:2798263-2799043	chr11:2798262-2798263		16.67
K	intron_retention		chr19	+	chr19:17450409-17451852				chr19:17450408-17450409;chr19:17451852-17451853		22.68
K	alternative_last_exon	CUFF.76	chr1	+	chr1:211570174-211599552	chr1:211570174-211570197	chr1:211599553-211599625	chr1:211570198-211570296			61.76
K	alternative_donor	CUFF.215,CUFF.239	chr12	-	chr12:48258961-48272750	chr12:48258961-48272598		chr12:48272599-48272750	chr12:48272750-48272751		20.22
N	alternative_acceptor	CUFF.386	chr16	+	chr16:21737980-21739561	chr16:21737980-21738432		chr16:21738433-21739561	chr16:21739561-21739562		0.00
N	mutually_exclusive	CUFF.509	chr19	-	chr19:6040253-6044203,chr19:6044294-6047417	chr19:6040253-6042054,chr19:6042135-6047417	chr19:6044204-6044293	chr19:6042055-6042134			25.00
N	jcn_only_AA	CUFF.693	chr21	+	chr21:15680941-15685264	chr21:15680941-15681292		chr21:15681293-15685264	chr21:15685264-15685265	chr21:15680874-15680940;chr21:15685265-15685452	16.67
N	jcn_only_AD		chr3	-	chr3:107576050-107585498	chr3:107576050-107577977					22.06
N	jcn_only_AA	CUFF.1004	chr7	-	chr7:110603622-111127293	chr7:111123785-111127293		chr7:110603622-111123784	chr7:110603621-110603622		5.06
K	alternative_first_exon	CUFF.628	chr2	+	chr2:101549464-101554214	chr2:101550623-101554214	chr2:101549372-101549463	chr2:101550525-101550622			20.74
K	alternative_donor	CUFF.765	chr3	-	chr3:107595034-107595301	chr3:107595034-107595281		chr3:107595282-107595301	chr3:107595301-107595302		53.93
K	intron_retention	CUFF.659	chr2	-	chr2:211081236-211082688				chr2:211081235-211081236;chr2:211082688-211082689		86.67
K	alternative_acceptor	CUFF.194	chr11	-	chr11:133710705-133711924	chr11:133710819-133711924		chr11:133710705-133710818	chr11:133710704-133710705		29.89
K	intron_retention		chr7	+	chr7:54617864-54618445				chr7:54617863-54617864;chr7:54618445-54618446		70.97
K	intron_retention	CUFF.1097	chr9	-	chr9:125613716-125616230				chr9:125613715-125613716;chr9:125616230-125616231		34.25
N	cassette	CUFF.653	chr2	+	chr2:200496619-200512396	chr2:200496619-200511776;chr2:200511903-200512396		chr2:200511777-200511902			75.00
K	jcn_only_AA	CUFF.496	chr18	-	chr18:66567475-66569424	chr18:66567509-66569424		chr18:66567475-66567508	chr18:66567474-66567475		38.75
K	alternative_first_exon	CUFF.133	chr10	+	chr10:124147500-124151818;chr10:124134478-124151818	chr10:124145704-124151818	chr10:124134342-124134477	chr10:124145508-124145703			76.42
N	jcn_only_AA		chr1	+	chr1:160137220-160141040	chr1:160137220-160139462		chr1:160139463-160141040	chr1:160141040-160141041		28.57
N	cassette	CUFF.1125	chrX	-	chrX:53570930-53571989	chrX:53570930-53571520;chrX:53571724-53571989		chrX:53571521-53571723			27.83
N	intron_retention		chr7	+	chr7:150817233-150820880				chr7:150817232-150817233;chr7:150820880-150820881		43.16
N	jcn_only_AA	CUFF.472	chr17	-	chr17:79478653-79478928	chr17:79478830-79478928		chr17:79478653-79478829	chr17:79478652-79478653		7.32
K	intron_retention	CUFF.1098	chr9	-	chr9:130953142-130953710				chr9:130953141-130953142;chr9:130953710-130953711		44.44
K	intron_retention	CUFF.984	chr7	+	chr7:75040118-75040690				chr7:75040117-75040118;chr7:75040690-75040691		10.26
N	cassette	CUFF.215	chr12	-	chr12:48272899-48293619;chr12:48272899-48298737	chr12:48272899-48276476;chr12:48276558-48293619,chr12:48276558-48298737		chr12:48276477-48276557			26.95
N	alternative_donor		chr17	-	chr17:1616199-1617149	chr17:1616199-1616996		chr17:1616997-1617149	chr17:1617149-1617150		73.12
N	jcn_only_AD		chr3	-	chr3:73453547-73610601;chr3:73453547-73651504;chr3:73453547-73523605;chr3:73453547-73605850;chr3:73453547-73618301	chr3:73453547-73482789					27.66
N	cassette	CUFF.280	chr14	+	chr14:76100040-76129397	chr14:76100040-76101252;chr14:76101357-76129397		chr14:76101253-76101356			18.42
N	intron_retention	CUFF.876	chr5	+	chr5:54456225-54456879				chr5:54456224-54456225;chr5:54456879-54456880		30.23
K	alternative_last_exon	CUFF.892	chr5	-	chr5:137194953-137223848	chr5:137219311-137223848	chr5:137194745-137194952	chr5:137218394-137219310			68.97
K	alternative_last_exon	CUFF.83	chr1	+	chr1:245246991-245250034,chr1:245246991-245254328,chr1:245246991-245285221;chr1:245246991-245250546;chr1:245246991-245250061	chr1:245246991-245254795	chr1:245250547-245251207;chr1:245250062-245250339	chr1:245254796-245255187			33.59
K	alternative_first_exon	CUFF.693	chr21	+	chr21:15642931-15651916	chr21:15646479-15651916	chr21:15642846-15642930	chr21:15646075-15646478		chr21:15651917-15651978	67.57
N	alternative_donor	CUFF.976	chr7	+	chr7:54614433-54614639;chr7:54612482-54614639	chr7:54613910-54614639		chr7:54612482-54613909;chr7:54613910-54614432	chr7:54612481-54612482;chr7:54613909-54613910		3.26
K	alternative_acceptor	CUFF.674	chr20	-	chr20:1517957-1532336	chr20:1517960-1532336		chr20:1517957-1517959	chr20:1517956-1517957		14.89
N	jcn_only_AA		chrX	+	chrX:47035986-47040613	chrX:47035986-47038501					89.19
K	intron_retention	CUFF.654	chr2	-	chr2:204306137-204309590				chr2:204306136-204306137;chr2:204309590-204309591		62.22
N	jcn_only_AA	CUFF.273	chr14	+	chr14:61518650-61518758	chr14:61518650-61518723		chr14:61518724-61518758	chr14:61518758-61518759		11.11
K	alternative_acceptor	CUFF.250	chr13	+	chr13:52028466-52034807	chr13:52028466-52034620		chr13:52034621-52034807	chr13:52034807-52034808		75.00
K	mutually_exclusive	CUFF.876	chr5	+	chr5:54456072-54456947,chr5:54457084-54459882	chr5:54456072-54456157,chr5:54456225-54459882	chr5:54456948-54457083	chr5:54456158-54456224			55.40
N	jcn_only_AA		chr12	+	chr12:58019248-58019407	chr12:58019248-58019364		chr12:58019365-58019407	chr12:58019407-58019408		95.80
K	coord_cassette	CUFF.654	chr2	-	chr2:204326649-204354306	chr2:204326649-204334961;chr2:204335037-204341798;chr2:204341880-204354306		chr2:204334962-204335036;chr2:204341799-204341879			46.34
K	jcn_only_AD	CUFF.931	chr6	+	chr6:46623772-46626698	chr6:46626266-46626698					30.00
K	cassette	CUFF.135	chr10	-	chr10:135060555-135061294	chr10:135060555-135061057;chr10:135061206-135061294		chr10:135061058-135061205			14.29
N	alternative_acceptor	CUFF.1118	chrX	-	chrX:19948773-19955622	chrX:19954017-19955622		chrX:19948773-19954016	chrX:19948772-19948773		55.56
N	jcn_only_AD	CUFF.306	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		87.18
K	intron_retention	CUFF.907	chr6	+	chr6:2988944-2989761				chr6:2988943-2988944;chr6:2989761-2989762		13.89
N	jcn_only_AD	CUFF.1039	chr8	+	chr8:74891097-74893389;chr8:74891407-74893389	chr8:74891111-74893389					48.21
N	cassette	CUFF.707	chr22	+	chr22:20755049-20759666	chr22:20755049-20755566;chr22:20755663-20759666		chr22:20755567-20755662			94.32
K	alternative_last_exon	CUFF.85	chr1	-	chr1:247320520-247322307,chr1:247320706-247322307;chr1:247302060-247322307	chr1:247287174-247322307	chr1:247319106-247320519;chr1:247301359-247302059	chr1:247285180-247287173			12.94
K	intron_retention	CUFF.673	chr2	+	chr2:242594759-242606059				chr2:242594758-242594759;chr2:242606059-242606060		78.43
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55714743-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55712848-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		6.69
K	intron_retention	CUFF.714	chr22	+	chr22:25916130-25916648				chr22:25916129-25916130;chr22:25916648-25916649		17.02
K	jcn_only_AA	CUFF.257,CUFF.285	chr14	+	chr14:77928586-77934425	chr14:77928586-77928984					83.68
K	intron_retention		chr17	-	chr17:57775340-57776231				chr17:57775339-57775340;chr17:57776231-57776232		18.18
N	jcn_only_AA	CUFF.765	chr3	-	chr3:107591328-107591814;chr3:107586425-107591814	chr3:107586273-107591814		chr3:107586273-107586424;chr3:107586425-107591327	chr3:107586272-107586273;chr3:107586424-107586425		46.96
K	intron_retention	CUFF.232	chr12	+	chr12:58016425-58016569				chr12:58016424-58016425;chr12:58016569-58016570		45.45
K	cassette	CUFF.384	chr16	-	chr16:15170508-15177369	chr16:15170508-15173854;chr16:15173954-15177369		chr16:15173855-15173953			98.71
N	jcn_only_AA	CUFF.701	chr21	-	chr21:43319457-43321730	chr21:43319472-43321730		chr21:43319457-43319471	chr21:43319456-43319457		57.14
K	intron_retention	CUFF.202	chr12	-	chr12:7086908-7087502				chr12:7086907-7086908;chr12:7087502-7087503		2.14
N	alternative_first_exon	CUFF.928	chr6	-	chr6:41491964-41516115;chr6:41491964-41515198	chr6:41491964-41513826,chr6:41491964-41513737	chr6:41515199-41515381	chr6:41513827-41513981			67.68
K	jcn_only_AA	CUFF.916	chr6	-	chr6:31508312-31509726	chr6:31508442-31509726		chr6:31508312-31508441	chr6:31508311-31508312		59.09
K	jcn_only_AA	CUFF.138	chr11	+	chr11:829541-829985	chr11:829541-829967		chr11:829968-829985	chr11:829985-829986	chr11:829360-829540;chr11:829986-830132	64.06
N	jcn_only_AD	CUFF.262,CUFF.278	chr14	-	chr14:31353881-31354618	chr14:31353881-31354173		chr14:31354174-31354618	chr14:31354618-31354619		32.26
K	coord_cassette	CUFF.320	chr15	-	chr15:47652295-47687757	chr15:47652295-47672653;chr15:47672793-47685518;chr15:47685683-47687757		chr15:47672654-47672792;chr15:47685519-47685682			36.36
N	intron_retention		chr16	-	chr16:30006165-30006861				chr16:30006164-30006165;chr16:30006861-30006862		31.58
N	jcn_only_AA	CUFF.389	chr16	+	chr16:22466187-22470675	chr16:22466187-22466770		chr16:22466771-22470675	chr16:22470675-22470676		4.62
N	jcn_only_AA	CUFF.1028	chr8	-	chr8:23225948-23282563	chr8:23261587-23282563					85.54
N	jcn_only_AD	CUFF.796	chr3	-	chr3:156262229-156266593;chr3:156262229-156266693	chr3:156262229-156266654		chr3:156266594-156266654;chr3:156266655-156266693	chr3:156266654-156266655;chr3:156266693-156266694		2.04
N	jcn_only_AD	CUFF.212	chr12	+	chr12:26112082-26147969	chr12:26126821-26147969		chr12:26112082-26126820	chr12:26112081-26112082		35.29
K	intron_retention	CUFF.897	chr5	-	chr5:141041357-141041609				chr5:141041356-141041357;chr5:141041609-141041610		28.57
N	alternative_donor	CUFF.889	chr5	+	chr5:128862150-128863440	chr5:128862209-128863440		chr5:128862150-128862208	chr5:128862149-128862150		83.33
N	jcn_only_AA	CUFF.230	chr12	-	chr12:56705180-56708634;chr12:56706670-56708634;chr12:56705199-56708634	chr12:56705238-56708634		chr12:56705180-56705198;chr12:56705199-56705237;chr12:56705238-56706669	chr12:56705179-56705180;chr12:56705198-56705199;chr12:56705237-56705238		10.53
N	jcn_only_AD		chr14	-	chr14:104251252-104263707	chr14:104251252-104260913					55.00
K	alternative_last_exon	CUFF.19	chr1	-	chr1:32827137-32827330	chr1:32827166-32827330	chr1:32826871-32827136	chr1:32827145-32827165			6.62
N	alternative_acceptor	CUFF.86	chr10	-	chr10:356033-372945	chr10:370960-372945		chr10:356033-370959	chr10:356032-356033		0.00
N	jcn_only_AA	CUFF.385	chr16	+	chr16:19580914-19584445	chr16:19580914-19584440		chr16:19584441-19584445	chr16:19584445-19584446		87.50
N	cassette	CUFF.905	chr6	+	chr6:320365-345853;chr6:311963-345853	chr6:311963-335113,chr6:320365-335113;chr6:335164-345853		chr6:335114-335163			43.21
N	jcn_only_AD		chr3	-	chr3:107568819-107572719	chr3:107568819-107569143		chr3:107569144-107572719	chr3:107572719-107572720		54.17
N	jcn_only_AD	CUFF.386	chr16	+	chr16:21716614-21721208	chr16:21716766-21721208		chr16:21716614-21716765	chr16:21716613-21716614		12.07
K	alternative_first_exon	CUFF.576,CUFF.654	chr2	-	chr2:676239-677288	chr2:676239-676573	chr2:677289-677534	chr2:676574-676796			81.58
K	coord_cassette	CUFF.218	chr12	-	chr12:49334972-49351092	chr12:49334972-49346895;chr12:49347058-49349880;chr12:49349981-49351092		chr12:49346896-49347057;chr12:49349881-49349980			55.07
K	jcn_only_AD	CUFF.252,CUFF.253	chr13	-	chr13:78492760-78493531	chr13:78492760-78493141		chr13:78493142-78493531	chr13:78493531-78493532		46.15
N	jcn_only_AA	CUFF.739	chr3	+	chr3:28357915-28358243;chr3:28357915-28360999	chr3:28357915-28360222		chr3:28358244-28360222;chr3:28360223-28360999	chr3:28360222-28360223;chr3:28360999-28361000		2.48
N	coord_cassette	CUFF.485	chr18	-	chr18:44272219-44336340	chr18:44272219-44284534;chr18:44284628-44301324;chr18:44301433-44336340		chr18:44284535-44284627;chr18:44301325-44301432			88.19
N	alternative_donor	CUFF.998	chr7	-	chr7:102251590-102252518;chr7:102251590-102257071	chr7:102251590-102256969		chr7:102252519-102256969;chr7:102256970-102257071	chr7:102256969-102256970;chr7:102257071-102257072		26.47
N	cassette	CUFF.1001	chr7	+	chr7:107224428-107236311	chr7:107224428-107234399;chr7:107234551-107236311		chr7:107234400-107234550			89.67
K	cassette	CUFF.540	chr19	+	chr19:36142252-36149495	chr19:36142252-36145472;chr19:36145574-36149495		chr19:36145473-36145573			64.44
K	jcn_only_AA	CUFF.619	chr2	-	chr2:86831602-86839281	chr2:86832542-86839281		chr2:86831602-86832541	chr2:86831601-86831602		54.00
N	alternative_donor	CUFF.86	chr10	-	chr10:415574-428586	chr10:415574-418952		chr10:418953-428586	chr10:428586-428587		0.00
N	alternative_acceptor	CUFF.716	chr22	+	chr22:29668421-29669726;chr22:29668421-29674119	chr22:29668421-29669729		chr22:29669727-29669729;chr22:29669730-29674119	chr22:29669729-29669730;chr22:29674119-29674120		55.17
K	cassette	CUFF.1108	chr9	+	chr9:139744590-139745206	chr9:139744590-139744957;chr9:139745013-139745206		chr9:139744958-139745012			60.79
N	jcn_only_AD	CUFF.852	chr4	-	chr4:152147239-152187237;chr4:152147239-152147319	chr4:152147239-152246392		chr4:152147320-152187237;chr4:152187238-152246392	chr4:152187237-152187238;chr4:152246392-152246393		4.21
N	alternative_last_exon	CUFF.149	chr11	-	chr11:6639008-6640426	chr11:6640147-6640426	chr11:6638857-6639007	chr11:6639665-6640146			96.96
K	intron_retention	CUFF.138	chr11	+	chr11:830133-830249				chr11:830132-830133;chr11:830249-830250	chr11:829986-830132;chr11:830250-830337	10.17
K	alternative_first_exon	CUFF.319	chr15	+	chr15:45741000-45752643	chr15:45751249-45752643	chr15:45740542-45740999	chr15:45751162-45751248			31.58
K	alternative_last_exon	CUFF.790	chr3	+	chr3:133407209-133419725	chr3:133407209-133418748	chr3:133419726-133419897	chr3:133418749-133419130			25.31
K	jcn_only_AA	CUFF.285,CUFF.301	chr14	+	chr14:106938645-106960260	chr14:106938645-106944774					64.29
K	alternative_donor	CUFF.1092	chr9	-	chr9:123555536-123555637	chr9:123555536-123555631		chr9:123555632-123555637	chr9:123555637-123555638		45.00
K	intron_retention	CUFF.393	chr16	-	chr16:30006785-30006861				chr16:30006784-30006785;chr16:30006861-30006862		8.47
N	intron_retention		chr17	-	chr17:1616199-1616996				chr17:1616198-1616199;chr17:1616996-1616997		67.91
K	intron_retention	CUFF.476	chr17	+	chr17:80438421-80438957				chr17:80438420-80438421;chr17:80438957-80438958		76.67
K	alternative_acceptor	CUFF.916	chr6	-	chr6:31508312-31509726	chr6:31508442-31509726		chr6:31508312-31508441	chr6:31508311-31508312		59.09
N	cassette	CUFF.782	chr3	-	chr3:125745323-125769740	chr3:125745323-125752449;chr3:125752522-125769740		chr3:125752450-125752521			86.24
N	jcn_only_AA	CUFF.163	chr11	+	chr11:63999437-63999865;chr11:63999437-63999901;chr11:63999437-64001365	chr11:63999437-63999981					3.93
K	alternative_first_exon	CUFF.560	chr19	-	chr19:51528923-51529793;chr19:51528923-51529011;chr19:51528923-51531199	chr19:51528923-51530712	chr19:51529794-51530493;chr19:51529012-51529110;chr19:51531200-51531383	chr19:51530713-51530984			28.24
K	alternative_last_exon	CUFF.775	chr3	-	chr3:120389380-120394638	chr3:120393837-120394638	chr3:120389055-120389379	chr3:120393353-120393836			87.88
K	cassette	CUFF.638	chr2	+	chr2:153497429-153504309	chr2:153497429-153499932;chr2:153500059-153504309		chr2:153499933-153500058			25.00
N	alternative_acceptor	CUFF.566	chr19	+	chr19:54648069-54649277;chr19:54648069-54649333	chr19:54648069-54649330		chr19:54649278-54649330;chr19:54649331-54649333	chr19:54649330-54649331;chr19:54649333-54649334		20.69
N	mutually_exclusive	CUFF.278	chr14	-	chr14:75143456-75151156,chr14:75151384-75152302	chr14:75143456-75149998,chr14:75150237-75152302	chr14:75151157-75151383	chr14:75149999-75150236		chr14:75143286-75143455;chr14:75152303-75152363	67.12
N	jcn_only_AA	CUFF.230	chr12	-	chr12:56706670-56708634;chr12:56705238-56708634;chr12:56705199-56708634	chr12:56705180-56708634		chr12:56705180-56705198;chr12:56705199-56705237;chr12:56705238-56706669	chr12:56705179-56705180;chr12:56705198-56705199;chr12:56705237-56705238		10.42
N	cassette	CUFF.467	chr17	-	chr17:76993727-77005745	chr17:76993727-76993921;chr17:76994046-77005745		chr17:76993922-76994045			98.34
K	jcn_only_AA	CUFF.102	chr10	+	chr10:35495980-35500583	chr10:35495980-35500181		chr10:35500182-35500583	chr10:35500583-35500584		44.98
N	alternative_donor	CUFF.880,CUFF.897	chr5	-	chr5:64907709-64909924	chr5:64907709-64909553		chr5:64909554-64909924	chr5:64909924-64909925		6.17
N	jcn_only_AD	CUFF.86	chr10	-	chr10:415574-428586	chr10:415574-418952		chr10:418953-428586	chr10:428586-428587		44.44
K	alternative_first_exon	CUFF.1004	chr7	-	chr7:111201980-111202519	chr7:111201980-111202499	chr7:111202520-111202671	chr7:111202500-111202515			7.58
K	intron_retention		chr16	+	chr16:89789592-89789667				chr16:89789591-89789592;chr16:89789667-89789668		5.88
N	intron_retention		chr3	-	chr3:141724387-141811902				chr3:141724386-141724387;chr3:141811902-141811903		26.83
K	intron_retention	CUFF.687	chr20	+	chr20:33589153-33589233				chr20:33589152-33589153;chr20:33589233-33589234		15.03
N	jcn_only_AD		chr14	+	chr14:76368568-76420766;chr14:76373021-76420766	chr14:76407838-76420766					25.00
K	alternative_acceptor	CUFF.1145	chrX	+	chrX:142113879-142121813	chrX:142113879-142121810		chrX:142121811-142121813	chrX:142121813-142121814	chrX:142113650-142113878;chrX:142121814-142122018	40.00
K	alternative_last_exon	CUFF.83	chr1	+	chr1:245246991-245250034,chr1:245246991-245254328,chr1:245246991-245285221;chr1:245246991-245250546;chr1:245246991-245254795	chr1:245246991-245250061	chr1:245250547-245251207;chr1:245254796-245255187	chr1:245250062-245250339			16.80
K	intron_retention	CUFF.1098	chr9	-	chr9:130948014-130953002				chr9:130948013-130948014;chr9:130953002-130953003		88.42
N	alternative_donor	CUFF.739	chr3	+	chr3:28357915-28360999;chr3:28358351-28360999	chr3:28360371-28360999		chr3:28357915-28358350;chr3:28358351-28360370	chr3:28357914-28357915;chr3:28358350-28358351		5.19
K	intron_retention	CUFF.647	chr2	-	chr2:175869809-175869933				chr2:175869808-175869809;chr2:175869933-175869934		9.88
N	jcn_only_AA	CUFF.49	chr1	-	chr1:153921121-153921590	chr1:153921377-153921590		chr1:153921121-153921376	chr1:153921120-153921121		15.62
N	jcn_only_AD		chr14	-	chr14:104224089-104245081;chr14:104224089-104225527	chr14:104224089-104230199					11.90
N	jcn_only_AD	CUFF.241	chr12	-	chr12:120158391-120287977	chr12:120158391-120159113					67.86
N	intron_retention		chr19	-	chr19:6191606-6191875				chr19:6191605-6191606;chr19:6191875-6191876		60.00
N	jcn_only_AD	CUFF.999	chr7	-	chr7:102453979-102462486	chr7:102453979-102454780		chr7:102454781-102462486	chr7:102462486-102462487		7.30
N	jcn_only_AD		chr7	-	chr7:110603622-111030626;chr7:110603622-111031893	chr7:110603622-111127293					67.57
N	cassette	CUFF.905	chr6	+	chr6:292561-345853	chr6:292561-311879;chr6:311915-345853		chr6:311880-311914			48.89
N	alternative_donor	CUFF.271	chr14	-	chr14:59946070-59950397;chr14:59946070-59950526	chr14:59946070-59950207		chr14:59950208-59950397;chr14:59950398-59950526	chr14:59950397-59950398;chr14:59950526-59950527		8.78
K	cassette	CUFF.412	chr16	+	chr16:77759482-77775478	chr16:77759482-77769724;chr16:77769884-77775478		chr16:77769725-77769883			70.21
K	intron_retention	CUFF.752	chr3	-	chr3:49350047-49362134				chr3:49350046-49350047;chr3:49362134-49362135		55.00
N	alternative_acceptor		chr7	-	chr7:37433521-37488462;chr7:37382368-37488462	chr7:37469360-37488462		chr7:37382368-37433520;chr7:37433521-37469359	chr7:37382367-37382368;chr7:37433520-37433521		0.00
K	intron_retention	CUFF.716	chr22	+	chr22:29687589-29688125				chr22:29687588-29687589;chr22:29688125-29688126		5.56
N	cassette	CUFF.441	chr17	+	chr17:35378314-35413900	chr17:35378314-35388910;chr17:35388983-35413900		chr17:35388911-35388982			15.91
K	intron_retention	CUFF.741	chr3	-	chr3:33431861-33434054				chr3:33431860-33431861;chr3:33434054-33434055		16.88
K	jcn_only_AD	CUFF.1014	chr7	+	chr7:148982588-148984655	chr7:148982788-148984655		chr7:148982588-148982787	chr7:148982587-148982588		25.00
N	jcn_only_AA		chr3	-	chr3:33686396-33700998	chr3:33700502-33700998					58.82
K	cassette	CUFF.971	chr7	-	chr7:37053041-37136223	chr7:37053041-37072951;chr7:37073018-37136223		chr7:37072952-37073017			14.81
N	jcn_only_AD	CUFF.572	chr2	-	chr2:110920710-110922264	chr2:110920710-110922096		chr2:110922097-110922264	chr2:110922264-110922265		18.18
N	intron_retention	CUFF.504	chr19	+	chr19:1438892-1439959				chr19:1438891-1438892;chr19:1439959-1439960		47.83
N	mutually_exclusive	CUFF.1116	chrX	-	chrX:15343275-15349711,chrX:15350115-15353622	chrX:15343275-15344035,chrX:15344169-15353622	chrX:15349712-15350114	chrX:15344036-15344168			7.14
K	jcn_only_AD	CUFF.1137	chrX	-	chrX:114358566-114364717	chrX:114358566-114361405					25.00
K	intron_retention	CUFF.530	chr19	+	chr19:17447537-17447628				chr19:17447536-17447537;chr19:17447628-17447629		73.53
N	cassette	CUFF.809	chr4	+	chr4:660404-663834	chr4:660404-661644;chr4:661796-663834		chr4:661645-661795			54.84
N	jcn_only_AA	CUFF.910	chr6	-	chr6:5144497-5216850;chr6:5138974-5216850;chr6:5187215-5216850	chr6:5113652-5216850		chr6:5113652-5138973;chr6:5138974-5144496;chr6:5144497-5187214	chr6:5113651-5113652;chr6:5138973-5138974;chr6:5144496-5144497		37.25
K	cassette	CUFF.459	chr17	-	chr17:61843555-61850771	chr17:61843555-61850136;chr17:61850224-61850771		chr17:61850137-61850223			4.08
N	alternative_donor	CUFF.201	chr12	+	chr12:4662256-4668022;chr12:4665717-4668022	chr12:4665669-4668022		chr12:4662256-4665668;chr12:4665669-4665716	chr12:4662255-4662256;chr12:4665668-4665669		17.24
K	intron_retention	CUFF.136	chr11	-	chr11:406539-406842				chr11:406538-406539;chr11:406842-406843		12.42
K	cassette	CUFF.393	chr16	-	chr16:30005130-30006423	chr16:30005130-30005226;chr16:30006165-30006423		chr16:30005227-30006164			41.46
K	jcn_only_AD	CUFF.133	chr10	+	chr10:124187833-124189139	chr10:124187937-124189139		chr10:124187833-124187936	chr10:124187832-124187833		99.52
N	alternative_first_exon	CUFF.212	chr12	+	chr12:26205536-26208168;chr12:26205930-26208168;chr12:26164755-26208168;chr12:26174452-26208168	chr12:26148064-26208168	chr12:26205414-26205929;chr12:26164591-26164754;chr12:26174353-26174451	chr12:26147970-26148063			12.50
K	intron_retention	CUFF.187	chr11	+	chr11:119056220-119056557				chr11:119056219-119056220;chr11:119056557-119056558		50.00
K	intron_retention	CUFF.1051	chr8	+	chr8:106646586-106800945				chr8:106646585-106646586;chr8:106800945-106800946		38.24
N	jcn_only_AA		chr14	-	chr14:104261001-104263707;chr14:104245159-104263707	chr14:104251252-104263707					34.62
N	alternative_acceptor	CUFF.426	chr17	-	chr17:15557746-15584178;chr17:15581036-15584178	chr17:15580997-15584178		chr17:15557746-15580996;chr17:15580997-15581035	chr17:15557745-15557746;chr17:15580996-15580997		0.00
K	intron_retention	CUFF.983	chr7	-	chr7:74984930-74988197				chr7:74984929-74984930;chr7:74988197-74988198		62.50
N	alternative_donor		chr7	+	chr7:54617864-54636823	chr7:54621767-54636823		chr7:54617864-54621766	chr7:54617863-54617864		66.67
K	alternative_first_exon	CUFF.200	chr12	+	chr12:4430470-4440445	chr12:4433930-4440445	chr12:4430371-4430469	chr12:4433745-4433929			80.60
K	intron_retention	CUFF.464	chr17	+	chr17:66522054-66523980				chr17:66522053-66522054;chr17:66523980-66523981		1.25
K	jcn_only_AA	CUFF.20	chr1	-	chr1:33647023-33647594	chr1:33647096-33647594		chr1:33647023-33647095	chr1:33647022-33647023		70.59
N	intron_retention		chr17	+	chr17:66511294-66511534				chr17:66511293-66511294;chr17:66511534-66511535		73.08
K	intron_retention	CUFF.457	chr17	+	chr17:61566494-61568314				chr17:61566493-61566494;chr17:61568314-61568315		9.64
K	coord_cassette	CUFF.824	chr4	-	chr4:36014454-36047600	chr4:36014454-36017007;chr4:36017255-36017521;chr4:36017581-36020765;chr4:36020909-36047600		chr4:36017008-36017254;chr4:36017522-36017580;chr4:36020766-36020908			21.21
K	alternative_first_exon	CUFF.296	chr14	+	chr14:103187422-103188523	chr14:103187715-103188523	chr14:103187177-103187421	chr14:103187657-103187714			10.87
N	alternative_acceptor	CUFF.119	chr10	-	chr10:78637649-78647048;chr10:78637652-78647048	chr10:78644776-78647048		chr10:78637649-78637651;chr10:78637652-78644775	chr10:78637648-78637649;chr10:78637651-78637652		15.00
K	alternative_donor	CUFF.550	chr19	+	chr19:44764156-44768466;chr19:44764362-44768466	chr19:44764092-44768466		chr19:44764092-44764155;chr19:44764156-44764361	chr19:44764091-44764092;chr19:44764155-44764156		6.82
K	intron_retention	CUFF.418	chr17	+	chr17:1944916-1945061				chr17:1944915-1944916;chr17:1945061-1945062		42.70
K	jcn_only_AA	CUFF.426	chr17	-	chr17:15586472-15587509	chr17:15586686-15587509		chr17:15586472-15586685	chr17:15586471-15586472		5.07
N	jcn_only_AD		chr14	-	chr14:104224089-104245081;chr14:104224089-104230199	chr14:104224089-104225527					30.95
K	cassette	CUFF.464	chr17	+	chr17:66524042-66525010	chr17:66524042-66524771;chr17:66524861-66525010		chr17:66524772-66524860			7.96
N	alternative_donor	CUFF.333	chr15	-	chr15:66783056-66786752	chr15:66783056-66786614		chr15:66786615-66786752	chr15:66786752-66786753		88.51
K	cassette	CUFF.356	chr15	+	chr15:94408878-94421262	chr15:94408878-94412919;chr15:94413063-94421262		chr15:94412920-94413062			40.00
K	cassette	CUFF.110	chr10	-	chr10:69583151-69597691	chr10:69583151-69587299;chr10:69587442-69597691		chr10:69587300-69587441		chr10:69583072-69583150;chr10:69597692-69597991	9.80
N	jcn_only_AD	CUFF.1004	chr7	-	chr7:110603622-111030626;chr7:110603622-111127293	chr7:110603622-111031893					23.87
N	jcn_only_AA	CUFF.151	chr11	-	chr11:8950976-8953688	chr11:8951081-8953688		chr11:8950976-8951080	chr11:8950975-8950976		87.61
N	cassette	CUFF.333	chr15	-	chr15:66786891-66789979;chr15:66786891-66789827	chr15:66786891-66787667;chr15:66787758-66789979,chr15:66787758-66789827		chr15:66787668-66787757			88.76
N	cassette	CUFF.481	chr18	+	chr18:12009987-12014263	chr18:12009987-12012168;chr18:12012215-12014263		chr18:12012169-12012214			87.08
K	jcn_only_AD	CUFF.1073	chr9	+	chr9:43915898-43920248	chr9:43915980-43920248		chr9:43915898-43915979	chr9:43915897-43915898		82.35
N	jcn_only_AA	CUFF.336,CUFF.340	chr15	+	chr15:74758472-74771400	chr15:74758472-74771384		chr15:74771385-74771400	chr15:74771400-74771401		16.33
K	alternative_first_exon	CUFF.641	chr2	+	chr2:169659184-169668076	chr2:169667936-169668076	chr2:169658891-169659183	chr2:169667865-169667935			4.31
K	intron_retention	CUFF.506	chr19	+	chr19:4318949-4322982				chr19:4318948-4318949;chr19:4322982-4322983		29.49
N	alternative_acceptor	CUFF.1066	chr9	-	chr9:15185405-15186941	chr9:15185527-15186941		chr9:15185405-15185526	chr9:15185404-15185405		4.62
K	mutually_exclusive	CUFF.673	chr2	+	chr2:242594063-242598522,chr2:242598603-242606059	chr2:242594063-242594685,chr2:242594759-242606059	chr2:242598523-242598602	chr2:242594686-242594758			64.71
K	alternative_first_exon	CUFF.836,CUFF.838	chr4	-	chr4:77979789-77987401;chr4:77979789-77985865	chr4:77979789-77996624	chr4:77987402-77987558;chr4:77985866-77986241	chr4:77996625-77997233			39.46
N	jcn_only_AA	CUFF.940	chr6	+	chr6:46638966-46644383	chr6:46638966-46644119		chr6:46644120-46644383	chr6:46644383-46644384		42.86
K	intron_retention	CUFF.557	chr19	+	chr19:50304879-50304978				chr19:50304878-50304879;chr19:50304978-50304979		11.36
K	jcn_only_AA	CUFF.253	chr13	-	chr13:97640030-97642011	chr13:97640088-97642011		chr13:97640030-97640087	chr13:97640029-97640030		85.60
N	alternative_last_exon		chr5	+	chr5:134181903-134190587	chr5:134181903-134182352	chr5:134190588-134195523	chr5:134182353-134182553			100.00
N	intron_retention		chr19	+	chr19:17448474-17448707				chr19:17448473-17448474;chr19:17448707-17448708		43.75
N	alternative_donor	CUFF.102	chr10	+	chr10:35464928-35467816;chr10:35437420-35467816;chr10:35416122-35467816;chr10:35456732-35467816;chr10:35464634-35467816	chr10:35426808-35467816		chr10:35416122-35426807;chr10:35426808-35437419;chr10:35437420-35456731;chr10:35456732-35464633;chr10:35464634-35464927	chr10:35416121-35416122;chr10:35426807-35426808;chr10:35437419-35437420;chr10:35456731-35456732;chr10:35464633-35464634		0.00
K	alternative_donor	CUFF.333	chr15	-	chr15:66786891-66787667	chr15:66786891-66787240		chr15:66787241-66787667	chr15:66787667-66787668		25.79
N	intron_retention		chr17	-	chr17:79994890-79995489				chr17:79994889-79994890;chr17:79995489-79995490		91.71
N	jcn_only_AA		chr19	-	chr19:6192041-6199490;chr19:6176455-6199490	chr19:6192065-6199490					13.64
N	cassette	CUFF.572	chr2	-	chr2:260703-263210;chr2:253116-264781;chr2:253116-263210	chr2:260703-262630,chr2:253116-262630;chr2:262787-264781,chr2:262787-263210		chr2:262631-262786			26.71
K	jcn_only_AD	CUFF.1066,CUFF.1084	chr9	-	chr9:104188921-104192090	chr9:104188921-104189763					28.57
K	alternative_first_exon	CUFF.526	chr19	+	chr19:16191886-16192722,chr19:16187508-16192722;chr19:16186983-16192722	chr19:16191253-16192722	chr19:16186857-16186982	chr19:16191160-16191252			10.78
K	jcn_only_AD	CUFF.176	chr11	-	chr11:102933144-102936997	chr11:102933144-102935003					90.99
N	jcn_only_AA	CUFF.167	chr11	+	chr11:67786363-67786638	chr11:67786363-67786534		chr11:67786535-67786638	chr11:67786638-67786639		3.08
K	intron_retention	CUFF.336	chr15	+	chr15:74753977-74773545				chr15:74753976-74753977;chr15:74773545-74773546		71.05
N	cassette	CUFF.927	chr6	-	chr6:39859156-39864972	chr6:39859156-39859398;chr6:39859540-39864972		chr6:39859399-39859539			57.14
N	jcn_only_AD	CUFF.769	chr3	+	chr3:119187954-119188666;chr3:119187854-119188666	chr3:119188106-119188666		chr3:119187854-119187953;chr3:119187954-119188105	chr3:119187853-119187854;chr3:119187953-119187954		44.83
N	jcn_only_AA		chr2	+	chr2:680152-696540	chr2:680152-681255		chr2:681256-696540	chr2:696540-696541		35.29
K	coord_cassette	CUFF.829	chr4	-	chr4:56471517-56475286	chr4:56471517-56473464;chr4:56473516-56473603;chr4:56473634-56475286		chr4:56473465-56473515;chr4:56473604-56473633			53.45
K	intron_retention	CUFF.526	chr19	+	chr19:16212601-16213657				chr19:16212600-16212601;chr19:16213657-16213658		73.08
N	jcn_only_AD	CUFF.28	chr1	+	chr1:70820795-70832126;chr1:70820892-70832126;chr1:70820791-70832126	chr1:70832012-70832126		chr1:70820791-70820794;chr1:70820795-70820891;chr1:70820892-70832011	chr1:70820790-70820791;chr1:70820794-70820795;chr1:70820891-70820892		8.24
K	cassette	CUFF.988	chr7	-	chr7:86569432-86571333	chr7:86569432-86570667;chr7:86570702-86571333		chr7:86570668-86570701			25.93
K	alternative_first_exon	CUFF.79	chr1	+	chr1:224371121-224377278;chr1:224371534-224377278	chr1:224363650-224377278	chr1:224370860-224371120;chr1:224371312-224371533	chr1:224363458-224363649			13.64
N	alternative_acceptor	CUFF.765	chr3	-	chr3:107568819-107572719;chr3:107569199-107572719	chr3:107567966-107572719		chr3:107567966-107568818;chr3:107568819-107569198	chr3:107567965-107567966;chr3:107568818-107568819		83.78
N	cassette	CUFF.1052	chr8	+	chr8:107726214-107752570	chr8:107726214-107751685;chr8:107751812-107752570		chr8:107751686-107751811			90.00
N	jcn_only_AD	CUFF.604	chr2	-	chr2:61749819-61753554	chr2:61749819-61752404		chr2:61752405-61753554	chr2:61753554-61753555		4.73
N	jcn_only_AD	CUFF.998	chr7	-	chr7:102251590-102256969;chr7:102251590-102252518	chr7:102251590-102257071		chr7:102252519-102256969;chr7:102256970-102257071	chr7:102256969-102256970;chr7:102257071-102257072		34.29
K	alternative_first_exon	CUFF.796	chr3	-	chr3:156271571-156272745;chr3:156271571-156272525	chr3:156271571-156271781	chr3:156272746-156272973;chr3:156272526-156272688	chr3:156271782-156271977			35.87
K	intron_retention	CUFF.265	chr14	+	chr14:50246394-50246465				chr14:50246393-50246394;chr14:50246465-50246466		81.25
N	jcn_only_AA	CUFF.810	chr4	+	chr4:186283866-186290903	chr4:186283866-186284538		chr4:186284539-186290903	chr4:186290903-186290904		96.12
K	intron_retention	CUFF.509	chr19	-	chr19:6007814-6008116				chr19:6007813-6007814;chr19:6008116-6008117		32.93
K	alternative_first_exon	CUFF.481	chr18	+	chr18:11999187-12009881	chr18:12008591-12009881	chr18:11999053-11999186	chr18:12008493-12008590			3.89
K	intron_retention		chr11	-	chr11:2187999-2188116				chr11:2187998-2187999;chr11:2188116-2188117		13.08
N	alternative_donor	CUFF.230	chr12	-	chr12:56709027-56709690;chr12:56709027-56709500	chr12:56709027-56709604		chr12:56709501-56709604;chr12:56709605-56709690	chr12:56709604-56709605;chr12:56709690-56709691		60.26
K	alternative_acceptor	CUFF.239	chr12	-	chr12:113596915-113599074	chr12:113596918-113599074		chr12:113596915-113596917	chr12:113596914-113596915		6.38
N	alternative_donor	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55816792-55833019	chr18:55722109-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		0.00
K	cassette	CUFF.304	chr15	+	chr15:25225232-25244116	chr15:25225232-25226921;chr15:25227585-25244116		chr15:25226922-25227584			75.00
N	alternative_acceptor	CUFF.786	chr3	-	chr3:127299007-127313642	chr3:127310794-127313642		chr3:127299007-127310793	chr3:127299006-127299007		7.84
N	cassette	CUFF.1042	chr8	-	chr8:80965666-81083659	chr8:80965666-80976712;chr8:80976829-81083659		chr8:80976713-80976828			55.80
K	coord_cassette	CUFF.787	chr3	+	chr3:132948196-133109023	chr3:132948196-133097185;chr3:133097401-133098595;chr3:133100006-133109023		chr3:133097186-133097400;chr3:133098596-133100005			40.00
K	intron_retention	CUFF.4	chr1	+	chr1:11082308-11083249				chr1:11082307-11082308;chr1:11083249-11083250		28.57
N	alternative_donor	CUFF.418	chr17	+	chr17:1939948-1940128	chr17:1939981-1940128		chr17:1939948-1939980	chr17:1939947-1939948		83.33
K	intron_retention	CUFF.50	chr1	+	chr1:155180686-155181182				chr1:155180685-155180686;chr1:155181182-155181183		21.05
K	alternative_last_exon	CUFF.777	chr3	+	chr3:122880303-122928045	chr3:122880303-122880726	chr3:122928046-122928246	chr3:122880727-122881038			53.12
K	intron_retention	CUFF.1008	chr7	-	chr7:127255150-127255454				chr7:127255149-127255150;chr7:127255454-127255455		26.83
N	jcn_only_AD		chr7	-	chr7:117424509-117431344	chr7:117424509-117426439					60.00
K	jcn_only_AA	CUFF.61,CUFF.65	chr1	+	chr1:171123354-171130296	chr1:171123354-171130202		chr1:171130203-171130296	chr1:171130296-171130297		58.82
K	alternative_first_exon	CUFF.83	chr1	+	chr1:245165535-245180543;chr1:245133101-245180543	chr1:245133746-245180543	chr1:245132920-245133100	chr1:245133631-245133745			32.43
N	jcn_only_AD		chr3	-	chr3:73453547-73482789;chr3:73453547-73610601;chr3:73453547-73651504;chr3:73453547-73605850;chr3:73453547-73618301	chr3:73453547-73523605					28.26
K	intron_retention	CUFF.152	chr11	-	chr11:10823322-10823595				chr11:10823321-10823322;chr11:10823595-10823596		80.00
K	alternative_first_exon	CUFF.847	chr4	-	chr4:120116724-120133681	chr4:120116724-120116865	chr4:120133682-120133883	chr4:120116866-120116996			61.29
N	alternative_acceptor		chr17	+	chr17:61555460-61557129;chr17:61555460-61556367	chr17:61555460-61556171		chr17:61556172-61556367;chr17:61556368-61557129	chr17:61556367-61556368;chr17:61557129-61557130		17.39
N	intron_retention		chr17	-	chr17:79220859-79225292				chr17:79220858-79220859;chr17:79225292-79225293	chr17:79225293-79226483	70.59
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55919287-55983213	chr18:55981822-55983213		chr18:55919287-55981821	chr18:55919286-55919287		2.50
K	cassette	CUFF.673	chr2	+	chr2:242577140-242590424	chr2:242577140-242577675;chr2:242577786-242590424		chr2:242577676-242577785			1.30
K	alternative_last_exon	CUFF.837,CUFF.850	chr4	+	chr4:77192922-77230296	chr4:77192922-77211054	chr4:77230297-77232371	chr4:77211055-77211134			6.45
N	jcn_only_AA		chr15	+	chr15:24811948-24814929;chr15:24811948-24813043;chr15:24811948-24813038	chr15:24811948-24813677					20.00
N	alternative_donor	CUFF.628	chr2	+	chr2:101565943-101580519	chr2:101579296-101580519		chr2:101565943-101579295	chr2:101565942-101565943		0.00
N	jcn_only_AA	CUFF.197	chr12	+	chr12:53861628-53862563	chr12:53861628-53862560		chr12:53862561-53862563	chr12:53862563-53862564		46.49
N	alternative_first_exon	CUFF.725	chr22	+	chr22:45181982-45182336,chr22:45173110-45182336;chr22:45131043-45182336;chr22:45162070-45182336;chr22:45122515-45182336	chr22:45148508-45182336	chr22:45130907-45131042;chr22:45161745-45162069;chr22:45122457-45122514	chr22:45148371-45148507			21.88
K	mutually_exclusive	CUFF.258	chr14	+	chr14:24459569-24473545,chr14:24473602-24475094	chr14:24459569-24470592,chr14:24470727-24475094	chr14:24473546-24473601	chr14:24470593-24470726			45.45
N	alternative_acceptor	CUFF.940	chr6	+	chr6:46638966-46644383	chr6:46638966-46644119		chr6:46644120-46644383	chr6:46644383-46644384		70.37
N	coord_cassette	CUFF.234	chr12	+	chr12:69214155-69233053	chr12:69214155-69218142;chr12:69218211-69218334;chr12:69218432-69233053		chr12:69218143-69218210;chr12:69218335-69218431			71.63
N	alternative_acceptor	CUFF.792	chr3	-	chr3:133910819-133913925	chr3:133910828-133913925		chr3:133910819-133910827	chr3:133910818-133910819		18.46
N	alternative_donor		chr7	-	chr7:37382368-37433424;chr7:37382368-37392635;chr7:37382368-37488277;chr7:37382368-37488462	chr7:37382368-37382655		chr7:37382656-37392635;chr7:37392636-37433424;chr7:37433425-37488277;chr7:37488278-37488462	chr7:37392635-37392636;chr7:37433424-37433425;chr7:37488277-37488278;chr7:37488462-37488463		0.00
K	alternative_donor	CUFF.658	chr2	-	chr2:207953306-207988497;chr2:207953306-207989067	chr2:207953306-207988699		chr2:207988498-207988699;chr2:207988700-207989067	chr2:207988699-207988700;chr2:207989067-207989068		10.62
K	alternative_first_exon	CUFF.669	chr2	+	chr2:241396887-241398446,chr2:241381924-241398446;chr2:241392512-241398446;chr2:241397535-241398446	chr2:241394438-241398446	chr2:241392147-241392511;chr2:241397319-241397534	chr2:241394347-241394437			3.31
K	cassette	CUFF.360	chr15	-	chr15:102197240-102201914	chr15:102197240-102197987;chr15:102198061-102201914		chr15:102197988-102198060			76.56
K	intron_retention	CUFF.1048	chr8	-	chr8:99057317-99057574				chr8:99057316-99057317;chr8:99057574-99057575		43.86
K	alternative_acceptor	CUFF.404	chr16	-	chr16:67968575-67968699	chr16:67968598-67968699		chr16:67968575-67968597	chr16:67968574-67968575	chr16:67968700-67968851;chr16:67968307-67968574	62.69
N	alternative_donor	CUFF.419,CUFF.472	chr17	-	chr17:5403271-5405056	chr17:5403271-5403350		chr17:5403351-5405056	chr17:5405056-5405057		76.00
N	jcn_only_AA	CUFF.464	chr17	+	chr17:46986183-46993437	chr17:46986183-46988169					68.18
N	alternative_acceptor	CUFF.728	chr22	-	chr22:51018232-51018402	chr22:51018260-51018402		chr22:51018232-51018259	chr22:51018231-51018232		94.07
K	intron_retention	CUFF.151	chr11	-	chr11:8949230-8950923				chr11:8949229-8949230;chr11:8950923-8950924		64.22
N	intron_retention		chr6	-	chr6:43480837-43481096				chr6:43480836-43480837;chr6:43481096-43481097		95.74
N	jcn_only_AA	CUFF.114	chr10	-	chr10:73973036-73975964;chr10:73975868-73975964;chr10:73975613-73975964;chr10:73973110-73975964	chr10:73973090-73975964					27.27
N	alternative_donor	CUFF.1062	chr8	+	chr8:144375236-144377909	chr8:144377641-144377909		chr8:144375236-144377640	chr8:144375235-144375236		1.20
N	jcn_only_AA		chr14	+	chr14:76243194-76245921	chr14:76243194-76245917					36.67
N	jcn_only_AD	CUFF.1039	chr8	+	chr8:74891407-74893389;chr8:74891111-74893389	chr8:74891097-74893389					7.14
N	alternative_acceptor	CUFF.352	chr15	-	chr15:90414779-90431752;chr15:90421533-90431752	chr15:90420657-90431752		chr15:90414779-90420656;chr15:90420657-90421532	chr15:90414778-90414779;chr15:90420656-90420657		2.13
K	coord_cassette	CUFF.34	chr1	-	chr1:106132408-106146784	chr1:106132408-106143891;chr1:106144008-106145898;chr1:106146181-106146784		chr1:106143892-106144007;chr1:106145899-106146180			48.72
K	intron_retention	CUFF.920	chr6	+	chr6:32122172-32122363				chr6:32122171-32122172;chr6:32122363-32122364		36.84
N	intron_retention		chr12	-	chr12:7086688-7087582				chr12:7086687-7086688;chr12:7087582-7087583		91.82
K	cassette	CUFF.1013	chr7	+	chr7:136554166-136699566	chr7:136554166-136676933;chr7:136677012-136699566		chr7:136676934-136677011			34.15
N	cassette	CUFF.1066	chr9	-	chr9:15192694-15203820	chr9:15192694-15199858;chr9:15199924-15203820		chr9:15199859-15199923			89.06
K	intron_retention	CUFF.114	chr10	-	chr10:73973090-73975964				chr10:73973089-73973090;chr10:73975964-73975965		22.97
N	jcn_only_AA	CUFF.765	chr3	-	chr3:107568819-107572719;chr3:107569199-107572719	chr3:107567966-107572719		chr3:107567966-107568818;chr3:107568819-107569198	chr3:107567965-107567966;chr3:107568818-107568819		54.39
N	cassette	CUFF.387	chr16	+	chr16:21969921-21973780	chr16:21969921-21972648;chr16:21972787-21973780		chr16:21972649-21972786			22.22
N	jcn_only_AA	CUFF.530,CUFF.531	chr19	+	chr19:17581517-17597371;chr19:17581517-17598268	chr19:17581517-17594690					5.13
K	intron_retention	CUFF.604	chr2	-	chr2:61711241-61712902				chr2:61711240-61711241;chr2:61712902-61712903		6.43
N	mutually_exclusive	CUFF.136	chr11	-	chr11:407958-408694,chr11:408894-409867	chr11:407958-408072,chr11:408207-409867	chr11:408695-408893	chr11:408073-408206			17.83
K	jcn_only_AD	CUFF.859	chr4	+	chr4:191012637-191013578	chr4:191013443-191013578		chr4:191012637-191013442	chr4:191012636-191012637		46.67
K	alternative_acceptor	CUFF.626	chr2	+	chr2:99232997-99234630	chr2:99232997-99234608		chr2:99234609-99234630	chr2:99234630-99234631		31.67
N	intron_retention		chr11	-	chr11:10821304-10821790				chr11:10821303-10821304;chr11:10821790-10821791		51.67
N	jcn_only_AA		chr2	-	chr2:242440263-242440892;chr2:242440493-242440892	chr2:242440335-242440892					14.93
N	jcn_only_AD	CUFF.325	chr15	+	chr15:57384090-57458599;chr15:57426699-57458599;chr15:57401516-57458599	chr15:57422171-57458599		chr15:57384090-57401515;chr15:57401516-57422170;chr15:57422171-57426698	chr15:57384089-57384090;chr15:57401515-57401516;chr15:57422170-57422171		13.59
N	intron_retention	CUFF.390	chr16	-	chr16:23504780-23505619				chr16:23504779-23504780;chr16:23505619-23505620	chr16:23504681-23504779;chr16:23505620-23505699	94.05
N	alternative_first_exon	CUFF.160	chr11	+	chr11:61596070-61605249;chr11:61584169-61605249	chr11:61594904-61605249	chr11:61583838-61584168	chr11:61594787-61594903		chr11:61605250-61605360	38.46
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		85.21
K	intron_retention	CUFF.722	chr22	+	chr22:37707569-37708060				chr22:37707568-37707569;chr22:37708060-37708061		15.79
N	alternative_donor	CUFF.230	chr12	-	chr12:56709027-56709604;chr12:56709027-56709500	chr12:56709027-56709690		chr12:56709501-56709604;chr12:56709605-56709690	chr12:56709604-56709605;chr12:56709690-56709691		30.77
N	intron_retention		chr3	-	chr3:107560867-107560951				chr3:107560866-107560867;chr3:107560951-107560952		68.75
N	alternative_acceptor	CUFF.980	chr7	+	chr7:73108381-73111934;chr7:73108381-73110735	chr7:73108381-73111795		chr7:73110736-73111795;chr7:73111796-73111934	chr7:73111795-73111796;chr7:73111934-73111935		2.60
N	jcn_only_AD	CUFF.1098	chr9	-	chr9:130941184-130941267;chr9:130941184-130941351	chr9:130941184-130941522		chr9:130941268-130941351;chr9:130941352-130941522	chr9:130941351-130941352;chr9:130941522-130941523		13.75
N	jcn_only_AD	CUFF.657	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		4.17
N	intron_retention	CUFF.504	chr19	+	chr19:1438892-1439714				chr19:1438891-1438892;chr19:1439714-1439715		84.00
K	jcn_only_AA	CUFF.569	chr19	-	chr19:56321705-56343328	chr19:56329603-56343328					30.16
N	jcn_only_AA	CUFF.163,CUFF.165	chr11	+	chr11:63999437-63999901;chr11:63999437-64001365;chr11:63999437-63999981	chr11:63999437-63999865					25.36
N	alternative_donor	CUFF.232	chr12	+	chr12:58014837-58015045	chr12:58014876-58015045		chr12:58014837-58014875	chr12:58014836-58014837		85.71
K	cassette	CUFF.728	chr22	-	chr22:51012145-51012763	chr22:51012145-51012236;chr22:51012351-51012763		chr22:51012237-51012350			52.91
K	intron_retention	CUFF.728	chr22	-	chr22:51007511-51007764				chr22:51007510-51007511;chr22:51007764-51007765		31.25
N	coord_cassette	CUFF.1052	chr8	+	chr8:107726214-107752570	chr8:107726214-107749747;chr8:107749829-107751685;chr8:107751812-107752570		chr8:107749748-107749828;chr8:107751686-107751811			87.88
K	jcn_only_AD	CUFF.183	chr11	-	chr11:118532439-118533496	chr11:118532439-118532598					31.88
K	intron_retention	CUFF.50	chr1	+	chr1:155181338-155181917				chr1:155181337-155181338;chr1:155181917-155181918		26.32
N	cassette	CUFF.1116	chrX	-	chrX:15343275-15349711	chrX:15343275-15344035;chrX:15344169-15349711		chrX:15344036-15344168			25.81
N	cassette	CUFF.138	chr11	+	chr11:830714-831223	chr11:830714-830865;chr11:831033-831223		chr11:830866-831032		chr11:830621-830713;chr11:831224-831295	79.41
N	jcn_only_AD	CUFF.588,CUFF.647	chr2	-	chr2:175677211-175689161	chr2:175677211-175686456		chr2:175686457-175689161	chr2:175689161-175689162		13.83
N	alternative_donor		chr14	-	chr14:92105595-92112480;chr14:92105595-92126180	chr14:92105595-92136157		chr14:92112481-92126180;chr14:92126181-92136157	chr14:92126180-92126181;chr14:92136157-92136158		100.00
K	intron_retention	CUFF.267	chr14	-	chr14:52472568-52473254				chr14:52472567-52472568;chr14:52473254-52473255		5.88
N	jcn_only_AA	CUFF.894	chr5	+	chr5:139815843-139818078;chr5:139815843-139818087	chr5:139815843-139818045		chr5:139818046-139818078;chr5:139818079-139818087	chr5:139818078-139818079;chr5:139818087-139818088	chr5:139815689-139815842;chr5:139818088-139818202	12.50
N	jcn_only_AA	CUFF.278	chr14	-	chr14:75152364-75158743	chr14:75157854-75158743		chr14:75152364-75157853	chr14:75152363-75152364	chr14:75158744-75159031;chr14:75152303-75152363	14.93
N	alternative_donor	CUFF.769	chr3	+	chr3:119188106-119188666;chr3:119187854-119188666	chr3:119187954-119188666		chr3:119187854-119187953;chr3:119187954-119188105	chr3:119187853-119187854;chr3:119187953-119187954		40.00
N	intron_retention		chrX	+	chrX:153607898-153608049				chrX:153607897-153607898;chrX:153608049-153608050		59.09
K	intron_retention	CUFF.782	chr3	-	chr3:125743749-125745177				chr3:125743748-125743749;chr3:125745177-125745178		36.84
N	alternative_donor	CUFF.589	chr2	-	chr2:27708371-27712481	chr2:27708371-27709025		chr2:27709026-27712481	chr2:27712481-27712482		0.00
N	alternative_donor	CUFF.352	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		0.47
N	jcn_only_AD		chr16	-	chr16:57513598-57513756;chr16:57513598-57517869	chr16:57513598-57513772					35.00
N	alternative_donor	CUFF.83	chr1	+	chr1:245222761-245245384	chr1:245238914-245245384		chr1:245222761-245238913	chr1:245222760-245222761		0.00
K	cassette	CUFF.467	chr17	-	chr17:76994046-76996181;chr17:76994046-77005745	chr17:76994046-76994229;chr17:76994369-76996181,chr17:76994369-77005745		chr17:76994230-76994368			37.06
N	coord_cassette	CUFF.234	chr12	+	chr12:69207409-69233053	chr12:69207409-69222550;chr12:69222712-69229608;chr12:69229765-69233053		chr12:69222551-69222711;chr12:69229609-69229764			73.68
N	cassette	CUFF.310	chr15	+	chr15:40545491-40556981	chr15:40545491-40555999;chr15:40556121-40556981		chr15:40556000-40556120			25.93
N	jcn_only_AD	CUFF.49	chr1	-	chr1:153921121-153921590	chr1:153921121-153921309		chr1:153921310-153921590	chr1:153921590-153921591		15.62
K	alternative_first_exon	CUFF.272	chr14	-	chr14:60030578-60031764	chr14:60030578-60031075	chr14:60031765-60031993	chr14:60031076-60031246			54.90
K	intron_retention	CUFF.1098	chr9	-	chr9:130943079-130947825				chr9:130943078-130943079;chr9:130947825-130947826		10.42
N	alternative_acceptor	CUFF.197	chr12	+	chr12:53861628-53862563	chr12:53861628-53862560		chr12:53862561-53862563	chr12:53862563-53862564		35.79
N	cassette	CUFF.905	chr6	+	chr6:292561-311879	chr6:292561-304627;chr6:304662-311879		chr6:304628-304661			80.61
K	mutually_exclusive	CUFF.811	chr4	-	chr4:1701798-1713600,chr4:1713718-1713856	chr4:1701798-1705322,chr4:1705428-1713856	chr4:1713601-1713717	chr4:1705323-1705427			56.67
K	cassette	CUFF.436	chr17	+	chr17:29677337-29683477	chr17:29677337-29679274;chr17:29679433-29683477		chr17:29679275-29679432			41.03
N	alternative_donor	CUFF.280	chr14	+	chr14:76259444-76286349	chr14:76269597-76286349		chr14:76259444-76269596	chr14:76259443-76259444		12.82
N	intron_retention		chr11	-	chr11:8496364-8502080				chr11:8496363-8496364;chr11:8502080-8502081		92.47
N	jcn_only_AA	CUFF.945	chr6	-	chr6:128313855-128316606	chr6:128316412-128316606		chr6:128313855-128316411	chr6:128313854-128313855		42.11
N	cassette	CUFF.38	chr1	-	chr1:114424620-114429870;chr1:114423763-114429870	chr1:114423763-114429158,chr1:114424620-114429158;chr1:114429281-114429870		chr1:114429159-114429280			23.40
K	alternative_donor	CUFF.712	chr22	+	chr22:24717292-24720187	chr22:24718887-24720187		chr22:24717292-24718886	chr22:24717291-24717292	chr22:24720188-24720395;chr22:24717256-24717291	70.83
K	alternative_last_exon	CUFF.868,CUFF.894	chr5	+	chr5:139918669-139921756	chr5:139918669-139918943	chr5:139921757-139921866	chr5:139918944-139919540		chr5:139918504-139918668	98.76
N	alternative_donor	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55714743-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55712848-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		2.56
N	cassette	CUFF.765	chr3	-	chr3:107586273-107596159;chr3:107591874-107596748	chr3:107586273-107594976,chr3:107591874-107594976;chr3:107595034-107596159,chr3:107595034-107596748		chr3:107594977-107595033			93.28
K	alternative_first_exon	CUFF.476	chr17	+	chr17:80417325-80417867,chr17:80417000-80417867,chr17:80416385-80417867;chr17:80416394-80417867	chr17:80416707-80417867	chr17:80415966-80416393	chr17:80416507-80416706			66.17
N	jcn_only_AA	CUFF.531	chr19	+	chr19:17581517-17594690;chr19:17581517-17597371	chr19:17581517-17598268					15.79
K	alternative_acceptor	CUFF.431	chr17	-	chr17:21437283-21438688	chr17:21437833-21438688		chr17:21437283-21437832	chr17:21437282-21437283		7.61
N	cassette	CUFF.432	chr17	+	chr17:25969375-25972886;chr17:25969375-25972339	chr17:25969375-25970550;chr17:25970647-25972886,chr17:25970647-25972339		chr17:25970551-25970646			65.43
N	alternative_donor	CUFF.490	chr18	+	chr18:55919287-55983213	chr18:55981822-55983213		chr18:55919287-55981821	chr18:55919286-55919287		0.00
K	jcn_only_AA	CUFF.52	chr1	-	chr1:156449139-156450625	chr1:156449589-156450625					22.22
N	cassette	CUFF.793	chr3	-	chr3:141724387-141868024	chr3:141724387-141820576;chr3:141820684-141868024		chr3:141820577-141820683			82.61
K	cassette	CUFF.858	chr4	+	chr4:186267805-186274638	chr4:186267805-186272598;chr4:186272764-186274638		chr4:186272599-186272763			83.75
N	alternative_donor	CUFF.709	chr22	-	chr22:21829590-21830290	chr22:21829590-21830280		chr22:21830281-21830290	chr22:21830290-21830291		45.90
K	intron_retention	CUFF.733	chr3	+	chr3:13976988-13977417				chr3:13976987-13976988;chr3:13977417-13977418		3.80
N	jcn_only_AA	CUFF.589	chr2	-	chr2:27672964-27676250	chr2:27676138-27676250		chr2:27672964-27676137	chr2:27672963-27672964		15.03
K	alternative_donor	CUFF.682	chr20	-	chr20:30009482-30011622	chr20:30009482-30011612		chr20:30011613-30011622	chr20:30011622-30011623		69.59
N	intron_retention		chr9	-	chr9:35079533-35079727				chr9:35079532-35079533;chr9:35079727-35079728		45.45
N	coord_cassette	CUFF.1080	chr9	-	chr9:86474287-86495211	chr9:86474287-86482598;chr9:86482776-86485433;chr9:86485548-86495211		chr9:86482599-86482775;chr9:86485434-86485547			71.43
K	alternative_first_exon	CUFF.37,CUFF.53	chr1	-	chr1:113471975-113472502,chr1:113471975-113497897;chr1:113471975-113498656;chr1:113471975-113478445	chr1:113471975-113499460	chr1:113498657-113498975;chr1:113478446-113478667	chr1:113499461-113499724			33.33
K	mutually_exclusive	CUFF.567	chr19	+	chr19:55084903-55085542,chr19:55085579-55085767	chr19:55084903-55085164,chr19:55085380-55085767	chr19:55085543-55085578	chr19:55085165-55085379			88.89
N	alternative_first_exon		chr1	-	chr1:120548212-120611947	chr1:120548212-120572528	chr1:120611948-120612315	chr1:120572529-120572610			90.24
K	alternative_first_exon	CUFF.622	chr2	-	chr2:88892924-88894986	chr2:88892924-88893430	chr2:88894987-88895181	chr2:88893431-88893662			74.07
N	alternative_acceptor	CUFF.722	chr22	+	chr22:37695348-37696947;chr22:37695348-37696110	chr22:37695348-37696193		chr22:37696111-37696193;chr22:37696194-37696947	chr22:37696193-37696194;chr22:37696947-37696948		2.44
N	jcn_only_AA	CUFF.1119	chrX	-	chrX:20183080-20185706	chrX:20183179-20185706		chrX:20183080-20183178	chrX:20183079-20183080		89.47
N	alternative_donor	CUFF.780,CUFF.786	chr3	-	chr3:125007073-125032151	chr3:125007073-125011308		chr3:125011309-125032151	chr3:125032151-125032152		0.00
N	coord_cassette	CUFF.234	chr12	+	chr12:69218432-69233053	chr12:69218432-69222550;chr12:69222712-69229608;chr12:69229765-69233053		chr12:69222551-69222711;chr12:69229609-69229764			38.46
N	cassette	CUFF.971	chr7	-	chr7:37272800-37298785	chr7:37272800-37283960;chr7:37283997-37298785		chr7:37283961-37283996			63.64
K	intron_retention	CUFF.918	chr6	+	chr6:31935860-31936104				chr6:31935859-31935860;chr6:31936104-31936105		16.13
K	alternative_first_exon	CUFF.113,CUFF.114	chr10	-	chr10:73515224-73520624	chr10:73515224-73517334	chr10:73520625-73520681	chr10:73517335-73517482		chr10:73515116-73515223	97.14
N	jcn_only_AA	CUFF.316	chr15	-	chr15:44892831-44898222	chr15:44896396-44898222		chr15:44892831-44896395	chr15:44892830-44892831		12.00
K	intron_retention	CUFF.838	chr4	-	chr4:77977477-77979659				chr4:77977476-77977477;chr4:77979659-77979660		27.71
K	intron_retention	CUFF.998	chr7	-	chr7:102251590-102257071				chr7:102251589-102251590;chr7:102257071-102257072		29.41
N	jcn_only_AA		chr2	+	chr2:3464108-3464417;chr2:3464108-3466628	chr2:3464108-3469367		chr2:3464418-3466628;chr2:3466629-3469367	chr2:3466628-3466629;chr2:3469367-3469368		89.64
N	intron_retention		chr1	+	chr1:2100557-2100956				chr1:2100556-2100557;chr1:2100956-2100957		31.25
N	cassette	CUFF.564	chr19	+	chr19:52909897-52918376	chr19:52909897-52918191;chr19:52918293-52918376		chr19:52918192-52918292			75.00
K	cassette	CUFF.234	chr12	+	chr12:69218211-69222550	chr12:69218211-69218334;chr12:69218432-69222550		chr12:69218335-69218431			94.02
K	jcn_only_AD	CUFF.17	chr1	+	chr1:31769923-31782890	chr1:31769944-31782890		chr1:31769923-31769943	chr1:31769922-31769923		38.60
N	jcn_only_AD	CUFF.236	chr12	-	chr12:77254194-77256955	chr12:77254194-77256589		chr12:77256590-77256955	chr12:77256955-77256956		28.85
K	intron_retention	CUFF.946	chr6	-	chr6:133055523-133055618				chr6:133055522-133055523;chr6:133055618-133055619		4.96
N	alternative_donor	CUFF.336	chr15	+	chr15:74754440-74758376;chr15:74754373-74758376	chr15:74754369-74758376		chr15:74754369-74754372;chr15:74754373-74754439	chr15:74754368-74754369;chr15:74754372-74754373		31.43
N	jcn_only_AD	CUFF.575	chr2	-	chr2:110927576-110958997	chr2:110927576-110935999					91.67
N	jcn_only_AA	CUFF.481	chr18	+	chr18:12014373-12017612;chr18:12014373-12028041	chr18:12014373-12021700		chr18:12017613-12021700;chr18:12021701-12028041	chr18:12021700-12021701;chr18:12028041-12028042		5.29
K	alternative_acceptor	CUFF.311,CUFF.319	chr15	+	chr15:40752096-40754113	chr15:40752096-40754110		chr15:40754111-40754113	chr15:40754113-40754114		60.00
K	alternative_first_exon	CUFF.1030	chr8	-	chr8:29583940-29605530	chr8:29583940-29592686	chr8:29605531-29605716	chr8:29592687-29592739			45.45
K	intron_retention	CUFF.728	chr22	-	chr22:51019090-51020677				chr22:51019089-51019090;chr22:51020677-51020678		87.88
K	alternative_acceptor	CUFF.533	chr19	-	chr19:20236319-20243269	chr19:20236593-20243269		chr19:20236319-20236592	chr19:20236318-20236319		80.68
N	alternative_donor	CUFF.787	chr3	+	chr3:132757280-132764745	chr3:132760700-132764745		chr3:132757280-132760699	chr3:132757279-132757280		0.00
N	jcn_only_AA	CUFF.589	chr2	-	chr2:27670502-27670678	chr2:27670525-27670678		chr2:27670502-27670524	chr2:27670501-27670502		2.50
K	alternative_first_exon	CUFF.1052	chr8	+	chr8:107531368-107691437;chr8:107593480-107691437;chr8:107670314-107691437	chr8:107630412-107691437	chr8:107531171-107531367;chr8:107593125-107593479;chr8:107670221-107670313	chr8:107630316-107630411			7.43
K	intron_retention	CUFF.626	chr2	+	chr2:99225475-99226105				chr2:99225474-99225475;chr2:99226105-99226106		47.06
K	intron_retention	CUFF.555	chr19	-	chr19:49299587-49299684				chr19:49299586-49299587;chr19:49299684-49299685		80.83
N	intron_retention		chr15	+	chr15:97326820-97327382				chr15:97326819-97326820;chr15:97327382-97327383		82.86
N	coord_cassette	CUFF.273	chr14	+	chr14:61518854-61545547	chr14:61518854-61519066;chr14:61519704-61540565;chr14:61540660-61545547		chr14:61519067-61519703;chr14:61540566-61540659			90.70
N	jcn_only_AD	CUFF.182	chr11	+	chr11:118402242-118402489;chr11:118402317-118402489	chr11:118401950-118402489		chr11:118401950-118402241;chr11:118402242-118402316	chr11:118401949-118401950;chr11:118402241-118402242	chr11:118402490-118402586;chr11:118401663-118401949	80.39
K	cassette	CUFF.264	chr14	+	chr14:50069187-50080973	chr14:50069187-50074117;chr14:50074840-50080973		chr14:50074118-50074839			76.47
K	cassette	CUFF.445	chr17	-	chr17:40738910-40744073	chr17:40738910-40739851;chr17:40739883-40744073		chr17:40739852-40739882			62.35
N	mutually_exclusive	CUFF.671	chr2	-	chr2:242440212-242447420,chr2:242447551-242447919	chr2:242440212-242440892,chr2:242441124-242447919	chr2:242447421-242447550	chr2:242440893-242441123			19.44
N	jcn_only_AD	CUFF.278,CUFF.289	chr14	-	chr14:92105595-92126180;chr14:92105595-92136157	chr14:92105595-92112480		chr14:92112481-92126180;chr14:92126181-92136157	chr14:92126180-92126181;chr14:92136157-92136158		9.68
K	intron_retention	CUFF.114	chr10	-	chr10:73892940-73921295				chr10:73892939-73892940;chr10:73921295-73921296		73.17
K	alternative_first_exon	CUFF.523	chr19	-	chr19:14436244-14474683	chr19:14436244-14458126	chr19:14474684-14474802	chr19:14458127-14458221			83.64
N	alternative_acceptor	CUFF.352	chr15	-	chr15:90420657-90431752;chr15:90421533-90431752	chr15:90414779-90431752		chr15:90414779-90420656;chr15:90420657-90421532	chr15:90414778-90414779;chr15:90420656-90420657		97.34
K	coord_cassette	CUFF.524	chr19	-	chr19:14862484-14867049	chr19:14862484-14863140;chr19:14863339-14865765;chr19:14865940-14867049		chr19:14863141-14863338;chr19:14865766-14865939			73.47
K	alternative_acceptor	CUFF.162	chr11	+	chr11:63669803-63670075	chr11:63669803-63670072		chr11:63670073-63670075	chr11:63670075-63670076		29.03
K	alternative_first_exon	CUFF.415	chr16	+	chr16:89788254-89788938;chr16:89786991-89788938	chr16:89787685-89788938	chr16:89787884-89788253;chr16:89786808-89786990	chr16:89787360-89787684			15.84
N	alternative_acceptor	CUFF.167	chr11	+	chr11:67790230-67793476	chr11:67790230-67791675		chr11:67791676-67793476	chr11:67793476-67793477		1.47
N	cassette	CUFF.809	chr4	+	chr4:649796-650662	chr4:649796-650033;chr4:650082-650662		chr4:650034-650081			71.43
N	jcn_only_AA	CUFF.716	chr22	+	chr22:29668421-29669726;chr22:29668421-29674119	chr22:29668421-29669729		chr22:29669727-29669729;chr22:29669730-29674119	chr22:29669729-29669730;chr22:29674119-29674120		77.60
N	jcn_only_AD	CUFF.336	chr15	+	chr15:74771620-74773391	chr15:74773256-74773391		chr15:74771620-74773255	chr15:74771619-74771620		15.38
K	alternative_donor	CUFF.332	chr15	-	chr15:66645294-66678987	chr15:66645294-66678757		chr15:66678758-66678987	chr15:66678987-66678988		50.00
N	jcn_only_AA	CUFF.695	chr21	-	chr21:15981890-15985196	chr21:15984967-15985196		chr21:15981890-15984966	chr21:15981889-15981890		23.91
K	intron_retention	CUFF.330	chr15	+	chr15:64446952-64447589				chr15:64446951-64446952;chr15:64447589-64447590		71.05
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55711941-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		36.62
K	jcn_only_AD	CUFF.703	chr21	-	chr21:47556409-47556892;chr21:47556409-47556828	chr21:47556409-47556898		chr21:47556829-47556892;chr21:47556893-47556898	chr21:47556892-47556893;chr21:47556898-47556899		47.73
K	intron_retention	CUFF.432	chr17	+	chr17:25970647-25972339				chr17:25970646-25970647;chr17:25972339-25972340		14.81
N	alternative_acceptor		chr1	+	chr1:200860531-200867519	chr1:200860531-200867434		chr1:200867435-200867519	chr1:200867519-200867520		78.08
K	intron_retention	CUFF.404	chr16	-	chr16:67970389-67970596				chr16:67970388-67970389;chr16:67970596-67970597	chr16:67970301-67970388;chr16:67970597-67971076	51.85
N	alternative_acceptor	CUFF.2	chr1	+	chr1:2101044-2103493	chr1:2101044-2102991		chr1:2102992-2103493	chr1:2103493-2103494		2.24
K	alternative_last_exon	CUFF.606	chr2	-	chr2:68358578-68361833	chr2:68359138-68361833	chr2:68358409-68358577	chr2:68358812-68359137			58.06
N	cassette	CUFF.737	chr3	-	chr3:27183074-27203951	chr3:27183074-27184935;chr3:27184966-27203951		chr3:27184936-27184965			78.57
K	jcn_only_AD	CUFF.781	chr3	+	chr3:125635563-125637706	chr3:125635661-125637706		chr3:125635563-125635660	chr3:125635562-125635563		31.71
N	jcn_only_AD	CUFF.232	chr12	+	chr12:58014837-58015045	chr12:58014876-58015045		chr12:58014837-58014875	chr12:58014836-58014837		91.88
K	jcn_only_AA	CUFF.454	chr17	-	chr17:57777238-57784731;chr17:57777551-57784731	chr17:57756906-57784731					32.43
N	jcn_only_AA	CUFF.755	chr3	+	chr3:186743306-186756529	chr3:186743306-186756182		chr3:186756183-186756529	chr3:186756529-186756530		10.53
N	alternative_donor	CUFF.231	chr12	+	chr12:57853985-57857447	chr12:57854339-57857447		chr12:57853985-57854338	chr12:57853984-57853985		58.82
N	jcn_only_AD		chr3	-	chr3:141772992-141868024	chr3:141772992-141811902		chr3:141811903-141868024	chr3:141868024-141868025		55.74
K	alternative_acceptor	CUFF.4	chr1	+	chr1:11083387-11084358	chr1:11083387-11084120		chr1:11084121-11084358	chr1:11084358-11084359		91.59
N	jcn_only_AD	CUFF.1092	chr9	-	chr9:15211396-15267911	chr9:15211396-15214136					96.55
K	alternative_acceptor	CUFF.363,CUFF.407	chr16	+	chr16:105550-105793	chr16:105550-105776		chr16:105777-105793	chr16:105793-105794		66.13
K	jcn_only_AA	CUFF.716	chr22	+	chr22:29668242-29668374	chr22:29668242-29668368		chr22:29668369-29668374	chr22:29668374-29668375		96.97
N	cassette	CUFF.758	chr3	-	chr3:57563115-57570110	chr3:57563115-57569624;chr3:57569788-57570110		chr3:57569625-57569787			72.97
K	cassette	CUFF.222	chr12	-	chr12:52962174-52963642	chr12:52962174-52963273;chr12:52963316-52963642		chr12:52963274-52963315			86.67
K	intron_retention	CUFF.225	chr12	+	chr12:53854210-53854798				chr12:53854209-53854210;chr12:53854798-53854799		83.33
N	jcn_only_AD	CUFF.516,CUFF.537	chr19	-	chr19:33954969-33968951	chr19:33954969-33967985		chr19:33967986-33968951	chr19:33968951-33968952		9.11
N	jcn_only_AA	CUFF.176	chr11	-	chr11:102937297-102953476	chr11:102950727-102953476		chr11:102937297-102950726	chr11:102937296-102937297		19.38
K	alternative_acceptor	CUFF.557	chr19	+	chr19:50308834-50308981	chr19:50308834-50308917		chr19:50308918-50308981	chr19:50308981-50308982		93.15
N	alternative_acceptor	CUFF.278	chr14	-	chr14:75138187-75139533	chr14:75138724-75139533		chr14:75138187-75138723	chr14:75138186-75138187	chr14:75139534-75139655;chr14:75138111-75138186	5.71
K	cassette	CUFF.114	chr10	-	chr10:73857209-73862607;chr10:73857209-73887839	chr10:73857209-73862091;chr10:73862171-73862607,chr10:73862171-73887839		chr10:73862092-73862170			24.31
K	alternative_donor	CUFF.903	chr5	+	chr5:177636434-177637132	chr5:177636449-177637132		chr5:177636434-177636448	chr5:177636433-177636434		63.16
N	jcn_only_AA	CUFF.785,CUFF.787	chr3	+	chr3:133100006-133109023	chr3:133100006-133105267		chr3:133105268-133109023	chr3:133109023-133109024		12.20
K	mutually_exclusive	CUFF.127	chr10	+	chr10:103113986-103213257,chr10:103213314-103221737	chr10:103113986-103190101,chr10:103190210-103221737	chr10:103213258-103213313	chr10:103190102-103190209			75.00
N	alternative_donor	CUFF.140	chr11	-	chr11:406060-406348	chr11:406060-406141		chr11:406142-406348	chr11:406348-406349		39.56
N	jcn_only_AA	CUFF.802	chr3	+	chr3:186769135-186790636	chr3:186769135-186782307		chr3:186782308-186790636	chr3:186790636-186790637		11.88
N	alternative_acceptor	CUFF.119	chr10	-	chr10:79396274-79397022;chr10:79163782-79397022	chr10:79396328-79397022		chr10:79163782-79396273;chr10:79396274-79396327	chr10:79163781-79163782;chr10:79396273-79396274		0.00
K	intron_retention	CUFF.4	chr1	+	chr1:11082299-11083249				chr1:11082298-11082299;chr1:11083249-11083250		57.14
N	jcn_only_AA	CUFF.119	chr10	-	chr10:78644776-78647048;chr10:78637652-78647048	chr10:78637649-78647048		chr10:78637649-78637651;chr10:78637652-78644775	chr10:78637648-78637649;chr10:78637651-78637652		5.88
K	intron_retention	CUFF.728	chr22	-	chr22:51017089-51017464				chr22:51017088-51017089;chr22:51017464-51017465		83.61
K	jcn_only_AD	CUFF.894	chr5	+	chr5:139917820-139918503	chr5:139917847-139918503		chr5:139917820-139917846	chr5:139917819-139917820	chr5:139918504-139918668;chr5:139917671-139917819	33.67
N	jcn_only_AD	CUFF.303	chr15	+	chr15:24758885-24778841	chr15:24766978-24778841		chr15:24758885-24766977	chr15:24758884-24758885		74.29
N	jcn_only_AA	CUFF.3,CUFF.83	chr1	+	chr1:245180629-245222687	chr1:245180629-245193956		chr1:245193957-245222687	chr1:245222687-245222688		3.68
N	jcn_only_AA	CUFF.1070	chr9	-	chr9:35077397-35078601	chr9:35078341-35078601		chr9:35077397-35078340	chr9:35077396-35077397		64.44
N	coord_cassette	CUFF.24	chr1	+	chr1:54360221-54375603	chr1:54360221-54368729;chr1:54368940-54370338;chr1:54370483-54375603		chr1:54368730-54368939;chr1:54370339-54370482			79.55
N	jcn_only_AD	CUFF.334	chr15	-	chr15:67700814-67713672	chr15:67700814-67705840		chr15:67705841-67713672	chr15:67713672-67713673		58.82
K	intron_retention	CUFF.543	chr19	+	chr19:40486362-40486568				chr19:40486361-40486362;chr19:40486568-40486569		7.14
N	jcn_only_AA	CUFF.856	chr4	-	chr4:162402322-162421167	chr4:162416633-162421167		chr4:162402322-162416632	chr4:162402321-162402322		12.84
K	alternative_donor	CUFF.545	chr19	-	chr19:41355886-41356151	chr19:41355886-41356141		chr19:41356142-41356151	chr19:41356151-41356152		57.14
K	cassette	CUFF.117	chr10	-	chr10:75479058-75480295	chr10:75479058-75479764;chr10:75479953-75480295		chr10:75479765-75479952			33.33
K	intron_retention	CUFF.662	chr2	+	chr2:219457431-219458891				chr2:219457430-219457431;chr2:219458891-219458892		53.23
N	jcn_only_AD	CUFF.954	chr6	+	chr6:161413116-161455290	chr6:161443260-161455290		chr6:161413116-161443259	chr6:161413115-161413116	chr6:161455291-161455481;chr6:161412759-161413115	93.75
N	jcn_only_AD	CUFF.2	chr1	+	chr1:1987002-1987922	chr1:1987316-1987922		chr1:1987002-1987315	chr1:1987001-1987002		9.35
N	alternative_donor	CUFF.237	chr12	-	chr12:7086688-7087582	chr12:7086688-7086759		chr12:7086760-7087582	chr12:7087582-7087583		87.92
K	intron_retention	CUFF.167	chr11	+	chr11:67788996-67795518				chr11:67788995-67788996;chr11:67795518-67795519		28.00
N	jcn_only_AA	CUFF.114	chr10	-	chr10:73973036-73975964;chr10:73973090-73975964;chr10:73975613-73975964;chr10:73973110-73975964	chr10:73975868-73975964					11.48
K	jcn_only_AA	CUFF.148	chr11	-	chr11:6623446-6624633	chr11:6623495-6624633		chr11:6623446-6623494	chr11:6623445-6623446		60.00
N	alternative_donor	CUFF.468,CUFF.472	chr17	-	chr17:79478653-79478928	chr17:79478653-79478788		chr17:79478789-79478928	chr17:79478928-79478929		1.94
K	alternative_first_exon	CUFF.308	chr15	+	chr15:31294234-31327955	chr15:31327860-31327955	chr15:31294140-31294233	chr15:31327773-31327859			62.96
N	intron_retention		chr16	-	chr16:57513598-57513772				chr16:57513597-57513598;chr16:57513772-57513773		78.12
K	jcn_only_AD	CUFF.236	chr12	-	chr12:77260042-77272742	chr12:77260042-77272717		chr12:77272718-77272742	chr12:77272742-77272743		65.43
N	jcn_only_AA	CUFF.67	chr1	+	chr1:196913069-196918584;chr1:196913069-196918565	chr1:196913069-196918746		chr1:196918566-196918584;chr1:196918585-196918746	chr1:196918584-196918585;chr1:196918746-196918747	chr1:196912830-196913068;chr1:196918747-196918779	14.49
K	jcn_only_AD	CUFF.473	chr17	-	chr17:79894738-79895137;chr17:79894738-79895133	chr17:79894738-79895055		chr17:79895056-79895133;chr17:79895134-79895137	chr17:79895133-79895134;chr17:79895137-79895138	chr17:79894624-79894737;chr17:79895138-79895264	27.27
K	alternative_last_exon	CUFF.550	chr19	+	chr19:44771115-44777457;chr19:44771115-44771532	chr19:44771115-44777051	chr19:44777458-44779568;chr19:44771533-44772456	chr19:44777052-44777453			25.47
K	jcn_only_AA	CUFF.272	chr14	-	chr14:60018141-60027836	chr14:60018155-60027836		chr14:60018141-60018154	chr14:60018140-60018141		79.10
K	cassette	CUFF.118	chr10	-	chr10:76269268-76287523	chr10:76269268-76276480;chr10:76276660-76287523		chr10:76276481-76276659			39.53
K	cassette	CUFF.875	chr5	-	chr5:54442685-54468765	chr5:54442685-54468415;chr5:54468479-54468765		chr5:54468416-54468478			19.32
N	alternative_donor		chr5	-	chr5:178050418-178057554	chr5:178050418-178053946		chr5:178053947-178057554	chr5:178057554-178057555		92.21
N	intron_retention		chr3	-	chr3:125775357-125786789				chr3:125775356-125775357;chr3:125786789-125786790		40.00
N	alternative_acceptor		chr8	+	chr8:7123432-7131717	chr8:7123432-7124095		chr8:7124096-7131717	chr8:7131717-7131718	chr8:7123323-7123431	89.29
K	intron_retention	CUFF.720	chr22	-	chr22:30742509-30748939				chr22:30742508-30742509;chr22:30748939-30748940		22.22
K	cassette	CUFF.777	chr3	+	chr3:122843191-122864368	chr3:122843191-122849326;chr3:122849464-122864368		chr3:122849327-122849463			41.67
K	intron_retention	CUFF.379	chr16	+	chr16:4559540-4559629				chr16:4559539-4559540;chr16:4559629-4559630		0.54
N	jcn_only_AD	CUFF.809	chr4	+	chr4:661731-663834	chr4:661796-663834		chr4:661731-661795	chr4:661730-661731		21.59
N	cassette	CUFF.331	chr15	-	chr15:64658275-64673156	chr15:64658275-64668941;chr15:64669105-64673156		chr15:64668942-64669104			90.12
N	alternative_acceptor	CUFF.1018	chr7	-	chr7:156589187-156619298	chr7:156616618-156619298		chr7:156589187-156616617	chr7:156589186-156589187		0.98
N	jcn_only_AA	CUFF.578,CUFF.598	chr2	+	chr2:38177739-38201182	chr2:38177739-38178375		chr2:38178376-38201182	chr2:38201182-38201183		23.40
K	jcn_only_AA	CUFF.87	chr10	+	chr10:5077809-5138601	chr10:5077809-5120061					94.19
N	alternative_donor	CUFF.1000	chr7	+	chr7:107204192-107205032;chr7:107204693-107205032;chr7:107204655-107205032	chr7:107204505-107205032		chr7:107204192-107204504;chr7:107204505-107204654;chr7:107204655-107204692	chr7:107204191-107204192;chr7:107204504-107204505;chr7:107204654-107204655		26.32
N	intron_retention	CUFF.504	chr19	+	chr19:1438892-1439966				chr19:1438891-1438892;chr19:1439966-1439967		36.67
N	intron_retention		chr6	+	chr6:31936239-31936677				chr6:31936238-31936239;chr6:31936677-31936678		92.31
K	jcn_only_AD	CUFF.273	chr14	+	chr14:61451522-61482621	chr14:61453876-61482621					20.26
K	alternative_first_exon	CUFF.651	chr2	+	chr2:191334376-191334483;chr2:191307732-191334483	chr2:191302288-191334483	chr2:191334148-191334375;chr2:191307225-191307731	chr2:191300703-191302287			22.86
N	alternative_acceptor		chr16	-	chr16:57513598-57513756	chr16:57513601-57513756		chr16:57513598-57513600	chr16:57513597-57513598		84.38
N	jcn_only_AA		chr11	-	chr11:558980-559346	chr11:559063-559346		chr11:558980-559062	chr11:558979-558980		52.17
K	jcn_only_AD	CUFF.239	chr12	-	chr12:113599803-113600736	chr12:113599803-113600700		chr12:113600701-113600736	chr12:113600736-113600737		5.80
N	jcn_only_AD		chr3	-	chr3:33686396-33700465;chr3:33686396-33686835;chr3:33686396-33686773;chr3:33686396-33686494	chr3:33686396-33700998					2.59
N	alternative_acceptor	CUFF.867	chr5	-	chr5:37309370-37310653	chr5:37309675-37310653		chr5:37309370-37309674	chr5:37309369-37309370		5.26
K	intron_retention	CUFF.572	chr2	-	chr2:218109-218745				chr2:218108-218109;chr2:218745-218746		89.51
K	jcn_only_AD	CUFF.524,CUFF.542	chr19	-	chr19:39924059-39924161;chr19:39924059-39924157	chr19:39924059-39924133		chr19:39924134-39924157;chr19:39924158-39924161	chr19:39924157-39924158;chr19:39924161-39924162		29.43
N	alternative_first_exon	CUFF.576	chr2	-	chr2:675631-677288	chr2:675631-676573,chr2:675631-675757	chr2:677289-677534	chr2:676574-676796			22.76
K	mutually_exclusive	CUFF.1099	chr9	+	chr9:130985140-130988313,chr9:130988453-130996299	chr9:130985140-130986529,chr9:130986669-130996299	chr9:130988314-130988452	chr9:130986530-130986668			38.46
N	alternative_acceptor	CUFF.775	chr3	-	chr3:120352176-120357301	chr3:120352438-120357301		chr3:120352176-120352437	chr3:120352175-120352176		42.86
N	cassette	CUFF.1033	chr8	-	chr8:56652778-56663522;chr8:56656180-56663522	chr8:56652778-56657619,chr8:56656180-56657619;chr8:56657681-56663522		chr8:56657620-56657680			52.87
N	jcn_only_AA	CUFF.683	chr20	+	chr20:30135410-30136479	chr20:30135410-30136182					58.06
N	intron_retention		chr19	+	chr19:50303275-50303353				chr19:50303274-50303275;chr19:50303353-50303354		84.62
K	cassette	CUFF.520	chr19	-	chr19:11537392-11537692	chr19:11537392-11537502;chr19:11537605-11537692		chr19:11537503-11537604			65.79
K	cassette	CUFF.520	chr19	-	chr19:11537861-11541718	chr19:11537861-11541518;chr19:11541597-11541718		chr19:11541519-11541596			77.78
K	jcn_only_AA	CUFF.866	chr5	-	chr5:36668814-36725215	chr5:36705954-36725215					80.00
N	jcn_only_AD		chr3	-	chr3:73453547-73482789;chr3:73453547-73610601;chr3:73453547-73523605;chr3:73453547-73605850;chr3:73453547-73618301	chr3:73453547-73651504					4.26
K	cassette	CUFF.112	chr10	+	chr10:70661228-70666466	chr10:70661228-70665981;chr10:70666094-70666466		chr10:70665982-70666093			65.52
N	cassette	CUFF.478	chr18	+	chr18:158715-163307	chr18:158715-162982;chr18:163175-163307		chr18:162983-163174			54.35
N	alternative_first_exon	CUFF.1010	chr7	+	chr7:129008393-129019481;chr7:129017465-129019481	chr7:129015768-129019481	chr7:129007884-129008392;chr7:129017358-129017464	chr7:129015629-129015767			3.51
N	alternative_donor	CUFF.201	chr12	+	chr12:4653071-4654947	chr12:4654479-4654947		chr12:4653071-4654478	chr12:4653070-4653071		22.22
K	alternative_first_exon	CUFF.974	chr7	-	chr7:38937730-38948753;chr7:38937730-38971877	chr7:38937730-38969071	chr7:38948754-38948829;chr7:38971878-38972082	chr7:38969072-38969203			17.50
N	jcn_only_AD	CUFF.280	chr14	+	chr14:76259444-76286349	chr14:76269597-76286349		chr14:76259444-76269596	chr14:76259443-76259444		81.87
K	cassette	CUFF.879	chr5	-	chr5:60199544-60214091	chr5:60199544-60200618;chr5:60200701-60214091		chr5:60200619-60200700			78.02
N	coord_cassette	CUFF.647	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			82.22
N	alternative_donor	CUFF.765	chr3	-	chr3:107572902-107573976	chr3:107572902-107573500		chr3:107573501-107573976	chr3:107573976-107573977		36.00
N	cassette	CUFF.63	chr1	-	chr1:169696667-169697198;chr1:169696667-169698326	chr1:169696667-169696879;chr1:169697069-169698326,chr1:169697069-169697198		chr1:169696880-169697068			64.95
K	mutually_exclusive	CUFF.829	chr4	-	chr4:56466743-56473464,chr4:56473516-56473603	chr4:56466743-56471441,chr4:56471517-56473603	chr4:56473465-56473515	chr4:56471442-56471516			60.00
K	alternative_acceptor	CUFF.166	chr11	-	chr11:67766776-67766988	chr11:67766846-67766988		chr11:67766776-67766845	chr11:67766775-67766776		16.67
K	alternative_first_exon	CUFF.831	chr4	+	chr4:57775206-57776795	chr4:57775754-57776795	chr4:57774990-57775205	chr4:57775332-57775753			36.07
N	intron_retention		chr7	-	chr7:102236555-102240306				chr7:102236554-102236555;chr7:102240306-102240307		58.49
N	cassette	CUFF.989	chr7	+	chr7:91609648-91622198	chr7:91609648-91621471;chr7:91621526-91622198		chr7:91621472-91621525			33.33
N	cassette	CUFF.155	chr11	+	chr11:36467991-36483891	chr11:36467991-36472758;chr11:36472886-36483891		chr11:36472759-36472885			30.43
N	alternative_donor	CUFF.914	chr6	+	chr6:29943295-29945430	chr6:29945281-29945430		chr6:29943295-29945280	chr6:29943294-29943295		7.14
K	intron_retention	CUFF.673	chr2	+	chr2:242592785-242592926				chr2:242592784-242592785;chr2:242592926-242592927		6.36
K	intron_retention	CUFF.1027	chr8	-	chr8:22011727-22012072				chr8:22011726-22011727;chr8:22012072-22012073		32.35
N	intron_retention	CUFF.852	chr4	-	chr4:152065203-152065371				chr4:152065202-152065203;chr4:152065371-152065372		78.12
K	cassette	CUFF.66	chr1	-	chr1:174084788-174124764	chr1:174084788-174091221;chr1:174091331-174124764		chr1:174091222-174091330			80.67
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		15.87
K	cassette	CUFF.515	chr19	-	chr19:8140075-8145886	chr19:8140075-8140166;chr19:8140296-8145886		chr19:8140167-8140295			47.76
N	jcn_only_AA	CUFF.581	chr2	-	chr2:4020665-4021134;chr2:4009394-4021134;chr2:4020693-4021134;chr2:4009485-4021134	chr2:4015879-4021134		chr2:4009394-4009484;chr2:4009485-4015878;chr2:4015879-4020664;chr2:4020665-4020692	chr2:4009393-4009394;chr2:4009484-4009485;chr2:4015878-4015879;chr2:4020664-4020665		18.48
N	jcn_only_AA	CUFF.504	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		3.08
N	coord_cassette	CUFF.393	chr16	-	chr16:30006165-30006861	chr16:30006165-30006423;chr16:30006539-30006663;chr16:30006785-30006861		chr16:30006424-30006538;chr16:30006664-30006784			66.67
N	jcn_only_AA	CUFF.929	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		7.86
N	jcn_only_AA	CUFF.504	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		5.40
K	alternative_first_exon	CUFF.1109	chr9	+	chr9:139780732-139793164;chr9:139780994-139793164;chr9:139777163-139793164	chr9:139784995-139793164	chr9:139780437-139780731;chr9:139780897-139780993;chr9:139777119-139777162	chr9:139784801-139784994			12.00
K	alternative_first_exon	CUFF.611	chr2	-	chr2:73285726-73286222,chr2:73285726-73298168,chr2:73285726-73302708;chr2:73285726-73286136;chr2:73285726-73298732	chr2:73285726-73297588	chr2:73286137-73286312;chr2:73298733-73298921	chr2:73297589-73298469			40.97
K	cassette	CUFF.848	chr4	+	chr4:120376289-120381337	chr4:120376289-120379125;chr4:120379326-120381337		chr4:120379126-120379325			18.57
N	cassette	CUFF.102	chr10	+	chr10:35468205-35490378;chr10:35468205-35495822	chr10:35468205-35477127;chr10:35477317-35495822,chr10:35477317-35490378		chr10:35477128-35477316			50.24
N	jcn_only_AD	CUFF.358	chr15	+	chr15:97327061-97327382;chr15:97326975-97327382	chr15:97326820-97327382		chr15:97326820-97326974;chr15:97326975-97327060	chr15:97326819-97326820;chr15:97326974-97326975		6.38
N	jcn_only_AD	CUFF.751	chr3	-	chr3:46982556-47017842;chr3:46982556-47018126	chr3:46982556-47007473		chr3:47007474-47017842;chr3:47017843-47018126	chr3:47017842-47017843;chr3:47018126-47018127		6.83
N	alternative_first_exon	CUFF.106	chr10	-	chr10:46113709-46116227;chr10:46113709-46143741	chr10:46113709-46120030	chr10:46116228-46116411;chr10:46143742-46143982	chr10:46120031-46120085			47.30
K	alternative_acceptor	CUFF.168	chr11	+	chr11:67820553-67820828	chr11:67820553-67820825		chr11:67820826-67820828	chr11:67820828-67820829		62.50
N	alternative_donor	CUFF.310	chr15	+	chr15:40532004-40532799;chr15:40509869-40532799;chr15:40531337-40532799	chr15:40532297-40532799		chr15:40509869-40531336;chr15:40531337-40532003;chr15:40532004-40532296	chr15:40509868-40509869;chr15:40531336-40531337;chr15:40532003-40532004		0.00
N	jcn_only_AA	CUFF.432	chr17	+	chr17:25967800-25969263	chr17:25967800-25967990		chr17:25967991-25969263	chr17:25969263-25969264		41.95
K	intron_retention	CUFF.407	chr16	+	chr16:70404289-70405274				chr16:70404288-70404289;chr16:70405274-70405275		13.85
K	cassette	CUFF.929	chr6	-	chr6:43481372-43483626	chr6:43481372-43483332;chr6:43483440-43483626		chr6:43483333-43483439			98.94
K	intron_retention	CUFF.1075	chr9	-	chr9:46687684-46687798				chr9:46687683-46687684;chr9:46687798-46687799		20.90
N	alternative_acceptor	CUFF.566	chr19	+	chr19:54657578-54657680;chr19:54657578-54659046	chr19:54657578-54658995		chr19:54657681-54658995;chr19:54658996-54659046	chr19:54658995-54658996;chr19:54659046-54659047		9.66
N	alternative_first_exon	CUFF.1130	chrX	+	chrX:78003532-78010287	chrX:78006809-78010287	chrX:78003129-78003531	chrX:78006707-78006808			73.53
K	coord_cassette	CUFF.407	chr16	+	chr16:70390151-70398919	chr16:70390151-70390725;chr16:70390810-70395320;chr16:70395414-70398445;chr16:70398549-70398919		chr16:70390726-70390809;chr16:70395321-70395413;chr16:70398446-70398548			19.31
N	jcn_only_AD	CUFF.1000	chr7	+	chr7:107207632-107211589	chr7:107208311-107211589		chr7:107207632-107208310	chr7:107207631-107207632		6.67
K	cassette	CUFF.970	chr7	+	chr7:34724297-34851381;chr7:34724297-34867012	chr7:34724297-34818073;chr7:34818178-34851381,chr7:34818178-34867012		chr7:34818074-34818177			51.15
N	alternative_acceptor	CUFF.869	chr5	+	chr5:40936588-40937653	chr5:40936588-40937339		chr5:40937340-40937653	chr5:40937653-40937654		6.56
N	jcn_only_AA		chr19	+	chr19:17597767-17597982	chr19:17597767-17597908		chr19:17597909-17597982	chr19:17597982-17597983		25.00
K	alternative_last_exon	CUFF.385	chr16	+	chr16:19710971-19716437	chr16:19710971-19711699	chr16:19716438-19718212	chr16:19711700-19712547			90.23
K	coord_cassette	CUFF.232	chr12	+	chr12:58017882-58018648	chr12:58017882-58018282;chr12:58018390-58018506;chr12:58018577-58018648		chr12:58018283-58018389;chr12:58018507-58018576			61.54
K	alternative_donor	CUFF.235	chr12	+	chr12:72094659-72097756	chr12:72094806-72097756		chr12:72094659-72094805	chr12:72094658-72094659		30.30
N	jcn_only_AD	CUFF.86	chr10	-	chr10:532471-735433	chr10:532471-629528		chr10:629529-735433	chr10:735433-735434		0.93
N	alternative_acceptor	CUFF.49	chr1	-	chr1:153921121-153921590	chr1:153921377-153921590		chr1:153921121-153921376	chr1:153921120-153921121		3.57
N	jcn_only_AD	CUFF.703	chr21	-	chr21:47566242-47570032	chr21:47566242-47566704		chr21:47566705-47570032	chr21:47570032-47570033		11.11
N	alternative_donor	CUFF.390	chr16	-	chr16:23505700-23507009;chr16:23505700-23507034	chr16:23505700-23507014		chr16:23507010-23507014;chr16:23507015-23507034	chr16:23507014-23507015;chr16:23507034-23507035	chr16:23505624-23505699;chr16:23507035-23507099	61.99
K	alternative_first_exon	CUFF.884	chr5	-	chr5:82969369-82971106;chr5:82969369-82970344;chr5:82969369-82978143;chr5:82969369-83016607	chr5:82969369-82969951	chr5:82970345-82970701;chr5:82978144-82978427;chr5:83016608-83017432	chr5:82969952-82970139			11.32
K	intron_retention	CUFF.676	chr20	-	chr20:3171885-3172410				chr20:3171884-3171885;chr20:3172410-3172411		4.14
K	intron_retention	CUFF.384	chr16	-	chr16:15154031-15155645				chr16:15154030-15154031;chr16:15155645-15155646		44.44
K	coord_cassette	CUFF.887	chr5	-	chr5:127396937-127418426	chr5:127396937-127412638;chr5:127412786-127417664;chr5:127417887-127418426		chr5:127412639-127412785;chr5:127417665-127417886			17.07
K	intron_retention	CUFF.1001	chr7	+	chr7:107220812-107221203				chr7:107220811-107220812;chr7:107221203-107221204		86.79
K	alternative_acceptor	CUFF.709	chr22	-	chr22:21832391-21832873	chr22:21832451-21832873		chr22:21832391-21832450	chr22:21832390-21832391		17.12
N	jcn_only_AD	CUFF.657	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		6.25
N	alternative_donor	CUFF.551	chr19	+	chr19:45251386-45254483	chr19:45252304-45254483		chr19:45251386-45252303	chr19:45251385-45251386		90.91
N	jcn_only_AD	CUFF.489	chr18	-	chr18:47329224-47337765;chr18:47329224-47340051;chr18:47329224-47339094;chr18:47329224-47340186;chr18:47329224-47339838	chr18:47329224-47340101		chr18:47337766-47339094;chr18:47339095-47339838;chr18:47339839-47340051;chr18:47340052-47340101;chr18:47340102-47340186	chr18:47339094-47339095;chr18:47339838-47339839;chr18:47340051-47340052;chr18:47340101-47340102;chr18:47340186-47340187		28.19
N	alternative_donor	CUFF.780	chr3	-	chr3:125032501-125042152;chr3:125032501-125033780	chr3:125032501-125042231		chr3:125033781-125042152;chr3:125042153-125042231	chr3:125042152-125042153;chr3:125042231-125042232		3.12
N	alternative_donor	CUFF.358	chr15	+	chr15:97326820-97327382;chr15:97327061-97327382	chr15:97326975-97327382		chr15:97326820-97326974;chr15:97326975-97327060	chr15:97326819-97326820;chr15:97326974-97326975		6.76
K	alternative_first_exon	CUFF.1010	chr7	+	chr7:128991503-129019478;chr7:129008393-129019478	chr7:129015768-129019478	chr7:129007884-129008392	chr7:129015629-129015767			30.65
N	alternative_acceptor	CUFF.725	chr22	+	chr22:45148508-45182336	chr22:45148508-45173041		chr22:45173042-45182336	chr22:45182336-45182337		2.94
K	intron_retention	CUFF.1033	chr8	-	chr8:56663717-56668802				chr8:56663716-56663717;chr8:56668802-56668803		4.88
K	coord_cassette	CUFF.944	chr6	+	chr6:126329619-126332398	chr6:126329619-126329802;chr6:126329892-126330480;chr6:126330581-126332398		chr6:126329803-126329891;chr6:126330481-126330580			12.62
N	jcn_only_AD	CUFF.663	chr2	+	chr2:220094623-220094949;chr2:220094703-220094949	chr2:220094681-220094949		chr2:220094623-220094680;chr2:220094681-220094702	chr2:220094622-220094623;chr2:220094680-220094681		6.71
N	cassette	CUFF.1096	chr9	+	chr9:125047567-125048317	chr9:125047567-125048058;chr9:125048226-125048317		chr9:125048059-125048225			75.68
N	cassette	CUFF.61	chr1	+	chr1:167190196-167301706;chr1:167190196-167272710	chr1:167190196-167210643;chr1:167210848-167301706,chr1:167210848-167272710		chr1:167210644-167210847			24.04
K	intron_retention	CUFF.180	chr11	+	chr11:117073889-117074022				chr11:117073888-117073889;chr11:117074022-117074023		20.37
N	cassette	CUFF.97	chr10	-	chr10:27040713-27047990;chr10:27040713-27054146	chr10:27040713-27044583;chr10:27044671-27047990,chr10:27044671-27054146		chr10:27044584-27044670			65.79
K	intron_retention	CUFF.848	chr4	+	chr4:120419059-120433505				chr4:120419058-120419059;chr4:120433505-120433506		68.57
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55816792-55833019	chr18:55722109-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		3.52
K	jcn_only_AA	CUFF.252	chr13	-	chr13:78470694-78473993	chr13:78472470-78473993		chr13:78470694-78472469	chr13:78470693-78470694		66.67
N	jcn_only_AA	CUFF.352	chr15	-	chr15:90378746-90380846	chr15:90378876-90380846		chr15:90378746-90378875	chr15:90378745-90378746		97.39
K	cassette	CUFF.278	chr14	-	chr14:75165560-75179635	chr14:75165560-75168371;chr14:75168478-75179635		chr14:75168372-75168477		chr14:75165467-75165559;chr14:75179636-75179896	64.44
K	jcn_only_AA	CUFF.187	chr11	+	chr11:119056662-119057324	chr11:119056662-119056800		chr11:119056801-119057324	chr11:119057324-119057325		97.30
N	jcn_only_AD	CUFF.273	chr14	+	chr14:61512886-61517229	chr14:61515016-61517229		chr14:61512886-61515015	chr14:61512885-61512886		14.77
K	mutually_exclusive	CUFF.97	chr10	-	chr10:27059275-27060003,chr10:27060019-27065993	chr10:27059275-27059451,chr10:27059470-27065993	chr10:27060004-27060018	chr10:27059452-27059469			24.00
N	intron_retention	CUFF.394	chr16	+	chr16:31368423-31368573				chr16:31368422-31368423;chr16:31368573-31368574		50.00
N	jcn_only_AA	CUFF.966	chr7	-	chr7:22162140-22165221	chr7:22165040-22165221		chr7:22162140-22165039	chr7:22162139-22162140		70.00
K	intron_retention	CUFF.179	chr11	+	chr11:115267610-115267983				chr11:115267609-115267610;chr11:115267983-115267984		13.56
K	intron_retention	CUFF.598	chr2	+	chr2:38244379-38244720				chr2:38244378-38244379;chr2:38244720-38244721		9.15
K	intron_retention	CUFF.148	chr11	-	chr11:6621496-6621715				chr11:6621495-6621496;chr11:6621715-6621716		80.00
N	jcn_only_AA	CUFF.114	chr10	-	chr10:73973036-73975964;chr10:73973090-73975964;chr10:73975868-73975964;chr10:73975613-73975964	chr10:73973110-73975964					30.48
K	intron_retention	CUFF.703	chr21	-	chr21:47557249-47558421				chr21:47557248-47557249;chr21:47558421-47558422		11.59
K	intron_retention	CUFF.708	chr22	+	chr22:21058517-21058598				chr22:21058516-21058517;chr22:21058598-21058599		4.83
N	intron_retention		chr7	+	chr7:107220747-107224326				chr7:107220746-107220747;chr7:107224326-107224327		39.71
K	alternative_first_exon	CUFF.115	chr10	-	chr10:74103270-74113099	chr10:74103270-74104707	chr10:74113100-74113606	chr10:74104708-74104885			75.86
K	cassette	CUFF.618	chr2	-	chr2:86393768-86398330	chr2:86393768-86397871;chr2:86397968-86398330		chr2:86397872-86397967			97.17
N	jcn_only_AD	CUFF.1098	chr9	-	chr9:130929444-130931330;chr9:130929444-130931354	chr9:130929444-130929817		chr9:130929818-130931330;chr9:130931331-130931354	chr9:130931330-130931331;chr9:130931354-130931355		11.43
N	jcn_only_AD	CUFF.2	chr1	+	chr1:2087532-2100956	chr1:2100557-2100956		chr1:2087532-2100556	chr1:2087531-2087532		7.75
N	jcn_only_AA	CUFF.685	chr20	-	chr20:31115717-31123243	chr20:31121289-31123243		chr20:31115717-31121288	chr20:31115716-31115717		28.00
N	coord_cassette	CUFF.707	chr22	+	chr22:20748953-20754921	chr22:20748953-20749622;chr22:20749709-20753884;chr22:20753981-20754921		chr22:20749623-20749708;chr22:20753885-20753980			76.00
K	alternative_first_exon	CUFF.449	chr17	-	chr17:46685458-46710875;chr17:46685458-46685590	chr17:46685458-46687880	chr17:46710876-46710987;chr17:46685591-46685727	chr17:46687881-46688379			55.56
N	alternative_donor		chr2	-	chr2:242872-244626;chr2:242872-243502	chr2:242872-247537		chr2:243503-244626;chr2:244627-247537	chr2:244626-244627;chr2:247537-247538		97.22
N	intron_retention		chr4	-	chr4:99405593-99407888				chr4:99405592-99405593;chr4:99407888-99407889		30.30
N	jcn_only_AD	CUFF.802	chr3	+	chr3:186649184-186681572;chr3:186660216-186681572;chr3:186648624-186681572;chr3:186648928-186681572	chr3:186666727-186681572		chr3:186648624-186648927;chr3:186648928-186649183;chr3:186649184-186660215;chr3:186660216-186666726	chr3:186648623-186648624;chr3:186648927-186648928;chr3:186649183-186649184;chr3:186660215-186660216		4.88
K	alternative_first_exon	CUFF.549	chr19	-	chr19:43724395-43727042	chr19:43724395-43724782	chr19:43727043-43727110	chr19:43724783-43725071			75.00
K	intron_retention	CUFF.936	chr6	+	chr6:90322090-90323510				chr6:90322089-90322090;chr6:90323510-90323511		20.18
K	intron_retention	CUFF.532	chr19	+	chr19:18119394-18119519				chr19:18119393-18119394;chr19:18119519-18119520		14.63
N	jcn_only_AA		chr15	+	chr15:57555473-57565230	chr15:57555473-57565227		chr15:57565228-57565230	chr15:57565230-57565231		82.55
K	jcn_only_AD	CUFF.875	chr5	-	chr5:54410147-54415640	chr5:54410147-54415628		chr5:54415629-54415640	chr5:54415640-54415641		92.19
K	cassette	CUFF.486	chr18	-	chr18:44435579-44470542	chr18:44435579-44444126;chr18:44444212-44470542		chr18:44444127-44444211			83.78
K	jcn_only_AD	CUFF.232	chr12	+	chr12:58019102-58019192	chr12:58019114-58019192		chr12:58019102-58019113	chr12:58019101-58019102		35.77
K	jcn_only_AA	CUFF.249	chr13	+	chr13:51796706-51805483	chr13:51796706-51799256					64.86
N	cassette	CUFF.515	chr19	-	chr19:8154555-8154982	chr19:8154555-8154777;chr19:8154844-8154982		chr19:8154778-8154843			84.21
N	coord_cassette	CUFF.342	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			66.67
K	alternative_last_exon	CUFF.121	chr10	-	chr10:80722644-80808530	chr10:80804270-80808530	chr10:80722581-80722643	chr10:80803807-80804269			84.31
N	jcn_only_AD	CUFF.769	chr3	+	chr3:119188106-119188666;chr3:119187954-119188666	chr3:119187854-119188666		chr3:119187854-119187953;chr3:119187954-119188105	chr3:119187853-119187854;chr3:119187953-119187954		15.52
K	jcn_only_AA	CUFF.645	chr2	-	chr2:174072387-174136238	chr2:174080565-174136238					17.11
K	intron_retention	CUFF.641	chr2	+	chr2:169712721-169713199				chr2:169712720-169712721;chr2:169713199-169713200		7.69
K	intron_retention	CUFF.394	chr16	+	chr16:31393218-31393788				chr16:31393217-31393218;chr16:31393788-31393789		55.17
N	alternative_donor	CUFF.498	chr18	-	chr18:72914296-72920374;chr18:72914296-72920315	chr18:72914296-72917147		chr18:72917148-72920315;chr18:72920316-72920374	chr18:72920315-72920316;chr18:72920374-72920375		1.61
N	jcn_only_AD	CUFF.638	chr2	+	chr2:153476233-153481951	chr2:153479072-153481951		chr2:153476233-153479071	chr2:153476232-153476233		14.29
K	jcn_only_AA	CUFF.1000	chr7	+	chr7:107215756-107216853	chr7:107215756-107216810		chr7:107216811-107216853	chr7:107216853-107216854		93.41
N	alternative_acceptor		chr16	-	chr16:57513598-57513772	chr16:57513601-57513772		chr16:57513598-57513600	chr16:57513597-57513598		78.12
N	alternative_first_exon	CUFF.212	chr12	+	chr12:26205536-26208168;chr12:26148064-26208168;chr12:26205930-26208168;chr12:26164755-26208168	chr12:26174452-26208168	chr12:26147970-26148063;chr12:26205414-26205929;chr12:26164591-26164754	chr12:26174353-26174451			25.00
K	alternative_acceptor	CUFF.1096	chr9	+	chr9:125028060-125033231	chr9:125028060-125033142		chr9:125033143-125033231	chr9:125033231-125033232		84.62
N	alternative_acceptor		chr19	+	chr19:17448474-17448816;chr19:17448474-17448707	chr19:17448474-17448682		chr19:17448683-17448707;chr19:17448708-17448816	chr19:17448707-17448708;chr19:17448816-17448817		30.08
N	intron_retention		chr11	-	chr11:10827595-10828801				chr11:10827594-10827595;chr11:10828801-10828802		80.19
N	coord_cassette	CUFF.726	chr22	+	chr22:47158746-47189397	chr22:47158746-47188416;chr22:47188474-47188564;chr22:47188702-47189397		chr22:47188417-47188473;chr22:47188565-47188701			93.33
K	alternative_first_exon	CUFF.106	chr10	-	chr10:46159291-46167719;chr10:46159291-46168126	chr10:46159291-46167697	chr10:46168127-46168325	chr10:46167698-46167796			49.23
N	alternative_acceptor	CUFF.418	chr17	+	chr17:80416707-80417875	chr17:80416707-80417867		chr17:80417868-80417875	chr17:80417875-80417876		92.57
N	intron_retention		chr11	+	chr11:61595697-61595966				chr11:61595696-61595697;chr11:61595966-61595967		28.57
N	alternative_acceptor	CUFF.765	chr3	-	chr3:107568819-107572719;chr3:107567966-107572719	chr3:107569199-107572719		chr3:107567966-107568818;chr3:107568819-107569198	chr3:107567965-107567966;chr3:107568818-107568819		8.11
K	jcn_only_AD	CUFF.492	chr18	-	chr18:61064487-61067280	chr18:61064487-61066474				chr18:61064267-61064486	41.94
N	jcn_only_AA	CUFF.1000	chr7	+	chr7:107207632-107211589	chr7:107207632-107208199		chr7:107208200-107211589	chr7:107211589-107211590		14.63
N	cassette	CUFF.707	chr22	+	chr22:20748953-20754921	chr22:20748953-20749622;chr22:20749709-20754921		chr22:20749623-20749708			80.95
K	intron_retention	CUFF.114	chr10	-	chr10:73973036-73975964				chr10:73973035-73973036;chr10:73975964-73975965		53.60
N	jcn_only_AD	CUFF.506	chr19	+	chr19:4323144-4323344;chr19:4323211-4323344	chr19:4323235-4323344		chr19:4323144-4323210;chr19:4323211-4323234	chr19:4323143-4323144;chr19:4323210-4323211		33.86
K	alternative_donor	CUFF.993	chr7	+	chr7:92158239-92158789	chr7:92158498-92158789		chr7:92158239-92158497	chr7:92158238-92158239		86.11
N	alternative_acceptor	CUFF.902	chr5	-	chr5:162439295-162516250	chr5:162465480-162516250		chr5:162439295-162465479	chr5:162439294-162439295		0.00
K	intron_retention		chr8	+	chr8:144356973-144357147				chr8:144356972-144356973;chr8:144357147-144357148		10.27
N	alternative_donor	CUFF.631	chr2	+	chr2:109065737-109066088	chr2:109065746-109066088		chr2:109065737-109065745	chr2:109065736-109065737		3.61
K	jcn_only_AD	CUFF.704,CUFF.709	chr22	-	chr22:18082862-18095577	chr22:18082862-18083857					90.72
N	alternative_acceptor	CUFF.151	chr11	-	chr11:8950976-8953688	chr11:8951081-8953688		chr11:8950976-8951080	chr11:8950975-8950976		81.94
N	intron_retention		chr17	+	chr17:25969375-25972886				chr17:25969374-25969375;chr17:25972886-25972887		31.82
K	cassette	CUFF.912	chr6	+	chr6:28109808-28116093	chr6:28109808-28112108;chr6:28112203-28116093		chr6:28112109-28112202			75.00
K	intron_retention	CUFF.468	chr17	-	chr17:79225413-79225994				chr17:79225412-79225413;chr17:79225994-79225995	chr17:79224584-79225412;chr17:79225995-79226483	41.00
K	intron_retention	CUFF.905	chr6	+	chr6:348275-348768				chr6:348274-348275;chr6:348768-348769		25.74
K	intron_retention	CUFF.241	chr12	-	chr12:120172163-120172964				chr12:120172162-120172163;chr12:120172964-120172965		71.93
N	jcn_only_AA	CUFF.984	chr7	+	chr7:75042211-75044162	chr7:75042211-75043917		chr7:75043918-75044162	chr7:75044162-75044163		44.44
K	jcn_only_AA	CUFF.1010	chr7	+	chr7:129008393-129019481	chr7:129008393-129019478		chr7:129019479-129019481	chr7:129019481-129019482		57.58
N	intron_retention		chr11	+	chr11:118402242-118402489				chr11:118402241-118402242;chr11:118402489-118402490	chr11:118401663-118402241;chr11:118402490-118402586	67.63
N	jcn_only_AA		chr3	+	chr3:8775677-8819162	chr3:8775677-8787211		chr3:8787212-8819162	chr3:8819162-8819163		82.86
K	jcn_only_AA	CUFF.425	chr17	-	chr17:15498141-15499827	chr17:15498205-15499827		chr17:15498141-15498204	chr17:15498140-15498141		46.34
K	alternative_first_exon	CUFF.999	chr7	-	chr7:102696195-102715142	chr7:102696195-102714692	chr7:102715143-102715367	chr7:102714693-102715071			63.92
K	intron_retention	CUFF.230	chr12	-	chr12:56705199-56708634				chr12:56705198-56705199;chr12:56708634-56708635		32.00
K	alternative_last_exon	CUFF.1095	chr9	-	chr9:124895254-124910390	chr9:124906658-124910390	chr9:124894745-124895253	chr9:124906242-124906657			62.39
N	coord_cassette	CUFF.945	chr6	-	chr6:128320050-128326228	chr6:128320050-128322340;chr6:128322353-128324341;chr6:128324378-128326228		chr6:128322341-128322352;chr6:128324342-128324377			85.48
N	mutually_exclusive	CUFF.786	chr3	-	chr3:127294109-127294591,chr3:127294653-127294782	chr3:127294109-127294245,chr3:127294349-127294782	chr3:127294592-127294652	chr3:127294246-127294348			44.44
N	intron_retention		chr8	-	chr8:80976829-81083441				chr8:80976828-80976829;chr8:81083441-81083442		40.91
N	jcn_only_AA	CUFF.40	chr1	+	chr1:145575405-145578061	chr1:145575405-145577651		chr1:145577652-145578061	chr1:145578061-145578062		68.57
K	intron_retention	CUFF.161	chr11	-	chr11:62365614-62365798				chr11:62365613-62365614;chr11:62365798-62365799		37.65
K	alternative_first_exon	CUFF.1057	chr8	-	chr8:126958427-126963429	chr8:126958427-126963157	chr8:126963430-126963565	chr8:126963158-126963429			36.84
N	cassette	CUFF.77	chr1	-	chr1:213173726-213178374	chr1:213173726-213174127;chr1:213174255-213178374		chr1:213174128-213174254			79.66
K	intron_retention	CUFF.393	chr16	-	chr16:30004879-30004960				chr16:30004878-30004879;chr16:30004960-30004961		47.06
N	alternative_donor		chr3	-	chr3:141772992-141868024	chr3:141772992-141811902		chr3:141811903-141868024	chr3:141868024-141868025		0.00
K	intron_retention	CUFF.429	chr17	-	chr17:20279149-20279443				chr17:20279148-20279149;chr17:20279443-20279444		26.03
N	alternative_acceptor	CUFF.61	chr1	+	chr1:167345393-167353093	chr1:167345393-167345789		chr1:167345790-167353093	chr1:167353093-167353094		0.83
K	intron_retention	CUFF.138	chr11	+	chr11:827319-828259				chr11:827318-827319;chr11:828259-828260	chr11:827215-827318;chr11:828260-828772	85.71
K	cassette	CUFF.228	chr12	-	chr12:56566489-56567479	chr12:56566489-56566720;chr12:56566814-56567479		chr12:56566721-56566813			29.55
N	alternative_donor		chr7	-	chr7:37954056-37966281	chr7:37954056-37955694		chr7:37955695-37966281	chr7:37966281-37966282		37.50
N	jcn_only_AD	CUFF.325	chr15	+	chr15:57213297-57355947	chr15:57293583-57355947		chr15:57213297-57293582	chr15:57213296-57213297		43.97
K	jcn_only_AD	CUFF.1075,CUFF.1080	chr9	-	chr9:46686830-46687553	chr9:46686830-46687372		chr9:46687373-46687553	chr9:46687553-46687554		31.71
K	alternative_first_exon	CUFF.350	chr15	-	chr15:84873728-84898603	chr15:84873728-84873982	chr15:84898604-84898964	chr15:84873983-84874071			72.50
K	alternative_first_exon	CUFF.578	chr2	+	chr2:1158976-1161233;chr2:1133496-1161233	chr2:1159412-1161233	chr2:1133454-1133495	chr2:1159330-1159411			3.45
N	coord_cassette	CUFF.114	chr10	-	chr10:73956748-73972944	chr10:73956748-73958206;chr10:73958424-73963184;chr10:73963283-73970489;chr10:73970590-73971945;chr10:73972044-73972944		chr10:73958207-73958423;chr10:73963185-73963282;chr10:73970490-73970589;chr10:73971946-73972043			34.62
K	jcn_only_AA	CUFF.168	chr11	+	chr11:67820553-67820828	chr11:67820553-67820825		chr11:67820826-67820828	chr11:67820828-67820829		76.92
K	jcn_only_AD	CUFF.703	chr21	-	chr21:47556409-47556892;chr21:47556409-47556898	chr21:47556409-47556828		chr21:47556829-47556892;chr21:47556893-47556898	chr21:47556892-47556893;chr21:47556898-47556899		43.51
K	intron_retention	CUFF.529	chr19	-	chr19:16654417-16655074				chr19:16654416-16654417;chr19:16655074-16655075		18.60
N	intron_retention	CUFF.350	chr15	-	chr15:84873269-84873347				chr15:84873268-84873269;chr15:84873347-84873348		80.39
N	alternative_donor	CUFF.316,CUFF.352	chr15	-	chr15:44881613-44884528	chr15:44881613-44882618		chr15:44882619-44884528	chr15:44884528-44884529		27.59
N	intron_retention		chr12	+	chr12:69210619-69233541				chr12:69210618-69210619;chr12:69233541-69233542		93.95
K	cassette	CUFF.349	chr15	-	chr15:83689515-83698887	chr15:83689515-83697367;chr15:83697481-83698887		chr15:83697368-83697480			97.03
K	intron_retention	CUFF.363	chr16	+	chr16:106421-106538				chr16:106420-106421;chr16:106538-106539		58.62
N	alternative_acceptor	CUFF.481	chr18	+	chr18:12014373-12021700;chr18:12014373-12028041	chr18:12014373-12017612		chr18:12017613-12021700;chr18:12021701-12028041	chr18:12021700-12021701;chr18:12028041-12028042		1.09
N	alternative_acceptor		chr7	+	chr7:7222452-7273933	chr7:7222452-7249057		chr7:7249058-7273933	chr7:7273933-7273934		0.00
K	cassette	CUFF.1014	chr7	+	chr7:148984868-148989301	chr7:148984868-148987028;chr7:148987130-148989301		chr7:148987029-148987129			64.52
K	intron_retention	CUFF.19	chr1	-	chr1:32827137-32827330				chr1:32827136-32827137;chr1:32827330-32827331		12.73
K	cassette	CUFF.463	chr17	-	chr17:66268909-66274229	chr17:66268909-66270067;chr17:66270212-66274229		chr17:66270068-66270211			78.57
N	alternative_donor	CUFF.1052	chr8	+	chr8:107691521-107695426	chr8:107694774-107695426		chr8:107691521-107694773	chr8:107691520-107691521		0.65
K	intron_retention	CUFF.1144	chrX	-	chrX:134290954-134291240				chrX:134290953-134290954;chrX:134291240-134291241		63.64
N	cassette	CUFF.332	chr15	-	chr15:66641776-66644466	chr15:66641776-66643862;chr15:66643939-66644466		chr15:66643863-66643938			66.67
N	jcn_only_AA	CUFF.1110	chrX	+	chrX:1404814-1407411	chrX:1404814-1406066		chrX:1406067-1407411	chrX:1407411-1407412		1.99
N	jcn_only_AD		chr11	-	chr11:6633050-6633604	chr11:6633050-6633188					98.02
K	cassette	CUFF.782	chr3	-	chr3:125752522-125786789	chr3:125752522-125769785;chr3:125769894-125786789		chr3:125769786-125769893			80.14
N	alternative_donor	CUFF.140	chr11	-	chr11:118927130-118927785	chr11:118927130-118927730		chr11:118927731-118927785	chr11:118927785-118927786		86.76
N	jcn_only_AD	CUFF.292	chr14	+	chr14:92792323-92900255	chr14:92874779-92900255		chr14:92792323-92874778	chr14:92792322-92792323		89.62
N	alternative_donor		chr14	-	chr14:59941245-59942586	chr14:59941245-59941445		chr14:59941446-59942586	chr14:59942586-59942587		28.85
N	jcn_only_AA	CUFF.119	chr10	-	chr10:78637649-78647048;chr10:78637652-78647048	chr10:78644776-78647048		chr10:78637649-78637651;chr10:78637652-78644775	chr10:78637648-78637649;chr10:78637651-78637652		55.07
N	jcn_only_AA	CUFF.125	chr10	+	chr10:35485028-35495822	chr10:35485028-35490378		chr10:35490379-35495822	chr10:35495822-35495823		37.21
N	jcn_only_AD	CUFF.1052	chr8	+	chr8:107691521-107695426	chr8:107694774-107695426		chr8:107691521-107694773	chr8:107691520-107691521		15.00
N	jcn_only_AA		chr3	-	chr3:33638227-33644443	chr3:33644082-33644443					91.80
K	intron_retention		chr16	+	chr16:3118012-3118180				chr16:3118011-3118012;chr16:3118180-3118181		2.07
K	alternative_acceptor	CUFF.241	chr12	-	chr12:120172163-120172964	chr12:120172212-120172964		chr12:120172163-120172211	chr12:120172162-120172163		85.32
N	cassette	CUFF.102	chr10	+	chr10:35464634-35468061	chr10:35464634-35467816;chr10:35467915-35468061		chr10:35467817-35467914			96.93
K	alternative_acceptor	CUFF.576	chr2	-	chr2:675631-677288	chr2:676239-677288		chr2:675631-676238	chr2:675630-675631		45.57
N	jcn_only_AA	CUFF.236	chr12	-	chr12:77254194-77256955	chr12:77256740-77256955		chr12:77254194-77256739	chr12:77254193-77254194		27.45
K	intron_retention		chr6	+	chr6:31927178-31927786				chr6:31927177-31927178;chr6:31927786-31927787		21.21
N	alternative_acceptor		chr17	+	chr17:60783831-60784792;chr17:60783831-60813446	chr17:60783831-60803388		chr17:60784793-60803388;chr17:60803389-60813446	chr17:60803388-60803389;chr17:60813446-60813447		0.00
N	jcn_only_AD	CUFF.976	chr7	+	chr7:54614433-54614639;chr7:54612482-54614639	chr7:54613910-54614639		chr7:54612482-54613909;chr7:54613910-54614432	chr7:54612481-54612482;chr7:54613909-54613910		18.37
K	intron_retention	CUFF.161	chr11	-	chr11:62363810-62363929				chr11:62363809-62363810;chr11:62363929-62363930		14.52
K	alternative_first_exon	CUFF.189	chr11	-	chr11:119291640-119293822;chr11:119291640-119295607	chr11:119291640-119292320	chr11:119293823-119294855;chr11:119295608-119295794	chr11:119292321-119292419			9.72
K	intron_retention		chr11	+	chr11:830714-830865				chr11:830713-830714;chr11:830865-830866	chr11:830621-830713;chr11:830866-831032	45.45
K	intron_retention	CUFF.663	chr2	+	chr2:220100308-220100429				chr2:220100307-220100308;chr2:220100429-220100430		30.38
N	alternative_donor	CUFF.683	chr20	+	chr20:30115386-30125981	chr20:30115854-30125981		chr20:30115386-30115853	chr20:30115385-30115386	chr20:30125982-30126064;chr20:30115287-30115385	1.21
N	intron_retention	CUFF.241	chr12	-	chr12:120148426-120148853				chr12:120148425-120148426;chr12:120148853-120148854		68.97
N	intron_retention		chr19	-	chr19:41938968-41939441				chr19:41938967-41938968;chr19:41939441-41939442		69.01
K	alternative_first_exon	CUFF.435	chr17	+	chr17:29422388-29483000	chr17:29455526-29483000	chr17:29421905-29422387	chr17:29455432-29455525			66.00
K	intron_retention	CUFF.482	chr18	+	chr18:12658205-12658572				chr18:12658204-12658205;chr18:12658572-12658573		16.67
K	alternative_acceptor	CUFF.410	chr16	-	chr16:75579853-75589701	chr16:75579976-75589701		chr16:75579853-75579975	chr16:75579852-75579853		20.00
K	alternative_first_exon	CUFF.889	chr5	+	chr5:129019967-129030412	chr5:129023908-129030412	chr5:129019813-129019966	chr5:129023695-129023907			96.95
N	jcn_only_AD	CUFF.790	chr3	+	chr3:133407209-133419725	chr3:133418468-133419725		chr3:133407209-133418467	chr3:133407208-133407209		1.71
N	mutually_exclusive	CUFF.726	chr22	+	chr22:47189739-47274548,chr22:47274620-47287161	chr22:47189739-47193340,chr22:47193518-47287161	chr22:47274549-47274619	chr22:47193341-47193517			63.89
N	alternative_donor	CUFF.1051	chr8	+	chr8:106456610-106573590	chr8:106541198-106573590		chr8:106456610-106541197	chr8:106456609-106456610		0.00
K	alternative_first_exon	CUFF.579	chr2	+	chr2:3383611-3391390	chr2:3383648-3391390	chr2:3383446-3383610	chr2:3383611-3383647			56.00
K	jcn_only_AA	CUFF.845	chr4	-	chr4:99399898-99403155	chr4:99399962-99403155		chr4:99399898-99399961	chr4:99399897-99399898		97.62
K	intron_retention	CUFF.457	chr17	+	chr17:61564435-61566008				chr17:61564434-61564435;chr17:61566008-61566009		41.86
K	alternative_last_exon	CUFF.983	chr7	-	chr7:74881027-74977921	chr7:74973331-74977921	chr7:74880819-74881026	chr7:74973248-74973330			62.50
N	cassette	CUFF.232	chr12	+	chr12:58018390-58018648	chr12:58018390-58018506;chr12:58018577-58018648		chr12:58018507-58018576			21.28
K	intron_retention	CUFF.504	chr19	+	chr19:1438892-1440017				chr19:1438891-1438892;chr19:1440017-1440018		4.90
N	cassette	CUFF.941	chr6	+	chr6:112604395-112627530	chr6:112604395-112604499;chr6:112604730-112627530		chr6:112604500-112604729			71.01
N	intron_retention		chr16	+	chr16:3115496-3115642				chr16:3115495-3115496;chr16:3115642-3115643		80.46
K	intron_retention		chr17	-	chr17:79479387-79479759				chr17:79479386-79479387;chr17:79479759-79479760		20.66
N	cassette	CUFF.572	chr2	-	chr2:260703-263210;chr2:253116-263210	chr2:260703-262630,chr2:253116-262630;chr2:262751-263210		chr2:262631-262750			49.33
K	cassette	CUFF.726	chr22	+	chr22:47158746-47188416	chr22:47158746-47185208;chr22:47185369-47188416		chr22:47185209-47185368			49.46
N	coord_cassette	CUFF.707	chr22	+	chr22:20748953-20759666	chr22:20748953-20754921;chr22:20755049-20755566;chr22:20755663-20759666		chr22:20754922-20755048;chr22:20755567-20755662			91.53
N	alternative_first_exon		chr11	-	chr11:8474454-8615629	chr11:8474454-8476290	chr11:8615630-8615928	chr11:8476291-8476379			85.94
K	cassette	CUFF.412	chr16	+	chr16:77756515-77775478	chr16:77756515-77759327;chr16:77759482-77775478		chr16:77759328-77759481			79.22
N	alternative_acceptor	CUFF.929	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		8.39
K	cassette	CUFF.841	chr4	+	chr4:81115394-81117505	chr4:81115394-81117166;chr4:81117279-81117505		chr4:81117167-81117278			31.34
N	alternative_donor	CUFF.325	chr15	+	chr15:57384090-57458599;chr15:57426699-57458599;chr15:57422171-57458599	chr15:57401516-57458599		chr15:57384090-57401515;chr15:57401516-57422170;chr15:57422171-57426698	chr15:57384089-57384090;chr15:57401515-57401516;chr15:57422170-57422171		0.00
N	jcn_only_AA	CUFF.497	chr18	-	chr18:67563282-67613969	chr18:67611805-67613969		chr18:67563282-67611804	chr18:67563281-67563282		33.33
K	cassette	CUFF.109	chr10	+	chr10:60029065-60036876	chr10:60029065-60035877;chr10:60035973-60036876		chr10:60035878-60035972			81.48
K	cassette	CUFF.223	chr12	-	chr12:52992897-52994810	chr12:52992897-52993054;chr12:52993087-52994810		chr12:52993055-52993086			41.67
K	cassette	CUFF.1018	chr7	-	chr7:156556490-156589082	chr7:156556490-156572348;chr7:156572427-156589082		chr7:156572349-156572426			26.97
K	intron_retention	CUFF.425	chr17	-	chr17:15501968-15508536				chr17:15501967-15501968;chr17:15508536-15508537		81.48
K	intron_retention	CUFF.671	chr2	-	chr2:242437765-242438053				chr2:242437764-242437765;chr2:242438053-242438054		26.67
N	alternative_acceptor	CUFF.765	chr3	-	chr3:107591328-107591814;chr3:107586273-107591814	chr3:107586425-107591814		chr3:107586273-107586424;chr3:107586425-107591327	chr3:107586272-107586273;chr3:107586424-107586425		51.00
N	cassette	CUFF.773	chr3	-	chr3:119246689-119255983	chr3:119246689-119248688;chr3:119248785-119255983		chr3:119248689-119248784			35.00
N	alternative_acceptor		chr4	+	chr4:647109-647640	chr4:647109-647225		chr4:647226-647640	chr4:647640-647641		27.45
N	jcn_only_AD	CUFF.961	chr7	+	chr7:6641772-6647590	chr7:6647229-6647590		chr7:6641772-6647228	chr7:6641771-6641772		14.49
K	jcn_only_AD	CUFF.993	chr7	+	chr7:92158239-92158789	chr7:92158498-92158789		chr7:92158239-92158497	chr7:92158238-92158239		83.87
N	cassette	CUFF.259	chr14	+	chr14:24564055-24567411	chr14:24564055-24566100;chr14:24566347-24567411		chr14:24566101-24566346			96.36
N	intron_retention		chr7	+	chr7:107214267-107215632				chr7:107214266-107214267;chr7:107215632-107215633		53.85
N	intron_retention		chr11	+	chr11:118402549-118403062				chr11:118402548-118402549;chr11:118403062-118403063	chr11:118401663-118402548;chr11:118403063-118403176	95.14
N	jcn_only_AA		chr3	+	chr3:51741184-51749077	chr3:51741184-51742863					66.67
N	intron_retention		chr19	+	chr19:17450409-17451915				chr19:17450408-17450409;chr19:17451915-17451916		74.51
N	jcn_only_AD	CUFF.453	chr17	-	chr17:56082403-56083870;chr17:56082403-56082774	chr17:56082403-56082758		chr17:56082759-56082774;chr17:56082775-56083870	chr17:56082774-56082775;chr17:56083870-56083871		62.50
N	intron_retention		chr12	+	chr12:26205536-26208211				chr12:26205535-26205536;chr12:26208211-26208212		75.89
N	coord_cassette	CUFF.524	chr19	-	chr19:14863339-14867049	chr19:14863339-14865765;chr19:14865940-14866465;chr19:14866657-14867049		chr19:14865766-14865939;chr19:14866466-14866656			56.90
N	alternative_donor	CUFF.633	chr2	-	chr2:110959072-110962476	chr2:110959072-110959949		chr2:110959950-110962476	chr2:110962476-110962477		0.00
N	alternative_acceptor	CUFF.520	chr19	-	chr19:11541841-11545593	chr19:11545352-11545593		chr19:11541841-11545351	chr19:11541840-11541841		0.00
K	alternative_last_exon	CUFF.1028	chr8	-	chr8:23186100-23190913;chr8:23186079-23190913	chr8:23189522-23190913	chr8:23185895-23186078	chr8:23188858-23189521			46.62
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55713021-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		8.45
K	jcn_only_AD	CUFF.1018	chr7	-	chr7:156619439-156626446	chr7:156619439-156626432		chr7:156626433-156626446	chr7:156626446-156626447		19.78
N	alternative_acceptor	CUFF.147	chr11	-	chr11:5687504-5699433	chr11:5691178-5699433		chr11:5687504-5691177	chr11:5687503-5687504		12.50
K	intron_retention	CUFF.232	chr12	+	chr12:58017697-58017785				chr12:58017696-58017697;chr12:58017785-58017786		5.13
N	mutually_exclusive	CUFF.980	chr7	+	chr7:73101231-73105245,chr7:73105343-73106925	chr7:73101231-73101328,chr7:73101426-73106925	chr7:73105246-73105342	chr7:73101329-73101425			84.44
K	alternative_first_exon	CUFF.345	chr15	-	chr15:80200027-80215793	chr15:80200027-80206929	chr15:80215794-80216138	chr15:80206930-80207027			8.64
K	intron_retention	CUFF.152	chr11	-	chr11:10825966-10826459				chr11:10825965-10825966;chr11:10826459-10826460		8.21
N	jcn_only_AA	CUFF.268,CUFF.270	chr14	+	chr14:55494190-55498606	chr14:55494190-55498580		chr14:55498581-55498606	chr14:55498606-55498607		18.42
K	alternative_first_exon	CUFF.728	chr22	-	chr22:51020787-51039578	chr22:51020787-51020986	chr22:51039579-51039939	chr22:51020987-51021428			71.11
N	jcn_only_AA	CUFF.535	chr19	-	chr19:21637275-21639262	chr19:21638407-21639262		chr19:21637275-21638406	chr19:21637274-21637275		11.27
N	alternative_acceptor	CUFF.273	chr14	+	chr14:61512886-61514965;chr14:61512886-61517229	chr14:61512886-61514868		chr14:61514869-61514965;chr14:61514966-61517229	chr14:61514965-61514966;chr14:61517229-61517230		0.00
K	jcn_only_AD	CUFF.903	chr5	+	chr5:177636434-177637132	chr5:177636449-177637132		chr5:177636434-177636448	chr5:177636433-177636434		70.83
N	jcn_only_AD	CUFF.971	chr7	-	chr7:37382368-37433424;chr7:37382368-37392635;chr7:37382368-37488462;chr7:37382368-37382655	chr7:37382368-37488277		chr7:37382656-37392635;chr7:37392636-37433424;chr7:37433425-37488277;chr7:37488278-37488462	chr7:37392635-37392636;chr7:37433424-37433425;chr7:37488277-37488278;chr7:37488462-37488463		13.04
K	alternative_acceptor	CUFF.793	chr3	-	chr3:141693034-141697361	chr3:141693037-141697361		chr3:141693034-141693036	chr3:141693033-141693034		30.00
N	intron_retention		chr11	-	chr11:406060-406348				chr11:406059-406060;chr11:406348-406349		44.16
K	mutually_exclusive	CUFF.1113	chrX	-	chrX:8997460-8998301,chrX:8998402-9000170	chrX:8997460-8998162,chrX:8998248-9000170	chrX:8998302-8998401	chrX:8998163-8998247			10.71
N	alternative_donor	CUFF.509	chr19	-	chr19:6047516-6049146;chr19:6047516-6110403;chr19:6047516-6057172;chr19:6047516-6072015	chr19:6047516-6148241		chr19:6049147-6057172;chr19:6057173-6072015;chr19:6072016-6110403;chr19:6110404-6148241	chr19:6057172-6057173;chr19:6072015-6072016;chr19:6110403-6110404;chr19:6148241-6148242		92.31
N	jcn_only_AD	CUFF.230	chr12	-	chr12:56709027-56709604;chr12:56709027-56709500	chr12:56709027-56709690		chr12:56709501-56709604;chr12:56709605-56709690	chr12:56709604-56709605;chr12:56709690-56709691		21.43
K	jcn_only_AA	CUFF.1001	chr7	+	chr7:107234551-107236313	chr7:107234551-107236311		chr7:107236312-107236313	chr7:107236313-107236314		92.83
N	alternative_donor	CUFF.28	chr1	+	chr1:70832012-70832126;chr1:70820892-70832126;chr1:70820791-70832126	chr1:70820795-70832126		chr1:70820791-70820794;chr1:70820795-70820891;chr1:70820892-70832011	chr1:70820790-70820791;chr1:70820794-70820795;chr1:70820891-70820892		7.69
N	alternative_donor	CUFF.1098	chr9	-	chr9:130941184-130941267;chr9:130941184-130941351	chr9:130941184-130941522		chr9:130941268-130941351;chr9:130941352-130941522	chr9:130941351-130941352;chr9:130941522-130941523		8.27
K	coord_cassette	CUFF.675	chr20	+	chr20:2840454-2841094	chr20:2840454-2840699;chr20:2840798-2840884;chr20:2841014-2841094		chr20:2840700-2840797;chr20:2840885-2841013			13.33
N	jcn_only_AD		chr9	-	chr9:15214248-15224337;chr9:15214248-15249915;chr9:15214248-15224357	chr9:15214248-15225914					61.29
K	jcn_only_AA	CUFF.894	chr5	+	chr5:139866646-139884405	chr5:139866646-139876104				chr5:139866543-139866645	45.45
N	alternative_donor	CUFF.879	chr5	-	chr5:127398193-127418661	chr5:127398193-127418426		chr5:127418427-127418661	chr5:127418661-127418662		82.28
N	jcn_only_AA	CUFF.347	chr15	-	chr15:83358206-83378345	chr15:83358687-83378345		chr15:83358206-83358686	chr15:83358205-83358206		31.76
N	alternative_acceptor	CUFF.119	chr10	-	chr10:78644776-78647048;chr10:78637649-78647048	chr10:78637652-78647048		chr10:78637649-78637651;chr10:78637652-78644775	chr10:78637648-78637649;chr10:78637651-78637652		65.00
N	jcn_only_AD	CUFF.802	chr3	+	chr3:186660216-186681572;chr3:186648624-186681572;chr3:186648928-186681572;chr3:186666727-186681572	chr3:186649184-186681572		chr3:186648624-186648927;chr3:186648928-186649183;chr3:186649184-186660215;chr3:186660216-186666726	chr3:186648623-186648624;chr3:186648927-186648928;chr3:186649183-186649184;chr3:186660215-186660216		5.26
K	alternative_first_exon	CUFF.618	chr2	-	chr2:86408496-86422460	chr2:86408496-86422044	chr2:86422461-86422991	chr2:86422045-86422140			11.11
N	jcn_only_AA	CUFF.709	chr22	-	chr22:21828970-21829499	chr22:21829090-21829499		chr22:21828970-21829089	chr22:21828969-21828970		11.88
N	cassette	CUFF.555	chr19	-	chr19:49310332-49314065;chr19:49310332-49314240	chr19:49310332-49311012;chr19:49311494-49314065,chr19:49311494-49314240		chr19:49311013-49311493			30.06
N	jcn_only_AD	CUFF.802	chr3	+	chr3:186649184-186681572;chr3:186648624-186681572;chr3:186648928-186681572;chr3:186666727-186681572	chr3:186660216-186681572		chr3:186648624-186648927;chr3:186648928-186649183;chr3:186649184-186660215;chr3:186660216-186666726	chr3:186648623-186648624;chr3:186648927-186648928;chr3:186649183-186649184;chr3:186660215-186660216		4.07
K	intron_retention		chr16	-	chr16:4463406-4466459				chr16:4463405-4463406;chr16:4466459-4466460		11.68
K	coord_cassette	CUFF.87	chr10	+	chr10:5120170-5138601	chr10:5120170-5122937;chr10:5123094-5123873;chr10:5124078-5138601		chr10:5122938-5123093;chr10:5123874-5124077			48.00
N	intron_retention	CUFF.83	chr1	+	chr1:245133746-245165422				chr1:245133745-245133746;chr1:245165422-245165423		16.67
N	alternative_acceptor	CUFF.647	chr2	-	chr2:175677211-175689161	chr2:175686508-175689161		chr2:175677211-175686507	chr2:175677210-175677211		0.41
K	jcn_only_AA	CUFF.112,CUFF.122	chr10	+	chr10:70661228-70666039	chr10:70661228-70665981		chr10:70665982-70666039	chr10:70666039-70666040		34.78
N	alternative_acceptor	CUFF.340,CUFF.357	chr15	+	chr15:77713347-77750745	chr15:77713347-77740060		chr15:77740061-77750745	chr15:77750745-77750746		0.00
N	cassette	CUFF.476	chr17	+	chr17:80441656-80443372	chr17:80441656-80442688;chr17:80442827-80443372		chr17:80442689-80442826			94.51
K	jcn_only_AD	CUFF.893	chr5	+	chr5:137514892-137515348	chr5:137515023-137515348		chr5:137514892-137515022	chr5:137514891-137514892		4.76
K	jcn_only_AA	CUFF.59	chr1	-	chr1:161953126-161953385	chr1:161953196-161953385		chr1:161953126-161953195	chr1:161953125-161953126		37.14
N	cassette	CUFF.1098	chr9	-	chr9:130950214-130952966;chr9:130948056-130952966	chr9:130948056-130952607,chr9:130950214-130952607;chr9:130952724-130952966		chr9:130952608-130952723			77.60
K	intron_retention	CUFF.2	chr1	+	chr1:1991031-2066700				chr1:1991030-1991031;chr1:2066700-2066701		41.43
K	alternative_acceptor	CUFF.595,CUFF.631	chr2	+	chr2:109102365-109102966	chr2:109102365-109102890		chr2:109102891-109102966	chr2:109102966-109102967		97.48
N	jcn_only_AA	CUFF.453	chr17	-	chr17:56081080-56082283	chr17:56081363-56082283		chr17:56081080-56081362	chr17:56081079-56081080		3.69
K	cassette	CUFF.1099	chr9	+	chr9:130988453-130996299	chr9:130988453-130994264;chr9:130994404-130996299		chr9:130994265-130994403			56.52
K	intron_retention	CUFF.484	chr18	-	chr18:14969572-14969674				chr18:14969571-14969572;chr18:14969674-14969675		24.14
N	intron_retention		chr1	+	chr1:222802037-222838940				chr1:222802036-222802037;chr1:222838940-222838941		75.68
K	intron_retention	CUFF.1129	chrX	-	chrX:53658435-53658518				chrX:53658434-53658435;chrX:53658518-53658519		91.67
N	alternative_donor	CUFF.945	chr6	-	chr6:128313855-128316393;chr6:128313855-128316606	chr6:128313855-128316591		chr6:128316394-128316591;chr6:128316592-128316606	chr6:128316591-128316592;chr6:128316606-128316607		2.50
N	jcn_only_AD		chr19	-	chr19:33984244-34003498;chr19:33984244-33991843	chr19:33984244-34001933					42.50
K	alternative_donor	CUFF.115,CUFF.118	chr10	-	chr10:74094376-74095591	chr10:74094376-74095537		chr10:74095538-74095591	chr10:74095591-74095592		88.89
N	jcn_only_AA	CUFF.519	chr19	+	chr19:17611686-17615263	chr19:17611686-17612081		chr19:17612082-17615263	chr19:17615263-17615264		34.88
K	coord_cassette	CUFF.264	chr14	+	chr14:50069187-50080973	chr14:50069187-50070269;chr14:50070337-50074117;chr14:50074840-50079189;chr14:50079343-50080973		chr14:50070270-50070336;chr14:50074118-50074839;chr14:50079190-50079342			40.74
K	alternative_donor	CUFF.376,CUFF.406	chr16	-	chr16:70266708-70267326	chr16:70266708-70267315		chr16:70267316-70267326	chr16:70267326-70267327		18.37
K	jcn_only_AD	CUFF.1121	chrX	+	chrX:45129987-45184737	chrX:45184464-45184737					71.93
K	cassette	CUFF.555	chr19	-	chr19:49298722-49299684	chr19:49298722-49299403;chr19:49299587-49299684		chr19:49299404-49299586			32.30
N	jcn_only_AD		chr15	-	chr15:90414779-90421496;chr15:90414779-90420537	chr15:90414779-90431752		chr15:90420538-90421496;chr15:90421497-90431752	chr15:90421496-90421497;chr15:90431752-90431753		63.99
K	intron_retention	CUFF.225	chr12	+	chr12:53849155-53849244				chr12:53849154-53849155;chr12:53849244-53849245		3.15
K	cassette	CUFF.726	chr22	+	chr22:47188474-47189397	chr22:47188474-47188564;chr22:47188702-47189397		chr22:47188565-47188701			28.70
K	alternative_acceptor	CUFF.1008	chr7	-	chr7:127251040-127251588	chr7:127251261-127251588		chr7:127251040-127251260	chr7:127251039-127251040		80.95
K	alternative_first_exon	CUFF.963,CUFF.988	chr7	-	chr7:7594821-7605544	chr7:7594821-7603867	chr7:7605545-7606627	chr7:7603868-7604023			47.83
K	jcn_only_AD	CUFF.1024	chr8	+	chr8:7123432-7124095	chr8:7123438-7124095		chr8:7123432-7123437	chr8:7123431-7123432	chr8:7124096-7125058;chr8:7123323-7123431	91.01
N	alternative_donor	CUFF.820	chr4	+	chr4:6911233-6925099;chr4:6912329-6925099	chr4:6911679-6925099		chr4:6911233-6911678;chr4:6911679-6912328	chr4:6911232-6911233;chr4:6911678-6911679		0.00
K	cassette	CUFF.829	chr4	-	chr4:56471517-56475286	chr4:56471517-56473603;chr4:56473634-56475286		chr4:56473604-56473633			51.20
N	jcn_only_AD	CUFF.1066,CUFF.1078	chr9	-	chr9:15214248-15225914;chr9:15214248-15249915;chr9:15214248-15224357	chr9:15214248-15224337					20.97
N	intron_retention		chr3	+	chr3:97662415-97663677				chr3:97662414-97662415;chr3:97663677-97663678		83.33
K	alternative_last_exon	CUFF.200,CUFF.212	chr12	+	chr12:26220647-26231965	chr12:26220647-26221629	chr12:26231966-26232924	chr12:26221630-26225899			62.50
K	alternative_first_exon	CUFF.258	chr14	+	chr14:24439542-24459390	chr14:24458285-24459390	chr14:24439057-24439541	chr14:24457961-24458284			75.00
K	jcn_only_AD	CUFF.414	chr16	-	chr16:87811607-87812592	chr16:87811607-87812413		chr16:87812414-87812592	chr16:87812592-87812593		51.85
K	cassette	CUFF.165	chr11	+	chr11:65480530-65481063	chr11:65480530-65480818;chr11:65480975-65481063		chr11:65480819-65480974			27.57
K	alternative_acceptor	CUFF.560	chr19	-	chr19:51525921-51526347	chr19:51525954-51526347		chr19:51525921-51525953	chr19:51525920-51525921		87.07
K	mutually_exclusive	CUFF.291	chr14	-	chr14:92195824-92245318,chr14:92245415-92246919	chr14:92195824-92203037,chr14:92203194-92246919	chr14:92245319-92245414	chr14:92203038-92203193		chr14:92195745-92195823;chr14:92246920-92247139	11.36
K	intron_retention	CUFF.551	chr19	+	chr19:45260673-45260902				chr19:45260672-45260673;chr19:45260902-45260903		51.16
K	alternative_donor	CUFF.1039	chr8	+	chr8:74884857-74888064	chr8:74885229-74888064		chr8:74884857-74885228	chr8:74884856-74884857		40.82
N	cassette	CUFF.426	chr17	-	chr17:15546131-15562115;chr17:15546131-15580489	chr17:15546131-15554404;chr17:15555261-15580489,chr17:15555261-15562115		chr17:15554405-15555260			63.44
N	cassette	CUFF.716	chr22	+	chr22:29674206-29682911	chr22:29674206-29678378;chr22:29678547-29682911		chr22:29678379-29678546			90.37
K	intron_retention	CUFF.739	chr3	+	chr3:28357915-28358243				chr3:28357914-28357915;chr3:28358243-28358244		88.51
N	jcn_only_AD	CUFF.657	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		12.50
K	intron_retention	CUFF.230	chr12	-	chr12:56708751-56708913				chr12:56708750-56708751;chr12:56708913-56708914		10.83
K	intron_retention	CUFF.464	chr17	+	chr17:66509120-66511534				chr17:66509119-66509120;chr17:66511534-66511535		10.34
K	cassette	CUFF.209	chr12	-	chr12:22643153-22659644	chr12:22643153-22646156;chr12:22646272-22659644		chr12:22646157-22646271			41.62
K	intron_retention	CUFF.1032	chr8	-	chr8:38001905-38002739				chr8:38001904-38001905;chr8:38002739-38002740		13.64
N	cassette	CUFF.287	chr14	+	chr14:83117341-83153657	chr14:83117341-83151723;chr14:83151776-83153657		chr14:83151724-83151775			94.67
N	alternative_donor	CUFF.1148	chrX	-	chrX:46382561-46387784	chrX:46382561-46387769		chrX:46387770-46387784	chrX:46387784-46387785		52.38
N	alternative_last_exon	CUFF.278	chr14	-	chr14:75127644-75130601	chr14:75130526-75130601	chr14:75127595-75127643	chr14:75127869-75130525		chr14:75130602-75130777	91.46
K	intron_retention	CUFF.49	chr1	-	chr1:153925311-153925741				chr1:153925310-153925311;chr1:153925741-153925742		67.35
K	intron_retention	CUFF.671	chr2	-	chr2:242438830-242439587				chr2:242438829-242438830;chr2:242439587-242439588		30.14
N	jcn_only_AD	CUFF.899	chr5	-	chr5:178047675-178050256	chr5:178047675-178049393		chr5:178049394-178050256	chr5:178050256-178050257		6.00
K	intron_retention	CUFF.351	chr15	+	chr15:89878601-89878879				chr15:89878600-89878601;chr15:89878879-89878880		34.78
N	jcn_only_AD	CUFF.396	chr16	-	chr16:57509870-57513353	chr16:57509870-57512455		chr16:57512456-57513353	chr16:57513353-57513354		10.97
N	alternative_donor	CUFF.796	chr3	-	chr3:156261059-156262096	chr3:156261059-156262082		chr3:156262083-156262096	chr3:156262096-156262097		5.04
K	cassette	CUFF.1033	chr8	-	chr8:56663717-56675193	chr8:56663717-56668802;chr8:56668971-56675193		chr8:56668803-56668970			89.89
N	alternative_donor	CUFF.271	chr14	-	chr14:59946070-59950526;chr14:59946070-59950207	chr14:59946070-59950397		chr14:59950208-59950397;chr14:59950398-59950526	chr14:59950397-59950398;chr14:59950526-59950527		23.41
N	alternative_donor	CUFF.1146	chrX	+	chrX:148864250-148867418;chrX:148863691-148867418	chrX:148863659-148867418		chrX:148863659-148863690;chrX:148863691-148864249	chrX:148863658-148863659;chrX:148863690-148863691		73.68
N	cassette	CUFF.795	chr3	-	chr3:155485459-155520320	chr3:155485459-155493489;chr3:155493638-155520320		chr3:155493490-155493637			90.91
K	coord_cassette	CUFF.146	chr11	+	chr11:3424187-3427728	chr11:3424187-3424822;chr11:3424883-3426083;chr11:3426194-3427728		chr11:3424823-3424882;chr11:3426084-3426193			30.22
N	jcn_only_AA	CUFF.611	chr2	-	chr2:73228704-73247367	chr2:73228708-73247367		chr2:73228704-73228707	chr2:73228703-73228704		96.33
N	jcn_only_AA	CUFF.316	chr15	-	chr15:44878049-44881449	chr15:44880837-44881449		chr15:44878049-44880836	chr15:44878048-44878049		29.63
N	jcn_only_AD	CUFF.90	chr10	+	chr10:6271144-6274857;chr10:6266177-6274857;chr10:6270182-6274857;chr10:6268329-6274857	chr10:6273278-6274857					21.36
K	cassette	CUFF.344	chr15	+	chr15:78807450-78819721	chr15:78807450-78810929;chr15:78811116-78819721		chr15:78810930-78811115			44.86
K	cassette	CUFF.1074	chr9	-	chr9:46661549-46662447	chr9:46661549-46661770;chr9:46661861-46662447		chr9:46661771-46661860			56.67
K	intron_retention	CUFF.78	chr1	+	chr1:222835675-222837339				chr1:222835674-222835675;chr1:222837339-222837340		68.37
N	intron_retention		chr17	-	chr17:76988223-76988491				chr17:76988222-76988223;chr17:76988491-76988492		91.89
K	cassette	CUFF.563	chr19	+	chr19:52264484-52271897	chr19:52264484-52265669;chr19:52265789-52271897		chr19:52265670-52265788			14.93
N	alternative_donor	CUFF.1033	chr8	-	chr8:56676540-56685785;chr8:56676540-56685534	chr8:56676540-56685827		chr8:56685535-56685785;chr8:56685786-56685827	chr8:56685785-56685786;chr8:56685827-56685828		78.86
N	jcn_only_AA	CUFF.1066	chr9	-	chr9:15214248-15225914	chr9:15224504-15225914		chr9:15214248-15224503	chr9:15214247-15214248		48.65
K	intron_retention	CUFF.1108	chr9	+	chr9:139744590-139744957				chr9:139744589-139744590;chr9:139744957-139744958		3.77
N	alternative_donor	CUFF.506	chr19	+	chr19:4323144-4323344;chr19:4323211-4323344	chr19:4323235-4323344		chr19:4323144-4323210;chr19:4323211-4323234	chr19:4323143-4323144;chr19:4323210-4323211		26.67
N	cassette	CUFF.473	chr17	-	chr17:79892366-79892801;chr17:79891253-79892801	chr17:79892366-79892528,chr17:79891253-79892528;chr17:79892622-79892801		chr17:79892529-79892621		chr17:79891183-79891252;chr17:79892802-79893023	85.80
N	coord_cassette	CUFF.106	chr10	-	chr10:46147482-46158989	chr10:46147482-46148431;chr10:46148508-46158027;chr10:46158130-46158989		chr10:46148432-46148507;chr10:46158028-46158129			71.79
K	intron_retention	CUFF.341	chr15	+	chr15:78080488-78080722				chr15:78080487-78080488;chr15:78080722-78080723		22.73
N	jcn_only_AD	CUFF.509	chr19	-	chr19:6047516-6148241;chr19:6047516-6049146;chr19:6047516-6110403;chr19:6047516-6057172	chr19:6047516-6072015		chr19:6049147-6057172;chr19:6057173-6072015;chr19:6072016-6110403;chr19:6110404-6148241	chr19:6057172-6057173;chr19:6072015-6072016;chr19:6110403-6110404;chr19:6148241-6148242		13.04
N	jcn_only_AA	CUFF.371	chr16	+	chr16:2203224-2203578	chr16:2203224-2203319		chr16:2203320-2203578	chr16:2203578-2203579		17.58
N	jcn_only_AA		chr15	-	chr15:90414779-90421496	chr15:90420657-90421496		chr15:90414779-90420656	chr15:90414778-90414779		53.33
N	alternative_donor	CUFF.579	chr2	+	chr2:3453249-3461391;chr2:3461001-3461391	chr2:3447663-3461391		chr2:3447663-3453248;chr2:3453249-3461000	chr2:3447662-3447663;chr2:3453248-3453249		98.38
K	alternative_acceptor	CUFF.253	chr13	-	chr13:97640030-97642011	chr13:97640088-97642011		chr13:97640030-97640087	chr13:97640029-97640030		79.31
N	jcn_only_AD		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		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		65.84
N	cassette	CUFF.172	chr11	-	chr11:77885630-77899618	chr11:77885630-77897726;chr11:77897863-77899618		chr11:77897727-77897862			85.71
N	cassette	CUFF.374	chr16	+	chr16:3117615-3118180;chr16:3117417-3118180	chr16:3117615-3117984,chr16:3117417-3117984;chr16:3118012-3118180		chr16:3117985-3118011			92.90
N	jcn_only_AD	CUFF.752	chr3	-	chr3:33617768-33623312	chr3:33617768-33618693					30.30
K	jcn_only_AD	CUFF.53	chr1	-	chr1:156908306-156909339	chr1:156908306-156908940		chr1:156908941-156909339	chr1:156909339-156909340		56.38
N	alternative_donor	CUFF.386	chr16	+	chr16:21693147-21696550	chr16:21695874-21696550		chr16:21693147-21695873	chr16:21693146-21693147		33.33
N	jcn_only_AD		chr1	+	chr1:245246991-245285221	chr1:245270600-245285221		chr1:245246991-245270599	chr1:245246990-245246991		36.36
N	intron_retention		chr22	+	chr22:29695271-29695588				chr22:29695270-29695271;chr22:29695588-29695589		19.23
N	cassette	CUFF.524	chr19	-	chr19:14862484-14867049	chr19:14862484-14863140;chr19:14863339-14867049		chr19:14863141-14863338			78.33
N	intron_retention		chr17	-	chr17:1616190-1616996				chr17:1616189-1616190;chr17:1616996-1616997		64.19
K	cassette	CUFF.476	chr17	+	chr17:80436795-80438957	chr17:80436795-80438282;chr17:80438421-80438957		chr17:80438283-80438420			2.13
K	intron_retention	CUFF.984	chr7	+	chr7:75042211-75044162				chr7:75042210-75042211;chr7:75044162-75044163		78.26
K	intron_retention	CUFF.19	chr1	-	chr1:32827478-32827558				chr1:32827477-32827478;chr1:32827558-32827559		4.84
K	coord_cassette	CUFF.445	chr17	-	chr17:40744181-40761103	chr17:40744181-40748550;chr17:40748646-40757265;chr17:40757310-40761103		chr17:40748551-40748645;chr17:40757266-40757309			25.00
N	alternative_donor	CUFF.1115	chrX	-	chrX:13801641-13803740	chrX:13801641-13801897		chrX:13801898-13803740	chrX:13803740-13803741		1.69
K	intron_retention	CUFF.571	chr19	+	chr19:58965712-58966549				chr19:58965711-58965712;chr19:58966549-58966550	chr19:58965595-58965711;chr19:58966550-58969200	54.81
K	cassette	CUFF.693	chr21	+	chr21:15695909-15709500	chr21:15695909-15708400;chr21:15708579-15709500		chr21:15708401-15708578		chr21:15695833-15695908;chr21:15709501-15709561	85.71
K	cassette	CUFF.217	chr12	-	chr12:48393909-48398019	chr12:48393909-48394767;chr12:48394878-48398019		chr12:48394768-48394877			63.33
N	jcn_only_AA		chr19	-	chr19:6192065-6199490;chr19:6176455-6199490	chr19:6192041-6199490					11.36
K	intron_retention	CUFF.869	chr5	+	chr5:40972697-40976851				chr5:40972696-40972697;chr5:40976851-40976852		35.71
K	jcn_only_AD	CUFF.1085	chr9	-	chr9:104239452-104251395	chr9:104239452-104242952					30.00
K	cassette	CUFF.569	chr19	-	chr19:56313106-56320134	chr19:56313106-56319218;chr19:56319381-56320134		chr19:56319219-56319380			45.16
N	intron_retention		chr7	+	chr7:107204505-107205032				chr7:107204504-107204505;chr7:107205032-107205033		58.24
N	alternative_acceptor		chr11	-	chr11:8496614-8498796	chr11:8498299-8498796		chr11:8496614-8498298	chr11:8496613-8496614		27.27
N	alternative_acceptor		chr19	+	chr19:54648069-54649330;chr19:54648069-54649277	chr19:54648069-54649333		chr19:54649278-54649330;chr19:54649331-54649333	chr19:54649330-54649331;chr19:54649333-54649334		75.86
K	alternative_acceptor	CUFF.169,CUFF.179	chr11	+	chr11:115267610-115267986	chr11:115267610-115267983		chr11:115267984-115267986	chr11:115267986-115267987		49.15
N	alternative_acceptor	CUFF.765	chr3	-	chr3:107591328-107591814;chr3:107586425-107591814	chr3:107586273-107591814		chr3:107586273-107586424;chr3:107586425-107591327	chr3:107586272-107586273;chr3:107586424-107586425		49.00
K	jcn_only_AD	CUFF.524,CUFF.569	chr19	-	chr19:14876383-14883153	chr19:14876383-14876469					93.04
N	jcn_only_AD		chrX	-	chrX:20258724-20284681	chrX:20258724-20259710		chrX:20259711-20284681	chrX:20284681-20284682		11.11
K	intron_retention	CUFF.747	chr3	-	chr3:38051303-38051394				chr3:38051302-38051303;chr3:38051394-38051395		26.32
K	intron_retention	CUFF.13	chr1	-	chr1:27429804-27432375				chr1:27429803-27429804;chr1:27432375-27432376		55.56
N	jcn_only_AA		chr7	+	chr7:75039744-75044162	chr7:75039744-75039888					91.67
K	cassette	CUFF.817	chr4	-	chr4:6087357-6114448	chr4:6087357-6107199;chr4:6107695-6114448		chr4:6107200-6107694			81.25
N	jcn_only_AA	CUFF.988	chr7	-	chr7:86542382-86544038	chr7:86542521-86544038		chr7:86542382-86542520	chr7:86542381-86542382		94.91
N	alternative_acceptor	CUFF.716	chr22	+	chr22:29668421-29669729;chr22:29668421-29674119	chr22:29668421-29669726		chr22:29669727-29669729;chr22:29669730-29674119	chr22:29669729-29669730;chr22:29674119-29674120		13.79
N	jcn_only_AA	CUFF.919	chr6	-	chr6:31938530-31938688	chr6:31938603-31938688		chr6:31938530-31938602	chr6:31938529-31938530		58.29
N	coord_cassette	CUFF.743	chr3	-	chr3:33543261-33557514	chr3:33543261-33552049;chr3:33552257-33556071;chr3:33556172-33557514		chr3:33552050-33552256;chr3:33556072-33556171			47.06
N	cassette	CUFF.419	chr17	-	chr17:5421208-5424843	chr17:5421208-5424200;chr17:5424333-5424843		chr17:5424201-5424332			56.52
K	cassette	CUFF.410	chr16	-	chr16:75576582-75589701	chr16:75576582-75579723;chr16:75579976-75589701		chr16:75579724-75579975			42.57
K	alternative_last_exon	CUFF.579	chr2	+	chr2:3482705-3488490	chr2:3482705-3482989	chr2:3488491-3488961	chr2:3482990-3483436			86.92
K	cassette	CUFF.887	chr5	-	chr5:127302621-127412638	chr5:127302621-127396835;chr5:127396937-127412638		chr5:127396836-127396936			23.33
K	alternative_first_exon	CUFF.258	chr14	+	chr14:24459569-24464240	chr14:24460162-24464240	chr14:24459391-24459568	chr14:24460067-24460161			4.12
K	jcn_only_AA	CUFF.352	chr15	-	chr15:90432369-90437112	chr15:90432373-90437112		chr15:90432369-90432372	chr15:90432368-90432369		66.67
N	alternative_acceptor	CUFF.576	chr2	-	chr2:675631-676573	chr2:676239-676573		chr2:675631-676238	chr2:675630-675631		91.57
K	intron_retention		chr11	-	chr11:10827595-10828366				chr11:10827594-10827595;chr11:10828366-10828367		21.33
N	coord_cassette	CUFF.426	chr17	-	chr17:15546131-15584178	chr17:15546131-15562115;chr17:15562191-15580489;chr17:15580595-15580888;chr17:15581036-15584178		chr17:15562116-15562190;chr17:15580490-15580594;chr17:15580889-15581035			59.02
K	cassette	CUFF.983	chr7	-	chr7:74981241-74982815	chr7:74981241-74982536;chr7:74982650-74982815		chr7:74982537-74982649			88.00
N	cassette	CUFF.741	chr3	-	chr3:33444397-33450727	chr3:33444397-33450181;chr3:33450290-33450727		chr3:33450182-33450289			45.45
K	intron_retention		chr9	+	chr9:43908524-43909283				chr9:43908523-43908524;chr9:43909283-43909284		33.33
N	jcn_only_AA	CUFF.581	chr2	-	chr2:4020665-4021134;chr2:4009394-4021134;chr2:4015879-4021134;chr2:4020693-4021134	chr2:4009485-4021134		chr2:4009394-4009484;chr2:4009485-4015878;chr2:4015879-4020664;chr2:4020665-4020692	chr2:4009393-4009394;chr2:4009484-4009485;chr2:4015878-4015879;chr2:4020664-4020665		39.81
K	intron_retention	CUFF.555	chr19	-	chr19:49310332-49314240				chr19:49310331-49310332;chr19:49314240-49314241		5.16
N	alternative_last_exon		chr7	+	chr7:91732141-91739435	chr7:91732141-91734991	chr7:91739436-91740085	chr7:91734992-91735077			87.10
N	alternative_acceptor		chr1	+	chr1:32540679-32541267	chr1:32540679-32541203		chr1:32541204-32541267	chr1:32541267-32541268		94.34
K	jcn_only_AA	CUFF.209	chr12	-	chr12:22611490-22612425	chr12:22611520-22612425		chr12:22611490-22611519	chr12:22611489-22611490		89.52
N	intron_retention		chr17	-	chr17:76993412-76993572				chr17:76993411-76993412;chr17:76993572-76993573		84.84
K	intron_retention	CUFF.905	chr6	+	chr6:348842-350821				chr6:348841-348842;chr6:350821-350822		27.42
K	intron_retention	CUFF.473	chr17	-	chr17:79890840-79891182				chr17:79890839-79890840;chr17:79891182-79891183	chr17:79890161-79890839;chr17:79891183-79891252	94.39
N	intron_retention		chr12	+	chr12:52404992-52407470				chr12:52404991-52404992;chr12:52407470-52407471		52.63
K	alternative_first_exon	CUFF.1136	chrX	+	chrX:107335067-107369306	chrX:107335110-107369306	chrX:107334833-107335066	chrX:107335077-107335109			6.31
N	jcn_only_AA	CUFF.743	chr3	-	chr3:33592888-33600798	chr3:33600668-33600798		chr3:33592888-33600667	chr3:33592887-33592888		31.15
K	alternative_first_exon	CUFF.248	chr13	+	chr13:33590452-33627903	chr13:33591398-33627903	chr13:33590207-33590451	chr13:33590476-33591397			85.00
K	jcn_only_AA	CUFF.807	chr3	-	chr3:196214450-196229743	chr3:196215555-196229743					12.50
N	alternative_donor	CUFF.155	chr11	+	chr11:36322621-36415395;chr11:36398255-36415395	chr11:36383732-36415395		chr11:36322621-36383731;chr11:36383732-36398254	chr11:36322620-36322621;chr11:36383731-36383732		0.00
N	alternative_donor	CUFF.396	chr16	-	chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57521007;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57514241		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		0.00
N	alternative_donor	CUFF.703	chr21	-	chr21:47566242-47570032	chr21:47566242-47566704		chr21:47566705-47570032	chr21:47570032-47570033		1.23
K	jcn_only_AA	CUFF.423	chr17	+	chr17:6353393-6353681	chr17:6353393-6353558		chr17:6353559-6353681	chr17:6353681-6353682		79.57
K	intron_retention	CUFF.265	chr14	+	chr14:50246525-50246930				chr14:50246524-50246525;chr14:50246930-50246931		48.96
N	intron_retention		chr16	+	chr16:3115657-3115784				chr16:3115656-3115657;chr16:3115784-3115785		50.00
N	jcn_only_AD	CUFF.890	chr5	+	chr5:131658049-131662969	chr5:131660336-131662969		chr5:131658049-131660335	chr5:131658048-131658049		62.96
N	alternative_donor	CUFF.502	chr18	+	chr18:77867357-77875412	chr18:77867906-77875412		chr18:77867357-77867905	chr18:77867356-77867357		25.00
K	cassette	CUFF.436	chr17	+	chr17:29657517-29661855	chr17:29657517-29661681;chr17:29661749-29661855		chr17:29661682-29661748			9.62
K	cassette	CUFF.1055	chr8	-	chr8:120756634-120758944	chr8:120756634-120757120;chr8:120757277-120758944		chr8:120757121-120757276			93.75
K	intron_retention	CUFF.21	chr1	-	chr1:41486606-41487294				chr1:41486605-41486606;chr1:41487294-41487295		83.33
N	jcn_only_AA	CUFF.704	chr22	-	chr22:18096087-18111368	chr22:18102293-18111368					91.53
K	coord_cassette	CUFF.162	chr11	+	chr11:63672516-63676348	chr11:63672516-63673559;chr11:63673587-63675731;chr11:63675777-63676348		chr11:63673560-63673586;chr11:63675732-63675776			37.50
K	mutually_exclusive	CUFF.1102	chr9	+	chr9:133320383-133326988,chr9:133327431-133327610	chr9:133320383-133325658,chr9:133325721-133327610	chr9:133326989-133327430	chr9:133325659-133325720			53.33
N	cassette	CUFF.515	chr19	-	chr19:8161891-8165784	chr19:8161891-8162172;chr19:8162299-8165784		chr19:8162173-8162298			25.29
K	cassette	CUFF.447	chr17	-	chr17:42113669-42114779	chr17:42113669-42114229;chr17:42114471-42114779		chr17:42114230-42114470			18.37
N	jcn_only_AA	CUFF.67	chr1	+	chr1:196913069-196918584;chr1:196913069-196918746	chr1:196913069-196918565		chr1:196918566-196918584;chr1:196918585-196918746	chr1:196918584-196918585;chr1:196918746-196918747	chr1:196912830-196913068;chr1:196918747-196918779	28.99
K	cassette	CUFF.114	chr10	-	chr10:73970590-73972944	chr10:73970590-73971945;chr10:73972044-73972944		chr10:73971946-73972043			6.33
N	jcn_only_AD	CUFF.504	chr19	+	chr19:1438892-1440017	chr19:1439826-1440017		chr19:1438892-1439825	chr19:1438891-1438892		8.78
N	cassette	CUFF.178	chr11	+	chr11:107917097-107923386	chr11:107917097-107920616;chr11:107920794-107923386		chr11:107920617-107920793			57.69
N	alternative_donor	CUFF.453	chr17	-	chr17:56082403-56082774;chr17:56082403-56082758	chr17:56082403-56083870		chr17:56082759-56082774;chr17:56082775-56083870	chr17:56082774-56082775;chr17:56083870-56083871		24.14
K	intron_retention		chr10	-	chr10:73956748-73963184				chr10:73956747-73956748;chr10:73963184-73963185		5.05
N	jcn_only_AA		chr12	+	chr12:13366756-13367504	chr12:13366756-13367467		chr12:13367468-13367504	chr12:13367504-13367505		59.65
N	jcn_only_AD	CUFF.971	chr7	-	chr7:37256301-37262219	chr7:37256301-37257316		chr7:37257317-37262219	chr7:37262219-37262220		27.27
K	alternative_first_exon	CUFF.1113,CUFF.1148	chrX	-	chrX:152988744-152988962,chrX:152988744-152989409,chrX:152988744-152989470,chrX:152988744-152989788;chrX:152988744-152989941	chrX:152988744-152989655	chrX:152989942-152990241	chrX:152989656-152989838			18.69
K	jcn_only_AD	CUFF.85	chr1	-	chr1:247287174-247322307	chr1:247287174-247302017					46.67
N	cassette	CUFF.880	chr5	-	chr5:64910047-64920020	chr5:64910047-64913919;chr5:64914083-64920020		chr5:64913920-64914082			95.00
N	jcn_only_AD	CUFF.292	chr14	+	chr14:92915504-92920243;chr14:92915561-92920243	chr14:92918991-92920243		chr14:92915504-92915560;chr14:92915561-92918990	chr14:92915503-92915504;chr14:92915560-92915561		26.67
K	alternative_first_exon	CUFF.317,CUFF.337	chr15	-	chr15:45470505-45490969;chr15:45470505-45473304;chr15:45470505-45479651	chr15:45470505-45492924	chr15:45473305-45473474;chr15:45479652-45480154	chr15:45492925-45493434			22.22
N	jcn_only_AA		chr17	+	chr17:61904875-61905033;chr17:61904875-61905210;chr17:61904875-61905188;chr17:61904875-61905478	chr17:61904875-61905497					54.89
N	alternative_acceptor	CUFF.1073,CUFF.1096	chr9	+	chr9:43853617-43861002;chr9:43853617-43861005	chr9:43853617-43854068		chr9:43854069-43861002;chr9:43861003-43861005	chr9:43861002-43861003;chr9:43861005-43861006		27.27
N	alternative_acceptor	CUFF.777	chr3	+	chr3:186714462-186756529	chr3:186714462-186723929		chr3:186723930-186756529	chr3:186756529-186756530		15.00
K	cassette	CUFF.975	chr7	+	chr7:44250724-44251845	chr7:44250724-44251152;chr7:44251204-44251845		chr7:44251153-44251203			78.42
N	alternative_donor	CUFF.923	chr6	+	chr6:34434048-34494019;chr6:34452922-34494019	chr6:34482846-34494019		chr6:34434048-34452921;chr6:34452922-34482845	chr6:34434047-34434048;chr6:34452921-34452922		0.00
K	cassette	CUFF.811	chr4	-	chr4:1705428-1713856	chr4:1705428-1713600;chr4:1713718-1713856		chr4:1713601-1713717			67.31
K	intron_retention	CUFF.747	chr3	-	chr3:38051545-38051621				chr3:38051544-38051545;chr3:38051621-38051622		43.75
N	cassette	CUFF.793	chr3	-	chr3:141697525-141724282;chr3:141697525-141713861	chr3:141697525-141712379;chr3:141712428-141724282,chr3:141712428-141713861		chr3:141712380-141712427			74.68
K	cassette	CUFF.1051	chr8	+	chr8:106370866-106431371	chr8:106370866-106427102;chr8:106427235-106431371		chr8:106427103-106427234			15.69
N	jcn_only_AA		chr17	+	chr17:61904875-61905033;chr17:61904875-61905210;chr17:61904875-61905188;chr17:61904875-61905497	chr17:61904875-61905478					18.05
N	alternative_acceptor	CUFF.879	chr5	-	chr5:60186914-60194102	chr5:60189471-60194102		chr5:60186914-60189470	chr5:60186913-60186914		5.32
N	jcn_only_AA		chr14	+	chr14:76219299-76230957	chr14:76219299-76224173					65.12
N	jcn_only_AA	CUFF.1002	chr7	-	chr7:107572823-107575859	chr7:107572939-107575859		chr7:107572823-107572938	chr7:107572822-107572823		33.33
N	alternative_acceptor	CUFF.102	chr10	+	chr10:35477317-35495822	chr10:35477317-35490378		chr10:35490379-35495822	chr10:35495822-35495823		0.87
N	cassette	CUFF.927	chr6	-	chr6:39856832-39864972	chr6:39856832-39859081;chr6:39859156-39864972		chr6:39859082-39859155			40.00
K	jcn_only_AD	CUFF.243	chr12	-	chr12:133181171-133181291	chr12:133181171-133181286		chr12:133181287-133181291	chr12:133181291-133181292		5.88
K	intron_retention	CUFF.278	chr14	-	chr14:75130526-75130601				chr14:75130525-75130526;chr14:75130601-75130602	chr14:75130215-75130525;chr14:75130602-75130777	7.32
N	alternative_donor	CUFF.102	chr10	+	chr10:35464928-35467816;chr10:35437420-35467816;chr10:35426808-35467816;chr10:35416122-35467816;chr10:35464634-35467816	chr10:35456732-35467816		chr10:35416122-35426807;chr10:35426808-35437419;chr10:35437420-35456731;chr10:35456732-35464633;chr10:35464634-35464927	chr10:35416121-35416122;chr10:35426807-35426808;chr10:35437419-35437420;chr10:35456731-35456732;chr10:35464633-35464634		0.00
N	alternative_acceptor	CUFF.230	chr12	-	chr12:56706670-56708634;chr12:56705238-56708634;chr12:56705199-56708634	chr12:56705180-56708634		chr12:56705180-56705198;chr12:56705199-56705237;chr12:56705238-56706669	chr12:56705179-56705180;chr12:56705198-56705199;chr12:56705237-56705238		15.62
N	alternative_donor	CUFF.377,CUFF.410	chr16	-	chr16:4411471-4411985	chr16:4411471-4411749		chr16:4411750-4411985	chr16:4411985-4411986		60.36
K	cassette	CUFF.412	chr16	+	chr16:77769884-77775478	chr16:77769884-77770546;chr16:77770641-77775478		chr16:77770547-77770640			52.83
N	intron_retention		chr6	-	chr6:31939359-31939705				chr6:31939358-31939359;chr6:31939705-31939706		91.94
K	mutually_exclusive	CUFF.132	chr10	-	chr10:123629554-123659380,chr10:123659510-123661905	chr10:123629554-123658355,chr10:123658485-123661905	chr10:123659381-123659509	chr10:123658356-123658484			23.94
N	jcn_only_AD	CUFF.708	chr22	+	chr22:21056998-21057293	chr22:21057182-21057293		chr22:21056998-21057181	chr22:21056997-21056998		16.77
K	alternative_acceptor	CUFF.21	chr1	-	chr1:41483652-41485897	chr1:41483829-41485897		chr1:41483652-41483828	chr1:41483651-41483652		92.73
K	alternative_donor	CUFF.763	chr3	-	chr3:93646252-93692517	chr3:93646252-93692406		chr3:93692407-93692517	chr3:93692517-93692518		97.58
N	alternative_acceptor	CUFF.669	chr2	+	chr2:241404164-241404272	chr2:241404164-241404251		chr2:241404252-241404272	chr2:241404272-241404273		2.12
K	intron_retention	CUFF.298	chr14	-	chr14:104201001-104201336				chr14:104201000-104201001;chr14:104201336-104201337		14.36
K	alternative_donor	CUFF.1075,CUFF.1080	chr9	-	chr9:46686830-46687553	chr9:46686830-46687372		chr9:46687373-46687553	chr9:46687553-46687554		33.33
N	jcn_only_AD	CUFF.589	chr2	-	chr2:27708371-27712481	chr2:27708371-27709025		chr2:27709026-27712481	chr2:27712481-27712482		7.69
K	cassette	CUFF.1096	chr9	+	chr9:125033355-125047447	chr9:125033355-125042721;chr9:125042878-125047447		chr9:125042722-125042877			93.58
N	alternative_donor	CUFF.802	chr3	+	chr3:186649184-186681572;chr3:186660216-186681572;chr3:186648624-186681572;chr3:186648928-186681572	chr3:186666727-186681572		chr3:186648624-186648927;chr3:186648928-186649183;chr3:186649184-186660215;chr3:186660216-186666726	chr3:186648623-186648624;chr3:186648927-186648928;chr3:186649183-186649184;chr3:186660215-186660216		0.00
N	cassette	CUFF.737	chr3	-	chr3:27244049-27297786	chr3:27244049-27257222;chr3:27257372-27297786		chr3:27257223-27257371			30.61
K	coord_cassette	CUFF.584	chr2	-	chr2:11587901-11593707	chr2:11587901-11590137;chr2:11590253-11591776;chr2:11591933-11593707		chr2:11590138-11590252;chr2:11591777-11591932			62.31
K	intron_retention	CUFF.576	chr2	-	chr2:676239-677288				chr2:676238-676239;chr2:677288-677289		77.27
K	cassette	CUFF.816	chr4	-	chr4:3949948-3952865	chr4:3949948-3951174;chr4:3951320-3952865		chr4:3951175-3951319			54.50
N	mutually_exclusive	CUFF.473	chr17	-	chr17:79891253-79892528,chr17:79892622-79892801	chr17:79891253-79892201,chr17:79892366-79892801	chr17:79892529-79892621	chr17:79892202-79892365		chr17:79891183-79891252;chr17:79892802-79893023	50.00
N	jcn_only_AA	CUFF.269	chr14	+	chr14:58899176-58899829;chr14:58899176-58909423	chr14:58899176-58906787		chr14:58899830-58906787;chr14:58906788-58909423	chr14:58906787-58906788;chr14:58909423-58909424		29.73
K	jcn_only_AD	CUFF.232	chr12	+	chr12:58019471-58019780	chr12:58019536-58019780		chr12:58019471-58019535	chr12:58019470-58019471		94.44
K	intron_retention	CUFF.1002	chr7	-	chr7:107570065-107571800				chr7:107570064-107570065;chr7:107571800-107571801		85.86
N	jcn_only_AD		chr15	-	chr15:90420657-90431752	chr15:90420657-90421496		chr15:90421497-90431752	chr15:90431752-90431753		13.11
N	jcn_only_AD		chr3	-	chr3:71777775-71778224;chr3:71777775-71803794	chr3:71777775-71803365					14.08
N	jcn_only_AD	CUFF.693	chr21	+	chr21:15680941-15685264	chr21:15681420-15685264		chr21:15680941-15681419	chr21:15680940-15680941	chr21:15685265-15685452;chr21:15680874-15680940	23.08
N	alternative_donor	CUFF.578	chr2	+	chr2:1263214-1271136	chr2:1266722-1271136		chr2:1263214-1266721	chr2:1263213-1263214		10.53
N	jcn_only_AD		chr3	-	chr3:33686396-33700998;chr3:33686396-33700465;chr3:33686396-33686835;chr3:33686396-33686494	chr3:33686396-33686773					34.69
K	cassette	CUFF.879	chr5	-	chr5:60199544-60214091	chr5:60199544-60200614;chr5:60200701-60214091		chr5:60200615-60200700			68.25
N	alternative_acceptor		chr7	-	chr7:117424509-117431344	chr7:117426480-117431344		chr7:117424509-117426479	chr7:117424508-117424509		0.00
N	alternative_acceptor	CUFF.593	chr2	+	chr2:27724097-27726380	chr2:27724097-27724556		chr2:27724557-27726380	chr2:27726380-27726381		9.38
K	jcn_only_AD	CUFF.4	chr1	+	chr1:11082299-11083249	chr1:11082308-11083249		chr1:11082299-11082307	chr1:11082298-11082299		75.34
K	intron_retention	CUFF.267	chr14	-	chr14:52486897-52495439				chr14:52486896-52486897;chr14:52495439-52495440		25.71
K	alternative_acceptor	CUFF.382	chr16	+	chr16:14020614-14021978	chr16:14020614-14021884		chr16:14021885-14021978	chr16:14021978-14021979		39.02
N	alternative_acceptor	CUFF.426	chr17	-	chr17:15557746-15584178;chr17:15580997-15584178	chr17:15581036-15584178		chr17:15557746-15580996;chr17:15580997-15581035	chr17:15557745-15557746;chr17:15580996-15580997		9.09
K	jcn_only_AA	CUFF.324	chr15	-	chr15:55790009-55790404	chr15:55790058-55790404		chr15:55790009-55790057	chr15:55790008-55790009		70.55
N	jcn_only_AD		chr18	-	chr18:67614769-67623849;chr18:67614769-67628827	chr18:67614769-67623990		chr18:67623850-67623990;chr18:67623991-67628827	chr18:67623990-67623991;chr18:67628827-67628828		25.93
K	jcn_only_AA	CUFF.240	chr12	-	chr12:113646065-113658801	chr12:113646315-113658801		chr12:113646065-113646314	chr12:113646064-113646065		28.57
N	jcn_only_AA		chr8	+	chr8:144373938-144375141	chr8:144373938-144374312		chr8:144374313-144375141	chr8:144375141-144375142		15.00
K	cassette	CUFF.427	chr17	+	chr17:15611562-15638243	chr17:15611562-15619372;chr17:15620628-15638243		chr17:15619373-15620627			35.85
N	jcn_only_AA	CUFF.945	chr6	-	chr6:128540242-128561179	chr6:128556750-128561179		chr6:128540242-128556749	chr6:128540241-128540242		5.56
N	jcn_only_AD	CUFF.1119	chrX	-	chrX:20252933-20285156	chrX:20252933-20258686		chrX:20258687-20285156	chrX:20285156-20285157		47.06
N	intron_retention		chr7	+	chr7:150835401-150837065				chr7:150835400-150835401;chr7:150837065-150837066		81.63
K	alternative_last_exon	CUFF.271	chr14	-	chr14:59941245-59942586;chr14:59927892-59942586	chr14:59939809-59942586	chr14:59927690-59927891	chr14:59939236-59939808			83.87
K	intron_retention	CUFF.927	chr6	-	chr6:39851801-39853526				chr6:39851800-39851801;chr6:39853526-39853527		76.92
N	intron_retention		chr14	+	chr14:61518854-61545547				chr14:61518853-61518854;chr14:61545547-61545548		80.00
N	jcn_only_AD	CUFF.201	chr12	+	chr12:4665669-4668022;chr12:4665717-4668022	chr12:4662256-4668022		chr12:4662256-4665668;chr12:4665669-4665716	chr12:4662255-4662256;chr12:4665668-4665669		20.22
N	jcn_only_AD		chr6	-	chr6:43483929-43484464	chr6:43483929-43484233		chr6:43484234-43484464	chr6:43484464-43484465		86.21
K	alternative_first_exon	CUFF.658	chr2	-	chr2:208030431-208031480;chr2:208030431-208031717	chr2:208030431-208030636	chr2:208031481-208031578;chr2:208031718-208032084	chr2:208030637-208030969			70.19
K	alternative_first_exon	CUFF.858	chr4	+	chr4:186209237-186231788	chr4:186217185-186231788	chr4:186209166-186209236	chr4:186217004-186217184			18.42
K	cassette	CUFF.704	chr22	-	chr22:18096087-18102226	chr22:18096087-18101799;chr22:18101894-18102226		chr22:18101800-18101893			4.65
K	alternative_last_exon	CUFF.411	chr16	-	chr16:76170264-76181457	chr16:76174302-76181457	chr16:76169937-76170263	chr16:76174260-76174301			53.85
K	intron_retention		chr17	-	chr17:1616350-1616996				chr17:1616349-1616350;chr17:1616996-1616997		5.07
K	jcn_only_AA	CUFF.439	chr17	+	chr17:33640726-33648755	chr17:33640726-33648753		chr17:33648754-33648755	chr17:33648755-33648756		59.09
N	cassette	CUFF.1018	chr7	-	chr7:156619439-156685621	chr7:156619439-156626432;chr7:156626487-156685621		chr7:156626433-156626486			62.96
K	jcn_only_AA	CUFF.703	chr21	-	chr21:47556968-47557152	chr21:47556988-47557152		chr21:47556968-47556987	chr21:47556967-47556968		49.64
N	jcn_only_AA	CUFF.225	chr12	+	chr12:53865592-53873189	chr12:53865592-53868652		chr12:53868653-53873189	chr12:53873189-53873190		2.26
K	cassette	CUFF.931	chr6	+	chr6:46630236-46636445	chr6:46630236-46632510;chr6:46632624-46636445		chr6:46632511-46632623			87.32
K	intron_retention	CUFF.390	chr16	-	chr16:23504909-23505623				chr16:23504908-23504909;chr16:23505623-23505624	chr16:23504681-23504908;chr16:23505624-23505699	46.01
K	alternative_last_exon	CUFF.714	chr22	+	chr22:25855483-25905149;chr22:25855483-25856833	chr22:25855483-25915889	chr22:25905150-25905309;chr22:25856834-25857720	chr22:25915890-25916129			51.52
K	intron_retention	CUFF.665	chr2	+	chr2:232028442-232029913				chr2:232028441-232028442;chr2:232029913-232029914		34.62
N	cassette	CUFF.211	chr12	-	chr12:25702481-25706002	chr12:25702481-25705804;chr12:25705924-25706002		chr12:25705805-25705923			95.18
N	cassette	CUFF.936	chr6	+	chr6:90276816-90312747	chr6:90276816-90305634;chr6:90305734-90312747		chr6:90305635-90305733			87.66
K	coord_cassette	CUFF.945	chr6	-	chr6:128326390-128330274	chr6:128326390-128327170;chr6:128327201-128329190;chr6:128329233-128330274		chr6:128327171-128327200;chr6:128329191-128329232			28.95
K	intron_retention	CUFF.298	chr14	-	chr14:104201417-104204030				chr14:104201416-104201417;chr14:104204030-104204031		14.53
K	intron_retention	CUFF.453	chr17	-	chr17:56081080-56082283				chr17:56081079-56081080;chr17:56082283-56082284		2.41
K	alternative_last_exon	CUFF.1082	chr9	+	chr9:95600023-95646187	chr9:95600023-95600538	chr9:95646188-95646282	chr9:95600539-95600836			97.44
N	coord_cassette	CUFF.467	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			97.54
K	jcn_only_AD	CUFF.235	chr12	+	chr12:72094659-72097756	chr12:72094806-72097756		chr12:72094659-72094805	chr12:72094658-72094659		30.30
N	jcn_only_AA	CUFF.170	chr11	+	chr11:118402587-118402960;chr11:118402587-118403124;chr11:118402587-118403004	chr11:118402587-118402811				chr11:118401663-118402586	59.21
N	jcn_only_AD	CUFF.2	chr1	+	chr1:2101044-2103493	chr1:2103085-2103493		chr1:2101044-2103084	chr1:2101043-2101044		13.82
K	intron_retention	CUFF.526	chr19	+	chr19:16204409-16204493				chr19:16204408-16204409;chr19:16204493-16204494		50.72
K	intron_retention	CUFF.562	chr19	+	chr19:52076655-52084643				chr19:52076654-52076655;chr19:52084643-52084644		35.48
N	coord_cassette	CUFF.683	chr20	+	chr20:30132839-30137866	chr20:30132839-30136767;chr20:30136918-30137009;chr20:30137136-30137866		chr20:30136768-30136917;chr20:30137010-30137135		chr20:30132750-30132838;chr20:30137867-30137965	76.97
K	alternative_donor	CUFF.920	chr6	+	chr6:32122172-32122363;chr6:32122182-32122363	chr6:32122024-32122363		chr6:32122024-32122171;chr6:32122172-32122181	chr6:32122023-32122024;chr6:32122171-32122172		14.66
K	alternative_donor	CUFF.539	chr19	+	chr19:35642377-35642535	chr19:35642386-35642535		chr19:35642377-35642385	chr19:35642376-35642377		62.50
N	cassette	CUFF.184	chr11	-	chr11:118919599-118920267	chr11:118919599-118919729;chr11:118919916-118920267		chr11:118919730-118919915			86.75
K	intron_retention	CUFF.149	chr11	-	chr11:6636561-6636672				chr11:6636560-6636561;chr11:6636672-6636673		10.32
K	mutually_exclusive	CUFF.403	chr16	+	chr16:67233660-67234094,chr16:67234265-67234353	chr16:67233660-67233853,chr16:67233905-67234353	chr16:67234095-67234264	chr16:67233854-67233904			88.89
N	alternative_donor	CUFF.436	chr17	+	chr17:29687722-29701030	chr17:29694297-29701030		chr17:29687722-29694296	chr17:29687721-29687722		12.50
K	alternative_last_exon	CUFF.85	chr1	-	chr1:247302060-247322307;chr1:247287174-247322307	chr1:247320520-247322307,chr1:247320706-247322307	chr1:247301359-247302059;chr1:247285180-247287173	chr1:247319106-247320519			72.94
N	cassette	CUFF.377	chr16	-	chr16:4466963-4475478	chr16:4466963-4470359;chr16:4470555-4475478		chr16:4470360-4470554			90.00
K	jcn_only_AA	CUFF.943	chr6	-	chr6:116988076-116989728	chr6:116988371-116989728		chr6:116988076-116988370	chr6:116988075-116988076		68.29
N	jcn_only_AA	CUFF.193	chr11	-	chr11:124766952-124767621;chr11:124767158-124767621	chr11:124767529-124767621		chr11:124766952-124767157;chr11:124767158-124767528	chr11:124766951-124766952;chr11:124767157-124767158		32.00
N	alternative_donor	CUFF.531	chr19	+	chr19:17611442-17615263;chr19:17612229-17615263	chr19:17611686-17615263		chr19:17611442-17611685;chr19:17611686-17612228	chr19:17611441-17611442;chr19:17611685-17611686		40.00
N	intron_retention		chr2	-	chr2:242441124-242447919				chr2:242441123-242441124;chr2:242447919-242447920		60.00
N	alternative_donor	CUFF.225	chr12	+	chr12:53846161-53848509;chr12:53847068-53848509;chr12:53837558-53848509	chr12:53846760-53848509		chr12:53837558-53846160;chr12:53846161-53846759;chr12:53846760-53847067	chr12:53837557-53837558;chr12:53846160-53846161;chr12:53846759-53846760		10.00
K	intron_retention	CUFF.532	chr19	+	chr19:18121168-18121380				chr19:18121167-18121168;chr19:18121380-18121381		44.83
K	jcn_only_AA	CUFF.402	chr16	-	chr16:67223587-67223873	chr16:67223671-67223873		chr16:67223587-67223670	chr16:67223586-67223587		32.69
K	intron_retention	CUFF.535	chr19	-	chr19:21636580-21637184				chr19:21636579-21636580;chr19:21637184-21637185		1.98
K	alternative_first_exon	CUFF.820	chr4	+	chr4:6925839-6969030	chr4:6956066-6969030	chr4:6925100-6925838	chr4:6955862-6956065			41.41
N	jcn_only_AD	CUFF.918	chr6	+	chr6:31937094-31937291	chr6:31937198-31937291		chr6:31937094-31937197	chr6:31937093-31937094		64.06
K	alternative_donor	CUFF.879,CUFF.880	chr5	-	chr5:60199544-60200618	chr5:60199544-60200614		chr5:60200615-60200618	chr5:60200618-60200619		7.95
N	cassette	CUFF.765	chr3	-	chr3:107586273-107594976;chr3:107586425-107596748	chr3:107586425-107591814,chr3:107586273-107591814;chr3:107591874-107594976,chr3:107591874-107596748		chr3:107591815-107591873			75.38
K	jcn_only_AA	CUFF.674	chr20	-	chr20:1517957-1532336	chr20:1517960-1532336		chr20:1517957-1517959	chr20:1517956-1517957		25.93
K	intron_retention	CUFF.140	chr11	-	chr11:2187289-2187709				chr11:2187288-2187289;chr11:2187709-2187710		12.98
K	intron_retention	CUFF.604	chr2	-	chr2:61709675-61710091				chr2:61709674-61709675;chr2:61710091-61710092		44.95
N	jcn_only_AA	CUFF.786	chr3	-	chr3:127299007-127309725	chr3:127309436-127309725		chr3:127299007-127309435	chr3:127299006-127299007		18.75
K	alternative_first_exon	CUFF.1016	chr7	+	chr7:150812729-150813879,chr7:150813738-150813879,chr7:150809332-150813879,chr7:150783097-150813879,chr7:150784160-150813879,chr7:150787635-150813879;chr7:150783148-150813879	chr7:150784292-150813879	chr7:150782918-150783147	chr7:150783779-150784291			18.94
K	cassette	CUFF.940	chr6	+	chr6:112386201-112389407	chr6:112386201-112388171;chr6:112388236-112389407		chr6:112388172-112388235			11.04
K	cassette	CUFF.662	chr2	+	chr2:219445464-219447693	chr2:219445464-219445717;chr2:219445838-219447693		chr2:219445718-219445837			43.03
K	jcn_only_AA	CUFF.945	chr6	-	chr6:128330411-128385902	chr6:128330414-128385902		chr6:128330411-128330413	chr6:128330410-128330411		97.44
N	jcn_only_AA	CUFF.685	chr20	-	chr20:31062546-31099149;chr20:31074605-31099149	chr20:31097744-31099149					9.62
K	alternative_first_exon	CUFF.569	chr19	-	chr19:56344282-56348075	chr19:56344282-56347701	chr19:56348076-56348251	chr19:56347702-56347892			29.41
N	jcn_only_AD	CUFF.155	chr11	+	chr11:36383732-36415395;chr11:36322621-36415395	chr11:36398255-36415395		chr11:36322621-36383731;chr11:36383732-36398254	chr11:36322620-36322621;chr11:36383731-36383732		94.07
N	alternative_donor	CUFF.639	chr2	+	chr2:160615847-160619390	chr2:160615870-160619390		chr2:160615847-160615869	chr2:160615846-160615847		11.11
N	jcn_only_AA	CUFF.1073	chr9	+	chr9:43853617-43854068;chr9:43853617-43861005	chr9:43853617-43861002		chr9:43854069-43861002;chr9:43861003-43861005	chr9:43861002-43861003;chr9:43861005-43861006		17.65
K	intron_retention	CUFF.393	chr16	-	chr16:30006539-30006663				chr16:30006538-30006539;chr16:30006663-30006664		40.38
K	alternative_last_exon	CUFF.425	chr17	-	chr17:15492542-15499827	chr17:15498141-15499827,chr17:15498205-15499827	chr17:15491607-15492541	chr17:15498062-15498140			54.90
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		74.42
K	cassette	CUFF.285	chr14	+	chr14:77934528-77935419	chr14:77934528-77934799;chr14:77934852-77935419		chr14:77934800-77934851			79.87
N	alternative_donor		chr14	-	chr14:59939809-59941156;chr14:59939809-59941445	chr14:59939809-59942586		chr14:59941157-59941445;chr14:59941446-59942586	chr14:59941445-59941446;chr14:59942586-59942587		90.10
N	coord_cassette	CUFF.234	chr12	+	chr12:69203073-69233053	chr12:69203073-69218142;chr12:69218211-69218334;chr12:69218432-69233053		chr12:69218143-69218210;chr12:69218335-69218431			47.66
K	jcn_only_AA	CUFF.36	chr1	+	chr1:110212194-110213935	chr1:110212194-110213908		chr1:110213909-110213935	chr1:110213935-110213936		55.32
K	intron_retention	CUFF.673	chr2	+	chr2:242598603-242606059				chr2:242598602-242598603;chr2:242606059-242606060		19.17
K	intron_retention	CUFF.566	chr19	+	chr19:54657578-54659046				chr19:54657577-54657578;chr19:54659046-54659047		75.19
N	jcn_only_AD	CUFF.457	chr17	+	chr17:61568730-61571282;chr17:61567390-61571282	chr17:61571021-61571282		chr17:61567390-61568729;chr17:61568730-61571020	chr17:61567389-61567390;chr17:61568729-61568730		95.67
K	intron_retention	CUFF.1135	chrX	-	chrX:106184863-106185205				chrX:106184862-106184863;chrX:106185205-106185206		69.70
K	alternative_first_exon	CUFF.822	chr4	+	chr4:13659479-13831403	chr4:13821896-13831403	chr4:13659371-13659478	chr4:13821679-13821895			55.56
N	alternative_first_exon	CUFF.891	chr5	+	chr5:134181428-134190587;chr5:134181903-134190587	chr5:134182554-134190587	chr5:134181338-134181427;chr5:134181764-134181902	chr5:134182156-134182553			89.58
N	jcn_only_AD	CUFF.340	chr15	+	chr15:77750839-77756581	chr15:77750901-77756581		chr15:77750839-77750900	chr15:77750838-77750839		5.53
N	alternative_first_exon	CUFF.889	chr5	+	chr5:128796176-128844769	chr5:128797451-128844769	chr5:128795958-128796175	chr5:128796795-128797450			44.44
K	intron_retention	CUFF.714	chr22	+	chr22:25855483-25856833				chr22:25855482-25855483;chr22:25856833-25856834		73.33
K	alternative_first_exon	CUFF.782	chr3	-	chr3:125787090-125789043,chr3:125787090-125791995,chr3:125787090-125802718;chr3:125787090-125797816;chr3:125787090-125802771	chr3:125787090-125802935,chr3:125787090-125802896	chr3:125797817-125797915;chr3:125802772-125802870	chr3:125802936-125803219			57.53
K	intron_retention	CUFF.530	chr19	+	chr19:17447967-17448682				chr19:17447966-17447967;chr19:17448682-17448683		63.89
K	alternative_acceptor	CUFF.1069	chr9	+	chr9:34993442-34996391	chr9:34993442-34996261		chr9:34996262-34996391	chr9:34996391-34996392		79.22
K	jcn_only_AD	CUFF.502	chr18	+	chr18:77875468-77890985	chr18:77875534-77890985		chr18:77875468-77875533	chr18:77875467-77875468		45.45
N	alternative_acceptor	CUFF.182	chr11	+	chr11:118405071-118416833;chr11:118405071-118405221	chr11:118405071-118406222		chr11:118405222-118406222;chr11:118406223-118416833	chr11:118406222-118406223;chr11:118416833-118416834	chr11:118404981-118405070	0.00
N	cassette	CUFF.941	chr6	+	chr6:112558118-112668493	chr6:112558118-112664599;chr6:112664981-112668493		chr6:112664600-112664980			95.50
K	intron_retention	CUFF.100	chr10	-	chr10:30301980-30302411				chr10:30301979-30301980;chr10:30302411-30302412		20.00
K	cassette	CUFF.584	chr2	-	chr2:11587901-11593707	chr2:11587901-11591327;chr2:11591933-11593707		chr2:11591328-11591932			55.09
K	intron_retention	CUFF.848	chr4	+	chr4:120414593-120415587				chr4:120414592-120414593;chr4:120415587-120415588		80.18
N	cassette	CUFF.985	chr7	-	chr7:75054992-75066792	chr7:75054992-75055643;chr7:75055736-75066792		chr7:75055644-75055735			36.67
N	alternative_acceptor	CUFF.945	chr6	-	chr6:128540242-128561179	chr6:128556750-128561179		chr6:128540242-128556749	chr6:128540241-128540242		0.00
N	alternative_donor	CUFF.460	chr17	+	chr17:61907310-61907630	chr17:61907550-61907630		chr17:61907310-61907549	chr17:61907309-61907310		92.84
K	mutually_exclusive	CUFF.1040	chr8	+	chr8:75262814-75272371,chr8:75272546-75274118	chr8:75262814-75263508,chr8:75263702-75274118	chr8:75272372-75272545	chr8:75263509-75263701			53.40
N	alternative_donor	CUFF.976	chr7	+	chr7:54612482-54614639;chr7:54613910-54614639	chr7:54614433-54614639		chr7:54612482-54613909;chr7:54613910-54614432	chr7:54612481-54612482;chr7:54613909-54613910		4.35
K	jcn_only_AA	CUFF.1030	chr8	-	chr8:29535521-29583671	chr8:29582536-29583671					50.00
N	alternative_donor	CUFF.852	chr4	-	chr4:152147239-152246392;chr4:152147239-152147319	chr4:152147239-152187237		chr4:152147320-152187237;chr4:152187238-152246392	chr4:152187237-152187238;chr4:152246392-152246393		0.00
N	alternative_last_exon	CUFF.73	chr1	+	chr1:230203154-230338882	chr1:230203154-230227335	chr1:230338883-230339036	chr1:230227336-230227874			92.16
N	alternative_acceptor	CUFF.734	chr3	+	chr3:19992554-20017092;chr3:19992554-20017134;chr3:19992554-20012039	chr3:19992554-20017078		chr3:20012040-20017078;chr3:20017079-20017092;chr3:20017093-20017134	chr3:20017078-20017079;chr3:20017092-20017093;chr3:20017134-20017135		81.30
N	intron_retention		chr2	-	chr2:177042550-177042742				chr2:177042549-177042550;chr2:177042742-177042743		75.00
N	jcn_only_AA	CUFF.163	chr11	+	chr11:63999437-63999865;chr11:63999437-63999901;chr11:63999437-63999981	chr11:63999437-64001365					3.21
K	alternative_acceptor	CUFF.530	chr19	+	chr19:17447967-17448816	chr19:17447967-17448682		chr19:17448683-17448816	chr19:17448816-17448817		85.71
K	intron_retention	CUFF.1151	chrX	+	chrX:153608728-153609112				chrX:153608727-153608728;chrX:153609112-153609113		14.29
K	mutually_exclusive	CUFF.263	chr14	+	chr14:39944160-39961458,chr14:39961761-39982820	chr14:39944160-39954220,chr14:39954462-39982820	chr14:39961459-39961760	chr14:39954221-39954461			36.17
K	intron_retention	CUFF.468	chr17	-	chr17:79220862-79225292				chr17:79220861-79220862;chr17:79225292-79225293	chr17:79225293-79226483	55.56
N	jcn_only_AA	CUFF.377	chr16	-	chr16:4411471-4411985	chr16:4411805-4411985		chr16:4411471-4411804	chr16:4411470-4411471		26.67
N	jcn_only_AA		chr3	+	chr3:119196296-119198754;chr3:119196296-119197180	chr3:119196296-119198897		chr3:119197181-119198754;chr3:119198755-119198897	chr3:119198754-119198755;chr3:119198897-119198898		31.25
N	alternative_first_exon		chr3	-	chr3:49354912-49362134	chr3:49354912-49355741	chr3:49362135-49362196	chr3:49355742-49356244			92.86
K	alternative_donor	CUFF.658	chr2	-	chr2:207953306-207989067;chr2:207953306-207988699	chr2:207953306-207988497		chr2:207988498-207988699;chr2:207988700-207989067	chr2:207988699-207988700;chr2:207989067-207989068		43.36
N	cassette	CUFF.998	chr7	-	chr7:102240836-102246304	chr7:102240836-102242770;chr7:102242853-102246304		chr7:102242771-102242852			93.58
K	intron_retention	CUFF.895	chr5	+	chr5:140027510-140028055				chr5:140027509-140027510;chr5:140028055-140028056		5.68
N	alternative_donor	CUFF.316	chr15	-	chr15:44907765-44912387	chr15:44907765-44912322		chr15:44912323-44912387	chr15:44912387-44912388		47.62
K	alternative_donor	CUFF.1012	chr7	+	chr7:134249522-134252909	chr7:134250299-134252909		chr7:134249522-134250298	chr7:134249521-134249522		82.76
N	intron_retention		chr17	+	chr17:35378314-35413900				chr17:35378313-35378314;chr17:35413900-35413901		50.67
K	intron_retention	CUFF.1096	chr9	+	chr9:125027825-125033142				chr9:125027824-125027825;chr9:125033142-125033143		41.59
N	cassette	CUFF.407	chr16	+	chr16:70390151-70394679;chr16:70390151-70395320	chr16:70390151-70390725;chr16:70390810-70394679,chr16:70390810-70395320		chr16:70390726-70390809			47.67
K	intron_retention	CUFF.371	chr16	+	chr16:2203224-2203578				chr16:2203223-2203224;chr16:2203578-2203579		13.38
K	alternative_acceptor	CUFF.982	chr7	-	chr7:74607950-74608617	chr7:74607952-74608617		chr7:74607950-74607951	chr7:74607949-74607950		12.50
K	jcn_only_AD	CUFF.1109	chr9	+	chr9:139794973-139802521	chr9:139795129-139802521		chr9:139794973-139795128	chr9:139794972-139794973		47.65
K	intron_retention	CUFF.394	chr16	+	chr16:31382819-31382950				chr16:31382818-31382819;chr16:31382950-31382951		27.78
N	jcn_only_AD	CUFF.971	chr7	-	chr7:37382368-37433424;chr7:37382368-37392635;chr7:37382368-37488277;chr7:37382368-37382655	chr7:37382368-37488462		chr7:37382656-37392635;chr7:37392636-37433424;chr7:37433425-37488277;chr7:37488278-37488462	chr7:37392635-37392636;chr7:37433424-37433425;chr7:37488277-37488278;chr7:37488462-37488463		4.26
N	alternative_last_exon	CUFF.928	chr6	-	chr6:41462632-41513826	chr6:41491964-41513826	chr6:41462591-41462631	chr6:41491546-41491963			9.28
N	jcn_only_AD		chr22	-	chr22:51016364-51016512;chr22:51016364-51016814	chr22:51016364-51016977		chr22:51016513-51016814;chr22:51016815-51016977	chr22:51016814-51016815;chr22:51016977-51016978		45.71
K	jcn_only_AA	CUFF.530	chr19	+	chr19:17447967-17448816	chr19:17447967-17448682		chr19:17448683-17448816	chr19:17448816-17448817		72.22
N	jcn_only_AD		chr14	-	chr14:104263856-104313344;chr14:104263856-104313635;chr14:104263856-104306415	chr14:104263856-104313111					3.53
K	jcn_only_AA	CUFF.647	chr2	-	chr2:175816931-175869933	chr2:175869809-175869933					83.91
N	alternative_first_exon	CUFF.954	chr6	+	chr6:161488329-161491639;chr6:161413116-161491639	chr6:161471012-161491639	chr6:161412759-161413115	chr6:161469648-161471011		chr6:161491640-161491882	78.38
N	cassette	CUFF.509	chr19	-	chr19:6042135-6047417	chr19:6042135-6044203;chr19:6044294-6047417		chr19:6044204-6044293			93.33
K	jcn_only_AD	CUFF.304	chr15	+	chr15:25223466-25225093	chr15:25224790-25225093					75.00
K	alternative_last_exon	CUFF.319	chr15	+	chr15:45768751-45769966;chr15:45768751-45789310	chr15:45768751-45804570	chr15:45769967-45770054;chr15:45789311-45789564	chr15:45804571-45804647			39.44
K	jcn_only_AD	CUFF.520,CUFF.547	chr19	-	chr19:41938314-41939441	chr19:41938314-41939176					48.04
N	jcn_only_AD	CUFF.292	chr14	+	chr14:92915561-92920243;chr14:92918991-92920243	chr14:92915504-92920243		chr14:92915504-92915560;chr14:92915561-92918990	chr14:92915503-92915504;chr14:92915560-92915561		11.11
N	intron_retention		chr11	+	chr11:115268247-115268300				chr11:115268246-115268247;chr11:115268300-115268301		90.72
K	alternative_first_exon	CUFF.415	chr16	+	chr16:89787685-89788938;chr16:89788254-89788938	chr16:89786991-89788938	chr16:89787360-89787684;chr16:89787884-89788253	chr16:89786808-89786990			23.76
N	cassette	CUFF.347	chr15	-	chr15:83350333-83357909	chr15:83350333-83357487;chr15:83357584-83357909		chr15:83357488-83357583			89.89
K	intron_retention	CUFF.423	chr17	+	chr17:6353393-6353558				chr17:6353392-6353393;chr17:6353558-6353559		3.90
N	intron_retention	CUFF.236	chr12	-	chr12:77254194-77256589				chr12:77254193-77254194;chr12:77256589-77256590		61.54
K	cassette	CUFF.644	chr2	+	chr2:171376051-171399415	chr2:171376051-171381014;chr2:171381137-171399415		chr2:171381015-171381136			35.29
N	intron_retention		chr22	+	chr22:50920193-50920265				chr22:50920192-50920193;chr22:50920265-50920266		15.38
N	jcn_only_AD	CUFF.639	chr2	+	chr2:160585687-160599571	chr2:160590594-160599571		chr2:160585687-160590593	chr2:160585686-160585687		1.36
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		39.39
N	jcn_only_AD	CUFF.50	chr1	+	chr1:155180207-155180338	chr1:155180227-155180338		chr1:155180207-155180226	chr1:155180206-155180207		16.92
N	jcn_only_AA	CUFF.274	chr14	-	chr14:69584993-69585910	chr14:69584996-69585910		chr14:69584993-69584995	chr14:69584992-69584993		73.68
K	cassette	CUFF.112	chr10	+	chr10:70679738-70694554	chr10:70679738-70693954;chr10:70694117-70694554		chr10:70693955-70694116			60.87
K	intron_retention		chr3	-	chr3:141713984-141719093				chr3:141713983-141713984;chr3:141719093-141719094		20.00
K	intron_retention	CUFF.460	chr17	+	chr17:61907550-61907630				chr17:61907549-61907550;chr17:61907630-61907631		0.43
N	cassette	CUFF.775	chr3	-	chr3:120352438-120360435;chr3:120352176-120360435	chr3:120352438-120357301,chr3:120352176-120357301;chr3:120357429-120360435		chr3:120357302-120357428			45.83
K	alternative_last_exon	CUFF.30	chr1	-	chr1:85718386-85724206	chr1:85723155-85724206	chr1:85715639-85718385	chr1:85723027-85723154			76.92
N	mutually_exclusive	CUFF.331	chr15	-	chr15:64658275-64673156,chr15:64673238-64673524	chr15:64658275-64668941,chr15:64669105-64673524	chr15:64673157-64673237	chr15:64668942-64669104			53.85
K	alternative_donor	CUFF.239	chr12	-	chr12:113617811-113618785	chr12:113617811-113618733		chr12:113618734-113618785	chr12:113618785-113618786		48.15
K	alternative_last_exon	CUFF.792	chr3	-	chr3:133794058-133894452	chr3:133878218-133894452	chr3:133793879-133794057	chr3:133878044-133878217			72.50
K	alternative_donor	CUFF.252,CUFF.253	chr13	-	chr13:78492760-78493531	chr13:78492760-78493141		chr13:78493142-78493531	chr13:78493531-78493532		41.67
K	intron_retention	CUFF.728	chr22	-	chr22:51018260-51018402				chr22:51018259-51018260;chr22:51018402-51018403		79.03
N	jcn_only_AA	CUFF.182	chr11	+	chr11:118405071-118405221;chr11:118405071-118406222	chr11:118405071-118416833		chr11:118405222-118406222;chr11:118406223-118416833	chr11:118406222-118406223;chr11:118416833-118416834	chr11:118404981-118405070	17.39
K	alternative_last_exon	CUFF.887	chr5	-	chr5:127396337-127396835;chr5:127302621-127396835;chr5:127292614-127396835	chr5:127359991-127396835	chr5:127301504-127302620;chr5:127292496-127292613	chr5:127359827-127359990			12.00
N	cassette	CUFF.758	chr3	-	chr3:57563115-57570110;chr3:57563115-57582800	chr3:57563115-57569624;chr3:57569735-57570110,chr3:57569735-57582800		chr3:57569625-57569734			59.65
K	intron_retention	CUFF.673	chr2	+	chr2:242591390-242592926				chr2:242591389-242591390;chr2:242592926-242592927		6.51
K	jcn_only_AD	CUFF.450	chr17	+	chr17:46990328-46993437	chr17:46990384-46993437		chr17:46990328-46990383	chr17:46990327-46990328		54.00
N	intron_retention		chr16	+	chr16:3115712-3115781				chr16:3115711-3115712;chr16:3115781-3115782		77.97
K	alternative_first_exon	CUFF.1151	chrX	+	chrX:153607927-153608301	chrX:153608155-153608301	chrX:153607505-153607926	chrX:153607992-153608154			78.43
K	intron_retention	CUFF.485	chr18	-	chr18:44268883-44272131				chr18:44268882-44268883;chr18:44272131-44272132		7.04
N	alternative_donor	CUFF.49	chr1	-	chr1:153921121-153921590	chr1:153921121-153921309		chr1:153921310-153921590	chr1:153921590-153921591		22.86
N	cassette	CUFF.1042	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			35.06
N	jcn_only_AD		chr16	-	chr16:23507100-23530907	chr16:23507100-23521641		chr16:23521642-23530907	chr16:23530907-23530908	chr16:23507015-23507099	95.96
N	intron_retention		chr17	+	chr17:61904875-61905210				chr17:61904874-61904875;chr17:61905210-61905211		58.62
N	alternative_acceptor	CUFF.187	chr11	+	chr11:119056338-119056630	chr11:119056338-119056557		chr11:119056558-119056630	chr11:119056630-119056631		30.77
K	intron_retention	CUFF.754	chr3	-	chr3:49462487-49462799				chr3:49462486-49462487;chr3:49462799-49462800		39.22
K	cassette	CUFF.150	chr11	-	chr11:8457687-8474368	chr11:8457687-8462224;chr11:8462301-8474368		chr11:8462225-8462300			94.87
K	alternative_last_exon	CUFF.578,CUFF.579	chr2	+	chr2:1133496-1161233	chr2:1133496-1156117	chr2:1161234-1161321	chr2:1156118-1157357			15.38
K	intron_retention	CUFF.160	chr11	+	chr11:61630542-61630753				chr11:61630541-61630542;chr11:61630753-61630754	chr11:61630444-61630541;chr11:61630754-61630850	51.32
N	cassette	CUFF.999	chr7	-	chr7:102668006-102669797	chr7:102668006-102669046;chr7:102669196-102669797		chr7:102669047-102669195			92.71
K	intron_retention	CUFF.980	chr7	+	chr7:73101062-73101147				chr7:73101061-73101062;chr7:73101147-73101148		9.88
K	jcn_only_AD	CUFF.483	chr18	+	chr18:14797854-14808549	chr18:14803824-14808549					36.07
K	jcn_only_AA	CUFF.257	chr14	+	chr14:23390330-23392180	chr14:23390330-23392177		chr14:23392178-23392180	chr14:23392180-23392181		87.86
K	intron_retention	CUFF.50	chr1	+	chr1:155180419-155181917				chr1:155180418-155180419;chr1:155181917-155181918		6.82
N	mutually_exclusive	CUFF.476	chr17	+	chr17:80426773-80436446,chr17:80436544-80436675	chr17:80426773-80430439,chr17:80430575-80436675	chr17:80436447-80436543	chr17:80430440-80430574			66.99
K	cassette	CUFF.787	chr3	+	chr3:132948196-133109023	chr3:132948196-133098595;chr3:133100006-133109023		chr3:133098596-133100005			81.82
N	jcn_only_AD	CUFF.456	chr17	+	chr17:60784969-60813446;chr17:60783831-60813446	chr17:60777141-60813446		chr17:60777141-60783830;chr17:60783831-60784968	chr17:60777140-60777141;chr17:60783830-60783831		84.71
K	cassette	CUFF.644	chr2	+	chr2:171356319-171371430	chr2:171356319-171358294;chr2:171358376-171371430		chr2:171358295-171358375			89.36
K	jcn_only_AA	CUFF.1092	chr9	-	chr9:123550465-123555426	chr9:123550557-123555426		chr9:123550465-123550556	chr9:123550464-123550465		76.92
N	jcn_only_AD	CUFF.631	chr2	+	chr2:109065737-109066088	chr2:109065746-109066088		chr2:109065737-109065745	chr2:109065736-109065737		7.26
N	jcn_only_AD	CUFF.879	chr5	-	chr5:60200701-60214091	chr5:60200701-60203106		chr5:60203107-60214091	chr5:60214091-60214092		3.19
N	alternative_acceptor	CUFF.966	chr7	-	chr7:22233074-22233532	chr7:22233396-22233532		chr7:22233074-22233395	chr7:22233073-22233074		13.95
N	alternative_acceptor	CUFF.278	chr14	-	chr14:75152364-75158743	chr14:75157854-75158743		chr14:75152364-75157853	chr14:75152363-75152364	chr14:75158744-75159031;chr14:75152303-75152363	0.00
N	intron_retention		chr17	+	chr17:66508637-66511534				chr17:66508636-66508637;chr17:66511534-66511535		61.29
N	jcn_only_AD	CUFF.631	chr2	+	chr2:109085541-109086106	chr2:109085789-109086106		chr2:109085541-109085788	chr2:109085540-109085541		69.01
N	alternative_donor	CUFF.942	chr6	-	chr6:114283559-114292020;chr6:114283559-114289797	chr6:114283559-114332294		chr6:114289798-114292020;chr6:114292021-114332294	chr6:114292020-114292021;chr6:114332294-114332295		90.00
N	coord_cassette	CUFF.793	chr3	-	chr3:141713984-141811902	chr3:141713984-141719093;chr3:141719197-141724282;chr3:141724387-141811902		chr3:141719094-141719196;chr3:141724283-141724386			79.41
N	alternative_acceptor	CUFF.652	chr2	-	chr2:197298183-197458231	chr2:197358100-197458231		chr2:197298183-197358099	chr2:197298182-197298183		0.00
K	cassette	CUFF.228	chr12	-	chr12:56557550-56558431	chr12:56557550-56558086;chr12:56558153-56558431		chr12:56558087-56558152			21.88
K	intron_retention	CUFF.716	chr22	+	chr22:29684776-29686401				chr22:29684775-29684776;chr22:29686401-29686402		16.44
K	intron_retention	CUFF.1000	chr7	+	chr7:107207632-107211589				chr7:107207631-107207632;chr7:107211589-107211590		39.13
K	alternative_first_exon	CUFF.385	chr16	+	chr16:19613046-19619499	chr16:19619184-19619499	chr16:19612986-19613045	chr16:19619042-19619183			60.14
K	alternative_donor	CUFF.687	chr20	+	chr20:33589330-33589750	chr20:33589396-33589750		chr20:33589330-33589395	chr20:33589329-33589330		2.05
K	alternative_last_exon	CUFF.714	chr22	+	chr22:25855483-25915889;chr22:25855483-25856833	chr22:25855483-25905149	chr22:25915890-25916129;chr22:25856834-25857720	chr22:25905150-25905309			18.18
N	jcn_only_AD	CUFF.475	chr17	-	chr17:79993940-79994057;chr17:79993940-79994022	chr17:79993940-79994066		chr17:79994023-79994057;chr17:79994058-79994066	chr17:79994057-79994058;chr17:79994066-79994067		86.59
N	intron_retention		chr11	-	chr11:6637735-6638589				chr11:6637734-6637735;chr11:6638589-6638590		14.93
N	jcn_only_AD	CUFF.347	chr15	-	chr15:83358206-83366608;chr15:83358206-83378345;chr15:83358206-83358514	chr15:83358206-83377523		chr15:83358515-83366608;chr15:83366609-83377523;chr15:83377524-83378345	chr15:83366608-83366609;chr15:83377523-83377524;chr15:83378345-83378346		3.25
N	jcn_only_AA	CUFF.321	chr15	-	chr15:50822127-50830905	chr15:50824425-50830905		chr15:50822127-50824424	chr15:50822126-50822127		8.13
N	jcn_only_AD	CUFF.221	chr12	+	chr12:52404926-52407470	chr12:52404992-52407470		chr12:52404926-52404991	chr12:52404925-52404926		28.12
N	jcn_only_AA	CUFF.765	chr3	-	chr3:107591328-107591814;chr3:107586273-107591814	chr3:107586425-107591814		chr3:107586273-107586424;chr3:107586425-107591327	chr3:107586272-107586273;chr3:107586424-107586425		50.16
N	intron_retention		chr12	-	chr12:102874179-102874364				chr12:102874178-102874179;chr12:102874364-102874365		10.34
K	intron_retention	CUFF.830	chr4	+	chr4:57302095-57302427				chr4:57302094-57302095;chr4:57302427-57302428		96.84
N	alternative_acceptor	CUFF.823	chr4	+	chr4:20552522-20555427	chr4:20552522-20554050		chr4:20554051-20555427	chr4:20555427-20555428		11.11
K	alternative_first_exon	CUFF.269	chr14	+	chr14:58906879-58909423;chr14:58899176-58909423	chr14:58908062-58909423	chr14:58899106-58899175	chr14:58907688-58908061			20.83
K	alternative_donor	CUFF.636	chr2	+	chr2:133070569-133074681	chr2:133070573-133074681		chr2:133070569-133070572	chr2:133070568-133070569		62.50
K	intron_retention	CUFF.673	chr2	+	chr2:242608101-242610140				chr2:242608100-242608101;chr2:242610140-242610141		3.98
K	alternative_last_exon	CUFF.1	chr1	+	chr1:1656203-1667255	chr1:1656203-1661684	chr1:1667256-1667503	chr1:1661685-1663435			64.29
N	alternative_acceptor	CUFF.1001	chr7	+	chr7:107236448-107240841	chr7:107236448-107240676		chr7:107240677-107240841	chr7:107240841-107240842		1.83
K	intron_retention	CUFF.543	chr19	+	chr19:40485892-40485976				chr19:40485891-40485892;chr19:40485976-40485977		5.36
K	intron_retention		chr14	+	chr14:24563644-24563974				chr14:24563643-24563644;chr14:24563974-24563975		8.36
N	intron_retention		chr2	-	chr2:4007227-4007505				chr2:4007226-4007227;chr2:4007505-4007506		91.67
N	jcn_only_AD	CUFF.389	chr16	+	chr16:22448814-22462940	chr16:22449059-22462940		chr16:22448814-22449058	chr16:22448813-22448814		30.00
N	cassette	CUFF.1116	chrX	-	chrX:15339895-15343141	chrX:15339895-15342786;chrX:15342994-15343141		chrX:15342787-15342993			95.31
N	coord_cassette	CUFF.269	chr14	+	chr14:58979346-59014498	chr14:58979346-59006788;chr14:59006855-59010600;chr14:59010686-59014498		chr14:59006789-59006854;chr14:59010601-59010685			33.33
N	cassette	CUFF.936	chr6	+	chr6:90326377-90331640	chr6:90326377-90327672;chr6:90327751-90331640		chr6:90327673-90327750			56.31
K	alternative_first_exon	CUFF.586	chr2	+	chr2:16535569-16573520	chr2:16536536-16573520	chr2:16535524-16535568	chr2:16536374-16536535			75.00
K	intron_retention	CUFF.55	chr1	-	chr1:158590257-158592772				chr1:158590256-158590257;chr1:158592772-158592773		4.15
K	alternative_last_exon	CUFF.304,CUFF.344	chr15	+	chr15:78819906-78829641	chr15:78819906-78825551	chr15:78829642-78829714	chr15:78825552-78826104			82.89
N	jcn_only_AD		chr17	-	chr17:79894070-79898625;chr17:79894070-79900171	chr17:79894070-79894623		chr17:79894624-79898625;chr17:79898626-79900171	chr17:79898625-79898626;chr17:79900171-79900172	chr17:79893999-79894069	94.24
N	alternative_first_exon	CUFF.188	chr11	-	chr11:119244232-119249716;chr11:119244232-119246933	chr11:119244232-119252182	chr11:119249717-119249914;chr11:119246934-119247108	chr11:119252183-119252421			2.44
N	jcn_only_AD	CUFF.572	chr2	-	chr2:230045-231022	chr2:230045-230546		chr2:230547-231022	chr2:231022-231023		5.77
N	cassette	CUFF.941	chr6	+	chr6:112558118-112627530	chr6:112558118-112604255;chr6:112604395-112627530		chr6:112604256-112604394			89.74
N	jcn_only_AA	CUFF.485	chr18	-	chr18:44268831-44272131	chr18:44268883-44272131		chr18:44268831-44268882	chr18:44268830-44268831		87.61
K	jcn_only_AD	CUFF.658	chr2	-	chr2:207953306-207988497;chr2:207953306-207989067	chr2:207953306-207988699		chr2:207988498-207988699;chr2:207988700-207989067	chr2:207988699-207988700;chr2:207989067-207989068		4.23
K	alternative_donor	CUFF.859	chr4	+	chr4:191012637-191013578	chr4:191013443-191013578		chr4:191012637-191013442	chr4:191012636-191012637		71.43
K	intron_retention	CUFF.709	chr22	-	chr22:21829590-21830290				chr22:21829589-21829590;chr22:21830290-21830291		45.90
N	alternative_acceptor	CUFF.482	chr18	+	chr18:55862966-55912658	chr18:55862966-55895061		chr18:55895062-55912658	chr18:55912658-55912659		0.00
K	alternative_last_exon	CUFF.641	chr2	+	chr2:169711971-169713199	chr2:169711971-169712395	chr2:169713200-169713288	chr2:169712396-169712494			11.22
K	intron_retention	CUFF.675	chr20	+	chr20:2844730-2844824				chr20:2844729-2844730;chr20:2844824-2844825		29.55
N	alternative_acceptor	CUFF.171	chr11	-	chr11:75520420-75522468;chr11:75514563-75522468	chr11:75514771-75522468		chr11:75514563-75514770;chr11:75514771-75520419	chr11:75514562-75514563;chr11:75514770-75514771		51.22
N	jcn_only_AD		chr11	-	chr11:67771269-67772276	chr11:67771269-67771417		chr11:67771418-67772276	chr11:67772276-67772277		93.55
K	alternative_first_exon	CUFF.540	chr19	+	chr19:36139796-36142134;chr19:36139306-36142134	chr19:36139811-36142134	chr19:36139125-36139305	chr19:36139554-36139810			48.15
K	intron_retention		chr11	-	chr11:118919599-118919729				chr11:118919598-118919599;chr11:118919729-118919730		8.25
N	alternative_donor	CUFF.879	chr5	-	chr5:60224787-60240758	chr5:60224787-60227933		chr5:60227934-60240758	chr5:60240758-60240759		0.00
N	cassette	CUFF.374	chr16	+	chr16:3115496-3117377	chr16:3115496-3115784;chr16:3115828-3117377		chr16:3115785-3115827			94.55
N	intron_retention		chr19	+	chr19:16191886-16192722				chr19:16191885-16191886;chr19:16192722-16192723		44.44
K	jcn_only_AA	CUFF.519	chr19	+	chr19:11467653-11468335	chr19:11467653-11468294		chr19:11468295-11468335	chr19:11468335-11468336		73.02
K	intron_retention		chrX	+	chrX:1409403-1413220				chrX:1409402-1409403;chrX:1413220-1413221		4.87
K	intron_retention	CUFF.508	chr19	-	chr19:5894866-5896463				chr19:5894865-5894866;chr19:5896463-5896464		38.18
K	intron_retention		chr18	+	chr18:163454-178932				chr18:163453-163454;chr18:178932-178933		45.45
K	intron_retention		chr17	+	chr17:61574347-61574497				chr17:61574346-61574347;chr17:61574497-61574498		3.24
K	alternative_first_exon	CUFF.312	chr15	+	chr15:40780407-40800530	chr15:40800267-40800530	chr15:40780240-40780406	chr15:40800174-40800266			26.92
N	intron_retention		chr10	+	chr10:35437420-35464780				chr10:35437419-35437420;chr10:35464780-35464781		29.41
N	jcn_only_AA	CUFF.457	chr17	+	chr17:60783831-60803388;chr17:60783831-60813446	chr17:60783831-60784792		chr17:60784793-60803388;chr17:60803389-60813446	chr17:60803388-60803389;chr17:60813446-60813447		43.75
N	jcn_only_AD		chr22	+	chr22:37697061-37699294	chr22:37698073-37699294		chr22:37697061-37698072	chr22:37697060-37697061		70.97
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		99.06
N	jcn_only_AD		chr11	-	chr11:10821304-10821790	chr11:10821304-10821636		chr11:10821637-10821790	chr11:10821790-10821791		39.58
K	jcn_only_AD	CUFF.115,CUFF.118	chr10	-	chr10:74094376-74095591	chr10:74094376-74095537		chr10:74095538-74095591	chr10:74095591-74095592		85.71
N	jcn_only_AD	CUFF.531	chr19	+	chr19:17611442-17615263;chr19:17612229-17615263	chr19:17611686-17615263		chr19:17611442-17611685;chr19:17611686-17612228	chr19:17611441-17611442;chr19:17611685-17611686		39.44
N	intron_retention		chr16	+	chr16:3115496-3115781				chr16:3115495-3115496;chr16:3115781-3115782		45.07
K	alternative_first_exon	CUFF.224,CUFF.241	chr12	-	chr12:120221856-120222763	chr12:120221856-120221992	chr12:120222764-120222869	chr12:120221993-120222009			7.69
N	alternative_acceptor	CUFF.497	chr18	-	chr18:67563282-67613969	chr18:67611805-67613969		chr18:67563282-67611804	chr18:67563281-67563282		0.00
N	jcn_only_AD	CUFF.315	chr15	-	chr15:42300064-42305882	chr15:42300064-42302276		chr15:42302277-42305882	chr15:42305882-42305883	chr15:42299927-42300063;chr15:42305883-42305955	50.00
N	alternative_donor	CUFF.663	chr2	+	chr2:220094623-220094949;chr2:220094703-220094949	chr2:220094681-220094949		chr2:220094623-220094680;chr2:220094681-220094702	chr2:220094622-220094623;chr2:220094680-220094681		7.26
K	alternative_donor	CUFF.1097	chr9	-	chr9:125612102-125613378	chr9:125612102-125613359		chr9:125613360-125613378	chr9:125613378-125613379		74.07
N	intron_retention		chr17	+	chr17:61907310-61907492				chr17:61907309-61907310;chr17:61907492-61907493		61.80
N	alternative_acceptor	CUFF.701	chr21	-	chr21:43319457-43321730	chr21:43319472-43321730		chr21:43319457-43319471	chr21:43319456-43319457		40.00
K	intron_retention	CUFF.114	chr10	-	chr10:73892940-73912626				chr10:73892939-73892940;chr10:73912626-73912627		3.68
N	alternative_donor	CUFF.728	chr22	-	chr22:51018232-51018485	chr22:51018232-51018402		chr22:51018403-51018485	chr22:51018485-51018486		17.83
N	jcn_only_AA	CUFF.722	chr22	+	chr22:37697061-37697921;chr22:37697061-37699294	chr22:37697061-37697975		chr22:37697922-37697975;chr22:37697976-37699294	chr22:37697975-37697976;chr22:37699294-37699295		4.74
N	intron_retention		chr7	+	chr7:75045049-75045258				chr7:75045048-75045049;chr7:75045258-75045259		83.33
K	coord_cassette	CUFF.1096	chr9	+	chr9:125047567-125054027	chr9:125047567-125048058;chr9:125048226-125048317;chr9:125048446-125054027		chr9:125048059-125048225;chr9:125048318-125048445			39.34
N	intron_retention		chr17	-	chr17:1616199-1617149				chr17:1616198-1616199;chr17:1617149-1617150		77.54
N	cassette	CUFF.478	chr18	+	chr18:180340-196636	chr18:180340-192841;chr18:192901-196636		chr18:192842-192900			58.33
N	jcn_only_AA	CUFF.386	chr16	+	chr16:21737980-21739561	chr16:21737980-21738432		chr16:21738433-21739561	chr16:21739561-21739562		3.61
K	cassette	CUFF.468	chr17	-	chr17:79220862-79225292	chr17:79220862-79223869;chr17:79223894-79225292		chr17:79223870-79223893		chr17:79225293-79226483	41.18
K	alternative_first_exon	CUFF.755	chr3	+	chr3:51741184-51742863	chr3:51741671-51742863	chr3:51741086-51741183	chr3:51741364-51741670			85.25
N	alternative_acceptor	CUFF.557	chr19	+	chr19:50305399-50306205	chr19:50305399-50305790		chr19:50305791-50306205	chr19:50306205-50306206		29.63
K	jcn_only_AA	CUFF.501	chr18	+	chr18:77441518-77455224	chr18:77441518-77443042					24.18
K	mutually_exclusive	CUFF.1069	chr9	+	chr9:34989829-34990664,chr9:34990810-34993196	chr9:34989829-34990495,chr9:34990609-34993196	chr9:34990665-34990809	chr9:34990496-34990608			80.00
N	alternative_donor	CUFF.879	chr5	-	chr5:60214216-60217880	chr5:60214216-60214338		chr5:60214339-60217880	chr5:60217880-60217881		3.12
K	cassette	CUFF.71	chr1	-	chr1:202861788-202863311	chr1:202861788-202862366;chr1:202862554-202863311		chr1:202862367-202862553			53.85
N	alternative_acceptor	CUFF.929	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		40.15
K	alternative_last_exon	CUFF.1042	chr8	-	chr8:80915416-80954854	chr8:80950471-80954854	chr8:80915234-80915415	chr8:80947023-80950470			92.90
N	mutually_exclusive	CUFF.172	chr11	-	chr11:77885630-77897726,chr11:77897863-77899618	chr11:77885630-77888784,chr11:77889032-77899618	chr11:77897727-77897862	chr11:77888785-77889031			75.00
K	intron_retention	CUFF.53	chr1	-	chr1:156914990-156915836				chr1:156914989-156914990;chr1:156915836-156915837		21.21
K	alternative_donor	CUFF.1109	chr9	+	chr9:139794973-139802521	chr9:139795129-139802521		chr9:139794973-139795128	chr9:139794972-139794973		42.58
K	intron_retention	CUFF.550	chr19	+	chr19:44764156-44768466				chr19:44764155-44764156;chr19:44768466-44768467		43.18
K	intron_retention	CUFF.1102	chr9	+	chr9:133346903-133352257				chr9:133346902-133346903;chr9:133352257-133352258		17.74
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55895140-55912658;chr18:55833094-55912658;chr18:55865102-55912658;chr18:55895121-55912658;chr18:55862966-55912658	chr18:55888990-55912658		chr18:55833094-55862965;chr18:55862966-55865101;chr18:55865102-55888989;chr18:55888990-55895120;chr18:55895121-55895139	chr18:55833093-55833094;chr18:55862965-55862966;chr18:55865101-55865102;chr18:55888989-55888990;chr18:55895120-55895121		2.33
N	alternative_acceptor		chr17	+	chr17:61574347-61584416	chr17:61574347-61574497		chr17:61574498-61584416	chr17:61584416-61584417		88.57
N	coord_cassette	CUFF.572	chr2	-	chr2:253116-264781	chr2:253116-263210;chr2:263373-263563;chr2:263763-264781		chr2:263211-263372;chr2:263564-263762			20.69
K	cassette	CUFF.258	chr14	+	chr14:24459569-24473545;chr14:24459569-24470071	chr14:24459569-24464240;chr14:24464343-24473545,chr14:24464343-24470071		chr14:24464241-24464342			53.49
N	jcn_only_AD	CUFF.887,CUFF.902	chr5	-	chr5:127338515-127359826	chr5:127338515-127339335		chr5:127339336-127359826	chr5:127359826-127359827		31.34
K	cassette	CUFF.893	chr5	+	chr5:137520887-137521649	chr5:137520887-137521200;chr5:137521400-137521649		chr5:137521201-137521399			75.71
N	jcn_only_AD		chr15	+	chr15:24811360-24811802;chr15:24780954-24811802	chr15:24803469-24811802					29.41
N	jcn_only_AA		chr4	+	chr4:120449945-120471533	chr4:120449945-120464907					67.50
K	alternative_first_exon	CUFF.759	chr3	+	chr3:68055888-68466429	chr3:68300062-68466429	chr3:68055308-68055887	chr3:68299942-68300061			64.58
K	cassette	CUFF.1103	chr9	-	chr9:135742341-135750501	chr9:135742341-135749726;chr9:135749827-135750501		chr9:135749727-135749826			50.00
K	intron_retention	CUFF.951	chr6	+	chr6:145157075-145157436				chr6:145157074-145157075;chr6:145157436-145157437		14.00
N	jcn_only_AA	CUFF.352	chr15	-	chr15:90420657-90431752;chr15:90421533-90431752	chr15:90414779-90431752		chr15:90414779-90420656;chr15:90420657-90421532	chr15:90414778-90414779;chr15:90420656-90420657		55.29
K	intron_retention	CUFF.382	chr16	+	chr16:14020614-14021978				chr16:14020613-14020614;chr16:14021978-14021979		62.12
K	intron_retention	CUFF.1092	chr9	-	chr9:123555536-123555631				chr9:123555535-123555536;chr9:123555631-123555632		21.05
N	jcn_only_AA	CUFF.685	chr20	-	chr20:31097744-31099149;chr20:31074605-31099149	chr20:31062546-31099149					61.54
K	intron_retention	CUFF.618	chr2	-	chr2:86398469-86400772				chr2:86398468-86398469;chr2:86400772-86400773		36.67
K	alternative_first_exon	CUFF.286	chr14	-	chr14:81864925-81893445	chr14:81864925-81884506	chr14:81893446-81893556	chr14:81884507-81884595		chr14:81864639-81864924	14.81
K	intron_retention	CUFF.741	chr3	-	chr3:33450290-33450727				chr3:33450289-33450290;chr3:33450727-33450728		87.27
K	jcn_only_AD	CUFF.703	chr21	-	chr21:47556409-47556898;chr21:47556409-47556828	chr21:47556409-47556892		chr21:47556829-47556892;chr21:47556893-47556898	chr21:47556892-47556893;chr21:47556898-47556899		9.09
N	cassette	CUFF.743	chr3	-	chr3:33602464-33612218	chr3:33602464-33612181;chr3:33612185-33612218		chr3:33612182-33612184			81.08
K	alternative_first_exon	CUFF.782	chr3	-	chr3:125787090-125789043,chr3:125787090-125791995,chr3:125787090-125802718;chr3:125787090-125802771;chr3:125787090-125802935,chr3:125787090-125802896	chr3:125787090-125797816	chr3:125802772-125802870;chr3:125802936-125803219	chr3:125797817-125797915			25.87
N	intron_retention		chr16	-	chr16:23505700-23507034				chr16:23505699-23505700;chr16:23507034-23507035	chr16:23505624-23505699;chr16:23507035-23507099	36.84
K	jcn_only_AD	CUFF.505	chr19	-	chr19:2427323-2427456	chr19:2427323-2427411		chr19:2427412-2427456	chr19:2427456-2427457		18.52
N	intron_retention		chr19	+	chr19:17597767-17597982				chr19:17597766-17597767;chr19:17597982-17597983		85.71
K	cassette	CUFF.342	chr15	-	chr15:78500445-78537610	chr15:78500445-78501486;chr15:78501592-78537610		chr15:78501487-78501591			83.33
K	alternative_last_exon	CUFF.342	chr15	-	chr15:78471174-78471891	chr15:78471323-78471891	chr15:78470956-78471173	chr15:78471225-78471322			23.68
K	intron_retention	CUFF.54	chr1	-	chr1:158464345-158464444				chr1:158464344-158464345;chr1:158464444-158464445		12.20
K	coord_cassette	CUFF.904	chr5	-	chr5:178032384-178039416	chr5:178032384-178032825;chr5:178032867-178035376;chr5:178035460-178039416		chr5:178032826-178032866;chr5:178035377-178035459			9.38
K	intron_retention	CUFF.316	chr15	-	chr15:44912602-44913956				chr15:44912601-44912602;chr15:44913956-44913957		33.33
N	mutually_exclusive	CUFF.209	chr12	-	chr12:22643153-22659644,chr12:22659754-22666227	chr12:22643153-22646156,chr12:22646272-22666227	chr12:22659645-22659753	chr12:22646157-22646271			7.58
K	jcn_only_AD	CUFF.954	chr6	+	chr6:161514872-161518111	chr6:161514884-161518111		chr6:161514872-161514883	chr6:161514871-161514872	chr6:161518112-161518208;chr6:161514805-161514871	91.53
N	alternative_first_exon	CUFF.755	chr3	+	chr3:51741184-51749077;chr3:51747327-51749077	chr3:51748138-51749077	chr3:51741086-51741183;chr3:51746489-51747326	chr3:51747980-51748137			88.22
K	alternative_first_exon	CUFF.1018,CUFF.998	chr7	-	chr7:156629580-156685621	chr7:156629580-156685163	chr7:156685622-156686004	chr7:156685164-156685270			10.37
K	alternative_first_exon	CUFF.1143	chrX	+	chrX:134193765-134254454	chrX:134250853-134254454	chrX:134193715-134193764	chrX:134250683-134250852			18.60
K	cassette	CUFF.595	chr2	+	chr2:33540337-33572433	chr2:33540337-33567904;chr2:33568031-33572433		chr2:33567905-33568030			13.44
K	intron_retention	CUFF.121	chr10	-	chr10:80721165-80721655				chr10:80721164-80721165;chr10:80721655-80721656		25.00
N	alternative_donor	CUFF.276	chr14	-	chr14:71227900-71249939;chr14:71227900-71267383	chr14:71227900-71232158		chr14:71232159-71249939;chr14:71249940-71267383	chr14:71249939-71249940;chr14:71267383-71267384		0.00
K	alternative_donor	CUFF.390,CUFF.406	chr16	-	chr16:70254784-70255156	chr16:70254784-70255152		chr16:70255153-70255156	chr16:70255156-70255157		33.33
K	jcn_only_AD	CUFF.354	chr15	+	chr15:91290721-91292596	chr15:91290892-91292596		chr15:91290721-91290891	chr15:91290720-91290721		77.14
K	alternative_donor	CUFF.1124	chrX	+	chrX:47039437-47039610	chrX:47039440-47039610		chrX:47039437-47039439	chrX:47039436-47039437		13.51
N	cassette	CUFF.217	chr12	-	chr12:48392215-48398019	chr12:48392215-48393701;chr12:48393909-48398019		chr12:48393702-48393908			85.71
N	jcn_only_AD	CUFF.322,CUFF.352	chr15	-	chr15:90432373-90437112	chr15:90432373-90437108		chr15:90437109-90437112	chr15:90437112-90437113		5.88
K	alternative_first_exon	CUFF.890	chr5	+	chr5:131630703-131647853	chr5:131631315-131647853	chr5:131630136-131630702	chr5:131631031-131631314			92.16
N	jcn_only_AD	CUFF.686	chr20	+	chr20:33114149-33122431	chr20:33118039-33122431		chr20:33114149-33118038	chr20:33114148-33114149		15.00
K	cassette	CUFF.195	chr12	-	chr12:332401-333157	chr12:332401-332911;chr12:333012-333157		chr12:332912-333011			18.87
N	alternative_donor	CUFF.86	chr10	-	chr10:410523-412214	chr10:410523-410754		chr10:410755-412214	chr10:412214-412215		25.00
N	intron_retention		chr9	-	chr9:130941184-130941522				chr9:130941183-130941184;chr9:130941522-130941523		92.14
N	jcn_only_AA		chr14	-	chr14:104225643-104245081;chr14:104224089-104245081	chr14:104230817-104245081					6.98
N	jcn_only_AD	CUFF.329	chr15	+	chr15:63128273-63131054	chr15:63128318-63131054		chr15:63128273-63128317	chr15:63128272-63128273		21.05
K	intron_retention		chr16	-	chr16:4445341-4455491				chr16:4445340-4445341;chr16:4455491-4455492		14.34
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		4.65
N	mutually_exclusive	CUFF.18	chr1	+	chr1:32541424-32542764,chr1:32542920-32557275	chr1:32541424-32542363,chr1:32542448-32557275	chr1:32542765-32542919	chr1:32542364-32542447			26.32
N	jcn_only_AA	CUFF.332	chr15	-	chr15:66645294-66678987	chr15:66672279-66678987		chr15:66645294-66672278	chr15:66645293-66645294		35.71
K	cassette	CUFF.1001	chr7	+	chr7:107253878-107258772	chr7:107253878-107254098;chr7:107254178-107258772		chr7:107254099-107254177			93.64
N	cassette	CUFF.471	chr17	-	chr17:79354385-79358928;chr17:79355741-79358928	chr17:79355741-79358745,chr17:79354385-79358745;chr17:79358833-79358928		chr17:79358746-79358832			73.01
K	alternative_first_exon	CUFF.750,CUFF.784	chr3	-	chr3:45721564-45730511	chr3:45721564-45729867	chr3:45730512-45730720	chr3:45729868-45730374			79.66
K	jcn_only_AA	CUFF.546	chr19	-	chr19:41533165-41533447	chr19:41533170-41533447		chr19:41533165-41533169	chr19:41533164-41533165		16.67
K	alternative_acceptor	CUFF.20	chr1	-	chr1:33647023-33647594	chr1:33647096-33647594		chr1:33647023-33647095	chr1:33647022-33647023		60.00
K	mutually_exclusive	CUFF.132	chr10	-	chr10:123629554-123661905,chr10:123662136-123670420	chr10:123629554-123659380,chr10:123659510-123670420	chr10:123661906-123662135	chr10:123659381-123659509			10.34
K	cassette	CUFF.306	chr15	+	chr15:29385424-29390692	chr15:29385424-29386480;chr15:29386517-29390692		chr15:29386481-29386516			5.43
N	jcn_only_AA	CUFF.390	chr16	-	chr16:23504843-23505623;chr16:23504909-23505623	chr16:23504780-23505623		chr16:23504780-23504842;chr16:23504843-23504908	chr16:23504779-23504780;chr16:23504842-23504843	chr16:23505624-23505699;chr16:23504681-23504779	16.34
N	jcn_only_AD	CUFF.821,CUFF.833	chr4	-	chr4:69057035-69071752	chr4:69057035-69057124		chr4:69057125-69071752	chr4:69071752-69071753		23.33
N	alternative_donor		chr7	+	chr7:150831656-150838984	chr7:150837204-150838984		chr7:150831656-150837203	chr7:150831655-150831656		17.65
N	jcn_only_AD	CUFF.310	chr15	+	chr15:40532297-40532799;chr15:40509869-40532799;chr15:40531337-40532799	chr15:40532004-40532799		chr15:40509869-40531336;chr15:40531337-40532003;chr15:40532004-40532296	chr15:40509868-40509869;chr15:40531336-40531337;chr15:40532003-40532004		13.04
K	coord_cassette	CUFF.900	chr5	-	chr5:149782876-149785821	chr5:149782876-149784242;chr5:149784331-149784647;chr5:149784744-149785821		chr5:149784243-149784330;chr5:149784648-149784743			59.49
N	jcn_only_AA		chr11	+	chr11:827712-828259	chr11:827712-828229		chr11:828230-828259	chr11:828259-828260	chr11:828260-828772	62.50
N	intron_retention		chr16	+	chr16:3115689-3115784				chr16:3115688-3115689;chr16:3115784-3115785		29.14
N	jcn_only_AD	CUFF.1018,CUFF.998	chr7	-	chr7:102251590-102256969;chr7:102251590-102257071	chr7:102251590-102252518		chr7:102252519-102256969;chr7:102256970-102257071	chr7:102256969-102256970;chr7:102257071-102257072		42.86
N	jcn_only_AA	CUFF.1062	chr8	+	chr8:144375236-144377909	chr8:144375236-144377548		chr8:144377549-144377909	chr8:144377909-144377910		0.81
N	jcn_only_AD	CUFF.506	chr19	+	chr19:4306039-4306194	chr19:4306067-4306194		chr19:4306039-4306066	chr19:4306038-4306039		2.96
N	alternative_acceptor	CUFF.929	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		2.55
N	jcn_only_AA	CUFF.276	chr14	-	chr14:71200060-71201102	chr14:71200516-71201102		chr14:71200060-71200515	chr14:71200059-71200060		78.02
N	cassette	CUFF.829	chr4	-	chr4:56471517-56473603;chr4:56466743-56473603	chr4:56466743-56473464,chr4:56471517-56473464;chr4:56473516-56473603		chr4:56473465-56473515			75.00
N	cassette	CUFF.709	chr22	-	chr22:21830450-21832078	chr22:21830450-21830932;chr22:21831054-21832078		chr22:21830933-21831053			89.19
K	cassette	CUFF.402	chr16	-	chr16:67218508-67218804	chr16:67218508-67218588;chr16:67218714-67218804		chr16:67218589-67218713			90.32
N	intron_retention		chr2	+	chr2:220095128-220096981				chr2:220095127-220095128;chr2:220096981-220096982		53.57
N	jcn_only_AA	CUFF.167	chr11	+	chr11:67790230-67793476	chr11:67790230-67791675		chr11:67791676-67793476	chr11:67793476-67793477		3.60
K	cassette	CUFF.371	chr16	+	chr16:2200053-2201569	chr16:2200053-2201130;chr16:2201317-2201569		chr16:2201131-2201316			23.33
K	jcn_only_AA	CUFF.675	chr20	+	chr20:2842351-2843710	chr20:2842351-2842450					56.67
K	intron_retention	CUFF.310	chr15	+	chr15:40558697-40559123				chr15:40558696-40558697;chr15:40559123-40559124		31.25
N	jcn_only_AD		chr3	-	chr3:156262229-156266593;chr3:156262229-156266654	chr3:156262229-156266693		chr3:156266594-156266654;chr3:156266655-156266693	chr3:156266654-156266655;chr3:156266693-156266694		95.92
N	intron_retention		chr21	-	chr21:15984967-15985196				chr21:15984966-15984967;chr21:15985196-15985197		70.27
K	alternative_last_exon	CUFF.1115	chrX	-	chrX:13791150-13794356	chrX:13792744-13794356	chrX:13789062-13791149	chrX:13791979-13792743			85.00
K	intron_retention	CUFF.265	chr14	+	chr14:50241397-50244556				chr14:50241396-50241397;chr14:50244556-50244557		62.99
K	intron_retention	CUFF.475	chr17	-	chr17:79994520-79994596				chr17:79994519-79994520;chr17:79994596-79994597		6.75
K	intron_retention	CUFF.720	chr22	-	chr22:30736371-30736683				chr22:30736370-30736371;chr22:30736683-30736684		30.51
K	intron_retention	CUFF.1033	chr8	-	chr8:56668971-56685827				chr8:56668970-56668971;chr8:56685827-56685828		48.98
K	intron_retention	CUFF.2	chr1	+	chr1:2087532-2100956				chr1:2087531-2087532;chr1:2100956-2100957		20.12
K	coord_cassette	CUFF.1103	chr9	-	chr9:135742341-135753558	chr9:135742341-135749726;chr9:135749827-135750501;chr9:135750587-135753558		chr9:135749727-135749826;chr9:135750502-135750586			3.91
K	jcn_only_AD	CUFF.18	chr1	+	chr1:32538653-32540551	chr1:32538700-32540551		chr1:32538653-32538699	chr1:32538652-32538653		8.64
K	alternative_acceptor	CUFF.643	chr2	-	chr2:169783801-169787174	chr2:169783873-169787174		chr2:169783801-169783872	chr2:169783800-169783801	chr2:169787175-169787372;chr2:169783666-169783800	83.33
K	alternative_first_exon	CUFF.786	chr3	-	chr3:127299007-127306912,chr3:127299007-127310732;chr3:127299007-127313642;chr3:127299007-127309252	chr3:127299007-127309725	chr3:127313643-127313776;chr3:127309253-127309667	chr3:127309726-127309965			16.77
K	alternative_first_exon	CUFF.284	chr14	-	chr14:77275987-77276431;chr14:77275987-77278647	chr14:77275987-77280649	chr14:77276432-77276597;chr14:77278648-77278744	chr14:77280650-77280764			31.17
K	alternative_donor	CUFF.473	chr17	-	chr17:79894738-79895137;chr17:79894738-79895133	chr17:79894738-79895055		chr17:79895056-79895133;chr17:79895134-79895137	chr17:79895133-79895134;chr17:79895137-79895138	chr17:79894624-79894737;chr17:79895138-79895264	17.58
N	cassette	CUFF.416	chr17	-	chr17:651273-655372	chr17:651273-653053;chr17:653150-655372		chr17:653054-653149			90.15
N	coord_cassette	CUFF.136	chr11	-	chr11:408894-414822	chr11:408894-409216;chr11:409309-409867;chr11:410028-414822		chr11:409217-409308;chr11:409868-410027			97.29
K	intron_retention		chr16	-	chr16:4445341-4466459				chr16:4445340-4445341;chr16:4466459-4466460		10.42
N	alternative_acceptor	CUFF.755,CUFF.762	chr3	+	chr3:75500554-75505767	chr3:75500554-75501682		chr3:75501683-75505767	chr3:75505767-75505768		5.41
K	intron_retention	CUFF.1115	chrX	-	chrX:13835315-13835376				chrX:13835314-13835315;chrX:13835376-13835377		16.39
N	alternative_first_exon	CUFF.188	chr11	-	chr11:119244232-119249716;chr11:119244232-119252182	chr11:119244232-119246933	chr11:119249717-119249914;chr11:119252183-119252421	chr11:119246934-119247108			42.68
K	intron_retention		chr11	-	chr11:8496614-8502080				chr11:8496613-8496614;chr11:8502080-8502081		1.54
N	jcn_only_AA		chr14	+	chr14:76241974-76243089	chr14:76241974-76243047					54.55
K	alternative_acceptor	CUFF.812	chr4	-	chr4:2934418-2934832	chr4:2934486-2934832		chr4:2934418-2934485	chr4:2934417-2934418		98.02
N	alternative_donor	CUFF.2	chr1	+	chr1:2106753-2116021	chr1:2113354-2116021		chr1:2106753-2113353	chr1:2106752-2106753		0.00
K	jcn_only_AA	CUFF.180	chr11	+	chr11:117070149-117073717	chr11:117070149-117070348					85.06
N	jcn_only_AA	CUFF.777	chr3	+	chr3:122864440-122864964	chr3:122864440-122864945		chr3:122864946-122864964	chr3:122864964-122864965		64.86
N	jcn_only_AD	CUFF.578	chr2	+	chr2:1263214-1271136	chr2:1266722-1271136		chr2:1263214-1266721	chr2:1263213-1263214		55.26
K	cassette	CUFF.741	chr3	-	chr3:33454320-33458249	chr3:33454320-33457497;chr3:33457593-33458249		chr3:33457498-33457592			88.81
N	jcn_only_AD	CUFF.271	chr14	-	chr14:59946070-59950397;chr14:59946070-59950526	chr14:59946070-59950207		chr14:59950208-59950397;chr14:59950398-59950526	chr14:59950397-59950398;chr14:59950526-59950527		9.33
K	intron_retention	CUFF.1018	chr7	-	chr7:156471045-156471770				chr7:156471044-156471045;chr7:156471770-156471771		35.00
N	jcn_only_AD		chr7	+	chr7:54617864-54636823	chr7:54621767-54636823		chr7:54617864-54621766	chr7:54617863-54617864		19.23
N	intron_retention		chr7	+	chr7:107204655-107205032				chr7:107204654-107204655;chr7:107205032-107205033		60.00
N	intron_retention		chr16	+	chr16:3115689-3115781				chr16:3115688-3115689;chr16:3115781-3115782		83.61
K	intron_retention		chr2	-	chr2:242447551-242447857				chr2:242447550-242447551;chr2:242447857-242447858		32.00
K	alternative_first_exon	CUFF.1054	chr8	+	chr8:118541049-118552121	chr8:118543067-118552121	chr8:118540890-118541048	chr8:118542531-118543066			74.74
K	intron_retention	CUFF.862	chr5	-	chr5:2746901-2747654				chr5:2746900-2746901;chr5:2747654-2747655		25.00
N	alternative_donor	CUFF.652	chr2	-	chr2:197298183-197458231	chr2:197298183-197357967		chr2:197357968-197458231	chr2:197458231-197458232		0.00
K	alternative_first_exon	CUFF.1073	chr9	+	chr9:43907538-43908435	chr9:43908211-43908435	chr9:43907404-43907537	chr9:43907580-43908210			87.50
N	coord_cassette	CUFF.436	chr17	+	chr17:29576138-29585361	chr17:29576138-29579955;chr17:29580019-29584704;chr17:29584745-29585361		chr17:29579956-29580018;chr17:29584705-29584744			81.48
N	alternative_donor	CUFF.595	chr2	+	chr2:33487889-33488360	chr2:33487892-33488360		chr2:33487889-33487891	chr2:33487888-33487889		5.31
K	cassette	CUFF.24	chr1	+	chr1:54360221-54370338	chr1:54360221-54368729;chr1:54368940-54370338		chr1:54368730-54368939			26.57
N	jcn_only_AA		chr17	+	chr17:60783831-60784792;chr17:60783831-60813446	chr17:60783831-60803388		chr17:60784793-60803388;chr17:60803389-60813446	chr17:60803388-60803389;chr17:60813446-60813447		11.76
K	jcn_only_AA	CUFF.1113	chrX	-	chrX:9050777-9130837	chrX:9130355-9130837					50.00
N	jcn_only_AA	CUFF.1066	chr9	-	chr9:15250009-15267911;chr9:15226011-15267911	chr9:15211396-15267911					1.01
N	intron_retention		chr16	-	chr16:4463406-4466785				chr16:4463405-4463406;chr16:4466785-4466786		93.02
N	jcn_only_AA	CUFF.56	chr1	+	chr1:160151822-160156065	chr1:160151822-160152481		chr1:160152482-160156065	chr1:160156065-160156066		6.45
K	alternative_first_exon	CUFF.1052	chr8	+	chr8:107593480-107691437;chr8:107670314-107691437;chr8:107630412-107691437	chr8:107531368-107691437	chr8:107593125-107593479;chr8:107670221-107670313;chr8:107630316-107630411	chr8:107531171-107531367			12.16
K	coord_cassette	CUFF.132	chr10	-	chr10:123673409-123687358	chr10:123673409-123681863;chr10:123681927-123683780;chr10:123683845-123687358		chr10:123681864-123681926;chr10:123683781-123683844			89.01
N	cassette	CUFF.683	chr20	+	chr20:30154099-30156922	chr20:30154099-30155880;chr20:30156084-30156922		chr20:30155881-30156083			28.65
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		62.90
K	cassette	CUFF.743	chr3	-	chr3:33552257-33557514	chr3:33552257-33556071;chr3:33556172-33557514		chr3:33556072-33556171			8.97
N	jcn_only_AD	CUFF.138	chr11	+	chr11:828964-829359	chr11:829184-829359		chr11:828964-829183	chr11:828963-828964	chr11:829360-829540;chr11:828852-828963	77.05
N	alternative_acceptor	CUFF.823	chr4	+	chr4:20570628-20591266	chr4:20570628-20574856		chr4:20574857-20591266	chr4:20591266-20591267		0.00
K	cassette	CUFF.211	chr12	-	chr12:25699489-25702259	chr12:25699489-25700158;chr12:25700286-25702259		chr12:25700159-25700285			36.00
N	jcn_only_AD		chr14	+	chr14:76187047-76198680	chr14:76198577-76198680					28.26
K	cassette	CUFF.410	chr16	-	chr16:75576582-75579723	chr16:75576582-75579249;chr16:75579394-75579723		chr16:75579250-75579393			37.59
N	jcn_only_AD	CUFF.323	chr15	+	chr15:55700985-55710420	chr15:55709958-55710420		chr15:55700985-55709957	chr15:55700984-55700985		30.51
K	intron_retention	CUFF.743	chr3	-	chr3:33612185-33612218				chr3:33612184-33612185;chr3:33612218-33612219		74.79
N	jcn_only_AA	CUFF.350	chr15	-	chr15:84871773-84872928;chr15:84872839-84872928	chr15:84871760-84872928		chr15:84871760-84871772;chr15:84871773-84872838	chr15:84871759-84871760;chr15:84871772-84871773		16.13
K	intron_retention		chr6	-	chr6:31938925-31939096				chr6:31938924-31938925;chr6:31939096-31939097		47.13
K	cassette	CUFF.133	chr10	+	chr10:124186548-124189139	chr10:124186548-124187791;chr10:124187937-124189139		chr10:124187792-124187936			98.09
K	cassette	CUFF.349	chr15	-	chr15:83687606-83698887	chr15:83687606-83689426;chr15:83689515-83698887		chr15:83689427-83689514			97.87
N	jcn_only_AA	CUFF.1117	chrX	+	chrX:15706982-15711085	chrX:15706982-15709260		chrX:15709261-15711085	chrX:15711085-15711086		10.34
N	intron_retention	CUFF.24	chr1	+	chr1:54360029-54360111				chr1:54360028-54360029;chr1:54360111-54360112		93.57
N	alternative_donor	CUFF.56	chr1	+	chr1:160146353-160147308	chr1:160146393-160147308		chr1:160146353-160146392	chr1:160146352-160146353		44.83
N	coord_cassette	CUFF.278	chr14	-	chr14:75143456-75151156	chr14:75143456-75144881;chr14:75145033-75149998;chr14:75150237-75151156		chr14:75144882-75145032;chr14:75149999-75150236		chr14:75143286-75143455;chr14:75151157-75151383	50.00
N	jcn_only_AA	CUFF.426	chr17	-	chr17:15584268-15586167	chr17:15584537-15586167		chr17:15584268-15584536	chr17:15584267-15584268		11.36
N	jcn_only_AD	CUFF.310	chr15	+	chr15:40532297-40532799;chr15:40532004-40532799;chr15:40531337-40532799	chr15:40509869-40532799		chr15:40509869-40531336;chr15:40531337-40532003;chr15:40532004-40532296	chr15:40509868-40509869;chr15:40531336-40531337;chr15:40532003-40532004		8.70
N	alternative_donor	CUFF.769	chr3	+	chr3:119187954-119188666;chr3:119187854-119188666	chr3:119188106-119188666		chr3:119187854-119187953;chr3:119187954-119188105	chr3:119187853-119187854;chr3:119187953-119187954		42.00
N	cassette	CUFF.1110	chrX	+	chrX:1414350-1422815	chrX:1414350-1419383;chrX:1419520-1422815		chrX:1419384-1419519			93.58
K	mutually_exclusive	CUFF.995	chr7	-	chr7:99032892-99057708,chr7:99057817-99063751	chr7:99032892-99045574,chr7:99045812-99063751	chr7:99057709-99057816	chr7:99045575-99045811			75.00
N	cassette	CUFF.476	chr17	+	chr17:80426773-80436675;chr17:80430575-80436675	chr17:80430575-80436446,chr17:80426773-80436446;chr17:80436544-80436675		chr17:80436447-80436543			44.05
N	jcn_only_AD	CUFF.457	chr17	+	chr17:61568730-61571282;chr17:61571021-61571282	chr17:61567390-61571282		chr17:61567390-61568729;chr17:61568730-61571020	chr17:61567389-61567390;chr17:61568729-61568730		1.08
N	alternative_donor	CUFF.390	chr16	-	chr16:23505700-23507009;chr16:23505700-23507014	chr16:23505700-23507034		chr16:23507010-23507014;chr16:23507015-23507034	chr16:23507014-23507015;chr16:23507034-23507035	chr16:23505624-23505699;chr16:23507035-23507099	5.43
K	alternative_first_exon	CUFF.651	chr2	+	chr2:191302288-191334483;chr2:191307732-191334483	chr2:191334376-191334483	chr2:191300703-191302287;chr2:191307225-191307731	chr2:191334148-191334375			52.14
N	cassette	CUFF.683	chr20	+	chr20:30132839-30137866	chr20:30132839-30136831;chr20:30136918-30137866		chr20:30136832-30136917		chr20:30132750-30132838;chr20:30137867-30137965	87.35
K	cassette	CUFF.646	chr2	-	chr2:175216454-175243650	chr2:175216454-175234714;chr2:175234743-175243650		chr2:175234715-175234742			33.33
K	alternative_last_exon	CUFF.997	chr7	-	chr7:100818093-100823322	chr7:100822418-100823322	chr7:100816903-100818092	chr7:100822378-100822417			15.00
N	jcn_only_AD	CUFF.951	chr6	+	chr6:144904737-144999541;chr6:144981412-144999541	chr6:144898425-144999541		chr6:144898425-144904736;chr6:144904737-144981411	chr6:144898424-144898425;chr6:144904736-144904737		26.32
N	alternative_acceptor	CUFF.1070	chr9	-	chr9:35077397-35078601	chr9:35078341-35078601		chr9:35077397-35078340	chr9:35077396-35077397		46.67
N	alternative_first_exon		chr9	-	chr9:125652825-125667388	chr9:125652825-125655187	chr9:125667389-125667652	chr9:125655188-125655305			62.22
N	cassette	CUFF.1007	chr7	-	chr7:117385985-117396608	chr7:117385985-117386066;chr7:117386154-117396608		chr7:117386067-117386153			5.52
K	intron_retention	CUFF.576	chr2	-	chr2:675631-675757				chr2:675630-675631;chr2:675757-675758		58.75
N	alternative_acceptor	CUFF.765	chr3	-	chr3:107572902-107573976;chr3:107573542-107573976	chr3:107572807-107573976		chr3:107572807-107572901;chr3:107572902-107573541	chr3:107572806-107572807;chr3:107572901-107572902		15.22
N	alternative_donor	CUFF.979	chr7	+	chr7:65579902-65592690;chr7:65579958-65592690	chr7:65591631-65592690		chr7:65579902-65579957;chr7:65579958-65591630	chr7:65579901-65579902;chr7:65579957-65579958		0.00
N	cassette	CUFF.201	chr12	+	chr12:4653078-4657257;chr12:4653071-4657257	chr12:4653078-4655474,chr12:4653071-4655474;chr12:4655585-4657257		chr12:4655475-4655584			57.36
N	jcn_only_AD	CUFF.579	chr2	+	chr2:3405665-3425651	chr2:3425558-3425651		chr2:3405665-3425557	chr2:3405664-3405665		33.80
K	intron_retention	CUFF.6	chr1	-	chr1:11709932-11710001				chr1:11709931-11709932;chr1:11710001-11710002		16.67
K	mutually_exclusive	CUFF.618	chr2	-	chr2:86393768-86398330,chr2:86398469-86400772	chr2:86393768-86397871,chr2:86397965-86400772	chr2:86398331-86398468	chr2:86397872-86397964			90.00
K	intron_retention	CUFF.472	chr17	-	chr17:79478135-79478213				chr17:79478134-79478135;chr17:79478213-79478214		31.88
K	jcn_only_AA	CUFF.969	chr7	+	chr7:30791921-30793349	chr7:30791921-30793346		chr7:30793347-30793349	chr7:30793349-30793350		57.14
N	intron_retention		chr14	-	chr14:104206401-104313878				chr14:104206400-104206401;chr14:104313878-104313879		49.02
N	alternative_last_exon		chr16	+	chr16:19586445-19589625;chr16:19586445-19592846	chr16:19586445-19590373	chr16:19592847-19592975	chr16:19590374-19590451			28.57
N	jcn_only_AD		chr17	-	chr17:1616199-1617149	chr17:1616199-1616996		chr17:1616997-1617149	chr17:1617149-1617150		36.44
N	jcn_only_AD	CUFF.758	chr3	-	chr3:57582951-57583365	chr3:57582951-57583058		chr3:57583059-57583365	chr3:57583365-57583366		45.83
N	jcn_only_AD		chr2	-	chr2:177042550-177042742	chr2:177042550-177042730		chr2:177042731-177042742	chr2:177042742-177042743		41.67
N	alternative_acceptor		chr14	+	chr14:76286505-76330009	chr14:76286505-76286945		chr14:76286946-76330009	chr14:76330009-76330010		29.41
N	alternative_acceptor	CUFF.874	chr5	+	chr5:52161652-52177704	chr5:52161652-52162871		chr5:52162872-52177704	chr5:52177704-52177705		0.00
K	alternative_last_exon	CUFF.492	chr18	-	chr18:61060783-61064266	chr18:61060800-61064266	chr18:61060642-61060782	chr18:61060784-61060799		chr18:61064267-61064486	22.92
N	alternative_acceptor		chr14	+	chr14:61512886-61514868;chr14:61512886-61514965	chr14:61512886-61517229		chr14:61514869-61514965;chr14:61514966-61517229	chr14:61514965-61514966;chr14:61517229-61517230		100.00
N	jcn_only_AA	CUFF.396	chr16	-	chr16:57509870-57513353	chr16:57512575-57513353		chr16:57509870-57512574	chr16:57509869-57509870		10.97
K	alternative_acceptor	CUFF.546	chr19	-	chr19:41533165-41533447	chr19:41533170-41533447		chr19:41533165-41533169	chr19:41533164-41533165		9.09
N	jcn_only_AD	CUFF.611	chr2	-	chr2:73198815-73215386	chr2:73198815-73208137		chr2:73208138-73215386	chr2:73215386-73215387		42.00
K	intron_retention	CUFF.59	chr1	-	chr1:161953196-161953385				chr1:161953195-161953196;chr1:161953385-161953386		82.19
K	intron_retention	CUFF.593	chr2	+	chr2:27729447-27729654				chr2:27729446-27729447;chr2:27729654-27729655		11.36
K	jcn_only_AA	CUFF.1037,CUFF.1061	chr8	+	chr8:144349655-144356873	chr8:144349655-144351529					61.90
K	jcn_only_AD	CUFF.500	chr18	-	chr18:76737430-76738785	chr18:76737430-76738462		chr18:76738463-76738785	chr18:76738785-76738786		32.79
N	alternative_donor		chr17	-	chr17:1616350-1617149	chr17:1616350-1616996		chr17:1616997-1617149	chr17:1617149-1617150		80.55
N	alternative_acceptor	CUFF.472	chr17	-	chr17:79479142-79479257	chr17:79479169-79479257		chr17:79479142-79479168	chr17:79479141-79479142		91.35
K	cassette	CUFF.1138	chrX	+	chrX:114536689-114540769	chrX:114536689-114537864;chrX:114537984-114540769		chrX:114537865-114537983			23.81
K	intron_retention	CUFF.548	chr19	-	chr19:42734544-42734830				chr19:42734543-42734544;chr19:42734830-42734831		69.77
N	intron_retention		chr15	+	chr15:77713177-77750795				chr15:77713176-77713177;chr15:77750795-77750796		16.67
K	alternative_last_exon	CUFF.524	chr19	-	chr19:14877922-14883153;chr19:14879747-14883153	chr19:14876383-14883153	chr19:14877790-14877921;chr19:14879520-14879746	chr19:14876336-14876382			3.63
N	intron_retention		chr14	+	chr14:76156666-76165530				chr14:76156665-76156666;chr14:76165530-76165531		48.15
N	jcn_only_AD	CUFF.374	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		35.53
N	alternative_acceptor		chr11	+	chr11:827712-828259	chr11:827712-828229		chr11:828230-828259	chr11:828259-828260	chr11:828260-828772	75.00
K	intron_retention	CUFF.314	chr15	+	chr15:41222881-41223700				chr15:41222880-41222881;chr15:41223700-41223701		55.56
K	cassette	CUFF.936	chr6	+	chr6:90337416-90338830	chr6:90337416-90337965;chr6:90338061-90338830		chr6:90337966-90338060			25.93
K	alternative_first_exon	CUFF.4	chr1	+	chr1:11072486-11073772	chr1:11072801-11073772	chr1:11072324-11072485	chr1:11072646-11072800			56.41
N	intron_retention		chr19	+	chr19:17449381-17449989				chr19:17449380-17449381;chr19:17449989-17449990		84.62
K	coord_cassette	CUFF.107	chr10	+	chr10:48216059-48221504	chr10:48216059-48216427;chr10:48216497-48218794;chr10:48218864-48221504		chr10:48216428-48216496;chr10:48218795-48218863			50.00
K	intron_retention	CUFF.1014	chr7	+	chr7:148982588-148984655				chr7:148982587-148982588;chr7:148984655-148984656		18.75
K	cassette	CUFF.939	chr6	+	chr6:111306342-111312949	chr6:111306342-111310230;chr6:111310269-111312949		chr6:111310231-111310268			77.50
N	jcn_only_AA		chr19	-	chr19:33984244-34001933	chr19:33991908-34001933					52.78
K	alternative_first_exon	CUFF.245	chr13	-	chr13:24334357-24380088	chr13:24334357-24334671	chr13:24380089-24380208	chr13:24334672-24334791			84.78
K	intron_retention	CUFF.705	chr22	+	chr22:19420131-19420787				chr22:19420130-19420131;chr22:19420787-19420788		80.77
K	alternative_last_exon	CUFF.391	chr16	-	chr16:25097094-25114671;chr16:25112007-25114671	chr16:25098045-25114671	chr16:25096913-25097093;chr16:25111790-25112006	chr16:25097561-25098044			36.36
N	alternative_donor	CUFF.490	chr18	+	chr18:55895140-55912658;chr18:55833094-55912658;chr18:55895121-55912658;chr18:55862966-55912658;chr18:55888990-55912658	chr18:55865102-55912658		chr18:55833094-55862965;chr18:55862966-55865101;chr18:55865102-55888989;chr18:55888990-55895120;chr18:55895121-55895139	chr18:55833093-55833094;chr18:55862965-55862966;chr18:55865101-55865102;chr18:55888989-55888990;chr18:55895120-55895121		0.00
N	alternative_acceptor	CUFF.472	chr17	-	chr17:79478653-79478928	chr17:79478830-79478928		chr17:79478653-79478829	chr17:79478652-79478653		4.40
N	jcn_only_AD	CUFF.432	chr17	+	chr17:25969375-25974055	chr17:25973615-25974055					97.44
N	jcn_only_AA		chr14	-	chr14:59939809-59941445	chr14:59941245-59941445		chr14:59939809-59941244	chr14:59939808-59939809		62.50
K	jcn_only_AA	CUFF.454	chr17	-	chr17:57756906-57784731;chr17:57777238-57784731	chr17:57777551-57784731					56.76
K	cassette	CUFF.618	chr2	-	chr2:86397965-86400772	chr2:86397965-86398330;chr2:86398436-86400772		chr2:86398331-86398435			90.32
K	cassette	CUFF.183	chr11	-	chr11:118533906-118550247	chr11:118533906-118534047;chr11:118534149-118550247		chr11:118534048-118534148			33.87
K	intron_retention	CUFF.377	chr16	-	chr16:4414415-4414597				chr16:4414414-4414415;chr16:4414597-4414598		13.64
N	intron_retention		chr15	+	chr15:77756730-77759524				chr15:77756729-77756730;chr15:77759524-77759525		70.37
K	cassette	CUFF.900	chr5	-	chr5:149782189-149785821;chr5:149782189-149784242	chr5:149782189-149782683;chr5:149782876-149785821,chr5:149782876-149784242		chr5:149782684-149782875			54.76
N	jcn_only_AA		chr16	-	chr16:57513598-57513772	chr16:57513601-57513772		chr16:57513598-57513600	chr16:57513597-57513598		50.00
N	intron_retention		chr2	+	chr2:3469467-3481462				chr2:3469466-3469467;chr2:3481462-3481463		61.36
N	alternative_donor		chr15	-	chr15:83358206-83366608;chr15:83358206-83358514;chr15:83358206-83377523	chr15:83358206-83378345		chr15:83358515-83366608;chr15:83366609-83377523;chr15:83377524-83378345	chr15:83366608-83366609;chr15:83377523-83377524;chr15:83378345-83378346		98.15
K	intron_retention	CUFF.223	chr12	-	chr12:52979620-52979746				chr12:52979619-52979620;chr12:52979746-52979747		91.80
N	alternative_first_exon	CUFF.460	chr17	+	chr17:61907862-61908395	chr17:61908296-61908395	chr17:61907631-61907861	chr17:61908009-61908295			98.84
K	jcn_only_AD	CUFF.550	chr19	+	chr19:44764156-44768466;chr19:44764092-44768466	chr19:44764362-44768466		chr19:44764092-44764155;chr19:44764156-44764361	chr19:44764091-44764092;chr19:44764155-44764156		56.25
N	alternative_acceptor	CUFF.726	chr22	+	chr22:47308085-47370185	chr22:47308085-47309229		chr22:47309230-47370185	chr22:47370185-47370186		0.00
N	coord_cassette	CUFF.97	chr10	-	chr10:27040713-27054146	chr10:27040713-27044583;chr10:27044671-27047990;chr10:27048168-27054146		chr10:27044584-27044670;chr10:27047991-27048167			91.67
N	jcn_only_AD		chr15	+	chr15:24813330-24814929;chr15:24813711-24814929	chr15:24811948-24814929					47.62
N	alternative_donor	CUFF.456	chr17	+	chr17:60784969-60813446;chr17:60777141-60813446	chr17:60783831-60813446		chr17:60777141-60783830;chr17:60783831-60784968	chr17:60777140-60777141;chr17:60783830-60783831		1.35
N	alternative_acceptor	CUFF.371	chr16	+	chr16:2203224-2203578	chr16:2203224-2203319		chr16:2203320-2203578	chr16:2203578-2203579		20.00
N	cassette	CUFF.726	chr22	+	chr22:47193518-47287161	chr22:47193518-47274548;chr22:47274620-47287161		chr22:47274549-47274619			65.22
N	intron_retention		chr7	+	chr7:73101426-73106925				chr7:73101425-73101426;chr7:73106925-73106926		17.31
K	jcn_only_AD	CUFF.60	chr1	+	chr1:166808842-166810191	chr1:166809007-166810191		chr1:166808842-166809006	chr1:166808841-166808842		59.09
N	cassette	CUFF.728	chr22	-	chr22:51014765-51015285	chr22:51014765-51014964;chr22:51015067-51015285		chr22:51014965-51015066			83.13
N	alternative_acceptor	CUFF.1110	chrX	+	chrX:1404814-1407411	chrX:1404814-1406066		chrX:1406067-1407411	chrX:1407411-1407412		0.34
N	alternative_donor	CUFF.325	chr15	+	chr15:57426699-57458599;chr15:57401516-57458599;chr15:57422171-57458599	chr15:57384090-57458599		chr15:57384090-57401515;chr15:57401516-57422170;chr15:57422171-57426698	chr15:57384089-57384090;chr15:57401515-57401516;chr15:57422170-57422171		100.00
K	intron_retention	CUFF.1028	chr8	-	chr8:23177566-23179642				chr8:23177565-23177566;chr8:23179642-23179643		25.45
N	jcn_only_AA	CUFF.858	chr4	+	chr4:120379233-120381897	chr4:120379233-120381337		chr4:120381338-120381897	chr4:120381897-120381898		48.61
K	intron_retention		chr16	+	chr16:3117417-3117554				chr16:3117416-3117417;chr16:3117554-3117555		18.77
K	intron_retention	CUFF.751	chr3	-	chr3:46963630-46963725				chr3:46963629-46963630;chr3:46963725-46963726		14.29
N	alternative_acceptor	CUFF.1016	chr7	+	chr7:150817233-150820880	chr7:150817233-150819811		chr7:150819812-150820880	chr7:150820880-150820881		80.51
K	alternative_last_exon	CUFF.36	chr1	+	chr1:110214206-110217368;chr1:110214206-110215824;chr1:110214206-110251102	chr1:110214206-110224430	chr1:110215825-110215963;chr1:110251103-110252171	chr1:110224431-110224456			56.32
N	alternative_acceptor	CUFF.786	chr3	-	chr3:127299007-127309725	chr3:127309436-127309725		chr3:127299007-127309435	chr3:127299006-127299007		7.14
N	alternative_donor	CUFF.579	chr2	+	chr2:3464108-3469367	chr2:3466843-3469367		chr2:3464108-3466842	chr2:3464107-3464108		2.17
K	cassette	CUFF.228	chr12	-	chr12:56565217-56566211	chr12:56565217-56565462;chr12:56565722-56566211		chr12:56565463-56565721			85.71
K	cassette	CUFF.225	chr12	+	chr12:53848654-53849244	chr12:53848654-53849130;chr12:53849155-53849244		chr12:53849131-53849154			96.38
N	alternative_donor	CUFF.86	chr10	-	chr10:532471-735433	chr10:532471-629528		chr10:629529-735433	chr10:735433-735434		0.00
K	alternative_donor	CUFF.403	chr16	+	chr16:67234710-67234792	chr16:67234712-67234792		chr16:67234710-67234711	chr16:67234709-67234710		84.51
N	intron_retention		chr22	-	chr22:21831031-21832078				chr22:21831030-21831031;chr22:21832078-21832079		88.46
N	intron_retention		chr17	+	chr17:61904973-61906217				chr17:61904972-61904973;chr17:61906217-61906218		78.57
K	mutually_exclusive	CUFF.97	chr10	-	chr10:27040713-27047990,chr10:27048165-27054146	chr10:27040713-27044583,chr10:27044671-27054146	chr10:27047991-27048164	chr10:27044584-27044670			20.00
N	jcn_only_AD		chr19	-	chr19:6192041-6199490	chr19:6192041-6199486					52.38
K	cassette	CUFF.936	chr6	+	chr6:90326377-90327672	chr6:90326377-90326592;chr6:90326676-90327672		chr6:90326593-90326675			41.35
K	jcn_only_AA	CUFF.110	chr10	-	chr10:69575888-69583071	chr10:69575892-69583071		chr10:69575888-69575891	chr10:69575887-69575888	chr10:69583072-69583150;chr10:69575798-69575887	52.00
K	cassette	CUFF.999	chr7	-	chr7:102669866-102696090	chr7:102669866-102695534;chr7:102695626-102696090		chr7:102695535-102695625			15.71
K	alternative_donor	CUFF.688	chr20	-	chr20:34246937-34252800	chr20:34246937-34252723		chr20:34252724-34252800	chr20:34252800-34252801		17.65
N	jcn_only_AA	CUFF.722	chr22	+	chr22:37695348-37696193;chr22:37695348-37696947	chr22:37695348-37696110		chr22:37696111-37696193;chr22:37696194-37696947	chr22:37696193-37696194;chr22:37696947-37696948		3.53
N	intron_retention		chr17	+	chr17:61905284-61905497				chr17:61905283-61905284;chr17:61905497-61905498		41.46
K	alternative_first_exon	CUFF.560	chr19	-	chr19:51528923-51530712;chr19:51528923-51529793;chr19:51528923-51531199	chr19:51528923-51529011	chr19:51530713-51530984;chr19:51529794-51530493;chr19:51531200-51531383	chr19:51529012-51529110			15.29
N	intron_retention		chr5	-	chr5:149781568-149785821				chr5:149781567-149781568;chr5:149785821-149785822		42.06
N	jcn_only_AD		chr5	-	chr5:178050418-178057554	chr5:178050418-178053946		chr5:178053947-178057554	chr5:178057554-178057555		99.24
K	jcn_only_AA	CUFF.812	chr4	-	chr4:2934137-2934326	chr4:2934240-2934326		chr4:2934137-2934239	chr4:2934136-2934137		97.95
K	jcn_only_AA	CUFF.160	chr11	+	chr11:61608198-61615630	chr11:61608198-61615292		chr11:61615293-61615630	chr11:61615630-61615631	chr11:61608096-61608197;chr11:61615631-61615756	37.13
K	cassette	CUFF.528	chr19	-	chr19:16596069-16606561	chr19:16596069-16601177;chr19:16601382-16606561		chr19:16601178-16601381			60.00
K	alternative_first_exon	CUFF.317	chr15	-	chr15:45470505-45490969;chr15:45470505-45473304;chr15:45470505-45492924	chr15:45470505-45479651	chr15:45473305-45473474;chr15:45492925-45493434	chr15:45479652-45480154			24.07
N	jcn_only_AD	CUFF.984	chr7	+	chr7:75040010-75040937	chr7:75040858-75040937		chr7:75040010-75040857	chr7:75040009-75040010		76.47
K	cassette	CUFF.34	chr1	-	chr1:106132408-106146784	chr1:106132408-106145898;chr1:106146181-106146784		chr1:106145899-106146180			68.75
N	coord_cassette	CUFF.278	chr14	-	chr14:75159032-75179635	chr14:75159032-75165466;chr14:75165560-75168371;chr14:75168478-75179635		chr14:75165467-75165559;chr14:75168372-75168477		chr14:75158744-75159031;chr14:75179636-75179896	50.82
K	alternative_acceptor	CUFF.240	chr12	-	chr12:113646065-113658801	chr12:113646315-113658801		chr12:113646065-113646314	chr12:113646064-113646065		24.24
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		25.00
K	jcn_only_AD	CUFF.403	chr16	+	chr16:67234710-67234792	chr16:67234712-67234792		chr16:67234710-67234711	chr16:67234709-67234710		91.67
N	jcn_only_AA		chr7	-	chr7:37469360-37488462;chr7:37382368-37488462	chr7:37433521-37488462		chr7:37382368-37433520;chr7:37433521-37469359	chr7:37382367-37382368;chr7:37433520-37433521		46.94
K	alternative_last_exon	CUFF.683	chr20	+	chr20:30149540-30150215;chr20:30149540-30156922	chr20:30149540-30154012	chr20:30156923-30157469	chr20:30154013-30154142			83.39
K	intron_retention	CUFF.109	chr10	+	chr10:60047518-60048035				chr10:60047517-60047518;chr10:60048035-60048036		60.87
K	intron_retention	CUFF.180	chr11	+	chr11:117074601-117074930				chr11:117074600-117074601;chr11:117074930-117074931		2.59
K	jcn_only_AA	CUFF.482,CUFF.495	chr18	+	chr18:12658343-12658572	chr18:12658343-12658549		chr18:12658550-12658572	chr18:12658572-12658573		64.00
N	alternative_first_exon	CUFF.725	chr22	+	chr22:45181982-45182336,chr22:45173110-45182336;chr22:45131043-45182336;chr22:45148508-45182336;chr22:45162070-45182336	chr22:45122515-45182336	chr22:45130907-45131042;chr22:45148371-45148507;chr22:45161745-45162069	chr22:45122457-45122514			6.25
N	jcn_only_AD	CUFF.849	chr4	+	chr4:124571485-124573941	chr4:124571488-124573941		chr4:124571485-124571487	chr4:124571484-124571485		65.93
K	cassette	CUFF.611	chr2	-	chr2:73247394-73250316	chr2:73247394-73249650;chr2:73249706-73250316		chr2:73249651-73249705			93.12
N	intron_retention		chr15	-	chr15:83350333-83357909				chr15:83350332-83350333;chr15:83357909-83357910		82.00
K	jcn_only_AA	CUFF.1008	chr7	-	chr7:127251731-127251998	chr7:127251903-127251998		chr7:127251731-127251902	chr7:127251730-127251731		15.38
K	alternative_donor	CUFF.406	chr16	-	chr16:70265062-70265339	chr16:70265062-70265225		chr16:70265226-70265339	chr16:70265339-70265340		25.40
N	jcn_only_AA	CUFF.176	chr11	-	chr11:102960039-102962412	chr11:102960048-102962412		chr11:102960039-102960047	chr11:102960038-102960039		54.55
K	alternative_donor	CUFF.782	chr3	-	chr3:125787090-125802935	chr3:125787090-125802896		chr3:125802897-125802935	chr3:125802935-125802936		34.68
N	alternative_acceptor	CUFF.1002	chr7	-	chr7:107642179-107643293	chr7:107642830-107643293		chr7:107642179-107642829	chr7:107642178-107642179		18.87
N	intron_retention		chr12	-	chr12:56705180-56708634				chr12:56705179-56705180;chr12:56708634-56708635		79.59
N	jcn_only_AD		chr14	-	chr14:92105595-92112480;chr14:92105595-92126180	chr14:92105595-92136157		chr14:92112481-92126180;chr14:92126181-92136157	chr14:92126180-92126181;chr14:92136157-92136158		86.67
N	jcn_only_AA	CUFF.385	chr16	+	chr16:19592976-19598714;chr16:19592976-19603111	chr16:19592976-19612985					23.33
K	alternative_last_exon	CUFF.270	chr14	+	chr14:59377061-59475751	chr14:59377061-59415030	chr14:59475752-59475952	chr14:59415031-59415059			63.04
N	jcn_only_AA	CUFF.189	chr11	-	chr11:119291089-119291578;chr11:119291097-119291578	chr11:119291046-119291578		chr11:119291046-119291088;chr11:119291089-119291096	chr11:119291045-119291046;chr11:119291088-119291089		3.42
K	intron_retention	CUFF.189	chr11	-	chr11:119290142-119290760				chr11:119290141-119290142;chr11:119290760-119290761		34.69
N	jcn_only_AA		chr5	+	chr5:54456225-54456879	chr5:54456225-54456821		chr5:54456822-54456879	chr5:54456879-54456880		25.00
K	intron_retention	CUFF.975	chr7	+	chr7:44250531-44250621				chr7:44250530-44250531;chr7:44250621-44250622		13.33
N	jcn_only_AA		chr14	+	chr14:58899176-58906787;chr14:58899176-58899829	chr14:58899176-58909423		chr14:58899830-58906787;chr14:58906788-58909423	chr14:58906787-58906788;chr14:58909423-58909424		60.81
N	jcn_only_AD		chr17	+	chr17:61904875-61905478	chr17:61905284-61905478					27.27
K	cassette	CUFF.11	chr1	-	chr1:25554727-25558594	chr1:25554727-25555488;chr1:25555615-25558594		chr1:25555489-25555614			20.34
N	cassette	CUFF.234	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			58.70
K	alternative_donor	CUFF.354	chr15	+	chr15:91290721-91292596	chr15:91290892-91292596		chr15:91290721-91290891	chr15:91290720-91290721		72.41
N	alternative_acceptor	CUFF.321	chr15	-	chr15:50822127-50830905	chr15:50824425-50830905		chr15:50822127-50824424	chr15:50822126-50822127		1.74
N	coord_cassette	CUFF.234	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			37.78
K	cassette	CUFF.97	chr10	-	chr10:27059275-27065993	chr10:27059275-27059451;chr10:27059470-27065993		chr10:27059452-27059469			35.29
N	jcn_only_AD	CUFF.489	chr18	-	chr18:47329224-47337765;chr18:47329224-47340051;chr18:47329224-47339094;chr18:47329224-47340186;chr18:47329224-47340101	chr18:47329224-47339838		chr18:47337766-47339094;chr18:47339095-47339838;chr18:47339839-47340051;chr18:47340052-47340101;chr18:47340102-47340186	chr18:47339094-47339095;chr18:47339838-47339839;chr18:47340051-47340052;chr18:47340101-47340102;chr18:47340186-47340187		14.77
K	jcn_only_AA	CUFF.982	chr7	-	chr7:74607950-74608617	chr7:74607952-74608617		chr7:74607950-74607951	chr7:74607949-74607950		22.22
N	cassette	CUFF.83	chr1	+	chr1:245133746-245222687;chr1:245165535-245222687	chr1:245133746-245180543,chr1:245165535-245180543;chr1:245180629-245222687		chr1:245180544-245180628			75.00
N	alternative_donor		chr11	-	chr11:10821304-10821790	chr11:10821304-10821636		chr11:10821637-10821790	chr11:10821790-10821791		49.12
N	alternative_acceptor		chr3	+	chr3:119196296-119198754;chr3:119196296-119197180	chr3:119196296-119198897		chr3:119197181-119198754;chr3:119198755-119198897	chr3:119198754-119198755;chr3:119198897-119198898		6.02
N	jcn_only_AA	CUFF.402	chr16	-	chr16:67221042-67222922	chr16:67222844-67222922					68.49
K	intron_retention	CUFF.714	chr22	+	chr22:25855483-25915889				chr22:25855482-25855483;chr22:25915889-25915890		16.13
K	intron_retention	CUFF.446	chr17	-	chr17:41738762-41739238				chr17:41738761-41738762;chr17:41739238-41739239		10.53
N	alternative_acceptor	CUFF.1119	chrX	-	chrX:20190987-20193281	chrX:20190990-20193281		chrX:20190987-20190989	chrX:20190986-20190987		11.63
N	jcn_only_AD	CUFF.1146	chrX	+	chrX:148863691-148867418;chrX:148863659-148867418	chrX:148864250-148867418		chrX:148863659-148863690;chrX:148863691-148864249	chrX:148863658-148863659;chrX:148863690-148863691		29.03
K	alternative_acceptor	CUFF.595	chr2	+	chr2:33572578-33585669	chr2:33572578-33585663		chr2:33585664-33585669	chr2:33585669-33585670		98.66
K	alternative_first_exon	CUFF.132	chr10	-	chr10:123683845-123687861	chr10:123683845-123687358	chr10:123687862-123688391	chr10:123687359-123687551			42.86
K	intron_retention	CUFF.187	chr11	+	chr11:119056338-119056630				chr11:119056337-119056338;chr11:119056630-119056631		25.00
N	cassette	CUFF.298	chr14	-	chr14:104208629-104212709	chr14:104208629-104208990;chr14:104209161-104212709		chr14:104208991-104209160			77.55
K	intron_retention	CUFF.647	chr2	-	chr2:175711686-175779785				chr2:175711685-175711686;chr2:175779785-175779786		22.12
K	intron_retention	CUFF.336	chr15	+	chr15:74753760-74754223				chr15:74753759-74753760;chr15:74754223-74754224		60.53
N	alternative_donor	CUFF.537,CUFF.542	chr19	-	chr19:33878388-33878795	chr19:33878388-33878560		chr19:33878561-33878795	chr19:33878795-33878796		11.43
K	jcn_only_AA	CUFF.244,CUFF.249	chr13	+	chr13:21205242-21228014	chr13:21205242-21212470					13.65
K	jcn_only_AA	CUFF.1096	chr9	+	chr9:125028060-125033231	chr9:125028060-125033142		chr9:125033143-125033231	chr9:125033231-125033232		53.12
N	intron_retention		chr11	+	chr11:63999437-64001365				chr11:63999436-63999437;chr11:64001365-64001366		70.97
K	alternative_first_exon	CUFF.167	chr11	+	chr11:67782546-67782766;chr11:67776163-67782766	chr11:67777863-67782766	chr11:67775961-67776162	chr11:67777704-67777862			83.83
K	alternative_acceptor	CUFF.1010	chr7	+	chr7:129008393-129019481	chr7:129008393-129019478		chr7:129019479-129019481	chr7:129019481-129019482		39.13
K	alternative_first_exon	CUFF.1016	chr7	+	chr7:150815720-150817073	chr7:150816342-150817073	chr7:150815592-150815719	chr7:150816243-150816341			33.24
N	alternative_donor	CUFF.663	chr2	+	chr2:220095073-220096649;chr2:220094623-220096649	chr2:220095128-220096649		chr2:220094623-220095072;chr2:220095073-220095127	chr2:220094622-220094623;chr2:220095072-220095073		46.51
N	cassette	CUFF.184	chr11	-	chr11:118926556-118927785	chr11:118926556-118926781;chr11:118926880-118927785		chr11:118926782-118926879			50.89
N	intron_retention		chrX	-	chrX:15343275-15349711				chrX:15343274-15343275;chrX:15349711-15349712		68.06
K	jcn_only_AA	CUFF.812	chr4	-	chr4:2934905-2935293	chr4:2934937-2935293		chr4:2934905-2934936	chr4:2934904-2934905		98.28
N	alternative_donor	CUFF.490	chr18	+	chr18:56033461-56034977	chr18:56034459-56034977		chr18:56033461-56034458	chr18:56033460-56033461		2.80
N	alternative_donor	CUFF.821,CUFF.833	chr4	-	chr4:69057035-69071752	chr4:69057035-69057124		chr4:69057125-69071752	chr4:69071752-69071753		0.00
N	jcn_only_AD	CUFF.708	chr22	+	chr22:21056595-21056873	chr22:21056749-21056873		chr22:21056595-21056748	chr22:21056594-21056595		38.60
N	jcn_only_AA	CUFF.716	chr22	+	chr22:29668421-29669729;chr22:29668421-29669726	chr22:29668421-29674119		chr22:29669727-29669729;chr22:29669730-29674119	chr22:29669729-29669730;chr22:29674119-29674120		3.60
K	intron_retention		chr16	+	chr16:3115496-3115784				chr16:3115495-3115496;chr16:3115784-3115785		27.59
N	jcn_only_AD		chr10	+	chr10:35437420-35464780	chr10:35464634-35464780					58.33
K	intron_retention	CUFF.49	chr1	-	chr1:153925112-153925280				chr1:153925111-153925112;chr1:153925280-153925281		68.89
K	jcn_only_AA	CUFF.262	chr14	-	chr14:31358462-31358589	chr14:31358484-31358589		chr14:31358462-31358483	chr14:31358461-31358462		45.45
K	alternative_last_exon	CUFF.1135	chrX	-	chrX:106059017-106236459;chrX:106235661-106236459	chrX:106229431-106236459	chrX:106057101-106059016;chrX:106235518-106235660	chrX:106229213-106229430			33.33
N	mutually_exclusive	CUFF.152	chr11	-	chr11:10827595-10828801,chr11:10828929-10829823	chr11:10827595-10828366,chr11:10828433-10829823	chr11:10828802-10828928	chr11:10828367-10828432			66.67
K	intron_retention	CUFF.530	chr19	+	chr19:17449551-17449762				chr19:17449550-17449551;chr19:17449762-17449763		45.85
K	intron_retention	CUFF.894	chr5	+	chr5:139918669-139918943				chr5:139918668-139918669;chr5:139918943-139918944	chr5:139918504-139918668;chr5:139918944-139919441	9.00
N	alternative_acceptor	CUFF.709	chr22	-	chr22:21841217-21841853	chr22:21841265-21841853		chr22:21841217-21841264	chr22:21841216-21841217		2.38
N	jcn_only_AD	CUFF.579	chr2	+	chr2:3464108-3469367	chr2:3466843-3469367		chr2:3464108-3466842	chr2:3464107-3464108		5.86
N	cassette	CUFF.665	chr2	+	chr2:232026224-232029913	chr2:232026224-232028348;chr2:232028442-232029913		chr2:232028349-232028441			69.57
K	intron_retention	CUFF.812	chr4	-	chr4:2932681-2932787				chr4:2932680-2932681;chr4:2932787-2932788		28.39
N	alternative_acceptor	CUFF.611	chr2	-	chr2:73228704-73247367	chr2:73228708-73247367		chr2:73228704-73228707	chr2:73228703-73228704		92.86
N	jcn_only_AA		chr17	+	chr17:60783831-60784792;chr17:60783831-60803388	chr17:60783831-60813446		chr17:60784793-60803388;chr17:60803389-60813446	chr17:60803388-60803389;chr17:60813446-60813447		43.75
K	intron_retention	CUFF.330	chr15	+	chr15:64444526-64444836				chr15:64444525-64444526;chr15:64444836-64444837		75.00
K	cassette	CUFF.273	chr14	+	chr14:61497242-61504342	chr14:61497242-61503776;chr14:61503860-61504342		chr14:61503777-61503859			93.80
N	jcn_only_AA	CUFF.579,CUFF.666	chr2	+	chr2:3405665-3425651	chr2:3405665-3425470		chr2:3425471-3425651	chr2:3425651-3425652		28.79
N	alternative_first_exon		chr14	-	chr14:104202540-104205015	chr14:104202540-104204030	chr14:104205016-104205149	chr14:104204031-104204197			89.86
K	jcn_only_AA	CUFF.709	chr22	-	chr22:21832391-21832873	chr22:21832451-21832873		chr22:21832391-21832450	chr22:21832390-21832391		22.69
N	cassette	CUFF.509	chr19	-	chr19:6002882-6007022	chr19:6002882-6004211;chr19:6004310-6007022		chr19:6004212-6004309			65.96
N	jcn_only_AA	CUFF.417	chr17	-	chr17:1617309-1617664	chr17:1617340-1617664		chr17:1617309-1617339	chr17:1617308-1617309		1.93
N	alternative_donor	CUFF.475	chr17	-	chr17:79993940-79994066;chr17:79993940-79994022	chr17:79993940-79994057		chr17:79994023-79994057;chr17:79994058-79994066	chr17:79994057-79994058;chr17:79994066-79994067		3.41
N	jcn_only_AA		chr15	+	chr15:40531337-40545378	chr15:40531337-40532799					39.47
K	alternative_acceptor	CUFF.1032	chr8	-	chr8:38005846-38006158	chr8:38005878-38006158		chr8:38005846-38005877	chr8:38005845-38005846		16.05
K	alternative_first_exon	CUFF.197	chr12	+	chr12:1684008-1740463,chr12:1739393-1740463,chr12:1738538-1740463;chr12:1639176-1740463;chr12:1640117-1740463	chr12:1726310-1740463	chr12:1639057-1639175;chr12:1639910-1640116	chr12:1725805-1726309			29.84
N	alternative_first_exon		chr11	-	chr11:102954056-102962515	chr11:102954056-102959955	chr11:102962516-102963030	chr11:102959956-102960047			48.77
N	jcn_only_AD	CUFF.225	chr12	+	chr12:53846161-53848509;chr12:53847068-53848509;chr12:53837558-53848509	chr12:53846760-53848509		chr12:53837558-53846160;chr12:53846161-53846759;chr12:53846760-53847067	chr12:53837557-53837558;chr12:53846160-53846161;chr12:53846759-53846760		16.10
N	alternative_donor	CUFF.316	chr15	-	chr15:44892831-44898222	chr15:44892831-44896302		chr15:44896303-44898222	chr15:44898222-44898223		0.00
N	jcn_only_AD	CUFF.102	chr10	+	chr10:35464928-35467816;chr10:35437420-35467816;chr10:35426808-35467816;chr10:35416122-35467816;chr10:35456732-35467816	chr10:35464634-35467816		chr10:35416122-35426807;chr10:35426808-35437419;chr10:35437420-35456731;chr10:35456732-35464633;chr10:35464634-35464927	chr10:35416121-35416122;chr10:35426807-35426808;chr10:35437419-35437420;chr10:35456731-35456732;chr10:35464633-35464634		4.43
K	intron_retention		chr17	-	chr17:1615694-1616996				chr17:1615693-1615694;chr17:1616996-1616997		30.23
N	alternative_donor	CUFF.827,CUFF.856	chr4	-	chr4:162463846-162508606	chr4:162463846-162473639		chr4:162473640-162508606	chr4:162508606-162508607		0.00
N	coord_cassette	CUFF.924	chr6	-	chr6:35477090-35479424	chr6:35477090-35477410;chr6:35477528-35477603;chr6:35477706-35478637;chr6:35478788-35479424		chr6:35477411-35477527;chr6:35477604-35477705;chr6:35478638-35478787			82.08
K	cassette	CUFF.143	chr11	+	chr11:2466715-2549157	chr11:2466715-2542708;chr11:2542801-2549157		chr11:2542709-2542800			63.16
N	jcn_only_AD	CUFF.102	chr10	+	chr10:35464928-35467816;chr10:35437420-35467816;chr10:35426808-35467816;chr10:35456732-35467816;chr10:35464634-35467816	chr10:35416122-35467816		chr10:35416122-35426807;chr10:35426808-35437419;chr10:35437420-35456731;chr10:35456732-35464633;chr10:35464634-35464927	chr10:35416121-35416122;chr10:35426807-35426808;chr10:35437419-35437420;chr10:35456731-35456732;chr10:35464633-35464634		8.03
N	alternative_donor	CUFF.603	chr2	+	chr2:48996261-49003418;chr2:48996214-49003418	chr2:48898820-49003418		chr2:48898820-48996213;chr2:48996214-48996260	chr2:48898819-48898820;chr2:48996213-48996214		100.00
K	cassette	CUFF.424	chr17	-	chr17:8638573-8644791	chr17:8638573-8638707;chr17:8638930-8644791		chr17:8638708-8638929			60.00
K	intron_retention	CUFF.929	chr6	-	chr6:43480302-43480498				chr6:43480301-43480302;chr6:43480498-43480499		23.99
K	intron_retention	CUFF.239	chr12	-	chr12:113599188-113599697				chr12:113599187-113599188;chr12:113599697-113599698		77.94
N	mutually_exclusive	CUFF.374	chr16	+	chr16:3117615-3118180,chr16:3118241-3118990	chr16:3117615-3117984,chr16:3118012-3118990	chr16:3118181-3118240	chr16:3117985-3118011			86.67
N	cassette	CUFF.578	chr2	+	chr2:1094097-1133307	chr2:1094097-1099090;chr2:1099129-1133307		chr2:1099091-1099128			82.93
N	jcn_only_AD		chr17	+	chr17:29706376-29708890;chr17:29706042-29708890	chr17:29707246-29708890					7.59
K	intron_retention	CUFF.147	chr11	-	chr11:5685404-5686885				chr11:5685403-5685404;chr11:5686885-5686886		38.20
N	alternative_donor	CUFF.887,CUFF.902	chr5	-	chr5:127338515-127359826	chr5:127338515-127339335		chr5:127339336-127359826	chr5:127359826-127359827		2.13
N	jcn_only_AA	CUFF.1082	chr9	+	chr9:95591446-95599058	chr9:95591446-95591955		chr9:95591956-95599058	chr9:95599058-95599059		30.00
N	jcn_only_AD		chr3	-	chr3:33467234-33482168	chr3:33467234-33481227		chr3:33481228-33482168	chr3:33482168-33482169		26.92
N	alternative_acceptor	CUFF.1016	chr7	+	chr7:150825772-150831486	chr7:150825772-150828158		chr7:150828159-150831486	chr7:150831486-150831487		1.87
N	jcn_only_AD	CUFF.924	chr6	-	chr6:35478788-35479956	chr6:35478788-35479424		chr6:35479425-35479956	chr6:35479956-35479957		41.67
K	intron_retention	CUFF.561	chr19	-	chr19:51532469-51532597				chr19:51532468-51532469;chr19:51532597-51532598		24.14
N	jcn_only_AD		chr1	+	chr1:167298544-167301706;chr1:167227155-167301706	chr1:167288294-167301706					70.83
N	alternative_donor	CUFF.68	chr1	+	chr1:200860531-200867434	chr1:200864216-200867434		chr1:200860531-200864215	chr1:200860530-200860531		0.00
K	intron_retention	CUFF.187	chr11	+	chr11:119058854-119059063				chr11:119058853-119058854;chr11:119059063-119059064		33.61
K	cassette	CUFF.726	chr22	+	chr22:47188474-47189397	chr22:47188474-47188564;chr22:47188660-47189397		chr22:47188565-47188659			25.45
N	alternative_donor	CUFF.576	chr2	-	chr2:675631-676573	chr2:675631-675757		chr2:675758-676573	chr2:676573-676574		90.41
N	alternative_acceptor	CUFF.236	chr12	-	chr12:77254194-77256955	chr12:77256740-77256955		chr12:77254194-77256739	chr12:77254193-77254194		51.32
N	cassette	CUFF.579	chr2	+	chr2:3469467-3482616	chr2:3469467-3481465;chr2:3481567-3482616		chr2:3481466-3481566			84.97
N	jcn_only_AD	CUFF.802	chr3	+	chr3:186769135-186790636	chr3:186782405-186790636		chr3:186769135-186782404	chr3:186769134-186769135		9.18
N	alternative_acceptor	CUFF.560	chr19	-	chr19:51528923-51529793	chr19:51528955-51529793		chr19:51528923-51528954	chr19:51528922-51528923		3.16
N	intron_retention		chr19	+	chr19:45261731-45261980				chr19:45261730-45261731;chr19:45261980-45261981		80.95
N	jcn_only_AD	CUFF.352	chr15	-	chr15:90414779-90420537;chr15:90414779-90431752	chr15:90414779-90421496		chr15:90420538-90421496;chr15:90421497-90431752	chr15:90421496-90421497;chr15:90431752-90431753		4.91
K	alternative_first_exon	CUFF.306	chr15	+	chr15:29347039-29367123	chr15:29363303-29367123	chr15:29346048-29347038	chr15:29362790-29363302			63.04
K	intron_retention	CUFF.532	chr19	+	chr19:18120849-18121004				chr19:18120848-18120849;chr19:18121004-18121005		22.92
N	jcn_only_AD	CUFF.572	chr2	-	chr2:242872-247537;chr2:242872-243502	chr2:242872-244626		chr2:243503-244626;chr2:244627-247537	chr2:244626-244627;chr2:247537-247538		8.45
N	intron_retention		chr12	+	chr12:58019248-58019407				chr12:58019247-58019248;chr12:58019407-58019408		85.86
K	alternative_last_exon	CUFF.593	chr2	+	chr2:27731119-27741654	chr2:27731119-27732393	chr2:27741655-27741804	chr2:27732394-27732692			30.00
N	alternative_donor	CUFF.1098	chr9	-	chr9:130929444-130929817;chr9:130929444-130931354	chr9:130929444-130931330		chr9:130929818-130931330;chr9:130931331-130931354	chr9:130931330-130931331;chr9:130931354-130931355		64.29
K	intron_retention	CUFF.747	chr3	-	chr3:38050923-38051143				chr3:38050922-38050923;chr3:38051143-38051144		20.41
K	cassette	CUFF.34	chr1	-	chr1:106132408-106145898	chr1:106132408-106143891;chr1:106144008-106145898		chr1:106143892-106144007			38.10
N	intron_retention		chr7	-	chr7:107580804-107591670				chr7:107580803-107580804;chr7:107591670-107591671		97.64
K	intron_retention	CUFF.707	chr22	+	chr22:20748625-20748852				chr22:20748624-20748625;chr22:20748852-20748853		86.11
N	alternative_donor	CUFF.1033	chr8	-	chr8:56676540-56685827;chr8:56676540-56685534	chr8:56676540-56685785		chr8:56685535-56685785;chr8:56685786-56685827	chr8:56685785-56685786;chr8:56685827-56685828		16.57
N	cassette	CUFF.18	chr1	+	chr1:32542448-32557275;chr1:32541424-32557275	chr1:32542448-32542764,chr1:32541424-32542764;chr1:32542920-32557275		chr1:32542765-32542919			62.21
K	jcn_only_AA	CUFF.418	chr17	+	chr17:1945170-1946269	chr17:1945170-1945898		chr17:1945899-1946269	chr17:1946269-1946270		87.68
N	alternative_first_exon	CUFF.310	chr15	+	chr15:40545491-40555999	chr15:40549288-40555999	chr15:40545379-40545490	chr15:40549189-40549287			69.23
N	alternative_acceptor	CUFF.481	chr18	+	chr18:12014373-12017612;chr18:12014373-12028041	chr18:12014373-12021700		chr18:12017613-12021700;chr18:12021701-12028041	chr18:12021700-12021701;chr18:12028041-12028042		0.00
N	alternative_acceptor	CUFF.193	chr11	-	chr11:124767529-124767621;chr11:124767158-124767621	chr11:124766952-124767621		chr11:124766952-124767157;chr11:124767158-124767528	chr11:124766951-124766952;chr11:124767157-124767158		7.41
N	alternative_acceptor	CUFF.734	chr3	+	chr3:19992554-20017134;chr3:19992554-20017078;chr3:19992554-20012039	chr3:19992554-20017092		chr3:20012040-20017078;chr3:20017079-20017092;chr3:20017093-20017134	chr3:20017078-20017079;chr3:20017092-20017093;chr3:20017134-20017135		10.57
K	alternative_last_exon	CUFF.1061,CUFF.1063	chr8	+	chr8:144822119-144826029	chr8:144822119-144823921	chr8:144826030-144828507	chr8:144823922-144824580			28.12
K	alternative_last_exon	CUFF.1029	chr8	+	chr8:27517057-27534085	chr8:27517057-27528416	chr8:27534086-27534293	chr8:27528417-27530618		chr8:27516013-27517056	73.68
N	jcn_only_AA	CUFF.879	chr5	-	chr5:60186914-60194102	chr5:60189471-60194102		chr5:60186914-60189470	chr5:60186913-60186914		2.20
K	cassette	CUFF.1155	chrY	-	chrY:24032860-24037971	chrY:24032860-24034774;chrY:24034953-24037971		chrY:24034775-24034952		chrY:24032707-24032859;chrY:24037972-24038075	48.89
N	jcn_only_AA	CUFF.189	chr11	-	chr11:119291089-119291578;chr11:119291046-119291578	chr11:119291097-119291578		chr11:119291046-119291088;chr11:119291089-119291096	chr11:119291045-119291046;chr11:119291088-119291089		91.45
N	alternative_donor	CUFF.1119	chrX	-	chrX:20252933-20285156	chrX:20252933-20258686		chrX:20258687-20285156	chrX:20285156-20285157		0.00
N	alternative_donor	CUFF.329	chr15	+	chr15:63128273-63131054	chr15:63128318-63131054		chr15:63128273-63128317	chr15:63128272-63128273		16.67
N	jcn_only_AA	CUFF.1119	chrX	-	chrX:20190987-20193281	chrX:20190990-20193281		chrX:20190987-20190989	chrX:20190986-20190987		7.32
K	cassette	CUFF.176	chr11	-	chr11:102937297-102953984	chr11:102937297-102953476;chr11:102953569-102953984		chr11:102953477-102953568			52.82
N	cassette	CUFF.1016	chr7	+	chr7:150815720-150819811	chr7:150815720-150817073;chr7:150817233-150819811		chr7:150817074-150817232			90.94
N	cassette	CUFF.1007	chr7	-	chr7:117364787-117368142	chr7:117364787-117365105;chr7:117365312-117368142		chr7:117365106-117365311			77.78
N	alternative_acceptor	CUFF.687	chr20	+	chr20:33589889-33589979	chr20:33589889-33589961		chr20:33589962-33589979	chr20:33589979-33589980		78.35
K	cassette	CUFF.530	chr19	+	chr19:17449551-17449931	chr19:17449551-17449762;chr19:17449836-17449931		chr19:17449763-17449835			89.17
N	alternative_donor	CUFF.1114,CUFF.1115	chrX	-	chrX:13798109-13801483	chrX:13798109-13799033		chrX:13799034-13801483	chrX:13801483-13801484		0.62
K	intron_retention	CUFF.448	chr17	-	chr17:42340095-42340219				chr17:42340094-42340095;chr17:42340219-42340220		39.13
K	alternative_acceptor	CUFF.550,CUFF.564	chr19	+	chr19:52901158-52901706	chr19:52901158-52901619		chr19:52901620-52901706	chr19:52901706-52901707		85.71
N	cassette	CUFF.998	chr7	-	chr7:102242853-102249207	chr7:102242853-102246304;chr7:102246435-102249207		chr7:102246305-102246434			87.07
N	intron_retention		chr16	-	chr16:4411805-4411985				chr16:4411804-4411805;chr16:4411985-4411986		84.00
N	alternative_donor	CUFF.966	chr7	-	chr7:22233652-22259484	chr7:22233652-22234187		chr7:22234188-22259484	chr7:22259484-22259485		0.00
K	alternative_acceptor	CUFF.969	chr7	+	chr7:30791921-30793349	chr7:30791921-30793346		chr7:30793347-30793349	chr7:30793349-30793350		40.00
N	cassette	CUFF.426	chr17	-	chr17:15580595-15584178	chr17:15580595-15580888;chr17:15581036-15584178		chr17:15580889-15581035			91.03
N	intron_retention		chr4	-	chr4:77977254-77987401				chr4:77977253-77977254;chr4:77987401-77987402		86.00
K	alternative_donor	CUFF.858	chr4	+	chr4:186185653-186188122	chr4:186185765-186188122		chr4:186185653-186185764	chr4:186185652-186185653		63.64
K	intron_retention	CUFF.975	chr7	+	chr7:44247798-44250621				chr7:44247797-44247798;chr7:44250621-44250622		31.43
N	alternative_donor	CUFF.579	chr2	+	chr2:3447663-3461391;chr2:3461001-3461391	chr2:3453249-3461391		chr2:3447663-3453248;chr2:3453249-3461000	chr2:3447662-3447663;chr2:3453248-3453249		1.08
K	alternative_first_exon	CUFF.862	chr5	-	chr5:2749902-2752772	chr5:2749902-2751278	chr5:2752773-2753066	chr5:2751279-2751776			29.17
N	intron_retention		chr16	-	chr16:23478100-23478752				chr16:23478099-23478100;chr16:23478752-23478753		58.33
N	jcn_only_AD	CUFF.197	chr12	+	chr12:1754228-1754959;chr12:1749143-1754959	chr12:1742072-1754959					42.11
K	alternative_last_exon	CUFF.647	chr2	-	chr2:175689247-175711607	chr2:175702065-175711607	chr2:175689162-175689246	chr2:175701789-175702064			38.58
N	alternative_acceptor		chr22	+	chr22:29521405-29533489	chr22:29521405-29533329		chr22:29533330-29533489	chr22:29533489-29533490		72.09
K	intron_retention	CUFF.166	chr11	-	chr11:67770646-67771126				chr11:67770645-67770646;chr11:67771126-67771127		10.29
K	alternative_donor	CUFF.187	chr11	+	chr11:119056220-119056630	chr11:119056338-119056630		chr11:119056220-119056337	chr11:119056219-119056220		14.68
N	alternative_acceptor	CUFF.67	chr1	+	chr1:196913069-196918584;chr1:196913069-196918565	chr1:196913069-196918746		chr1:196918566-196918584;chr1:196918585-196918746	chr1:196918584-196918585;chr1:196918746-196918747	chr1:196912830-196913068;chr1:196918747-196918779	14.93
N	jcn_only_AD	CUFF.333	chr15	-	chr15:66783056-66786752	chr15:66783056-66786614		chr15:66786615-66786752	chr15:66786752-66786753		81.63
K	intron_retention	CUFF.631	chr2	+	chr2:109111942-109113425				chr2:109111941-109111942;chr2:109113425-109113426		81.82
K	intron_retention	CUFF.881	chr5	-	chr5:69493218-69497694				chr5:69493217-69493218;chr5:69497694-69497695		82.05
N	cassette	CUFF.726	chr22	+	chr22:47189739-47274548	chr22:47189739-47193340;chr22:47193518-47274548		chr22:47193341-47193517			78.38
K	jcn_only_AD	CUFF.332	chr15	-	chr15:66645294-66678987	chr15:66645294-66678757		chr15:66678758-66678987	chr15:66678987-66678988		47.06
K	intron_retention	CUFF.845	chr4	-	chr4:99399898-99403155				chr4:99399897-99399898;chr4:99403155-99403156		95.00
K	intron_retention	CUFF.1118	chrX	-	chrX:19932387-19932468				chrX:19932386-19932387;chrX:19932468-19932469		68.18
N	coord_cassette	CUFF.234	chr12	+	chr12:69207409-69222550	chr12:69207409-69214104;chr12:69214155-69218142;chr12:69218211-69222550		chr12:69214105-69214154;chr12:69218143-69218210			83.33
K	intron_retention	CUFF.900	chr5	-	chr5:149786524-149786714				chr5:149786523-149786524;chr5:149786714-149786715		9.03
K	coord_cassette	CUFF.321	chr15	-	chr15:50833462-50838669	chr15:50833462-50835794;chr15:50835991-50836783;chr15:50836979-50838669		chr15:50835795-50835990;chr15:50836784-50836978			28.17
N	jcn_only_AA	CUFF.802	chr3	+	chr3:186756662-186760441	chr3:186756662-186759704		chr3:186759705-186760441	chr3:186760441-186760442		11.48
K	alternative_last_exon	CUFF.1089	chr9	+	chr9:116791253-116794927,chr9:116791253-116794924	chr9:116791253-116793083	chr9:116794928-116795008	chr9:116793084-116793256			61.90
K	alternative_acceptor	CUFF.171	chr11	-	chr11:75522582-75524647	chr11:75522615-75524647		chr11:75522582-75522614	chr11:75522581-75522582		38.57
N	jcn_only_AD		chr19	-	chr19:41944320-41946385;chr19:41944320-41945378	chr19:41944320-41945786		chr19:41945379-41945786;chr19:41945787-41946385	chr19:41945786-41945787;chr19:41946385-41946386		54.83
K	jcn_only_AA	CUFF.643	chr2	-	chr2:169783801-169787174	chr2:169783873-169787174		chr2:169783801-169783872	chr2:169783800-169783801	chr2:169787175-169787372;chr2:169783666-169783800	87.50
N	alternative_donor		chr17	-	chr17:79894070-79898625;chr17:79894070-79900171	chr17:79894070-79894623		chr17:79894624-79898625;chr17:79898626-79900171	chr17:79898625-79898626;chr17:79900171-79900172	chr17:79893999-79894069	63.16
K	alternative_first_exon	CUFF.12,CUFF.55	chr1	-	chr1:26231230-26231539,chr1:26231230-26231634;chr1:26231230-26232342;chr1:26231230-26232879	chr1:26231230-26233278	chr1:26232343-26232694;chr1:26232880-26232975	chr1:26233279-26233581			35.66
K	alternative_acceptor	CUFF.575	chr2	-	chr2:280150-283110	chr2:280153-283110		chr2:280150-280152	chr2:280149-280150		3.44
N	alternative_donor	CUFF.606	chr2	-	chr2:68374700-68384392;chr2:68374700-68384058	chr2:68374700-68384505		chr2:68384059-68384392;chr2:68384393-68384505	chr2:68384392-68384393;chr2:68384505-68384506		18.18
N	intron_retention		chr1	-	chr1:213186761-213188567				chr1:213186760-213186761;chr1:213188567-213188568		85.11
N	cassette	CUFF.524	chr19	-	chr19:14863339-14867049	chr19:14863339-14865765;chr19:14865940-14867049		chr19:14865766-14865939			75.25
K	alternative_last_exon	CUFF.902	chr5	-	chr5:162516353-162852808	chr5:162683994-162852808	chr5:162516251-162516352	chr5:162683776-162683993			53.97
N	alternative_acceptor	CUFF.919	chr6	-	chr6:31938530-31938688	chr6:31938603-31938688		chr6:31938530-31938602	chr6:31938529-31938530		67.36
K	alternative_donor	CUFF.628	chr2	+	chr2:101541757-101549371	chr2:101541763-101549371		chr2:101541757-101541762	chr2:101541756-101541757		13.61
K	intron_retention	CUFF.298	chr14	-	chr14:104200260-104200703				chr14:104200259-104200260;chr14:104200703-104200704		12.11
N	jcn_only_AA	CUFF.289	chr14	-	chr14:92105595-92136157	chr14:92126326-92136157		chr14:92105595-92126325	chr14:92105594-92105595		7.14
K	intron_retention		chr2	-	chr2:253116-262630				chr2:253115-253116;chr2:262630-262631		13.46
N	alternative_donor	CUFF.758	chr3	-	chr3:57582951-57583365	chr3:57582951-57583058		chr3:57583059-57583365	chr3:57583365-57583366		48.00
K	alternative_first_exon	CUFF.911	chr6	-	chr6:13470863-13472212;chr6:13470863-13486869	chr6:13470863-13486242	chr6:13472213-13472325;chr6:13486870-13487974	chr6:13486243-13486491			35.00
N	alternative_donor	CUFF.922	chr6	+	chr6:33240504-33243573	chr6:33243435-33243573		chr6:33240504-33243434	chr6:33240503-33240504		2.86
K	cassette	CUFF.712	chr22	+	chr22:24765289-24808615	chr22:24765289-24807555;chr22:24807673-24808615		chr22:24807556-24807672		chr22:24765186-24765288;chr22:24808616-24808675	18.18
N	cassette	CUFF.276	chr14	-	chr14:71201216-71204961	chr14:71201216-71202677;chr14:71202747-71204961		chr14:71202678-71202746			10.75
K	intron_retention	CUFF.382	chr16	+	chr16:14020614-14021884				chr16:14020613-14020614;chr16:14021884-14021885		65.31
N	jcn_only_AA		chr19	-	chr19:33984244-34003498	chr19:34002062-34003498					73.68
N	alternative_donor	CUFF.739	chr3	+	chr3:28360371-28360999;chr3:28358351-28360999	chr3:28357915-28360999		chr3:28357915-28358350;chr3:28358351-28360370	chr3:28357914-28357915;chr3:28358350-28358351		79.26
K	alternative_first_exon	CUFF.658	chr2	-	chr2:208030431-208030636;chr2:208030431-208031717	chr2:208030431-208031480	chr2:208030637-208030969;chr2:208031718-208032084	chr2:208031481-208031578			2.88
K	alternative_first_exon	CUFF.1001	chr7	+	chr7:107220812-107221203;chr7:107221091-107221203	chr7:107220747-107221203	chr7:107220751-107220811;chr7:107220910-107221090	chr7:107220422-107220746			69.66
N	alternative_donor	CUFF.407	chr16	+	chr16:70380952-70384459	chr16:70381894-70384459		chr16:70380952-70381893	chr16:70380951-70380952		0.79
N	coord_cassette	CUFF.651	chr2	+	chr2:191273230-191300702	chr2:191273230-191280017;chr2:191280140-191298052;chr2:191298119-191300702		chr2:191280018-191280139;chr2:191298053-191298118			63.16
N	alternative_donor	CUFF.303	chr15	+	chr15:24758885-24778841	chr15:24766978-24778841		chr15:24758885-24766977	chr15:24758884-24758885		14.29
N	jcn_only_AA		chr14	+	chr14:76201633-76203908;chr14:76201633-76210719	chr14:76201633-76211437					16.35
K	jcn_only_AA	CUFF.758	chr3	-	chr3:57569760-57570110;chr3:57569735-57570110	chr3:57569788-57570110		chr3:57569735-57569759;chr3:57569760-57569787	chr3:57569734-57569735;chr3:57569759-57569760		39.05
K	alternative_last_exon	CUFF.852	chr4	-	chr4:152096827-152097685	chr4:152096848-152097685	chr4:152095822-152096826	chr4:152096833-152096847			8.16
K	intron_retention	CUFF.802	chr3	+	chr3:186790736-186791946				chr3:186790735-186790736;chr3:186791946-186791947		8.05
K	jcn_only_AD	CUFF.144	chr11	-	chr11:2905365-2906431	chr11:2905365-2905899		chr11:2905900-2906431	chr11:2906431-2906432		92.39
K	intron_retention	CUFF.1118	chrX	-	chrX:19931598-19932269				chrX:19931597-19931598;chrX:19932269-19932270		82.35
N	jcn_only_AA	CUFF.869,CUFF.878	chr5	+	chr5:56510021-56526672	chr5:56510021-56517202		chr5:56517203-56526672	chr5:56526672-56526673	chr5:56509901-56510020;chr5:56526673-56526796	69.05
N	mutually_exclusive	CUFF.393	chr16	-	chr16:30005130-30006423,chr16:30006785-30006861	chr16:30005130-30005226,chr16:30006165-30006861	chr16:30006424-30006784	chr16:30005227-30006164			27.03
K	alternative_last_exon	CUFF.1103	chr9	-	chr9:135730313-135739051	chr9:135736985-135739051	chr9:135730244-135730312	chr9:135736910-135736984			5.10
N	intron_retention		chr2	-	chr2:253116-264083				chr2:253115-253116;chr2:264083-264084		60.00
K	alternative_last_exon	CUFF.1097	chr9	-	chr9:125627937-125639749	chr9:125637648-125639749	chr9:125627628-125627936	chr9:125635970-125637647			72.31
N	cassette	CUFF.942	chr6	-	chr6:114281183-114292020;chr6:114281183-114289797	chr6:114281183-114283530;chr6:114283559-114289797,chr6:114283559-114292020		chr6:114283531-114283558			31.15
K	cassette	CUFF.1109	chr9	+	chr9:139815668-139818303	chr9:139815668-139816833;chr9:139816946-139818303		chr9:139816834-139816945			29.33
N	jcn_only_AA	CUFF.325	chr15	+	chr15:57574797-57578354;chr15:57574797-57583026	chr15:57574797-57591423		chr15:57578355-57583026;chr15:57583027-57591423	chr15:57583026-57583027;chr15:57591423-57591424		8.66
K	intron_retention	CUFF.709	chr22	-	chr22:21831054-21832078				chr22:21831053-21831054;chr22:21832078-21832079		47.19
N	alternative_donor	CUFF.151	chr11	-	chr11:8941998-8947009	chr11:8941998-8942840		chr11:8942841-8947009	chr11:8947009-8947010		0.00
N	intron_retention		chr17	-	chr17:1616220-1616996				chr17:1616219-1616220;chr17:1616996-1616997		84.00
N	jcn_only_AA		chr2	+	chr2:220095128-220096981	chr2:220095128-220096649					86.73
K	jcn_only_AD	CUFF.324,CUFF.338	chr15	-	chr15:55742566-55783320	chr15:55742566-55759127					71.90
K	alternative_last_exon	CUFF.159	chr11	-	chr11:61517215-61523106	chr11:61521918-61523106	chr11:61516015-61517214	chr11:61521420-61521917			44.93
N	intron_retention		chr2	-	chr2:242440335-242440892				chr2:242440334-242440335;chr2:242440892-242440893		77.78
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		20.93
K	jcn_only_AD	CUFF.286	chr14	-	chr14:81745084-81837331	chr14:81745084-81772975				chr14:81743245-81745083	72.73
K	alternative_last_exon	CUFF.662	chr2	+	chr2:219457431-219458891,chr2:219457431-219458830	chr2:219457431-219458250	chr2:219458892-219461803	chr2:219458251-219458642			38.78
K	cassette	CUFF.403	chr16	+	chr16:67233905-67234353	chr16:67233905-67234094;chr16:67234265-67234353		chr16:67234095-67234264			56.31
K	intron_retention	CUFF.547	chr19	-	chr19:41938314-41939176				chr19:41938313-41938314;chr19:41939176-41939177		64.49
K	alternative_acceptor	CUFF.758	chr3	-	chr3:57569788-57570110;chr3:57569735-57570110	chr3:57569760-57570110		chr3:57569735-57569759;chr3:57569760-57569787	chr3:57569734-57569735;chr3:57569759-57569760		4.88
N	jcn_only_AD	CUFF.56	chr1	+	chr1:160146353-160147308	chr1:160146393-160147308		chr1:160146353-160146392	chr1:160146352-160146353		60.98
K	intron_retention	CUFF.330	chr15	+	chr15:64445884-64446133				chr15:64445883-64445884;chr15:64446133-64446134		19.48
N	alternative_acceptor	CUFF.739	chr3	+	chr3:28357915-28360222;chr3:28357915-28360999	chr3:28357915-28358243		chr3:28358244-28360222;chr3:28360223-28360999	chr3:28360222-28360223;chr3:28360999-28361000		3.54
K	intron_retention	CUFF.187	chr11	+	chr11:119056875-119057187				chr11:119056874-119056875;chr11:119057187-119057188		28.34
K	alternative_first_exon	CUFF.564	chr19	+	chr19:52901154-52901619,chr19:52901158-52901619	chr19:52901274-52901619	chr19:52901102-52901153	chr19:52901181-52901273			8.06
K	alternative_donor	CUFF.875	chr5	-	chr5:54410147-54415640	chr5:54410147-54415628		chr5:54415629-54415640	chr5:54415640-54415641		87.50
K	alternative_first_exon	CUFF.1113	chrX	-	chrX:9130946-9132333	chrX:9130946-9131117	chrX:9132334-9132709	chrX:9131118-9131318			38.46
N	cassette	CUFF.786	chr3	-	chr3:127294109-127294782;chr3:127294349-127294782	chr3:127294109-127294591,chr3:127294349-127294591;chr3:127294653-127294782		chr3:127294592-127294652			85.14
N	jcn_only_AD	CUFF.979	chr7	+	chr7:65579902-65592690;chr7:65591631-65592690	chr7:65579958-65592690		chr7:65579902-65579957;chr7:65579958-65591630	chr7:65579901-65579902;chr7:65579957-65579958		67.69
K	cassette	CUFF.87	chr10	+	chr10:5120170-5138601	chr10:5120170-5122937;chr10:5123094-5138601		chr10:5122938-5123093			43.48
K	intron_retention	CUFF.716	chr22	+	chr22:29694886-29695223				chr22:29694885-29694886;chr22:29695223-29695224		10.40
K	jcn_only_AD	CUFF.636	chr2	+	chr2:133070569-133074681	chr2:133070573-133074681		chr2:133070569-133070572	chr2:133070568-133070569		76.92
K	alternative_last_exon	CUFF.768	chr3	+	chr3:112048234-112051032	chr3:112048234-112049096	chr3:112051033-112051638	chr3:112049097-112049232			45.45
K	alternative_first_exon	CUFF.197	chr12	+	chr12:1684008-1740463,chr12:1739393-1740463,chr12:1738538-1740463;chr12:1639176-1740463;chr12:1726310-1740463	chr12:1640117-1740463	chr12:1639057-1639175;chr12:1725805-1726309	chr12:1639910-1640116			41.13
K	intron_retention	CUFF.561	chr19	-	chr19:51537897-51538061				chr19:51537896-51537897;chr19:51538061-51538062		1.46
K	intron_retention	CUFF.1032	chr8	-	chr8:38005846-38006158				chr8:38005845-38005846;chr8:38006158-38006159		8.11
N	jcn_only_AD	CUFF.489	chr18	-	chr18:47329224-47337765;chr18:47329224-47340051;chr18:47329224-47339094;chr18:47329224-47339838;chr18:47329224-47340101	chr18:47329224-47340186		chr18:47337766-47339094;chr18:47339095-47339838;chr18:47339839-47340051;chr18:47340052-47340101;chr18:47340102-47340186	chr18:47339094-47339095;chr18:47339838-47339839;chr18:47340051-47340052;chr18:47340101-47340102;chr18:47340186-47340187		4.70
N	cassette	CUFF.162	chr11	+	chr11:63672516-63676348;chr11:63673587-63676348	chr11:63672516-63675731,chr11:63673587-63675731;chr11:63675777-63676348		chr11:63675732-63675776			53.93
N	cassette	CUFF.234	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			46.58
N	cassette	CUFF.478	chr18	+	chr18:163454-178932;chr18:163454-180235	chr18:163454-166786;chr18:166820-180235,chr18:166820-178932		chr18:166787-166819			31.03
N	alternative_acceptor	CUFF.56	chr1	+	chr1:160151822-160156065	chr1:160151822-160152481		chr1:160152482-160156065	chr1:160156065-160156066		1.42
N	intron_retention	CUFF.1148	chrX	-	chrX:152988744-152989409				chrX:152988743-152988744;chrX:152989409-152989410		60.71
N	alternative_first_exon	CUFF.188	chr11	-	chr11:2187780-2188664	chr11:2187780-2187862	chr11:2188665-2188746	chr11:2187863-2188007			96.31
K	alternative_acceptor	CUFF.426	chr17	-	chr17:15586472-15587509	chr17:15586686-15587509		chr17:15586472-15586685	chr17:15586471-15586472		14.85
K	cassette	CUFF.278	chr14	-	chr14:75150237-75152302	chr14:75150237-75151156;chr14:75151384-75152302		chr14:75151157-75151383		chr14:75149999-75150236;chr14:75152303-75152363	53.09
N	alternative_acceptor	CUFF.151	chr11	-	chr11:8941998-8947009	chr11:8943063-8947009		chr11:8941998-8943062	chr11:8941997-8941998		4.00
K	intron_retention	CUFF.161	chr11	-	chr11:62364888-62365081				chr11:62364887-62364888;chr11:62365081-62365082		10.91
N	intron_retention		chr3	-	chr3:125741776-125745235				chr3:125741775-125741776;chr3:125745235-125745236		95.06
N	alternative_donor	CUFF.979	chr7	+	chr7:65579958-65592690;chr7:65591631-65592690	chr7:65579902-65592690		chr7:65579902-65579957;chr7:65579958-65591630	chr7:65579901-65579902;chr7:65579957-65579958		31.25
N	alternative_donor	CUFF.1131	chrX	-	chrX:85282562-85302487	chrX:85282562-85302250		chrX:85302251-85302487	chrX:85302487-85302488		2.78
N	alternative_acceptor	CUFF.182	chr11	+	chr11:118405071-118405221;chr11:118405071-118406222	chr11:118405071-118416833		chr11:118405222-118406222;chr11:118406223-118416833	chr11:118406222-118406223;chr11:118416833-118416834	chr11:118404981-118405070	49.12
N	alternative_donor	CUFF.1018,CUFF.998	chr7	-	chr7:102251590-102256969;chr7:102251590-102257071	chr7:102251590-102252518		chr7:102252519-102256969;chr7:102256970-102257071	chr7:102256969-102256970;chr7:102257071-102257072		2.94
N	alternative_donor	CUFF.325	chr15	+	chr15:57535749-57543547	chr15:57540280-57543547		chr15:57535749-57540279	chr15:57535748-57535749		10.91
N	jcn_only_AA	CUFF.352	chr15	-	chr15:90420657-90431752;chr15:90414779-90431752	chr15:90421533-90431752		chr15:90414779-90420656;chr15:90420657-90421532	chr15:90414778-90414779;chr15:90420656-90420657		12.69
K	alternative_first_exon	CUFF.67	chr1	+	chr1:196789033-196918584	chr1:196913069-196918584	chr1:196788898-196789032	chr1:196912830-196913068		chr1:196918585-196918779	80.00
K	intron_retention	CUFF.557	chr19	+	chr19:50308834-50308981				chr19:50308833-50308834;chr19:50308981-50308982		88.64
K	intron_retention	CUFF.149	chr11	-	chr11:6640147-6640426				chr11:6640146-6640147;chr11:6640426-6640427		4.56
N	jcn_only_AD	CUFF.83	chr1	+	chr1:245222761-245245384	chr1:245238914-245245384		chr1:245222761-245238913	chr1:245222760-245222761		3.76
K	intron_retention	CUFF.1031	chr8	-	chr8:30643506-30657232				chr8:30643505-30643506;chr8:30657232-30657233		39.82
N	alternative_acceptor	CUFF.28	chr1	+	chr1:70820791-70832126	chr1:70820791-70831828		chr1:70831829-70832126	chr1:70832126-70832127		10.11
N	alternative_acceptor	CUFF.1110	chrX	+	chrX:1393712-1401301	chrX:1393712-1400763		chrX:1400764-1401301	chrX:1401301-1401302		62.41
K	intron_retention	CUFF.410	chr16	-	chr16:75575354-75576499				chr16:75575353-75575354;chr16:75576499-75576500		11.80
K	intron_retention		chr11	+	chr11:118403177-118403631				chr11:118403176-118403177;chr11:118403631-118403632	chr11:118402865-118403176;chr11:118403632-118403922	14.01
K	intron_retention		chr19	+	chr19:17597767-17597908				chr19:17597766-17597767;chr19:17597908-17597909		95.00
K	alternative_first_exon	CUFF.6	chr1	-	chr1:11710892-11715696;chr1:11710892-11713447	chr1:11710892-11714375	chr1:11715697-11715916;chr1:11713448-11713601	chr1:11714376-11714739			57.14
K	intron_retention	CUFF.944	chr6	+	chr6:126319281-126319368				chr6:126319280-126319281;chr6:126319368-126319369		32.58
N	jcn_only_AD	CUFF.350	chr15	-	chr15:64658275-64665896	chr15:64658275-64665354		chr15:64665355-64665896	chr15:64665896-64665897		77.42
K	alternative_first_exon	CUFF.152	chr11	-	chr11:10823983-10827453	chr11:10823983-10824576	chr11:10827454-10827841	chr11:10824577-10824675			48.57
N	jcn_only_AD	CUFF.457	chr17	+	chr17:61571021-61571282;chr17:61567390-61571282	chr17:61568730-61571282		chr17:61567390-61568729;chr17:61568730-61571020	chr17:61567389-61567390;chr17:61568729-61568730		3.24
K	alternative_last_exon	CUFF.425	chr17	-	chr17:15472345-15496650	chr17:15492542-15496650	chr17:15472205-15472344	chr17:15491607-15492541			79.41
N	jcn_only_AA	CUFF.426	chr17	-	chr17:15557746-15584178;chr17:15580997-15584178	chr17:15581036-15584178		chr17:15557746-15580996;chr17:15580997-15581035	chr17:15557745-15557746;chr17:15580996-15580997		86.92
N	cassette	CUFF.486	chr18	-	chr18:44471018-44500021	chr18:44471018-44483489;chr18:44483597-44500021		chr18:44483490-44483596			92.31
K	coord_cassette	CUFF.975	chr7	+	chr7:44247798-44251845	chr7:44247798-44250440;chr7:44250531-44250621;chr7:44250724-44251845		chr7:44250441-44250530;chr7:44250622-44250723			54.55
N	jcn_only_AD	CUFF.407	chr16	+	chr16:70380952-70384459	chr16:70381894-70384459		chr16:70380952-70381893	chr16:70380951-70380952		6.72
N	jcn_only_AA		chr1	+	chr1:32540679-32541267	chr1:32540679-32541203		chr1:32541204-32541267	chr1:32541267-32541268		95.62
K	intron_retention	CUFF.474	chr17	-	chr17:79916872-79917346				chr17:79916871-79916872;chr17:79917346-79917347		2.02
K	alternative_acceptor	CUFF.504	chr19	+	chr19:1438428-1438809	chr19:1438428-1438805		chr19:1438806-1438809	chr19:1438809-1438810		78.51
N	alternative_donor	CUFF.951	chr6	+	chr6:145119127-145124171	chr6:145120610-145124171		chr6:145119127-145120609	chr6:145119126-145119127		0.00
K	cassette	CUFF.944	chr6	+	chr6:126320760-126329537	chr6:126320760-126327987;chr6:126328101-126329537		chr6:126327988-126328100			12.50
K	cassette	CUFF.875	chr5	-	chr5:54415747-54420630	chr5:54415747-54416252;chr5:54416379-54420630		chr5:54416253-54416378			45.76
K	intron_retention		chr14	+	chr14:50249176-50249259				chr14:50249175-50249176;chr14:50249259-50249260		24.00
K	intron_retention	CUFF.494	chr18	+	chr18:61826223-61826329				chr18:61826222-61826223;chr18:61826329-61826330		44.00
N	alternative_acceptor		chr19	+	chr19:17597767-17597982	chr19:17597767-17597908		chr19:17597909-17597982	chr19:17597982-17597983		75.00
K	intron_retention	CUFF.1048	chr8	-	chr8:99055004-99057574				chr8:99055003-99055004;chr8:99057574-99057575		31.11
K	intron_retention	CUFF.221	chr12	+	chr12:52404926-52407470				chr12:52404925-52404926;chr12:52407470-52407471		30.30
N	coord_cassette	CUFF.905	chr6	+	chr6:292561-345853	chr6:292561-304627;chr6:304662-311879;chr6:311915-345853		chr6:304628-304661;chr6:311880-311914			70.51
K	intron_retention	CUFF.666	chr2	+	chr2:232258622-232259365				chr2:232258621-232258622;chr2:232259365-232259366		38.46
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		73.17
N	jcn_only_AA	CUFF.786	chr3	-	chr3:127299007-127309252	chr3:127307004-127309252		chr3:127299007-127307003	chr3:127299006-127299007		19.79
K	alternative_donor	CUFF.542	chr19	-	chr19:39924059-39924133;chr19:39924059-39924157	chr19:39924059-39924161		chr19:39924134-39924157;chr19:39924158-39924161	chr19:39924157-39924158;chr19:39924161-39924162		85.07
K	intron_retention	CUFF.490	chr18	+	chr18:56056425-56057877				chr18:56056424-56056425;chr18:56057877-56057878		2.51
K	alternative_acceptor	CUFF.872,CUFF.878	chr5	+	chr5:50685767-50687176	chr5:50685767-50687107		chr5:50687108-50687176	chr5:50687176-50687177	chr5:50685480-50685766;chr5:50687177-50687275	77.12
N	jcn_only_AD	CUFF.631	chr2	+	chr2:109068923-109085435	chr2:109079142-109085435		chr2:109068923-109079141	chr2:109068922-109068923		21.62
K	intron_retention	CUFF.683	chr20	+	chr20:30149540-30154012				chr20:30149539-30149540;chr20:30154012-30154013		26.34
N	alternative_acceptor	CUFF.1119	chrX	-	chrX:20252933-20285156	chrX:20258788-20285156		chrX:20252933-20258787	chrX:20252932-20252933		0.00
N	jcn_only_AA	CUFF.419	chr17	-	chr17:5405193-5421065;chr17:5409298-5421065	chr17:5418838-5421065					89.91
K	alternative_first_exon	CUFF.2	chr1	+	chr1:2006573-2066700,chr1:2043257-2066700,chr1:2005369-2066700,chr1:2013900-2066700,chr1:2036335-2066700,chr1:2029995-2066700,chr1:2065440-2066700,chr1:2006819-2066700,chr1:2005715-2066700,chr1:2047750-2066700;chr1:1991031-2066700;chr1:2066526-2066700	chr1:2006207-2066700	chr1:1990980-1991030;chr1:2066291-2066525	chr1:2006119-2006206			1.50
N	cassette	CUFF.234	chr12	+	chr12:69207409-69214104;chr12:69203073-69214104	chr12:69207409-69210591,chr12:69203073-69210591;chr12:69210726-69214104		chr12:69210592-69210725			27.11
N	alternative_donor	CUFF.324,CUFF.352	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		0.47
N	jcn_only_AA	CUFF.155	chr11	+	chr11:61584169-61605249	chr11:61584169-61588852				chr11:61583838-61584168	75.36
N	alternative_acceptor	CUFF.432	chr17	+	chr17:25967800-25969263	chr17:25967800-25967990		chr17:25967991-25969263	chr17:25969263-25969264		11.19
N	jcn_only_AD	CUFF.325	chr15	+	chr15:57426699-57458599;chr15:57401516-57458599;chr15:57422171-57458599	chr15:57384090-57458599		chr15:57384090-57401515;chr15:57401516-57422170;chr15:57422171-57426698	chr15:57384089-57384090;chr15:57401515-57401516;chr15:57422170-57422171		73.08
N	alternative_donor	CUFF.374	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		20.48
N	alternative_first_exon	CUFF.176	chr11	-	chr11:2187999-2188664	chr11:2187999-2188116	chr11:2188665-2188746	chr11:2188117-2188324			97.42
K	intron_retention	CUFF.224	chr12	-	chr12:53468569-53468878				chr12:53468568-53468569;chr12:53468878-53468879		11.86
N	jcn_only_AA	CUFF.171	chr11	-	chr11:75520420-75522468;chr11:75514563-75522468	chr11:75514771-75522468		chr11:75514563-75514770;chr11:75514771-75520419	chr11:75514562-75514563;chr11:75514770-75514771		40.48
N	jcn_only_AA	CUFF.211	chr12	-	chr12:25673010-25679702	chr12:25679153-25679702					95.90
K	alternative_donor	CUFF.414	chr16	-	chr16:87811607-87812592	chr16:87811607-87812413		chr16:87812414-87812592	chr16:87812592-87812593		50.00
N	jcn_only_AD		chr14	-	chr14:59941245-59942586	chr14:59941245-59941445		chr14:59941446-59942586	chr14:59942586-59942587		21.28
N	jcn_only_AA		chr10	+	chr10:35485071-35495822	chr10:35485071-35490378		chr10:35490379-35495822	chr10:35495822-35495823		9.32
N	jcn_only_AD		chr3	-	chr3:73453547-73482789;chr3:73453547-73610601;chr3:73453547-73651504;chr3:73453547-73523605;chr3:73453547-73605850	chr3:73453547-73618301					8.51
K	jcn_only_AD	CUFF.858	chr4	+	chr4:186185653-186188122	chr4:186185765-186188122		chr4:186185653-186185764	chr4:186185652-186185653		71.93
N	alternative_acceptor	CUFF.661	chr2	+	chr2:219222458-219222759	chr2:219222458-219222708		chr2:219222709-219222759	chr2:219222759-219222760		37.50
N	alternative_donor	CUFF.236	chr12	-	chr12:77254194-77256955	chr12:77254194-77256589		chr12:77256590-77256955	chr12:77256955-77256956		31.48
K	intron_retention	CUFF.1000	chr7	+	chr7:107215756-107216853				chr7:107215755-107215756;chr7:107216853-107216854		78.95
K	intron_retention	CUFF.53	chr1	-	chr1:156908306-156908940				chr1:156908305-156908306;chr1:156908940-156908941		14.52
K	alternative_donor	CUFF.370	chr16	+	chr16:2141610-2142889	chr16:2141616-2142889		chr16:2141610-2141615	chr16:2141609-2141610		5.52
N	alternative_donor		chr4	-	chr4:152147239-152246392;chr4:152147239-152187237	chr4:152147239-152147319		chr4:152147320-152187237;chr4:152187238-152246392	chr4:152187237-152187238;chr4:152246392-152246393		0.00
K	intron_retention	CUFF.1101	chr9	-	chr9:131484854-131486272				chr9:131484853-131484854;chr9:131486272-131486273		11.98
N	alternative_donor	CUFF.848	chr4	+	chr4:120381976-120382871	chr4:120381983-120382871		chr4:120381976-120381982	chr4:120381975-120381976		67.88
K	jcn_only_AA	CUFF.228	chr12	-	chr12:56578877-56579938	chr12:56578896-56579938		chr12:56578877-56578895	chr12:56578876-56578877		31.82
K	alternative_first_exon	CUFF.658	chr2	-	chr2:208030431-208031480;chr2:208030431-208030636	chr2:208030431-208031717	chr2:208031481-208031578;chr2:208030637-208030969	chr2:208031718-208032084			26.92
N	intron_retention		chr2	+	chr2:220095073-220096981				chr2:220095072-220095073;chr2:220096981-220096982		30.08
N	alternative_first_exon	CUFF.212	chr12	+	chr12:26148064-26173077	chr12:26164755-26173077	chr12:26147970-26148063	chr12:26164591-26164754			95.40
K	cassette	CUFF.836	chr4	-	chr4:77102255-77116859	chr4:77102255-77105809;chr4:77105934-77116859		chr4:77105810-77105933			40.00
K	jcn_only_AD	CUFF.944	chr6	+	chr6:126342412-126359850	chr6:126342427-126359850		chr6:126342412-126342426	chr6:126342411-126342412		91.23
N	coord_cassette	CUFF.114	chr10	-	chr10:73956748-73972944	chr10:73956748-73963184;chr10:73963283-73970489;chr10:73970590-73971945;chr10:73972044-73972944		chr10:73963185-73963282;chr10:73970490-73970589;chr10:73971946-73972043			60.00
K	alternative_first_exon	CUFF.37	chr1	-	chr1:113471975-113472502,chr1:113471975-113497897;chr1:113471975-113498656;chr1:113471975-113499460	chr1:113471975-113478445	chr1:113498657-113498975;chr1:113499461-113499724	chr1:113478446-113478667			28.99
K	alternative_last_exon	CUFF.876,CUFF.890	chr5	+	chr5:131649462-131657876	chr5:131649462-131656557	chr5:131657877-131658048	chr5:131656558-131656763			89.92
K	cassette	CUFF.1008	chr7	-	chr7:127251731-127253075	chr7:127251731-127251998;chr7:127252055-127253075		chr7:127251999-127252054			67.57
K	alternative_acceptor	CUFF.225	chr12	+	chr12:53854928-53856276	chr12:53854928-53856264		chr12:53856265-53856276	chr12:53856276-53856277		40.67
K	intron_retention	CUFF.225	chr12	+	chr12:53854928-53856276				chr12:53854927-53854928;chr12:53856276-53856277		15.24
N	cassette	CUFF.946	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			49.50
K	intron_retention	CUFF.589	chr2	-	chr2:27706805-27707093				chr2:27706804-27706805;chr2:27707093-27707094		37.04
N	intron_retention		chr7	-	chr7:107569651-107569856				chr7:107569650-107569651;chr7:107569856-107569857		82.43
N	coord_cassette	CUFF.490	chr18	+	chr18:56001125-56016768	chr18:56001125-56008909;chr18:56009030-56010137;chr18:56010336-56016768		chr18:56008910-56009029;chr18:56010138-56010335			53.70
N	alternative_donor	CUFF.911	chr6	-	chr6:114289861-114292020	chr6:114289861-114291643		chr6:114291644-114292020	chr6:114292020-114292021		61.76
N	alternative_acceptor	CUFF.734	chr3	+	chr3:19992554-20017092;chr3:19992554-20017134;chr3:19992554-20017078	chr3:19992554-20012039		chr3:20012040-20017078;chr3:20017079-20017092;chr3:20017093-20017134	chr3:20017078-20017079;chr3:20017092-20017093;chr3:20017134-20017135		0.00
N	cassette	CUFF.639	chr2	+	chr2:160619505-160623794	chr2:160619505-160621136;chr2:160621186-160623794		chr2:160621137-160621185			45.21
K	alternative_acceptor	CUFF.187	chr11	+	chr11:119056662-119057324	chr11:119056662-119056800		chr11:119056801-119057324	chr11:119057324-119057325		95.74
K	cassette	CUFF.588	chr2	-	chr2:25180844-25186273	chr2:25180844-25181415;chr2:25181471-25186273		chr2:25181416-25181470			81.44
N	jcn_only_AD	CUFF.1098	chr9	-	chr9:130929444-130929817;chr9:130929444-130931354	chr9:130929444-130931330		chr9:130929818-130931330;chr9:130931331-130931354	chr9:130931330-130931331;chr9:130931354-130931355		76.86
N	alternative_donor	CUFF.498	chr18	-	chr18:72914296-72917147;chr18:72914296-72920315	chr18:72914296-72920374		chr18:72917148-72920315;chr18:72920316-72920374	chr18:72920315-72920316;chr18:72920374-72920375		11.29
N	jcn_only_AA	CUFF.152	chr11	-	chr11:10821157-10821636	chr11:10821304-10821636		chr11:10821157-10821303	chr11:10821156-10821157		76.00
N	alternative_donor	CUFF.325	chr15	+	chr15:57213297-57355947	chr15:57293583-57355947		chr15:57213297-57293582	chr15:57213296-57213297		0.00
K	alternative_last_exon	CUFF.524	chr19	-	chr19:14847057-14854231	chr19:14852899-14854231	chr19:14843106-14847056	chr19:14852807-14852898			5.63
K	intron_retention	CUFF.833	chr4	-	chr4:69054335-69056965				chr4:69054334-69054335;chr4:69056965-69056966		66.67
N	jcn_only_AD	CUFF.490	chr18	+	chr18:56024485-56031499	chr18:56027291-56031499		chr18:56024485-56027290	chr18:56024484-56024485		12.78
N	alternative_acceptor	CUFF.715	chr22	+	chr22:29538089-29563031	chr22:29538089-29550325		chr22:29550326-29563031	chr22:29563031-29563032		0.00
K	intron_retention	CUFF.330	chr15	+	chr15:64444942-64445443				chr15:64444941-64444942;chr15:64445443-64445444		18.18
K	intron_retention	CUFF.176	chr11	-	chr11:102960039-102962412				chr11:102960038-102960039;chr11:102962412-102962413		50.00
N	intron_retention		chr3	-	chr3:141697525-141713861				chr3:141697524-141697525;chr3:141713861-141713862		73.73
N	alternative_last_exon		chr5	+	chr5:56531860-56542126	chr5:56531860-56532939	chr5:56542127-56542311	chr5:56532940-56533411		chr5:56531793-56531859	75.34
N	intron_retention		chr17	-	chr17:56081363-56082283				chr17:56081362-56081363;chr17:56082283-56082284		33.33
N	jcn_only_AD	CUFF.456	chr17	+	chr17:60784969-60813446;chr17:60777141-60813446	chr17:60783831-60813446		chr17:60777141-60783830;chr17:60783831-60784968	chr17:60777140-60777141;chr17:60783830-60783831		8.33
N	alternative_acceptor	CUFF.826	chr4	-	chr4:36152667-36160351	chr4:36159173-36160351		chr4:36152667-36159172	chr4:36152666-36152667		0.00
N	cassette	CUFF.265	chr14	+	chr14:50247041-50249087	chr14:50247041-50247420;chr14:50247494-50249087		chr14:50247421-50247493			96.69
N	alternative_donor		chr19	-	chr19:6047516-6148241;chr19:6047516-6049146;chr19:6047516-6057172;chr19:6047516-6072015	chr19:6047516-6110403		chr19:6049147-6057172;chr19:6057173-6072015;chr19:6072016-6110403;chr19:6110404-6148241	chr19:6057172-6057173;chr19:6072015-6072016;chr19:6110403-6110404;chr19:6148241-6148242		7.69
K	intron_retention	CUFF.929	chr6	-	chr6:43481372-43483332				chr6:43481371-43481372;chr6:43483332-43483333		1.85
K	alternative_last_exon	CUFF.321	chr15	-	chr15:50805710-50821993;chr15:50793035-50821993	chr15:50793249-50821993	chr15:50792759-50793034	chr15:50793047-50793248			16.33
K	alternative_acceptor	CUFF.848	chr4	+	chr4:120415679-120418965	chr4:120415679-120418816		chr4:120418817-120418965	chr4:120418965-120418966		59.91
N	jcn_only_AD	CUFF.966	chr7	-	chr7:22206767-22232984	chr7:22206767-22231146		chr7:22231147-22232984	chr7:22232984-22232985		16.00
N	jcn_only_AD	CUFF.347	chr15	-	chr15:83358206-83366608;chr15:83358206-83378345;chr15:83358206-83377523	chr15:83358206-83358514		chr15:83358515-83366608;chr15:83366609-83377523;chr15:83377524-83378345	chr15:83366608-83366609;chr15:83377523-83377524;chr15:83378345-83378346		22.86
K	alternative_last_exon	CUFF.324	chr15	-	chr15:55703354-55724694	chr15:55722978-55724694	chr15:55703307-55703353	chr15:55722409-55722977			75.49
N	alternative_first_exon	CUFF.769	chr3	+	chr3:119196296-119198754	chr3:119197322-119198754	chr3:119196160-119196295	chr3:119196874-119197321			99.27
N	jcn_only_AA	CUFF.310	chr15	+	chr15:24803469-24811802	chr15:24803469-24811235					23.08
K	jcn_only_AA	CUFF.311	chr15	+	chr15:40756747-40757542	chr15:40756747-40757533		chr15:40757534-40757542	chr15:40757542-40757543		50.00
N	jcn_only_AD	CUFF.751	chr3	-	chr3:46982556-47007473;chr3:46982556-47017842	chr3:46982556-47018126		chr3:47007474-47017842;chr3:47017843-47018126	chr3:47017842-47017843;chr3:47018126-47018127		49.69
K	alternative_first_exon	CUFF.782,CUFF.796	chr3	-	chr3:156271571-156272525;chr3:156271571-156271781	chr3:156271571-156272745	chr3:156272526-156272688;chr3:156271782-156271977	chr3:156272746-156272973			35.87
K	alternative_first_exon	CUFF.905	chr6	+	chr6:291701-304627	chr6:292561-304627	chr6:291589-291700	chr6:292017-292560			93.55
N	jcn_only_AA	CUFF.765	chr3	-	chr3:107572902-107573976;chr3:107573542-107573976	chr3:107572807-107573976		chr3:107572807-107572901;chr3:107572902-107573541	chr3:107572806-107572807;chr3:107572901-107572902		7.69
K	alternative_first_exon	CUFF.701	chr21	-	chr21:43342195-43362255	chr21:43342195-43346680	chr21:43362256-43362368	chr21:43346681-43346777			8.51
N	cassette	CUFF.673	chr2	+	chr2:242590751-242592926;chr2:242590751-242592721	chr2:242590751-242591298;chr2:242591390-242592926,chr2:242591390-242592721		chr2:242591299-242591389			32.13
K	intron_retention	CUFF.140	chr11	-	chr11:2188716-2189095				chr11:2188715-2188716;chr11:2189095-2189096		8.00
N	intron_retention		chr17	-	chr17:40738156-40761103				chr17:40738155-40738156;chr17:40761103-40761104		31.91
K	alternative_last_exon	CUFF.23	chr1	-	chr1:53883339-53905447	chr1:53904722-53905447	chr1:53883200-53883338	chr1:53903907-53904721			60.00
N	jcn_only_AD		chr14	-	chr14:59939809-59941156;chr14:59939809-59941445	chr14:59939809-59942586		chr14:59941157-59941445;chr14:59941446-59942586	chr14:59941445-59941446;chr14:59942586-59942587		83.98
K	jcn_only_AA	CUFF.187	chr11	+	chr11:119056220-119056557;chr11:119056220-119056630	chr11:119056220-119056633		chr11:119056558-119056630;chr11:119056631-119056633	chr11:119056630-119056631;chr11:119056633-119056634		55.69
N	alternative_donor	CUFF.354	chr15	+	chr15:91304486-91306195	chr15:91305653-91306195		chr15:91304486-91305652	chr15:91304485-91304486		8.33
K	alternative_first_exon	CUFF.114	chr10	-	chr10:73912747-73921295	chr10:73912747-73918703	chr10:73921296-73921432	chr10:73918704-73918801			4.11
N	alternative_donor	CUFF.286	chr14	-	chr14:81893557-81902664	chr14:81893557-81902431		chr14:81902432-81902664	chr14:81902664-81902665	chr14:81893446-81893556	30.77
K	jcn_only_AA	CUFF.1061	chr8	+	chr8:144351691-144356873;chr8:144351691-144356889	chr8:144351691-144354565					7.69
N	mutually_exclusive	CUFF.782	chr3	-	chr3:125752522-125786789,chr3:125787090-125820271	chr3:125752522-125769785,chr3:125769894-125820271	chr3:125786790-125787089	chr3:125769786-125769893			55.56
N	alternative_donor		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		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		18.92
N	jcn_only_AA	CUFF.274	chr14	-	chr14:69542129-69558390	chr14:69557874-69558390		chr14:69542129-69557873	chr14:69542128-69542129		14.63
N	alternative_acceptor	CUFF.189	chr11	-	chr11:119291046-119291578;chr11:119291097-119291578	chr11:119291089-119291578		chr11:119291046-119291088;chr11:119291089-119291096	chr11:119291045-119291046;chr11:119291088-119291089		6.76
N	alternative_first_exon	CUFF.683	chr20	+	chr20:30137925-30147413	chr20:30142633-30147413	chr20:30137867-30137924	chr20:30142380-30142632			99.01
K	alternative_first_exon	CUFF.376	chr16	-	chr16:4254636-4289634	chr16:4254636-4256727	chr16:4289635-4289799	chr16:4256728-4258105			13.33
K	jcn_only_AA	CUFF.403	chr16	+	chr16:67234872-67235311	chr16:67234872-67235287		chr16:67235288-67235311	chr16:67235311-67235312		60.47
N	intron_retention		chr8	+	chr8:144356973-144358172				chr8:144356972-144356973;chr8:144358172-144358173		94.64
K	jcn_only_AD	CUFF.1012	chr7	+	chr7:134249522-134252909	chr7:134250299-134252909		chr7:134249522-134250298	chr7:134249521-134249522		88.64
N	jcn_only_AD		chr3	-	chr3:33686396-33700998;chr3:33686396-33686835;chr3:33686396-33686773;chr3:33686396-33686494	chr3:33686396-33700465					8.12
N	jcn_only_AD	CUFF.971	chr7	-	chr7:37382368-37392635;chr7:37382368-37488277;chr7:37382368-37488462;chr7:37382368-37382655	chr7:37382368-37433424		chr7:37382656-37392635;chr7:37392636-37433424;chr7:37433425-37488277;chr7:37488278-37488462	chr7:37392635-37392636;chr7:37433424-37433425;chr7:37488277-37488278;chr7:37488462-37488463		52.17
N	jcn_only_AD	CUFF.818	chr4	-	chr4:83821377-83821524	chr4:83821377-83821486		chr4:83821487-83821524	chr4:83821524-83821525		95.76
K	intron_retention	CUFF.83	chr1	+	chr1:245133746-245180543				chr1:245133745-245133746;chr1:245180543-245180544		23.44
N	jcn_only_AD	CUFF.457	chr17	+	chr17:61562331-61562596;chr17:61562428-61562596	chr17:61561903-61562596		chr17:61561903-61562330;chr17:61562331-61562427	chr17:61561902-61561903;chr17:61562330-61562331		9.52
K	jcn_only_AA	CUFF.550,CUFF.566	chr19	+	chr19:44768529-44770350	chr19:44768529-44770307		chr19:44770308-44770350	chr19:44770350-44770351		12.93
N	intron_retention		chr11	+	chr11:828260-828574				chr11:828259-828260;chr11:828574-828575	chr11:828230-828259;chr11:828575-828772	64.97
N	jcn_only_AD	CUFF.506	chr19	+	chr19:4323235-4323344;chr19:4323211-4323344	chr19:4323144-4323344		chr19:4323144-4323210;chr19:4323211-4323234	chr19:4323143-4323144;chr19:4323210-4323211		6.30
K	mutually_exclusive	CUFF.567	chr19	+	chr19:55084903-55085542,chr19:55085579-55085767	chr19:55084903-55085297,chr19:55085380-55085767	chr19:55085543-55085578	chr19:55085298-55085379			88.33
K	cassette	CUFF.798	chr3	-	chr3:173628660-173632679	chr3:173628660-173630335;chr3:173630408-173632679		chr3:173630336-173630407			8.96
N	intron_retention		chr17	+	chr17:61568730-61571282				chr17:61568729-61568730;chr17:61571282-61571283		65.38
K	jcn_only_AA	CUFF.311,CUFF.319	chr15	+	chr15:40752096-40754113	chr15:40752096-40754110		chr15:40754111-40754113	chr15:40754113-40754114		75.00
K	cassette	CUFF.73	chr1	+	chr1:207287631-207288760	chr1:207287631-207288020;chr1:207288117-207288760		chr1:207288021-207288116			47.17
N	jcn_only_AD	CUFF.728	chr22	-	chr22:51018232-51018485	chr22:51018232-51018402		chr22:51018403-51018485	chr22:51018485-51018486		6.19
K	intron_retention	CUFF.146	chr11	+	chr11:3427946-3428851				chr11:3427945-3427946;chr11:3428851-3428852		70.80
K	intron_retention		chr1	+	chr1:245246991-245254795				chr1:245246990-245246991;chr1:245254795-245254796		12.07
K	alternative_first_exon	CUFF.919,CUFF.933	chr6	-	chr6:75975055-75994117	chr6:75975055-75977356	chr6:75994118-75994748	chr6:75977357-75977464			25.00
N	jcn_only_AA	CUFF.1101	chr9	-	chr9:131484854-131486272	chr9:131485019-131486272		chr9:131484854-131485018	chr9:131484853-131484854		11.16
N	alternative_donor	CUFF.265	chr14	+	chr14:50235340-50238311	chr14:50235810-50238311		chr14:50235340-50235809	chr14:50235339-50235340		13.64
K	intron_retention	CUFF.387	chr16	+	chr16:21976827-21979948				chr16:21976826-21976827;chr16:21979948-21979949		30.43
N	cassette	CUFF.773	chr3	-	chr3:119246689-119263396	chr3:119246689-119255983;chr3:119256266-119263396		chr3:119255984-119256265			32.88
N	jcn_only_AD	CUFF.352	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		3.48
K	alternative_first_exon	CUFF.184	chr11	-	chr11:118926880-118926990,chr11:118926880-118927711,chr11:118926880-118927737,chr11:118926880-118927863;chr11:118926880-118927730	chr11:118926880-118927515	chr11:118927731-118928009	chr11:118927516-118927646			11.76
K	cassette	CUFF.360	chr15	-	chr15:102194934-102197124	chr15:102194934-102196069;chr15:102196224-102197124		chr15:102196070-102196223			16.67
K	alternative_first_exon	CUFF.1028	chr8	-	chr8:23186079-23186485;chr8:23186079-23198504	chr8:23186079-23190913	chr8:23198505-23198716	chr8:23190914-23191189			71.67
K	intron_retention	CUFF.475	chr17	-	chr17:79994758-79994964				chr17:79994757-79994758;chr17:79994964-79994965		53.95
N	jcn_only_AA	CUFF.504	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		75.00
K	alternative_acceptor	CUFF.273	chr14	+	chr14:61545646-61550272	chr14:61545646-61550267		chr14:61550268-61550272	chr14:61550272-61550273		53.85
N	alternative_donor		chr9	-	chr9:104293842-104295734	chr9:104293842-104294958		chr9:104294959-104295734	chr9:104295734-104295735		40.00
N	jcn_only_AD	CUFF.1098	chr9	-	chr9:130929444-130929817;chr9:130929444-130931330	chr9:130929444-130931354		chr9:130929818-130931330;chr9:130931331-130931354	chr9:130931330-130931331;chr9:130931354-130931355		11.43
K	cassette	CUFF.876	chr5	+	chr5:54456225-54459882	chr5:54456225-54456821;chr5:54457084-54459882		chr5:54456822-54457083			44.95
K	jcn_only_AD	CUFF.334	chr15	-	chr15:67722739-67758831	chr15:67722739-67752029					98.86
K	cassette	CUFF.975	chr7	+	chr7:44247798-44251845	chr7:44247798-44250621;chr7:44250724-44251845		chr7:44250622-44250723			48.72
K	intron_retention	CUFF.805	chr3	-	chr3:193560545-193560866				chr3:193560544-193560545;chr3:193560866-193560867		89.74
K	alternative_acceptor	CUFF.1092	chr9	-	chr9:123550465-123555426	chr9:123550557-123555426		chr9:123550465-123550556	chr9:123550464-123550465		80.00
N	coord_cassette	CUFF.486	chr18	-	chr18:44471018-44500021	chr18:44471018-44473393;chr18:44473495-44483489;chr18:44483597-44500021		chr18:44473394-44473494;chr18:44483490-44483596			78.57
K	alternative_last_exon	CUFF.598	chr2	+	chr2:38231360-38239745;chr2:38231360-38294124	chr2:38231360-38244328	chr2:38294125-38294383	chr2:38244329-38244378			71.60
K	cassette	CUFF.350	chr15	-	chr15:84873269-84873538	chr15:84873269-84873351;chr15:84873444-84873538		chr15:84873352-84873443			60.00
N	alternative_donor	CUFF.663	chr2	+	chr2:220094681-220094949;chr2:220094703-220094949	chr2:220094623-220094949		chr2:220094623-220094680;chr2:220094681-220094702	chr2:220094622-220094623;chr2:220094680-220094681		83.24
K	jcn_only_AA	CUFF.418	chr17	+	chr17:1939386-1939822	chr17:1939386-1939722		chr17:1939723-1939822	chr17:1939822-1939823		8.93
K	alternative_first_exon	CUFF.1112	chrX	-	chrX:2408814-2418857	chrX:2408814-2418351	chrX:2418858-2419086	chrX:2418352-2418597			38.71
K	intron_retention	CUFF.475	chr17	-	chr17:79995424-79995506				chr17:79995423-79995424;chr17:79995506-79995507		45.95
N	alternative_donor		chr3	-	chr3:127313777-127317038	chr3:127313777-127314294		chr3:127314295-127317038	chr3:127317038-127317039		52.38
K	alternative_acceptor	CUFF.347	chr15	-	chr15:83331986-83332311	chr15:83332048-83332311		chr15:83331986-83332047	chr15:83331985-83331986		29.76
N	cassette	CUFF.132	chr10	-	chr10:123673409-123683780	chr10:123673409-123681863;chr10:123681927-123683780		chr10:123681864-123681926			97.81
N	alternative_donor	CUFF.306	chr15	+	chr15:29288010-29346047	chr15:29336632-29346047		chr15:29288010-29336631	chr15:29288009-29288010		0.00
K	alternative_donor	CUFF.18	chr1	+	chr1:32538653-32540551	chr1:32538700-32540551		chr1:32538653-32538699	chr1:32538652-32538653		7.50
N	jcn_only_AA	CUFF.722	chr22	+	chr22:37697061-37697921;chr22:37697061-37697975	chr22:37697061-37699294		chr22:37697922-37697975;chr22:37697976-37699294	chr22:37697975-37697976;chr22:37699294-37699295		4.74
N	alternative_acceptor	CUFF.722	chr22	+	chr22:37697061-37697921;chr22:37697061-37699294	chr22:37697061-37697975		chr22:37697922-37697975;chr22:37697976-37699294	chr22:37697975-37697976;chr22:37699294-37699295		3.92
N	cassette	CUFF.298	chr14	-	chr14:104212891-104213269	chr14:104212891-104212988;chr14:104213198-104213269		chr14:104212989-104213197			98.68
K	alternative_first_exon	CUFF.72	chr1	-	chr1:205593020-205600759	chr1:205593020-205594759	chr1:205600760-205601148	chr1:205594760-205594885			69.57
N	intron_retention		chr17	+	chr17:61907310-61907630				chr17:61907309-61907310;chr17:61907630-61907631		11.11
K	intron_retention	CUFF.1001	chr7	+	chr7:107234551-107236313				chr7:107234550-107234551;chr7:107236313-107236314		37.50
K	intron_retention	CUFF.36	chr1	+	chr1:110211994-110212092				chr1:110211993-110211994;chr1:110212092-110212093		35.02
N	alternative_donor	CUFF.877	chr5	-	chr5:54577344-54579030	chr5:54577344-54578943		chr5:54578944-54579030	chr5:54579030-54579031		25.00
K	cassette	CUFF.816	chr4	-	chr4:3949948-3954837	chr4:3949948-3952865;chr4:3952947-3954837		chr4:3952866-3952946			89.47
N	intron_retention	CUFF.426	chr17	-	chr17:15584268-15584364				chr17:15584267-15584268;chr17:15584364-15584365		74.07
K	intron_retention	CUFF.314	chr15	+	chr15:41222315-41222822				chr15:41222314-41222315;chr15:41222822-41222823		44.44
K	alternative_first_exon	CUFF.1111	chrX	+	chrX:1515542-1517717	chrX:1516118-1517717	chrX:1515245-1515541	chrX:1515866-1516117			43.59
N	alternative_acceptor	CUFF.1073	chr9	+	chr9:43853617-43861002;chr9:43853617-43854068	chr9:43853617-43861005		chr9:43854069-43861002;chr9:43861003-43861005	chr9:43861002-43861003;chr9:43861005-43861006		45.45
N	intron_retention		chr6	-	chr6:31938530-31938688				chr6:31938529-31938530;chr6:31938688-31938689		75.08
N	jcn_only_AD	CUFF.838	chr4	-	chr4:74459311-74481607	chr4:74459311-74464356		chr4:74464357-74481607	chr4:74481607-74481608		57.14
N	jcn_only_AD		chr10	-	chr10:78637652-78647048	chr10:78637652-78644746		chr10:78644747-78647048	chr10:78647048-78647049		34.15
N	intron_retention		chr17	+	chr17:61908786-61908865				chr17:61908785-61908786;chr17:61908865-61908866		37.15
N	alternative_acceptor	CUFF.152	chr11	-	chr11:10821157-10821636	chr11:10821304-10821636		chr11:10821157-10821303	chr11:10821156-10821157		84.21
N	cassette	CUFF.971	chr7	-	chr7:36917723-36934458	chr7:36917723-36927164;chr7:36927278-36934458		chr7:36927165-36927277			93.52
K	intron_retention	CUFF.252	chr13	-	chr13:78492760-78493531				chr13:78492759-78492760;chr13:78493531-78493532		36.36
N	intron_retention		chr11	+	chr11:118403177-118403804				chr11:118403176-118403177;chr11:118403804-118403805	chr11:118402865-118403176;chr11:118403805-118403922	89.63
N	jcn_only_AA	CUFF.273	chr14	+	chr14:61512886-61514868;chr14:61512886-61517229	chr14:61512886-61514965		chr14:61514869-61514965;chr14:61514966-61517229	chr14:61514965-61514966;chr14:61517229-61517230		5.81
K	alternative_last_exon	CUFF.319	chr15	+	chr15:45768751-45804570;chr15:45768751-45769966	chr15:45768751-45789310	chr15:45804571-45804647;chr15:45769967-45770054	chr15:45789311-45789564			57.75
N	cassette	CUFF.980	chr7	+	chr7:73101426-73106925;chr7:73101231-73106925	chr7:73101231-73105245,chr7:73101426-73105245;chr7:73105343-73106925		chr7:73105246-73105342			23.94
N	jcn_only_AA		chr2	-	chr2:242440493-242440892;chr2:242440335-242440892	chr2:242440263-242440892					41.79
K	jcn_only_AA	CUFF.144	chr11	-	chr11:2905141-2905228	chr11:2905146-2905228		chr11:2905141-2905145	chr11:2905140-2905141		39.45
K	alternative_last_exon	CUFF.685	chr20	-	chr20:31044199-31062403	chr20:31052921-31062403,chr20:31052938-31062403	chr20:31043921-31044198	chr20:31052485-31052920			89.86
K	intron_retention	CUFF.601	chr2	-	chr2:46840925-46842075				chr2:46840924-46840925;chr2:46842075-46842076		78.79
N	jcn_only_AA		chr15	+	chr15:24811948-24814929;chr15:24811948-24813043;chr15:24811948-24813677	chr15:24811948-24813038					45.45
N	alternative_acceptor	CUFF.68	chr1	+	chr1:200877016-200877857	chr1:200877016-200877243		chr1:200877244-200877857	chr1:200877857-200877858		63.64
N	alternative_donor	CUFF.709,CUFF.728	chr22	-	chr22:51020292-51020677	chr22:51020292-51020457		chr22:51020458-51020677	chr22:51020677-51020678		20.83
K	alternative_first_exon	CUFF.24	chr1	+	chr1:54356968-54359986	chr1:54357950-54359986	chr1:54356821-54356967	chr1:54357819-54357949			41.30
K	cassette	CUFF.951	chr6	+	chr6:145142155-145148746	chr6:145142155-145148483;chr6:145148523-145148746		chr6:145148484-145148522			55.00
K	alternative_first_exon	CUFF.1059	chr8	-	chr8:133851626-133856470	chr8:133851626-133854636	chr8:133856471-133856543	chr8:133854637-133855371			52.54
K	alternative_first_exon	CUFF.200	chr12	+	chr12:4440484-4446204	chr12:4444818-4446204	chr12:4440446-4440483	chr12:4444614-4444817			88.16
K	alternative_donor	CUFF.891	chr5	+	chr5:134190853-134193046	chr5:134191018-134193046		chr5:134190853-134191017	chr5:134190852-134190853		84.09
K	alternative_donor	CUFF.419,CUFF.467	chr17	-	chr17:5436305-5436623	chr17:5436305-5436611		chr17:5436612-5436623	chr17:5436623-5436624		1.37
K	cassette	CUFF.491	chr18	-	chr18:57106811-57115214	chr18:57106811-57106908;chr18:57107049-57115214		chr18:57106909-57107048			54.55
N	alternative_first_exon	CUFF.752	chr3	-	chr3:49349088-49355741;chr3:49349088-49362134	chr3:49349088-49351303	chr3:49355742-49356244;chr3:49362135-49362196	chr3:49351304-49351556			84.85
N	jcn_only_AA		chr7	-	chr7:117424509-117431344	chr7:117426480-117431344		chr7:117424509-117426479	chr7:117424508-117424509		60.00
K	alternative_first_exon	CUFF.152,CUFF.173	chr11	-	chr11:94705358-94706661	chr11:94705358-94706452,chr11:94705358-94706436	chr11:94706662-94706776	chr11:94706453-94706532			20.75
N	jcn_only_AD	CUFF.489,CUFF.492	chr18	-	chr18:47329224-47340051;chr18:47329224-47339094;chr18:47329224-47340186;chr18:47329224-47339838;chr18:47329224-47340101	chr18:47329224-47337765		chr18:47337766-47339094;chr18:47339095-47339838;chr18:47339839-47340051;chr18:47340052-47340101;chr18:47340102-47340186	chr18:47339094-47339095;chr18:47339838-47339839;chr18:47340051-47340052;chr18:47340101-47340102;chr18:47340186-47340187		4.03
K	alternative_last_exon	CUFF.526,CUFF.551	chr19	+	chr19:45251386-45254483	chr19:45251386-45251951	chr19:45254484-45254637	chr19:45251952-45252348			97.14
N	cassette	CUFF.999	chr7	-	chr7:102566822-102603979	chr7:102566822-102572327;chr7:102572381-102603979		chr7:102572328-102572380			94.53
N	intron_retention		chr16	+	chr16:3115712-3115784				chr16:3115711-3115712;chr16:3115784-3115785		35.94
N	jcn_only_AA	CUFF.247	chr13	+	chr13:31192194-31195900	chr13:31192194-31195209		chr13:31195210-31195900	chr13:31195900-31195901		13.33
K	jcn_only_AA	CUFF.1029,CUFF.1047	chr8	+	chr8:98817693-98827555	chr8:98817693-98827531		chr8:98827532-98827555	chr8:98827555-98827556		46.94
N	alternative_acceptor	CUFF.929	chr6	-	chr6:43480837-43481096	chr6:43480939-43481096		chr6:43480837-43480938	chr6:43480836-43480837		92.35
K	intron_retention	CUFF.184	chr11	-	chr11:118926052-118926204				chr11:118926051-118926052;chr11:118926204-118926205		3.97
N	alternative_acceptor		chr15	+	chr15:40545491-40549043;chr15:40545491-40555999	chr15:40545491-40556004		chr15:40549044-40555999;chr15:40556000-40556004	chr15:40555999-40556000;chr15:40556004-40556005		97.62
N	alternative_donor	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57521007;chr16:57513601-57514206	chr16:57513601-57513756		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		0.00
K	coord_cassette	CUFF.467	chr17	-	chr17:76994369-77005745	chr17:76994369-76996181;chr17:76996353-77001453;chr17:77001564-77005745		chr17:76996182-76996352;chr17:77001454-77001563			81.01
K	cassette	CUFF.145	chr11	+	chr11:3239790-3242799	chr11:3239790-3240929;chr11:3241019-3242799		chr11:3240930-3241018		chr11:3239562-3239789;chr11:3242800-3244361	50.00
N	intron_retention	CUFF.576	chr2	-	chr2:675631-676573				chr2:675630-675631;chr2:676573-676574		84.78
N	jcn_only_AA	CUFF.114	chr10	-	chr10:73973090-73975964;chr10:73975868-73975964;chr10:73975613-73975964;chr10:73973110-73975964	chr10:73973036-73975964					27.62
N	cassette	CUFF.835	chr4	-	chr4:74447586-74450896	chr4:74447586-74447905;chr4:74448008-74450896		chr4:74447906-74448007			63.64
N	alternative_acceptor		chr15	-	chr15:90414779-90421496	chr15:90420657-90421496		chr15:90414779-90420656	chr15:90414778-90414779		6.67
N	cassette	CUFF.782	chr3	-	chr3:125769894-125820271	chr3:125769894-125786789;chr3:125787090-125820271		chr3:125786790-125787089			98.03
N	alternative_donor	CUFF.310	chr15	+	chr15:40532297-40532799;chr15:40532004-40532799;chr15:40509869-40532799	chr15:40531337-40532799		chr15:40509869-40531336;chr15:40531337-40532003;chr15:40532004-40532296	chr15:40509868-40509869;chr15:40531336-40531337;chr15:40532003-40532004		0.00
K	alternative_first_exon	CUFF.165	chr11	+	chr11:65479917-65480236	chr11:65480069-65480236	chr11:65479405-65479916	chr11:65479971-65480068			5.08
K	alternative_donor	CUFF.647,CUFF.659	chr2	-	chr2:175816931-175869933	chr2:175816931-175869621		chr2:175869622-175869933	chr2:175869933-175869934		82.50
N	jcn_only_AA		chr7	+	chr7:7222452-7273933	chr7:7222452-7249057		chr7:7249058-7273933	chr7:7273933-7273934		31.82
K	intron_retention	CUFF.386	chr16	+	chr16:21716359-21716489				chr16:21716358-21716359;chr16:21716489-21716490		19.64
K	intron_retention	CUFF.460	chr17	+	chr17:61904567-61904777				chr17:61904566-61904567;chr17:61904777-61904778		28.07
K	cassette	CUFF.463	chr17	-	chr17:66274469-66287226	chr17:66274469-66279137;chr17:66279265-66287226		chr17:66279138-66279264			34.78
K	alternative_acceptor	CUFF.177	chr11	-	chr11:104915386-104916017	chr11:104915659-104916017		chr11:104915386-104915658	chr11:104915385-104915386		59.38
N	jcn_only_AA		chr19	-	chr19:6148341-6199486;chr19:6176455-6199486	chr19:6192041-6199486					13.92
K	jcn_only_AD	CUFF.902,CUFF.904	chr5	-	chr5:162516353-162852808	chr5:162516353-162683856					9.38
N	jcn_only_AA	CUFF.390	chr16	-	chr16:23504843-23505623;chr16:23504780-23505623	chr16:23504909-23505623		chr16:23504780-23504842;chr16:23504843-23504908	chr16:23504779-23504780;chr16:23504842-23504843	chr16:23505624-23505699;chr16:23504681-23504779	57.52
N	jcn_only_AD		chr7	+	chr7:150831656-150837065	chr7:150835401-150837065		chr7:150831656-150835400	chr7:150831655-150831656		40.91
K	jcn_only_AA	CUFF.774,CUFF.785	chr3	+	chr3:119530574-119531643	chr3:119530574-119531532		chr3:119531533-119531643	chr3:119531643-119531644		90.77
N	intron_retention		chr17	-	chr17:1616190-1617149				chr17:1616189-1616190;chr17:1617149-1617150		70.62
N	alternative_acceptor	CUFF.589	chr2	-	chr2:27708371-27712481	chr2:27709110-27712481		chr2:27708371-27709109	chr2:27708370-27708371		0.00
N	alternative_acceptor	CUFF.274	chr14	-	chr14:69542129-69558390	chr14:69557874-69558390		chr14:69542129-69557873	chr14:69542128-69542129		5.41
N	jcn_only_AD	CUFF.657	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		77.08
K	intron_retention	CUFF.1120	chrX	+	chrX:24382349-24382540				chrX:24382348-24382349;chrX:24382540-24382541		60.00
K	cassette	CUFF.394	chr16	+	chr16:31383106-31383917	chr16:31383106-31383698;chr16:31383831-31383917		chr16:31383699-31383830			73.33
K	intron_retention	CUFF.733	chr3	+	chr3:13978186-13978482				chr3:13978185-13978186;chr3:13978482-13978483		5.00
K	cassette	CUFF.45	chr1	+	chr1:147563999-147566014	chr1:147563999-147564303;chr1:147564350-147566014		chr1:147564304-147564349			83.33
K	alternative_first_exon	CUFF.751	chr3	-	chr3:47018271-47023421	chr3:47018271-47020963	chr3:47023422-47023599	chr3:47020964-47021069			30.77
K	cassette	CUFF.954	chr6	+	chr6:161529892-161530786	chr6:161529892-161529982;chr6:161530074-161530786		chr6:161529983-161530073		chr6:161529775-161529891;chr6:161530787-161530946	11.00
K	alternative_first_exon	CUFF.1113,CUFF.1119	chrX	-	chrX:9001117-9050619	chrX:9001117-9001892	chrX:9050620-9050776	chrX:9001893-9002215			72.73
N	alternative_donor	CUFF.780	chr3	-	chr3:125032501-125042152;chr3:125032501-125042231	chr3:125032501-125033780		chr3:125033781-125042152;chr3:125042153-125042231	chr3:125042152-125042153;chr3:125042231-125042232		0.00
N	intron_retention		chr3	-	chr3:124951499-124951952				chr3:124951498-124951499;chr3:124951952-124951953		67.12
K	intron_retention	CUFF.919	chr6	-	chr6:31938256-31938382				chr6:31938255-31938256;chr6:31938382-31938383		29.68
K	intron_retention	CUFF.407	chr16	+	chr16:70400166-70400526				chr16:70400165-70400166;chr16:70400526-70400527		63.10
N	jcn_only_AA	CUFF.566	chr19	+	chr19:54657578-54657680;chr19:54657578-54659046	chr19:54657578-54658995		chr19:54657681-54658995;chr19:54658996-54659046	chr19:54658995-54658996;chr19:54659046-54659047		10.42
K	alternative_first_exon	CUFF.823	chr4	+	chr4:20255618-20258294	chr4:20256699-20258294	chr4:20254883-20255617	chr4:20256490-20256698			87.50
K	alternative_first_exon	CUFF.645	chr2	-	chr2:174072387-174136238	chr2:174072387-174074374	chr2:174136239-174136404	chr2:174074375-174074673			31.08
N	alternative_donor	CUFF.336	chr15	+	chr15:74754369-74758376;chr15:74754373-74758376	chr15:74754440-74758376		chr15:74754369-74754372;chr15:74754373-74754439	chr15:74754368-74754369;chr15:74754372-74754373		2.86
K	alternative_first_exon	CUFF.255	chr13	-	chr13:102527647-103053820	chr13:102527647-102568802	chr13:103053821-103054124	chr13:102568803-102569070			66.67
K	intron_retention	CUFF.144	chr11	-	chr11:2906697-2906863				chr11:2906696-2906697;chr11:2906863-2906864		70.97
K	alternative_last_exon	CUFF.119	chr10	-	chr10:78823902-78832854;chr10:78799396-78832854	chr10:78831404-78832854	chr10:78799286-78799395	chr10:78830906-78831403			65.74
K	jcn_only_AA	CUFF.112	chr10	+	chr10:70673036-70673146	chr10:70673036-70673105		chr10:70673106-70673146	chr10:70673146-70673147		48.65
N	alternative_donor	CUFF.201	chr12	+	chr12:4662256-4668022;chr12:4665669-4668022	chr12:4665717-4668022		chr12:4662256-4665668;chr12:4665669-4665716	chr12:4662255-4662256;chr12:4665668-4665669		18.97
N	jcn_only_AA		chr15	+	chr15:57574797-57583026;chr15:57574797-57591423	chr15:57574797-57578354		chr15:57578355-57583026;chr15:57583027-57591423	chr15:57583026-57583027;chr15:57591423-57591424		81.89
K	intron_retention	CUFF.624	chr2	+	chr2:96192968-96194965				chr2:96192967-96192968;chr2:96194965-96194966		55.56
N	jcn_only_AA		chr7	-	chr7:37469360-37488462;chr7:37433521-37488462	chr7:37382368-37488462		chr7:37382368-37433520;chr7:37433521-37469359	chr7:37382367-37382368;chr7:37433520-37433521		4.08
K	alternative_first_exon	CUFF.12	chr1	-	chr1:26231230-26231539,chr1:26231230-26231634;chr1:26231230-26232342;chr1:26231230-26233278	chr1:26231230-26232879	chr1:26232343-26232694;chr1:26233279-26233581	chr1:26232880-26232975			6.20
N	jcn_only_AD	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57515373;chr16:57513601-57521042;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;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		1.43
N	alternative_donor	CUFF.61	chr1	+	chr1:167345393-167353093	chr1:167345825-167353093		chr1:167345393-167345824	chr1:167345392-167345393		1.65
K	intron_retention	CUFF.557	chr19	+	chr19:50306634-50308709				chr19:50306633-50306634;chr19:50308709-50308710		9.80
N	jcn_only_AD	CUFF.737	chr3	-	chr3:71777775-71803794;chr3:71777775-71803365	chr3:71777775-71778224					60.56
K	intron_retention	CUFF.876	chr5	+	chr5:54460008-54460427				chr5:54460007-54460008;chr5:54460427-54460428		37.55
K	alternative_last_exon	CUFF.1026	chr8	+	chr8:17491723-17501079	chr8:17491723-17500121	chr8:17501080-17501679	chr8:17500122-17500642			79.58
K	cassette	CUFF.713	chr22	-	chr22:25155957-25158364	chr22:25155957-25157845;chr22:25157929-25158364		chr22:25157846-25157928			30.00
N	alternative_donor	CUFF.490	chr18	+	chr18:56001125-56008909	chr18:56008402-56008909		chr18:56001125-56008401	chr18:56001124-56001125		80.00
N	alternative_donor	CUFF.598	chr2	+	chr2:38224658-38231133	chr2:38230170-38231133		chr2:38224658-38230169	chr2:38224657-38224658		1.19
K	cassette	CUFF.1089	chr9	+	chr9:116795009-116798579	chr9:116795009-116797470;chr9:116797516-116798579		chr9:116797471-116797515			42.86
K	alternative_last_exon	CUFF.246	chr13	-	chr13:25525627-25542343	chr13:25541592-25542343	chr13:25525535-25525626	chr13:25541320-25541591			67.65
N	cassette	CUFF.838	chr4	-	chr4:77969816-77977114	chr4:77969816-77976302;chr4:77976534-77977114		chr4:77976303-77976533			69.49
K	alternative_first_exon	CUFF.473	chr17	-	chr17:79894738-79894845,chr17:79894738-79895068,chr17:79894738-79895103;chr17:79894738-79895403	chr17:79894738-79895137,chr17:79894738-79895133,chr17:79894738-79895055	chr17:79895404-79895626	chr17:79895138-79895264		chr17:79894624-79894737	59.03
N	alternative_donor		chr3	-	chr3:124996654-125042231	chr3:124996654-124997967		chr3:124997968-125042231	chr3:125042231-125042232		6.25
N	alternative_donor	CUFF.1125,CUFF.1137	chrX	-	chrX:53569501-53570846	chrX:53569501-53570801		chrX:53570802-53570846	chrX:53570846-53570847		13.59
K	intron_retention	CUFF.1065	chr9	+	chr9:12192-12292				chr9:12191-12192;chr9:12292-12293		16.67
K	cassette	CUFF.981	chr7	+	chr7:73275597-73279322	chr7:73275597-73275798;chr7:73275922-73279322		chr7:73275799-73275921			12.96
K	coord_cassette	CUFF.975	chr7	+	chr7:44247798-44251845	chr7:44247798-44250621;chr7:44250724-44251152;chr7:44251204-44251845		chr7:44250622-44250723;chr7:44251153-44251203			72.03
N	alternative_donor	CUFF.604	chr2	-	chr2:61749819-61753554	chr2:61749819-61752404		chr2:61752405-61753554	chr2:61753554-61753555		11.44
N	alternative_donor	CUFF.579	chr2	+	chr2:3392442-3405547	chr2:3393551-3405547		chr2:3392442-3393550	chr2:3392441-3392442		20.00
N	alternative_donor	CUFF.221	chr12	+	chr12:52404926-52407470	chr12:52404992-52407470		chr12:52404926-52404991	chr12:52404925-52404926		20.69
N	jcn_only_AD	CUFF.951	chr6	+	chr6:144981412-144999541;chr6:144898425-144999541	chr6:144904737-144999541		chr6:144898425-144904736;chr6:144904737-144981411	chr6:144898424-144898425;chr6:144904736-144904737		63.16
K	intron_retention	CUFF.225	chr12	+	chr12:53854928-53856264				chr12:53854927-53854928;chr12:53856264-53856265		12.21
K	intron_retention	CUFF.876	chr5	+	chr5:54456072-54456947				chr5:54456071-54456072;chr5:54456947-54456948		42.34
N	alternative_donor	CUFF.1146	chrX	+	chrX:148864250-148867418;chrX:148863659-148867418	chrX:148863691-148867418		chrX:148863659-148863690;chrX:148863691-148864249	chrX:148863658-148863659;chrX:148863690-148863691		21.05
N	jcn_only_AD	CUFF.880,CUFF.897	chr5	-	chr5:64907709-64909924	chr5:64907709-64909553		chr5:64909554-64909924	chr5:64909924-64909925		18.28
N	alternative_acceptor	CUFF.877	chr5	-	chr5:54569206-54570441	chr5:54569255-54570441		chr5:54569206-54569254	chr5:54569205-54569206		20.59
N	intron_retention		chr19	+	chr19:52909897-52918376				chr19:52909896-52909897;chr19:52918376-52918377		89.29
N	jcn_only_AD		chr14	-	chr14:104224089-104230199;chr14:104224089-104225527	chr14:104224089-104245081					57.14
N	cassette	CUFF.106	chr10	-	chr10:46147482-46158989	chr10:46147482-46148431;chr10:46148508-46158989		chr10:46148432-46148507			79.63
K	intron_retention	CUFF.755	chr3	+	chr3:51747327-51747979				chr3:51747326-51747327;chr3:51747979-51747980		0.86
N	alternative_acceptor	CUFF.390	chr16	-	chr16:23504843-23505623;chr16:23504909-23505623	chr16:23504780-23505623		chr16:23504780-23504842;chr16:23504843-23504908	chr16:23504779-23504780;chr16:23504842-23504843	chr16:23505624-23505699;chr16:23504681-23504779	16.45
N	alternative_donor		chr18	-	chr18:67614769-67623849;chr18:67614769-67628827	chr18:67614769-67623990		chr18:67623850-67623990;chr18:67623991-67628827	chr18:67623990-67623991;chr18:67628827-67628828		9.09
N	alternative_donor	CUFF.457	chr17	+	chr17:61554705-61555291	chr17:61555152-61555291		chr17:61554705-61555151	chr17:61554704-61554705		24.19
K	cassette	CUFF.213	chr12	+	chr12:27627847-27641392	chr12:27627847-27628514;chr12:27628665-27641392		chr12:27628515-27628664			90.91
K	alternative_first_exon	CUFF.99	chr10	+	chr10:28033878-28056286	chr10:28053703-28056286	chr10:28033715-28033877	chr10:28053580-28053702			43.75
N	jcn_only_AA		chr22	+	chr22:21057981-21058255	chr22:21057981-21058106		chr22:21058107-21058255	chr22:21058255-21058256		5.75
N	cassette	CUFF.1073	chr9	+	chr9:43908524-43915825	chr9:43908524-43915359;chr9:43915591-43915825		chr9:43915360-43915590			92.35
N	alternative_acceptor	CUFF.352	chr15	-	chr15:90420657-90431752;chr15:90414779-90431752	chr15:90421533-90431752		chr15:90414779-90420656;chr15:90420657-90421532	chr15:90414778-90414779;chr15:90420656-90420657		0.53
N	cassette	CUFF.215	chr12	-	chr12:48276558-48298737;chr12:48272899-48298737	chr12:48276558-48293619,chr12:48272899-48293619;chr12:48293742-48298737		chr12:48293620-48293741			63.04
N	intron_retention		chr22	+	chr22:21058172-21058255				chr22:21058171-21058172;chr22:21058255-21058256		91.67
K	intron_retention	CUFF.136	chr11	-	chr11:406994-407061				chr11:406993-406994;chr11:407061-407062		10.07
N	jcn_only_AD		chr14	+	chr14:76219299-76230957	chr14:76224213-76230957					68.75
N	alternative_donor	CUFF.673	chr2	+	chr2:242610857-242611605;chr2:242610841-242611605	chr2:242610821-242611605		chr2:242610821-242610840;chr2:242610841-242610856	chr2:242610820-242610821;chr2:242610840-242610841		70.59
N	intron_retention		chr14	-	chr14:59941245-59941445				chr14:59941244-59941245;chr14:59941445-59941446		47.37
N	alternative_donor	CUFF.673	chr2	+	chr2:242610821-242611605;chr2:242610841-242611605	chr2:242610857-242611605		chr2:242610821-242610840;chr2:242610841-242610856	chr2:242610820-242610821;chr2:242610840-242610841		17.65
K	alternative_last_exon	CUFF.211	chr12	-	chr12:25652931-25656671;chr12:25629395-25656671;chr12:25562365-25656671;chr12:25655973-25656671	chr12:25650729-25656671	chr12:25628947-25629394;chr12:25562143-25562364;chr12:25655879-25655972	chr12:25650631-25650728			2.48
N	alternative_donor		chr4	-	chr4:36231268-36245312	chr4:36231268-36245230		chr4:36245231-36245312	chr4:36245312-36245313		82.61
K	cassette	CUFF.601	chr2	-	chr2:46808731-46819613	chr2:46808731-46815213;chr2:46815319-46819613		chr2:46815214-46815318			49.30
N	alternative_donor	CUFF.793	chr3	-	chr3:141820684-141868024	chr3:141820684-141844990		chr3:141844991-141868024	chr3:141868024-141868025		0.00
N	alternative_donor	CUFF.769	chr3	+	chr3:119188106-119188666;chr3:119187954-119188666	chr3:119187854-119188666		chr3:119187854-119187953;chr3:119187954-119188105	chr3:119187853-119187854;chr3:119187953-119187954		18.00
K	intron_retention	CUFF.734	chr3	+	chr3:19992554-20017078				chr3:19992553-19992554;chr3:20017078-20017079		2.93
N	intron_retention	CUFF.894	chr5	+	chr5:139915124-139916922				chr5:139915123-139915124;chr5:139916922-139916923	chr5:139914947-139915123	79.31
K	intron_retention	CUFF.998	chr7	-	chr7:102234690-102234893				chr7:102234689-102234690;chr7:102234893-102234894		61.11
N	jcn_only_AA	CUFF.703	chr21	-	chr21:47571895-47572820	chr21:47571920-47572820		chr21:47571895-47571919	chr21:47571894-47571895		7.04
K	jcn_only_AA	CUFF.506,CUFF.550	chr19	+	chr19:4304759-4306020;chr19:4304759-4305981	chr19:4304759-4305942		chr19:4305943-4305981;chr19:4305982-4306020	chr19:4305981-4305982;chr19:4306020-4306021		82.44
K	intron_retention	CUFF.460	chr17	+	chr17:61908296-61908395				chr17:61908295-61908296;chr17:61908395-61908396		2.12
K	intron_retention	CUFF.1098	chr9	-	chr9:130929160-130929373				chr9:130929159-130929160;chr9:130929373-130929374		3.00
K	cassette	CUFF.530	chr19	+	chr19:17445932-17448816	chr19:17445932-17447628;chr19:17447844-17448816		chr19:17447629-17447843			98.68
K	cassette	CUFF.436	chr17	+	chr17:29576138-29584704	chr17:29576138-29579955;chr17:29580019-29584704		chr17:29579956-29580018			61.76
K	jcn_only_AA	CUFF.246	chr13	-	chr13:25507675-25525534	chr13:25517160-25525534					35.48
K	intron_retention		chr14	+	chr14:61518854-61519066				chr14:61518853-61518854;chr14:61519066-61519067		25.93
N	alternative_acceptor		chr12	+	chr12:13366756-13367504	chr12:13366756-13367467		chr12:13367468-13367504	chr12:13367504-13367505		50.54
K	alternative_acceptor	CUFF.144	chr11	-	chr11:2905141-2905228	chr11:2905146-2905228		chr11:2905141-2905145	chr11:2905140-2905141		24.14
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		12.90
K	cassette	CUFF.781	chr3	+	chr3:125635563-125639667	chr3:125635563-125637706;chr3:125637770-125639667		chr3:125637707-125637769			90.62
N	cassette	CUFF.317	chr15	-	chr15:45464277-45467416	chr15:45464277-45464344;chr15:45464517-45467416		chr15:45464345-45464516			90.32
N	cassette	CUFF.167	chr11	+	chr11:67782930-67786241	chr11:67782930-67785996;chr11:67786107-67786241		chr11:67785997-67786106			97.70
K	alternative_first_exon	CUFF.189	chr11	-	chr11:119291640-119292320;chr11:119291640-119295607	chr11:119291640-119293822	chr11:119292321-119292419;chr11:119295608-119295794	chr11:119293823-119294855			58.33
K	alternative_last_exon	CUFF.504,CUFF.526	chr19	+	chr19:16204564-16212073	chr19:16204564-16206073	chr19:16212074-16213657	chr19:16206074-16206172			9.26
N	cassette	CUFF.184	chr11	-	chr11:118926284-118926781	chr11:118926284-118926461;chr11:118926556-118926781		chr11:118926462-118926555			50.23
K	alternative_last_exon	CUFF.920	chr6	+	chr6:32125498-32130344	chr6:32125498-32125616	chr6:32130345-32130436	chr6:32125617-32126119			69.44
N	jcn_only_AD		chr18	-	chr18:72914296-72917147;chr18:72914296-72920374	chr18:72914296-72920315		chr18:72917148-72920315;chr18:72920316-72920374	chr18:72920315-72920316;chr18:72920374-72920375		88.24
N	alternative_donor	CUFF.310	chr15	+	chr15:40558697-40564424	chr15:40559199-40564424		chr15:40558697-40559198	chr15:40558696-40558697		28.26
K	alternative_last_exon	CUFF.524	chr19	-	chr19:14879747-14883153;chr19:14876383-14883153	chr19:14877922-14883153	chr19:14879520-14879746;chr19:14876336-14876382	chr19:14877790-14877921			45.16
N	jcn_only_AA	CUFF.663	chr2	+	chr2:220094623-220096649;chr2:220094623-220094949	chr2:220094623-220097211					15.56
K	alternative_last_exon	CUFF.117	chr10	-	chr10:75476951-75478917	chr10:75477924-75478917	chr10:75476806-75476950	chr10:75477773-75477923			61.11
N	alternative_donor	CUFF.951	chr6	+	chr6:144981412-144999541;chr6:144898425-144999541	chr6:144904737-144999541		chr6:144898425-144904736;chr6:144904737-144981411	chr6:144898424-144898425;chr6:144904736-144904737		16.67
N	intron_retention		chr8	-	chr8:80976829-81083659				chr8:80976828-80976829;chr8:81083659-81083660		10.45
N	cassette	CUFF.426	chr17	-	chr17:15535029-15539349	chr17:15535029-15535822;chr17:15535989-15539349		chr17:15535823-15535988			82.71
K	intron_retention		chr17	-	chr17:79479387-79479489				chr17:79479386-79479387;chr17:79479489-79479490		15.38
N	alternative_acceptor	CUFF.1000	chr7	+	chr7:107207632-107211589	chr7:107207632-107208199		chr7:107208200-107211589	chr7:107211589-107211590		35.19
N	jcn_only_AA	CUFF.418	chr17	+	chr17:80416385-80417867	chr17:80416385-80417150		chr17:80417151-80417867	chr17:80417867-80417868		38.71
K	alternative_acceptor	CUFF.406	chr16	-	chr16:70267574-70268076	chr16:70267606-70268076		chr16:70267574-70267605	chr16:70267573-70267574		57.14
N	alternative_acceptor	CUFF.998	chr7	-	chr7:102236555-102240306	chr7:102236577-102240306		chr7:102236555-102236576	chr7:102236554-102236555		51.11
K	intron_retention	CUFF.709	chr22	-	chr22:21832451-21832873				chr22:21832450-21832451;chr22:21832873-21832874		18.18
N	alternative_acceptor		chr12	+	chr12:58019248-58019407	chr12:58019248-58019364		chr12:58019365-58019407	chr12:58019407-58019408		93.94
K	intron_retention	CUFF.572	chr2	-	chr2:263763-264781				chr2:263762-263763;chr2:264781-264782		12.00
K	intron_retention	CUFF.975	chr7	+	chr7:44247798-44250440				chr7:44247797-44247798;chr7:44250440-44250441		14.19
N	intron_retention		chr22	-	chr22:30735024-30736197				chr22:30735023-30735024;chr22:30736197-30736198		22.58
N	alternative_acceptor		chr11	+	chr11:118404845-118404983	chr11:118404845-118404980		chr11:118404981-118404983	chr11:118404983-118404984	chr11:118404744-118404844;chr11:118404984-118405070	62.50
K	coord_cassette	CUFF.407	chr16	+	chr16:70390151-70398919	chr16:70390151-70395320;chr16:70395414-70398445;chr16:70398549-70398919		chr16:70395321-70395413;chr16:70398446-70398548			19.86
N	cassette	CUFF.150	chr11	-	chr11:8496614-8615290	chr11:8496614-8602360;chr11:8602508-8615290		chr11:8602361-8602507			70.00
N	alternative_donor	CUFF.12,CUFF.53	chr1	-	chr1:156918291-156921364	chr1:156918291-156918364		chr1:156918365-156921364	chr1:156921364-156921365		22.22
K	cassette	CUFF.567	chr19	+	chr19:55084903-55085542	chr19:55084903-55085164;chr19:55085380-55085542		chr19:55085165-55085379			81.69
K	intron_retention		chr11	+	chr11:118401950-118402489				chr11:118401949-118401950;chr11:118402489-118402490	chr11:118401663-118401949;chr11:118402490-118402586	23.42
N	cassette	CUFF.426	chr17	-	chr17:15580595-15584178	chr17:15580595-15580888;chr17:15580997-15584178		chr17:15580889-15580996			77.59
K	intron_retention	CUFF.895	chr5	+	chr5:140039781-140040342				chr5:140039780-140039781;chr5:140040342-140040343		41.46
N	cassette	CUFF.1027	chr8	-	chr8:22011553-22012072	chr8:22011553-22011654;chr8:22011727-22012072		chr8:22011655-22011726			91.38
N	alternative_donor	CUFF.298	chr14	-	chr14:104209161-104212709	chr14:104209161-104210227		chr14:104210228-104212709	chr14:104212709-104212710		33.33
K	alternative_last_exon	CUFF.704	chr22	-	chr22:18082862-18095577	chr22:18083948-18095577	chr22:18082793-18082861	chr22:18083390-18083947			90.41
N	jcn_only_AD	CUFF.1000	chr7	+	chr7:107204505-107205032;chr7:107204693-107205032;chr7:107204655-107205032	chr7:107204192-107205032		chr7:107204192-107204504;chr7:107204505-107204654;chr7:107204655-107204692	chr7:107204191-107204192;chr7:107204504-107204505;chr7:107204654-107204655		15.85
N	alternative_acceptor	CUFF.504	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		3.62
N	jcn_only_AA	CUFF.138,CUFF.179	chr11	+	chr11:827460-828259	chr11:827460-828229		chr11:828230-828259	chr11:828259-828260	chr11:827215-827459;chr11:828260-828772	80.85
N	jcn_only_AD	CUFF.918	chr6	+	chr6:31935860-31936104	chr6:31935897-31936104		chr6:31935860-31935896	chr6:31935859-31935860		36.07
N	alternative_acceptor	CUFF.786	chr3	-	chr3:127299007-127309252	chr3:127307004-127309252		chr3:127299007-127307003	chr3:127299006-127299007		0.00
N	intron_retention	CUFF.716	chr22	+	chr22:29694886-29695184				chr22:29694885-29694886;chr22:29695184-29695185		65.38
N	alternative_first_exon		chr11	-	chr11:6639008-6640426	chr11:6639008-6640006	chr11:6640427-6640525	chr11:6640007-6640146			98.45
N	intron_retention		chr11	+	chr11:118402317-118402489				chr11:118402316-118402317;chr11:118402489-118402490	chr11:118401663-118402316;chr11:118402490-118402586	76.52
N	jcn_only_AD	CUFF.197	chr12	+	chr12:1742072-1754959;chr12:1749143-1754959	chr12:1754228-1754959					19.13
K	intron_retention	CUFF.423	chr17	+	chr17:6353393-6353681				chr17:6353392-6353393;chr17:6353681-6353682		42.42
K	alternative_donor	CUFF.187	chr11	+	chr11:119058368-119058648	chr11:119058410-119058648		chr11:119058368-119058409	chr11:119058367-119058368		82.17
N	alternative_donor	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55711941-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55758860-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		2.56
N	intron_retention	CUFF.648	chr2	-	chr2:177042223-177042742				chr2:177042222-177042223;chr2:177042742-177042743		68.18
K	intron_retention	CUFF.261	chr14	-	chr14:24684869-24684942				chr14:24684868-24684869;chr14:24684942-24684943		57.14
K	intron_retention	CUFF.604	chr2	-	chr2:61722749-61724013				chr2:61722748-61722749;chr2:61724013-61724014		12.00
K	cassette	CUFF.121	chr10	-	chr10:80705747-80721010	chr10:80705747-80720261;chr10:80720474-80721010		chr10:80720262-80720473			29.41
K	intron_retention	CUFF.244	chr13	+	chr13:21237526-21237636				chr13:21237525-21237526;chr13:21237636-21237637		3.95
K	cassette	CUFF.979	chr7	+	chr7:65592728-65595730	chr7:65592728-65595113;chr7:65595236-65595730		chr7:65595114-65595235			20.83
N	alternative_acceptor	CUFF.385	chr16	+	chr16:19580914-19584445	chr16:19580914-19584440		chr16:19584441-19584445	chr16:19584445-19584446		77.27
N	coord_cassette	CUFF.980	chr7	+	chr7:73106977-73111934	chr7:73106977-73107658;chr7:73107745-73107953;chr7:73108000-73111934		chr7:73107659-73107744;chr7:73107954-73107999			35.65
N	intron_retention		chr11	-	chr11:6632684-6632894				chr11:6632683-6632684;chr11:6632894-6632895		83.13
N	alternative_donor	CUFF.506	chr19	+	chr19:4323144-4323344;chr19:4323235-4323344	chr19:4323211-4323344		chr19:4323144-4323210;chr19:4323211-4323234	chr19:4323143-4323144;chr19:4323210-4323211		65.71
N	jcn_only_AA	CUFF.647	chr2	-	chr2:175677211-175689161	chr2:175686508-175689161		chr2:175677211-175686507	chr2:175677210-175677211		11.96
K	alternative_donor	CUFF.418	chr17	+	chr17:1945170-1945898	chr17:1945526-1945898		chr17:1945170-1945525	chr17:1945169-1945170		27.17
K	intron_retention	CUFF.377	chr16	-	chr16:4409623-4410278				chr16:4409622-4409623;chr16:4410278-4410279		25.96
K	intron_retention	CUFF.647	chr2	-	chr2:175711686-175712040				chr2:175711685-175711686;chr2:175712040-175712041		11.93
N	jcn_only_AD	CUFF.306	chr15	+	chr15:29288010-29346047	chr15:29336632-29346047		chr15:29288010-29336631	chr15:29288009-29288010		6.98
K	intron_retention		chr20	+	chr20:30137925-30142548				chr20:30137924-30137925;chr20:30142548-30142549	chr20:30137867-30137924	10.68
N	alternative_donor	CUFF.489	chr18	-	chr18:47329224-47337765;chr18:47329224-47339094;chr18:47329224-47340186;chr18:47329224-47339838;chr18:47329224-47340101	chr18:47329224-47340051		chr18:47337766-47339094;chr18:47339095-47339838;chr18:47339839-47340051;chr18:47340052-47340101;chr18:47340102-47340186	chr18:47339094-47339095;chr18:47339838-47339839;chr18:47340051-47340052;chr18:47340101-47340102;chr18:47340186-47340187		41.38
K	jcn_only_AD	CUFF.763	chr3	-	chr3:93646252-93692517	chr3:93646252-93692406		chr3:93692407-93692517	chr3:93692517-93692518		98.80
N	jcn_only_AA	CUFF.1018	chr7	-	chr7:156589187-156619298	chr7:156616618-156619298		chr7:156589187-156616617	chr7:156589186-156589187		8.18
K	alternative_donor	CUFF.232	chr12	+	chr12:58019471-58019780	chr12:58019536-58019780		chr12:58019471-58019535	chr12:58019470-58019471		92.51
K	intron_retention		chr11	-	chr11:10821304-10821636				chr11:10821303-10821304;chr11:10821636-10821637		59.57
N	jcn_only_AD	CUFF.481	chr18	+	chr18:12014373-12028041	chr18:12021822-12028041		chr18:12014373-12021821	chr18:12014372-12014373		5.70
N	alternative_donor	CUFF.208	chr12	+	chr12:21011506-21174394	chr12:21172315-21174394		chr12:21011506-21172314	chr12:21011505-21011506		0.00
N	alternative_donor	CUFF.254	chr13	-	chr13:24460646-24463270	chr13:24460646-24462816		chr13:24462817-24463270	chr13:24463270-24463271		69.57
N	jcn_only_AA	CUFF.67	chr1	+	chr1:196913069-196918746;chr1:196913069-196918565	chr1:196913069-196918584		chr1:196918566-196918584;chr1:196918585-196918746	chr1:196918584-196918585;chr1:196918746-196918747	chr1:196912830-196913068;chr1:196918747-196918779	56.52
K	jcn_only_AA	CUFF.872,CUFF.878	chr5	+	chr5:50685767-50687176	chr5:50685767-50687107		chr5:50687108-50687176	chr5:50687176-50687177	chr5:50685480-50685766;chr5:50687177-50687275	83.02
N	coord_cassette	CUFF.202	chr12	-	chr12:7091066-7125577	chr12:7091066-7091836;chr12:7091944-7092592;chr12:7092701-7108732;chr12:7108792-7125577		chr12:7091837-7091943;chr12:7092593-7092700;chr12:7108733-7108791			63.40
K	intron_retention	CUFF.4	chr1	+	chr1:11085266-11085607				chr1:11085265-11085266;chr1:11085607-11085608		30.00
N	alternative_donor	CUFF.1069	chr9	+	chr9:34991414-34993196	chr9:34992984-34993196		chr9:34991414-34992983	chr9:34991413-34991414		3.12
N	coord_cassette	CUFF.816	chr4	-	chr4:3945100-3954837	chr4:3945100-3949816;chr4:3949948-3951174;chr4:3951320-3952865;chr4:3952947-3954837		chr4:3949817-3949947;chr4:3951175-3951319;chr4:3952866-3952946			76.60
N	jcn_only_AA	CUFF.468	chr17	-	chr17:79220041-79220684	chr17:79220474-79220684		chr17:79220041-79220473	chr17:79220040-79220041		96.36
N	jcn_only_AD	CUFF.769	chr3	+	chr3:119205780-119207775	chr3:119205884-119207775		chr3:119205780-119205883	chr3:119205779-119205780		56.25
N	alternative_donor	CUFF.890	chr5	+	chr5:131658049-131662969	chr5:131660336-131662969		chr5:131658049-131660335	chr5:131658048-131658049		16.67
K	intron_retention	CUFF.845	chr4	-	chr4:99403327-99407888				chr4:99403326-99403327;chr4:99407888-99407889		6.33
N	coord_cassette	CUFF.436	chr17	+	chr17:29664899-29667522	chr17:29664899-29665042;chr17:29665158-29665721;chr17:29665824-29667522		chr17:29665043-29665157;chr17:29665722-29665823			51.43
K	alternative_first_exon	CUFF.1031	chr8	-	chr8:30657272-30671402;chr8:30657272-30669835	chr8:30657272-30667505	chr8:30669836-30670477	chr8:30667506-30667847			58.48
K	cassette	CUFF.50	chr1	+	chr1:155180419-155182175	chr1:155180419-155181917;chr1:155182011-155182175		chr1:155181918-155182010			52.63
K	intron_retention		chr11	-	chr11:118926284-118926461				chr11:118926283-118926284;chr11:118926461-118926462		27.81
N	intron_retention		chr17	-	chr17:79994199-79994259				chr17:79994198-79994199;chr17:79994259-79994260		70.73
N	cassette	CUFF.202	chr12	-	chr12:7088742-7090755	chr12:7088742-7090165;chr12:7090345-7090755		chr12:7090166-7090344			98.95
N	cassette	CUFF.647	chr2	-	chr2:175742857-175816891	chr2:175742857-175779785;chr2:175779900-175816891		chr2:175779786-175779899			84.00
K	intron_retention	CUFF.401	chr16	+	chr16:66613602-66614041				chr16:66613601-66613602;chr16:66614041-66614042		62.79
N	jcn_only_AA	CUFF.919	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		31.07
K	alternative_last_exon	CUFF.965	chr7	-	chr7:19153547-19156293	chr7:19155755-19156293	chr7:19153500-19153546	chr7:19155029-19155754			38.98
N	intron_retention		chr19	+	chr19:50304257-50304659				chr19:50304256-50304257;chr19:50304659-50304660		57.14
K	alternative_first_exon	CUFF.838	chr4	-	chr4:77979789-77996624;chr4:77979789-77987401	chr4:77979789-77985865	chr4:77996625-77997233;chr4:77987402-77987558	chr4:77985866-77986241			18.37
N	intron_retention		chr3	-	chr3:33481349-33481950				chr3:33481348-33481349;chr3:33481950-33481951		54.55
N	alternative_acceptor	CUFF.1119	chrX	-	chrX:20183080-20185706	chrX:20183179-20185706		chrX:20183080-20183178	chrX:20183079-20183080		85.37
K	cassette	CUFF.486	chr18	-	chr18:44471018-44497284	chr18:44471018-44483489;chr18:44483599-44497284		chr18:44483490-44483598			54.29
N	alternative_acceptor		chr18	+	chr18:77875534-77905317	chr18:77875534-77890985		chr18:77890986-77905317	chr18:77905317-77905318		0.00
N	alternative_donor	CUFF.423	chr17	+	chr17:6352728-6353347	chr17:6353099-6353347		chr17:6352728-6353098	chr17:6352727-6352728		3.06
N	alternative_acceptor	CUFF.728	chr22	-	chr22:51009963-51010434	chr22:51009969-51010434		chr22:51009963-51009968	chr22:51009962-51009963		71.01
N	jcn_only_AD	CUFF.547,CUFF.560	chr19	-	chr19:41944320-41946385;chr19:41944320-41945786	chr19:41944320-41945378		chr19:41945379-41945786;chr19:41945787-41946385	chr19:41945786-41945787;chr19:41946385-41946386		21.43
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		95.12
N	jcn_only_AD		chr18	+	chr18:55833094-55895061;chr18:55862966-55895061	chr18:55888990-55895061		chr18:55833094-55862965;chr18:55862966-55888989	chr18:55833093-55833094;chr18:55862965-55862966		40.38
K	intron_retention	CUFF.560	chr19	-	chr19:51526485-51527300				chr19:51526484-51526485;chr19:51527300-51527301		5.43
K	alternative_first_exon	CUFF.674,CUFF.682	chr20	-	chr20:30009482-30016345	chr20:30009482-30011622,chr20:30009482-30011612	chr20:30016346-30016438	chr20:30011623-30011759			96.43
K	intron_retention	CUFF.316	chr15	-	chr15:44890572-44890828				chr15:44890571-44890572;chr15:44890828-44890829		42.37
N	alternative_first_exon	CUFF.163	chr11	+	chr11:63999437-64001365	chr11:64000338-64001365	chr11:63999302-63999436	chr11:64000176-64000337			95.86
N	jcn_only_AA	CUFF.1066	chr9	-	chr9:15250009-15267911;chr9:15211396-15267911	chr9:15226011-15267911					21.61
K	alternative_acceptor	CUFF.506,CUFF.550	chr19	+	chr19:4304759-4306020;chr19:4304759-4305981	chr19:4304759-4305942		chr19:4305943-4305981;chr19:4305982-4306020	chr19:4305981-4305982;chr19:4306020-4306021		72.34
N	intron_retention		chr2	+	chr2:242594063-242606059				chr2:242594062-242594063;chr2:242606059-242606060		89.77
N	alternative_acceptor		chr6	-	chr6:114281183-114291643	chr6:114289861-114291643		chr6:114281183-114289860	chr6:114281182-114281183		4.17
N	jcn_only_AA		chr14	+	chr14:76368568-76372897;chr14:76368568-76420766	chr14:76368568-76407766					45.10
K	alternative_last_exon	CUFF.307	chr15	+	chr15:30771397-30776704	chr15:30771397-30772944	chr15:30776705-30776892	chr15:30772945-30773339			44.83
K	intron_retention	CUFF.184	chr11	-	chr11:118923142-118923348				chr11:118923141-118923142;chr11:118923348-118923349		14.13
N	alternative_donor	CUFF.342	chr15	-	chr15:78501592-78537610	chr15:78501592-78504890		chr15:78504891-78537610	chr15:78537610-78537611		8.33
N	alternative_first_exon	CUFF.450	chr17	+	chr17:46986183-46993437	chr17:46990328-46993437,chr17:46990384-46993437	chr17:46985731-46986182	chr17:46990196-46990327			86.05
N	alternative_acceptor	CUFF.894	chr5	+	chr5:139815843-139818045;chr5:139815843-139818078	chr5:139815843-139818087		chr5:139818046-139818078;chr5:139818079-139818087	chr5:139818078-139818079;chr5:139818087-139818088	chr5:139815689-139815842;chr5:139818088-139818202	52.38
K	jcn_only_AA	CUFF.506	chr19	+	chr19:4304759-4306020;chr19:4304759-4305942	chr19:4304759-4305981		chr19:4305943-4305981;chr19:4305982-4306020	chr19:4305981-4305982;chr19:4306020-4306021		12.31
N	jcn_only_AD		chr1	+	chr1:167298544-167301706;chr1:167288294-167301706	chr1:167227155-167301706					20.00
K	alternative_first_exon	CUFF.197	chr12	+	chr12:1684008-1740463,chr12:1739393-1740463,chr12:1738538-1740463;chr12:1640117-1740463;chr12:1726310-1740463	chr12:1639176-1740463	chr12:1639910-1640116;chr12:1725805-1726309	chr12:1639057-1639175			8.87
K	alternative_first_exon	CUFF.140,CUFF.193	chr11	-	chr11:124766952-124768293	chr11:124766952-124767621	chr11:124768294-124768472	chr11:124767622-124768201			30.00
K	alternative_acceptor	CUFF.148	chr11	-	chr11:6623446-6624633	chr11:6623495-6624633		chr11:6623446-6623494	chr11:6623445-6623446		56.52
K	jcn_only_AA	CUFF.1028	chr8	-	chr8:23186079-23198504	chr8:23191137-23198504					25.00
N	alternative_donor	CUFF.481	chr18	+	chr18:12014373-12028041	chr18:12021822-12028041		chr18:12014373-12021821	chr18:12014372-12014373		1.09
N	mutually_exclusive	CUFF.38	chr1	-	chr1:114423763-114429158,chr1:114429281-114429870	chr1:114423763-114424394,chr1:114424620-114429870	chr1:114429159-114429280	chr1:114424395-114424619			78.18
N	alternative_acceptor	CUFF.920,CUFF.922	chr6	+	chr6:33240504-33243573	chr6:33240504-33243276		chr6:33243277-33243573	chr6:33243573-33243574		9.93
K	alternative_first_exon	CUFF.195	chr12	-	chr12:335681-336730	chr12:335681-335818	chr12:336731-336834	chr12:335819-336182			61.02
K	cassette	CUFF.584	chr2	-	chr2:11593925-11605897	chr2:11593925-11597304;chr2:11597360-11605897		chr2:11597305-11597359			65.03
N	jcn_only_AD	CUFF.884	chr5	-	chr5:36703067-36705822	chr5:36703067-36705781		chr5:36705782-36705822	chr5:36705822-36705823		90.24
K	intron_retention	CUFF.453	chr17	-	chr17:56082962-56083161				chr17:56082961-56082962;chr17:56083161-56083162		9.80
N	cassette	CUFF.852	chr4	-	chr4:152080505-152095821	chr4:152080505-152086740;chr4:152086849-152095821		chr4:152086741-152086848			81.25
K	intron_retention	CUFF.1092	chr9	-	chr9:123550465-123555426				chr9:123550464-123550465;chr9:123555426-123555427		78.57
K	alternative_donor	CUFF.500	chr18	-	chr18:76737430-76738785	chr18:76737430-76738462		chr18:76738463-76738785	chr18:76738785-76738786		37.88
N	intron_retention		chr16	-	chr16:57513601-57514241				chr16:57513600-57513601;chr16:57514241-57514242		88.89
N	jcn_only_AD	CUFF.962	chr7	+	chr7:7197058-7273933	chr7:7222452-7273933		chr7:7197058-7222451	chr7:7197057-7197058		45.45
K	intron_retention	CUFF.187	chr11	+	chr11:119058410-119058648				chr11:119058409-119058410;chr11:119058648-119058649		35.00
N	alternative_acceptor	CUFF.436,CUFF.464	chr17	+	chr17:29687722-29701030	chr17:29687722-29694242		chr17:29694243-29701030	chr17:29701030-29701031		0.00
K	cassette	CUFF.119	chr10	-	chr10:78734332-78771724	chr10:78734332-78737300;chr10:78737397-78771724		chr10:78737301-78737396			20.00
N	jcn_only_AD	CUFF.976	chr7	+	chr7:54612482-54614639;chr7:54613910-54614639	chr7:54614433-54614639		chr7:54612482-54613909;chr7:54613910-54614432	chr7:54612481-54612482;chr7:54613909-54613910		23.97
N	alternative_donor		chrX	-	chrX:20258724-20284681	chrX:20258724-20259710		chrX:20259711-20284681	chrX:20284681-20284682		0.00
N	alternative_acceptor	CUFF.1000	chr7	+	chr7:107211712-107215632	chr7:107211712-107214148		chr7:107214149-107215632	chr7:107215632-107215633		5.59
N	jcn_only_AA	CUFF.572	chr2	-	chr2:262751-263210	chr2:262787-263210		chr2:262751-262786	chr2:262750-262751		28.89
K	alternative_first_exon	CUFF.85	chr1	-	chr1:247302060-247322307	chr1:247302060-247313159	chr1:247322308-247322368	chr1:247313160-247313289			38.10
K	intron_retention	CUFF.830	chr4	+	chr4:57302142-57302427				chr4:57302141-57302142;chr4:57302427-57302428		89.81
N	jcn_only_AD	CUFF.650	chr2	+	chr2:186662254-186678271	chr2:186673861-186678271					50.00
N	jcn_only_AD	CUFF.489	chr18	-	chr18:47329224-47337765;chr18:47329224-47339094;chr18:47329224-47340186;chr18:47329224-47339838;chr18:47329224-47340101	chr18:47329224-47340051		chr18:47337766-47339094;chr18:47339095-47339838;chr18:47339839-47340051;chr18:47340052-47340101;chr18:47340102-47340186	chr18:47339094-47339095;chr18:47339838-47339839;chr18:47340051-47340052;chr18:47340101-47340102;chr18:47340186-47340187		44.30
N	alternative_donor	CUFF.475	chr17	-	chr17:79993940-79994057;chr17:79993940-79994022	chr17:79993940-79994066		chr17:79994023-79994057;chr17:79994058-79994066	chr17:79994057-79994058;chr17:79994066-79994067		84.38
K	alternative_acceptor	CUFF.894	chr5	+	chr5:139865318-139866590	chr5:139865318-139866542		chr5:139866543-139866590	chr5:139866590-139866591	chr5:139865174-139865317;chr5:139866591-139866645	63.64
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		20.97
K	intron_retention	CUFF.900	chr5	-	chr5:149781814-149782125				chr5:149781813-149781814;chr5:149782125-149782126		3.25
K	cassette	CUFF.316	chr15	-	chr15:44859791-44862722	chr15:44859791-44861595;chr15:44861704-44862722		chr15:44861596-44861703			85.11
N	jcn_only_AD		chr15	+	chr15:24780954-24811802;chr15:24803469-24811802	chr15:24811360-24811802					60.29
K	intron_retention	CUFF.936	chr6	+	chr6:90337416-90337965				chr6:90337415-90337416;chr6:90337965-90337966		58.00
K	intron_retention	CUFF.161	chr11	-	chr11:62365863-62365993				chr11:62365862-62365863;chr11:62365993-62365994		41.35
K	mutually_exclusive	CUFF.765	chr3	-	chr3:107576050-107591814,chr3:107591874-107594976	chr3:107576050-107586157,chr3:107586273-107594976	chr3:107591815-107591873	chr3:107586158-107586272			39.11
K	intron_retention	CUFF.1002	chr7	-	chr7:107572939-107575859				chr7:107572938-107572939;chr7:107575859-107575860		90.62
N	jcn_only_AD	CUFF.923	chr6	+	chr6:34434048-34494019;chr6:34452922-34494019	chr6:34482846-34494019		chr6:34434048-34452921;chr6:34452922-34482845	chr6:34434047-34434048;chr6:34452921-34452922		55.88
N	alternative_donor	CUFF.136	chr11	-	chr11:410028-417293;chr11:410028-414822	chr11:410028-417324		chr11:414823-417293;chr11:417294-417324	chr11:417293-417294;chr11:417324-417325		11.24
N	alternative_donor	CUFF.802	chr3	+	chr3:186649184-186681572;chr3:186660216-186681572;chr3:186648624-186681572;chr3:186666727-186681572	chr3:186648928-186681572		chr3:186648624-186648927;chr3:186648928-186649183;chr3:186649184-186660215;chr3:186660216-186666726	chr3:186648623-186648624;chr3:186648927-186648928;chr3:186649183-186649184;chr3:186660215-186660216		17.42
N	alternative_donor	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55722109-55833019	chr18:55816792-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		0.00
K	intron_retention	CUFF.316	chr15	-	chr15:44876757-44877833				chr15:44876756-44876757;chr15:44877833-44877834		26.32
K	alternative_first_exon	CUFF.105	chr10	-	chr10:44273299-44274154	chr10:44273299-44274029	chr10:44274155-44274362	chr10:44274030-44274074			69.23
N	alternative_acceptor	CUFF.581	chr2	-	chr2:4020665-4021134;chr2:4009394-4021134;chr2:4015879-4021134;chr2:4020693-4021134	chr2:4009485-4021134		chr2:4009394-4009484;chr2:4009485-4015878;chr2:4015879-4020664;chr2:4020665-4020692	chr2:4009393-4009394;chr2:4009484-4009485;chr2:4015878-4015879;chr2:4020664-4020665		66.13
N	alternative_acceptor	CUFF.988	chr7	-	chr7:86542382-86544038	chr7:86542521-86544038		chr7:86542382-86542520	chr7:86542381-86542382		95.42
N	jcn_only_AA		chr1	-	chr1:113471975-113497897	chr1:113472657-113497897		chr1:113471975-113472656	chr1:113471974-113471975		54.55
N	alternative_donor	CUFF.1043	chr8	+	chr8:82192910-82195600	chr8:82193549-82195600		chr8:82192910-82193548	chr8:82192909-82192910		3.80
K	alternative_first_exon	CUFF.588	chr2	-	chr2:25190163-25194284;chr2:25190163-25194686	chr2:25190163-25194424	chr2:25194687-25194963	chr2:25194425-25194523			4.46
K	cassette	CUFF.97	chr10	-	chr10:27059275-27065993	chr10:27059275-27060003;chr10:27060019-27065993		chr10:27060004-27060018			63.33
N	alternative_acceptor	CUFF.310	chr15	+	chr15:40545491-40556004;chr15:40545491-40555999	chr15:40545491-40549043		chr15:40549044-40555999;chr15:40556000-40556004	chr15:40555999-40556000;chr15:40556004-40556005		0.00
N	jcn_only_AD	CUFF.752,CUFF.765	chr3	-	chr3:107567966-107575926;chr3:107567966-107572719	chr3:107567966-107568669					28.36
K	alternative_last_exon	CUFF.848	chr4	+	chr4:120419059-120433505	chr4:120419059-120420715	chr4:120433506-120433619	chr4:120420716-120421501			54.17
N	alternative_donor	CUFF.336	chr15	+	chr15:74771620-74773391	chr15:74773256-74773391		chr15:74771620-74773255	chr15:74771619-74771620		8.33
K	jcn_only_AD	CUFF.953	chr6	-	chr6:151754366-151757580	chr6:151754366-151757554		chr6:151757555-151757580	chr6:151757580-151757581		44.44
N	cassette	CUFF.673	chr2	+	chr2:242590751-242592926;chr2:242591390-242592926	chr2:242590751-242592721,chr2:242591390-242592721;chr2:242592785-242592926		chr2:242592722-242592784			23.71
K	intron_retention	CUFF.269	chr14	+	chr14:58908062-58909423				chr14:58908061-58908062;chr14:58909423-58909424		21.43
N	jcn_only_AD	CUFF.189	chr11	-	chr11:2192001-2192926	chr11:2192001-2192914		chr11:2192915-2192926	chr11:2192926-2192927		10.53
N	jcn_only_AD	CUFF.1098,CUFF.1101	chr9	-	chr9:131484854-131486272	chr9:131484854-131486230		chr9:131486231-131486272	chr9:131486272-131486273		1.55
N	alternative_donor	CUFF.460	chr17	+	chr17:61904884-61907492	chr17:61907310-61907492		chr17:61904884-61907309	chr17:61904883-61904884		47.42
N	jcn_only_AD	CUFF.182	chr11	+	chr11:118402242-118402489;chr11:118401950-118402489	chr11:118402317-118402489		chr11:118401950-118402241;chr11:118402242-118402316	chr11:118401949-118401950;chr11:118402241-118402242	chr11:118402490-118402586;chr11:118401663-118401949	7.44
K	intron_retention	CUFF.418	chr17	+	chr17:1939386-1939722				chr17:1939385-1939386;chr17:1939722-1939723		58.33
N	alternative_acceptor	CUFF.316	chr15	-	chr15:44892831-44898222	chr15:44896396-44898222		chr15:44892831-44896395	chr15:44892830-44892831		0.00
K	jcn_only_AA	CUFF.1089	chr9	+	chr9:116791253-116794927	chr9:116791253-116794924		chr9:116794925-116794927	chr9:116794927-116794928		17.65
K	cassette	CUFF.1009	chr7	+	chr7:128850955-128851476	chr7:128850955-128851223;chr7:128851352-128851476		chr7:128851224-128851351			38.89
N	cassette	CUFF.354	chr15	+	chr15:91306388-91310139	chr15:91306388-91308525;chr15:91308645-91310139		chr15:91308526-91308644			86.00
K	cassette	CUFF.1118	chrX	-	chrX:19935453-19947902	chrX:19935453-19941275;chrX:19941526-19947902		chrX:19941276-19941525			29.90
K	alternative_acceptor	CUFF.920	chr6	+	chr6:32121414-32121972	chr6:32121414-32121775		chr6:32121776-32121972	chr6:32121972-32121973		86.36
N	intron_retention		chr7	+	chr7:107204693-107205032				chr7:107204692-107204693;chr7:107205032-107205033		89.80
K	intron_retention	CUFF.693	chr21	+	chr21:15660868-15663890				chr21:15660867-15660868;chr21:15663890-15663891	chr21:15660725-15660867;chr21:15663891-15664068	21.74
N	cassette	CUFF.918	chr6	+	chr6:31928872-31929323	chr6:31928872-31928972;chr6:31929164-31929323		chr6:31928973-31929163			79.17
K	jcn_only_AA	CUFF.524	chr19	-	chr19:14866657-14867049	chr19:14866690-14867049		chr19:14866657-14866689	chr19:14866656-14866657		65.71
N	alternative_acceptor	CUFF.765	chr3	-	chr3:107559252-107560951	chr3:107560867-107560951		chr3:107559252-107560866	chr3:107559251-107559252		72.22
N	jcn_only_AD	CUFF.579	chr2	+	chr2:3453249-3461391;chr2:3461001-3461391	chr2:3447663-3461391		chr2:3447663-3453248;chr2:3453249-3461000	chr2:3447662-3447663;chr2:3453248-3453249		71.94
K	intron_retention	CUFF.340	chr15	+	chr15:77771664-77775311				chr15:77771663-77771664;chr15:77775311-77775312		15.45
K	alternative_first_exon	CUFF.1	chr1	+	chr1:1656203-1667255	chr1:1664284-1667255	chr1:1655886-1656202	chr1:1664001-1664283			45.83
K	alternative_first_exon	CUFF.139	chr11	-	chr11:1782699-1785021	chr11:1782699-1783362	chr11:1785022-1785281	chr11:1783363-1783697			68.00
K	intron_retention	CUFF.193	chr11	-	chr11:124766567-124766827				chr11:124766566-124766567;chr11:124766827-124766828		41.51
N	alternative_donor	CUFF.547	chr19	-	chr19:41944320-41945378;chr19:41944320-41945786	chr19:41944320-41946385		chr19:41945379-41945786;chr19:41945787-41946385	chr19:41945786-41945787;chr19:41946385-41946386		25.41
N	jcn_only_AD	CUFF.550	chr19	+	chr19:44771115-44777051	chr19:44771298-44777051		chr19:44771115-44771297	chr19:44771114-44771115		10.34
K	cassette	CUFF.450	chr17	+	chr17:46988243-46993437	chr17:46988243-46990195;chr17:46990328-46993437		chr17:46990196-46990327			61.11
N	jcn_only_AD	CUFF.276	chr14	-	chr14:71227900-71249939;chr14:71227900-71267383	chr14:71227900-71232158		chr14:71232159-71249939;chr14:71249940-71267383	chr14:71249939-71249940;chr14:71267383-71267384		70.45
K	intron_retention	CUFF.782	chr3	-	chr3:125725472-125725559				chr3:125725471-125725472;chr3:125725559-125725560		18.91
N	jcn_only_AD	CUFF.1000	chr7	+	chr7:107204192-107205032;chr7:107204693-107205032;chr7:107204655-107205032	chr7:107204505-107205032		chr7:107204192-107204504;chr7:107204505-107204654;chr7:107204655-107204692	chr7:107204191-107204192;chr7:107204504-107204505;chr7:107204654-107204655		46.91
K	alternative_donor	CUFF.140,CUFF.184	chr11	-	chr11:2190926-2192926	chr11:2190926-2192914		chr11:2192915-2192926	chr11:2192926-2192927		17.24
N	jcn_only_AA	CUFF.852	chr4	-	chr4:152065203-152069073	chr4:152065441-152069073		chr4:152065203-152065440	chr4:152065202-152065203		15.62
K	cassette	CUFF.107	chr10	+	chr10:48231815-48235818	chr10:48231815-48235121;chr10:48235174-48235818		chr10:48235122-48235173			53.85
K	intron_retention	CUFF.377	chr16	-	chr16:4408105-4408367				chr16:4408104-4408105;chr16:4408367-4408368		5.77
K	alternative_last_exon	CUFF.83	chr1	+	chr1:245246991-245250034,chr1:245246991-245254328,chr1:245246991-245285221;chr1:245246991-245254795;chr1:245246991-245250061	chr1:245246991-245250546	chr1:245254796-245255187;chr1:245250062-245250339	chr1:245250547-245251207			34.38
N	alternative_acceptor	CUFF.976	chr7	+	chr7:129015768-129019481	chr7:129015768-129019478		chr7:129019479-129019481	chr7:129019481-129019482		81.25
N	alternative_donor	CUFF.276	chr14	-	chr14:71227900-71232158;chr14:71227900-71267383	chr14:71227900-71249939		chr14:71232159-71249939;chr14:71249940-71267383	chr14:71249939-71249940;chr14:71267383-71267384		0.00
N	jcn_only_AA		chr14	-	chr14:104230817-104245081;chr14:104224089-104245081	chr14:104225643-104245081					37.21
K	intron_retention	CUFF.557	chr19	+	chr19:50306447-50306543				chr19:50306446-50306447;chr19:50306543-50306544		4.76
N	cassette	CUFF.475	chr17	-	chr17:79994890-79995506	chr17:79994890-79995325;chr17:79995418-79995506		chr17:79995326-79995417			91.33
K	cassette	CUFF.359	chr15	-	chr15:99514388-99548657	chr15:99514388-99544415;chr15:99544509-99548657		chr15:99544416-99544508			88.89
K	jcn_only_AD	CUFF.952	chr6	+	chr6:150206810-150240322	chr6:150217376-150240322					46.15
K	jcn_only_AD	CUFF.712	chr22	+	chr22:24717292-24720187	chr22:24718887-24720187		chr22:24717292-24718886	chr22:24717291-24717292	chr22:24720188-24720395;chr22:24717256-24717291	61.11
N	jcn_only_AA	CUFF.460	chr17	+	chr17:61904884-61907492	chr17:61904884-61904979		chr17:61904980-61907492	chr17:61907492-61907493		22.73
N	jcn_only_AD	CUFF.102	chr10	+	chr10:35464928-35467816;chr10:35437420-35467816;chr10:35426808-35467816;chr10:35416122-35467816;chr10:35464634-35467816	chr10:35456732-35467816		chr10:35416122-35426807;chr10:35426808-35437419;chr10:35437420-35456731;chr10:35456732-35464633;chr10:35464634-35464927	chr10:35416121-35416122;chr10:35426807-35426808;chr10:35437419-35437420;chr10:35456731-35456732;chr10:35464633-35464634		8.25
N	cassette	CUFF.172	chr11	-	chr11:77885630-77899618	chr11:77885630-77888784;chr11:77889032-77899618		chr11:77888785-77889031			97.01
K	intron_retention	CUFF.418	chr17	+	chr17:1939386-1939822				chr17:1939385-1939386;chr17:1939822-1939823		20.31
N	alternative_donor	CUFF.671	chr2	-	chr2:242435950-242436714;chr2:242435950-242437030	chr2:242435950-242436596		chr2:242436597-242436714;chr2:242436715-242437030	chr2:242436714-242436715;chr2:242437030-242437031		11.24
K	intron_retention		chr16	-	chr16:23505700-23507009				chr16:23505699-23505700;chr16:23507009-23507010	chr16:23505624-23505699;chr16:23507010-23507099	4.11
N	alternative_donor	CUFF.899	chr5	-	chr5:178047675-178050256	chr5:178047675-178049393		chr5:178049394-178050256	chr5:178050256-178050257		22.95
N	alternative_acceptor	CUFF.765	chr3	-	chr3:107573542-107573976;chr3:107572807-107573976	chr3:107572902-107573976		chr3:107572807-107572901;chr3:107572902-107573541	chr3:107572806-107572807;chr3:107572901-107572902		67.39
N	alternative_first_exon	CUFF.212	chr12	+	chr12:26205536-26208168;chr12:26148064-26208168;chr12:26164755-26208168;chr12:26174452-26208168	chr12:26205930-26208168	chr12:26147970-26148063;chr12:26164591-26164754;chr12:26174353-26174451	chr12:26205414-26205929			11.11
K	alternative_first_exon	CUFF.486	chr18	-	chr18:44486279-44497284;chr18:44486279-44497964	chr18:44486279-44500021	chr18:44497285-44497510;chr18:44497965-44498061	chr18:44500022-44500200			23.94
K	alternative_first_exon	CUFF.1119	chrX	-	chrX:20227523-20252875	chrX:20227523-20236917	chrX:20252876-20252932	chrX:20236918-20237117			60.00
K	intron_retention	CUFF.728	chr22	-	chr22:51018232-51018485				chr22:51018231-51018232;chr22:51018485-51018486		52.47
K	cassette	CUFF.1018	chr7	-	chr7:156626487-156629506	chr7:156626487-156627171;chr7:156627270-156629506		chr7:156627172-156627269			26.83
N	mutually_exclusive	CUFF.876	chr5	+	chr5:54456072-54456821,chr5:54457084-54459882	chr5:54456072-54456157,chr5:54456225-54459882	chr5:54456822-54457083	chr5:54456158-54456224			59.90
K	intron_retention	CUFF.931	chr6	+	chr6:46636531-46644383				chr6:46636530-46636531;chr6:46644383-46644384		48.15
K	cassette	CUFF.920	chr6	+	chr6:32121414-32122363	chr6:32121414-32121972;chr6:32122182-32122363		chr6:32121973-32122181			52.28
K	coord_cassette	CUFF.78	chr1	+	chr1:222824246-222826349	chr1:222824246-222825318;chr1:222825391-222825569;chr1:222825675-222826349		chr1:222825319-222825390;chr1:222825570-222825674			68.75
K	cassette	CUFF.1009	chr7	+	chr7:128848693-128850203	chr7:128848693-128849129;chr7:128849239-128850203		chr7:128849130-128849238			30.00
K	jcn_only_AA	CUFF.1121	chrX	+	chrX:45184847-45192754	chrX:45184847-45192518		chrX:45192519-45192754	chrX:45192754-45192755		44.83
N	intron_retention		chr17	-	chr17:56082403-56083870				chr17:56082402-56082403;chr17:56083870-56083871		97.95
K	alternative_acceptor	CUFF.496	chr18	-	chr18:66567475-66569424	chr18:66567509-66569424		chr18:66567475-66567508	chr18:66567474-66567475		24.62
K	alternative_donor	CUFF.715	chr22	+	chr22:29469210-29490245	chr22:29469216-29490245		chr22:29469210-29469215	chr22:29469209-29469210		40.00
N	jcn_only_AA	CUFF.519	chr19	+	chr19:11468416-11470146;chr19:11468416-11470207	chr19:11468416-11470282		chr19:11470147-11470207;chr19:11470208-11470282	chr19:11470207-11470208;chr19:11470282-11470283		37.50
N	jcn_only_AA		chr11	-	chr11:10828867-10830251	chr11:10830056-10830251					46.15
N	intron_retention		chr7	+	chr7:150837204-150838984				chr7:150837203-150837204;chr7:150838984-150838985		12.20
N	jcn_only_AD	CUFF.1062	chr8	+	chr8:144375236-144377909	chr8:144377641-144377909		chr8:144375236-144377640	chr8:144375235-144375236		1.20
K	intron_retention	CUFF.68	chr1	+	chr1:200883724-200884202				chr1:200883723-200883724;chr1:200884202-200884203		40.00
N	jcn_only_AD	CUFF.140	chr11	-	chr11:118927130-118927785	chr11:118927130-118927730		chr11:118927731-118927785	chr11:118927785-118927786		30.77
K	alternative_donor	CUFF.1092,CUFF.1098	chr9	-	chr9:123550557-123555426	chr9:123550557-123555164		chr9:123555165-123555426	chr9:123555426-123555427		41.18
N	jcn_only_AD	CUFF.1066	chr9	-	chr9:15214248-15224337;chr9:15214248-15225914;chr9:15214248-15249915	chr9:15214248-15224357					12.70
N	cassette	CUFF.1018	chr7	-	chr7:156619439-156685621	chr7:156619439-156626446;chr7:156626487-156685621		chr7:156626447-156626486			80.95
K	cassette	CUFF.375	chr16	+	chr16:3194326-3194743	chr16:3194326-3194453;chr16:3194649-3194743		chr16:3194454-3194648			61.11
K	intron_retention	CUFF.195	chr12	-	chr12:347177-369016				chr12:347176-347177;chr12:369016-369017		62.16
N	jcn_only_AD		chr1	+	chr1:70820791-70831828	chr1:70820892-70831828		chr1:70820791-70820891	chr1:70820790-70820791		51.85
N	jcn_only_AA	CUFF.880	chr5	-	chr5:64900873-64905069	chr5:64902995-64905069		chr5:64900873-64902994	chr5:64900872-64900873		34.00
K	intron_retention	CUFF.547	chr19	-	chr19:41939340-41939441				chr19:41939339-41939340;chr19:41939441-41939442		4.19
K	cassette	CUFF.828	chr4	+	chr4:37839236-37841469	chr4:37839236-37841138;chr4:37841306-37841469		chr4:37841139-37841305			90.62
N	intron_retention		chr17	-	chr17:79478605-79478952				chr17:79478604-79478605;chr17:79478952-79478953		81.16
N	cassette	CUFF.974	chr7	-	chr7:38908854-38948753	chr7:38908854-38937690;chr7:38937730-38948753		chr7:38937691-38937729			82.22
N	jcn_only_AA		chr3	-	chr3:33673864-33686248	chr3:33673867-33686248					2.43
N	jcn_only_AA		chr2	+	chr2:101609990-101612257	chr2:101609990-101611861		chr2:101611862-101612257	chr2:101612257-101612258		65.00
N	alternative_donor	CUFF.752,CUFF.796	chr3	-	chr3:156262229-156266693;chr3:156262229-156266654	chr3:156262229-156266593		chr3:156266594-156266654;chr3:156266655-156266693	chr3:156266654-156266655;chr3:156266693-156266694		1.24
K	cassette	CUFF.402	chr16	-	chr16:67220561-67220923	chr16:67220561-67220661;chr16:67220788-67220923		chr16:67220662-67220787			12.82
N	alternative_donor	CUFF.457	chr17	+	chr17:61562331-61562596;chr17:61562428-61562596	chr17:61561903-61562596		chr17:61561903-61562330;chr17:61562331-61562427	chr17:61561902-61561903;chr17:61562330-61562331		17.86
K	cassette	CUFF.310	chr15	+	chr15:40545491-40556981	chr15:40545491-40556004;chr15:40556121-40556981		chr15:40556005-40556120			38.93
N	jcn_only_AA	CUFF.869	chr5	+	chr5:40936588-40937653	chr5:40936588-40937339		chr5:40937340-40937653	chr5:40937653-40937654		8.06
K	intron_retention	CUFF.555	chr19	-	chr19:49310332-49311012				chr19:49310331-49310332;chr19:49311012-49311013		44.29
N	jcn_only_AA	CUFF.910	chr6	-	chr6:5113652-5216850;chr6:5138974-5216850;chr6:5187215-5216850	chr6:5144497-5216850		chr6:5113652-5138973;chr6:5138974-5144496;chr6:5144497-5187214	chr6:5113651-5113652;chr6:5138973-5138974;chr6:5144496-5144497		21.57
N	alternative_donor	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;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;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		13.51
K	alternative_donor	CUFF.180	chr11	+	chr11:117070149-117073717	chr11:117070546-117073717		chr11:117070149-117070545	chr11:117070148-117070149		93.16
N	cassette	CUFF.725	chr22	+	chr22:45244941-45258154	chr22:45244941-45255610;chr22:45255715-45258154		chr22:45255611-45255714			94.12
K	alternative_last_exon	CUFF.1048	chr8	-	chr8:99054947-99057170;chr8:99037967-99057170	chr8:99055004-99057170	chr8:99037079-99037966	chr8:99054873-99055003			77.06
K	cassette	CUFF.90	chr10	+	chr10:6263491-6265920	chr10:6263491-6264817;chr10:6264948-6265920		chr10:6264818-6264947			96.91
K	intron_retention	CUFF.984	chr7	+	chr7:75040858-75040937				chr7:75040857-75040858;chr7:75040937-75040938		40.91
N	jcn_only_AA	CUFF.61	chr1	+	chr1:167345393-167353093	chr1:167345393-167345789		chr1:167345790-167353093	chr1:167353093-167353094		8.46
K	intron_retention	CUFF.330	chr15	+	chr15:64445539-64445850				chr15:64445538-64445539;chr15:64445850-64445851		24.24
K	intron_retention	CUFF.432	chr17	+	chr17:25970647-25972886				chr17:25970646-25970647;chr17:25972886-25972887		14.29
K	jcn_only_AD	CUFF.1018,CUFF.971	chr7	-	chr7:156516873-156526870	chr7:156516873-156518128					55.21
N	alternative_donor	CUFF.358	chr15	+	chr15:97326820-97327382;chr15:97326975-97327382	chr15:97327061-97327382		chr15:97326820-97326974;chr15:97326975-97327060	chr15:97326819-97326820;chr15:97326974-97326975		85.14
K	cassette	CUFF.829	chr4	-	chr4:56475347-56496568	chr4:56475347-56482504;chr4:56482553-56496568		chr4:56482505-56482552			73.79
N	intron_retention		chr2	+	chr2:219461022-219461057				chr2:219461021-219461022;chr2:219461057-219461058		15.38
N	intron_retention		chr12	+	chr12:58018390-58018648				chr12:58018389-58018390;chr12:58018648-58018649		35.65
K	alternative_first_exon	CUFF.1061	chr8	+	chr8:144349655-144356873	chr8:144351691-144356873	chr8:144349524-144349654	chr8:144351469-144351690			77.89
K	intron_retention	CUFF.307	chr15	+	chr15:30773111-30776704				chr15:30773110-30773111;chr15:30776704-30776705		46.15
K	alternative_acceptor	CUFF.1089,CUFF.1109	chr9	+	chr9:116779065-116791189	chr9:116779065-116791012		chr9:116791013-116791189	chr9:116791189-116791190		82.30
N	intron_retention		chr9	-	chr9:131485019-131486272				chr9:131485018-131485019;chr9:131486272-131486273		35.14
N	jcn_only_AA	CUFF.792	chr3	-	chr3:133910819-133913925	chr3:133910828-133913925		chr3:133910819-133910827	chr3:133910818-133910819		28.38
K	intron_retention		chr11	-	chr11:8474454-8476290				chr11:8474453-8474454;chr11:8476290-8476291		6.90
N	alternative_donor	CUFF.476	chr17	+	chr17:80439088-80441591	chr17:80441181-80441591		chr17:80439088-80441180	chr17:80439087-80439088		0.28
N	cassette	CUFF.278	chr14	-	chr14:75159032-75179635	chr14:75159032-75165466;chr14:75165560-75179635		chr14:75165467-75165559		chr14:75158744-75159031;chr14:75179636-75179896	52.38
N	alternative_last_exon		chr10	+	chr10:5138770-5141518	chr10:5138770-5139625	chr10:5141519-5141641	chr10:5139626-5139854			88.32
N	mutually_exclusive	CUFF.136	chr11	-	chr11:407958-408694,chr11:408894-414822	chr11:407958-408072,chr11:408207-414822	chr11:408695-408893	chr11:408073-408206			17.83
N	jcn_only_AD	CUFF.606,CUFF.622	chr2	-	chr2:68374700-68384392;chr2:68374700-68384505	chr2:68374700-68384058		chr2:68384059-68384392;chr2:68384393-68384505	chr2:68384392-68384393;chr2:68384505-68384506		20.00
N	alternative_acceptor	CUFF.298	chr14	-	chr14:104202540-104205015	chr14:104204198-104205015		chr14:104202540-104204197	chr14:104202539-104202540		90.00
N	alternative_donor	CUFF.879	chr5	-	chr5:60200701-60214091	chr5:60200701-60203106		chr5:60203107-60214091	chr5:60214091-60214092		1.09
N	jcn_only_AA	CUFF.340,CUFF.357	chr15	+	chr15:77713347-77750745	chr15:77713347-77740060		chr15:77740061-77750745	chr15:77750745-77750746		3.57
K	intron_retention		chr19	-	chr19:6026249-6039990				chr19:6026248-6026249;chr19:6039990-6039991		26.73
N	intron_retention		chr12	+	chr12:53846760-53848509				chr12:53846759-53846760;chr12:53848509-53848510		64.15
K	jcn_only_AD	CUFF.1055	chr8	-	chr8:120818642-120843916	chr8:120818642-120831585					16.67
K	cassette	CUFF.94	chr10	+	chr10:18240955-18250509	chr10:18240955-18242119;chr10:18242467-18250509		chr10:18242120-18242466			23.33
K	jcn_only_AD	CUFF.658	chr2	-	chr2:207953306-207988497;chr2:207953306-207988699	chr2:207953306-207989067		chr2:207988498-207988699;chr2:207988700-207989067	chr2:207988699-207988700;chr2:207989067-207989068		73.24
N	intron_retention		chr21	+	chr21:15646434-15646458				chr21:15646433-15646434;chr21:15646458-15646459	chr21:15646075-15646433;chr21:15646459-15646478	63.64
N	jcn_only_AD	CUFF.316,CUFF.352	chr15	-	chr15:44881613-44884528	chr15:44881613-44882618		chr15:44882619-44884528	chr15:44884528-44884529		44.74
K	alternative_first_exon	CUFF.512	chr19	-	chr19:6216525-6217964	chr19:6216525-6216746	chr19:6217965-6218052	chr19:6216747-6217022			72.00
K	jcn_only_AD	CUFF.687	chr20	+	chr20:33589330-33589750	chr20:33589396-33589750		chr20:33589330-33589395	chr20:33589329-33589330		4.03
N	coord_cassette	CUFF.385	chr16	+	chr16:19621738-19637498	chr16:19621738-19623049;chr16:19623121-19627435;chr16:19627514-19628007;chr16:19628131-19637498		chr16:19623050-19623120;chr16:19627436-19627513;chr16:19628008-19628130			95.50
K	jcn_only_AA	CUFF.1027	chr8	-	chr8:22012977-22013849	chr8:22013023-22013849		chr8:22012977-22013022	chr8:22012976-22012977		89.66
N	jcn_only_AA	CUFF.504	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		10.80
N	cassette	CUFF.1080	chr9	-	chr9:86514720-86523366	chr9:86514720-86517974;chr9:86518934-86523366		chr9:86517975-86518933			64.29
K	alternative_first_exon	CUFF.104	chr10	+	chr10:43572780-43607546	chr10:43606914-43607546	chr10:43572433-43572779	chr10:43606655-43606913			28.57
N	jcn_only_AD		chr11	-	chr11:10828929-10829080;chr11:10828929-10829291	chr11:10828929-10829720		chr11:10829081-10829291;chr11:10829292-10829720	chr11:10829291-10829292;chr11:10829720-10829721		20.00
K	intron_retention	CUFF.426	chr17	-	chr17:15586472-15587509				chr17:15586471-15586472;chr17:15587509-15587510		11.08
N	alternative_donor	CUFF.315	chr15	-	chr15:42300064-42305882	chr15:42300064-42302276		chr15:42302277-42305882	chr15:42305882-42305883	chr15:42299927-42300063;chr15:42305883-42305955	0.00
N	jcn_only_AD	CUFF.974	chr7	-	chr7:38869929-38902144	chr7:38869929-38870815		chr7:38870816-38902144	chr7:38902144-38902145		31.93
N	intron_retention		chr3	+	chr3:28360371-28360999				chr3:28360370-28360371;chr3:28360999-28361000		41.67
N	jcn_only_AA	CUFF.786	chr3	-	chr3:127299007-127313642	chr3:127310794-127313642		chr3:127299007-127310793	chr3:127299006-127299007		11.32
N	alternative_donor	CUFF.818,CUFF.856	chr4	-	chr4:162577647-162680562	chr4:162577647-162585967		chr4:162585968-162680562	chr4:162680562-162680563		0.00
N	alternative_donor	CUFF.464	chr17	+	chr17:66511708-66518896	chr17:66511718-66518896		chr17:66511708-66511717	chr17:66511707-66511708		97.86
N	cassette	CUFF.809	chr4	+	chr4:645878-647640	chr4:645878-646284;chr4:646343-647640		chr4:646285-646342			66.67
K	intron_retention	CUFF.160	chr11	+	chr11:61608004-61608095				chr11:61608003-61608004;chr11:61608095-61608096	chr11:61607913-61608003;chr11:61608096-61608197	51.68
N	jcn_only_AD		chr3	-	chr3:27394411-27410715;chr3:27394411-27409013	chr3:27394411-27410521					15.38
K	cassette	CUFF.765	chr3	-	chr3:107576050-107591814	chr3:107576050-107586157;chr3:107586425-107591814		chr3:107586158-107586424			57.65
N	jcn_only_AA	CUFF.709	chr22	-	chr22:21841217-21841853	chr22:21841265-21841853		chr22:21841217-21841264	chr22:21841216-21841217		2.38
K	jcn_only_AA	CUFF.654	chr2	-	chr2:204354810-204355936	chr2:204354813-204355936		chr2:204354810-204354812	chr2:204354809-204354810		91.37
K	cassette	CUFF.61	chr1	+	chr1:167353189-167365522	chr1:167353189-167358824;chr1:167358999-167365522		chr1:167358825-167358998			98.48
K	cassette	CUFF.945	chr6	-	chr6:128718834-128841403	chr6:128718834-128730438;chr6:128730478-128841403		chr6:128730439-128730477			33.33
N	mutually_exclusive	CUFF.1098	chr9	-	chr9:130948056-130952607,chr9:130952724-130952966	chr9:130948056-130950141,chr9:130950214-130952966	chr9:130952608-130952723	chr9:130950142-130950213			7.69
N	jcn_only_AA	CUFF.754	chr3	-	chr3:49463856-49466540	chr3:49463862-49466540		chr3:49463856-49463861	chr3:49463855-49463856		88.64
N	jcn_only_AA	CUFF.722	chr22	+	chr22:37695348-37696947;chr22:37695348-37696110	chr22:37695348-37696193		chr22:37696111-37696193;chr22:37696194-37696947	chr22:37696193-37696194;chr22:37696947-37696948		4.71
K	alternative_last_exon	CUFF.286	chr14	-	chr14:81728276-81737013	chr14:81734842-81737013	chr14:81726910-81728275	chr14:81734293-81734841		chr14:81737014-81737216	83.78
K	jcn_only_AD	CUFF.658	chr2	-	chr2:207953306-207989067;chr2:207953306-207988699	chr2:207953306-207988497		chr2:207988498-207988699;chr2:207988700-207989067	chr2:207988699-207988700;chr2:207989067-207989068		22.86
N	jcn_only_AD	CUFF.187	chr11	+	chr11:119056220-119056557	chr11:119056338-119056557		chr11:119056220-119056337	chr11:119056219-119056220		31.82
N	alternative_donor	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;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;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		0.00
K	alternative_first_exon	CUFF.486	chr18	-	chr18:44486279-44497284;chr18:44486279-44500021	chr18:44486279-44497964	chr18:44497285-44497510;chr18:44500022-44500200	chr18:44497965-44498061			25.35
K	cassette	CUFF.1102	chr9	+	chr9:133320383-133327610	chr9:133320383-133326988;chr9:133327431-133327610		chr9:133326989-133327430			70.00
N	jcn_only_AD		chr14	-	chr14:104263856-104313635;chr14:104263856-104313111;chr14:104263856-104306415	chr14:104263856-104313344					25.88
K	cassette	CUFF.145	chr11	+	chr11:3239790-3242799	chr11:3239790-3241456;chr11:3241590-3242799		chr11:3241457-3241589		chr11:3239562-3239789;chr11:3242800-3244361	50.00
N	jcn_only_AA	CUFF.1073	chr9	+	chr9:43853617-43861002;chr9:43853617-43854068	chr9:43853617-43861005		chr9:43854069-43861002;chr9:43861003-43861005	chr9:43861002-43861003;chr9:43861005-43861006		14.71
N	alternative_donor	CUFF.1052	chr8	+	chr8:107738538-107749747;chr8:107726214-107749747	chr8:107738486-107749747		chr8:107726214-107738485;chr8:107738486-107738537	chr8:107726213-107726214;chr8:107738485-107738486		0.00
N	intron_retention		chr20	+	chr20:30136597-30136831				chr20:30136596-30136597;chr20:30136831-30136832	chr20:30136832-30136917	59.55
N	jcn_only_AA	CUFF.874	chr5	+	chr5:52177854-52183646	chr5:52177854-52178711		chr5:52178712-52183646	chr5:52183646-52183647		44.00
N	jcn_only_AD	CUFF.780	chr3	-	chr3:125032501-125042152;chr3:125032501-125042231	chr3:125032501-125033780		chr3:125033781-125042152;chr3:125042153-125042231	chr3:125042152-125042153;chr3:125042231-125042232		3.36
K	alternative_first_exon	CUFF.201	chr12	+	chr12:4658003-4662148	chr12:4659714-4662148	chr12:4657853-4658002	chr12:4659620-4659713			14.85
N	jcn_only_AD		chr22	+	chr22:37699444-37705252	chr22:37700328-37705252					81.82
N	jcn_only_AD	CUFF.90	chr10	+	chr10:6271144-6274857;chr10:6266177-6274857;chr10:6273278-6274857;chr10:6268329-6274857	chr10:6270182-6274857					11.65
K	alternative_last_exon	CUFF.122	chr10	+	chr10:88993347-88994873	chr10:88993347-88993679	chr10:88994874-88996734	chr10:88993680-88994735			61.54
N	alternative_acceptor		chr17	+	chr17:25965381-25967668	chr17:25965381-25967597		chr17:25967598-25967668	chr17:25967668-25967669		83.76
N	intron_retention		chr7	+	chr7:75044077-75044162				chr7:75044076-75044077;chr7:75044162-75044163		87.50
K	alternative_first_exon	CUFF.1031	chr8	-	chr8:30643824-30648712	chr8:30643824-30643947	chr8:30648713-30648831	chr8:30643948-30644044			6.35
N	alternative_donor	CUFF.530	chr19	+	chr19:17447967-17448682	chr19:17448474-17448682		chr19:17447967-17448473	chr19:17447966-17447967		72.63
N	alternative_donor	CUFF.389	chr16	+	chr16:22448814-22462940	chr16:22449059-22462940		chr16:22448814-22449058	chr16:22448813-22448814		36.36
N	alternative_acceptor	CUFF.918	chr6	+	chr6:31936316-31936462	chr6:31936316-31936399		chr6:31936400-31936462	chr6:31936462-31936463		9.92
N	intron_retention		chr16	+	chr16:89789592-89789686				chr16:89789591-89789592;chr16:89789686-89789687		63.16
K	intron_retention	CUFF.241	chr12	-	chr12:120135644-120135780				chr12:120135643-120135644;chr12:120135780-120135781		7.00
K	intron_retention	CUFF.184	chr11	-	chr11:118925773-118925896				chr11:118925772-118925773;chr11:118925896-118925897		13.28
N	jcn_only_AD	CUFF.419,CUFF.472	chr17	-	chr17:5403271-5405056	chr17:5403271-5403350		chr17:5403351-5405056	chr17:5405056-5405057		79.31
K	intron_retention	CUFF.59	chr1	-	chr1:161953126-161953385				chr1:161953125-161953126;chr1:161953385-161953386		73.49
N	jcn_only_AD		chr15	+	chr15:24811360-24811802;chr15:24803469-24811802	chr15:24780954-24811802					8.82
N	alternative_acceptor	CUFF.119	chr10	-	chr10:79396328-79397022;chr10:79163782-79397022	chr10:79396274-79397022		chr10:79163782-79396273;chr10:79396274-79396327	chr10:79163781-79163782;chr10:79396273-79396274		0.00
K	cassette	CUFF.618	chr2	-	chr2:86397965-86400772	chr2:86397965-86398330;chr2:86398469-86400772		chr2:86398331-86398468			90.00
K	intron_retention	CUFF.657	chr2	+	chr2:207653628-207655295				chr2:207653627-207653628;chr2:207655295-207655296		3.33
K	intron_retention	CUFF.517	chr19	+	chr19:10394171-10394233				chr19:10394170-10394171;chr19:10394233-10394234		82.56
N	intron_retention	CUFF.769	chr3	+	chr3:119196296-119197180				chr3:119196295-119196296;chr3:119197180-119197181		96.42
N	jcn_only_AD	CUFF.161	chr11	-	chr11:410028-417324;chr11:410028-417293	chr11:410028-414822		chr11:414823-417293;chr11:417294-417324	chr11:417293-417294;chr11:417324-417325		88.45
K	cassette	CUFF.483	chr18	+	chr18:14791491-14796341	chr18:14791491-14796219;chr18:14796249-14796341		chr18:14796220-14796248			21.88
K	jcn_only_AA	CUFF.506	chr19	+	chr19:4304759-4305981;chr19:4304759-4305942	chr19:4304759-4306020		chr19:4305943-4305981;chr19:4305982-4306020	chr19:4305981-4305982;chr19:4306020-4306021		4.62
K	coord_cassette	CUFF.524	chr19	-	chr19:14862484-14867049	chr19:14862484-14863140;chr19:14863339-14865765;chr19:14865940-14866465;chr19:14866657-14867049		chr19:14863141-14863338;chr19:14865766-14865939;chr19:14866466-14866656			67.09
N	jcn_only_AD	CUFF.780,CUFF.786	chr3	-	chr3:125007073-125032151	chr3:125007073-125011308		chr3:125011309-125032151	chr3:125032151-125032152		68.29
N	alternative_donor		chr4	+	chr4:120434076-120449894	chr4:120434126-120449894		chr4:120434076-120434125	chr4:120434075-120434076		67.65
N	jcn_only_AD	CUFF.728	chr22	-	chr22:51016364-51016512;chr22:51016364-51016977	chr22:51016364-51016814		chr22:51016513-51016814;chr22:51016815-51016977	chr22:51016814-51016815;chr22:51016977-51016978		51.89
K	intron_retention	CUFF.241	chr12	-	chr12:120220442-120221711				chr12:120220441-120220442;chr12:120221711-120221712		90.24
K	alternative_last_exon	CUFF.39	chr1	-	chr1:120529706-120539619	chr1:120539370-120539619	chr1:120529583-120529705	chr1:120535306-120539369			98.82
K	intron_retention	CUFF.761	chr3	-	chr3:73432957-73433799				chr3:73432956-73432957;chr3:73433799-73433800		88.73
K	intron_retention	CUFF.273	chr14	+	chr14:61448101-61449225				chr14:61448100-61448101;chr14:61449225-61449226		38.68
N	alternative_donor	CUFF.708	chr22	+	chr22:21058172-21058255;chr22:21057981-21058255	chr22:21058040-21058255		chr22:21057981-21058039;chr22:21058040-21058171	chr22:21057980-21057981;chr22:21058039-21058040		58.76
K	alternative_first_exon	CUFF.76	chr1	+	chr1:211556268-211564957	chr1:211564013-211564957	chr1:211556052-211556267	chr1:211563906-211564012			28.57
N	jcn_only_AA	CUFF.86	chr10	-	chr10:410523-412214	chr10:410962-412214		chr10:410523-410961	chr10:410522-410523		78.57
N	alternative_donor	CUFF.306	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		0.00
K	cassette	CUFF.936	chr6	+	chr6:90327751-90333128	chr6:90327751-90331640;chr6:90331746-90333128		chr6:90331641-90331745			97.83
N	jcn_only_AD	CUFF.639	chr2	+	chr2:160615847-160619390	chr2:160615870-160619390		chr2:160615847-160615869	chr2:160615846-160615847		21.31
N	alternative_acceptor	CUFF.493	chr18	+	chr18:55888990-55912658	chr18:55888990-55895061		chr18:55895062-55912658	chr18:55912658-55912659		0.00
N	intron_retention		chr11	+	chr11:830714-831223				chr11:830713-830714;chr11:831223-831224	chr11:830621-830713;chr11:831224-831295	74.07
K	jcn_only_AA	CUFF.177	chr11	-	chr11:104915386-104916017	chr11:104915659-104916017		chr11:104915386-104915658	chr11:104915385-104915386		62.86
N	intron_retention		chr12	-	chr12:77256740-77256955				chr12:77256739-77256740;chr12:77256955-77256956		46.15
N	jcn_only_AA	CUFF.663	chr2	+	chr2:220094623-220096649;chr2:220094623-220097211	chr2:220094623-220094949					66.22
K	alternative_first_exon	CUFF.531	chr19	+	chr19:17598339-17599816	chr19:17599749-17599816	chr19:17598269-17598338	chr19:17599505-17599748			97.53
N	alternative_donor	CUFF.852	chr4	-	chr4:152147239-152187237;chr4:152147239-152147319	chr4:152147239-152246392		chr4:152147320-152187237;chr4:152187238-152246392	chr4:152187237-152187238;chr4:152246392-152246393		100.00
N	cassette	CUFF.257	chr14	+	chr14:23392414-23395669	chr14:23392414-23393509;chr14:23393651-23395669		chr14:23393510-23393650			74.16
K	cassette	CUFF.407	chr16	+	chr16:70390151-70398919	chr16:70390151-70398445;chr16:70398549-70398919		chr16:70398446-70398548			24.03
K	jcn_only_AD	CUFF.516	chr19	-	chr19:10207250-10213243	chr19:10207250-10213227		chr19:10213228-10213243	chr19:10213243-10213244		21.74
N	alternative_donor	CUFF.696,CUFF.701	chr21	-	chr21:30971258-31015145	chr21:30971258-30973547		chr21:30973548-31015145	chr21:31015145-31015146		0.00
N	jcn_only_AA	CUFF.765	chr3	-	chr3:107568819-107572719;chr3:107567966-107572719	chr3:107569199-107572719		chr3:107567966-107568818;chr3:107568819-107569198	chr3:107567965-107567966;chr3:107568818-107568819		24.56
K	intron_retention		chr17	+	chr17:61571832-61573754				chr17:61571831-61571832;chr17:61573754-61573755		4.53
K	alternative_first_exon	CUFF.777	chr3	+	chr3:122786054-122808014	chr3:122786423-122808014	chr3:122785876-122786053	chr3:122786102-122786422			93.02
K	intron_retention	CUFF.504	chr19	+	chr19:1440253-1440347				chr19:1440252-1440253;chr19:1440347-1440348		7.63
N	alternative_donor	CUFF.971	chr7	-	chr7:37382368-37433424;chr7:37382368-37392635;chr7:37382368-37488277;chr7:37382368-37382655	chr7:37382368-37488462		chr7:37382656-37392635;chr7:37392636-37433424;chr7:37433425-37488277;chr7:37488278-37488462	chr7:37392635-37392636;chr7:37433424-37433425;chr7:37488277-37488278;chr7:37488462-37488463		40.00
N	alternative_donor	CUFF.490	chr18	+	chr18:55895140-55912658;chr18:55865102-55912658;chr18:55895121-55912658;chr18:55862966-55912658;chr18:55888990-55912658	chr18:55833094-55912658		chr18:55833094-55862965;chr18:55862966-55865101;chr18:55865102-55888989;chr18:55888990-55895120;chr18:55895121-55895139	chr18:55833093-55833094;chr18:55862965-55862966;chr18:55865101-55865102;chr18:55888989-55888990;chr18:55895120-55895121		100.00
K	cassette	CUFF.232	chr12	+	chr12:58018940-58019192	chr12:58018940-58019018;chr12:58019114-58019192		chr12:58019019-58019113			22.00
K	cassette	CUFF.956	chr6	-	chr6:170112636-170115803	chr6:170112636-170114828;chr6:170114939-170115803		chr6:170114829-170114938			80.00
N	jcn_only_AA	CUFF.823	chr4	+	chr4:20552522-20555427	chr4:20552522-20554050		chr4:20554051-20555427	chr4:20555427-20555428		15.79
N	alternative_donor	CUFF.998	chr7	-	chr7:102251590-102256969;chr7:102251590-102252518	chr7:102251590-102257071		chr7:102252519-102256969;chr7:102256970-102257071	chr7:102256969-102256970;chr7:102257071-102257072		70.59
N	alternative_donor	CUFF.165	chr11	+	chr11:65486221-65486343	chr11:65486247-65486343		chr11:65486221-65486246	chr11:65486220-65486221		2.30
K	alternative_donor	CUFF.550	chr19	+	chr19:44764156-44768466;chr19:44764092-44768466	chr19:44764362-44768466		chr19:44764092-44764155;chr19:44764156-44764361	chr19:44764091-44764092;chr19:44764155-44764156		54.55
K	alternative_first_exon	CUFF.340	chr15	+	chr15:77713437-77750745,chr15:77740154-77750745,chr15:77750627-77750745;chr15:77713080-77750745	chr15:77713347-77750745	chr15:77712661-77713079	chr15:77713239-77713346			15.23
N	jcn_only_AA	CUFF.849	chr4	+	chr4:124750343-124846338	chr4:124750343-124784729		chr4:124784730-124846338	chr4:124846338-124846339		6.03
N	jcn_only_AA	CUFF.419	chr17	-	chr17:5409298-5421065;chr17:5418838-5421065	chr17:5405193-5421065					7.34
K	alternative_last_exon	CUFF.785	chr3	+	chr3:126139073-126142167	chr3:126139073-126139472	chr3:126142168-126142219	chr3:126139473-126139777		chr3:126138946-126139072	72.55
K	intron_retention	CUFF.545	chr19	-	chr19:41350678-41351198				chr19:41350677-41350678;chr19:41351198-41351199		58.06
K	intron_retention	CUFF.894	chr5	+	chr5:139915124-139916973				chr5:139915123-139915124;chr5:139916973-139916974	chr5:139914947-139915123;chr5:139916974-139917174	33.33
N	jcn_only_AA		chr6	+	chr6:161413116-161491639	chr6:161413116-161455290				chr6:161412759-161413115	25.00
K	intron_retention	CUFF.230	chr12	-	chr12:56709027-56709690				chr12:56709026-56709027;chr12:56709690-56709691		53.85
K	intron_retention	CUFF.547	chr19	-	chr19:41937794-41938219				chr19:41937793-41937794;chr19:41938219-41938220		86.61
K	jcn_only_AD	CUFF.618,CUFF.633	chr2	-	chr2:110920713-110922264	chr2:110920713-110922096		chr2:110922097-110922264	chr2:110922264-110922265		13.33
K	alternative_acceptor	CUFF.457	chr17	+	chr17:61564435-61566008	chr17:61564435-61565930		chr17:61565931-61566008	chr17:61566008-61566009		51.69
N	cassette	CUFF.639	chr2	+	chr2:160569173-160585519	chr2:160569173-160572191;chr2:160572278-160585519		chr2:160572192-160572277			9.43
K	alternative_acceptor	CUFF.482,CUFF.495	chr18	+	chr18:12658343-12658572	chr18:12658343-12658549		chr18:12658550-12658572	chr18:12658572-12658573		50.00
K	jcn_only_AA	CUFF.643	chr2	-	chr2:169826726-169828356	chr2:169826867-169828356		chr2:169826726-169826866	chr2:169826725-169826726	chr2:169828357-169828560;chr2:169826555-169826725	37.50
K	jcn_only_AA	CUFF.36	chr1	+	chr1:110211994-110212257	chr1:110211994-110212092		chr1:110212093-110212257	chr1:110212257-110212258		93.26
N	alternative_acceptor	CUFF.417	chr17	-	chr17:1615941-1617149	chr17:1616350-1617149		chr17:1615941-1616349	chr17:1615940-1615941		98.10
K	jcn_only_AD	CUFF.1092	chr9	-	chr9:123555536-123555637	chr9:123555536-123555631		chr9:123555632-123555637	chr9:123555637-123555638		57.69
K	alternative_donor	CUFF.386	chr16	+	chr16:21712349-21716489	chr16:21712391-21716489		chr16:21712349-21712390	chr16:21712348-21712349		5.26
K	alternative_last_exon	CUFF.486	chr18	-	chr18:44483599-44497284	chr18:44486279-44497284	chr18:44483490-44483598	chr18:44485634-44486278			67.31
K	jcn_only_AD	CUFF.402,CUFF.406	chr16	-	chr16:67221741-67222806	chr16:67221741-67222623		chr16:67222624-67222806	chr16:67222806-67222807		57.14
N	alternative_acceptor		chr19	+	chr19:17450409-17451915	chr19:17450409-17451852		chr19:17451853-17451915	chr19:17451915-17451916		79.69
N	jcn_only_AD	CUFF.504	chr19	+	chr19:1440241-1440347	chr19:1440253-1440347		chr19:1440241-1440252	chr19:1440240-1440241		86.92
N	alternative_donor	CUFF.453	chr17	-	chr17:56082403-56083870;chr17:56082403-56082774	chr17:56082403-56082758		chr17:56082759-56082774;chr17:56082775-56083870	chr17:56082774-56082775;chr17:56083870-56083871		62.07
N	jcn_only_AD	CUFF.325	chr15	+	chr15:57384090-57458599;chr15:57401516-57458599;chr15:57422171-57458599	chr15:57426699-57458599		chr15:57384090-57401515;chr15:57401516-57422170;chr15:57422171-57426698	chr15:57384089-57384090;chr15:57401515-57401516;chr15:57422170-57422171		3.88
K	intron_retention	CUFF.716	chr22	+	chr22:29684776-29687553				chr22:29684775-29684776;chr22:29687553-29687554		20.00
K	intron_retention	CUFF.232	chr12	+	chr12:58019536-58019780				chr12:58019535-58019536;chr12:58019780-58019781		10.11
N	jcn_only_AD		chr7	-	chr7:36901342-36934613	chr7:36901342-36909997		chr7:36909998-36934613	chr7:36934613-36934614		88.41
K	intron_retention	CUFF.267	chr14	-	chr14:52478402-52481004				chr14:52478401-52478402;chr14:52481004-52481005		27.78
N	jcn_only_AD	CUFF.942	chr6	-	chr6:114283559-114292020;chr6:114283559-114332294	chr6:114283559-114289797		chr6:114289798-114292020;chr6:114292021-114332294	chr6:114292020-114292021;chr6:114332294-114332295		66.33
N	intron_retention		chr17	-	chr17:1615694-1617149				chr17:1615693-1615694;chr17:1617149-1617150		78.26
K	alternative_last_exon	CUFF.885	chr5	+	chr5:121358103-121411009	chr5:121358103-121362636	chr5:121411010-121411363	chr5:121362637-121364314			44.68
K	cassette	CUFF.547	chr19	-	chr19:41939579-41944122	chr19:41939579-41942296;chr19:41942378-41944122		chr19:41942297-41942377			41.32
K	alternative_acceptor	CUFF.550	chr19	+	chr19:44764092-44768480	chr19:44764092-44768466		chr19:44768467-44768480	chr19:44768480-44768481		22.22
K	intron_retention	CUFF.663	chr2	+	chr2:220100035-220100195				chr2:220100034-220100035;chr2:220100195-220100196		31.15
K	alternative_first_exon	CUFF.95	chr10	-	chr10:18831107-18834393	chr10:18831107-18833252	chr10:18834394-18834580	chr10:18833253-18833406			84.21
K	jcn_only_AA	CUFF.504	chr19	+	chr19:1438428-1438809	chr19:1438428-1438805		chr19:1438806-1438809	chr19:1438809-1438810		83.95
K	alternative_first_exon	CUFF.1062	chr8	+	chr8:144374455-144375141,chr8:144373938-144375141;chr8:144373029-144375141	chr8:144373781-144375141	chr8:144372915-144373028	chr8:144373337-144373780			80.00
K	alternative_acceptor	CUFF.834	chr4	-	chr4:70513414-70518905	chr4:70513417-70518905		chr4:70513414-70513416	chr4:70513413-70513414		59.26
N	intron_retention		chr10	-	chr10:73973110-73975964				chr10:73973109-73973110;chr10:73975964-73975965		14.67
K	cassette	CUFF.264	chr14	+	chr14:50065922-50069087	chr14:50065922-50068259;chr14:50068368-50069087		chr14:50068260-50068367			12.36
N	jcn_only_AD	CUFF.1018	chr7	-	chr7:117501371-117512157;chr7:117501371-117514054	chr7:117501371-117511643					42.86
K	alternative_first_exon	CUFF.1121	chrX	+	chrX:45042590-45184352	chrX:45182893-45184352	chrX:45042404-45042589	chrX:45182792-45182892			51.85
N	jcn_only_AA	CUFF.119	chr10	-	chr10:78644776-78647048;chr10:78637649-78647048	chr10:78637652-78647048		chr10:78637649-78637651;chr10:78637652-78644775	chr10:78637648-78637649;chr10:78637651-78637652		39.13
N	jcn_only_AD		chr4	+	chr4:120449945-120471533	chr4:120465001-120471533					67.50
K	intron_retention	CUFF.241	chr12	-	chr12:120151454-120152001				chr12:120151453-120151454;chr12:120152001-120152002		49.32
N	alternative_donor	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55711941-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		88.89
N	alternative_acceptor	CUFF.1066	chr9	-	chr9:15214248-15225914	chr9:15224504-15225914		chr9:15214248-15224503	chr9:15214247-15214248		2.56
N	jcn_only_AD	CUFF.737,CUFF.782	chr3	-	chr3:27329235-27332752	chr3:27329235-27332107		chr3:27332108-27332752	chr3:27332752-27332753		32.09
N	jcn_only_AD	CUFF.579	chr2	+	chr2:3461465-3464033	chr2:3462233-3464033		chr2:3461465-3462232	chr2:3461464-3461465		1.60
N	alternative_first_exon	CUFF.755	chr3	+	chr3:51741184-51749077;chr3:51748138-51749077	chr3:51747327-51749077	chr3:51741086-51741183;chr3:51747980-51748137	chr3:51746489-51747326			10.10
K	alternative_first_exon	CUFF.207	chr12	+	chr12:13349807-13366412	chr12:13364523-13366412	chr12:13349561-13349806	chr12:13364403-13364522			89.81
K	jcn_only_AA	CUFF.603,CUFF.673	chr2	+	chr2:242590527-242592926	chr2:242590527-242590678					98.53
N	jcn_only_AD	CUFF.476	chr17	+	chr17:80439088-80441591	chr17:80441181-80441591		chr17:80439088-80441180	chr17:80439087-80439088		3.21
N	cassette	CUFF.445	chr17	-	chr17:40744181-40762554	chr17:40744181-40761515;chr17:40761746-40762554		chr17:40761516-40761745			57.89
K	alternative_acceptor	CUFF.418	chr17	+	chr17:1945170-1946269	chr17:1945170-1945898		chr17:1945899-1946269	chr17:1946269-1946270		88.44
K	alternative_first_exon	CUFF.533,CUFF.569	chr19	-	chr19:56321705-56343328	chr19:56321705-56329269	chr19:56343329-56343460	chr19:56329270-56329603			56.00
N	intron_retention		chr11	+	chr11:36397709-36398178				chr11:36397708-36397709;chr11:36398178-36398179		94.25
K	intron_retention	CUFF.1042	chr8	-	chr8:80963864-80965516				chr8:80963863-80963864;chr8:80965516-80965517		8.89
N	intron_retention	CUFF.176	chr11	-	chr11:102960048-102962412				chr11:102960047-102960048;chr11:102962412-102962413		45.45
N	coord_cassette	CUFF.374	chr16	+	chr16:3117417-3118180	chr16:3117417-3117554;chr16:3117615-3117984;chr16:3118012-3118180		chr16:3117555-3117614;chr16:3117985-3118011			97.89
K	jcn_only_AA	CUFF.457	chr17	+	chr17:61564435-61566008	chr17:61564435-61565930		chr17:61565931-61566008	chr17:61566008-61566009		60.00
N	jcn_only_AA		chr11	-	chr11:8496614-8498796	chr11:8498299-8498796		chr11:8496614-8498298	chr11:8496613-8496614		55.56
K	alternative_first_exon	CUFF.495	chr18	+	chr18:63417617-63429882	chr18:63418387-63429882	chr18:63417398-63417616	chr18:63417851-63418386			40.91
N	jcn_only_AA	CUFF.338	chr15	-	chr15:77577421-77578764;chr15:77474383-77578764	chr15:77577398-77578764					3.57
K	alternative_last_exon	CUFF.106	chr10	-	chr10:46143983-46147413	chr10:46147074-46147413	chr10:46143742-46143982	chr10:46145500-46147073			36.36
K	jcn_only_AD	CUFF.472	chr17	-	chr17:79479387-79479759	chr17:79479387-79479640		chr17:79479641-79479759	chr17:79479759-79479760		9.43
N	intron_retention		chr17	+	chr17:61904875-61905497				chr17:61904874-61904875;chr17:61905497-61905498		25.51
K	cassette	CUFF.524	chr19	-	chr19:14865940-14867049	chr19:14865940-14866465;chr19:14866690-14867049		chr19:14866466-14866689			39.56
K	jcn_only_AD	CUFF.482	chr18	+	chr18:12658205-12658572	chr18:12658343-12658572		chr18:12658205-12658342	chr18:12658204-12658205		23.08
N	jcn_only_AA	CUFF.633	chr2	-	chr2:110936125-110937200	chr2:110936513-110937200		chr2:110936125-110936512	chr2:110936124-110936125		6.32
N	intron_retention		chr14	-	chr14:52481981-52485962				chr14:52481980-52481981;chr14:52485962-52485963		41.18
K	intron_retention		chr11	-	chr11:406060-406141				chr11:406059-406060;chr11:406141-406142		84.21
K	alternative_acceptor	CUFF.187	chr11	+	chr11:119056220-119056633;chr11:119056220-119056557	chr11:119056220-119056630		chr11:119056558-119056630;chr11:119056631-119056633	chr11:119056630-119056631;chr11:119056633-119056634		24.74
N	jcn_only_AA	CUFF.1097	chr9	-	chr9:125652825-125667388	chr9:125659856-125667388					58.06
K	intron_retention	CUFF.550	chr19	+	chr19:44764092-44768466				chr19:44764091-44764092;chr19:44768466-44768467		88.46
K	intron_retention	CUFF.298	chr14	-	chr14:104209161-104212709				chr14:104209160-104209161;chr14:104212709-104212710		80.28
N	cassette	CUFF.136	chr11	-	chr11:408207-414822;chr11:408207-409867	chr11:408207-408694;chr11:408894-409867,chr11:408894-414822		chr11:408695-408893			80.79
N	alternative_first_exon	CUFF.663	chr2	+	chr2:220094623-220097211	chr2:220097085-220097211	chr2:220094404-220094622	chr2:220096982-220097084			87.68
K	alternative_first_exon	CUFF.668	chr2	+	chr2:237476485-237489082	chr2:237478568-237489082	chr2:237476372-237476484	chr2:237478230-237478567			58.82
N	alternative_acceptor	CUFF.1101	chr9	-	chr9:131483810-131483929;chr9:131483782-131483929	chr9:131483760-131483929		chr9:131483760-131483781;chr9:131483782-131483809	chr9:131483759-131483760;chr9:131483781-131483782		10.84
K	jcn_only_AA	CUFF.713	chr22	-	chr22:25124342-25130050	chr22:25124369-25130050		chr22:25124342-25124368	chr22:25124341-25124342		38.89
K	cassette	CUFF.440	chr17	-	chr17:34500807-34502089	chr17:34500807-34501765;chr17:34501989-34502089		chr17:34501766-34501988			19.05
N	jcn_only_AD	CUFF.951	chr6	+	chr6:145119127-145124171	chr6:145120610-145124171		chr6:145119127-145120609	chr6:145119126-145119127		5.32
K	cassette	CUFF.78	chr1	+	chr1:222835675-222837339	chr1:222835675-222836229;chr1:222836374-222837339		chr1:222836230-222836373			31.11
N	cassette	CUFF.936	chr6	+	chr6:90312847-90321990	chr6:90312847-90315725;chr6:90315825-90321990		chr6:90315726-90315824			58.78
K	alternative_acceptor	CUFF.243	chr12	-	chr12:133181418-133182732	chr12:133181605-133182732		chr12:133181418-133181604	chr12:133181417-133181418		80.77
K	jcn_only_AA	CUFF.1061	chr8	+	chr8:144351691-144354565;chr8:144351691-144356889	chr8:144351691-144356873					38.71
K	intron_retention	CUFF.703	chr21	-	chr21:47556968-47557152				chr21:47556967-47556968;chr21:47557152-47557153		6.12
N	alternative_acceptor	CUFF.919	chr6	-	chr6:31938917-31939096	chr6:31938925-31939096		chr6:31938917-31938924	chr6:31938916-31938917		85.11
K	jcn_only_AA	CUFF.259,CUFF.280	chr14	+	chr14:24572465-24573050	chr14:24572465-24572718		chr14:24572719-24573050	chr14:24573050-24573051		94.05
K	intron_retention	CUFF.526	chr19	+	chr19:16186983-16192722				chr19:16186982-16186983;chr19:16192722-16192723		19.48
K	cassette	CUFF.46	chr1	+	chr1:150249041-150253245	chr1:150249041-150252053;chr1:150252153-150253245		chr1:150252054-150252152			20.00
N	alternative_donor	CUFF.1052	chr8	+	chr8:107738538-107749747;chr8:107738486-107749747	chr8:107726214-107749747		chr8:107726214-107738485;chr8:107738486-107738537	chr8:107726213-107726214;chr8:107738485-107738486		100.00
N	alternative_last_exon		chr6	+	chr6:112664981-112668493	chr6:112664981-112666240	chr6:112668494-112668609	chr6:112666241-112666617			76.52
K	alternative_first_exon	CUFF.154,CUFF.183	chr11	-	chr11:34226238-34378247	chr11:34226238-34264021	chr11:34378248-34379555	chr11:34264022-34264184			89.47
N	jcn_only_AD		chr16	-	chr16:67221042-67222922	chr16:67221042-67221127					62.30
K	intron_retention	CUFF.1048	chr8	-	chr8:99055004-99057170				chr8:99055003-99055004;chr8:99057170-99057171		36.21
N	intron_retention		chr3	-	chr3:125725408-125725956				chr3:125725407-125725408;chr3:125725956-125725957		77.23
K	cassette	CUFF.1048	chr8	-	chr8:99055004-99057574	chr8:99055004-99057170;chr8:99057317-99057574		chr8:99057171-99057316			53.96
N	jcn_only_AD	CUFF.852	chr4	-	chr4:152065203-152069073	chr4:152065203-152065371		chr4:152065372-152069073	chr4:152069073-152069074		20.59
K	cassette	CUFF.1018	chr7	-	chr7:156626487-156685621	chr7:156626487-156629506;chr7:156629580-156685621		chr7:156629507-156629579			81.45
K	intron_retention	CUFF.617	chr2	-	chr2:79365203-79365497				chr2:79365202-79365203;chr2:79365497-79365498		33.77
N	alternative_acceptor	CUFF.176	chr11	-	chr11:102960039-102962412	chr11:102960048-102962412		chr11:102960039-102960047	chr11:102960038-102960039		42.31
K	intron_retention	CUFF.12	chr1	-	chr1:26228174-26230131				chr1:26228173-26228174;chr1:26230131-26230132		2.30
K	coord_cassette	CUFF.18	chr1	+	chr1:32541424-32542764	chr1:32541424-32542164;chr1:32542248-32542363;chr1:32542448-32542764		chr1:32542165-32542247;chr1:32542364-32542447			63.10
K	cassette	CUFF.347	chr15	-	chr15:83333696-83334208	chr15:83333696-83333998;chr15:83334056-83334208		chr15:83333999-83334055			27.45
K	intron_retention	CUFF.464	chr17	+	chr17:66521100-66521894				chr17:66521099-66521100;chr17:66521894-66521895		1.67
N	intron_retention		chr5	-	chr5:178049461-178050256				chr5:178049460-178049461;chr5:178050256-178050257		21.05
N	jcn_only_AD		chr3	+	chr3:28283393-28304781	chr3:28295257-28304781					30.00
N	jcn_only_AA	CUFF.579	chr2	+	chr2:3447663-3461391	chr2:3447663-3460920		chr2:3460921-3461391	chr2:3461391-3461392		6.19
K	alternative_first_exon	CUFF.253	chr13	-	chr13:97644827-97646822	chr13:97644827-97646551	chr13:97646823-97647068	chr13:97646552-97646819			96.19
N	alternative_acceptor		chr4	+	chr4:130821810-130849722	chr4:130821810-130829788		chr4:130829789-130849722	chr4:130849722-130849723		0.00
N	alternative_acceptor	CUFF.310	chr15	+	chr15:40545491-40549043;chr15:40545491-40556004	chr15:40545491-40555999		chr15:40549044-40555999;chr15:40556000-40556004	chr15:40555999-40556000;chr15:40556004-40556005		2.38
N	jcn_only_AD	CUFF.1151	chrX	+	chrX:153607898-153608049	chrX:153607927-153608049		chrX:153607898-153607926	chrX:153607897-153607898		80.43
N	jcn_only_AD	CUFF.106	chr10	-	chr10:46135412-46143741	chr10:46135412-46135688		chr10:46135689-46143741	chr10:46143741-46143742		13.46
N	cassette	CUFF.980	chr7	+	chr7:73101231-73105245;chr7:73101231-73106925	chr7:73101231-73101328;chr7:73101426-73105245,chr7:73101426-73106925		chr7:73101329-73101425			40.33
K	jcn_only_AA	CUFF.1151	chrX	+	chrX:153607927-153608301	chrX:153607927-153608049					75.51
N	jcn_only_AD	CUFF.576	chr2	-	chr2:675631-676573	chr2:675631-675757		chr2:675758-676573	chr2:676573-676574		82.50
N	alternative_acceptor		chr1	+	chr1:78546545-78560635	chr1:78546545-78558440		chr1:78558441-78560635	chr1:78560635-78560636		33.33
K	alternative_first_exon	CUFF.872	chr5	+	chr5:50680565-50683323	chr5:50682461-50683323	chr5:50680375-50680564	chr5:50681955-50682460		chr5:50683324-50683583	87.66
K	alternative_last_exon	CUFF.495	chr18	+	chr18:63430289-63476939	chr18:63430289-63470350	chr18:63476940-63477234	chr18:63470351-63471132			55.17
K	alternative_last_exon	CUFF.581	chr2	-	chr2:4006532-4007153	chr2:4006986-4007153	chr2:4005148-4006531	chr2:4006795-4006985			70.91
K	alternative_last_exon	CUFF.460	chr17	+	chr17:61908296-61908395	chr17:61908296-61908379	chr17:61908396-61908586	chr17:61908380-61908395			0.98
N	cassette	CUFF.306	chr15	+	chr15:29131425-29140665	chr15:29131425-29139019;chr15:29139191-29140665		chr15:29139020-29139190			91.67
K	alternative_first_exon	CUFF.319	chr15	+	chr15:45742489-45768276	chr15:45752768-45768276	chr15:45742270-45742488	chr15:45752644-45752767			39.66
K	jcn_only_AD	CUFF.1092,CUFF.1098	chr9	-	chr9:123550557-123555426	chr9:123550557-123555164		chr9:123555165-123555426	chr9:123555426-123555427		33.33
N	jcn_only_AA	CUFF.720	chr22	-	chr22:30735169-30752718	chr22:30749062-30752718		chr22:30735169-30749061	chr22:30735168-30735169		97.72
N	alternative_acceptor	CUFF.485	chr18	-	chr18:44268831-44272131	chr18:44268883-44272131		chr18:44268831-44268882	chr18:44268830-44268831		83.43
K	jcn_only_AD	CUFF.387	chr16	+	chr16:21983444-21991867	chr16:21987565-21991867					62.50
N	jcn_only_AD		chr17	+	chr17:61555460-61557129	chr17:61556462-61557129		chr17:61555460-61556461	chr17:61555459-61555460		98.31
N	alternative_acceptor	CUFF.1000,CUFF.980	chr7	+	chr7:73108381-73111795;chr7:73108381-73111934	chr7:73108381-73110735		chr7:73110736-73111795;chr7:73111796-73111934	chr7:73111795-73111796;chr7:73111934-73111935		10.39
N	jcn_only_AA	CUFF.436,CUFF.464	chr17	+	chr17:29687722-29701030	chr17:29687722-29694242		chr17:29694243-29701030	chr17:29701030-29701031		19.23
N	jcn_only_AD	CUFF.765	chr3	-	chr3:107572902-107573976	chr3:107572902-107573500		chr3:107573501-107573976	chr3:107573976-107573977		44.19
N	alternative_donor	CUFF.704	chr22	-	chr22:51015464-51015784	chr22:51015464-51015752		chr22:51015753-51015784	chr22:51015784-51015785		81.48
K	intron_retention	CUFF.419	chr17	-	chr17:5487424-5487612				chr17:5487423-5487424;chr17:5487612-5487613		78.46
N	jcn_only_AA	CUFF.579	chr2	+	chr2:3464108-3464417;chr2:3464108-3469367	chr2:3464108-3466628		chr2:3464418-3466628;chr2:3466629-3469367	chr2:3466628-3466629;chr2:3469367-3469368		4.38
N	mutually_exclusive	CUFF.707	chr22	+	chr22:20748625-20749622,chr22:20749709-20754921	chr22:20748625-20748852,chr22:20748953-20754921	chr22:20749623-20749708	chr22:20748853-20748952			23.81
K	intron_retention	CUFF.547	chr19	-	chr19:41938314-41939441				chr19:41938313-41938314;chr19:41939441-41939442		14.52
K	intron_retention	CUFF.228	chr12	-	chr12:56578896-56579938				chr12:56578895-56578896;chr12:56579938-56579939		50.00
K	alternative_first_exon	CUFF.40	chr1	+	chr1:145577754-145578061;chr1:145575405-145578061	chr1:145576103-145578061	chr1:145575233-145575404	chr1:145575947-145576102			91.35
K	intron_retention	CUFF.464	chr17	+	chr17:66508690-66511534				chr17:66508689-66508690;chr17:66511534-66511535		14.81
N	alternative_acceptor	CUFF.833	chr4	-	chr4:69057243-69078079	chr4:69071816-69078079		chr4:69057243-69071815	chr4:69057242-69057243		0.00
N	jcn_only_AD	CUFF.217	chr12	-	chr12:48375613-48375889	chr12:48375613-48375727		chr12:48375728-48375889	chr12:48375889-48375890		8.57
K	alternative_first_exon	CUFF.12	chr1	-	chr1:26231230-26231539,chr1:26231230-26231634;chr1:26231230-26233278;chr1:26231230-26232879	chr1:26231230-26232342	chr1:26233279-26233581;chr1:26232880-26232975	chr1:26232343-26232694			26.36
K	jcn_only_AD	CUFF.545	chr19	-	chr19:41355886-41356151	chr19:41355886-41356141		chr19:41356142-41356151	chr19:41356151-41356152		73.33
K	alternative_first_exon	CUFF.245,CUFF.246	chr13	-	chr13:25525627-25542343	chr13:25525627-25541529	chr13:25542344-25542713	chr13:25541530-25541644			35.00
N	alternative_donor		chr8	-	chr8:99057628-99057942	chr8:99057628-99057735		chr8:99057736-99057942	chr8:99057942-99057943		92.73
K	alternative_donor	CUFF.601,CUFF.658	chr2	-	chr2:46842325-46844108	chr2:46842325-46843725		chr2:46843726-46844108	chr2:46844108-46844109		70.71
K	intron_retention		chr12	+	chr12:53861628-53862560				chr12:53861627-53861628;chr12:53862560-53862561		19.70
K	jcn_only_AA	CUFF.410	chr16	-	chr16:75579853-75589701	chr16:75579976-75589701		chr16:75579853-75579975	chr16:75579852-75579853		24.26
N	cassette	CUFF.501	chr18	+	chr18:77478017-77496354	chr18:77478017-77488906;chr18:77489070-77496354		chr18:77488907-77489069			75.00
K	intron_retention	CUFF.1151	chrX	+	chrX:153608380-153608593				chrX:153608379-153608380;chrX:153608593-153608594		33.77
K	cassette	CUFF.900	chr5	-	chr5:149785885-149792187	chr5:149785885-149786714;chr5:149786888-149792187		chr5:149786715-149786887			80.23
K	cassette	CUFF.816	chr4	-	chr4:3954901-3957050	chr4:3954901-3956686;chr4:3956761-3957050		chr4:3956687-3956760			21.17
K	intron_retention	CUFF.542	chr19	-	chr19:39924059-39924161				chr19:39924058-39924059;chr19:39924161-39924162		7.77
K	jcn_only_AD	CUFF.173	chr11	-	chr11:94705358-94706452	chr11:94705358-94706436		chr11:94706437-94706452	chr11:94706452-94706453		70.97
N	jcn_only_AA	CUFF.765	chr3	-	chr3:107573542-107573976;chr3:107572807-107573976	chr3:107572902-107573976		chr3:107572807-107572901;chr3:107572902-107573541	chr3:107572806-107572807;chr3:107572901-107572902		52.75
N	intron_retention		chr9	-	chr9:131483760-131483929				chr9:131483759-131483760;chr9:131483929-131483930		45.45
N	jcn_only_AD		chr6	-	chr6:128313855-128316393;chr6:128313855-128316591	chr6:128313855-128316606		chr6:128316394-128316591;chr6:128316592-128316606	chr6:128316591-128316592;chr6:128316606-128316607		55.00
N	alternative_acceptor	CUFF.894	chr5	+	chr5:139815843-139818078;chr5:139815843-139818087	chr5:139815843-139818045		chr5:139818046-139818078;chr5:139818079-139818087	chr5:139818078-139818079;chr5:139818087-139818088	chr5:139815689-139815842;chr5:139818088-139818202	4.76
K	jcn_only_AA	CUFF.440	chr17	-	chr17:34497370-34497912	chr17:34497494-34497912		chr17:34497370-34497493	chr17:34497369-34497370		20.51
K	alternative_last_exon	CUFF.285	chr14	+	chr14:77934852-77935419	chr14:77934852-77934932	chr14:77935420-77935912	chr14:77934933-77935184			47.01
K	coord_cassette	CUFF.218	chr12	-	chr12:49334972-49351092	chr12:49334972-49346895;chr12:49347058-49349880;chr12:49350319-49351092		chr12:49346896-49347057;chr12:49349881-49350318			53.03
N	alternative_first_exon	CUFF.212	chr12	+	chr12:26205536-26208211;chr12:26148064-26208211	chr12:26205930-26208211	chr12:26147970-26148063	chr12:26205414-26205929			82.23
K	intron_retention	CUFF.572	chr2	-	chr2:262787-264781				chr2:262786-262787;chr2:264781-264782		12.50
N	jcn_only_AA	CUFF.716	chr22	+	chr22:29694886-29695223	chr22:29694886-29695184		chr22:29695185-29695223	chr22:29695223-29695224		7.44
N	jcn_only_AA	CUFF.419	chr17	-	chr17:5405193-5421065;chr17:5418838-5421065	chr17:5409298-5421065					2.75
K	cassette	CUFF.1089	chr9	+	chr9:116750861-116764275	chr9:116750861-116760538;chr9:116760635-116764275		chr9:116760539-116760634			2.92
N	alternative_donor	CUFF.347	chr15	-	chr15:83358206-83366608;chr15:83358206-83378345;chr15:83358206-83377523	chr15:83358206-83358514		chr15:83358515-83366608;chr15:83366609-83377523;chr15:83377524-83378345	chr15:83366608-83366609;chr15:83377523-83377524;chr15:83378345-83378346		1.23
N	jcn_only_AA		chr11	+	chr11:36317989-36422546	chr11:36317989-36318920					73.58
K	intron_retention	CUFF.673	chr2	+	chr2:242590527-242590678				chr2:242590526-242590527;chr2:242590678-242590679		6.53
K	intron_retention	CUFF.375	chr16	+	chr16:3196087-3197258				chr16:3196086-3196087;chr16:3197258-3197259		42.86
N	alternative_acceptor	CUFF.137	chr11	-	chr11:558767-558855	chr11:558785-558855		chr11:558767-558784	chr11:558766-558767		20.97
K	intron_retention	CUFF.751	chr3	-	chr3:46964854-46965096				chr3:46964853-46964854;chr3:46965096-46965097		5.66
K	alternative_donor	CUFF.618,CUFF.633	chr2	-	chr2:110920713-110922264	chr2:110920713-110922096		chr2:110922097-110922264	chr2:110922264-110922265		13.33
K	intron_retention	CUFF.633	chr2	-	chr2:110883259-110886762				chr2:110883258-110883259;chr2:110886762-110886763		9.40
N	jcn_only_AD	CUFF.453	chr17	-	chr17:56082403-56082774;chr17:56082403-56082758	chr17:56082403-56083870		chr17:56082759-56082774;chr17:56082775-56083870	chr17:56082774-56082775;chr17:56083870-56083871		22.58
N	intron_retention		chr16	+	chr16:70389439-70390031				chr16:70389438-70389439;chr16:70390031-70390032		78.57
N	alternative_donor	CUFF.728	chr22	-	chr22:30735024-30736197	chr22:30735024-30735118		chr22:30735119-30736197	chr22:30736197-30736198		17.24
K	cassette	CUFF.1022	chr7	+	chr7:157647568-157649981	chr7:157647568-157648618;chr7:157648823-157649981		chr7:157648619-157648822			42.22
K	intron_retention	CUFF.557	chr19	+	chr19:50306263-50306363				chr19:50306262-50306263;chr19:50306363-50306364		7.22
N	jcn_only_AD		chr3	-	chr3:127313777-127317038	chr3:127313777-127314294		chr3:127314295-127317038	chr3:127317038-127317039		80.39
K	alternative_donor	CUFF.403	chr16	+	chr16:67233486-67233586	chr16:67233497-67233586		chr16:67233486-67233496	chr16:67233485-67233486		32.58
N	jcn_only_AA	CUFF.954	chr6	+	chr6:161455482-161469647	chr6:161455482-161469277		chr6:161469278-161469647	chr6:161469647-161469648	chr6:161455291-161455481;chr6:161469648-161471011	60.00
K	alternative_first_exon	CUFF.524	chr19	-	chr19:14885119-14887537	chr19:14885119-14887215	chr19:14887538-14887739	chr19:14887216-14887421			19.05
N	alternative_donor	CUFF.611	chr2	-	chr2:73215478-73226077	chr2:73215478-73221974		chr2:73221975-73226077	chr2:73226077-73226078		7.65
K	intron_retention	CUFF.958	chr7	+	chr7:208977-286380				chr7:208976-208977;chr7:286380-286381		50.00
N	intron_retention		chr2	+	chr2:241405787-241405862				chr2:241405786-241405787;chr2:241405862-241405863		61.19
K	intron_retention		chr2	+	chr2:220095128-220096649				chr2:220095127-220095128;chr2:220096649-220096650		16.67
K	intron_retention	CUFF.846	chr4	-	chr4:107845362-107845701				chr4:107845361-107845362;chr4:107845701-107845702		5.88
N	cassette	CUFF.218	chr12	-	chr12:49333563-49334730	chr12:49333563-49333779;chr12:49333891-49334730		chr12:49333780-49333890			66.37
N	jcn_only_AD	CUFF.317	chr15	-	chr15:84874072-84898653	chr15:84874072-84898603		chr15:84898604-84898653	chr15:84898653-84898654		77.78
K	intron_retention	CUFF.904	chr5	-	chr5:178044436-178045556				chr5:178044435-178044436;chr5:178045556-178045557		94.65
K	coord_cassette	CUFF.1033	chr8	-	chr8:56652778-56663522	chr8:56652778-56656039;chr8:56656180-56657619;chr8:56657681-56663522		chr8:56656040-56656179;chr8:56657620-56657680			43.10
N	alternative_donor	CUFF.358	chr15	+	chr15:97327061-97327382;chr15:97326975-97327382	chr15:97326820-97327382		chr15:97326820-97326974;chr15:97326975-97327060	chr15:97326819-97326820;chr15:97326974-97326975		8.11
K	intron_retention	CUFF.922	chr6	+	chr6:33244045-33244167				chr6:33244044-33244045;chr6:33244167-33244168		62.94
K	cassette	CUFF.132	chr10	-	chr10:123629554-123661905	chr10:123629554-123659380;chr10:123659510-123661905		chr10:123659381-123659509			66.67
N	alternative_acceptor	CUFF.171	chr11	-	chr11:75514771-75522468;chr11:75520420-75522468	chr11:75514563-75522468		chr11:75514563-75514770;chr11:75514771-75520419	chr11:75514562-75514563;chr11:75514770-75514771		47.56
K	intron_retention		chr8	-	chr8:80965666-80976712				chr8:80965665-80965666;chr8:80976712-80976713		9.29
K	alternative_last_exon	CUFF.685	chr20	-	chr20:31115717-31172371	chr20:31136689-31172371	chr20:31115561-31115716	chr20:31136234-31136688			50.00
K	coord_cassette	CUFF.387	chr16	+	chr16:21969921-21973780	chr16:21969921-21970659;chr16:21970877-21972648;chr16:21972787-21973780		chr16:21970660-21970876;chr16:21972649-21972786			21.76
K	alternative_acceptor	CUFF.440	chr17	-	chr17:34497370-34497912	chr17:34497494-34497912		chr17:34497370-34497493	chr17:34497369-34497370		16.22
N	intron_retention		chr7	-	chr7:36901342-36934613				chr7:36901341-36901342;chr7:36934613-36934614		30.43
K	alternative_last_exon	CUFF.1061	chr8	+	chr8:144356973-144357364,chr8:144356973-144358172;chr8:144356973-144358066	chr8:144356973-144357147	chr8:144358067-144359200	chr8:144357148-144357963			68.32
N	cassette	CUFF.856	chr4	-	chr4:162421287-162459317	chr4:162421287-162431549;chr4:162431577-162459317		chr4:162431550-162431576			84.82
N	jcn_only_AD	CUFF.1052	chr8	+	chr8:107738538-107749747;chr8:107726214-107749747	chr8:107738486-107749747		chr8:107726214-107738485;chr8:107738486-107738537	chr8:107726213-107726214;chr8:107738485-107738486		8.11
K	intron_retention	CUFF.894	chr5	+	chr5:139865318-139866590				chr5:139865317-139865318;chr5:139866590-139866591	chr5:139865174-139865317;chr5:139866591-139866645	75.00
K	alternative_acceptor	CUFF.654	chr2	-	chr2:204354810-204355936	chr2:204354813-204355936		chr2:204354810-204354812	chr2:204354809-204354810		84.00
N	jcn_only_AD		chr15	-	chr15:83358206-83366608;chr15:83358206-83358514;chr15:83358206-83377523	chr15:83358206-83378345		chr15:83358515-83366608;chr15:83366609-83377523;chr15:83377524-83378345	chr15:83366608-83366609;chr15:83377523-83377524;chr15:83378345-83378346		64.63
K	intron_retention	CUFF.371	chr16	+	chr16:2203047-2203146				chr16:2203046-2203047;chr16:2203146-2203147		29.08
N	jcn_only_AA	CUFF.1015	chr7	+	chr7:65579958-65610429	chr7:65579958-65592690					93.62
K	cassette	CUFF.725	chr22	+	chr22:45204319-45210551	chr22:45204319-45204885;chr22:45204979-45210551		chr22:45204886-45204978			10.00
N	jcn_only_AA	CUFF.1073	chr9	+	chr9:43818185-43822517	chr9:43818185-43819609		chr9:43819610-43822517	chr9:43822517-43822518		50.00
K	alternative_acceptor	CUFF.1073	chr9	+	chr9:43907538-43908435	chr9:43907538-43908111		chr9:43908112-43908435	chr9:43908435-43908436		93.98
K	jcn_only_AD	CUFF.187	chr11	+	chr11:119058368-119058648	chr11:119058410-119058648		chr11:119058368-119058409	chr11:119058367-119058368		79.82
N	jcn_only_AA	CUFF.1000	chr7	+	chr7:107211712-107215632	chr7:107211712-107214148		chr7:107214149-107215632	chr7:107215632-107215633		8.43
N	jcn_only_AA	CUFF.867	chr5	-	chr5:37309370-37310653	chr5:37309675-37310653		chr5:37309370-37309674	chr5:37309369-37309370		10.00
K	coord_cassette	CUFF.264	chr14	+	chr14:50069187-50080973	chr14:50069187-50074117;chr14:50074840-50079189;chr14:50079343-50080973		chr14:50074118-50074839;chr14:50079190-50079342			42.86
K	cassette	CUFF.385	chr16	+	chr16:19621738-19627435	chr16:19621738-19623049;chr16:19623121-19627435		chr16:19623050-19623120			34.98
K	jcn_only_AA	CUFF.956	chr6	-	chr6:170117997-170118883	chr6:170118003-170118883		chr6:170117997-170118002	chr6:170117996-170117997		90.20
K	cassette	CUFF.202	chr12	-	chr12:7090345-7090971	chr12:7090345-7090755;chr12:7090794-7090971		chr12:7090756-7090793			15.12
N	jcn_only_AD	CUFF.354	chr15	+	chr15:91304486-91306195	chr15:91305653-91306195		chr15:91304486-91305652	chr15:91304485-91304486		38.89
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		98.91
K	cassette	CUFF.58	chr1	-	chr1:161042676-161043509	chr1:161042676-161043014;chr1:161043090-161043509		chr1:161043015-161043089			19.05
K	jcn_only_AD	CUFF.818	chr4	-	chr4:6380300-6382767	chr4:6380300-6382723		chr4:6382724-6382767	chr4:6382767-6382768		65.29
N	mutually_exclusive	CUFF.486	chr18	-	chr18:44435579-44470542,chr18:44471018-44497284	chr18:44435579-44444126,chr18:44444212-44497284	chr18:44470543-44471017	chr18:44444127-44444211			33.33
N	jcn_only_AA	CUFF.728	chr22	-	chr22:51018232-51018402	chr22:51018260-51018402		chr22:51018232-51018259	chr22:51018231-51018232		88.14
N	cassette	CUFF.1052	chr8	+	chr8:107726214-107751685;chr8:107738538-107751685	chr8:107726214-107749747,chr8:107738538-107749747;chr8:107749829-107751685		chr8:107749748-107749828			63.04
K	intron_retention	CUFF.473	chr17	-	chr17:79894738-79895055				chr17:79894737-79894738;chr17:79895055-79895056	chr17:79894624-79894737;chr17:79895056-79895264	53.25
K	intron_retention	CUFF.228	chr12	-	chr12:56574886-56575265				chr12:56574885-56574886;chr12:56575265-56575266		88.35
K	alternative_donor	CUFF.133	chr10	+	chr10:124187833-124189139	chr10:124187937-124189139		chr10:124187833-124187936	chr10:124187832-124187833		99.13
K	alternative_first_exon	CUFF.764	chr3	+	chr3:97652352-97652537;chr3:97634581-97652537	chr3:97643256-97652537	chr3:97634454-97634580	chr3:97642964-97643255			85.71
N	jcn_only_AD	CUFF.696,CUFF.701	chr21	-	chr21:30971258-31015145	chr21:30971258-30973547		chr21:30973548-31015145	chr21:31015145-31015146		31.45
N	alternative_acceptor	CUFF.389	chr16	+	chr16:22466187-22470675	chr16:22466187-22466770		chr16:22466771-22470675	chr16:22470675-22470676		0.00
K	intron_retention		chr14	+	chr14:77929103-77930940				chr14:77929102-77929103;chr14:77930940-77930941		25.59
K	intron_retention	CUFF.604	chr2	-	chr2:61719884-61720049				chr2:61719883-61719884;chr2:61720049-61720050		33.33
N	mutually_exclusive	CUFF.946	chr6	-	chr6:133046119-133049879,chr6:133050073-133055391	chr6:133046119-133047860,chr6:133047978-133055391	chr6:133049880-133050072	chr6:133047861-133047977			64.29
N	cassette	CUFF.754	chr3	-	chr3:49462872-49463684	chr3:49462872-49463315;chr3:49463430-49463684		chr3:49463316-49463429			92.86
K	cassette	CUFF.427	chr17	+	chr17:15603092-15604465	chr17:15603092-15603361;chr17:15603483-15604465		chr17:15603362-15603482			58.82
N	jcn_only_AA	CUFF.53	chr1	-	chr1:156908306-156909339	chr1:156909078-156909339		chr1:156908306-156909077	chr1:156908305-156908306		47.44
K	cassette	CUFF.726	chr22	+	chr22:47158746-47188416	chr22:47158746-47184876;chr22:47184935-47188416		chr22:47184877-47184934			47.19
K	alternative_acceptor	CUFF.59	chr1	-	chr1:161953126-161953385	chr1:161953196-161953385		chr1:161953126-161953195	chr1:161953125-161953126		56.86
N	jcn_only_AD		chr4	-	chr4:36231268-36245312	chr4:36231268-36245230		chr4:36245231-36245312	chr4:36245312-36245313		86.21
K	intron_retention	CUFF.138	chr11	+	chr11:829541-829985				chr11:829540-829541;chr11:829985-829986	chr11:829360-829540;chr11:829986-830132	55.77
N	alternative_donor	CUFF.2	chr1	+	chr1:2101044-2103493	chr1:2103085-2103493		chr1:2101044-2103084	chr1:2101043-2101044		1.50
K	alternative_first_exon	CUFF.944	chr6	+	chr6:126307837-126314902;chr6:126307769-126314902	chr6:126307920-126314902	chr6:126307501-126307768	chr6:126307854-126307919			15.22
N	cassette	CUFF.387	chr16	+	chr16:21964778-21968737	chr16:21964778-21968555;chr16:21968640-21968737		chr16:21968556-21968639			76.92
N	jcn_only_AD	CUFF.683	chr20	+	chr20:30115386-30125981	chr20:30115854-30125981		chr20:30115386-30115853	chr20:30115385-30115386	chr20:30125982-30126064;chr20:30115287-30115385	3.78
K	cassette	CUFF.274	chr14	-	chr14:69589078-69619481	chr14:69589078-69616147;chr14:69616221-69619481		chr14:69616148-69616220			56.25
K	intron_retention	CUFF.138	chr11	+	chr11:831033-831223				chr11:831032-831033;chr11:831223-831224	chr11:830866-831032;chr11:831224-831295	63.10
N	alternative_acceptor	CUFF.633	chr2	-	chr2:110936125-110937200	chr2:110936513-110937200		chr2:110936125-110936512	chr2:110936124-110936125		3.26
N	alternative_donor	CUFF.762	chr3	+	chr3:75492798-75500360	chr3:75496448-75500360		chr3:75492798-75496447	chr3:75492797-75492798		0.00
K	intron_retention	CUFF.980	chr7	+	chr7:73108381-73111934				chr7:73108380-73108381;chr7:73111934-73111935		8.22
K	intron_retention	CUFF.1027	chr8	-	chr8:22012145-22012904				chr8:22012144-22012145;chr8:22012904-22012905		28.57
N	alternative_donor	CUFF.457	chr17	+	chr17:61562428-61562596;chr17:61561903-61562596	chr17:61562331-61562596		chr17:61561903-61562330;chr17:61562331-61562427	chr17:61561902-61561903;chr17:61562330-61562331		22.32
N	jcn_only_AD	CUFF.390	chr16	-	chr16:23505700-23507009;chr16:23505700-23507014	chr16:23505700-23507034		chr16:23507010-23507014;chr16:23507015-23507034	chr16:23507014-23507015;chr16:23507034-23507035	chr16:23505624-23505699;chr16:23507035-23507099	2.37
N	cassette	CUFF.162	chr11	+	chr11:63656437-63662630	chr11:63656437-63657693;chr11:63657768-63662630		chr11:63657694-63657767			81.82
K	alternative_last_exon	CUFF.785	chr3	+	chr3:126135352-126137297;chr3:126135352-126137300	chr3:126135352-126135614	chr3:126137301-126137368	chr3:126135615-126135803			77.08
N	alternative_donor	CUFF.578	chr2	+	chr2:1094097-1099090	chr2:1098397-1099090		chr2:1094097-1098396	chr2:1094096-1094097		3.12
K	cassette	CUFF.785	chr3	+	chr3:126114893-126126014	chr3:126114893-126115332;chr3:126115523-126126014		chr3:126115333-126115522			32.91
N	jcn_only_AA	CUFF.377	chr16	-	chr16:4445341-4455491	chr16:4447452-4455491		chr16:4445341-4447451	chr16:4445340-4445341		3.15
K	alternative_last_exon	CUFF.417	chr17	-	chr17:1616190-1616996,chr17:1616199-1616996,chr17:1616220-1616996;chr17:1615694-1616996	chr17:1616350-1616996	chr17:1614805-1615693	chr17:1615696-1616349			53.27
K	intron_retention	CUFF.663	chr2	+	chr2:220100818-220101043				chr2:220100817-220100818;chr2:220101043-220101044		45.45
N	jcn_only_AA	CUFF.28	chr1	+	chr1:70820791-70832126	chr1:70820791-70831828		chr1:70831829-70832126	chr1:70832126-70832127		13.33
N	alternative_acceptor	CUFF.350	chr15	-	chr15:84871760-84872928;chr15:84871773-84872928	chr15:84872839-84872928		chr15:84871760-84871772;chr15:84871773-84872838	chr15:84871759-84871760;chr15:84871772-84871773		8.33
K	alternative_donor	CUFF.219	chr12	-	chr12:50232799-50236636	chr12:50232799-50236168		chr12:50236169-50236636	chr12:50236636-50236637		95.45
N	alternative_donor	CUFF.884	chr5	-	chr5:36703067-36705822	chr5:36703067-36705781		chr5:36705782-36705822	chr5:36705822-36705823		84.62
K	intron_retention	CUFF.816	chr4	-	chr4:3948645-3949468				chr4:3948644-3948645;chr4:3949468-3949469		61.90
N	jcn_only_AA	CUFF.628	chr2	+	chr2:101565943-101584742;chr2:101565943-101580519	chr2:101565943-101579216					15.02
N	alternative_first_exon	CUFF.979	chr7	+	chr7:65579958-65610429	chr7:65599362-65610429	chr7:65579528-65579957	chr7:65599267-65599361			91.67
K	alternative_last_exon	CUFF.8	chr1	+	chr1:16382254-16383732	chr1:16382254-16382916	chr1:16383733-16383900	chr1:16382917-16383003			37.78
K	intron_retention	CUFF.1039	chr8	+	chr8:74888727-74890990				chr8:74888726-74888727;chr8:74890990-74890991		24.32
N	cassette	CUFF.1110	chrX	+	chrX:1419520-1428294	chrX:1419520-1424338;chrX:1424421-1428294		chrX:1424339-1424420			96.04
K	intron_retention	CUFF.377,CUFF.378	chr16	-	chr16:4405165-4405286				chr16:4405164-4405165;chr16:4405286-4405287		15.46
N	alternative_acceptor		chr7	-	chr7:37469360-37488462;chr7:37433521-37488462	chr7:37382368-37488462		chr7:37382368-37433520;chr7:37433521-37469359	chr7:37382367-37382368;chr7:37433520-37433521		100.00
N	cassette	CUFF.476	chr17	+	chr17:80426773-80436675;chr17:80426773-80436446	chr17:80426773-80430439;chr17:80430575-80436446,chr17:80430575-80436675		chr17:80430440-80430574			65.12
N	jcn_only_AD	CUFF.468,CUFF.472	chr17	-	chr17:79478653-79478928	chr17:79478653-79478788		chr17:79478789-79478928	chr17:79478928-79478929		5.59
K	cassette	CUFF.970	chr7	+	chr7:34888276-34889176	chr7:34888276-34888934;chr7:34889035-34889176		chr7:34888935-34889034			18.52
N	jcn_only_AA	CUFF.137	chr11	-	chr11:558980-560682	chr11:559499-560682		chr11:558980-559498	chr11:558979-558980		36.36
K	intron_retention	CUFF.707	chr22	+	chr22:20748625-20749622				chr22:20748624-20748625;chr22:20749622-20749623		35.71
N	jcn_only_AD	CUFF.436	chr17	+	chr17:29667602-29670026	chr17:29667664-29670026		chr17:29667602-29667663	chr17:29667601-29667602		45.76
N	jcn_only_AA	CUFF.775	chr3	-	chr3:120352176-120357301	chr3:120352438-120357301		chr3:120352176-120352437	chr3:120352175-120352176		12.64
N	alternative_last_exon	CUFF.140	chr11	-	chr11:2188263-2188664;chr11:2187999-2188664	chr11:2187780-2188664	chr11:2188117-2188262;chr11:2187863-2187998	chr11:2187043-2187779			2.88
K	jcn_only_AA	CUFF.662	chr2	+	chr2:219457431-219458891	chr2:219457431-219458830		chr2:219458831-219458891	chr2:219458891-219458892		68.13
N	alternative_acceptor	CUFF.396	chr16	-	chr16:57509870-57513353	chr16:57512575-57513353		chr16:57509870-57512574	chr16:57509869-57509870		4.29
N	alternative_donor	CUFF.924	chr6	-	chr6:35478788-35479956	chr6:35478788-35479424		chr6:35479425-35479956	chr6:35479956-35479957		46.15
K	intron_retention	CUFF.1070	chr9	-	chr9:35075080-35075275				chr9:35075079-35075080;chr9:35075275-35075276		28.95
N	coord_cassette	CUFF.426	chr17	-	chr17:15532513-15539349	chr17:15532513-15534932;chr17:15535029-15535822;chr17:15535989-15539349		chr17:15534933-15535028;chr17:15535823-15535988			94.51
N	alternative_donor	CUFF.2	chr1	+	chr1:2087532-2100956	chr1:2100557-2100956		chr1:2087532-2100556	chr1:2087531-2087532		4.38
N	intron_retention		chr17	-	chr17:79479387-79479631				chr17:79479386-79479387;chr17:79479631-79479632		21.43
K	intron_retention	CUFF.572	chr2	-	chr2:260898-262630				chr2:260897-260898;chr2:262630-262631		34.38
K	alternative_last_exon	CUFF.12	chr1	-	chr1:26212361-26227981	chr1:26227579-26227981	chr1:26210579-26212360	chr1:26226502-26227578			95.30
N	jcn_only_AD	CUFF.931	chr6	+	chr6:46636531-46644383	chr6:46638966-46644383					36.36
N	alternative_acceptor	CUFF.457	chr17	+	chr17:60783831-60803388;chr17:60783831-60813446	chr17:60783831-60784792		chr17:60784793-60803388;chr17:60803389-60813446	chr17:60803388-60803389;chr17:60813446-60813447		0.00
K	intron_retention	CUFF.646	chr2	-	chr2:175216454-175243650				chr2:175216453-175216454;chr2:175243650-175243651		54.84
K	jcn_only_AA	CUFF.194	chr11	-	chr11:133710705-133711924	chr11:133710819-133711924		chr11:133710705-133710818	chr11:133710704-133710705		33.70
N	jcn_only_AA	CUFF.737	chr3	-	chr3:27329235-27332752	chr3:27332246-27332752		chr3:27329235-27332245	chr3:27329234-27329235		3.95
N	jcn_only_AA	CUFF.208	chr12	+	chr12:21242864-21279041	chr12:21242864-21245446		chr12:21245447-21279041	chr12:21279041-21279042	chr12:21279042-21279191	48.53
N	jcn_only_AA		chr11	+	chr11:118402587-118402960;chr11:118402587-118402811;chr11:118402587-118403004	chr11:118402587-118403124				chr11:118401663-118402586	7.89
K	intron_retention	CUFF.1066	chr9	-	chr9:15185405-15186941				chr9:15185404-15185405;chr9:15186941-15186942		8.82
K	alternative_first_exon	CUFF.1117	chrX	+	chrX:15699171-15706783;chrX:15693696-15706783;chrX:15693092-15706783;chrX:15699311-15706783	chrX:15693902-15706783	chrX:15693624-15693695;chrX:15692971-15693091;chrX:15699124-15699310	chrX:15693813-15693901			40.00
N	jcn_only_AD	CUFF.176	chr11	-	chr11:102960048-102962515;chr11:102960048-102962244	chr11:102960048-102962412		chr11:102962245-102962412;chr11:102962413-102962515	chr11:102962412-102962413;chr11:102962515-102962516		12.95
K	intron_retention	CUFF.509	chr19	-	chr19:6008236-6010146				chr19:6008235-6008236;chr19:6010146-6010147		7.14
N	jcn_only_AA	CUFF.919	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		19.42
N	mutually_exclusive	CUFF.946	chr6	-	chr6:133046119-133049879,chr6:133050119-133055391	chr6:133046119-133047860,chr6:133047978-133055391	chr6:133049880-133050118	chr6:133047861-133047977			60.00
N	jcn_only_AD		chr14	+	chr14:76373021-76420766;chr14:76407838-76420766	chr14:76368568-76420766					8.06
K	jcn_only_AA	CUFF.875	chr5	-	chr5:54429357-54436141	chr5:54433465-54436141					77.02
K	alternative_donor	CUFF.998	chr7	-	chr7:102234690-102234938	chr7:102234690-102234893		chr7:102234894-102234938	chr7:102234938-102234939		33.33
N	jcn_only_AD	CUFF.537,CUFF.542	chr19	-	chr19:33878388-33878795	chr19:33878388-33878560		chr19:33878561-33878795	chr19:33878795-33878796		22.50
K	jcn_only_AD	CUFF.688	chr20	-	chr20:34246937-34252800	chr20:34246937-34252723		chr20:34252724-34252800	chr20:34252800-34252801		26.32
K	alternative_last_exon	CUFF.1135	chrX	-	chrX:106235661-106236459;chrX:106229431-106236459	chrX:106059017-106236459	chrX:106235518-106235660;chrX:106229213-106229430	chrX:106057101-106059016			40.00
N	jcn_only_AD	CUFF.673	chr2	+	chr2:242610857-242611605;chr2:242610821-242611605	chr2:242610841-242611605		chr2:242610821-242610840;chr2:242610841-242610856	chr2:242610820-242610821;chr2:242610840-242610841		4.40
K	jcn_only_AA	CUFF.169,CUFF.179	chr11	+	chr11:115267610-115267986	chr11:115267610-115267983		chr11:115267984-115267986	chr11:115267986-115267987		62.96
K	intron_retention	CUFF.519	chr19	+	chr19:11474496-11474836				chr19:11474495-11474496;chr19:11474836-11474837		34.09
K	intron_retention	CUFF.904	chr5	-	chr5:178046898-178050256				chr5:178046897-178046898;chr5:178050256-178050257		58.33
K	cassette	CUFF.907	chr6	+	chr6:2988266-2989761	chr6:2988266-2988661;chr6:2988944-2989761		chr6:2988662-2988943			72.22
N	alternative_donor	CUFF.638	chr2	+	chr2:153476233-153481951	chr2:153479072-153481951		chr2:153476233-153479071	chr2:153476232-153476233		0.00
N	alternative_donor	CUFF.818	chr4	-	chr4:83821377-83821524	chr4:83821377-83821486		chr4:83821487-83821524	chr4:83821524-83821525		92.37
N	cassette	CUFF.843	chr4	-	chr4:83819216-83821229;chr4:83816928-83821229	chr4:83816928-83820865,chr4:83819216-83820865;chr4:83820891-83821229		chr4:83820866-83820890			96.25
N	alternative_first_exon	CUFF.377	chr16	-	chr16:4445341-4447318;chr16:4445341-4466785;chr16:4445341-4455491	chr16:4445341-4466459	chr16:4466786-4466962;chr16:4455492-4455568	chr16:4466460-4466665			17.43
K	intron_retention	CUFF.434	chr17	+	chr17:26554520-26554633				chr17:26554519-26554520;chr17:26554633-26554634		80.00
K	cassette	CUFF.1116	chrX	-	chrX:15344169-15353622	chrX:15344169-15349711;chrX:15350115-15353622		chrX:15349712-15350114			89.66
N	intron_retention		chr19	+	chr19:17448079-17448816				chr19:17448078-17448079;chr19:17448816-17448817		67.83
N	alternative_acceptor	CUFF.377	chr16	-	chr16:4411471-4411985	chr16:4411805-4411985		chr16:4411471-4411804	chr16:4411470-4411471		54.17
K	intron_retention	CUFF.993	chr7	+	chr7:92164285-92166164				chr7:92164284-92164285;chr7:92166164-92166165		62.50
N	coord_cassette	CUFF.61	chr1	+	chr1:167190196-167301706	chr1:167190196-167210643;chr1:167210848-167272710;chr1:167272812-167301706		chr1:167210644-167210847;chr1:167272711-167272811			86.84
N	jcn_only_AD	CUFF.29	chr1	+	chr1:78445304-78546358	chr1:78512019-78546358		chr1:78445304-78512018	chr1:78445303-78445304		10.00
N	jcn_only_AD	CUFF.589,CUFF.609	chr2	-	chr2:27693963-27695116	chr2:27693963-27694099		chr2:27694100-27695116	chr2:27695116-27695117		70.59
N	alternative_donor		chr10	-	chr10:78637652-78647048	chr10:78637652-78644746		chr10:78644747-78647048	chr10:78647048-78647049		49.06
K	alternative_last_exon	CUFF.245	chr13	-	chr13:24415628-24432998	chr13:24416709-24432998	chr13:24415474-24415627	chr13:24416310-24416708			92.75
K	cassette	CUFF.641	chr2	+	chr2:169699628-169707593	chr2:169699628-169707345;chr2:169707517-169707593		chr2:169707346-169707516			2.71
K	cassette	CUFF.187	chr11	+	chr11:119057400-119058272	chr11:119057400-119057978;chr11:119058169-119058272		chr11:119057979-119058168			88.24
N	alternative_acceptor	CUFF.959	chr7	-	chr7:1778839-1781844	chr7:1779172-1781844		chr7:1778839-1779171	chr7:1778838-1778839		9.43
N	jcn_only_AD		chr2	-	chr2:73227617-73228657	chr2:73227617-73228653		chr2:73228654-73228657	chr2:73228657-73228658		94.85
N	jcn_only_AD	CUFF.709	chr22	-	chr22:21829590-21830290	chr22:21829590-21830280		chr22:21830281-21830290	chr22:21830290-21830291		49.23
N	alternative_donor	CUFF.708	chr22	+	chr22:21058040-21058255;chr22:21057981-21058255	chr22:21058172-21058255		chr22:21057981-21058039;chr22:21058040-21058171	chr22:21057980-21057981;chr22:21058039-21058040		11.31
N	cassette	CUFF.509	chr19	-	chr19:6040253-6044203	chr19:6040253-6042054;chr19:6042135-6044203		chr19:6042055-6042134			83.86
N	alternative_donor	CUFF.506	chr19	+	chr19:4323235-4323344;chr19:4323211-4323344	chr19:4323144-4323344		chr19:4323144-4323210;chr19:4323211-4323234	chr19:4323143-4323144;chr19:4323210-4323211		7.62
N	coord_cassette	CUFF.234	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			60.42
N	cassette	CUFF.374	chr16	+	chr16:3117417-3118180;chr16:3117417-3117984	chr16:3117417-3117554;chr16:3117615-3118180,chr16:3117615-3117984		chr16:3117555-3117614			62.14
K	jcn_only_AA	CUFF.946	chr6	-	chr6:133047978-133049879	chr6:133048152-133049879		chr6:133047978-133048151	chr6:133047977-133047978		42.11
K	coord_cassette	CUFF.647	chr2	-	chr2:175779900-175816891	chr2:175779900-175783261;chr2:175783294-175809615;chr2:175809672-175816891		chr2:175783262-175783293;chr2:175809616-175809671			45.74
K	alternative_last_exon	CUFF.533	chr19	-	chr19:20339293-20349096;chr19:20243397-20349096	chr19:20287619-20349096	chr19:20243270-20243396	chr19:20286854-20287618			34.33
K	alternative_donor	CUFF.482	chr18	+	chr18:12658205-12658572	chr18:12658343-12658572		chr18:12658205-12658342	chr18:12658204-12658205		25.00
N	cassette	CUFF.152	chr11	-	chr11:10827595-10828801	chr11:10827595-10828366;chr11:10828433-10828801		chr11:10828367-10828432			91.06
N	jcn_only_AD		chr16	-	chr16:57513598-57513772;chr16:57513598-57517869	chr16:57513598-57513756					25.00
N	alternative_donor	CUFF.240,CUFF.241	chr12	-	chr12:120148426-120149982	chr12:120148426-120148853		chr12:120148854-120149982	chr12:120149982-120149983		2.04
K	cassette	CUFF.467	chr17	-	chr17:76996353-77005745;chr17:76994046-77005745	chr17:76996353-77001453,chr17:76994046-77001453;chr17:77001564-77005745		chr17:77001454-77001563			28.21
N	alternative_donor	CUFF.106,CUFF.115	chr10	-	chr10:46143983-46147413	chr10:46143983-46145179		chr10:46145180-46147413	chr10:46147413-46147414		27.78
K	intron_retention		chr22	-	chr22:21830450-21830932				chr22:21830449-21830450;chr22:21830932-21830933		62.67
K	cassette	CUFF.999	chr7	-	chr7:102473422-102517913	chr7:102473422-102495223;chr7:102495308-102517913		chr7:102495224-102495307			80.82
N	alternative_donor		chr10	+	chr10:35416122-35426709	chr10:35416496-35426709		chr10:35416122-35416495	chr10:35416121-35416122		21.54
N	cassette	CUFF.1001	chr7	+	chr7:107220747-107224326	chr7:107220747-107221203;chr7:107221310-107224326		chr7:107221204-107221309			85.09
N	intron_retention		chr11	+	chr11:119059261-119059348				chr11:119059260-119059261;chr11:119059348-119059349		17.80
K	intron_retention	CUFF.156	chr11	-	chr11:57001333-57003265				chr11:57001332-57001333;chr11:57003265-57003266		11.11
N	jcn_only_AD	CUFF.1066	chr9	-	chr9:15214248-15224337;chr9:15214248-15225914;chr9:15214248-15224357	chr9:15214248-15249915					4.76
K	intron_retention	CUFF.1032	chr8	-	chr8:38001905-38003480				chr8:38001904-38001905;chr8:38003480-38003481		50.00
K	cassette	CUFF.218	chr12	-	chr12:49334972-49349880	chr12:49334972-49346895;chr12:49347058-49349880		chr12:49346896-49347057			62.34
N	jcn_only_AD	CUFF.273	chr14	+	chr14:61497242-61503776	chr14:61500832-61503776		chr14:61497242-61500831	chr14:61497241-61497242		13.00
N	alternative_donor	CUFF.1000	chr7	+	chr7:107207632-107211589	chr7:107208311-107211589		chr7:107207632-107208310	chr7:107207631-107207632		6.67
K	cassette	CUFF.313	chr15	-	chr15:41108452-41120584	chr15:41108452-41109429;chr15:41109546-41120584		chr15:41109430-41109545			52.00
K	intron_retention	CUFF.56	chr1	+	chr1:160137203-160141040				chr1:160137202-160137203;chr1:160141040-160141041		75.00
N	alternative_donor	CUFF.230,CUFF.239	chr12	-	chr12:113618864-113623082	chr12:113618864-113621527		chr12:113621528-113623082	chr12:113623082-113623083		20.00
K	intron_retention	CUFF.775	chr3	-	chr3:120369713-120371438				chr3:120369712-120369713;chr3:120371438-120371439		2.27
N	alternative_last_exon		chr12	+	chr12:26164755-26208168	chr12:26164755-26173077	chr12:26208169-26208379	chr12:26173078-26173529			71.30
K	intron_retention		chr17	-	chr17:15535029-15535822				chr17:15535028-15535029;chr17:15535822-15535823		24.72
N	jcn_only_AD	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57521042;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;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		3.91
K	cassette	CUFF.82	chr1	+	chr1:230385018-230390963	chr1:230385018-230386202;chr1:230386307-230390963		chr1:230386203-230386306			55.56
N	alternative_donor	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55713251-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		0.85
N	alternative_acceptor	CUFF.3,CUFF.83	chr1	+	chr1:245180629-245222687	chr1:245180629-245193956		chr1:245193957-245222687	chr1:245222687-245222688		0.00
K	cassette	CUFF.572	chr2	-	chr2:231192-234159	chr2:231192-233100;chr2:233230-234159		chr2:233101-233229			67.16
K	intron_retention	CUFF.557	chr19	+	chr19:50308834-50308917				chr19:50308833-50308834;chr19:50308917-50308918		21.53
K	intron_retention		chr12	+	chr12:13366756-13367467				chr12:13366755-13366756;chr12:13367467-13367468		66.67
N	jcn_only_AD	CUFF.106,CUFF.115	chr10	-	chr10:46143983-46147413	chr10:46143983-46145179		chr10:46145180-46147413	chr10:46147413-46147414		23.53
K	intron_retention	CUFF.530	chr19	+	chr19:17449065-17449173				chr19:17449064-17449065;chr19:17449173-17449174		5.46
N	coord_cassette	CUFF.611	chr2	-	chr2:73188378-73215386	chr2:73188378-73195576;chr2:73195663-73198698;chr2:73198815-73215386		chr2:73195577-73195662;chr2:73198699-73198814			24.72
N	alternative_first_exon	CUFF.1010	chr7	+	chr7:129015768-129019481;chr7:129017465-129019481	chr7:129008393-129019481	chr7:129015629-129015767;chr7:129017358-129017464	chr7:129007884-129008392			42.11
K	alternative_first_exon	CUFF.844	chr4	-	chr4:85416998-85418711	chr4:85416998-85417645	chr4:85418712-85419677	chr4:85417646-85418103			10.29
K	intron_retention	CUFF.617	chr2	-	chr2:79364054-79364349				chr2:79364053-79364054;chr2:79364349-79364350		47.83
K	intron_retention	CUFF.513	chr19	-	chr19:6375628-6375712				chr19:6375627-6375628;chr19:6375712-6375713		33.33
K	intron_retention		chr2	+	chr2:3469467-3481465				chr2:3469466-3469467;chr2:3481465-3481466		17.53
K	alternative_first_exon	CUFF.598	chr2	+	chr2:38179345-38201182;chr2:38156873-38201182	chr2:38177739-38201182	chr2:38156405-38156872	chr2:38177522-38177738			54.43
N	coord_cassette	CUFF.739	chr3	+	chr3:28333446-28357823	chr3:28333446-28334226;chr3:28334456-28335924;chr3:28336018-28357823		chr3:28334227-28334455;chr3:28335925-28336017			98.22
N	intron_retention		chr17	+	chr17:61904875-61905478				chr17:61904874-61904875;chr17:61905478-61905479		53.85
N	jcn_only_AA	CUFF.734	chr3	+	chr3:19992554-20017134;chr3:19992554-20017078;chr3:19992554-20012039	chr3:19992554-20017092		chr3:20012040-20017078;chr3:20017079-20017092;chr3:20017093-20017134	chr3:20017078-20017079;chr3:20017092-20017093;chr3:20017134-20017135		7.92
K	cassette	CUFF.457	chr17	+	chr17:61566153-61568314	chr17:61566153-61566301;chr17:61566494-61568314		chr17:61566302-61566493			85.23
K	intron_retention	CUFF.755	chr3	+	chr3:51747327-51749077				chr3:51747326-51747327;chr3:51749077-51749078		39.39
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		81.71
K	jcn_only_AD	CUFF.177	chr11	-	chr11:104915386-104916017	chr11:104915386-104915917		chr11:104915918-104916017	chr11:104916017-104916018		40.91
N	jcn_only_AD	CUFF.579	chr2	+	chr2:3453249-3461391;chr2:3447663-3461391	chr2:3461001-3461391		chr2:3447663-3453248;chr2:3453249-3461000	chr2:3447662-3447663;chr2:3453248-3453249		12.25
K	alternative_acceptor	CUFF.311	chr15	+	chr15:40756747-40757542	chr15:40756747-40757533		chr15:40757534-40757542	chr15:40757542-40757543		52.94
K	alternative_last_exon	CUFF.603	chr2	+	chr2:48898820-49003418	chr2:48898820-48906473	chr2:49003419-49003753	chr2:48906474-48906742			48.28
N	alternative_donor	CUFF.743,CUFF.796	chr3	-	chr3:33614847-33617660	chr3:33614847-33615964		chr3:33615965-33617660	chr3:33617660-33617661		0.47
K	jcn_only_AD	CUFF.1097	chr9	-	chr9:125612102-125613378	chr9:125612102-125613359		chr9:125613360-125613378	chr9:125613378-125613379		84.44
K	jcn_only_AD	CUFF.550	chr19	+	chr19:44764156-44768466;chr19:44764362-44768466	chr19:44764092-44768466		chr19:44764092-44764155;chr19:44764156-44764361	chr19:44764091-44764092;chr19:44764155-44764156		4.69
N	jcn_only_AA	CUFF.457	chr17	+	chr17:61555460-61556171;chr17:61555460-61556367	chr17:61555460-61557129		chr17:61556172-61556367;chr17:61556368-61557129	chr17:61556367-61556368;chr17:61557129-61557130		1.64
K	alternative_first_exon	CUFF.933	chr6	-	chr6:75977465-75993935	chr6:75977465-75982179	chr6:75993936-75994059	chr6:75982180-75982383			60.00
N	intron_retention		chr4	-	chr4:83821377-83821524				chr4:83821376-83821377;chr4:83821524-83821525		69.19
K	intron_retention	CUFF.1134	chrX	+	chrX:103357938-103358124				chrX:103357937-103357938;chrX:103358124-103358125	chrX:103357886-103357937;chrX:103358125-103358264	17.07
K	jcn_only_AD	CUFF.944	chr6	+	chr6:126317187-126319368	chr6:126319281-126319368					86.96
K	alternative_first_exon	CUFF.911	chr6	-	chr6:13470863-13486242;chr6:13470863-13486869	chr6:13470863-13472212	chr6:13486243-13486491;chr6:13486870-13487974	chr6:13472213-13472325			35.00
N	jcn_only_AD	CUFF.86	chr10	-	chr10:410523-412214	chr10:410523-410754		chr10:410755-412214	chr10:412214-412215		50.00
N	alternative_donor	CUFF.951	chr6	+	chr6:144904737-144999541;chr6:144898425-144999541	chr6:144981412-144999541		chr6:144898425-144904736;chr6:144904737-144981411	chr6:144898424-144898425;chr6:144904736-144904737		0.00
K	alternative_acceptor	CUFF.1098	chr9	-	chr9:130943079-130947825	chr9:130943094-130947825		chr9:130943079-130943093	chr9:130943078-130943079		66.92
N	jcn_only_AD	CUFF.852	chr4	-	chr4:152147239-152246392;chr4:152147239-152147319	chr4:152147239-152187237		chr4:152147320-152187237;chr4:152187238-152246392	chr4:152187237-152187238;chr4:152246392-152246393		4.17
N	intron_retention	CUFF.661	chr2	+	chr2:219222458-219222708				chr2:219222457-219222458;chr2:219222708-219222709		55.56
K	coord_cassette	CUFF.258	chr14	+	chr14:24459569-24470592	chr14:24459569-24470071;chr14:24470143-24470241;chr14:24470294-24470592		chr14:24470072-24470142;chr14:24470242-24470293			86.67
N	jcn_only_AA	CUFF.557	chr19	+	chr19:50305399-50306205	chr19:50305399-50305790		chr19:50305791-50306205	chr19:50306205-50306206		36.67
N	alternative_donor	CUFF.1052	chr8	+	chr8:107738486-107749747;chr8:107726214-107749747	chr8:107738538-107749747		chr8:107726214-107738485;chr8:107738486-107738537	chr8:107726213-107726214;chr8:107738485-107738486		0.00
N	jcn_only_AA	CUFF.468	chr17	-	chr17:79258696-79263490	chr17:79262746-79263490		chr17:79258696-79262745	chr17:79258695-79258696	chr17:79263491-79263608;chr17:79258650-79258695	55.71
N	coord_cassette	CUFF.234	chr12	+	chr12:69207409-69229608	chr12:69207409-69218142;chr12:69218211-69218334;chr12:69218432-69229608		chr12:69218143-69218210;chr12:69218335-69218431			57.30
K	alternative_first_exon	CUFF.114	chr10	-	chr10:73973090-73975534;chr10:73973090-73976578;chr10:73973090-73975539	chr10:73973090-73975964	chr10:73976579-73976962;chr10:73975540-73975867	chr10:73975965-73976126			30.53
N	jcn_only_AD	CUFF.598	chr2	+	chr2:38231360-38244328	chr2:38239793-38244328		chr2:38231360-38239792	chr2:38231359-38231360		5.56
K	cassette	CUFF.206	chr12	+	chr12:12765122-12788710	chr12:12765122-12785422;chr12:12785526-12788710		chr12:12785423-12785525			9.38
K	alternative_first_exon	CUFF.80	chr1	-	chr1:224396714-224400456	chr1:224396714-224397942	chr1:224400457-224401051	chr1:224397943-224398114			60.87
N	alternative_acceptor		chr12	-	chr12:49334972-49350767	chr12:49350134-49350767		chr12:49334972-49350133	chr12:49334971-49334972		7.14
N	jcn_only_AA	CUFF.426	chr17	-	chr17:15581036-15584178;chr17:15580997-15584178	chr17:15557746-15584178		chr17:15557746-15580996;chr17:15580997-15581035	chr17:15557745-15557746;chr17:15580996-15580997		8.40
K	intron_retention	CUFF.136	chr11	-	chr11:407535-407816				chr11:407534-407535;chr11:407816-407817		38.24
N	jcn_only_AD	CUFF.418	chr17	+	chr17:1939948-1940128	chr17:1939981-1940128		chr17:1939948-1939980	chr17:1939947-1939948		89.09
K	alternative_acceptor	CUFF.1089	chr9	+	chr9:116791253-116794927	chr9:116791253-116794924		chr9:116794925-116794927	chr9:116794927-116794928		9.68
K	intron_retention	CUFF.138	chr11	+	chr11:829541-829967				chr11:829540-829541;chr11:829967-829968	chr11:829360-829540;chr11:829968-830132	38.81
N	jcn_only_AA	CUFF.739	chr3	+	chr3:28357915-28360222;chr3:28357915-28360999	chr3:28357915-28358243		chr3:28358244-28360222;chr3:28360223-28360999	chr3:28360222-28360223;chr3:28360999-28361000		8.26
K	intron_retention	CUFF.165	chr11	+	chr11:65480306-65480392				chr11:65480305-65480306;chr11:65480392-65480393		1.20
K	jcn_only_AA	CUFF.299	chr14	+	chr14:105054647-105054958	chr14:105054647-105054914		chr14:105054915-105054958	chr14:105054958-105054959		44.00
N	jcn_only_AA	CUFF.929	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		1.42
N	jcn_only_AD	CUFF.933,CUFF.945	chr6	-	chr6:128313855-128316606;chr6:128313855-128316591	chr6:128313855-128316393		chr6:128316394-128316591;chr6:128316592-128316606	chr6:128316591-128316592;chr6:128316606-128316607		43.33
N	jcn_only_AD	CUFF.306	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		2.53
K	cassette	CUFF.604	chr2	-	chr2:61761039-61764696	chr2:61761039-61761692;chr2:61761814-61764696		chr2:61761693-61761813			24.00
K	alternative_last_exon	CUFF.419	chr17	-	chr17:5425107-5433800	chr17:5433379-5433800	chr17:5424844-5425106	chr17:5433172-5433378			14.55
N	alternative_acceptor	CUFF.922	chr6	+	chr6:33239900-33240404	chr6:33239900-33240363		chr6:33240364-33240404	chr6:33240404-33240405		3.33
K	intron_retention	CUFF.261	chr14	-	chr14:24683358-24683515				chr14:24683357-24683358;chr14:24683515-24683516		30.77
N	mutually_exclusive	CUFF.1042	chr8	-	chr8:80954904-80962679,chr8:80962707-80963761	chr8:80954904-80956401,chr8:80956444-80963761	chr8:80962680-80962706	chr8:80956402-80956443			12.50
K	cassette	CUFF.150	chr11	-	chr11:8414258-8457040	chr11:8414258-8435041;chr11:8435240-8457040		chr11:8435042-8435239			63.51
K	cassette	CUFF.410	chr16	-	chr16:75576582-75589701	chr16:75576582-75579723;chr16:75579853-75589701		chr16:75579724-75579852			52.51
N	jcn_only_AD	CUFF.1026	chr8	+	chr8:17434266-17434644	chr8:17434270-17434644		chr8:17434266-17434269	chr8:17434265-17434266		23.81
N	alternative_donor	CUFF.579	chr2	+	chr2:3469467-3481465	chr2:3476374-3481465		chr2:3469467-3476373	chr2:3469466-3469467		4.51
N	alternative_acceptor	CUFF.298	chr14	-	chr14:104201417-104204030	chr14:104202540-104204030		chr14:104201417-104202539	chr14:104201416-104201417		10.28
N	alternative_donor	CUFF.631	chr2	+	chr2:109068923-109085435	chr2:109079142-109085435		chr2:109068923-109079141	chr2:109068922-109068923		0.00
N	alternative_acceptor		chr14	+	chr14:58899176-58906787;chr14:58899176-58899829	chr14:58899176-58909423		chr14:58899830-58906787;chr14:58906788-58909423	chr14:58906787-58906788;chr14:58909423-58909424		93.75
N	jcn_only_AD	CUFF.942	chr6	-	chr6:114283559-114292020;chr6:114283559-114289797	chr6:114283559-114332294		chr6:114289798-114292020;chr6:114292021-114332294	chr6:114292020-114292021;chr6:114332294-114332295		18.37
N	alternative_donor	CUFF.598	chr2	+	chr2:38231360-38244328	chr2:38239793-38244328		chr2:38231360-38239792	chr2:38231359-38231360		0.65
K	cassette	CUFF.852	chr4	-	chr4:152100550-152108574	chr4:152100550-152102840;chr4:152102882-152108574		chr4:152102841-152102881			63.33
K	coord_cassette	CUFF.1073	chr9	+	chr9:43828222-43853496	chr9:43828222-43844143;chr9:43844316-43849744;chr9:43849852-43853496		chr9:43844144-43844315;chr9:43849745-43849851			41.67
N	intron_retention		chr16	-	chr16:57513601-57513756				chr16:57513600-57513601;chr16:57513756-57513757		67.50
K	mutually_exclusive	CUFF.61	chr1	+	chr1:167190196-167272710,chr1:167272812-167301706	chr1:167190196-167210643,chr1:167210848-167301706	chr1:167272711-167272811	chr1:167210644-167210847			6.32
K	intron_retention	CUFF.147	chr11	-	chr11:5686626-5686885				chr11:5686625-5686626;chr11:5686885-5686886		22.06
K	coord_cassette	CUFF.795	chr3	-	chr3:155520381-155523927	chr3:155520381-155521839;chr3:155521963-155523385;chr3:155523513-155523927		chr3:155521840-155521962;chr3:155523386-155523512			48.44
N	jcn_only_AD	CUFF.762	chr3	+	chr3:75492798-75500360	chr3:75496448-75500360		chr3:75492798-75496447	chr3:75492797-75492798		4.88
N	jcn_only_AA	CUFF.466	chr17	+	chr17:29706042-29708890	chr17:29706042-29706123					66.67
K	intron_retention	CUFF.504	chr19	+	chr19:1438428-1438809				chr19:1438427-1438428;chr19:1438809-1438810		74.76
N	alternative_last_exon	CUFF.509	chr19	-	chr19:6027346-6039990;chr19:6016283-6039990	chr19:6026249-6039990	chr19:6016101-6016282	chr19:6026125-6026248			53.00
N	alternative_acceptor	CUFF.490,CUFF.502	chr18	+	chr18:55833094-55912658	chr18:55833094-55895061		chr18:55895062-55912658	chr18:55912658-55912659		0.00
N	intron_retention		chr4	+	chr4:20618571-20622026				chr4:20618570-20618571;chr4:20622026-20622027		36.67
N	jcn_only_AD	CUFF.547	chr19	-	chr19:41944320-41945378;chr19:41944320-41945786	chr19:41944320-41946385		chr19:41945379-41945786;chr19:41945787-41946385	chr19:41945786-41945787;chr19:41946385-41946386		23.91
K	alternative_first_exon	CUFF.292	chr14	+	chr14:92788980-92792211	chr14:92790305-92792211	chr14:92788925-92788979	chr14:92790152-92790304			84.62
K	jcn_only_AD	CUFF.1150	chrX	+	chrX:153238312-153247300	chrX:153238338-153247300		chrX:153238312-153238337	chrX:153238311-153238312	chrX:153247301-153248646;chrX:153237778-153238311	63.89
K	intron_retention	CUFF.980	chr7	+	chr7:73107745-73107953				chr7:73107744-73107745;chr7:73107953-73107954		7.91
K	intron_retention	CUFF.330	chr15	+	chr15:64444050-64444441				chr15:64444049-64444050;chr15:64444441-64444442		29.09
K	cassette	CUFF.817	chr4	-	chr4:6055876-6058423	chr4:6055876-6056474;chr4:6056531-6058423		chr4:6056475-6056530			12.50
N	alternative_acceptor	CUFF.929	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		28.10
N	alternative_donor	CUFF.102	chr10	+	chr10:35464928-35467816;chr10:35437420-35467816;chr10:35426808-35467816;chr10:35416122-35467816;chr10:35456732-35467816	chr10:35464634-35467816		chr10:35416122-35426807;chr10:35426808-35437419;chr10:35437420-35456731;chr10:35456732-35464633;chr10:35464634-35464927	chr10:35416121-35416122;chr10:35426807-35426808;chr10:35437419-35437420;chr10:35456731-35456732;chr10:35464633-35464634		0.00
N	alternative_acceptor	CUFF.244,CUFF.256	chr13	+	chr13:103510769-103513856	chr13:103510769-103511260		chr13:103511261-103513856	chr13:103513856-103513857		0.00
K	intron_retention	CUFF.394	chr16	+	chr16:31368423-31368654				chr16:31368422-31368423;chr16:31368654-31368655		25.93
N	jcn_only_AA	CUFF.687	chr20	+	chr20:33589889-33589979	chr20:33589889-33589961		chr20:33589962-33589979	chr20:33589979-33589980		86.09
N	jcn_only_AD	CUFF.310	chr15	+	chr15:40532004-40532799;chr15:40509869-40532799;chr15:40531337-40532799	chr15:40532297-40532799		chr15:40509869-40531336;chr15:40531337-40532003;chr15:40532004-40532296	chr15:40509868-40509869;chr15:40531336-40531337;chr15:40532003-40532004		12.50
N	jcn_only_AD	CUFF.453,CUFF.475	chr17	-	chr17:56083889-56084304	chr17:56083889-56084267		chr17:56084268-56084304	chr17:56084304-56084305		32.35
N	intron_retention		chr16	+	chr16:19592976-19612985				chr16:19592975-19592976;chr16:19612985-19612986		77.05
N	intron_retention	CUFF.1148	chrX	-	chrX:152988744-152989788				chrX:152988743-152988744;chrX:152989788-152989789		65.00
N	alternative_first_exon	CUFF.138	chr11	+	chr11:827712-828229;chr11:826267-828229	chr11:827460-828229	chr11:826050-826266	chr11:827215-827459		chr11:828230-828772	47.27
K	cassette	CUFF.349	chr15	-	chr15:83710678-83725140	chr15:83710678-83718824;chr15:83718931-83725140		chr15:83718825-83718930			0.96
N	jcn_only_AD		chr7	-	chr7:37433521-37488462	chr7:37433521-37488277					20.69
N	jcn_only_AD	CUFF.265	chr14	+	chr14:50235340-50238311	chr14:50235810-50238311		chr14:50235340-50235809	chr14:50235339-50235340		19.15
K	jcn_only_AD	CUFF.386	chr16	+	chr16:21756358-21763255	chr16:21760282-21763255					2.68
K	intron_retention	CUFF.919	chr6	-	chr6:31937981-31938119				chr6:31937980-31937981;chr6:31938119-31938120		1.21
K	coord_cassette	CUFF.114	chr10	-	chr10:73857209-73887839	chr10:73857209-73862091;chr10:73862171-73862607;chr10:73862726-73887839		chr10:73862092-73862170;chr10:73862608-73862725			43.04
K	cassette	CUFF.658	chr2	-	chr2:207989129-208030190	chr2:207989129-208013705;chr2:208013925-208030190		chr2:208013706-208013924			24.64
N	alternative_donor	CUFF.225	chr12	+	chr12:53846760-53848509;chr12:53846161-53848509;chr12:53837558-53848509	chr12:53847068-53848509		chr12:53837558-53846160;chr12:53846161-53846759;chr12:53846760-53847067	chr12:53837557-53837558;chr12:53846160-53846161;chr12:53846759-53846760		30.00
K	cassette	CUFF.671	chr2	-	chr2:242440212-242447420	chr2:242440212-242440892;chr2:242441124-242447420		chr2:242440893-242441123			91.04
N	intron_retention		chr11	+	chr11:118401950-118403631				chr11:118401949-118401950;chr11:118403631-118403632	chr11:118401663-118401949;chr11:118403632-118403922	81.82
N	jcn_only_AA	CUFF.728	chr22	-	chr22:51009963-51010434	chr22:51009969-51010434		chr22:51009963-51009968	chr22:51009962-51009963		83.33
K	cassette	CUFF.119	chr10	-	chr10:78729826-78771724	chr10:78729826-78734244;chr10:78734332-78771724		chr10:78734245-78734331			23.53
K	jcn_only_AD	CUFF.126	chr10	+	chr10:101492167-101496002	chr10:101492318-101496002		chr10:101492167-101492317	chr10:101492166-101492167		29.03
K	intron_retention	CUFF.661	chr2	+	chr2:219221911-219222256				chr2:219221910-219221911;chr2:219222256-219222257		76.92
N	intron_retention		chr17	+	chr17:25965381-25967668				chr17:25965380-25965381;chr17:25967668-25967669		79.12
N	jcn_only_AD	CUFF.1114,CUFF.1115	chrX	-	chrX:13798109-13801483	chrX:13798109-13799033		chrX:13799034-13801483	chrX:13801483-13801484		9.66
K	intron_retention	CUFF.832	chr4	-	chr4:68927570-68927629				chr4:68927569-68927570;chr4:68927629-68927630		90.48
N	jcn_only_AD	CUFF.752	chr3	-	chr3:49330032-49331839	chr3:49330032-49330978		chr3:49330979-49331839	chr3:49331839-49331840		35.42
N	intron_retention		chr10	-	chr10:78644776-78647048				chr10:78644775-78644776;chr10:78647048-78647049		39.68
N	alternative_acceptor		chr12	+	chr12:26148064-26208211	chr12:26148064-26208168		chr12:26208169-26208211	chr12:26208211-26208212		42.86
N	intron_retention		chr18	-	chr18:44268831-44272131				chr18:44268830-44268831;chr18:44272131-44272132		68.89
N	intron_retention		chr17	+	chr17:80441619-80446077				chr17:80441618-80441619;chr17:80446077-80446078		55.32
N	intron_retention		chr12	+	chr12:69236305-69237543				chr12:69236304-69236305;chr12:69237543-69237544		78.85
K	alternative_first_exon	CUFF.685	chr20	-	chr20:31062546-31099149	chr20:31062546-31071164	chr20:31099150-31099259	chr20:31071165-31071394			42.50
N	cassette	CUFF.1072	chr9	+	chr9:35400441-35403163	chr9:35400441-35401947;chr9:35402005-35403163		chr9:35401948-35402004			91.67
N	intron_retention		chr11	+	chr11:828964-829359				chr11:828963-828964;chr11:829359-829360	chr11:828852-828963;chr11:829360-829540	89.06
N	jcn_only_AA		chr16	+	chr16:22448814-22466022	chr16:22448814-22462940					82.35
N	alternative_donor	CUFF.961	chr7	+	chr7:6641772-6647590	chr7:6647229-6647590		chr7:6641772-6647228	chr7:6641771-6641772		6.35
N	intron_retention		chr6	+	chr6:112375374-112375537				chr6:112375373-112375374;chr6:112375537-112375538		62.30
K	intron_retention	CUFF.146	chr11	+	chr11:3418637-3422988				chr11:3418636-3418637;chr11:3422988-3422989		10.99
K	alternative_first_exon	CUFF.953	chr6	-	chr6:151757690-151766442;chr6:151757690-151773150	chr6:151757690-151765600	chr6:151766443-151767007;chr6:151773151-151773335	chr6:151765601-151765760			18.37
N	cassette	CUFF.18	chr1	+	chr1:32541424-32557275;chr1:32541424-32542764	chr1:32541424-32542363;chr1:32542448-32542764,chr1:32542448-32557275		chr1:32542364-32542447			44.02
N	cassette	CUFF.189	chr11	-	chr11:119291097-119293822	chr11:119291097-119291578;chr11:119291640-119293822		chr11:119291579-119291639			85.50
N	alternative_donor	CUFF.761	chr3	-	chr3:73450161-73453298	chr3:73450161-73450919		chr3:73450920-73453298	chr3:73453298-73453299		1.45
N	alternative_donor		chr15	-	chr15:90420657-90431752	chr15:90420657-90421496		chr15:90421497-90431752	chr15:90431752-90431753		10.92
K	alternative_acceptor	CUFF.49	chr1	-	chr1:153925112-153925280	chr1:153925127-153925280		chr1:153925112-153925126	chr1:153925111-153925112		57.58
K	cassette	CUFF.273	chr14	+	chr14:61518854-61545527	chr14:61518854-61519066;chr14:61519704-61545527		chr14:61519067-61519703			80.72
K	coord_cassette	CUFF.661	chr2	+	chr2:219225383-219231746	chr2:219225383-219227457;chr2:219227626-219229350;chr2:219229476-219231746		chr2:219227458-219227625;chr2:219229351-219229475			41.67
N	jcn_only_AA	CUFF.36	chr1	+	chr1:167382352-167385285	chr1:167382352-167384736		chr1:167384737-167385285	chr1:167385285-167385286		66.67
K	intron_retention		chr11	-	chr11:5701469-5706245				chr11:5701468-5701469;chr11:5706245-5706246		64.00
K	intron_retention	CUFF.1108	chr9	+	chr9:139743233-139743562				chr9:139743232-139743233;chr9:139743562-139743563		90.09
N	jcn_only_AD		chr18	+	chr18:56001125-56008269	chr18:56002770-56008269		chr18:56001125-56002769	chr18:56001124-56001125		10.34
N	jcn_only_AA	CUFF.224	chr12	-	chr12:53467256-53468878	chr12:53468569-53468878					86.67
K	intron_retention	CUFF.180	chr11	+	chr11:117073910-117074022				chr11:117073909-117073910;chr11:117074022-117074023		4.04
N	jcn_only_AA	CUFF.734	chr3	+	chr3:19992554-20017092;chr3:19992554-20017134;chr3:19992554-20012039	chr3:19992554-20017078		chr3:20012040-20017078;chr3:20017079-20017092;chr3:20017093-20017134	chr3:20017078-20017079;chr3:20017092-20017093;chr3:20017134-20017135		83.26
N	alternative_first_exon	CUFF.1096	chr9	+	chr9:125027218-125033231	chr9:125028060-125033231	chr9:125026790-125027217	chr9:125027930-125028059			84.85
K	alternative_first_exon	CUFF.737,CUFF.786	chr3	-	chr3:27233734-27235551;chr3:27233734-27243000	chr3:27233734-27236027	chr3:27243001-27243071	chr3:27236028-27236204			26.47
K	alternative_last_exon	CUFF.645	chr2	-	chr2:174057785-174072274	chr2:174063553-174072274	chr2:174057669-174057784	chr2:174062378-174063552			38.10
N	alternative_acceptor	CUFF.722	chr22	+	chr22:37697061-37697921;chr22:37697061-37697975	chr22:37697061-37699294		chr22:37697922-37697975;chr22:37697976-37699294	chr22:37697975-37697976;chr22:37699294-37699295		17.65
N	cassette	CUFF.273	chr14	+	chr14:61509931-61512063	chr14:61509931-61510167;chr14:61510222-61512063		chr14:61510168-61510221			87.10
K	cassette	CUFF.1124	chrX	+	chrX:47038895-47039278	chrX:47038895-47039082;chrX:47039181-47039278		chrX:47039083-47039180			57.14
N	cassette	CUFF.945	chr6	-	chr6:128320050-128326228	chr6:128320050-128324341;chr6:128324378-128326228		chr6:128324342-128324377			87.67
K	intron_retention	CUFF.519	chr19	+	chr19:11470397-11470496				chr19:11470396-11470397;chr19:11470496-11470497		39.32
N	jcn_only_AD		chr4	-	chr4:152147239-152246392;chr4:152147239-152187237	chr4:152147239-152147319		chr4:152147320-152187237;chr4:152187238-152246392	chr4:152187237-152187238;chr4:152246392-152246393		91.67
N	alternative_last_exon		chr21	+	chr21:15646479-15659870	chr21:15646479-15651916	chr21:15659871-15660018	chr21:15651917-15651978		chr21:15646075-15646478	86.96
K	coord_cassette	CUFF.102	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			83.51
N	jcn_only_AA	CUFF.102	chr10	+	chr10:35477317-35495822	chr10:35477317-35490378		chr10:35490379-35495822	chr10:35495822-35495823		21.38
N	cassette	CUFF.537	chr19	-	chr19:33882386-33892626	chr19:33882386-33886995;chr19:33887062-33892626		chr19:33886996-33887061			92.98
K	cassette	CUFF.1004	chr7	-	chr7:110303778-110603555	chr7:110303778-110304879;chr7:110305069-110603555		chr7:110304880-110305068			61.22
K	intron_retention		chr12	-	chr12:48392215-48393701				chr12:48392214-48392215;chr12:48393701-48393702		9.68
K	intron_retention	CUFF.550	chr19	+	chr19:44764092-44768480				chr19:44764091-44764092;chr19:44768480-44768481		45.10
K	cassette	CUFF.581	chr2	-	chr2:4006532-4007505	chr2:4006532-4007153;chr2:4007365-4007505		chr2:4007154-4007364			97.84
N	jcn_only_AA		chr17	+	chr17:61905284-61905497	chr17:61905284-61905478					15.79
K	jcn_only_AD	CUFF.752,CUFF.775	chr3	-	chr3:49338125-49339870	chr3:49338125-49339816		chr3:49339817-49339870	chr3:49339870-49339871		87.80
N	alternative_donor	CUFF.138	chr11	+	chr11:828964-829359	chr11:829184-829359		chr11:828964-829183	chr11:828963-828964	chr11:829360-829540;chr11:828852-828963	88.43
N	jcn_only_AA	CUFF.86	chr10	-	chr10:356033-372945	chr10:370960-372945		chr10:356033-370959	chr10:356032-356033		92.31
K	jcn_only_AD	CUFF.396,CUFF.406	chr16	-	chr16:70268196-70274909	chr16:70268196-70268899					77.55
N	jcn_only_AD	CUFF.905	chr6	+	chr6:311963-335113	chr6:320365-335113		chr6:311963-320364	chr6:311962-311963		31.43
N	jcn_only_AA	CUFF.338	chr15	-	chr15:77577398-77578764;chr15:77474383-77578764	chr15:77577421-77578764					94.64
K	cassette	CUFF.21	chr1	-	chr1:41481901-41483306	chr1:41481901-41482905;chr1:41483050-41483306		chr1:41482906-41483049			61.82
N	jcn_only_AA	CUFF.661	chr2	+	chr2:219222458-219222759	chr2:219222458-219222708		chr2:219222709-219222759	chr2:219222759-219222760		44.44
N	jcn_only_AA	CUFF.966	chr7	-	chr7:22233074-22233532	chr7:22233396-22233532		chr7:22233074-22233395	chr7:22233073-22233074		11.90
K	alternative_first_exon	CUFF.557	chr19	+	chr19:50305399-50306205	chr19:50305857-50306205	chr19:50305238-50305398	chr19:50305647-50305856			80.49
K	intron_retention	CUFF.581	chr2	-	chr2:4007365-4007505				chr2:4007364-4007365;chr2:4007505-4007506		49.28
N	jcn_only_AD	CUFF.68	chr1	+	chr1:200860531-200867434	chr1:200864216-200867434		chr1:200860531-200864215	chr1:200860530-200860531		3.23
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	chr1:110215825-110215963			10.34
N	intron_retention		chr3	-	chr3:127294349-127294782				chr3:127294348-127294349;chr3:127294782-127294783		70.97
K	cassette	CUFF.823	chr4	+	chr4:20525801-20530571	chr4:20525801-20526771;chr4:20526796-20530571		chr4:20526772-20526795			27.27
N	jcn_only_AD	CUFF.460	chr17	+	chr17:61907310-61907630	chr17:61907550-61907630		chr17:61907310-61907549	chr17:61907309-61907310		95.56
K	jcn_only_AD	CUFF.124	chr10	+	chr10:96961943-96966964	chr10:96961953-96966964		chr10:96961943-96961952	chr10:96961942-96961943		85.29
K	intron_retention	CUFF.390	chr16	-	chr16:23504780-23505623				chr16:23504779-23504780;chr16:23505623-23505624	chr16:23504681-23504779;chr16:23505624-23505699	82.39
K	alternative_first_exon	CUFF.472	chr17	-	chr17:79479387-79479631,chr17:79479387-79481572,chr17:79479387-79490667;chr17:79479387-79479759,chr17:79479387-79479640	chr17:79479387-79479489	chr17:79479760-79479934	chr17:79479490-79479583			6.09
K	jcn_only_AD	CUFF.36	chr1	+	chr1:110212194-110213908	chr1:110212857-110213908					22.39
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55895140-55912658;chr18:55833094-55912658;chr18:55895121-55912658;chr18:55862966-55912658;chr18:55888990-55912658	chr18:55865102-55912658		chr18:55833094-55862965;chr18:55862966-55865101;chr18:55865102-55888989;chr18:55888990-55895120;chr18:55895121-55895139	chr18:55833093-55833094;chr18:55862965-55862966;chr18:55865101-55865102;chr18:55888989-55888990;chr18:55895120-55895121		32.68
N	jcn_only_AD		chr19	-	chr19:33984244-34003498;chr19:33984244-34001933	chr19:33984244-33991843					45.00
K	cassette	CUFF.920	chr6	+	chr6:32130400-32133914	chr6:32130400-32132355;chr6:32132435-32133914		chr6:32132356-32132434			37.50
K	alternative_last_exon	CUFF.665	chr2	+	chr2:231951896-232003449	chr2:231951896-231973277	chr2:232003450-232003564	chr2:231973278-231973916			56.41
K	cassette	CUFF.736	chr3	-	chr3:25657078-25660144	chr3:25657078-25659908;chr3:25660001-25660144		chr3:25659909-25660000			50.00
K	cassette	CUFF.797	chr3	-	chr3:165491295-165503932	chr3:165491295-165495504;chr3:165495584-165503932		chr3:165495505-165495583			5.34
K	alternative_last_exon	CUFF.953	chr6	-	chr6:151757690-151773150	chr6:151766961-151773150	chr6:151757283-151757689	chr6:151766443-151766960			69.70
K	cassette	CUFF.601	chr2	-	chr2:46839484-46842075	chr2:46839484-46840832;chr2:46840925-46842075		chr2:46840833-46840924			67.38
N	cassette	CUFF.848	chr4	+	chr4:120384135-120414487	chr4:120384135-120409799;chr4:120409873-120414487		chr4:120409800-120409872			93.02
N	intron_retention		chr6	+	chr6:46638966-46644383				chr6:46638965-46638966;chr6:46644383-46644384		69.23
K	intron_retention	CUFF.258	chr14	+	chr14:24470143-24470241				chr14:24470142-24470143;chr14:24470241-24470242		23.23
K	alternative_acceptor	CUFF.810	chr4	+	chr4:1126229-1126514	chr4:1126229-1126496		chr4:1126497-1126514	chr4:1126514-1126515		4.08
K	alternative_last_exon	CUFF.654	chr2	-	chr2:204259813-204309590	chr2:204306137-204309590,chr2:204306804-204309590	chr2:204258973-204259812	chr2:204304062-204306136			83.10
N	jcn_only_AA	CUFF.325,CUFF.354	chr15	+	chr15:57211105-57212099	chr15:57211105-57212089		chr15:57212090-57212099	chr15:57212099-57212100		95.12
N	mutually_exclusive	CUFF.998	chr7	-	chr7:102240836-102246304,chr7:102246435-102249207	chr7:102240836-102242770,chr7:102242853-102249207	chr7:102246305-102246434	chr7:102242771-102242852			66.67
K	intron_retention	CUFF.347	chr15	-	chr15:83357584-83357909				chr15:83357583-83357584;chr15:83357909-83357910		1.80
N	alternative_acceptor	CUFF.171	chr11	-	chr11:75514771-75522468;chr11:75514563-75522468	chr11:75520420-75522468		chr11:75514563-75514770;chr11:75514771-75520419	chr11:75514562-75514563;chr11:75514770-75514771		1.22
N	intron_retention		chr14	+	chr14:77929103-77935419				chr14:77929102-77929103;chr14:77935419-77935420		65.38
K	intron_retention	CUFF.25	chr1	-	chr1:54394114-54395711				chr1:54394113-54394114;chr1:54395711-54395712		23.33
K	intron_retention		chr12	+	chr12:58019248-58019364				chr12:58019247-58019248;chr12:58019364-58019365		1.85
K	intron_retention	CUFF.187	chr11	+	chr11:119056662-119056800				chr11:119056661-119056662;chr11:119056800-119056801		2.04
K	jcn_only_AA	CUFF.945	chr6	-	chr6:128540242-128643183	chr6:128563748-128643183					11.49
K	cassette	CUFF.101	chr10	-	chr10:35299371-35302626	chr10:35299371-35300775;chr10:35300893-35302626		chr10:35300776-35300892			70.15
K	intron_retention	CUFF.230	chr12	-	chr12:56705238-56708634				chr12:56705237-56705238;chr12:56708634-56708635		74.36
K	cassette	CUFF.811	chr4	-	chr4:1701798-1713600	chr4:1701798-1705322;chr4:1705428-1713600		chr4:1705323-1705427			68.25
N	jcn_only_AD	CUFF.18	chr1	+	chr1:32560573-32566042	chr1:32561364-32566042		chr1:32560573-32561363	chr1:32560572-32560573		1.76
N	jcn_only_AA	CUFF.686	chr20	+	chr20:30137925-30147413	chr20:30137925-30142548				chr20:30137867-30137924	99.07
K	alternative_first_exon	CUFF.709	chr22	-	chr22:21846384-21868418;chr22:21846384-21871613	chr22:21846384-21868422	chr22:21871614-21871914	chr22:21868423-21868617			60.26
N	alternative_acceptor	CUFF.273	chr14	+	chr14:61518650-61518758	chr14:61518650-61518723		chr14:61518724-61518758	chr14:61518758-61518759		8.20
N	jcn_only_AA	CUFF.114	chr10	-	chr10:73973036-73975964;chr10:73973090-73975964;chr10:73975868-73975964;chr10:73973110-73975964	chr10:73975613-73975964					2.86
K	intron_retention	CUFF.617	chr2	-	chr2:79363203-79363915				chr2:79363202-79363203;chr2:79363915-79363916		44.00
K	alternative_first_exon	CUFF.820	chr4	+	chr4:6969152-6995910	chr4:6989077-6995910	chr4:6969031-6969151	chr4:6988992-6989076			3.64
N	alternative_donor	CUFF.102	chr10	+	chr10:35464928-35467816;chr10:35426808-35467816;chr10:35416122-35467816;chr10:35456732-35467816;chr10:35464634-35467816	chr10:35437420-35467816		chr10:35416122-35426807;chr10:35426808-35437419;chr10:35437420-35456731;chr10:35456732-35464633;chr10:35464634-35464927	chr10:35416121-35416122;chr10:35426807-35426808;chr10:35437419-35437420;chr10:35456731-35456732;chr10:35464633-35464634		6.82
N	alternative_donor		chr15	-	chr15:90414779-90421496;chr15:90414779-90420537	chr15:90414779-90431752		chr15:90420538-90421496;chr15:90421497-90431752	chr15:90421496-90421497;chr15:90431752-90431753		92.89
K	coord_cassette	CUFF.4	chr1	+	chr1:11074023-11078789	chr1:11074023-11075580;chr1:11075704-11076900;chr1:11077065-11078789		chr1:11075581-11075703;chr1:11076901-11077064			23.08
K	cassette	CUFF.1103	chr9	-	chr9:135742341-135753558	chr9:135742341-135750501;chr9:135750587-135753558		chr9:135750502-135750586			6.11
K	alternative_first_exon	CUFF.721	chr22	+	chr22:31688685-31733653	chr22:31731403-31733653	chr22:31688485-31688684	chr22:31731241-31731402			90.77
K	alternative_first_exon	CUFF.884	chr5	-	chr5:82969369-82971106;chr5:82969369-82970344;chr5:82969369-82969951;chr5:82969369-82978143	chr5:82969369-83016607	chr5:82970345-82970701;chr5:82969952-82970139;chr5:82978144-82978427	chr5:83016608-83017432			0.00
K	alternative_last_exon	CUFF.782	chr3	-	chr3:125741776-125745177	chr3:125743749-125745177	chr3:125741629-125741775	chr3:125743554-125743748			49.36
N	alternative_donor	CUFF.374	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		26.19
N	jcn_only_AD	CUFF.423	chr17	+	chr17:6352728-6353347	chr17:6353099-6353347		chr17:6352728-6353098	chr17:6352727-6352728		3.55
K	jcn_only_AA	CUFF.806	chr3	-	chr3:194063432-194071970	chr3:194063435-194071970		chr3:194063432-194063434	chr3:194063431-194063432		44.44
N	cassette	CUFF.136	chr11	-	chr11:408207-414822;chr11:408894-414822	chr11:408894-409867,chr11:408207-409867;chr11:410028-414822		chr11:409868-410027			89.74
N	coord_cassette	CUFF.829	chr4	-	chr4:56466743-56473603	chr4:56466743-56471441;chr4:56471517-56473464;chr4:56473516-56473603		chr4:56471442-56471516;chr4:56473465-56473515			93.67
K	intron_retention	CUFF.716	chr22	+	chr22:29684745-29688488				chr22:29684744-29684745;chr22:29688488-29688489		85.19
K	jcn_only_AD	CUFF.253	chr13	-	chr13:97642064-97644761	chr13:97642064-97644675		chr13:97644676-97644761	chr13:97644761-97644762		92.37
K	alternative_donor	CUFF.705	chr22	+	chr22:19420131-19420787	chr22:19420383-19420787		chr22:19420131-19420382	chr22:19420130-19420131		90.57
K	jcn_only_AA	CUFF.244	chr13	+	chr13:21141396-21148518	chr13:21141396-21141808					78.69
N	cassette	CUFF.681	chr20	-	chr20:29966195-29978225	chr20:29966195-29976125;chr20:29976163-29978225		chr20:29976126-29976162			77.27
N	jcn_only_AD		chr3	-	chr3:73453547-73482789;chr3:73453547-73610601;chr3:73453547-73651504;chr3:73453547-73523605;chr3:73453547-73618301	chr3:73453547-73605850					26.09
N	alternative_donor	CUFF.1146	chrX	+	chrX:148863691-148867418;chrX:148863659-148867418	chrX:148864250-148867418		chrX:148863659-148863690;chrX:148863691-148864249	chrX:148863658-148863659;chrX:148863690-148863691		5.26
N	jcn_only_AD	CUFF.671	chr2	-	chr2:242435950-242436714;chr2:242435950-242437030	chr2:242435950-242436596		chr2:242436597-242436714;chr2:242436715-242437030	chr2:242436714-242436715;chr2:242437030-242437031		9.20
N	alternative_acceptor	CUFF.929	chr6	-	chr6:43481372-43483332	chr6:43483045-43483332		chr6:43481372-43483044	chr6:43481371-43481372		0.56
K	cassette	CUFF.944	chr6	+	chr6:126329892-126332398	chr6:126329892-126330480;chr6:126330581-126332398		chr6:126330481-126330580			66.67
N	cassette	CUFF.984	chr7	+	chr7:75044513-75045258	chr7:75044513-75044869;chr7:75045057-75045258		chr7:75044870-75045056			89.13
K	alternative_first_exon	CUFF.841	chr4	+	chr4:81105210-81112625	chr4:81106673-81112625	chr4:81104961-81105209	chr4:81106398-81106672			77.08
N	cassette	CUFF.946	chr6	-	chr6:133046119-133049879;chr6:133046119-133055391	chr6:133046119-133047860;chr6:133048152-133049879,chr6:133048152-133055391		chr6:133047861-133048151			56.32
N	jcn_only_AA		chr14	+	chr14:76286505-76330009	chr14:76286505-76286945		chr14:76286946-76330009	chr14:76330009-76330010		97.70
N	cassette	CUFF.683	chr20	+	chr20:30132839-30137866	chr20:30132839-30136767;chr20:30136918-30137866		chr20:30136768-30136917		chr20:30132750-30132838;chr20:30137867-30137965	76.70
K	intron_retention	CUFF.464	chr17	+	chr17:66508690-66509050				chr17:66508689-66508690;chr17:66509050-66509051		89.55
N	jcn_only_AA	CUFF.119	chr10	-	chr10:78771802-78778770	chr10:78772316-78778770		chr10:78771802-78772315	chr10:78771801-78771802		12.63
N	jcn_only_AD	CUFF.316	chr15	-	chr15:44892831-44898222	chr15:44892831-44896302		chr15:44896303-44898222	chr15:44898222-44898223		6.38
K	cassette	CUFF.1039	chr8	+	chr8:74888197-74890990	chr8:74888197-74888539;chr8:74888727-74890990		chr8:74888540-74888726			52.50
K	jcn_only_AA	CUFF.860	chr5	-	chr5:471939-472793	chr5:472081-472793		chr5:471939-472080	chr5:471938-471939		76.84
K	alternative_first_exon	CUFF.170	chr11	+	chr11:74624828-74630577;chr11:74622471-74630577	chr11:74630071-74630577	chr11:74622307-74622470	chr11:74629982-74630070			2.94
N	cassette	CUFF.265	chr14	+	chr14:50249176-50249547	chr14:50249176-50249259;chr14:50249313-50249547		chr14:50249260-50249312			64.80
K	jcn_only_AA	CUFF.685	chr20	-	chr20:31052921-31062403	chr20:31052938-31062403		chr20:31052921-31052937	chr20:31052920-31052921		17.39
K	cassette	CUFF.90	chr10	+	chr10:6266177-6268154	chr10:6266177-6266468;chr10:6266587-6268154		chr10:6266469-6266586			7.21
N	jcn_only_AA	CUFF.739	chr3	+	chr3:28357915-28358243;chr3:28357915-28360222	chr3:28357915-28360999		chr3:28358244-28360222;chr3:28360223-28360999	chr3:28360222-28360223;chr3:28360999-28361000		89.17
N	intron_retention		chr14	+	chr14:24563464-24563974				chr14:24563463-24563464;chr14:24563974-24563975		86.08
K	alternative_donor	CUFF.15	chr1	+	chr1:28655636-28657107	chr1:28655692-28657107		chr1:28655636-28655691	chr1:28655635-28655636		95.77
N	jcn_only_AD	CUFF.182	chr11	+	chr11:118402317-118402489;chr11:118401950-118402489	chr11:118402242-118402489		chr11:118401950-118402241;chr11:118402242-118402316	chr11:118401949-118401950;chr11:118402241-118402242	chr11:118402490-118402586;chr11:118401663-118401949	12.40
N	intron_retention		chr2	+	chr2:242610857-242611605				chr2:242610856-242610857;chr2:242611605-242611606		90.91
N	cassette	CUFF.752	chr3	-	chr3:49336069-49339816	chr3:49336069-49337899;chr3:49338125-49339816		chr3:49337900-49338124			66.04
K	intron_retention	CUFF.794	chr3	-	chr3:149051187-149051299				chr3:149051186-149051187;chr3:149051299-149051300		66.67
K	intron_retention	CUFF.1151	chrX	+	chrX:153609163-153609241				chrX:153609162-153609163;chrX:153609241-153609242		19.12
N	jcn_only_AD	CUFF.1000	chr7	+	chr7:107204192-107205032;chr7:107204505-107205032;chr7:107204655-107205032	chr7:107204693-107205032		chr7:107204192-107204504;chr7:107204505-107204654;chr7:107204655-107204692	chr7:107204191-107204192;chr7:107204504-107204505;chr7:107204654-107204655		6.10
K	intron_retention		chr17	-	chr17:79479387-79479640				chr17:79479386-79479387;chr17:79479640-79479641		23.08
K	jcn_only_AD	CUFF.686	chr20	+	chr20:33104267-33114072	chr20:33104682-33114072		chr20:33104267-33104681	chr20:33104266-33104267		41.08
N	alternative_acceptor	CUFF.737	chr3	-	chr3:27297863-27326092	chr3:27320465-27326092		chr3:27297863-27320464	chr3:27297862-27297863		0.00
N	jcn_only_AA		chr15	+	chr15:40509869-40545378	chr15:40509869-40532799					25.00
K	jcn_only_AD	CUFF.564	chr19	+	chr19:52901154-52901619	chr19:52901158-52901619		chr19:52901154-52901157	chr19:52901153-52901154		40.28
K	alternative_donor	CUFF.136	chr11	-	chr11:407569-407851	chr11:407569-407816		chr11:407817-407851	chr11:407851-407852		89.44
N	jcn_only_AA	CUFF.497	chr18	-	chr18:67614769-67623990;chr18:67563282-67623990	chr18:67614670-67623990		chr18:67563282-67614669;chr18:67614670-67614768	chr18:67563281-67563282;chr18:67614669-67614670		16.67
N	jcn_only_AD	CUFF.358	chr15	+	chr15:97326820-97327382;chr15:97327061-97327382	chr15:97326975-97327382		chr15:97326820-97326974;chr15:97326975-97327060	chr15:97326819-97326820;chr15:97326974-97326975		6.45
K	cassette	CUFF.809	chr4	+	chr4:660404-663834	chr4:660404-661644;chr4:661731-663834		chr4:661645-661730			67.06
K	cassette	CUFF.23	chr1	-	chr1:53878941-53883199	chr1:53878941-53881072;chr1:53881197-53883199		chr1:53881073-53881196			66.30
N	jcn_only_AA	CUFF.1110	chrX	+	chrX:1393712-1401301	chrX:1393712-1400763		chrX:1400764-1401301	chrX:1401301-1401302		59.85
N	jcn_only_AD	CUFF.971	chr7	-	chr7:37382368-37433424;chr7:37382368-37488277;chr7:37382368-37488462;chr7:37382368-37382655	chr7:37382368-37392635		chr7:37382656-37392635;chr7:37392636-37433424;chr7:37433425-37488277;chr7:37488278-37488462	chr7:37392635-37392636;chr7:37433424-37433425;chr7:37488277-37488278;chr7:37488462-37488463		8.51
K	alternative_acceptor	CUFF.895	chr5	+	chr5:140031392-140031672	chr5:140031392-140031651		chr5:140031652-140031672	chr5:140031672-140031673		43.66
K	alternative_first_exon	CUFF.101	chr10	-	chr10:35360268-35379357;chr10:35360268-35379106;chr10:35360268-35378823	chr10:35360268-35363119	chr10:35379107-35379332;chr10:35378824-35378973	chr10:35363120-35363275			43.16
N	alternative_donor	CUFF.962	chr7	+	chr7:7197058-7273933	chr7:7222452-7273933		chr7:7197058-7222451	chr7:7197057-7197058		0.00
N	alternative_last_exon		chr7	+	chr7:150817233-150820880,chr7:150817233-150819811	chr7:150817233-150817606	chr7:150820881-150820973	chr7:150817607-150818208			78.09
K	coord_cassette	CUFF.1051	chr8	+	chr8:106801153-106810951	chr8:106801153-106807983;chr8:106808126-106808996;chr8:106809135-106810951		chr8:106807984-106808125;chr8:106808997-106809134			61.11
K	alternative_donor	CUFF.60	chr1	+	chr1:166808842-166810191	chr1:166809007-166810191		chr1:166808842-166809006	chr1:166808841-166808842		50.00
K	cassette	CUFF.545	chr19	-	chr19:41354669-41356151	chr19:41354669-41355722;chr19:41355886-41356151		chr19:41355723-41355885			63.79
K	jcn_only_AA	CUFF.506	chr19	+	chr19:4317278-4318380	chr19:4317278-4318342		chr19:4318343-4318380	chr19:4318380-4318381		55.17
N	intron_retention	CUFF.1135	chrX	-	chrX:106184863-106185167				chrX:106184862-106184863;chrX:106185167-106185168		80.00
K	intron_retention	CUFF.102	chr10	+	chr10:35495980-35500583				chr10:35495979-35495980;chr10:35500583-35500584		23.03
K	alternative_first_exon	CUFF.326,CUFF.345	chr15	-	chr15:61931912-62007313	chr15:61931912-61945387	chr15:62007314-62007451	chr15:61945388-61945400			61.54
N	alternative_acceptor	CUFF.966	chr7	-	chr7:22206767-22232984	chr7:22231261-22232984		chr7:22206767-22231260	chr7:22206766-22206767		0.00
N	jcn_only_AA	CUFF.910	chr6	-	chr6:5144497-5216850;chr6:5113652-5216850;chr6:5187215-5216850	chr6:5138974-5216850		chr6:5113652-5138973;chr6:5138974-5144496;chr6:5144497-5187214	chr6:5113651-5113652;chr6:5138973-5138974;chr6:5144496-5144497		5.88
N	alternative_acceptor	CUFF.945	chr6	-	chr6:128313855-128316606	chr6:128316412-128316606		chr6:128313855-128316411	chr6:128313854-128313855		5.71
K	jcn_only_AD	CUFF.146	chr11	+	chr11:3427841-3428851	chr11:3427946-3428851		chr11:3427841-3427945	chr11:3427840-3427841		67.80
K	jcn_only_AA	CUFF.693	chr21	+	chr21:15660868-15663890	chr21:15660868-15663606		chr21:15663607-15663890	chr21:15663890-15663891	chr21:15660725-15660867;chr21:15663891-15664068	21.74
K	alternative_last_exon	CUFF.335	chr15	+	chr15:69576672-69587411	chr15:69576672-69580746	chr15:69587412-69587760	chr15:69580747-69580903			37.23
N	jcn_only_AD	CUFF.1001	chr7	+	chr7:107236448-107240841	chr7:107240748-107240841		chr7:107236448-107240747	chr7:107236447-107236448		4.99
K	alternative_first_exon	CUFF.533	chr19	-	chr19:20243397-20349096;chr19:20243397-20351308	chr19:20243397-20261169	chr19:20349097-20349344;chr19:20351309-20351446	chr19:20261170-20261357			8.33
N	coord_cassette	CUFF.673	chr2	+	chr2:242590751-242592926	chr2:242590751-242591298;chr2:242591390-242592721;chr2:242592785-242592926		chr2:242591299-242591389;chr2:242592722-242592784			10.76
K	cassette	CUFF.699	chr21	+	chr21:40178045-40181958	chr21:40178045-40178374;chr21:40178733-40181958		chr21:40178375-40178732			89.58
K	alternative_first_exon	CUFF.974	chr7	-	chr7:38937730-38948753;chr7:38937730-38969071	chr7:38937730-38971877	chr7:38948754-38948829;chr7:38969072-38969203	chr7:38971878-38972082			27.50
K	alternative_donor	CUFF.473	chr17	-	chr17:79894738-79895133;chr17:79894738-79895055	chr17:79894738-79895137		chr17:79895056-79895133;chr17:79895134-79895137	chr17:79895133-79895134;chr17:79895137-79895138	chr17:79894624-79894737;chr17:79895138-79895264	52.75
N	alternative_donor	CUFF.2	chr1	+	chr1:1982141-1986879	chr1:1982452-1986879		chr1:1982141-1982451	chr1:1982140-1982141		49.07
K	alternative_last_exon	CUFF.812	chr4	-	chr4:2932878-2933281	chr4:2933193-2933281	chr4:2932288-2932877	chr4:2933102-2933192			74.26
K	cassette	CUFF.975	chr7	+	chr7:44247798-44250621	chr7:44247798-44250440;chr7:44250531-44250621		chr7:44250441-44250530			63.36
K	alternative_first_exon	CUFF.1032	chr8	-	chr8:38006273-38008272	chr8:38006273-38006593	chr8:38008273-38008783	chr8:38006594-38006685			19.10
K	jcn_only_AD	CUFF.240,CUFF.241	chr12	-	chr12:113633695-113645242	chr12:113633695-113635345					67.86
N	alternative_acceptor	CUFF.708	chr22	+	chr22:21056998-21057293	chr22:21056998-21057117		chr22:21057118-21057293	chr22:21057293-21057294		35.58
K	intron_retention	CUFF.1125	chrX	-	chrX:53569501-53570846				chrX:53569500-53569501;chrX:53570846-53570847		17.59
N	jcn_only_AA		chr2	-	chr2:61761039-61765626	chr2:61764723-61765626		chr2:61761039-61764722	chr2:61761038-61761039		55.56
N	cassette	CUFF.136	chr11	-	chr11:407958-408694	chr11:407958-408072;chr11:408207-408694		chr11:408073-408206			72.98
N	intron_retention		chr19	+	chr19:17448474-17448682				chr19:17448473-17448474;chr19:17448682-17448683		32.88
K	alternative_first_exon	CUFF.47	chr1	-	chr1:151158427-151167754	chr1:151158427-151162599,chr1:151158427-151162480	chr1:151167755-151167884	chr1:151162600-151162664			86.36
N	alternative_acceptor		chr15	+	chr15:57555473-57565230	chr15:57555473-57565227		chr15:57565228-57565230	chr15:57565230-57565231		70.11
K	intron_retention	CUFF.893	chr5	+	chr5:137515023-137515348				chr5:137515022-137515023;chr5:137515348-137515349		62.50
K	intron_retention	CUFF.1031	chr8	-	chr8:30648832-30651432				chr8:30648831-30648832;chr8:30651432-30651433		44.16
K	cassette	CUFF.324	chr15	-	chr15:55783455-55789909	chr15:55783455-55787325;chr15:55787401-55789909		chr15:55787326-55787400			26.07
N	intron_retention		chr7	+	chr7:107220747-107221090				chr7:107220746-107220747;chr7:107221090-107221091		67.86
N	intron_retention	CUFF.350	chr15	-	chr15:84871760-84872928				chr15:84871759-84871760;chr15:84872928-84872929		33.33
K	cassette	CUFF.124	chr10	+	chr10:96954435-96961741	chr10:96954435-96961197;chr10:96961279-96961741		chr10:96961198-96961278			30.30
N	jcn_only_AA	CUFF.1066	chr9	-	chr9:15226011-15267911;chr9:15211396-15267911	chr9:15250009-15267911					77.39
N	alternative_acceptor	CUFF.734	chr3	+	chr3:19992554-20017092;chr3:19992554-20017078;chr3:19992554-20012039	chr3:19992554-20017134		chr3:20012040-20017078;chr3:20017079-20017092;chr3:20017093-20017134	chr3:20017078-20017079;chr3:20017092-20017093;chr3:20017134-20017135		8.13
K	alternative_last_exon	CUFF.860	chr5	-	chr5:472709-472793;chr5:466642-472793	chr5:471939-472793,chr5:472081-472793	chr5:466239-466641	chr5:470533-471938			66.67
N	jcn_only_AA		chr14	-	chr14:104261001-104263707;chr14:104251252-104263707	chr14:104245159-104263707					16.67
K	intron_retention	CUFF.152	chr11	-	chr11:10825138-10825445				chr11:10825137-10825138;chr11:10825445-10825446		20.83
K	alternative_donor	CUFF.415	chr16	+	chr16:89793734-89795642	chr16:89793766-89795642		chr16:89793734-89793765	chr16:89793733-89793734		36.21
K	alternative_last_exon	CUFF.299,CUFF.301	chr14	+	chr14:106944969-106950170	chr14:106944969-106946393	chr14:106950171-106951557	chr14:106946394-106946588			45.71
N	intron_retention		chr15	-	chr15:90378746-90380846				chr15:90378745-90378746;chr15:90380846-90380847		91.30
K	intron_retention		chr17	+	chr17:80441656-80442688				chr17:80441655-80441656;chr17:80442688-80442689		23.46
N	alternative_donor	CUFF.611	chr2	-	chr2:73198815-73215386	chr2:73198815-73208137		chr2:73208138-73215386	chr2:73215386-73215387		6.45
K	cassette	CUFF.320	chr15	-	chr15:47652295-47687757	chr15:47652295-47672653;chr15:47672793-47687757		chr15:47672654-47672792			50.00
N	alternative_donor	CUFF.457	chr17	+	chr17:61568730-61571282;chr17:61567390-61571282	chr17:61571021-61571282		chr17:61567390-61568729;chr17:61568730-61571020	chr17:61567389-61567390;chr17:61568729-61568730		89.58
K	alternative_last_exon	CUFF.81	chr1	+	chr1:227597586-227617105	chr1:227597586-227613456	chr1:227617106-227618736	chr1:227613457-227613796			35.00
N	cassette	CUFF.306	chr15	+	chr15:29131425-29213842	chr15:29131425-29140665;chr15:29140756-29213842		chr15:29140666-29140755			76.19
N	cassette	CUFF.225	chr12	+	chr12:53861078-53862560	chr12:53861078-53861588;chr12:53861628-53862560		chr12:53861589-53861627			36.14
N	intron_retention		chr7	+	chr7:54617864-54636823				chr7:54617863-54617864;chr7:54636823-54636824		61.11
K	jcn_only_AA	CUFF.618	chr2	-	chr2:86397965-86398330	chr2:86397968-86398330		chr2:86397965-86397967	chr2:86397964-86397965		82.95
N	intron_retention		chr15	+	chr15:40545216-40545378				chr15:40545215-40545216;chr15:40545378-40545379		20.69
K	alternative_first_exon	CUFF.2	chr1	+	chr1:2006573-2066700,chr1:2043257-2066700,chr1:2005369-2066700,chr1:2013900-2066700,chr1:2036335-2066700,chr1:2029995-2066700,chr1:2065440-2066700,chr1:2006819-2066700,chr1:2005715-2066700,chr1:2047750-2066700;chr1:2066526-2066700;chr1:2006207-2066700	chr1:1991031-2066700	chr1:2066291-2066525;chr1:2006119-2006206	chr1:1990980-1991030			8.23
K	alternative_acceptor	CUFF.662	chr2	+	chr2:219457431-219458891	chr2:219457431-219458830		chr2:219458831-219458891	chr2:219458891-219458892		59.72
N	cassette	CUFF.211	chr12	-	chr12:25699489-25801427	chr12:25699489-25702259;chr12:25702481-25801427		chr12:25702260-25702480			92.72
N	alternative_acceptor	CUFF.212	chr12	+	chr12:13366510-13369377	chr12:13366510-13366614		chr12:13366615-13369377	chr12:13369377-13369378		79.45
N	jcn_only_AA	CUFF.769	chr3	+	chr3:119196296-119198897;chr3:119196296-119197180	chr3:119196296-119198754		chr3:119197181-119198754;chr3:119198755-119198897	chr3:119198754-119198755;chr3:119198897-119198898		25.00
K	intron_retention	CUFF.897	chr5	-	chr5:141052701-141052967				chr5:141052700-141052701;chr5:141052967-141052968		48.00
K	cassette	CUFF.589	chr2	-	chr2:27668317-27668611	chr2:27668317-27668419;chr2:27668497-27668611		chr2:27668420-27668496			86.60
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55711941-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55758860-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		29.23
K	intron_retention	CUFF.195	chr12	-	chr12:347177-347336				chr12:347176-347177;chr12:347336-347337		45.38
N	alternative_donor	CUFF.1070	chr9	-	chr9:35077397-35078601	chr9:35077397-35078137		chr9:35078138-35078601	chr9:35078601-35078602		42.86
K	cassette	CUFF.559	chr19	-	chr19:51483744-51485582	chr19:51483744-51485022;chr19:51485171-51485582		chr19:51485023-51485170			27.27
K	jcn_only_AA	CUFF.1145	chrX	+	chrX:142113879-142121813	chrX:142113879-142121810		chrX:142121811-142121813	chrX:142121813-142121814	chrX:142113650-142113878;chrX:142121814-142122018	57.14
N	alternative_acceptor	CUFF.519	chr19	+	chr19:11468416-11470282;chr19:11468416-11470207	chr19:11468416-11470146		chr19:11470147-11470207;chr19:11470208-11470282	chr19:11470207-11470208;chr19:11470282-11470283		3.81
K	jcn_only_AA	CUFF.431	chr17	-	chr17:21437283-21438688	chr17:21437833-21438688		chr17:21437283-21437832	chr17:21437282-21437283		5.56
K	cassette	CUFF.417	chr17	-	chr17:1617309-1619423	chr17:1617309-1617664;chr17:1617748-1619423		chr17:1617665-1617747			42.86
N	alternative_acceptor	CUFF.473	chr17	-	chr17:79893021-79893998	chr17:79893393-79893998		chr17:79893021-79893392	chr17:79893020-79893021	chr17:79893999-79894069;chr17:79892802-79893020	73.10
K	jcn_only_AA	CUFF.595	chr2	+	chr2:33572578-33585669	chr2:33572578-33585663		chr2:33585664-33585669	chr2:33585669-33585670		99.34
N	intron_retention		chr15	+	chr15:24819892-24820053				chr15:24819891-24819892;chr15:24820053-24820054		53.66
N	alternative_first_exon		chr1	-	chr1:213184801-213188954	chr1:213184801-213188490	chr1:213188955-213189168	chr1:213188491-213188896			65.38
N	cassette	CUFF.786	chr3	-	chr3:127294109-127294782;chr3:127294109-127294591	chr3:127294109-127294245;chr3:127294349-127294782,chr3:127294349-127294591		chr3:127294246-127294348			82.19
N	intron_retention		chr16	+	chr16:3117417-3117984				chr16:3117416-3117417;chr16:3117984-3117985		11.21
N	jcn_only_AD		chr3	-	chr3:27394411-27410521;chr3:27394411-27409013	chr3:27394411-27410715					66.67
N	alternative_donor		chr18	-	chr18:67614769-67628827;chr18:67614769-67623990	chr18:67614769-67623849		chr18:67623850-67623990;chr18:67623991-67628827	chr18:67623990-67623991;chr18:67628827-67628828		9.09
N	jcn_only_AD	CUFF.709,CUFF.728	chr22	-	chr22:51020292-51020677	chr22:51020292-51020457		chr22:51020458-51020677	chr22:51020677-51020678		24.00
K	intron_retention	CUFF.418	chr17	+	chr17:1944476-1944774				chr17:1944475-1944476;chr17:1944774-1944775		17.05
N	intron_retention		chr14	+	chr14:58894356-58894989				chr14:58894355-58894356;chr14:58894989-58894990		60.00
K	alternative_first_exon	CUFF.974	chr7	-	chr7:38937730-38971877;chr7:38937730-38969071	chr7:38937730-38948753	chr7:38971878-38972082;chr7:38969072-38969203	chr7:38948754-38948829			55.00
K	alternative_acceptor	CUFF.909	chr6	-	chr6:3155158-3155858	chr6:3155290-3155858		chr6:3155158-3155289	chr6:3155157-3155158		89.15
N	intron_retention		chr17	+	chr17:61555152-61555291				chr17:61555151-61555152;chr17:61555291-61555292		50.54
K	alternative_acceptor	CUFF.713	chr22	-	chr22:25124342-25130050	chr22:25124369-25130050		chr22:25124342-25124368	chr22:25124341-25124342		26.67
N	alternative_acceptor	CUFF.579	chr2	+	chr2:3447663-3461391	chr2:3447663-3460920		chr2:3460921-3461391	chr2:3461391-3461392		1.62
K	alternative_last_exon	CUFF.347	chr15	-	chr15:83355772-83357487;chr15:83350333-83357487	chr15:83357251-83357487	chr15:83350172-83350332	chr15:83355097-83357250			76.16
N	jcn_only_AA	CUFF.628	chr2	+	chr2:101565943-101579216;chr2:101565943-101580519	chr2:101565943-101584742					55.40
N	alternative_donor	CUFF.941	chr6	+	chr6:112558118-112604255	chr6:112600441-112604255		chr6:112558118-112600440	chr6:112558117-112558118		0.00
K	intron_retention	CUFF.40	chr1	+	chr1:145578480-145578636				chr1:145578479-145578480;chr1:145578636-145578637		89.80
K	alternative_first_exon	CUFF.126	chr10	+	chr10:101482868-101496002	chr10:101492167-101496002,chr10:101492318-101496002	chr10:101482675-101482867	chr10:101491924-101492166			80.95
K	cassette	CUFF.419	chr17	-	chr17:5437309-5442734	chr17:5437309-5440170;chr17:5440261-5442734		chr17:5440171-5440260			65.08
K	cassette	CUFF.662	chr2	+	chr2:219449445-219452308	chr2:219449445-219452027;chr2:219452124-219452308		chr2:219452028-219452123			52.11
N	jcn_only_AD		chr3	-	chr3:125741776-125745235	chr3:125741776-125745177		chr3:125745178-125745235	chr3:125745235-125745236		95.74
K	alternative_last_exon	CUFF.822	chr4	+	chr4:13831472-13961612	chr4:13831472-13930973	chr4:13961613-13961710	chr4:13930974-13932852			70.00
K	alternative_last_exon	CUFF.381	chr16	-	chr16:5651666-5661235	chr16:5660676-5661235	chr16:5651170-5651665	chr16:5660202-5660675			84.48
N	jcn_only_AD	CUFF.739	chr3	+	chr3:28360371-28360999;chr3:28358351-28360999	chr3:28357915-28360999		chr3:28357915-28358350;chr3:28358351-28360370	chr3:28357914-28357915;chr3:28358350-28358351		87.70
N	jcn_only_AD		chr6	+	chr6:112375365-112375537	chr6:112375374-112375537					50.00
N	alternative_donor	CUFF.737,CUFF.782	chr3	-	chr3:27329235-27332752	chr3:27329235-27332107		chr3:27332108-27332752	chr3:27332752-27332753		13.10
K	coord_cassette	CUFF.60	chr1	+	chr1:166810326-166818174	chr1:166810326-166815848;chr1:166815976-166816730;chr1:166816830-166818174		chr1:166815849-166815975;chr1:166816731-166816829			42.11
N	jcn_only_AA	CUFF.722	chr22	+	chr22:45173110-45182336	chr22:45173110-45181921		chr22:45181922-45182336	chr22:45182336-45182337		72.22
N	alternative_donor	CUFF.152,CUFF.176	chr11	-	chr11:10828929-10829720;chr11:10828929-10829291	chr11:10828929-10829080		chr11:10829081-10829291;chr11:10829292-10829720	chr11:10829291-10829292;chr11:10829720-10829721		21.62
N	alternative_acceptor	CUFF.317	chr15	-	chr15:45464201-45464344	chr15:45464277-45464344		chr15:45464201-45464276	chr15:45464200-45464201		9.47
K	alternative_donor	CUFF.858	chr4	+	chr4:186253868-186260532	chr4:186253914-186260532		chr4:186253868-186253913	chr4:186253867-186253868		93.33
K	intron_retention	CUFF.641	chr2	+	chr2:169711971-169713199				chr2:169711970-169711971;chr2:169713199-169713200		3.40
N	alternative_acceptor	CUFF.775	chr3	-	chr3:120371494-120389273	chr3:120371499-120389273		chr3:120371494-120371498	chr3:120371493-120371494		78.43
K	intron_retention	CUFF.432	chr17	+	chr17:25974145-25974295				chr17:25974144-25974145;chr17:25974295-25974296		16.00
K	jcn_only_AD	CUFF.561	chr19	-	chr19:51537396-51537840	chr19:51537396-51537680		chr19:51537681-51537840	chr19:51537840-51537841		80.92
N	jcn_only_AD	CUFF.201	chr12	+	chr12:4662256-4668022;chr12:4665669-4668022	chr12:4665717-4668022		chr12:4662256-4665668;chr12:4665669-4665716	chr12:4662255-4662256;chr12:4665668-4665669		39.13
N	jcn_only_AA	CUFF.787	chr3	+	chr3:133419898-133472438	chr3:133419898-133426336		chr3:133426337-133472438	chr3:133472438-133472439		82.05
N	jcn_only_AD	CUFF.102	chr10	+	chr10:35464928-35467816;chr10:35426808-35467816;chr10:35416122-35467816;chr10:35456732-35467816;chr10:35464634-35467816	chr10:35437420-35467816		chr10:35416122-35426807;chr10:35426808-35437419;chr10:35437420-35456731;chr10:35456732-35464633;chr10:35464634-35464927	chr10:35416121-35416122;chr10:35426807-35426808;chr10:35437419-35437420;chr10:35456731-35456732;chr10:35464633-35464634		37.97
K	intron_retention	CUFF.460	chr17	+	chr17:61908977-61909083				chr17:61908976-61908977;chr17:61909083-61909084		10.37
K	coord_cassette	CUFF.1098	chr9	-	chr9:130948056-130952966	chr9:130948056-130950141;chr9:130950214-130952607;chr9:130952724-130952966		chr9:130950142-130950213;chr9:130952608-130952723			74.17
N	jcn_only_AD	CUFF.325	chr15	+	chr15:57565461-57574642	chr15:57573991-57574642		chr15:57565461-57573990	chr15:57565460-57565461		11.90
K	intron_retention		chr17	+	chr17:35378314-35388910				chr17:35378313-35378314;chr17:35388910-35388911		63.64
K	alternative_first_exon	CUFF.1153	chrY	+	chrY:20883069-20893582	chrY:20891910-20893582	chrY:20882957-20883068	chrY:20891743-20891909			35.85
N	alternative_donor	CUFF.526	chr19	+	chr19:16199931-16204345	chr19:16203943-16204345		chr19:16199931-16203942	chr19:16199930-16199931		0.00
K	intron_retention	CUFF.1042	chr8	-	chr8:80954904-80963761				chr8:80954903-80954904;chr8:80963761-80963762		3.86
K	intron_retention	CUFF.851	chr4	-	chr4:142244773-142245955				chr4:142244772-142244773;chr4:142245955-142245956		31.58
N	coord_cassette	CUFF.316	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			83.33
K	alternative_first_exon	CUFF.138	chr11	+	chr11:827712-828259;chr11:826267-828259	chr11:827319-828259,chr11:827460-828259	chr11:826050-826266	chr11:827215-827318		chr11:828260-828772	15.71
N	alternative_acceptor	CUFF.504	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		19.00
K	jcn_only_AD	CUFF.542	chr19	-	chr19:39924059-39924133;chr19:39924059-39924157	chr19:39924059-39924161		chr19:39924134-39924157;chr19:39924158-39924161	chr19:39924157-39924158;chr19:39924161-39924162		68.02
N	cassette	CUFF.490	chr18	+	chr18:55919287-55989656	chr18:55919287-55983213;chr18:55983265-55989656		chr18:55983214-55983264			98.44
N	alternative_donor	CUFF.155	chr11	+	chr11:36397709-36440804	chr11:36424929-36440804		chr11:36397709-36424928	chr11:36397708-36397709		54.55
K	jcn_only_AD	CUFF.550	chr19	+	chr19:44764362-44768466;chr19:44764092-44768466	chr19:44764156-44768466		chr19:44764092-44764155;chr19:44764156-44764361	chr19:44764091-44764092;chr19:44764155-44764156		39.68
K	alternative_last_exon	CUFF.940	chr6	+	chr6:112375609-112382193	chr6:112375609-112375825	chr6:112382194-112382491	chr6:112375826-112376184			46.11
N	alternative_donor	CUFF.905	chr6	+	chr6:311963-335113	chr6:320365-335113		chr6:311963-320364	chr6:311962-311963		7.69
K	cassette	CUFF.895	chr5	+	chr5:140028123-140031298	chr5:140028123-140028467;chr5:140028566-140031298		chr5:140028468-140028565			23.62
K	jcn_only_AD	CUFF.894	chr5	+	chr5:139909382-139916973	chr5:139915124-139916973				chr5:139916974-139917174	80.60
N	jcn_only_AD	CUFF.663	chr2	+	chr2:220095073-220096649;chr2:220094623-220096649	chr2:220095128-220096649		chr2:220094623-220095072;chr2:220095073-220095127	chr2:220094622-220094623;chr2:220095072-220095073		52.15
N	jcn_only_AD	CUFF.652	chr2	-	chr2:197298183-197458231	chr2:197298183-197357967		chr2:197357968-197458231	chr2:197458231-197458232		20.00
N	intron_retention		chr3	-	chr3:124951499-124953143				chr3:124951498-124951499;chr3:124953143-124953144		64.00
N	intron_retention		chr2	-	chr2:242440263-242440892				chr2:242440262-242440263;chr2:242440892-242440893		62.16
K	intron_retention	CUFF.812	chr4	-	chr4:2933193-2933551				chr4:2933192-2933193;chr4:2933551-2933552		71.01
K	cassette	CUFF.1082	chr9	+	chr9:95588861-95599058	chr9:95588861-95591219;chr9:95591446-95599058		chr9:95591220-95591445			85.71
N	intron_retention		chr17	+	chr17:61904875-61905033				chr17:61904874-61904875;chr17:61905033-61905034		84.38
N	alternative_donor	CUFF.28	chr1	+	chr1:70832012-70832126;chr1:70820795-70832126;chr1:70820791-70832126	chr1:70820892-70832126		chr1:70820791-70820794;chr1:70820795-70820891;chr1:70820892-70832011	chr1:70820790-70820791;chr1:70820794-70820795;chr1:70820891-70820892		23.08
N	intron_retention		chr16	-	chr16:23504843-23505623				chr16:23504842-23504843;chr16:23505623-23505624	chr16:23504681-23504842;chr16:23505624-23505699	70.04
K	cassette	CUFF.820	chr4	+	chr4:7008454-7011603	chr4:7008454-7009250;chr4:7009353-7011603		chr4:7009251-7009352			20.30
N	cassette	CUFF.321	chr15	-	chr15:50831049-50838669	chr15:50831049-50833245;chr15:50833462-50838669		chr15:50833246-50833461			84.78
N	alternative_acceptor	CUFF.1117	chrX	+	chrX:15706982-15711085	chrX:15706982-15709260		chrX:15709261-15711085	chrX:15711085-15711086		2.50
N	jcn_only_AA	CUFF.493	chr18	+	chr18:55888990-55912658	chr18:55888990-55895061		chr18:55895062-55912658	chr18:55912658-55912659		77.78
K	cassette	CUFF.845	chr4	-	chr4:99403327-99407888	chr4:99403327-99405549;chr4:99405750-99407888		chr4:99405550-99405749			7.50
N	intron_retention		chr17	-	chr17:40738156-40739851				chr17:40738155-40738156;chr17:40739851-40739852		25.00
K	jcn_only_AD	CUFF.519	chr19	+	chr19:11474496-11474836	chr19:11474512-11474836		chr19:11474496-11474511	chr19:11474495-11474496		17.14
N	intron_retention		chr2	-	chr2:263373-264781				chr2:263372-263373;chr2:264781-264782		14.29
N	intron_retention		chr17	+	chr17:61905284-61905478				chr17:61905283-61905284;chr17:61905478-61905479		80.43
N	jcn_only_AD	CUFF.23	chr1	-	chr1:53904722-53905447	chr1:53904722-53905099		chr1:53905100-53905447	chr1:53905447-53905448		15.00
N	alternative_acceptor		chr16	+	chr16:3194833-3195668	chr16:3194833-3194984		chr16:3194985-3195668	chr16:3195668-3195669		70.00
N	alternative_acceptor	CUFF.633	chr2	-	chr2:110920710-110922264	chr2:110920713-110922264		chr2:110920710-110920712	chr2:110920709-110920710		47.06
N	jcn_only_AA		chr17	+	chr17:25965381-25967668	chr17:25965381-25967597		chr17:25967598-25967668	chr17:25967668-25967669		84.68
N	cassette	CUFF.1042	chr8	-	chr8:80976829-81083659	chr8:80976829-81032049;chr8:81032120-81083659		chr8:81032050-81032119			30.23
N	jcn_only_AD		chr15	+	chr15:24819892-24820053	chr15:24819961-24820053					38.71
N	alternative_acceptor	CUFF.577	chr2	+	chr2:33477912-33482434	chr2:33477912-33482350		chr2:33482351-33482434	chr2:33482434-33482435		86.39
K	cassette	CUFF.450	chr17	+	chr17:46988243-46993437	chr17:46988243-46990195;chr17:46990384-46993437		chr17:46990196-46990383			65.00
N	jcn_only_AD		chr14	+	chr14:76368568-76420766;chr14:76407838-76420766	chr14:76373021-76420766					67.48
N	cassette	CUFF.877	chr5	-	chr5:54593227-54603214	chr5:54593227-54594418;chr5:54594493-54603214		chr5:54594419-54594492			45.00
K	intron_retention	CUFF.1075	chr9	-	chr9:46686830-46687372				chr9:46686829-46686830;chr9:46687372-46687373		59.38
K	alternative_last_exon	CUFF.864	chr5	+	chr5:36177395-36183941	chr5:36177395-36181919	chr5:36183942-36184515	chr5:36181920-36182917		chr5:36177287-36177394	78.23
K	cassette	CUFF.202	chr12	-	chr12:7092701-7125577	chr12:7092701-7108732;chr12:7108792-7125577		chr12:7108733-7108791			1.69
N	jcn_only_AD	CUFF.1007,CUFF.999	chr7	-	chr7:117432836-117450818	chr7:117432836-117433466		chr7:117433467-117450818	chr7:117450818-117450819		27.27
K	alternative_donor	CUFF.528	chr19	-	chr19:16593597-16594740	chr19:16593597-16594572		chr19:16594573-16594740	chr19:16594740-16594741		80.00
K	alternative_first_exon	CUFF.176,CUFF.193	chr11	-	chr11:124767158-124767483;chr11:124767158-124768293	chr11:124767158-124767621	chr11:124768294-124768472	chr11:124767622-124768201			47.62
N	cassette	CUFF.611	chr2	-	chr2:73172229-73195576	chr2:73172229-73188259;chr2:73188378-73195576		chr2:73188260-73188377			67.90
N	jcn_only_AA	CUFF.390	chr16	-	chr16:23504780-23505623;chr16:23504909-23505623	chr16:23504843-23505623		chr16:23504780-23504842;chr16:23504843-23504908	chr16:23504779-23504780;chr16:23504842-23504843	chr16:23505624-23505699;chr16:23504681-23504779	26.14
K	alternative_first_exon	CUFF.234	chr12	+	chr12:69202272-69202987	chr12:69202867-69202987	chr12:69201956-69202271	chr12:69202759-69202866			39.32
N	alternative_donor	CUFF.457	chr17	+	chr17:61562331-61562596;chr17:61561903-61562596	chr17:61562428-61562596		chr17:61561903-61562330;chr17:61562331-61562427	chr17:61561902-61561903;chr17:61562330-61562331		59.82
K	coord_cassette	CUFF.584	chr2	-	chr2:11593925-11605897	chr2:11593925-11597304;chr2:11597360-11598406;chr2:11598478-11605897		chr2:11597305-11597359;chr2:11598407-11598477			27.85
K	intron_retention	CUFF.579	chr2	+	chr2:3469480-3482616				chr2:3469479-3469480;chr2:3482616-3482617		71.05
N	jcn_only_AD	CUFF.961	chr7	+	chr7:6641772-6647167	chr7:6642384-6647167		chr7:6641772-6642383	chr7:6641771-6641772		35.00
K	alternative_last_exon	CUFF.479	chr18	-	chr18:4775123-4946880	chr18:4807995-4946880	chr18:4775053-4775122	chr18:4807841-4807994			70.83
N	alternative_acceptor	CUFF.566	chr19	+	chr19:54648069-54649330;chr19:54648069-54649333	chr19:54648069-54649277		chr19:54649278-54649330;chr19:54649331-54649333	chr19:54649330-54649331;chr19:54649333-54649334		3.45
K	cassette	CUFF.618	chr2	-	chr2:86393768-86398330	chr2:86393768-86397871;chr2:86397965-86398330		chr2:86397872-86397964			95.83
K	intron_retention		chr5	-	chr5:178043950-178044344				chr5:178043949-178043950;chr5:178044344-178044345		58.49
K	cassette	CUFF.725	chr22	+	chr22:45198045-45210551	chr22:45198045-45204186;chr22:45204319-45210551		chr22:45204187-45204318			88.14
N	cassette	CUFF.758	chr3	-	chr3:57569735-57582800;chr3:57563115-57582800	chr3:57569735-57570110,chr3:57563115-57570110;chr3:57570192-57582800		chr3:57570111-57570191			63.57
N	alternative_donor	CUFF.823	chr4	+	chr4:20570628-20591266	chr4:20574884-20591266		chr4:20570628-20574883	chr4:20570627-20570628		65.00
N	alternative_donor	CUFF.18	chr1	+	chr1:32560573-32566042	chr1:32561364-32566042		chr1:32560573-32561363	chr1:32560572-32560573		0.89
K	alternative_donor	CUFF.542	chr19	-	chr19:39924402-39926297	chr19:39924402-39926246		chr19:39926247-39926297	chr19:39926297-39926298		33.14
N	alternative_donor		chr11	-	chr11:10828929-10829080;chr11:10828929-10829291	chr11:10828929-10829720		chr11:10829081-10829291;chr11:10829292-10829720	chr11:10829291-10829292;chr11:10829720-10829721		24.32
N	jcn_only_AD	CUFF.998	chr7	-	chr7:102251590-102252518;chr7:102251590-102257071	chr7:102251590-102256969		chr7:102252519-102256969;chr7:102256970-102257071	chr7:102256969-102256970;chr7:102257071-102257072		22.86
K	intron_retention	CUFF.243	chr12	-	chr12:133181418-133182732				chr12:133181417-133181418;chr12:133182732-133182733		88.37
K	jcn_only_AA	CUFF.1023	chr8	-	chr8:2452792-2453715	chr8:2452795-2453715		chr8:2452792-2452794	chr8:2452791-2452792		32.14
K	cassette	CUFF.1102	chr9	+	chr9:133333977-133342111	chr9:133333977-133339497;chr9:133339555-133342111		chr9:133339498-133339554			81.25
K	intron_retention	CUFF.812	chr4	-	chr4:2932878-2932953				chr4:2932877-2932878;chr4:2932953-2932954		55.11
N	jcn_only_AD	CUFF.1004	chr7	-	chr7:111161506-111201906	chr7:111161506-111172573		chr7:111172574-111201906	chr7:111201906-111201907		5.26
K	alternative_first_exon	CUFF.137,CUFF.152	chr11	-	chr11:558980-559346;chr11:558980-560682	chr11:558980-559968	chr11:560683-560864	chr11:559969-560172			33.33
N	coord_cassette	CUFF.102	chr10	+	chr10:35464634-35477127	chr10:35464634-35467816;chr10:35467915-35468061;chr10:35468205-35477127		chr10:35467817-35467914;chr10:35468062-35468204			91.26
K	cassette	CUFF.830	chr4	+	chr4:57308027-57312860	chr4:57308027-57312522;chr4:57312544-57312860		chr4:57312523-57312543			31.11
K	cassette	CUFF.354	chr15	+	chr15:91298169-91303823	chr15:91298169-91303376;chr15:91303510-91303823		chr15:91303377-91303509			80.00
K	cassette	CUFF.22	chr1	+	chr1:47139892-47152344	chr1:47139892-47147852;chr1:47147937-47152344		chr1:47147853-47147936			7.58
K	cassette	CUFF.502	chr18	+	chr18:77891076-77893494	chr18:77891076-77891574;chr18:77891690-77893494		chr18:77891575-77891689			9.68
N	mutually_exclusive	CUFF.725	chr22	+	chr22:45182487-45204186,chr22:45204319-45210551	chr22:45182487-45197956,chr22:45198045-45210551	chr22:45204187-45204318	chr22:45197957-45198044			27.78
K	intron_retention	CUFF.149	chr11	-	chr11:6640499-6640614				chr11:6640498-6640499;chr11:6640614-6640615		3.69
K	cassette	CUFF.338	chr15	-	chr15:77578847-77712347	chr15:77578847-77657504;chr15:77657568-77712347		chr15:77657505-77657567			34.59
K	intron_retention	CUFF.259,CUFF.260	chr14	+	chr14:24568930-24569203				chr14:24568929-24568930;chr14:24569203-24569204		14.89
K	intron_retention	CUFF.55	chr1	-	chr1:158584097-158585005				chr1:158584096-158584097;chr1:158585005-158585006		1.89
N	intron_retention	CUFF.1108	chr9	+	chr9:139744590-139744954				chr9:139744589-139744590;chr9:139744954-139744955		33.33
K	alternative_last_exon	CUFF.716	chr22	+	chr22:29684776-29687550;chr22:29684776-29687553	chr22:29684776-29686401	chr22:29687554-29687588	chr22:29686402-29687550			67.71
N	coord_cassette	CUFF.316	chr15	-	chr15:44859791-44864880	chr15:44859791-44861595;chr15:44861704-44862722;chr15:44862857-44864880		chr15:44861596-44861703;chr15:44862723-44862856			73.17
K	cassette	CUFF.234	chr12	+	chr12:69207409-69210591	chr12:69207409-69208382;chr12:69208470-69210591		chr12:69208383-69208469			16.18
N	coord_cassette	CUFF.234	chr12	+	chr12:69203073-69210591	chr12:69203073-69207333;chr12:69207409-69208382;chr12:69208470-69210591		chr12:69207334-69207408;chr12:69208383-69208469			46.15
N	alternative_acceptor	CUFF.751	chr3	-	chr3:46982556-47017842	chr3:47007620-47017842		chr3:46982556-47007619	chr3:46982555-46982556		0.00
N	intron_retention		chr15	+	chr15:40531337-40545378				chr15:40531336-40531337;chr15:40545378-40545379		17.86
N	jcn_only_AD	CUFF.21,CUFF.44	chr1	-	chr1:41486606-41487294	chr1:41486606-41487201		chr1:41487202-41487294	chr1:41487294-41487295		80.00
K	alternative_first_exon	CUFF.716	chr22	+	chr22:29664339-29668204	chr22:29665652-29668204	chr22:29663905-29664338	chr22:29665568-29665651			1.59
N	coord_cassette	CUFF.202	chr12	-	chr12:7091066-7125577	chr12:7091066-7091836;chr12:7091944-7092592;chr12:7092701-7125577		chr12:7091837-7091943;chr12:7092593-7092700			87.04
K	alternative_donor	CUFF.157	chr11	+	chr11:57310815-57311096	chr11:57310848-57311096		chr11:57310815-57310847	chr11:57310814-57310815		58.33
K	coord_cassette	CUFF.728	chr22	-	chr22:51019090-51020677	chr22:51019090-51019848;chr22:51019983-51020177;chr22:51020292-51020677		chr22:51019849-51019982;chr22:51020178-51020291			84.42
K	intron_retention	CUFF.330	chr15	+	chr15:64445586-64445850				chr15:64445585-64445586;chr15:64445850-64445851		54.55
N	alternative_first_exon	CUFF.891	chr5	+	chr5:134182554-134190587;chr5:134181903-134190587	chr5:134181428-134190587	chr5:134182156-134182553;chr5:134181764-134181902	chr5:134181338-134181427			6.25
N	intron_retention		chr14	-	chr14:104202540-104204030				chr14:104202539-104202540;chr14:104204030-104204031		19.72
N	cassette	CUFF.385	chr16	+	chr16:19659205-19663297	chr16:19659205-19661703;chr16:19661782-19663297		chr16:19661704-19661781			84.51
N	coord_cassette	CUFF.524	chr19	-	chr19:14863339-14867049	chr19:14863339-14865765;chr19:14865940-14866465;chr19:14866690-14867049		chr19:14865766-14865939;chr19:14866466-14866689			59.02
K	alternative_first_exon	CUFF.977,CUFF.988	chr7	-	chr7:86548627-86550078;chr7:86548627-86554843	chr7:86548627-86549023	chr7:86554844-86554972	chr7:86549024-86549206			62.92
N	cassette	CUFF.1110	chrX	+	chrX:1401673-1407411	chrX:1401673-1404670;chrX:1404814-1407411		chrX:1404671-1404813			90.81
K	intron_retention	CUFF.1098	chr9	-	chr9:130940770-130940987				chr9:130940769-130940770;chr9:130940987-130940988		34.55
K	alternative_last_exon	CUFF.338	chr15	-	chr15:77451039-77471131	chr15:77470366-77471131	chr15:77447443-77451038	chr15:77470089-77470365			51.35
N	alternative_first_exon	CUFF.878	chr5	+	chr5:56531860-56542126	chr5:56533000-56542126	chr5:56531793-56531859	chr5:56532901-56532999		chr5:56542127-56542311	34.62
K	intron_retention	CUFF.918	chr6	+	chr6:31936867-31937056				chr6:31936866-31936867;chr6:31937056-31937057		9.80
N	alternative_donor	CUFF.23	chr1	-	chr1:53904722-53905447	chr1:53904722-53905099		chr1:53905100-53905447	chr1:53905447-53905448		12.82
N	alternative_acceptor	CUFF.1080	chr9	-	chr9:86506417-86514575	chr9:86513864-86514575		chr9:86506417-86513863	chr9:86506416-86506417		6.67
N	cassette	CUFF.671	chr2	-	chr2:242437103-242438053	chr2:242437103-242437649;chr2:242437765-242438053		chr2:242437650-242437764			91.04
K	cassette	CUFF.2	chr1	+	chr1:2075781-2077465	chr1:2075781-2076776;chr1:2076951-2077465		chr1:2076777-2076950			23.27
K	jcn_only_AD	CUFF.157	chr11	+	chr11:57310815-57311096	chr11:57310848-57311096		chr11:57310815-57310847	chr11:57310814-57310815		72.22
K	intron_retention	CUFF.709	chr22	-	chr22:21832391-21832873				chr22:21832390-21832391;chr22:21832873-21832874		10.68
N	alternative_donor		chr14	-	chr14:71227900-71249939;chr14:71227900-71232158	chr14:71227900-71267383		chr14:71232159-71249939;chr14:71249940-71267383	chr14:71249939-71249940;chr14:71267383-71267384		100.00
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		87.80
N	intron_retention	CUFF.758	chr3	-	chr3:57582951-57583058				chr3:57582950-57582951;chr3:57583058-57583059		82.81
N	alternative_acceptor	CUFF.167	chr11	+	chr11:67786363-67786638	chr11:67786363-67786534		chr11:67786535-67786638	chr11:67786638-67786639		3.08
K	cassette	CUFF.556	chr19	-	chr19:49316606-49316919	chr19:49316606-49316712;chr19:49316810-49316919		chr19:49316713-49316809			12.31
N	jcn_only_AD	CUFF.579	chr2	+	chr2:3469467-3481465	chr2:3476374-3481465		chr2:3469467-3476373	chr2:3469466-3469467		21.12
N	jcn_only_AA		chr3	+	chr3:186681715-186769036	chr3:186681715-186756529					92.05
K	cassette	CUFF.264	chr14	+	chr14:50069187-50074117	chr14:50069187-50070269;chr14:50070337-50074117		chr14:50070270-50070336			23.73
K	jcn_only_AD	CUFF.129	chr10	+	chr10:106937932-106970894	chr10:106961012-106970894					48.89
K	coord_cassette	CUFF.215	chr12	-	chr12:48272899-48298737	chr12:48272899-48276476;chr12:48276558-48293619;chr12:48293742-48298737		chr12:48276477-48276557;chr12:48293620-48293741			41.25
K	intron_retention	CUFF.1018	chr7	-	chr7:156469319-156471770				chr7:156469318-156469319;chr7:156471770-156471771		35.29
N	alternative_last_exon	CUFF.476	chr17	+	chr17:80442807-80446096	chr17:80442807-80443372	chr17:80446097-80448509	chr17:80443373-80443530			40.62
N	cassette	CUFF.611	chr2	-	chr2:73188378-73215386	chr2:73188378-73195576;chr2:73195663-73215386		chr2:73195577-73195662			21.18
N	intron_retention		chr2	+	chr2:220094703-220094949				chr2:220094702-220094703;chr2:220094949-220094950		94.20
N	jcn_only_AD	CUFF.633	chr2	-	chr2:110959072-110962476	chr2:110959072-110959949		chr2:110959950-110962476	chr2:110962476-110962477		4.04
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		22.61
K	intron_retention	CUFF.444	chr17	+	chr17:37822033-37822104				chr17:37822032-37822033;chr17:37822104-37822105		31.25
N	jcn_only_AA	CUFF.241	chr12	-	chr12:120128257-120135463	chr12:120128260-120135463		chr12:120128257-120128259	chr12:120128256-120128257		88.35
N	jcn_only_AA	CUFF.553	chr19	-	chr19:49116565-49117964	chr19:49117885-49117964		chr19:49116565-49117884	chr19:49116564-49116565		1.89
K	alternative_first_exon	CUFF.785	chr3	+	chr3:126152048-126153018	chr3:126152318-126153018	chr3:126151912-126152047	chr3:126152195-126152317		chr3:126153019-126153224	41.38
K	cassette	CUFF.291	chr14	-	chr14:92195824-92246919	chr14:92195824-92203037;chr14:92203194-92246919		chr14:92203038-92203193		chr14:92195745-92195823;chr14:92246920-92247139	50.00
N	alternative_acceptor		chr2	+	chr2:680152-696540	chr2:680152-681255		chr2:681256-696540	chr2:696540-696541		8.33
N	alternative_donor	CUFF.657	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		73.33
K	alternative_first_exon	CUFF.384	chr16	-	chr16:15186472-15188001	chr16:15186472-15187808	chr16:15188002-15188243	chr16:15187809-15187907			26.32
K	jcn_only_AD	CUFF.475	chr17	-	chr17:79994185-79994289	chr17:79994185-79994259		chr17:79994260-79994289	chr17:79994289-79994290		84.86
K	intron_retention	CUFF.377	chr16	-	chr16:4410365-4410444				chr16:4410364-4410365;chr16:4410444-4410445		10.11
N	jcn_only_AD		chr18	-	chr18:67614769-67628827;chr18:67614769-67623990	chr18:67614769-67623849		chr18:67623850-67623990;chr18:67623991-67628827	chr18:67623990-67623991;chr18:67628827-67628828		40.74
K	alternative_donor	CUFF.703	chr21	-	chr21:47556409-47556892;chr21:47556409-47556828	chr21:47556409-47556898		chr21:47556829-47556892;chr21:47556893-47556898	chr21:47556892-47556893;chr21:47556898-47556899		37.06
K	alternative_first_exon	CUFF.1036,CUFF.1057	chr8	-	chr8:69218834-69243541	chr8:69218834-69224378	chr8:69243542-69243726	chr8:69224379-69224536			91.04
K	intron_retention	CUFF.284	chr14	-	chr14:77270256-77270717				chr14:77270255-77270256;chr14:77270717-77270718		67.39
K	mutually_exclusive	CUFF.209	chr12	-	chr12:22666314-22672048,chr12:22672174-22676359	chr12:22666314-22670919,chr12:22671072-22676359	chr12:22672049-22672173	chr12:22670920-22671071			41.07
N	jcn_only_AA	CUFF.472	chr17	-	chr17:79479142-79479257	chr17:79479169-79479257		chr17:79479142-79479168	chr17:79479141-79479142		94.38
K	intron_retention	CUFF.209	chr12	-	chr12:22643153-22659644				chr12:22643152-22643153;chr12:22659644-22659645		5.61
N	alternative_donor	CUFF.160	chr11	+	chr11:61560501-61593503	chr11:61583899-61593503		chr11:61560501-61583898	chr11:61560500-61560501		0.00
N	alternative_acceptor		chr1	+	chr1:2005369-2066700	chr1:2005369-2029785		chr1:2029786-2066700	chr1:2066700-2066701		11.11
K	intron_retention	CUFF.907	chr6	+	chr6:2989968-2990102				chr6:2989967-2989968;chr6:2990102-2990103		73.53
K	cassette	CUFF.492	chr18	-	chr18:61071060-61077522	chr18:61071060-61074664;chr18:61074733-61077522		chr18:61074665-61074732		chr18:61070940-61071059;chr18:61077523-61077679	26.67
N	cassette	CUFF.24	chr1	+	chr1:54360221-54375603;chr1:54360221-54371767	chr1:54360221-54370338;chr1:54370483-54371767,chr1:54370483-54375603		chr1:54370339-54370482			85.08
N	intron_retention		chr2	-	chr2:242447551-242447919				chr2:242447550-242447551;chr2:242447919-242447920		41.18
K	intron_retention	CUFF.542	chr19	-	chr19:39924402-39926246				chr19:39924401-39924402;chr19:39926246-39926247		17.57
K	alternative_first_exon	CUFF.560	chr19	-	chr19:51528923-51530712;chr19:51528923-51529793;chr19:51528923-51529011	chr19:51528923-51531199	chr19:51530713-51530984;chr19:51529794-51530493;chr19:51529012-51529110	chr19:51531200-51531383			25.29
K	alternative_donor	CUFF.1018	chr7	-	chr7:156619439-156626446	chr7:156619439-156626432		chr7:156626433-156626446	chr7:156626446-156626447		19.34
N	alternative_acceptor	CUFF.394	chr16	+	chr16:31368423-31368654	chr16:31368423-31368573		chr16:31368574-31368654	chr16:31368654-31368655		23.08
K	alternative_first_exon	CUFF.237	chr12	-	chr12:102869578-102874096	chr12:102869578-102872264	chr12:102874097-102874378	chr12:102872265-102872513			94.01
K	intron_retention	CUFF.316	chr15	-	chr15:44888554-44888981				chr15:44888553-44888554;chr15:44888981-44888982		27.66
N	mutually_exclusive	CUFF.152	chr11	-	chr11:10827595-10828801,chr11:10828929-10830251	chr11:10827595-10828366,chr11:10828433-10830251	chr11:10828802-10828928	chr11:10828367-10828432			66.67
K	intron_retention	CUFF.1016	chr7	+	chr7:150817833-150820880				chr7:150817832-150817833;chr7:150820880-150820881		91.95
N	alternative_acceptor	CUFF.336,CUFF.340	chr15	+	chr15:74758472-74771400	chr15:74758472-74771384		chr15:74771385-74771400	chr15:74771400-74771401		8.89
N	cassette	CUFF.936	chr6	+	chr6:90333777-90337301	chr6:90333777-90334257;chr6:90334411-90337301		chr6:90334258-90334410			92.59
N	alternative_donor	CUFF.310	chr15	+	chr15:40532297-40532799;chr15:40509869-40532799;chr15:40531337-40532799	chr15:40532004-40532799		chr15:40509869-40531336;chr15:40531337-40532003;chr15:40532004-40532296	chr15:40509868-40509869;chr15:40531336-40531337;chr15:40532003-40532004		0.00
K	alternative_first_exon	CUFF.6	chr1	-	chr1:11710892-11715696;chr1:11710892-11714375	chr1:11710892-11713447	chr1:11715697-11715916;chr1:11714376-11714739	chr1:11713448-11713601			19.05
N	coord_cassette	CUFF.537	chr19	-	chr19:33904550-33968951	chr19:33904550-33953900;chr19:33953948-33954892;chr19:33954969-33968951		chr19:33953901-33953947;chr19:33954893-33954968			98.40
N	intron_retention		chr1	+	chr1:145578296-145578400				chr1:145578295-145578296;chr1:145578400-145578401		99.41
N	coord_cassette	CUFF.234	chr12	+	chr12:69207409-69233053	chr12:69207409-69218142;chr12:69218211-69218334;chr12:69218432-69233053		chr12:69218143-69218210;chr12:69218335-69218431			91.23
N	intron_retention		chr16	-	chr16:23478152-23478309				chr16:23478151-23478152;chr16:23478309-23478310		46.30
K	jcn_only_AD	CUFF.493	chr18	+	chr18:61323211-61377412	chr18:61370241-61377412					86.49
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55722109-55833019	chr18:55816792-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		1.76
N	alternative_donor	CUFF.606,CUFF.622	chr2	-	chr2:68374700-68384392;chr2:68374700-68384505	chr2:68374700-68384058		chr2:68384059-68384392;chr2:68384393-68384505	chr2:68384392-68384393;chr2:68384505-68384506		23.64
N	intron_retention		chr2	+	chr2:3469467-3482616				chr2:3469466-3469467;chr2:3482616-3482617		53.06
K	intron_retention	CUFF.1009	chr7	+	chr7:128848693-128849129				chr7:128848692-128848693;chr7:128849129-128849130		60.00
N	cassette	CUFF.342	chr15	-	chr15:78487069-78526712	chr15:78487069-78500343;chr15:78500445-78526712		chr15:78500344-78500444			88.00
N	jcn_only_AD	CUFF.704	chr22	-	chr22:51015464-51015784	chr22:51015464-51015752		chr22:51015753-51015784	chr22:51015784-51015785		88.19
K	intron_retention	CUFF.601	chr2	-	chr2:46842325-46844108				chr2:46842324-46842325;chr2:46844108-46844109		62.57
K	alternative_first_exon	CUFF.763,CUFF.786	chr3	-	chr3:127299007-127306912,chr3:127299007-127310732;chr3:127299007-127309252;chr3:127299007-127309725	chr3:127299007-127313642	chr3:127309253-127309667;chr3:127309726-127309965	chr3:127313643-127313776			21.56
K	jcn_only_AD	CUFF.1135	chrX	-	chrX:106224708-106235517	chrX:106224708-106228325					57.14
N	jcn_only_AD	CUFF.225	chr12	+	chr12:53846760-53848509;chr12:53846161-53848509;chr12:53847068-53848509	chr12:53837558-53848509		chr12:53837558-53846160;chr12:53846161-53846759;chr12:53846760-53847067	chr12:53837557-53837558;chr12:53846160-53846161;chr12:53846759-53846760		3.39
N	cassette	CUFF.385	chr16	+	chr16:19584564-19590373	chr16:19584564-19586419;chr16:19586445-19590373		chr16:19586420-19586444			85.29
N	alternative_acceptor		chr7	-	chr7:37382368-37488277	chr7:37433521-37488277		chr7:37382368-37433520	chr7:37382367-37382368		0.00
K	cassette	CUFF.1104	chr9	+	chr9:137772768-137775147	chr9:137772768-137774371;chr9:137774486-137775147		chr9:137774372-137774485			28.57
K	cassette	CUFF.900	chr5	-	chr5:149785885-149786714	chr5:149785885-149786443;chr5:149786524-149786714		chr5:149786444-149786523			91.93
K	alternative_first_exon	CUFF.449	chr17	-	chr17:46685458-46687880;chr17:46685458-46710875	chr17:46685458-46685590	chr17:46687881-46688379;chr17:46710876-46710987	chr17:46685591-46685727			25.00
K	intron_retention	CUFF.707	chr22	+	chr22:20753981-20754921				chr22:20753980-20753981;chr22:20754921-20754922		4.08
N	cassette	CUFF.176	chr11	-	chr11:102937297-102962515	chr11:102937297-102953984;chr11:102954056-102962515		chr11:102953985-102954055			83.54
K	intron_retention	CUFF.228	chr12	-	chr12:56577715-56577958				chr12:56577714-56577715;chr12:56577958-56577959		1.15
K	cassette	CUFF.228	chr12	-	chr12:56575864-56577958	chr12:56575864-56577644;chr12:56577715-56577958		chr12:56577645-56577714			62.57
K	intron_retention	CUFF.232	chr12	+	chr12:58018577-58018648				chr12:58018576-58018577;chr12:58018648-58018649		64.62
K	cassette	CUFF.278	chr14	-	chr14:75143456-75149998	chr14:75143456-75144881;chr14:75145033-75149998		chr14:75144882-75145032		chr14:75143286-75143455;chr14:75149999-75150236	31.08
N	mutually_exclusive	CUFF.946	chr6	-	chr6:133046119-133049879,chr6:133050119-133055391	chr6:133046119-133047860,chr6:133048152-133055391	chr6:133049880-133050118	chr6:133047861-133048151			52.00
N	alternative_acceptor		chr16	-	chr16:57513598-57517869	chr16:57513601-57517869		chr16:57513598-57513600	chr16:57513597-57513598		74.19
N	jcn_only_AD	CUFF.363	chr16	+	chr16:105543-105793	chr16:105550-105793		chr16:105543-105549	chr16:105542-105543		63.64
K	alternative_acceptor	CUFF.1112	chrX	-	chrX:2408811-2418857	chrX:2408814-2418857		chrX:2408811-2408813	chrX:2408810-2408811		85.71
K	alternative_last_exon	CUFF.980,CUFF.989	chr7	+	chr7:73112025-73117708	chr7:73112025-73112161	chr7:73117709-73119588	chr7:73112162-73112625			81.20
N	intron_retention		chr15	-	chr15:84874072-84898653				chr15:84874071-84874072;chr15:84898653-84898654		55.56
N	jcn_only_AD	CUFF.102	chr10	+	chr10:35464928-35467816;chr10:35437420-35467816;chr10:35416122-35467816;chr10:35456732-35467816;chr10:35464634-35467816	chr10:35426808-35467816		chr10:35416122-35426807;chr10:35426808-35437419;chr10:35437420-35456731;chr10:35456732-35464633;chr10:35464634-35464927	chr10:35416121-35416122;chr10:35426807-35426808;chr10:35437419-35437420;chr10:35456731-35456732;chr10:35464633-35464634		2.11
K	alternative_first_exon	CUFF.817	chr4	-	chr4:6114725-6201979	chr4:6114725-6196217	chr4:6201980-6202282	chr4:6196218-6196376			40.48
N	cassette	CUFF.457	chr17	+	chr17:61571832-61574158	chr17:61571832-61573754;chr17:61573878-61574158		chr17:61573755-61573877			79.28
N	jcn_only_AA	CUFF.497	chr18	-	chr18:67614769-67623990;chr18:67614670-67623990	chr18:67563282-67623990		chr18:67563282-67614669;chr18:67614670-67614768	chr18:67563281-67563282;chr18:67614669-67614670		25.00
N	jcn_only_AA		chr7	+	chr7:91730371-91732000	chr7:91730371-91731907		chr7:91731908-91732000	chr7:91732000-91732001		52.43
N	alternative_donor	CUFF.769	chr3	+	chr3:119205780-119207775	chr3:119205884-119207775		chr3:119205780-119205883	chr3:119205779-119205780		48.15
N	intron_retention		chr11	+	chr11:118402915-118403049				chr11:118402914-118402915;chr11:118403049-118403050	chr11:118402865-118402914;chr11:118403050-118403176	95.38
N	intron_retention		chr15	+	chr15:40531337-40532799				chr15:40531336-40531337;chr15:40532799-40532800		72.73
N	jcn_only_AA	CUFF.195	chr12	-	chr12:332401-344255	chr12:336835-344255					86.00
N	intron_retention		chr7	+	chr7:73111847-73111934				chr7:73111846-73111847;chr7:73111934-73111935		30.77
K	alternative_first_exon	CUFF.20	chr1	-	chr1:33631168-33646625	chr1:33631168-33642008	chr1:33646626-33647267	chr1:33642009-33642229			55.93
N	mutually_exclusive	CUFF.184	chr11	-	chr11:118926284-118926781,chr11:118926880-118927785	chr11:118926284-118926461,chr11:118926556-118927785	chr11:118926782-118926879	chr11:118926462-118926555			84.44
N	jcn_only_AD	CUFF.879	chr5	-	chr5:60214216-60217880	chr5:60214216-60214338		chr5:60214339-60217880	chr5:60217880-60217881		32.61
N	jcn_only_AA	CUFF.273	chr14	+	chr14:61512886-61514965;chr14:61512886-61517229	chr14:61512886-61514868		chr14:61514869-61514965;chr14:61514966-61517229	chr14:61514965-61514966;chr14:61517229-61517230		6.98
N	jcn_only_AA		chr14	+	chr14:76368568-76372897;chr14:76368568-76407766	chr14:76368568-76420766					9.80
K	alternative_first_exon	CUFF.712	chr22	+	chr22:24698353-24709280	chr22:24700421-24709280	chr22:24698163-24698352	chr22:24700330-24700420		chr22:24709281-24709434	20.83
K	jcn_only_AD	CUFF.473	chr17	-	chr17:79894738-79895137;chr17:79894738-79895055	chr17:79894738-79895133		chr17:79895056-79895133;chr17:79895134-79895137	chr17:79895133-79895134;chr17:79895137-79895138	chr17:79894624-79894737;chr17:79895138-79895264	35.88
N	intron_retention		chr3	-	chr3:120360541-120365819				chr3:120360540-120360541;chr3:120365819-120365820		71.43
K	intron_retention	CUFF.998	chr7	-	chr7:102246435-102249207				chr7:102246434-102246435;chr7:102249207-102249208		20.56
K	intron_retention	CUFF.1016	chr7	+	chr7:150820974-150825666				chr7:150820973-150820974;chr7:150825666-150825667		26.64
N	alternative_donor	CUFF.490	chr18	+	chr18:55912741-55916130	chr18:55914857-55916130		chr18:55912741-55914856	chr18:55912740-55912741		2.65
N	cassette	CUFF.998	chr7	-	chr7:102249902-102257071	chr7:102249902-102251532;chr7:102251590-102257071		chr7:102251533-102251589			69.49
K	intron_retention	CUFF.410	chr16	-	chr16:75589872-75589968				chr16:75589871-75589872;chr16:75589968-75589969		27.81
N	cassette	CUFF.102	chr10	+	chr10:35464634-35477127	chr10:35464634-35468061;chr10:35468205-35477127		chr10:35468062-35468204			91.92
K	alternative_first_exon	CUFF.464	chr17	+	chr17:66509112-66511127;chr17:66508284-66511127	chr17:66509120-66511127	chr17:66507921-66508283	chr17:66508946-66509119			30.00
K	intron_retention		chr16	+	chr16:70389439-70390014				chr16:70389438-70389439;chr16:70390014-70390015		27.13
N	jcn_only_AA	CUFF.633	chr2	-	chr2:110959072-110962476	chr2:110960057-110962476		chr2:110959072-110960056	chr2:110959071-110959072		5.00
K	intron_retention	CUFF.13	chr1	-	chr1:27425496-27425702				chr1:27425495-27425496;chr1:27425702-27425703		69.57
K	intron_retention	CUFF.402	chr16	-	chr16:67218714-67218804				chr16:67218713-67218714;chr16:67218804-67218805		79.17
N	alternative_donor	CUFF.317	chr15	-	chr15:84874072-84898653	chr15:84874072-84898603		chr15:84898604-84898653	chr15:84898653-84898654		66.67
K	intron_retention		chr17	+	chr17:25969375-25970550				chr17:25969374-25969375;chr17:25970550-25970551		16.18
N	jcn_only_AD	CUFF.531	chr19	+	chr19:17611442-17615263;chr19:17611686-17615263	chr19:17612229-17615263		chr19:17611442-17611685;chr19:17611686-17612228	chr19:17611441-17611442;chr19:17611685-17611686		28.17
K	alternative_last_exon	CUFF.1092	chr9	-	chr9:123515590-123533625	chr9:123527126-123533625	chr9:123514170-123515589	chr9:123526367-123527125		chr9:123533626-123533795	66.67
K	intron_retention	CUFF.259	chr14	+	chr14:24569423-24571961				chr14:24569422-24569423;chr14:24571961-24571962		21.08
K	cassette	CUFF.944	chr6	+	chr6:126329619-126332398	chr6:126329619-126329802;chr6:126329892-126332398		chr6:126329803-126329891			13.46
N	intron_retention	CUFF.1148	chrX	-	chrX:152988744-152989470				chrX:152988743-152988744;chrX:152989470-152989471		61.76
N	jcn_only_AD	CUFF.914	chr6	+	chr6:29943295-29945430	chr6:29945281-29945430		chr6:29943295-29945280	chr6:29943294-29943295		35.00
N	jcn_only_AA		chr14	+	chr14:76174051-76184203	chr14:76174051-76175521					86.96
K	alternative_first_exon	CUFF.449	chr17	-	chr17:46685458-46687880;chr17:46685458-46685590	chr17:46685458-46710875	chr17:46687881-46688379;chr17:46685591-46685727	chr17:46710876-46710987			19.44
N	jcn_only_AD	CUFF.1013	chr7	+	chr7:136554166-136676933	chr7:136635828-136676933		chr7:136554166-136635827	chr7:136554165-136554166		23.53
N	alternative_donor	CUFF.28	chr1	+	chr1:70832012-70832126;chr1:70820795-70832126;chr1:70820892-70832126	chr1:70820791-70832126		chr1:70820791-70820794;chr1:70820795-70820891;chr1:70820892-70832011	chr1:70820790-70820791;chr1:70820794-70820795;chr1:70820891-70820892		68.42
N	jcn_only_AD	CUFF.1115,CUFF.1135	chrX	-	chrX:13825889-13834962	chrX:13825889-13830989		chrX:13830990-13834962	chrX:13834962-13834963		27.87
N	jcn_only_AA	CUFF.581	chr2	-	chr2:4009394-4021134;chr2:4015879-4021134;chr2:4020693-4021134;chr2:4009485-4021134	chr2:4020665-4021134		chr2:4009394-4009484;chr2:4009485-4015878;chr2:4015879-4020664;chr2:4020665-4020692	chr2:4009393-4009394;chr2:4009484-4009485;chr2:4015878-4015879;chr2:4020664-4020665		22.38
K	intron_retention		chr16	-	chr16:23505700-23507014				chr16:23505699-23505700;chr16:23507014-23507015	chr16:23505624-23505699;chr16:23507015-23507099	2.73
K	intron_retention	CUFF.347	chr15	-	chr15:83357251-83357487				chr15:83357250-83357251;chr15:83357487-83357488		16.51
N	alternative_last_exon	CUFF.1061	chr8	+	chr8:74891097-74893389	chr8:74891097-74891313	chr8:74893390-74895115	chr8:74891314-74891406			95.45
K	intron_retention	CUFF.1008	chr7	-	chr7:127251731-127251998				chr7:127251730-127251731;chr7:127251998-127251999		24.14
N	cassette	CUFF.485	chr18	-	chr18:44272219-44336340	chr18:44272219-44284534;chr18:44284628-44336340		chr18:44284535-44284627			83.87
K	jcn_only_AD	CUFF.147	chr11	-	chr11:5685404-5686885	chr11:5685404-5686398		chr11:5686399-5686885	chr11:5686885-5686886		15.38
N	jcn_only_AA		chr12	-	chr12:49334972-49350767	chr12:49350134-49350767		chr12:49334972-49350133	chr12:49334971-49334972		40.91
K	alternative_last_exon	CUFF.1135	chrX	-	chrX:106059017-106236459;chrX:106229431-106236459	chrX:106235661-106236459	chrX:106057101-106059016;chrX:106229213-106229430	chrX:106235518-106235660			26.67
K	alternative_last_exon	CUFF.9	chr1	-	chr1:16934187-16935002;chr1:16921509-16935002	chr1:16928339-16935002	chr1:16921426-16921508	chr1:16925990-16928338			83.03
K	cassette	CUFF.136	chr11	-	chr11:406539-407061	chr11:406539-406842;chr11:406994-407061		chr11:406843-406993			66.49
N	jcn_only_AA	CUFF.579	chr2	+	chr2:3461465-3464033	chr2:3461465-3461565		chr2:3461566-3464033	chr2:3464033-3464034		13.21
K	intron_retention	CUFF.566	chr19	+	chr19:54657578-54657680				chr19:54657577-54657578;chr19:54657680-54657681		88.89
N	alternative_donor	CUFF.176	chr11	-	chr11:102960048-102962412;chr11:102960048-102962244	chr11:102960048-102962515		chr11:102962245-102962412;chr11:102962413-102962515	chr11:102962412-102962413;chr11:102962515-102962516		67.44
N	cassette	CUFF.946	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			51.43
N	jcn_only_AD	CUFF.820	chr4	+	chr4:6912329-6925099;chr4:6911679-6925099	chr4:6911233-6925099		chr4:6911233-6911678;chr4:6911679-6912328	chr4:6911232-6911233;chr4:6911678-6911679		86.00
N	alternative_last_exon		chr17	+	chr17:61907862-61908395	chr17:61907862-61908168	chr17:61908396-61908586	chr17:61908169-61908295			98.69
N	jcn_only_AA	CUFF.929	chr6	-	chr6:43481372-43483332	chr6:43483045-43483332		chr6:43481372-43483044	chr6:43481371-43481372		1.85
K	cassette	CUFF.1033	chr8	-	chr8:56668971-56685827	chr8:56668971-56676494;chr8:56676540-56685827		chr8:56676495-56676539			77.88
N	jcn_only_AD	CUFF.823	chr4	+	chr4:20570628-20591266	chr4:20574884-20591266		chr4:20570628-20574883	chr4:20570627-20570628		22.22
K	alternative_last_exon	CUFF.1099	chr9	+	chr9:131015417-131016932	chr9:131015417-131016287	chr9:131016933-131017615	chr9:131016288-131016510			25.00
N	jcn_only_AD	CUFF.464	chr17	+	chr17:66511708-66518896	chr17:66511718-66518896		chr17:66511708-66511717	chr17:66511707-66511708		98.87
K	alternative_first_exon	CUFF.1013	chr7	+	chr7:136553865-136554007;chr7:136553740-136554007	chr7:136553921-136554007	chr7:136553416-136553739	chr7:136553798-136553920			23.03
K	jcn_only_AA	CUFF.626,CUFF.666	chr2	+	chr2:232258622-232259491	chr2:232258622-232259365		chr2:232259366-232259491	chr2:232259491-232259492		48.98
K	intron_retention	CUFF.184	chr11	-	chr11:118919083-118919187				chr11:118919082-118919083;chr11:118919187-118919188		39.20
N	cassette	CUFF.1098	chr9	-	chr9:130948056-130952607;chr9:130948056-130952966	chr9:130948056-130950141;chr9:130950214-130952607,chr9:130950214-130952966		chr9:130950142-130950213			64.14
K	intron_retention	CUFF.988	chr7	-	chr7:86541488-86542256				chr7:86541487-86541488;chr7:86542256-86542257		85.88
N	intron_retention		chr6	-	chr6:31939459-31939705				chr6:31939458-31939459;chr6:31939705-31939706		86.50
N	intron_retention		chr7	-	chr7:107643417-107643555				chr7:107643416-107643417;chr7:107643555-107643556		58.18
K	alternative_first_exon	CUFF.3	chr1	+	chr1:10490626-10493898	chr1:10491459-10493898	chr1:10490073-10490625	chr1:10490809-10491458			46.43
K	alternative_first_exon	CUFF.641	chr2	+	chr2:169711971-169713199	chr2:169712721-169713199	chr2:169711862-169711970	chr2:169712622-169712720			8.12
N	jcn_only_AA	CUFF.734	chr3	+	chr3:19992554-20017092;chr3:19992554-20017078;chr3:19992554-20012039	chr3:19992554-20017134		chr3:20012040-20017078;chr3:20017079-20017092;chr3:20017093-20017134	chr3:20017078-20017079;chr3:20017092-20017093;chr3:20017134-20017135		4.17
N	alternative_donor		chr22	-	chr22:51016364-51016512;chr22:51016364-51016814	chr22:51016364-51016977		chr22:51016513-51016814;chr22:51016815-51016977	chr22:51016814-51016815;chr22:51016977-51016978		65.75
N	jcn_only_AD		chr22	+	chr22:45148508-45173041	chr22:45148621-45173041		chr22:45148508-45148620	chr22:45148507-45148508		71.43
K	intron_retention		chr2	+	chr2:220094623-220096649				chr2:220094622-220094623;chr2:220096649-220096650		39.71
N	intron_retention		chr17	-	chr17:15546131-15580489				chr17:15546130-15546131;chr17:15580489-15580490		61.36
K	alternative_last_exon	CUFF.887	chr5	-	chr5:127396337-127396835;chr5:127292614-127396835;chr5:127359991-127396835	chr5:127302621-127396835	chr5:127292496-127292613;chr5:127359827-127359990	chr5:127301504-127302620			36.00
K	intron_retention	CUFF.227	chr12	-	chr12:54757644-54758176				chr12:54757643-54757644;chr12:54758176-54758177		50.00
K	alternative_first_exon	CUFF.774	chr3	+	chr3:119501148-119526075	chr3:119501700-119526075	chr3:119499331-119501147	chr3:119501494-119501699			62.86
N	jcn_only_AA	CUFF.716	chr22	+	chr22:29668421-29669729;chr22:29668421-29674119	chr22:29668421-29669726		chr22:29669727-29669729;chr22:29669730-29674119	chr22:29669729-29669730;chr22:29674119-29674120		19.20
N	alternative_donor	CUFF.509	chr19	-	chr19:6047516-6148241;chr19:6047516-6049146;chr19:6047516-6110403;chr19:6047516-6057172	chr19:6047516-6072015		chr19:6049147-6057172;chr19:6057173-6072015;chr19:6072016-6110403;chr19:6110404-6148241	chr19:6057172-6057173;chr19:6072015-6072016;chr19:6110403-6110404;chr19:6148241-6148242		0.00
N	alternative_donor		chr3	-	chr3:33467234-33482168	chr3:33467234-33481227		chr3:33481228-33482168	chr3:33482168-33482169		13.64
N	alternative_acceptor		chr22	+	chr22:37697061-37699294;chr22:37697061-37697975	chr22:37697061-37697921		chr22:37697922-37697975;chr22:37697976-37699294	chr22:37697975-37697976;chr22:37699294-37699295		78.43
N	jcn_only_AD	CUFF.28	chr1	+	chr1:70832012-70832126;chr1:70820795-70832126;chr1:70820791-70832126	chr1:70820892-70832126		chr1:70820791-70820794;chr1:70820795-70820891;chr1:70820892-70832011	chr1:70820790-70820791;chr1:70820794-70820795;chr1:70820891-70820892		22.01
N	alternative_acceptor	CUFF.633	chr2	-	chr2:110959072-110962476	chr2:110960057-110962476		chr2:110959072-110960056	chr2:110959071-110959072		1.04
N	jcn_only_AA	CUFF.1000,CUFF.980	chr7	+	chr7:73108381-73111795;chr7:73108381-73111934	chr7:73108381-73110735		chr7:73110736-73111795;chr7:73111796-73111934	chr7:73111795-73111796;chr7:73111934-73111935		12.20
N	intron_retention	CUFF.728	chr22	-	chr22:51020292-51020457				chr22:51020291-51020292;chr22:51020457-51020458		38.46
N	jcn_only_AA	CUFF.919	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		30.10
N	jcn_only_AD	CUFF.155	chr11	+	chr11:36383732-36415395;chr11:36398255-36415395	chr11:36322621-36415395		chr11:36322621-36383731;chr11:36383732-36398254	chr11:36322620-36322621;chr11:36383731-36383732		2.98
K	coord_cassette	CUFF.845	chr4	-	chr4:99428880-99578690	chr4:99428880-99495607;chr4:99495734-99495894;chr4:99496057-99578690		chr4:99495608-99495733;chr4:99495895-99496056			86.89
K	intron_retention	CUFF.1070	chr9	-	chr9:35074430-35076518				chr9:35074429-35074430;chr9:35076518-35076519		8.46
N	jcn_only_AD	CUFF.579	chr2	+	chr2:3392442-3405547	chr2:3393551-3405547		chr2:3392442-3393550	chr2:3392441-3392442		49.37
K	alternative_last_exon	CUFF.550	chr19	+	chr19:44771115-44777051;chr19:44771115-44771532	chr19:44771115-44777457	chr19:44777052-44777453;chr19:44771533-44772456	chr19:44777458-44779568			29.25
N	jcn_only_AA	CUFF.303	chr15	+	chr15:24825478-24869114	chr15:24825478-24832713		chr15:24832714-24869114	chr15:24869114-24869115		2.99
N	intron_retention		chr19	+	chr19:17452543-17452964				chr19:17452542-17452543;chr19:17452964-17452965		63.64
K	alternative_first_exon	CUFF.934	chr6	+	chr6:88066222-88074678	chr6:88068920-88074678	chr6:88065834-88066221	chr6:88068775-88068919			32.00
K	intron_retention	CUFF.177	chr11	-	chr11:104915386-104916017				chr11:104915385-104915386;chr11:104916017-104916018		53.57
N	intron_retention		chr11	-	chr11:6632684-6633294				chr11:6632683-6632684;chr11:6633294-6633295		45.70
K	jcn_only_AD	CUFF.682	chr20	-	chr20:30009482-30011622	chr20:30009482-30011612		chr20:30011613-30011622	chr20:30011622-30011623		82.19
N	intron_retention		chr17	+	chr17:25969375-25972339				chr17:25969374-25969375;chr17:25972339-25972340		47.83
N	alternative_donor	CUFF.734	chr3	+	chr3:19992554-20017092	chr3:20012210-20017092		chr3:19992554-20012209	chr3:19992553-19992554		0.00
K	cassette	CUFF.360	chr15	-	chr15:102226266-102241288	chr15:102226266-102239533;chr15:102239639-102241288		chr15:102239534-102239638			8.51
K	intron_retention	CUFF.236	chr12	-	chr12:77254194-77256955				chr12:77254193-77254194;chr12:77256955-77256956		40.32
N	intron_retention		chr11	-	chr11:10821716-10821790				chr11:10821715-10821716;chr11:10821790-10821791		84.62
K	alternative_last_exon	CUFF.493	chr18	+	chr18:61377596-61390228	chr18:61377596-61378568	chr18:61390229-61391225	chr18:61378569-61378628			61.19
K	jcn_only_AD	CUFF.187	chr11	+	chr11:119056220-119056630	chr11:119056338-119056630		chr11:119056220-119056337	chr11:119056219-119056220		8.82
N	jcn_only_AA		chr1	+	chr1:2005369-2066700	chr1:2005369-2029785		chr1:2029786-2066700	chr1:2066700-2066701		30.43
K	alternative_first_exon	CUFF.838	chr4	-	chr4:77987559-77996251;chr4:77987559-77996624	chr4:77987559-77995942	chr4:77996625-77997233	chr4:77995943-77996097			16.98
K	intron_retention	CUFF.195	chr12	-	chr12:333283-333566				chr12:333282-333283;chr12:333566-333567		20.00
N	alternative_acceptor	CUFF.125	chr10	+	chr10:35485028-35495822	chr10:35485028-35490378		chr10:35490379-35495822	chr10:35495822-35495823		1.82
K	intron_retention	CUFF.146	chr11	+	chr11:3405515-3418346				chr11:3405514-3405515;chr11:3418346-3418347		13.38
N	jcn_only_AD	CUFF.342	chr15	-	chr15:78501592-78537610	chr15:78501592-78504890		chr15:78504891-78537610	chr15:78537610-78537611		15.38
K	alternative_first_exon	CUFF.415	chr16	+	chr16:89787685-89788938;chr16:89786991-89788938	chr16:89788254-89788938	chr16:89787360-89787684;chr16:89786808-89786990	chr16:89787884-89788253			60.40
N	alternative_donor	CUFF.1102	chr9	+	chr9:133346903-133352257	chr9:133351777-133352257		chr9:133346903-133351776	chr9:133346902-133346903		1.92
K	alternative_acceptor	CUFF.961	chr7	+	chr7:6630107-6631333	chr7:6630107-6631276		chr7:6631277-6631333	chr7:6631333-6631334		38.89
K	cassette	CUFF.999	chr7	-	chr7:102462651-102495223	chr7:102462651-102473286;chr7:102473422-102495223		chr7:102473287-102473421			34.82
N	jcn_only_AA	CUFF.768,CUFF.769	chr3	+	chr3:119196296-119198897;chr3:119196296-119198754	chr3:119196296-119197180		chr3:119197181-119198754;chr3:119198755-119198897	chr3:119198754-119198755;chr3:119198897-119198898		43.75
N	jcn_only_AA	CUFF.765	chr3	-	chr3:107559252-107560951	chr3:107560867-107560951		chr3:107559252-107560866	chr3:107559251-107559252		60.00
N	jcn_only_AD	CUFF.502	chr18	+	chr18:77867357-77875412	chr18:77867906-77875412		chr18:77867357-77867905	chr18:77867356-77867357		37.50
N	jcn_only_AD	CUFF.820	chr4	+	chr4:6911233-6925099;chr4:6911679-6925099	chr4:6912329-6925099		chr4:6911233-6911678;chr4:6911679-6912328	chr4:6911232-6911233;chr4:6911678-6911679		12.00
N	intron_retention	CUFF.426	chr17	-	chr17:15584268-15586174				chr17:15584267-15584268;chr17:15586174-15586175		60.61
K	cassette	CUFF.34	chr1	-	chr1:106148712-106161480	chr1:106148712-106155521;chr1:106155567-106161480		chr1:106155522-106155566			68.75
K	alternative_donor	CUFF.944	chr6	+	chr6:126342412-126359850	chr6:126342427-126359850		chr6:126342412-126342426	chr6:126342411-126342412		84.85
N	cassette	CUFF.234	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			26.97
N	alternative_donor	CUFF.722	chr22	+	chr22:37705365-37707028	chr22:37706074-37707028		chr22:37705365-37706073	chr22:37705364-37705365		34.78
K	intron_retention		chr4	-	chr4:83821377-83821486				chr4:83821376-83821377;chr4:83821486-83821487		2.05
N	alternative_acceptor	CUFF.1062	chr8	+	chr8:144375236-144377909	chr8:144375236-144377548		chr8:144377549-144377909	chr8:144377909-144377910		0.40
N	cassette	CUFF.829	chr4	-	chr4:56466743-56473464;chr4:56466743-56473603	chr4:56466743-56471441;chr4:56471517-56473603,chr4:56471517-56473464		chr4:56471442-56471516			85.62
N	jcn_only_AA	CUFF.178	chr11	+	chr11:107944225-107948902	chr11:107944225-107944526		chr11:107944527-107948902	chr11:107948902-107948903		80.00
N	intron_retention		chr2	-	chr2:242436794-242437030				chr2:242436793-242436794;chr2:242437030-242437031		38.46
N	alternative_acceptor	CUFF.1110	chrX	+	chrX:1424421-1428294	chrX:1424421-1424520		chrX:1424521-1428294	chrX:1428294-1428295		5.10
K	cassette	CUFF.263	chr14	+	chr14:39944160-39961458	chr14:39944160-39954220;chr14:39954462-39961458		chr14:39954221-39954461			26.51
K	cassette	CUFF.943	chr6	-	chr6:116973356-116979965	chr6:116973356-116977846;chr6:116978016-116979965		chr6:116977847-116978015			76.47
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		15.15
N	alternative_first_exon	CUFF.936	chr6	+	chr6:90143095-90305634	chr6:90276816-90305634	chr6:90142889-90143094	chr6:90276553-90276815			94.05
N	coord_cassette	CUFF.478	chr18	+	chr18:163454-180235	chr18:163454-166786;chr18:166820-178932;chr18:179038-180235		chr18:166787-166819;chr18:178933-179037			57.14
N	jcn_only_AA	CUFF.884	chr5	-	chr5:82969369-83016607	chr5:82971157-83016607		chr5:82969369-82971156	chr5:82969368-82969369		75.00
K	alternative_acceptor	CUFF.324	chr15	-	chr15:55790009-55790404	chr15:55790058-55790404		chr15:55790009-55790057	chr15:55790008-55790009		63.25
N	jcn_only_AA		chr5	+	chr5:36163859-36177066	chr5:36163859-36166620				chr5:36163747-36163858	84.72
K	jcn_only_AA	CUFF.241	chr12	-	chr12:120172163-120172964	chr12:120172212-120172964		chr12:120172163-120172211	chr12:120172162-120172163		90.64
K	alternative_last_exon	CUFF.364	chr16	+	chr16:583999-597558	chr16:583999-596816	chr16:597559-598307	chr16:596817-597466			38.46
K	intron_retention		chr17	-	chr17:56082403-56082774				chr17:56082402-56082403;chr17:56082774-56082775		98.85
K	alternative_last_exon	CUFF.486	chr18	-	chr18:44395313-44400895	chr18:44398411-44400895	chr18:44395275-44395312	chr18:44398068-44398410			75.00
K	intron_retention	CUFF.195	chr12	-	chr12:335681-335818				chr12:335680-335681;chr12:335818-335819		26.32
K	intron_retention	CUFF.152	chr11	-	chr11:10825751-10825833				chr11:10825750-10825751;chr11:10825833-10825834		60.85
N	alternative_donor	CUFF.385	chr16	+	chr16:19566643-19576172	chr16:19567069-19576172		chr16:19566643-19567068	chr16:19566642-19566643		80.95
K	alternative_first_exon	CUFF.371	chr16	+	chr16:2190951-2199941	chr16:2198980-2199941	chr16:2190733-2190950	chr16:2198793-2198979			74.36
K	alternative_first_exon	CUFF.134	chr10	-	chr10:127541212-127548171	chr10:127541212-127542529	chr10:127548172-127548544	chr10:127542530-127543428			92.98
K	alternative_donor	CUFF.1040	chr8	+	chr8:75263557-75272371	chr8:75263702-75272371		chr8:75263557-75263701	chr8:75263556-75263557		84.00
N	jcn_only_AD	CUFF.197	chr12	+	chr12:1742072-1754959;chr12:1754228-1754959	chr12:1749143-1754959					38.60
N	jcn_only_AD	CUFF.217	chr12	-	chr12:48381493-48383010	chr12:48381493-48382208		chr12:48382209-48383010	chr12:48383010-48383011		28.57
N	jcn_only_AD		chr2	+	chr2:101609990-101612257	chr2:101611043-101612257		chr2:101609990-101611042	chr2:101609989-101609990		33.33
K	cassette	CUFF.817	chr4	-	chr4:6066736-6081898	chr4:6066736-6080665;chr4:6080726-6081898		chr4:6080666-6080725			92.94
N	intron_retention		chr2	-	chr2:263369-264781				chr2:263368-263369;chr2:264781-264782		21.43
N	alternative_first_exon	CUFF.188	chr11	-	chr11:119244232-119246933;chr11:119244232-119252182	chr11:119244232-119249716	chr11:119246934-119247108;chr11:119252183-119252421	chr11:119249717-119249914			54.88
K	intron_retention	CUFF.917	chr6	+	chr6:31795803-31796033				chr6:31795802-31795803;chr6:31796033-31796034		38.10
N	intron_retention		chr17	+	chr17:29701148-29705905				chr17:29701147-29701148;chr17:29705905-29705906		68.57
N	alternative_acceptor	CUFF.165,CUFF.168	chr11	+	chr11:65479751-65479849	chr11:65479751-65479820		chr11:65479821-65479849	chr11:65479849-65479850		66.98
K	intron_retention		chr2	-	chr2:253116-263983				chr2:253115-253116;chr2:263983-263984		21.43
N	alternative_donor	CUFF.225	chr12	+	chr12:53846760-53848509;chr12:53847068-53848509;chr12:53837558-53848509	chr12:53846161-53848509		chr12:53837558-53846160;chr12:53846161-53846759;chr12:53846760-53847067	chr12:53837557-53837558;chr12:53846160-53846161;chr12:53846759-53846760		20.00
N	jcn_only_AD		chr17	+	chr17:29706376-29708890;chr17:29707246-29708890	chr17:29706042-29708890					25.32
N	jcn_only_AA	CUFF.385	chr16	+	chr16:19576273-19580745	chr16:19576273-19580565		chr16:19580566-19580745	chr16:19580745-19580746		5.36
N	coord_cassette	CUFF.17	chr1	+	chr1:31769923-31791955	chr1:31769923-31782890;chr1:31783012-31791013;chr1:31791084-31791955		chr1:31782891-31783011;chr1:31791014-31791083			89.29
N	alternative_acceptor	CUFF.755	chr3	+	chr3:186743306-186756529	chr3:186743306-186756182		chr3:186756183-186756529	chr3:186756529-186756530		2.86
K	jcn_only_AD	CUFF.262	chr14	-	chr14:31355533-31358348	chr14:31355533-31358325		chr14:31358326-31358348	chr14:31358348-31358349		37.50
N	jcn_only_AD	CUFF.336	chr15	+	chr15:74754440-74758376;chr15:74754369-74758376	chr15:74754373-74758376		chr15:74754369-74754372;chr15:74754373-74754439	chr15:74754368-74754369;chr15:74754372-74754373		77.59
K	alternative_donor	CUFF.505	chr19	-	chr19:2427323-2427456	chr19:2427323-2427411		chr19:2427412-2427456	chr19:2427456-2427457		12.00
K	alternative_first_exon	CUFF.486	chr18	-	chr18:44486279-44497964;chr18:44486279-44500021	chr18:44486279-44497284	chr18:44497965-44498061;chr18:44500022-44500200	chr18:44497285-44497510			50.70
K	alternative_last_exon	CUFF.208	chr12	+	chr12:21220318-21229385	chr12:21220318-21228193	chr12:21229386-21229503	chr12:21228194-21228760		chr12:21220238-21220317	35.45
K	alternative_donor	CUFF.894	chr5	+	chr5:139917820-139918503	chr5:139917847-139918503		chr5:139917820-139917846	chr5:139917819-139917820	chr5:139918504-139918668;chr5:139917671-139917819	25.29
N	alternative_donor		chr3	-	chr3:125741776-125745235	chr3:125741776-125745177		chr3:125745178-125745235	chr3:125745235-125745236		96.12
K	jcn_only_AD	CUFF.782	chr3	-	chr3:125787090-125802935	chr3:125787090-125802896		chr3:125802897-125802935	chr3:125802935-125802936		51.50
K	alternative_donor	CUFF.516	chr19	-	chr19:10204296-10204488	chr19:10204296-10204368		chr19:10204369-10204488	chr19:10204488-10204489		71.43
N	jcn_only_AD	CUFF.708	chr22	+	chr22:21058172-21058255;chr22:21057981-21058255	chr22:21058040-21058255		chr22:21057981-21058039;chr22:21058040-21058171	chr22:21057980-21057981;chr22:21058039-21058040		76.33
K	cassette	CUFF.1028	chr8	-	chr8:23225948-23261466	chr8:23225948-23239903;chr8:23240027-23261466		chr8:23239904-23240026			69.12
N	alternative_donor	CUFF.647	chr2	-	chr2:175809672-175816891	chr2:175809672-175809897		chr2:175809898-175816891	chr2:175816891-175816892		2.86
N	alternative_acceptor	CUFF.1052	chr8	+	chr8:107593480-107691437	chr8:107593480-107617009		chr8:107617010-107691437	chr8:107691437-107691438		0.00
K	alternative_donor	CUFF.53	chr1	-	chr1:156908306-156909339	chr1:156908306-156908940		chr1:156908941-156909339	chr1:156909339-156909340		40.58
N	alternative_acceptor	CUFF.852	chr4	-	chr4:152065203-152069073	chr4:152065441-152069073		chr4:152065203-152065440	chr4:152065202-152065203		46.00
N	coord_cassette	CUFF.213	chr12	+	chr12:27628665-27648612	chr12:27628665-27641392;chr12:27641481-27647232;chr12:27647290-27648612		chr12:27641393-27641480;chr12:27647233-27647289			89.36
N	jcn_only_AD		chr14	+	chr14:76150000-76156534	chr14:76156205-76156534					25.00
N	alternative_first_exon	CUFF.377	chr16	-	chr16:4445341-4447318;chr16:4445341-4466785;chr16:4445341-4466459	chr16:4445341-4455491	chr16:4466786-4466962;chr16:4466460-4466665	chr16:4455492-4455568			63.07
K	coord_cassette	CUFF.1136	chrX	+	chrX:107369418-107374489	chrX:107369418-107370022;chrX:107370325-107372010;chrX:107372083-107374489		chrX:107370023-107370324;chrX:107372011-107372082			42.06
K	alternative_first_exon	CUFF.17	chr1	+	chr1:31769923-31782890,chr1:31769944-31782890	chr1:31770061-31782890	chr1:31769842-31769922	chr1:31770007-31770060			2.44
K	intron_retention	CUFF.878	chr5	+	chr5:56533000-56542126				chr5:56532999-56533000;chr5:56542126-56542127	chr5:56532940-56532999;chr5:56542127-56542311	49.06
K	jcn_only_AD	CUFF.274,CUFF.289	chr14	-	chr14:69522329-69542061	chr14:69522329-69529100					50.00
N	jcn_only_AD	CUFF.561	chr19	-	chr19:51537897-51538061	chr19:51537897-51538050		chr19:51538051-51538061	chr19:51538061-51538062		4.93
N	coord_cassette	CUFF.604	chr2	-	chr2:61727030-61749745	chr2:61727030-61729130;chr2:61729176-61729383;chr2:61729446-61749745		chr2:61729131-61729175;chr2:61729384-61729445			89.47
K	intron_retention	CUFF.758	chr3	-	chr3:57569735-57582800				chr3:57569734-57569735;chr3:57582800-57582801		48.78
K	alternative_acceptor	CUFF.1023	chr8	-	chr8:2452792-2453715	chr8:2452795-2453715		chr8:2452792-2452794	chr8:2452791-2452792		17.39
K	alternative_acceptor	CUFF.506	chr19	+	chr19:4304759-4305981;chr19:4304759-4305942	chr19:4304759-4306020		chr19:4305943-4305981;chr19:4305982-4306020	chr19:4305981-4305982;chr19:4306020-4306021		12.77
N	intron_retention		chr3	-	chr3:141713984-141811902				chr3:141713983-141713984;chr3:141811902-141811903		63.16
K	jcn_only_AD	CUFF.768	chr3	+	chr3:112046542-112048192	chr3:112046554-112048192		chr3:112046542-112046553	chr3:112046541-112046542		58.06
N	alternative_acceptor	CUFF.189	chr11	-	chr11:119291089-119291578;chr11:119291046-119291578	chr11:119291097-119291578		chr11:119291046-119291088;chr11:119291089-119291096	chr11:119291045-119291046;chr11:119291088-119291089		87.84
N	alternative_donor	CUFF.119	chr10	-	chr10:78637649-78647048	chr10:78637649-78644746		chr10:78644747-78647048	chr10:78647048-78647049		86.67
N	jcn_only_AD	CUFF.1148	chrX	-	chrX:46382561-46387784	chrX:46382561-46387769		chrX:46387770-46387784	chrX:46387784-46387785		50.00
N	intron_retention		chr6	+	chr6:31935897-31936104				chr6:31935896-31935897;chr6:31936104-31936105		13.73
N	intron_retention	CUFF.371	chr16	+	chr16:2203224-2203319				chr16:2203223-2203224;chr16:2203319-2203320		44.23
K	intron_retention	CUFF.657	chr2	+	chr2:207655411-207656406				chr2:207655410-207655411;chr2:207656406-207656407		19.19
K	cassette	CUFF.387	chr16	+	chr16:21987565-21994408	chr16:21987565-21991867;chr16:21992022-21994408		chr16:21991868-21992021			60.32
N	alternative_donor	CUFF.182	chr11	+	chr11:118402317-118402489;chr11:118401950-118402489	chr11:118402242-118402489		chr11:118401950-118402241;chr11:118402242-118402316	chr11:118401949-118401950;chr11:118402241-118402242	chr11:118402490-118402586;chr11:118401663-118401949	14.72
N	jcn_only_AD	CUFF.1043	chr8	+	chr8:82192910-82195600	chr8:82193549-82195600		chr8:82192910-82193548	chr8:82192909-82192910		3.80
K	intron_retention	CUFF.49	chr1	-	chr1:153927466-153927540				chr1:153927465-153927466;chr1:153927540-153927541		9.09
N	alternative_donor	CUFF.1113,CUFF.1135	chrX	-	chrX:106184863-106185205	chrX:106184863-106185167		chrX:106185168-106185205	chrX:106185205-106185206		60.00
K	cassette	CUFF.1155	chrY	-	chrY:24027300-24028418	chrY:24027300-24027386;chrY:24027498-24028418		chrY:24027387-24027497		chrY:24027211-24027299;chrY:24028419-24028529	84.21
N	jcn_only_AD	CUFF.201	chr12	+	chr12:4653071-4654947	chr12:4654479-4654947		chr12:4653071-4654478	chr12:4653070-4653071		74.07
K	alternative_acceptor	CUFF.112,CUFF.122	chr10	+	chr10:70661228-70666039	chr10:70661228-70665981		chr10:70665982-70666039	chr10:70666039-70666040		16.67
K	intron_retention	CUFF.633	chr2	-	chr2:110882901-110883213				chr2:110882900-110882901;chr2:110883213-110883214		82.35
K	jcn_only_AA	CUFF.475	chr17	-	chr17:79995418-79995506	chr17:79995424-79995506		chr17:79995418-79995423	chr17:79995417-79995418		40.82
K	cassette	CUFF.581	chr2	-	chr2:4008147-4021134	chr2:4008147-4009359;chr2:4009485-4021134		chr2:4009360-4009484			98.17
K	intron_retention	CUFF.180	chr11	+	chr11:117070149-117070348				chr11:117070148-117070149;chr11:117070348-117070349		63.73
K	cassette	CUFF.683	chr20	+	chr20:30136918-30137866	chr20:30136918-30137009;chr20:30137136-30137866		chr20:30137010-30137135		chr20:30136832-30136917;chr20:30137867-30137965	40.60
N	jcn_only_AA	CUFF.531	chr19	+	chr19:17611442-17615263	chr19:17611442-17611520		chr19:17611521-17615263	chr19:17615263-17615264		55.77
K	alternative_acceptor	CUFF.165	chr11	+	chr11:65481320-65482130	chr11:65481320-65481965		chr11:65481966-65482130	chr11:65482130-65482131		90.72
N	cassette	CUFF.61	chr1	+	chr1:167190196-167301706;chr1:167210848-167301706	chr1:167190196-167272710,chr1:167210848-167272710;chr1:167272812-167301706		chr1:167272711-167272811			90.62
N	intron_retention		chr12	-	chr12:7088742-7090755				chr12:7088741-7088742;chr12:7090755-7090756		81.82
K	intron_retention	CUFF.232	chr12	+	chr12:58013662-58014124				chr12:58013661-58013662;chr12:58014124-58014125		56.67
N	jcn_only_AD	CUFF.1136	chrX	+	chrX:107395089-107396208	chrX:107395236-107396208		chrX:107395089-107395235	chrX:107395088-107395089		6.25
N	coord_cassette	CUFF.217	chr12	-	chr12:48392215-48398019	chr12:48392215-48393701;chr12:48393909-48394767;chr12:48394878-48398019		chr12:48393702-48393908;chr12:48394768-48394877			83.33
K	cassette	CUFF.828	chr4	+	chr4:37841882-37847253	chr4:37841882-37845984;chr4:37846175-37847253		chr4:37845985-37846174			78.18
N	jcn_only_AD	CUFF.1002,CUFF.999	chr7	-	chr7:107642179-107643293	chr7:107642179-107642571		chr7:107642572-107643293	chr7:107643293-107643294		32.81
N	coord_cassette	CUFF.211	chr12	-	chr12:25699489-25801427	chr12:25699489-25700158;chr12:25700286-25702259;chr12:25702481-25801427		chr12:25700159-25700285;chr12:25702260-25702480			72.50
N	jcn_only_AD	CUFF.708	chr22	+	chr22:21058329-21058475	chr22:21058345-21058475		chr22:21058329-21058344	chr22:21058328-21058329		5.63
N	jcn_only_AA	CUFF.566	chr19	+	chr19:54648069-54649330;chr19:54648069-54649333	chr19:54648069-54649277		chr19:54649278-54649330;chr19:54649331-54649333	chr19:54649330-54649331;chr19:54649333-54649334		8.11
N	jcn_only_AD	CUFF.489	chr18	-	chr18:47329224-47337765;chr18:47329224-47340051;chr18:47329224-47340186;chr18:47329224-47339838;chr18:47329224-47340101	chr18:47329224-47339094		chr18:47337766-47339094;chr18:47339095-47339838;chr18:47339839-47340051;chr18:47340052-47340101;chr18:47340102-47340186	chr18:47339094-47339095;chr18:47339838-47339839;chr18:47340051-47340052;chr18:47340101-47340102;chr18:47340186-47340187		4.03
N	jcn_only_AA		chr19	-	chr19:6192041-6199486;chr19:6176455-6199486	chr19:6148341-6199486					31.65
K	alternative_first_exon	CUFF.317	chr15	-	chr15:45470505-45490969;chr15:45470505-45479651;chr15:45470505-45492924	chr15:45470505-45473304	chr15:45479652-45480154;chr15:45492925-45493434	chr15:45473305-45473474			49.07
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		87.01
K	alternative_donor	CUFF.126	chr10	+	chr10:101492167-101496002	chr10:101492318-101496002		chr10:101492167-101492317	chr10:101492166-101492167		29.03
K	cassette	CUFF.834	chr4	-	chr4:70465113-70512647	chr4:70465113-70501408;chr4:70501541-70512647		chr4:70501409-70501540			37.93
K	jcn_only_AD	CUFF.386	chr16	+	chr16:21712349-21716489	chr16:21712391-21716489		chr16:21712349-21712390	chr16:21712348-21712349		10.00
N	jcn_only_AD	CUFF.974	chr7	-	chr7:38813845-38816278	chr7:38813845-38814788		chr7:38814789-38816278	chr7:38816278-38816279		15.79
K	cassette	CUFF.225	chr12	+	chr12:53853188-53854798	chr12:53853188-53854114;chr12:53854210-53854798		chr12:53854115-53854209			7.53
K	intron_retention	CUFF.931	chr6	+	chr6:46644481-46645347				chr6:46644480-46644481;chr6:46645347-46645348		32.94
N	jcn_only_AA	CUFF.894	chr5	+	chr5:139815843-139818045;chr5:139815843-139818087	chr5:139815843-139818078		chr5:139818046-139818078;chr5:139818079-139818087	chr5:139818078-139818079;chr5:139818087-139818088	chr5:139815689-139815842;chr5:139818088-139818202	53.12
N	alternative_acceptor	CUFF.193	chr11	-	chr11:124766952-124767621;chr11:124767529-124767621	chr11:124767158-124767621		chr11:124766952-124767157;chr11:124767158-124767528	chr11:124766951-124766952;chr11:124767157-124767158		72.22
K	jcn_only_AA	CUFF.1112	chrX	-	chrX:2408811-2418857	chrX:2408814-2418857		chrX:2408811-2408813	chrX:2408810-2408811		92.00
K	intron_retention	CUFF.665	chr2	+	chr2:231934883-231937046				chr2:231934882-231934883;chr2:231937046-231937047		4.12
K	intron_retention	CUFF.551	chr19	+	chr19:45261671-45261980				chr19:45261670-45261671;chr19:45261980-45261981		20.83
N	alternative_donor		chr17	+	chr17:61555460-61557129	chr17:61556462-61557129		chr17:61555460-61556461	chr17:61555459-61555460		97.78
N	jcn_only_AD	CUFF.95	chr10	-	chr10:76287751-76290264	chr10:76287751-76289050		chr10:76289051-76290264	chr10:76290264-76290265		85.42
N	intron_retention	CUFF.980	chr7	+	chr7:73108381-73111795				chr7:73108380-73108381;chr7:73111795-73111796		58.33
K	cassette	CUFF.903	chr5	+	chr5:177636434-177637553;chr5:177636449-177637553	chr5:177636449-177637132,chr5:177636434-177637132;chr5:177637274-177637553		chr5:177637133-177637273			28.24
N	jcn_only_AD	CUFF.276	chr14	-	chr14:71205116-71206758	chr14:71205116-71206614		chr14:71206615-71206758	chr14:71206758-71206759		2.25
K	intron_retention	CUFF.11	chr1	-	chr1:25558703-25558934				chr1:25558702-25558703;chr1:25558934-25558935		9.90
K	alternative_first_exon	CUFF.436	chr17	+	chr17:29592358-29652837	chr17:29645583-29652837	chr17:29592247-29592357	chr17:29645341-29645582			86.84
K	alternative_acceptor	CUFF.589	chr2	-	chr2:27703994-27706155	chr2:27704128-27706155		chr2:27703994-27704127	chr2:27703993-27703994		74.36
N	alternative_donor	CUFF.201	chr12	+	chr12:4665669-4668022;chr12:4665717-4668022	chr12:4662256-4668022		chr12:4662256-4665668;chr12:4665669-4665716	chr12:4662255-4662256;chr12:4665668-4665669		63.79
K	intron_retention	CUFF.876	chr5	+	chr5:54456072-54456157				chr5:54456071-54456072;chr5:54456157-54456158		6.07
K	intron_retention	CUFF.1102	chr9	+	chr9:133320383-133327610				chr9:133320382-133320383;chr9:133327610-133327611		62.50
K	cassette	CUFF.618	chr2	-	chr2:86397965-86400772	chr2:86397965-86398330;chr2:86398505-86400772		chr2:86398331-86398504			92.50
K	intron_retention	CUFF.418	chr17	+	chr17:1945170-1946269				chr17:1945169-1945170;chr17:1946269-1946270		73.20
N	jcn_only_AA	CUFF.520	chr19	-	chr19:11541841-11545593	chr19:11545352-11545593		chr19:11541841-11545351	chr19:11541840-11541841		5.45
K	alternative_first_exon	CUFF.101	chr10	-	chr10:35360268-35379357;chr10:35360268-35379106;chr10:35360268-35363119	chr10:35360268-35378823	chr10:35379107-35379332;chr10:35363120-35363275	chr10:35378824-35378973			26.32
K	intron_retention	CUFF.152	chr11	-	chr11:10820972-10821098				chr11:10820971-10820972;chr11:10821098-10821099		15.56
N	jcn_only_AA		chr7	-	chr7:107580804-107591670	chr7:107583065-107591670					72.00
N	alternative_acceptor	CUFF.86	chr10	-	chr10:410523-412214	chr10:410962-412214		chr10:410523-410961	chr10:410522-410523		62.50
N	alternative_acceptor	CUFF.579,CUFF.666	chr2	+	chr2:3405665-3425651	chr2:3405665-3425470		chr2:3425471-3425651	chr2:3425651-3425652		16.07
N	mutually_exclusive	CUFF.257	chr14	+	chr14:23390330-23393509,chr14:23393651-23395669	chr14:23390330-23392287,chr14:23392414-23395669	chr14:23393510-23393650	chr14:23392288-23392413			69.23
N	jcn_only_AA	CUFF.151	chr11	-	chr11:8941998-8947009	chr11:8943063-8947009		chr11:8941998-8943062	chr11:8941997-8941998		14.29
N	cassette	CUFF.338	chr15	-	chr15:77544869-77577299	chr15:77544869-77576224;chr15:77576373-77577299		chr15:77576225-77576372			85.42
K	alternative_acceptor	CUFF.683,CUFF.689	chr20	+	chr20:30132839-30136831	chr20:30132839-30136767		chr20:30136768-30136831	chr20:30136831-30136832	chr20:30132750-30132838;chr20:30136832-30136917	7.80
K	cassette	CUFF.921	chr6	+	chr6:32823983-32825781	chr6:32823983-32825039;chr6:32825172-32825781		chr6:32825040-32825171			74.51
N	alternative_last_exon	CUFF.396	chr16	-	chr16:57509132-57509761	chr16:57509533-57509761	chr16:57509012-57509131	chr16:57509364-57509532			98.25
K	intron_retention	CUFF.475	chr17	-	chr17:79994185-79994289				chr17:79994184-79994185;chr17:79994289-79994290		41.80
N	alternative_acceptor		chr5	+	chr5:54456225-54456879	chr5:54456225-54456821		chr5:54456822-54456879	chr5:54456879-54456880		30.23
K	alternative_first_exon	CUFF.752,CUFF.796	chr3	-	chr3:49373030-49377916	chr3:49373030-49377356	chr3:49377917-49378220	chr3:49377357-49377558			61.70
K	cassette	CUFF.106	chr10	-	chr10:46148508-46158989	chr10:46148508-46158027;chr10:46158130-46158989		chr10:46158028-46158129			46.88
K	jcn_only_AA	CUFF.111	chr10	+	chr10:69918385-69925239	chr10:69918385-69921485					62.50
K	jcn_only_AA	CUFF.1040,CUFF.1056	chr8	+	chr8:124629084-124646553	chr8:124629084-124637926				chr8:124628966-124629083	3.33
N	jcn_only_AA	CUFF.285	chr14	+	chr14:76368568-76420766;chr14:76368568-76407766	chr14:76368568-76372897					45.54
N	jcn_only_AA	CUFF.716	chr22	+	chr22:37699444-37705252	chr22:37699444-37700212					77.78
N	alternative_donor	CUFF.531	chr19	+	chr19:17612229-17615263;chr19:17611686-17615263	chr19:17611442-17615263		chr19:17611442-17611685;chr19:17611686-17612228	chr19:17611441-17611442;chr19:17611685-17611686		46.00
K	alternative_acceptor	CUFF.774,CUFF.785	chr3	+	chr3:119530574-119531643	chr3:119530574-119531532		chr3:119531533-119531643	chr3:119531643-119531644		88.46
K	jcn_only_AA	CUFF.8	chr1	+	chr1:16382019-16382172	chr1:16382019-16382169		chr1:16382170-16382172	chr1:16382172-16382173		43.40
K	intron_retention	CUFF.522	chr19	+	chr19:12917615-12917821				chr19:12917614-12917615;chr19:12917821-12917822		34.38
N	mutually_exclusive	CUFF.946	chr6	-	chr6:133046119-133049879,chr6:133050073-133055391	chr6:133046119-133047860,chr6:133048152-133055391	chr6:133049880-133050072	chr6:133047861-133048151			56.52
K	cassette	CUFF.486	chr18	-	chr18:44471018-44483489	chr18:44471018-44473393;chr18:44473495-44483489		chr18:44473394-44473494			16.28
K	cassette	CUFF.407	chr16	+	chr16:70390151-70398445	chr16:70390151-70395320;chr16:70395414-70398445		chr16:70395321-70395413			59.18
N	mutually_exclusive	CUFF.471	chr17	-	chr17:79354385-79358745,chr17:79358833-79358928	chr17:79354385-79355676,chr17:79355741-79358928	chr17:79358746-79358832	chr17:79355677-79355740			53.33
K	intron_retention	CUFF.49	chr1	-	chr1:153925127-153925280				chr1:153925126-153925127;chr1:153925280-153925281		87.80
K	intron_retention	CUFF.919	chr6	-	chr6:31938603-31938688				chr6:31938602-31938603;chr6:31938688-31938689		63.67
N	alternative_donor	CUFF.657	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		6.67
K	jcn_only_AA	CUFF.828	chr4	+	chr4:37831754-37841479	chr4:37831754-37836239					70.15
K	cassette	CUFF.649	chr2	-	chr2:177497854-177502189	chr2:177497854-177498092;chr2:177498469-177502189		chr2:177498093-177498468			34.48
K	intron_retention		chr11	-	chr11:67771269-67771417				chr11:67771268-67771269;chr11:67771417-67771418		34.59
N	alternative_donor	CUFF.188	chr11	-	chr11:6637735-6638589	chr11:6637735-6637891		chr11:6637892-6638589	chr11:6638589-6638590		30.09
N	jcn_only_AD	CUFF.2	chr1	+	chr1:2106753-2116021	chr1:2113354-2116021		chr1:2106753-2113353	chr1:2106752-2106753		2.04
N	intron_retention		chr11	+	chr11:118402587-118403631				chr11:118402586-118402587;chr11:118403631-118403632	chr11:118401663-118402586;chr11:118403632-118403922	82.69
K	coord_cassette	CUFF.1136	chrX	+	chrX:107377389-107381033	chrX:107377389-107377568;chrX:107377642-107380320;chrX:107380401-107381033		chrX:107377569-107377641;chrX:107380321-107380400			89.52
N	alternative_donor	CUFF.155	chr11	+	chr11:36459027-36472758	chr11:36467991-36472758		chr11:36459027-36467990	chr11:36459026-36459027		0.00
N	jcn_only_AA	CUFF.244,CUFF.256	chr13	+	chr13:103510769-103513856	chr13:103510769-103511260		chr13:103511261-103513856	chr13:103513856-103513857		66.67
N	alternative_donor	CUFF.489	chr18	-	chr18:47329224-47337765;chr18:47329224-47340051;chr18:47329224-47339094;chr18:47329224-47340186;chr18:47329224-47340101	chr18:47329224-47339838		chr18:47337766-47339094;chr18:47339095-47339838;chr18:47339839-47340051;chr18:47340052-47340101;chr18:47340102-47340186	chr18:47339094-47339095;chr18:47339838-47339839;chr18:47340051-47340052;chr18:47340101-47340102;chr18:47340186-47340187		14.94
N	alternative_donor		chr7	+	chr7:150831656-150837065	chr7:150835401-150837065		chr7:150831656-150835400	chr7:150831655-150831656		35.00
K	jcn_only_AD	CUFF.1124	chrX	+	chrX:47039437-47039610	chrX:47039440-47039610		chrX:47039437-47039439	chrX:47039436-47039437		23.81
N	jcn_only_AA	CUFF.490,CUFF.502	chr18	+	chr18:55833094-55912658	chr18:55833094-55895061		chr18:55895062-55912658	chr18:55912658-55912659		18.52
K	intron_retention	CUFF.228	chr12	-	chr12:56558153-56558431				chr12:56558152-56558153;chr12:56558431-56558432		66.67
N	jcn_only_AA	CUFF.137	chr11	-	chr11:558767-558855	chr11:558785-558855		chr11:558767-558784	chr11:558766-558767		30.99
K	intron_retention		chr17	+	chr17:25965381-25967597				chr17:25965380-25965381;chr17:25967597-25967598		8.70
N	alternative_donor		chr2	+	chr2:101609990-101612257	chr2:101611043-101612257		chr2:101609990-101611042	chr2:101609989-101609990		12.50
N	intron_retention		chr7	-	chr7:107572823-107575859				chr7:107572822-107572823;chr7:107575859-107575860		86.96
K	intron_retention	CUFF.389	chr16	+	chr16:22477140-22477517				chr16:22477139-22477140;chr16:22477517-22477518		43.75
N	alternative_donor	CUFF.139,CUFF.176	chr11	-	chr11:102960048-102962412;chr11:102960048-102962515	chr11:102960048-102962244		chr11:102962245-102962412;chr11:102962413-102962515	chr11:102962412-102962413;chr11:102962515-102962516		20.93
K	jcn_only_AD	CUFF.781	chr3	+	chr3:125639749-125643808	chr3:125642984-125643808					28.30
K	jcn_only_AD	CUFF.473	chr17	-	chr17:79894738-79895133;chr17:79894738-79895055	chr17:79894738-79895137		chr17:79895056-79895133;chr17:79895134-79895137	chr17:79895133-79895134;chr17:79895137-79895138	chr17:79894624-79894737;chr17:79895138-79895264	36.64
N	jcn_only_AA	CUFF.910	chr6	-	chr6:5144497-5216850;chr6:5113652-5216850;chr6:5138974-5216850	chr6:5187215-5216850		chr6:5113652-5138973;chr6:5138974-5144496;chr6:5144497-5187214	chr6:5113651-5113652;chr6:5138973-5138974;chr6:5144496-5144497		37.25
N	jcn_only_AA	CUFF.838	chr4	-	chr4:77977254-77987401	chr4:77979789-77987401		chr4:77977254-77979788	chr4:77977253-77977254		87.27
N	intron_retention		chr18	+	chr18:56002770-56008269				chr18:56002769-56002770;chr18:56008269-56008270		62.50
N	alternative_donor	CUFF.50	chr1	+	chr1:155180207-155180338	chr1:155180227-155180338		chr1:155180207-155180226	chr1:155180206-155180207		8.47
N	cassette	CUFF.707	chr22	+	chr22:20748953-20759666	chr22:20748953-20754921;chr22:20755049-20759666		chr22:20754922-20755048			78.26
K	alternative_acceptor	CUFF.961,CUFF.984	chr7	+	chr7:6631499-6634065	chr7:6631499-6634042		chr7:6634043-6634065	chr7:6634065-6634066		36.67
N	jcn_only_AA		chr16	+	chr16:3194833-3195668	chr16:3194833-3194984		chr16:3194985-3195668	chr16:3195668-3195669		70.00
K	alternative_first_exon	CUFF.768	chr3	+	chr3:112021562-112045368	chr3:112026046-112045368	chr3:112021325-112021561	chr3:112025901-112026045			63.16
N	intron_retention		chr17	-	chr17:15517057-15517146				chr17:15517056-15517057;chr17:15517146-15517147		85.37
K	alternative_acceptor	CUFF.506	chr19	+	chr19:4317278-4318380	chr19:4317278-4318342		chr19:4318343-4318380	chr19:4318380-4318381		44.29
N	intron_retention		chr5	-	chr5:64887330-64887698				chr5:64887329-64887330;chr5:64887698-64887699		75.00
N	jcn_only_AA	CUFF.918	chr6	+	chr6:31936316-31936462	chr6:31936316-31936399		chr6:31936400-31936462	chr6:31936462-31936463		13.87
K	cassette	CUFF.244	chr13	+	chr13:21179245-21189931	chr13:21179245-21188495;chr13:21188575-21189931		chr13:21188496-21188574			26.83
N	alternative_last_exon		chr7	+	chr7:73108000-73111934	chr7:73108000-73108321	chr7:73111935-73112024	chr7:73108322-73108405			88.04
N	intron_retention		chr3	-	chr3:33644082-33644443				chr3:33644081-33644082;chr3:33644443-33644444		34.12
K	alternative_first_exon	CUFF.611	chr2	-	chr2:73285726-73286222,chr2:73285726-73298168,chr2:73285726-73302708;chr2:73285726-73297588;chr2:73285726-73298732	chr2:73285726-73286136	chr2:73297589-73298469;chr2:73298733-73298921	chr2:73286137-73286312			8.94
N	jcn_only_AD	CUFF.53	chr1	-	chr1:156933387-156937778	chr1:156933387-156933483		chr1:156933484-156937778	chr1:156937778-156937779		89.19
K	jcn_only_AD	CUFF.376,CUFF.406	chr16	-	chr16:70266708-70267326	chr16:70266708-70267315		chr16:70267316-70267326	chr16:70267326-70267327		32.20
K	intron_retention	CUFF.663	chr2	+	chr2:220097914-220098007				chr2:220097913-220097914;chr2:220098007-220098008		60.25
N	jcn_only_AA	CUFF.631	chr2	+	chr2:109068923-109085435	chr2:109068923-109079043		chr2:109079044-109085435	chr2:109085435-109085436		12.12
K	intron_retention	CUFF.769	chr3	+	chr3:119207835-119209397				chr3:119207834-119207835;chr3:119209397-119209398		20.00
N	alternative_acceptor	CUFF.289	chr14	-	chr14:92105595-92136157	chr14:92126326-92136157		chr14:92105595-92126325	chr14:92105594-92105595		0.00
K	intron_retention		chr7	+	chr7:73101426-73105245				chr7:73101425-73101426;chr7:73105245-73105246		14.89
K	alternative_last_exon	CUFF.3	chr1	+	chr1:10500471-10511433	chr1:10500471-10502321	chr1:10511434-10512308	chr1:10502322-10502953			68.42
N	jcn_only_AD	CUFF.663	chr2	+	chr2:220095128-220096649;chr2:220095073-220096649	chr2:220094623-220096649		chr2:220094623-220095072;chr2:220095073-220095127	chr2:220094622-220094623;chr2:220095072-220095073		25.31
N	alternative_acceptor		chr12	+	chr12:26205536-26208211	chr12:26205536-26208168		chr12:26208169-26208211	chr12:26208211-26208212		38.64
N	alternative_donor	CUFF.971	chr7	-	chr7:37256301-37262219	chr7:37256301-37257316		chr7:37257317-37262219	chr7:37262219-37262220		0.00
K	coord_cassette	CUFF.63	chr1	-	chr1:169696667-169698326	chr1:169696667-169696879;chr1:169697069-169697198;chr1:169697388-169698326		chr1:169696880-169697068;chr1:169697199-169697387			64.00
N	alternative_last_exon	CUFF.212	chr12	+	chr12:26148064-26208211,chr12:26148064-26208168	chr12:26148064-26173077	chr12:26208212-26208379	chr12:26173078-26173529			19.05
K	jcn_only_AD	CUFF.322,CUFF.331	chr15	-	chr15:55483246-55484917	chr15:55483246-55484600		chr15:55484601-55484917	chr15:55484917-55484918		24.42
N	alternative_acceptor	CUFF.317	chr15	-	chr15:45470505-45492924	chr15:45491319-45492924		chr15:45470505-45491318	chr15:45470504-45470505		5.56
K	intron_retention	CUFF.139	chr11	-	chr11:1776259-1778553				chr11:1776258-1776259;chr11:1778553-1778554		31.67
K	cassette	CUFF.457	chr17	+	chr17:61562734-61563917	chr17:61562734-61563719;chr17:61563733-61563917		chr17:61563720-61563732			10.57
N	jcn_only_AD	CUFF.1051	chr8	+	chr8:106646586-106800945	chr8:106703164-106800945		chr8:106646586-106703163	chr8:106646585-106646586		12.50
N	alternative_acceptor		chr18	+	chr18:55713021-55833023	chr18:55713021-55833019		chr18:55833020-55833023	chr18:55833023-55833024		37.50
K	alternative_first_exon	CUFF.1109	chr9	+	chr9:139780732-139793164;chr9:139784995-139793164;chr9:139777163-139793164	chr9:139780994-139793164	chr9:139780437-139780731;chr9:139784801-139784994;chr9:139777119-139777162	chr9:139780897-139780993			33.60
K	alternative_first_exon	CUFF.971	chr7	-	chr7:36934623-37025527;chr7:36934623-37052903	chr7:36934623-37024519	chr7:37052904-37053040	chr7:37024520-37024712			35.98
K	cassette	CUFF.1136	chrX	+	chrX:107369418-107372010	chrX:107369418-107370022;chrX:107370325-107372010		chrX:107370023-107370324			61.00
K	intron_retention	CUFF.661	chr2	+	chr2:219225383-219231746				chr2:219225382-219225383;chr2:219231746-219231747		65.00
K	alternative_acceptor	CUFF.423	chr17	+	chr17:6353393-6353681	chr17:6353393-6353558		chr17:6353559-6353681	chr17:6353681-6353682		70.77
N	jcn_only_AD	CUFF.922	chr6	+	chr6:33240504-33243573	chr6:33243435-33243573		chr6:33240504-33243434	chr6:33240503-33240504		6.85
N	jcn_only_AA		chr15	+	chr15:24811948-24814929;chr15:24811948-24813677;chr15:24811948-24813038	chr15:24811948-24813043					13.64
K	alternative_first_exon	CUFF.284	chr14	-	chr14:77275987-77280649;chr14:77275987-77278647	chr14:77275987-77276431	chr14:77280650-77280764;chr14:77278648-77278744	chr14:77276432-77276597			58.44
N	jcn_only_AD	CUFF.1033	chr8	-	chr8:56676540-56685827;chr8:56676540-56685534	chr8:56676540-56685785		chr8:56685535-56685785;chr8:56685786-56685827	chr8:56685785-56685786;chr8:56685827-56685828		22.68
K	coord_cassette	CUFF.828	chr4	+	chr4:37848917-37857228	chr4:37848917-37850142;chr4:37850273-37851804;chr4:37851995-37857228		chr4:37850143-37850272;chr4:37851805-37851994			54.55
N	coord_cassette	CUFF.234	chr12	+	chr12:69207409-69222550	chr12:69207409-69218142;chr12:69218211-69218334;chr12:69218432-69222550		chr12:69218143-69218210;chr12:69218335-69218431			90.00
N	jcn_only_AD	CUFF.377,CUFF.410	chr16	-	chr16:4411471-4411985	chr16:4411471-4411749		chr16:4411750-4411985	chr16:4411985-4411986		25.42
N	intron_retention		chr11	+	chr11:118402587-118402960				chr11:118402586-118402587;chr11:118402960-118402961	chr11:118401663-118402586;chr11:118402961-118403176	95.31
N	intron_retention		chr4	+	chr4:120379233-120381897				chr4:120379232-120379233;chr4:120381897-120381898		48.61
K	coord_cassette	CUFF.765	chr3	-	chr3:107595034-107596748	chr3:107595034-107595301;chr3:107595379-107596159;chr3:107596345-107596748		chr3:107595302-107595378;chr3:107596160-107596344			34.81
N	jcn_only_AA	CUFF.971	chr7	-	chr7:37256301-37262219	chr7:37257362-37262219		chr7:37256301-37257361	chr7:37256300-37256301		29.41
K	cassette	CUFF.67	chr1	+	chr1:196913069-196919981	chr1:196913069-196918584;chr1:196918780-196919981		chr1:196918585-196918779		chr1:196912830-196913068;chr1:196919982-196920158	76.11
K	cassette	CUFF.664	chr2	+	chr2:228172636-228173919	chr2:228172636-228173614;chr2:228173793-228173919		chr2:228173615-228173792			6.35
K	intron_retention	CUFF.1073	chr9	+	chr9:43908211-43908435				chr9:43908210-43908211;chr9:43908435-43908436		93.91
K	intron_retention	CUFF.1008	chr7	-	chr7:127251903-127251998				chr7:127251902-127251903;chr7:127251998-127251999		66.67
K	cassette	CUFF.1105	chr9	+	chr9:138480579-138482636	chr9:138480579-138481256;chr9:138481331-138482636		chr9:138481257-138481330			63.92
K	intron_retention	CUFF.144	chr11	-	chr11:2905365-2906431				chr11:2905364-2905365;chr11:2906431-2906432		85.11
N	alternative_acceptor	CUFF.176	chr11	-	chr11:102937297-102953476	chr11:102950727-102953476		chr11:102937297-102950726	chr11:102937296-102937297		0.00
N	alternative_acceptor	CUFF.709	chr22	-	chr22:21828970-21829499	chr22:21829090-21829499		chr22:21828970-21829089	chr22:21828969-21828970		7.29
K	alternative_first_exon	CUFF.821	chr4	-	chr4:11401738-11431048	chr4:11401738-11430086	chr4:11431049-11431389	chr4:11430087-11430286			45.45
K	intron_retention		chr7	-	chr7:36901342-36909997				chr7:36901341-36901342;chr7:36909997-36909998		5.43
N	cassette	CUFF.209	chr12	-	chr12:22610096-22622642	chr12:22610096-22612425;chr12:22612477-22622642		chr12:22612426-22612476			94.64
N	jcn_only_AA	CUFF.426	chr17	-	chr17:15557746-15584178;chr17:15581036-15584178	chr17:15580997-15584178		chr17:15557746-15580996;chr17:15580997-15581035	chr17:15557745-15557746;chr17:15580996-15580997		5.04
K	alternative_first_exon	CUFF.958	chr7	+	chr7:193805-195553	chr7:195328-195553	chr7:192874-193804	chr7:195179-195327			50.00
K	cassette	CUFF.633	chr2	-	chr2:110881641-110883213	chr2:110881641-110882795;chr2:110882901-110883213		chr2:110882796-110882900			3.70
K	alternative_first_exon	CUFF.21	chr1	-	chr1:41486451-41487287	chr1:41486451-41486535	chr1:41487288-41487387	chr1:41486536-41486605			52.00
K	intron_retention	CUFF.176	chr11	-	chr11:102960048-102962515				chr11:102960047-102960048;chr11:102962515-102962516		27.50
N	coord_cassette	CUFF.273	chr14	+	chr14:61451522-61497162	chr14:61451522-61482621;chr14:61482675-61486258;chr14:61486299-61497162		chr14:61482622-61482674;chr14:61486259-61486298			92.89
N	alternative_acceptor	CUFF.722	chr22	+	chr22:45173110-45182336	chr22:45173110-45181921		chr22:45181922-45182336	chr22:45182336-45182337		64.29
K	jcn_only_AA	CUFF.884	chr5	-	chr5:82948641-82969242	chr5:82948644-82969242		chr5:82948641-82948643	chr5:82948640-82948641		87.80
K	coord_cassette	CUFF.989	chr7	+	chr7:91712970-91714808	chr7:91712970-91713953;chr7:91714018-91714132;chr7:91714255-91714808		chr7:91713954-91714017;chr7:91714133-91714254			89.74
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		96.88
N	intron_retention		chr22	-	chr22:51020525-51020677				chr22:51020524-51020525;chr22:51020677-51020678		47.06
K	alternative_last_exon	CUFF.961	chr7	+	chr7:6641772-6642294;chr7:6641772-6647590	chr7:6641772-6647167	chr7:6647591-6648456	chr7:6647168-6647511			16.67
K	coord_cassette	CUFF.463	chr17	-	chr17:66274469-66287226	chr17:66274469-66279137;chr17:66279265-66281685;chr17:66281784-66287226		chr17:66279138-66279264;chr17:66281686-66281783			28.57
K	alternative_donor	CUFF.232	chr12	+	chr12:58019102-58019192	chr12:58019114-58019192		chr12:58019102-58019113	chr12:58019101-58019102		21.00
N	jcn_only_AD	CUFF.352	chr15	-	chr15:90414779-90421496;chr15:90414779-90431752	chr15:90414779-90420537		chr15:90420538-90421496;chr15:90421497-90431752	chr15:90421496-90421497;chr15:90431752-90431753		30.88
K	alternative_first_exon	CUFF.410	chr16	-	chr16:75579853-75589701	chr16:75579853-75589116	chr16:75589702-75590268	chr16:75589117-75589215			14.29
N	alternative_acceptor	CUFF.504	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		1.36
K	intron_retention	CUFF.36	chr1	+	chr1:110211994-110212257				chr1:110211993-110211994;chr1:110212257-110212258		85.39
K	cassette	CUFF.264	chr14	+	chr14:50074840-50080973	chr14:50074840-50079189;chr14:50079343-50080973		chr14:50079190-50079342			23.81
K	cassette	CUFF.107	chr10	+	chr10:48221540-48231778	chr10:48221540-48229090;chr10:48229192-48231778		chr10:48229091-48229191			44.44
K	intron_retention	CUFF.445	chr17	-	chr17:40738910-40739851				chr17:40738909-40738910;chr17:40739851-40739852		41.18
K	alternative_last_exon	CUFF.337	chr15	-	chr15:75762341-75766029	chr15:75763172-75766029	chr15:75762079-75762340	chr15:75763021-75763171			42.86
N	alternative_acceptor	CUFF.919	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		21.88
N	jcn_only_AA	CUFF.504	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		4.88
N	alternative_last_exon	CUFF.945	chr6	-	chr6:128320050-128322340	chr6:128321476-128322340	chr6:128319865-128320049	chr6:128321038-128321475			83.81
K	alternative_last_exon	CUFF.337	chr15	-	chr15:75772256-75782548	chr15:75780119-75782548	chr15:75772189-75772255	chr15:75779531-75780118			98.28
K	intron_retention	CUFF.530	chr19	+	chr19:17447967-17448816				chr19:17447966-17447967;chr19:17448816-17448817		89.80
N	alternative_acceptor	CUFF.890	chr5	+	chr5:131658049-131662969	chr5:131658049-131660153		chr5:131660154-131662969	chr5:131662969-131662970		16.67
K	coord_cassette	CUFF.471	chr17	-	chr17:79354385-79358928	chr17:79354385-79355676;chr17:79355741-79358745;chr17:79358833-79358928		chr17:79355677-79355740;chr17:79358746-79358832			75.78
K	jcn_only_AD	CUFF.912	chr6	+	chr6:28116603-28117260	chr6:28116617-28117260		chr6:28116603-28116616	chr6:28116602-28116603		87.10
K	jcn_only_AA	CUFF.239	chr12	-	chr12:113596915-113599074	chr12:113596918-113599074		chr12:113596915-113596917	chr12:113596914-113596915		13.73
K	intron_retention		chr5	-	chr5:64887330-64887669				chr5:64887329-64887330;chr5:64887669-64887670		19.05
K	alternative_first_exon	CUFF.1055	chr8	-	chr8:120774849-120790258	chr8:120774849-120779242	chr8:120790259-120790369	chr8:120779243-120779444			88.89
K	alternative_acceptor	CUFF.506	chr19	+	chr19:4304759-4306020;chr19:4304759-4305942	chr19:4304759-4305981		chr19:4305943-4305981;chr19:4305982-4306020	chr19:4305981-4305982;chr19:4306020-4306021		14.89
N	jcn_only_AD		chr11	+	chr11:36397709-36398178	chr11:36397788-36398178					88.37
K	intron_retention	CUFF.728	chr22	-	chr22:51018701-51018786				chr22:51018700-51018701;chr22:51018786-51018787		59.26
N	jcn_only_AA		chr15	+	chr15:77756730-77759524	chr15:77756730-77759436		chr15:77759437-77759524	chr15:77759524-77759525		87.69
K	intron_retention	CUFF.165	chr11	+	chr11:65479917-65480236				chr11:65479916-65479917;chr11:65480236-65480237		11.34
N	jcn_only_AA		chr16	-	chr16:57513598-57517869	chr16:57513601-57517869		chr16:57513598-57513600	chr16:57513597-57513598		33.33
N	alternative_first_exon		chr15	-	chr15:55486558-55488550	chr15:55486558-55487501	chr15:55488551-55488889	chr15:55487502-55487597			35.29
K	jcn_only_AA	CUFF.1089,CUFF.1109	chr9	+	chr9:116779065-116791189	chr9:116779065-116791012		chr9:116791013-116791189	chr9:116791189-116791190		83.74
K	intron_retention	CUFF.754	chr3	-	chr3:49462308-49462381				chr3:49462307-49462308;chr3:49462381-49462382		20.93
N	jcn_only_AD	CUFF.603	chr2	+	chr2:48996261-49003418;chr2:48996214-49003418	chr2:48898820-49003418		chr2:48898820-48996213;chr2:48996214-48996260	chr2:48898819-48898820;chr2:48996213-48996214		71.70
N	alternative_donor	CUFF.971	chr7	-	chr7:37382368-37433424;chr7:37382368-37392635;chr7:37382368-37488462;chr7:37382368-37382655	chr7:37382368-37488277		chr7:37382656-37392635;chr7:37392636-37433424;chr7:37433425-37488277;chr7:37488278-37488462	chr7:37392635-37392636;chr7:37433424-37433425;chr7:37488277-37488278;chr7:37488462-37488463		60.00
K	jcn_only_AA	CUFF.556	chr19	-	chr19:49335990-49337532	chr19:49336010-49337532		chr19:49335990-49336009	chr19:49335989-49335990		8.09
N	alternative_donor	CUFF.352	chr15	-	chr15:90414779-90421496;chr15:90414779-90431752	chr15:90414779-90420537		chr15:90420538-90421496;chr15:90421497-90431752	chr15:90421496-90421497;chr15:90431752-90431753		6.09
N	alternative_acceptor		chr14	-	chr14:71227900-71249939	chr14:71232205-71249939		chr14:71227900-71232204	chr14:71227899-71227900		40.00
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	chr11:118404981-118405070	79.01
K	alternative_last_exon	CUFF.169	chr11	+	chr11:74108951-74195221	chr11:74108951-74139377	chr11:74195222-74195293	chr11:74139378-74139610		chr11:74108814-74108950	61.90
N	intron_retention		chr1	-	chr1:156909078-156909339				chr1:156909077-156909078;chr1:156909339-156909340		17.78
K	alternative_acceptor	CUFF.1037	chr8	+	chr8:71564130-71564769	chr8:71564130-71564745		chr8:71564746-71564769	chr8:71564769-71564770		2.78
N	alternative_first_exon		chr12	-	chr12:53467256-53468878	chr12:53467256-53468432	chr12:53468879-53469003	chr12:53468433-53468856			86.05
K	intron_retention	CUFF.532	chr19	+	chr19:18119928-18120400				chr19:18119927-18119928;chr19:18120400-18120401		29.41
K	cassette	CUFF.60	chr1	+	chr1:166810326-166816730	chr1:166810326-166815848;chr1:166815976-166816730		chr1:166815849-166815975			50.00
N	jcn_only_AD	CUFF.457	chr17	+	chr17:61562331-61562596;chr17:61561903-61562596	chr17:61562428-61562596		chr17:61561903-61562330;chr17:61562331-61562427	chr17:61561902-61561903;chr17:61562330-61562331		66.67
N	jcn_only_AA	CUFF.1016	chr7	+	chr7:150817233-150820880	chr7:150817233-150819811		chr7:150819812-150820880	chr7:150820880-150820881		61.70
N	cassette	CUFF.793	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			88.84
N	alternative_donor		chr18	+	chr18:55888990-55895061;chr18:55862966-55895061	chr18:55833094-55895061		chr18:55833094-55862965;chr18:55862966-55888989	chr18:55833093-55833094;chr18:55862965-55862966		100.00
K	alternative_last_exon	CUFF.1040	chr8	+	chr8:75275289-75400912	chr8:75275289-75276219	chr8:75400913-75401197	chr8:75276220-75277074			85.71
K	intron_retention	CUFF.171	chr11	-	chr11:75522615-75524647				chr11:75522614-75522615;chr11:75524647-75524648		73.08
K	jcn_only_AA	CUFF.595,CUFF.631	chr2	+	chr2:109102365-109102966	chr2:109102365-109102890		chr2:109102891-109102966	chr2:109102966-109102967		98.12
K	intron_retention	CUFF.946	chr6	-	chr6:133044194-133044872				chr6:133044193-133044194;chr6:133044872-133044873		14.29
N	jcn_only_AA	CUFF.531	chr19	+	chr19:17581517-17594690;chr19:17581517-17598268	chr19:17581517-17597371					81.58
N	jcn_only_AD		chr4	-	chr4:6537105-6565286	chr4:6537105-6557260					61.11
K	alternative_first_exon	CUFF.609	chr2	-	chr2:69870407-69870874,chr2:69870407-69870923;chr2:69870407-69901154	chr2:69870407-69870706	chr2:69901155-69901580	chr2:69870707-69871115			36.67
K	alternative_first_exon	CUFF.78	chr1	+	chr1:222806592-222818895	chr1:222817929-222818895	chr1:222806446-222806591	chr1:222817628-222817928			70.13
K	alternative_acceptor	CUFF.868	chr5	+	chr5:39521730-39524364	chr5:39521730-39524352		chr5:39524353-39524364	chr5:39524364-39524365		31.37
N	jcn_only_AD	CUFF.793	chr3	-	chr3:141820684-141868024	chr3:141820684-141844990		chr3:141844991-141868024	chr3:141868024-141868025		6.90
K	alternative_acceptor	CUFF.878,CUFF.885	chr5	+	chr5:56543043-56545280	chr5:56543043-56545235		chr5:56545236-56545280	chr5:56545280-56545281	chr5:56542902-56543042;chr5:56545281-56545403	57.78
N	jcn_only_AD	CUFF.820	chr4	+	chr4:6911233-6925099;chr4:6912329-6925099	chr4:6911679-6925099		chr4:6911233-6911678;chr4:6911679-6912328	chr4:6911232-6911233;chr4:6911678-6911679		2.00
K	alternative_donor	CUFF.676,CUFF.691	chr20	-	chr20:61991052-61992528	chr20:61991052-61992441		chr20:61992442-61992528	chr20:61992528-61992529		33.33
N	cassette	CUFF.988	chr7	-	chr7:86574363-86594219	chr7:86574363-86577042;chr7:86577239-86594219		chr7:86577043-86577238			84.09
K	mutually_exclusive	CUFF.97	chr10	-	chr10:27040713-27047990,chr10:27048168-27054146	chr10:27040713-27044583,chr10:27044671-27054146	chr10:27047991-27048167	chr10:27044584-27044670			18.18
N	mutually_exclusive	CUFF.647	chr2	-	chr2:175711686-175779785,chr2:175779900-175816891	chr2:175711686-175742567,chr2:175742857-175816891	chr2:175779786-175779899	chr2:175742568-175742856			23.64
K	cassette	CUFF.223	chr12	-	chr12:52981636-52985247	chr12:52981636-52984619;chr12:52984746-52985247		chr12:52984620-52984745			71.88
K	intron_retention		chr2	-	chr2:242447551-242447732				chr2:242447550-242447551;chr2:242447732-242447733		16.37
K	alternative_last_exon	CUFF.1139	chrX	-	chrX:119312412-119378618,chrX:119377887-119378618,chrX:119374209-119378618;chrX:119271100-119378618	chrX:119355498-119378618	chrX:119270952-119271099	chrX:119355102-119355497			60.42
K	alternative_first_exon	CUFF.133	chr10	+	chr10:124134323-124152696;chr10:124134364-124152696	chr10:124151889-124152696	chr10:124134212-124134322;chr10:124134325-124134363	chr10:124151819-124151888			93.46
K	alternative_first_exon	CUFF.518	chr19	+	chr19:11041001-11044036	chr19:11042937-11044036	chr19:11039690-11041000	chr19:11042708-11042936			20.83
N	jcn_only_AA	CUFF.97	chr10	-	chr10:27112235-27149675	chr10:27128713-27149675		chr10:27112235-27128712	chr10:27112234-27112235		7.14
N	jcn_only_AD	CUFF.396	chr16	-	chr16:57513601-57514241;chr16:57513601-57521157;chr16:57513601-57513772;chr16:57513601-57517869;chr16:57513601-57515373;chr16:57513601-57521042;chr16:57513601-57513756;chr16:57513601-57514206	chr16:57513601-57521007		chr16:57513757-57513772;chr16:57513773-57514206;chr16:57514207-57514241;chr16:57514242-57515373;chr16:57515374-57517869;chr16:57517870-57521007;chr16:57521008-57521042;chr16:57521043-57521157	chr16:57513772-57513773;chr16:57514206-57514207;chr16:57514241-57514242;chr16:57515373-57515374;chr16:57517869-57517870;chr16:57521007-57521008;chr16:57521042-57521043;chr16:57521157-57521158		7.83
K	intron_retention	CUFF.188	chr11	-	chr11:119229845-119229940				chr11:119229844-119229845;chr11:119229940-119229941		11.86
K	alternative_donor	CUFF.561	chr19	-	chr19:51537396-51537840	chr19:51537396-51537680		chr19:51537681-51537840	chr19:51537840-51537841		74.22
K	intron_retention	CUFF.187	chr11	+	chr11:119056220-119056633				chr11:119056219-119056220;chr11:119056633-119056634		9.27
K	alternative_last_exon	CUFF.36,CUFF.81	chr1	+	chr1:110214206-110217368;chr1:110214206-110215824;chr1:110214206-110224430	chr1:110214206-110251102	chr1:110215825-110215963;chr1:110224431-110224456	chr1:110251103-110252171			8.05
N	alternative_acceptor	CUFF.695	chr21	-	chr21:15981890-15985196	chr21:15984967-15985196		chr21:15981890-15984966	chr21:15981889-15981890		12.50
K	alternative_last_exon	CUFF.428,CUFF.435	chr17	+	chr17:17380580-17394592	chr17:17380580-17388613	chr17:17394593-17396637	chr17:17388614-17388978			70.00
N	cassette	CUFF.172	chr11	-	chr11:77885630-77888784	chr11:77885630-77887933;chr11:77888032-77888784		chr11:77887934-77888031			83.52
N	intron_retention	CUFF.725	chr22	+	chr22:45204319-45204551				chr22:45204318-45204319;chr22:45204551-45204552		82.14
N	alternative_donor	CUFF.999	chr7	-	chr7:102453979-102462486	chr7:102453979-102454780		chr7:102454781-102462486	chr7:102462486-102462487		0.00
N	jcn_only_AA	CUFF.566	chr19	+	chr19:54657578-54658995;chr19:54657578-54659046	chr19:54657578-54657680		chr19:54657681-54658995;chr19:54658996-54659046	chr19:54658995-54658996;chr19:54659046-54659047		22.92
N	cassette	CUFF.509	chr19	-	chr19:6044294-6110403	chr19:6044294-6047417;chr19:6047516-6110403		chr19:6047418-6047515			82.76
K	alternative_last_exon	CUFF.319	chr15	+	chr15:45741000-45753476	chr15:45741000-45752643	chr15:45753477-45753588	chr15:45752644-45753213			66.67
N	alternative_donor		chr3	-	chr3:156262229-156266593;chr3:156262229-156266654	chr3:156262229-156266693		chr3:156266594-156266654;chr3:156266655-156266693	chr3:156266654-156266655;chr3:156266693-156266694		97.11
K	intron_retention	CUFF.325	chr15	+	chr15:57535749-57543547				chr15:57535748-57535749;chr15:57543547-57543548		50.00
N	alternative_donor	CUFF.489	chr18	-	chr18:47329224-47337765;chr18:47329224-47340051;chr18:47329224-47339094;chr18:47329224-47340186;chr18:47329224-47339838	chr18:47329224-47340101		chr18:47337766-47339094;chr18:47339095-47339838;chr18:47339839-47340051;chr18:47340052-47340101;chr18:47340102-47340186	chr18:47339094-47339095;chr18:47339838-47339839;chr18:47340051-47340052;chr18:47340101-47340102;chr18:47340186-47340187		29.89
K	alternative_first_exon	CUFF.680	chr20	+	chr20:21284112-21307127	chr20:21307045-21307127	chr20:21283912-21284111	chr20:21306917-21307044			42.86
N	alternative_donor	CUFF.1098	chr9	-	chr9:130941184-130941522;chr9:130941184-130941267	chr9:130941184-130941351		chr9:130941268-130941351;chr9:130941352-130941522	chr9:130941351-130941352;chr9:130941522-130941523		57.14
N	jcn_only_AD	CUFF.1000	chr7	+	chr7:107204192-107205032;chr7:107204505-107205032;chr7:107204693-107205032	chr7:107204655-107205032		chr7:107204192-107204504;chr7:107204505-107204654;chr7:107204655-107204692	chr7:107204191-107204192;chr7:107204504-107204505;chr7:107204654-107204655		31.71
K	intron_retention	CUFF.136	chr11	-	chr11:406539-407061				chr11:406538-406539;chr11:407061-407062		23.17
K	intron_retention	CUFF.1032	chr8	-	chr8:38002834-38003480				chr8:38002833-38002834;chr8:38003480-38003481		8.93
K	alternative_first_exon	CUFF.1052	chr8	+	chr8:107531368-107691437;chr8:107670314-107691437;chr8:107630412-107691437	chr8:107593480-107691437	chr8:107531171-107531367;chr8:107670221-107670313;chr8:107630316-107630411	chr8:107593125-107593479			75.00
K	alternative_first_exon	CUFF.338	chr15	-	chr15:77474383-77578764	chr15:77474383-77544708	chr15:77578765-77578846	chr15:77544709-77544873			98.10
N	intron_retention		chr22	+	chr22:21058345-21058475				chr22:21058344-21058345;chr22:21058475-21058476		91.43
K	alternative_acceptor	CUFF.403	chr16	+	chr16:67234872-67235311	chr16:67234872-67235287		chr16:67235288-67235311	chr16:67235311-67235312		42.05
N	intron_retention	CUFF.21	chr1	-	chr1:41486606-41487201				chr1:41486605-41486606;chr1:41487201-41487202		45.45
N	alternative_acceptor	CUFF.67	chr1	+	chr1:196913069-196918746;chr1:196913069-196918565	chr1:196913069-196918584		chr1:196918566-196918584;chr1:196918585-196918746	chr1:196918584-196918585;chr1:196918746-196918747	chr1:196912830-196913068;chr1:196918747-196918779	61.19
N	cassette	CUFF.49	chr1	-	chr1:153921861-153924493	chr1:153921861-153923735;chr1:153924143-153924493		chr1:153923736-153924142			96.30
K	intron_retention	CUFF.604	chr2	-	chr2:61726049-61726847				chr2:61726048-61726049;chr2:61726847-61726848		39.53
N	intron_retention	CUFF.1033	chr8	-	chr8:56675588-56676195				chr8:56675587-56675588;chr8:56676195-56676196		54.55
K	alternative_first_exon	CUFF.360	chr15	-	chr15:102202020-102211688	chr15:102202020-102204372	chr15:102211689-102211789	chr15:102204373-102204465			17.07
N	cassette	CUFF.878	chr5	+	chr5:56472228-56526672	chr5:56472228-56509900;chr5:56510021-56526672		chr5:56509901-56510020		chr5:56471275-56472227;chr5:56526673-56526796	89.29
K	alternative_acceptor	CUFF.945	chr6	-	chr6:128330411-128385902	chr6:128330414-128385902		chr6:128330411-128330413	chr6:128330410-128330411		95.00
N	intron_retention		chr17	-	chr17:79477356-79477504				chr17:79477355-79477356;chr17:79477504-79477505		93.97
N	cassette	CUFF.816	chr4	-	chr4:3945100-3954837	chr4:3945100-3949816;chr4:3949948-3954837		chr4:3949817-3949947			69.44
K	alternative_first_exon	CUFF.648	chr2	-	chr2:177043827-177053146	chr2:177043827-177052792	chr2:177053147-177053302	chr2:177052793-177053021			33.93
K	intron_retention	CUFF.367	chr16	-	chr16:1370460-1372488				chr16:1370459-1370460;chr16:1372488-1372489		60.00
N	coord_cassette	CUFF.18	chr1	+	chr1:32541424-32557275	chr1:32541424-32542363;chr1:32542448-32542764;chr1:32542920-32557275		chr1:32542364-32542447;chr1:32542765-32542919			54.74
N	cassette	CUFF.802	chr3	+	chr3:186739793-186756529	chr3:186739793-186756179;chr3:186756280-186756529		chr3:186756180-186756279			96.61
K	intron_retention	CUFF.936	chr6	+	chr6:90337416-90338830				chr6:90337415-90337416;chr6:90338830-90338831		22.48
K	cassette	CUFF.146	chr11	+	chr11:3423960-3424822	chr11:3423960-3424144;chr11:3424187-3424822		chr11:3424145-3424186			63.54
K	jcn_only_AA	CUFF.246	chr13	-	chr13:25525627-25541529	chr13:25539719-25541529					78.85
K	jcn_only_AA	CUFF.278	chr14	-	chr14:75136830-75137464	chr14:75136846-75137464		chr14:75136830-75136845	chr14:75136829-75136830	chr14:75137465-75137574;chr14:75136650-75136829	28.00
K	cassette	CUFF.983	chr7	-	chr7:74981241-74984789	chr7:74981241-74982815;chr7:74982903-74984789		chr7:74982816-74982902			78.79
K	jcn_only_AA	CUFF.406	chr16	-	chr16:70267574-70268076	chr16:70267606-70268076		chr16:70267574-70267605	chr16:70267573-70267574		74.58
K	alternative_last_exon	CUFF.132	chr10	-	chr10:123503374-123549683	chr10:123542215-123549683	chr10:123499841-123503373	chr10:123541921-123542214			76.27
K	alternative_donor	CUFF.781	chr3	+	chr3:125635563-125637706	chr3:125635661-125637706		chr3:125635563-125635660	chr3:125635562-125635563		28.21
N	jcn_only_AA	CUFF.826	chr4	-	chr4:36152667-36160351	chr4:36159173-36160351		chr4:36152667-36159172	chr4:36152666-36152667		9.65
K	intron_retention	CUFF.896	chr5	+	chr5:140706205-140707336				chr5:140706204-140706205;chr5:140707336-140707337		24.56
N	jcn_only_AA	CUFF.307,CUFF.336	chr15	+	chr15:74771620-74773391	chr15:74771620-74772961		chr15:74772962-74773391	chr15:74773391-74773392		8.33
N	alternative_donor	CUFF.336	chr15	+	chr15:74754440-74758376;chr15:74754369-74758376	chr15:74754373-74758376		chr15:74754369-74754372;chr15:74754373-74754439	chr15:74754368-74754369;chr15:74754372-74754373		65.71
N	jcn_only_AA	CUFF.929	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		20.36
K	alternative_first_exon	CUFF.1000	chr7	+	chr7:107214267-107215632;chr7:107211712-107215632	chr7:107214329-107215632	chr7:107210458-107211711	chr7:107214273-107214328			20.00
N	alternative_acceptor	CUFF.640	chr2	-	chr2:166732743-166737188	chr2:166736478-166737188		chr2:166732743-166736477	chr2:166732742-166732743		12.50
K	jcn_only_AA	CUFF.895	chr5	+	chr5:140031392-140031672	chr5:140031392-140031651		chr5:140031652-140031672	chr5:140031672-140031673		62.03
N	alternative_donor	CUFF.1102	chr9	+	chr9:133355188-133355771	chr9:133355287-133355771		chr9:133355188-133355286	chr9:133355187-133355188		16.90
N	alternative_donor	CUFF.187	chr11	+	chr11:119056875-119057187	chr11:119056951-119057187		chr11:119056875-119056950	chr11:119056874-119056875		15.72
K	cassette	CUFF.446	chr17	-	chr17:41719401-41738433	chr17:41719401-41720855;chr17:41721029-41738433		chr17:41720856-41721028			73.49
K	intron_retention	CUFF.165	chr11	+	chr11:65480069-65480236				chr11:65480068-65480069;chr11:65480236-65480237		79.35
N	jcn_only_AA		chr2	+	chr2:1243549-1251098	chr2:1243549-1246509		chr2:1246510-1251098	chr2:1251098-1251099		30.43
N	intron_retention		chr8	-	chr8:80965666-81083659				chr8:80965665-80965666;chr8:81083659-81083660		6.15
K	cassette	CUFF.28	chr1	+	chr1:70832221-70833299	chr1:70832221-70832615;chr1:70832668-70833299		chr1:70832616-70832667			16.20
N	alternative_donor	CUFF.572	chr2	-	chr2:230045-231022	chr2:230045-230546		chr2:230547-231022	chr2:231022-231023		16.67
K	alternative_donor	CUFF.920	chr6	+	chr6:32122024-32122363;chr6:32122172-32122363	chr6:32122182-32122363		chr6:32122024-32122171;chr6:32122172-32122181	chr6:32122023-32122024;chr6:32122171-32122172		76.72
K	jcn_only_AA	CUFF.793	chr3	-	chr3:141693034-141697361	chr3:141693037-141697361		chr3:141693034-141693036	chr3:141693033-141693034		46.61
N	cassette	CUFF.278	chr14	-	chr14:75143456-75151156	chr14:75143456-75149998;chr14:75150237-75151156		chr14:75149999-75150236		chr14:75143286-75143455;chr14:75151157-75151383	70.65
K	cassette	CUFF.1045	chr8	+	chr8:92086140-92090583	chr8:92086140-92088819;chr8:92088960-92090583		chr8:92088820-92088959			84.85
K	intron_retention	CUFF.15	chr1	+	chr1:28661598-28662304				chr1:28661597-28661598;chr1:28662304-28662305		80.00
N	alternative_donor		chr1	+	chr1:245246991-245285221	chr1:245270600-245285221		chr1:245246991-245270599	chr1:245246990-245246991		12.50
N	alternative_acceptor	CUFF.1073	chr9	+	chr9:43818185-43822517	chr9:43818185-43819609		chr9:43819610-43822517	chr9:43822517-43822518		37.50
N	alternative_donor	CUFF.509,CUFF.555	chr19	-	chr19:6047516-6148241;chr19:6047516-6110403;chr19:6047516-6057172;chr19:6047516-6072015	chr19:6047516-6049146		chr19:6049147-6057172;chr19:6057173-6072015;chr19:6072016-6110403;chr19:6110404-6148241	chr19:6057172-6057173;chr19:6072015-6072016;chr19:6110403-6110404;chr19:6148241-6148242		0.00
K	alternative_acceptor	CUFF.47	chr1	-	chr1:151149508-151150476	chr1:151149541-151150476		chr1:151149508-151149540	chr1:151149507-151149508		22.41
K	jcn_only_AA	CUFF.464	chr17	+	chr17:66508690-66511534	chr17:66508690-66509050					9.21
N	intron_retention		chr17	+	chr17:66509112-66511127				chr17:66509111-66509112;chr17:66511127-66511128		73.33
K	alternative_last_exon	CUFF.90	chr10	+	chr10:6268329-6274857	chr10:6268329-6270158	chr10:6274858-6277593	chr10:6270159-6270310			85.71
N	alternative_acceptor	CUFF.1051	chr8	+	chr8:106456610-106573590	chr8:106456610-106463785		chr8:106463786-106573590	chr8:106573590-106573591		0.00
K	jcn_only_AD	CUFF.504	chr19	+	chr19:1438428-1438805	chr19:1438580-1438805		chr19:1438428-1438579	chr19:1438427-1438428		38.74
K	alternative_first_exon	CUFF.971,CUFF.999	chr7	-	chr7:102572381-102603979	chr7:102572381-102573767	chr7:102603980-102604112	chr7:102573768-102574200			41.67
K	alternative_last_exon	CUFF.468	chr17	-	chr17:79250934-79254408	chr17:79253961-79254408	chr17:79250831-79250933	chr17:79253402-79253960		chr17:79254409-79254533	87.76
N	coord_cassette	CUFF.726	chr22	+	chr22:47158746-47189397	chr22:47158746-47185208;chr22:47185369-47188416;chr22:47188474-47189397		chr22:47185209-47185368;chr22:47188417-47188473			92.16
K	jcn_only_AA	CUFF.483	chr18	+	chr18:14797854-14808549	chr18:14797854-14799099					41.79
N	alternative_donor	CUFF.739	chr3	+	chr3:28357915-28360999;chr3:28360371-28360999	chr3:28358351-28360999		chr3:28357915-28358350;chr3:28358351-28360370	chr3:28357914-28357915;chr3:28358350-28358351		15.56
K	intron_retention	CUFF.673	chr2	+	chr2:242610841-242611605				chr2:242610840-242610841;chr2:242611605-242611606		88.41
N	jcn_only_AA	CUFF.2	chr1	+	chr1:2101044-2103493	chr1:2101044-2102991		chr1:2102992-2103493	chr1:2103493-2103494		9.66
N	alternative_acceptor	CUFF.364,CUFF.386	chr16	+	chr16:21756358-21763255	chr16:21756358-21758618		chr16:21758619-21763255	chr16:21763255-21763256		0.91
K	cassette	CUFF.136	chr11	-	chr11:408894-409867	chr11:408894-409216;chr11:409309-409867		chr11:409217-409308			60.05
N	alternative_donor	CUFF.417	chr17	-	chr17:79263609-79269221	chr17:79263609-79268622		chr17:79268623-79269221	chr17:79269221-79269222	chr17:79263491-79263608	48.65
N	alternative_donor	CUFF.276	chr14	-	chr14:71205116-71206758	chr14:71205116-71206614		chr14:71206615-71206758	chr14:71206758-71206759		2.25
K	alternative_last_exon	CUFF.139	chr11	-	chr11:1775369-1776135	chr11:1775486-1776135	chr11:1774973-1775368	chr11:1775392-1775485			10.77
K	intron_retention	CUFF.554	chr19	-	chr19:49117594-49117696				chr19:49117593-49117594;chr19:49117696-49117697		61.54
N	cassette	CUFF.155	chr11	+	chr11:36398255-36422546	chr11:36398255-36415395;chr11:36415562-36422546		chr11:36415396-36415561			83.61
N	alternative_acceptor	CUFF.793	chr3	-	chr3:141697525-141712379	chr3:141708357-141712379		chr3:141697525-141708356	chr3:141697524-141697525		0.49
K	intron_retention	CUFF.669	chr2	+	chr2:241402930-241404032				chr2:241402929-241402930;chr2:241404032-241404033		10.11
N	alternative_donor	CUFF.1013	chr7	+	chr7:136554166-136676933	chr7:136635828-136676933		chr7:136554166-136635827	chr7:136554165-136554166		7.14
K	alternative_last_exon	CUFF.211	chr12	-	chr12:25652931-25656671;chr12:25650729-25656671;chr12:25629395-25656671;chr12:25655973-25656671	chr12:25562365-25656671	chr12:25650631-25650728;chr12:25628947-25629394;chr12:25655879-25655972	chr12:25562143-25562364			8.87
K	jcn_only_AA	CUFF.160	chr11	+	chr11:61615757-61624482	chr11:61615757-61616152				chr11:61615631-61615756	4.55
N	alternative_last_exon		chr11	+	chr11:36415562-36415945;chr11:36415562-36422546	chr11:36415562-36417663	chr11:36422547-36422835	chr11:36417664-36417838			53.62
K	coord_cassette	CUFF.349	chr15	-	chr15:83687606-83698887	chr15:83687606-83689426;chr15:83689515-83697367;chr15:83697481-83698887		chr15:83689427-83689514;chr15:83697368-83697480			98.78
N	jcn_only_AD	CUFF.716	chr22	+	chr22:29683124-29688125	chr22:29687589-29688125					59.30
N	alternative_acceptor	CUFF.504	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		2.26
K	cassette	CUFF.1136	chrX	+	chrX:107381222-107393381	chrX:107381222-107381342;chrX:107381422-107393381		chrX:107381343-107381421			88.89
N	intron_retention		chr7	+	chr7:75040010-75040690				chr7:75040009-75040010;chr7:75040690-75040691		77.78
K	alternative_acceptor	CUFF.140	chr11	-	chr11:2188716-2189095	chr11:2188747-2189095		chr11:2188716-2188746	chr11:2188715-2188716		14.81
N	cassette	CUFF.843	chr4	-	chr4:83816928-83820865;chr4:83816928-83821229	chr4:83816928-83819141;chr4:83819216-83821229,chr4:83819216-83820865		chr4:83819142-83819215			98.88
K	alternative_last_exon	CUFF.366,CUFF.374	chr16	+	chr16:603042-604553	chr16:603042-603338	chr16:604554-604734	chr16:603339-603595			15.52
N	cassette	CUFF.589	chr2	-	chr2:27676381-27676848	chr2:27676381-27676496;chr2:27676607-27676848		chr2:27676497-27676606			26.26
K	alternative_first_exon	CUFF.451	chr17	-	chr17:47304121-47307938	chr17:47304121-47307829	chr17:47307939-47308224	chr17:47307830-47307890			62.69
N	jcn_only_AA	CUFF.671	chr2	-	chr2:242435950-242437030	chr2:242436794-242437030		chr2:242435950-242436793	chr2:242435949-242435950		14.29
K	intron_retention	CUFF.633	chr2	-	chr2:110881641-110883213				chr2:110881640-110881641;chr2:110883213-110883214		17.46
N	jcn_only_AD	CUFF.531	chr19	+	chr19:17612229-17615263;chr19:17611686-17615263	chr19:17611442-17615263		chr19:17611442-17611685;chr19:17611686-17612228	chr19:17611441-17611442;chr19:17611685-17611686		32.39
K	alternative_first_exon	CUFF.1001	chr7	+	chr7:107220812-107221203;chr7:107220747-107221203	chr7:107221091-107221203	chr7:107220751-107220811;chr7:107220422-107220746	chr7:107220910-107221090			26.97
N	alternative_donor	CUFF.579	chr2	+	chr2:3461465-3464033	chr2:3462233-3464033		chr2:3461465-3462232	chr2:3461464-3461465		10.24
N	coord_cassette	CUFF.775	chr3	-	chr3:120360541-120365819	chr3:120360541-120363444;chr3:120363467-120365113;chr3:120365214-120365819		chr3:120363445-120363466;chr3:120365114-120365213			91.30
N	alternative_donor	CUFF.56	chr1	+	chr1:160137203-160141040	chr1:160137220-160141040		chr1:160137203-160137219	chr1:160137202-160137203		75.00
N	cassette	CUFF.126	chr10	+	chr10:101507148-101514285	chr10:101507148-101510125;chr10:101510154-101514285		chr10:101510126-101510153			91.11
N	intron_retention		chr6	-	chr6:133047978-133055391				chr6:133047977-133047978;chr6:133055391-133055392		42.86
K	coord_cassette	CUFF.773	chr3	-	chr3:119246689-119263396	chr3:119246689-119248688;chr3:119248785-119255983;chr3:119256266-119263396		chr3:119248689-119248784;chr3:119255984-119256265			15.52
N	alternative_donor	CUFF.389	chr16	+	chr16:22466187-22470675	chr16:22466927-22470675		chr16:22466187-22466926	chr16:22466186-22466187		1.59
K	intron_retention	CUFF.1131	chrX	-	chrX:85236814-85282494				chrX:85236813-85236814;chrX:85282494-85282495		14.29
K	cassette	CUFF.641	chr2	+	chr2:169668163-169684667	chr2:169668163-169681143;chr2:169681228-169684667		chr2:169681144-169681227			11.17
N	coord_cassette	CUFF.97	chr10	-	chr10:27040713-27054146	chr10:27040713-27044583;chr10:27044671-27047990;chr10:27048165-27054146		chr10:27044584-27044670;chr10:27047991-27048164			91.30
N	jcn_only_AA	CUFF.1037	chr8	+	chr8:71543526-71558279	chr8:71543526-71544669		chr8:71544670-71558279	chr8:71558279-71558280		12.50
K	intron_retention	CUFF.418	chr17	+	chr17:1945526-1945898				chr17:1945525-1945526;chr17:1945898-1945899		19.70
K	alternative_first_exon	CUFF.799	chr3	+	chr3:178866008-178916537	chr3:178867505-178916537	chr3:178865902-178866007	chr3:178867296-178867504			26.25
K	intron_retention	CUFF.464	chr17	+	chr17:66509120-66511127				chr17:66509119-66509120;chr17:66511127-66511128		72.73
N	intron_retention		chr2	-	chr2:61752469-61752626				chr2:61752468-61752469;chr2:61752626-61752627		92.31
N	jcn_only_AD	CUFF.728	chr22	-	chr22:30735024-30736197	chr22:30735024-30735118		chr22:30735119-30736197	chr22:30736197-30736198		48.94
K	alternative_last_exon	CUFF.994	chr7	+	chr7:93621479-93640352	chr7:93621479-93629608	chr7:93640353-93640522	chr7:93629609-93629684			40.62
N	intron_retention		chr2	-	chr2:242441124-242447857				chr2:242441123-242441124;chr2:242447857-242447858		90.70
K	alternative_acceptor	CUFF.812	chr4	-	chr4:2934905-2935293	chr4:2934937-2935293		chr4:2934905-2934936	chr4:2934904-2934905		96.75
N	intron_retention		chr7	+	chr7:150831656-150837065				chr7:150831655-150831656;chr7:150837065-150837066		18.75
K	intron_retention	CUFF.146	chr11	+	chr11:3405515-3422988				chr11:3405514-3405515;chr11:3422988-3422989		53.33
N	intron_retention		chr7	-	chr7:102242853-102249207				chr7:102242852-102242853;chr7:102249207-102249208		31.82
N	jcn_only_AD	CUFF.603	chr2	+	chr2:48898820-49003418;chr2:48996261-49003418	chr2:48996214-49003418		chr2:48898820-48996213;chr2:48996214-48996260	chr2:48898819-48898820;chr2:48996213-48996214		15.09
K	intron_retention	CUFF.583	chr2	+	chr2:9244290-9244564				chr2:9244289-9244290;chr2:9244564-9244565		32.35
N	alternative_donor	CUFF.1066	chr9	-	chr9:15226011-15267911	chr9:15226011-15232229		chr9:15232230-15267911	chr9:15267911-15267912		17.31
N	jcn_only_AD	CUFF.1124	chrX	+	chrX:47035986-47040613	chrX:47039906-47040613					95.45
N	jcn_only_AD	CUFF.1102	chr9	+	chr9:133355188-133355771	chr9:133355287-133355771		chr9:133355188-133355286	chr9:133355187-133355188		16.90
K	jcn_only_AA	CUFF.1032	chr8	-	chr8:38005846-38006158	chr8:38005878-38006158		chr8:38005846-38005877	chr8:38005845-38005846		21.84
N	alternative_acceptor		chr1	+	chr1:160137220-160141040	chr1:160137220-160139462		chr1:160139463-160141040	chr1:160141040-160141041		50.00
K	alternative_last_exon	CUFF.466	chr17	+	chr17:75543175-75557026	chr17:75543175-75544052	chr17:75557027-75559424	chr17:75544053-75544076			22.58
K	intron_retention	CUFF.457	chr17	+	chr17:61573785-61574893				chr17:61573784-61573785;chr17:61574893-61574894		88.62
N	cassette	CUFF.454	chr17	-	chr17:57775340-57784731	chr17:57775340-57776231;chr17:57777551-57784731		chr17:57776232-57777550			85.42
N	jcn_only_AA	CUFF.482	chr18	+	chr18:55862966-55912658	chr18:55862966-55895061		chr18:55895062-55912658	chr18:55912658-55912659		66.67
K	cassette	CUFF.508	chr19	-	chr19:5897009-5903622	chr19:5897009-5901345;chr19:5901466-5903622		chr19:5901346-5901465			47.06
N	alternative_acceptor	CUFF.119	chr10	-	chr10:79396328-79397022;chr10:79396274-79397022	chr10:79163782-79397022		chr10:79163782-79396273;chr10:79396274-79396327	chr10:79163781-79163782;chr10:79396273-79396274		100.00
N	jcn_only_AD	CUFF.271,CUFF.278	chr14	-	chr14:75138187-75139533	chr14:75138187-75138671		chr14:75138672-75139533	chr14:75139533-75139534	chr14:75138111-75138186;chr14:75139534-75139655	17.50
N	jcn_only_AD		chr2	-	chr2:242872-244626;chr2:242872-243502	chr2:242872-247537		chr2:243503-244626;chr2:244627-247537	chr2:244626-244627;chr2:247537-247538		48.61
K	mutually_exclusive	CUFF.563	chr19	+	chr19:52264484-52266614,chr19:52266771-52271897	chr19:52264484-52265669,chr19:52265789-52271897	chr19:52266615-52266770	chr19:52265670-52265788			52.63
K	alternative_first_exon	CUFF.1114	chrX	-	chrX:10535644-10645504	chrX:10535644-10588329	chrX:10645505-10645779	chrX:10588330-10588428			5.39
K	intron_retention	CUFF.358	chr15	+	chr15:97326975-97327382				chr15:97326974-97326975;chr15:97327382-97327383		89.09
N	cassette	CUFF.232	chr12	+	chr12:58017882-58018648	chr12:58017882-58018282;chr12:58018390-58018648		chr12:58018283-58018389			84.85
N	jcn_only_AA	CUFF.292	chr14	+	chr14:92922953-92949023	chr14:92922953-92923597		chr14:92923598-92949023	chr14:92949023-92949024		32.79
K	alternative_last_exon	CUFF.1117	chrX	+	chrX:15711182-15720904;chrX:15711182-15715362	chrX:15711182-15713793	chrX:15720905-15721927;chrX:15715363-15715961	chrX:15713794-15713856			9.09
N	alternative_acceptor	CUFF.189	chr11	-	chr11:119291089-119291578;chr11:119291097-119291578	chr11:119291046-119291578		chr11:119291046-119291088;chr11:119291089-119291096	chr11:119291045-119291046;chr11:119291088-119291089		5.41
K	intron_retention	CUFF.728	chr22	-	chr22:51017937-51018155				chr22:51017936-51017937;chr22:51018155-51018156		7.17
N	alternative_acceptor	CUFF.954	chr6	+	chr6:161471012-161491639	chr6:161471012-161488230		chr6:161488231-161491639	chr6:161491639-161491640	chr6:161469648-161471011;chr6:161491640-161491882	0.00
N	alternative_donor	CUFF.551	chr19	+	chr19:45254638-45259488	chr19:45258732-45259488		chr19:45254638-45258731	chr19:45254637-45254638		8.33
K	intron_retention	CUFF.158	chr11	+	chr11:59861032-59861436				chr11:59861031-59861032;chr11:59861436-59861437		63.64
K	jcn_only_AA	CUFF.1069	chr9	+	chr9:34993442-34996391	chr9:34993442-34996261		chr9:34996262-34996391	chr9:34996391-34996392		82.80
N	jcn_only_AD		chr18	-	chr18:67614769-67623849;chr18:67614769-67623990	chr18:67614769-67628827		chr18:67623850-67623990;chr18:67623991-67628827	chr18:67623990-67623991;chr18:67628827-67628828		33.33
K	intron_retention	CUFF.187	chr11	+	chr11:119058368-119058648				chr11:119058367-119058368;chr11:119058648-119058649		78.70
N	alternative_first_exon	CUFF.1010	chr7	+	chr7:129015768-129019481;chr7:129008393-129019481	chr7:129017465-129019481	chr7:129015629-129015767;chr7:129007884-129008392	chr7:129017358-129017464			54.39
N	jcn_only_AD	CUFF.28	chr1	+	chr1:70832012-70832126;chr1:70820892-70832126;chr1:70820791-70832126	chr1:70820795-70832126		chr1:70820791-70820794;chr1:70820795-70820891;chr1:70820892-70832011	chr1:70820790-70820791;chr1:70820794-70820795;chr1:70820891-70820892		6.74
N	jcn_only_AA	CUFF.310	chr15	+	chr15:40545491-40549043;chr15:40545491-40556004	chr15:40545491-40555999		chr15:40549044-40555999;chr15:40556000-40556004	chr15:40555999-40556000;chr15:40556004-40556005		3.70
K	intron_retention		chr12	+	chr12:69214155-69218142				chr12:69214154-69214155;chr12:69218142-69218143		1.74
K	alternative_donor	CUFF.818	chr4	-	chr4:6380300-6382767	chr4:6380300-6382723		chr4:6382724-6382767	chr4:6382767-6382768		48.70
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55895140-55912658;chr18:55833094-55912658;chr18:55865102-55912658;chr18:55862966-55912658;chr18:55888990-55912658	chr18:55895121-55912658		chr18:55833094-55862965;chr18:55862966-55865101;chr18:55865102-55888989;chr18:55888990-55895120;chr18:55895121-55895139	chr18:55833093-55833094;chr18:55862965-55862966;chr18:55865101-55865102;chr18:55888989-55888990;chr18:55895120-55895121		11.28
K	intron_retention	CUFF.221	chr12	+	chr12:52407565-52407660				chr12:52407564-52407565;chr12:52407660-52407661		11.45
N	intron_retention		chr11	+	chr11:118404267-118404571				chr11:118404266-118404267;chr11:118404571-118404572	chr11:118404572-118404602	38.18
K	intron_retention	CUFF.415	chr16	+	chr16:89804314-89804383				chr16:89804313-89804314;chr16:89804383-89804384		6.12
N	cassette	CUFF.162	chr11	+	chr11:63672516-63676348;chr11:63672516-63675731	chr11:63672516-63673559;chr11:63673587-63676348,chr11:63673587-63675731		chr11:63673560-63673586			34.41
K	alternative_first_exon	CUFF.62	chr1	-	chr1:169439425-169454800	chr1:169439425-169446392	chr1:169454801-169455266	chr1:169446393-169446995			27.27
N	jcn_only_AA	CUFF.966	chr7	-	chr7:22206767-22232984	chr7:22231261-22232984		chr7:22206767-22231260	chr7:22206766-22206767		41.67
K	coord_cassette	CUFF.148	chr11	-	chr11:6622006-6624633	chr11:6622006-6622155;chr11:6622833-6623081;chr11:6623446-6624633		chr11:6622156-6622832;chr11:6623082-6623445			87.76
N	jcn_only_AA	CUFF.497	chr18	-	chr18:67614007-67614596	chr18:67614306-67614596		chr18:67614007-67614305	chr18:67614006-67614007		70.77
N	alternative_donor	CUFF.1000	chr7	+	chr7:107204505-107205032;chr7:107204693-107205032;chr7:107204655-107205032	chr7:107204192-107205032		chr7:107204192-107204504;chr7:107204505-107204654;chr7:107204655-107204692	chr7:107204191-107204192;chr7:107204504-107204505;chr7:107204654-107204655		22.81
K	alternative_acceptor	CUFF.946	chr6	-	chr6:133055523-133055618	chr6:133055526-133055618		chr6:133055523-133055525	chr6:133055522-133055523		10.16
K	intron_retention	CUFF.347	chr15	-	chr15:83331005-83331445				chr15:83331004-83331005;chr15:83331445-83331446		40.59
K	jcn_only_AD	CUFF.887,CUFF.897	chr5	-	chr5:141050196-141050891	chr5:141050196-141050831		chr5:141050832-141050891	chr5:141050891-141050892		35.29
N	coord_cassette	CUFF.176	chr11	-	chr11:102937297-102962515	chr11:102937297-102953476;chr11:102953569-102953984;chr11:102954056-102962515		chr11:102953477-102953568;chr11:102953985-102954055			83.95
K	intron_retention	CUFF.330	chr15	+	chr15:64446202-64446585				chr15:64446201-64446202;chr15:64446585-64446586		52.11
N	jcn_only_AD	CUFF.68	chr1	+	chr1:200870288-200876961	chr1:200875624-200876961		chr1:200870288-200875623	chr1:200870287-200870288		66.67
K	jcn_only_AD	CUFF.493	chr18	+	chr18:61377596-61390228	chr18:61388221-61390228					72.92
K	intron_retention	CUFF.1075	chr9	-	chr9:46686830-46687553				chr9:46686829-46686830;chr9:46687553-46687554		34.88
N	jcn_only_AD	CUFF.271	chr14	-	chr14:59939809-59942586;chr14:59939809-59941156	chr14:59939809-59941445		chr14:59941157-59941445;chr14:59941446-59942586	chr14:59941445-59941446;chr14:59942586-59942587		2.90
N	cassette	CUFF.61	chr1	+	chr1:167341274-167345265	chr1:167341274-167343344;chr1:167343534-167345265		chr1:167343345-167343533			97.64
K	jcn_only_AA	CUFF.944	chr6	+	chr6:126307769-126314938	chr6:126307769-126314902		chr6:126314903-126314938	chr6:126314938-126314939		46.67
N	mutually_exclusive	CUFF.147	chr11	-	chr11:5686913-5688918,chr11:5688942-5699433	chr11:5686913-5687210,chr11:5687312-5699433	chr11:5688919-5688941	chr11:5687211-5687311			93.15
N	alternative_acceptor		chr19	+	chr19:52085136-52092800	chr19:52085136-52089879		chr19:52089880-52092800	chr19:52092800-52092801		80.00
K	intron_retention	CUFF.68	chr1	+	chr1:200883188-200883601				chr1:200883187-200883188;chr1:200883601-200883602		18.18
K	cassette	CUFF.17	chr1	+	chr1:31783012-31791955	chr1:31783012-31791013;chr1:31791084-31791955		chr1:31791014-31791083			55.56
N	coord_cassette	CUFF.793	chr3	-	chr3:141713984-141747420	chr3:141713984-141719093;chr3:141719197-141724282;chr3:141724387-141747420		chr3:141719094-141719196;chr3:141724283-141724386			79.41
K	intron_retention	CUFF.285	chr14	+	chr14:77924326-77925958				chr14:77924325-77924326;chr14:77925958-77925959		61.11
N	cassette	CUFF.445	chr17	-	chr17:40744181-40762554	chr17:40744181-40748550;chr17:40748646-40762554		chr17:40748551-40748645			73.33
N	jcn_only_AA	CUFF.1110	chrX	+	chrX:1424421-1428294	chrX:1424421-1424520		chrX:1424521-1428294	chrX:1428294-1428295		21.85
N	alternative_donor	CUFF.217	chr12	-	chr12:48381493-48383010	chr12:48381493-48382208		chr12:48382209-48383010	chr12:48383010-48383011		0.00
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		25.56
N	jcn_only_AD	CUFF.298	chr14	-	chr14:104209161-104212709	chr14:104209161-104210227		chr14:104210228-104212709	chr14:104212709-104212710		44.00
N	intron_retention	CUFF.152	chr11	-	chr11:10828929-10829823				chr11:10828928-10828929;chr11:10829823-10829824		61.29
N	jcn_only_AD	CUFF.165	chr11	+	chr11:65480527-65480818	chr11:65480530-65480818		chr11:65480527-65480529	chr11:65480526-65480527		92.35
K	cassette	CUFF.121	chr10	-	chr10:80825577-80827144	chr10:80825577-80826204;chr10:80826344-80827144		chr10:80826205-80826343			12.82
N	intron_retention		chr2	-	chr2:207989129-208031863				chr2:207989128-207989129;chr2:208031863-208031864		68.75
K	cassette	CUFF.232	chr12	+	chr12:58018940-58019192	chr12:58018940-58019018;chr12:58019102-58019192		chr12:58019019-58019101			25.95
K	cassette	CUFF.244	chr13	+	chr13:21230570-21237636	chr13:21230570-21237401;chr13:21237526-21237636		chr13:21237402-21237525			84.81
N	jcn_only_AD	CUFF.28	chr1	+	chr1:70832012-70832126;chr1:70820795-70832126;chr1:70820892-70832126	chr1:70820791-70832126		chr1:70820791-70820794;chr1:70820795-70820891;chr1:70820892-70832011	chr1:70820790-70820791;chr1:70820794-70820795;chr1:70820891-70820892		63.30
N	intron_retention		chr2	-	chr2:242432956-242434257				chr2:242432955-242432956;chr2:242434257-242434258		31.48
K	intron_retention	CUFF.1004	chr7	-	chr7:110603622-111127293				chr7:110603621-110603622;chr7:111127293-111127294		3.85
N	intron_retention		chr11	+	chr11:65480527-65480818				chr11:65480526-65480527;chr11:65480818-65480819		36.36
N	alternative_donor	CUFF.506	chr19	+	chr19:4306039-4306194	chr19:4306067-4306194		chr19:4306039-4306066	chr19:4306038-4306039		1.50
N	intron_retention		chr17	-	chr17:79994890-79995325				chr17:79994889-79994890;chr17:79995325-79995326		41.46
K	intron_retention		chr11	-	chr11:6637735-6637891				chr11:6637734-6637735;chr11:6637891-6637892		33.90
K	alternative_first_exon	CUFF.963	chr7	-	chr7:7592554-7594786	chr7:7592554-7594318	chr7:7594787-7594820	chr7:7594319-7594407			31.82
K	intron_retention	CUFF.566	chr19	+	chr19:54652479-54653294				chr19:54652478-54652479;chr19:54653294-54653295		16.67
K	alternative_first_exon	CUFF.726	chr22	+	chr22:47158746-47185208	chr22:47159229-47185208	chr22:47158463-47158745	chr22:47159127-47159228			74.14
N	jcn_only_AA	CUFF.919	chr6	-	chr6:31938917-31939096	chr6:31938925-31939096		chr6:31938917-31938924	chr6:31938916-31938917		85.57
N	alternative_acceptor	CUFF.178	chr11	+	chr11:107944225-107948902	chr11:107944225-107944526		chr11:107944527-107948902	chr11:107948902-107948903		42.86
K	intron_retention	CUFF.1134	chrX	+	chrX:103358265-103359942				chrX:103358264-103358265;chrX:103359942-103359943	chrX:103358125-103358264;chrX:103359943-103360609	70.59
N	alternative_acceptor	CUFF.426	chr17	-	chr17:15584268-15586167	chr17:15584537-15586167		chr17:15584268-15584536	chr17:15584267-15584268		10.34
K	coord_cassette	CUFF.1018	chr7	-	chr7:156626487-156685621	chr7:156626487-156627171;chr7:156627270-156629506;chr7:156629580-156685621		chr7:156627172-156627269;chr7:156629507-156629579			53.93
N	alternative_donor	CUFF.490	chr18	+	chr18:55895140-55912658;chr18:55833094-55912658;chr18:55865102-55912658;chr18:55862966-55912658;chr18:55888990-55912658	chr18:55895121-55912658		chr18:55833094-55862965;chr18:55862966-55865101;chr18:55865102-55888989;chr18:55888990-55895120;chr18:55895121-55895139	chr18:55833093-55833094;chr18:55862965-55862966;chr18:55865101-55865102;chr18:55888989-55888990;chr18:55895120-55895121		0.00
K	alternative_first_exon	CUFF.481	chr18	+	chr18:11981130-11999052;chr18:11981205-11999052	chr18:11981765-11999052	chr18:11980936-11981204	chr18:11981468-11981764			38.68
K	intron_retention	CUFF.158	chr11	+	chr11:59856135-59856222				chr11:59856134-59856135;chr11:59856222-59856223		50.00
K	intron_retention	CUFF.165	chr11	+	chr11:65480530-65480818				chr11:65480529-65480530;chr11:65480818-65480819		5.06
N	coord_cassette	CUFF.639	chr2	+	chr2:160569118-160585519	chr2:160569118-160571067;chr2:160571110-160572191;chr2:160572278-160585519		chr2:160571068-160571109;chr2:160572192-160572277			50.00
K	intron_retention	CUFF.1070	chr9	-	chr9:35079239-35079437				chr9:35079238-35079239;chr9:35079437-35079438		7.32
N	intron_retention		chr2	-	chr2:263373-264083				chr2:263372-263373;chr2:264083-264084		10.00
K	jcn_only_AD	CUFF.285	chr14	+	chr14:77928586-77934425	chr14:77932011-77934425					90.82
K	intron_retention	CUFF.734	chr3	+	chr3:19992554-20017092				chr3:19992553-19992554;chr3:20017092-20017093		45.71
N	intron_retention		chr16	-	chr16:4458199-4466480				chr16:4458198-4458199;chr16:4466480-4466481		88.24
N	alternative_acceptor	CUFF.36	chr1	+	chr1:167382352-167385285	chr1:167382352-167384736		chr1:167384737-167385285	chr1:167385285-167385286		71.88
K	intron_retention	CUFF.648	chr2	-	chr2:177042223-177042730				chr2:177042222-177042223;chr2:177042730-177042731		18.75
N	coord_cassette	CUFF.683	chr20	+	chr20:30132839-30137866	chr20:30132839-30136831;chr20:30136918-30137009;chr20:30137136-30137866		chr20:30136832-30136917;chr20:30137010-30137135		chr20:30132750-30132838;chr20:30137867-30137965	82.17
N	alternative_donor	CUFF.509	chr19	-	chr19:6047516-6148241;chr19:6047516-6049146;chr19:6047516-6110403;chr19:6047516-6072015	chr19:6047516-6057172		chr19:6049147-6057172;chr19:6057173-6072015;chr19:6072016-6110403;chr19:6110404-6148241	chr19:6057172-6057173;chr19:6072015-6072016;chr19:6110403-6110404;chr19:6148241-6148242		0.00
K	alternative_acceptor	CUFF.8	chr1	+	chr1:16382019-16382172	chr1:16382019-16382169		chr1:16382170-16382172	chr1:16382172-16382173		28.57
K	cassette	CUFF.647	chr2	-	chr2:175711686-175742567	chr2:175711686-175740515;chr2:175740594-175742567		chr2:175740516-175740593			79.22
N	jcn_only_AD	CUFF.385	chr16	+	chr16:19566643-19576172	chr16:19567069-19576172		chr16:19566643-19567068	chr16:19566642-19566643		89.61
K	cassette	CUFF.241	chr12	-	chr12:120146124-120148344	chr12:120146124-120148055;chr12:120148192-120148344		chr12:120148056-120148191			89.55
K	alternative_first_exon	CUFF.284	chr14	-	chr14:77275987-77280649;chr14:77275987-77276431	chr14:77275987-77278647	chr14:77280650-77280764;chr14:77276432-77276597	chr14:77278648-77278744			10.39
N	cassette	CUFF.225	chr12	+	chr12:53858637-53861004;chr12:53856352-53861004	chr12:53858637-53859715,chr12:53856352-53859715;chr12:53859758-53861004		chr12:53859716-53859757			88.67
N	alternative_donor	CUFF.396	chr16	-	chr16:57509870-57513353	chr16:57509870-57512455		chr16:57512456-57513353	chr16:57513353-57513354		1.92
K	cassette	CUFF.974	chr7	-	chr7:38835212-38836344	chr7:38835212-38836014;chr7:38836127-38836344		chr7:38836015-38836126			30.77
N	jcn_only_AD	CUFF.225	chr12	+	chr12:53846760-53848509;chr12:53847068-53848509;chr12:53837558-53848509	chr12:53846161-53848509		chr12:53837558-53846160;chr12:53846161-53846759;chr12:53846760-53847067	chr12:53837557-53837558;chr12:53846160-53846161;chr12:53846759-53846760		55.93
K	intron_retention	CUFF.47	chr1	-	chr1:151158097-151158273				chr1:151158096-151158097;chr1:151158273-151158274		39.82
K	cassette	CUFF.572	chr2	-	chr2:219002-229965	chr2:219002-224863;chr2:224921-229965		chr2:224864-224920			57.14
K	alternative_first_exon	CUFF.49	chr1	-	chr1:153925846-153930820	chr1:153925846-153926013	chr1:153930821-153931091	chr1:153926014-153926082			77.59
N	alternative_acceptor	CUFF.457	chr17	+	chr17:61555460-61557129;chr17:61555460-61556171	chr17:61555460-61556367		chr17:61556172-61556367;chr17:61556368-61557129	chr17:61556367-61556368;chr17:61557129-61557130		73.91
N	jcn_only_AA		chr3	-	chr3:73453547-73651504	chr3:73457412-73651504					71.43
N	alternative_first_exon	CUFF.416	chr17	-	chr17:653150-654890;chr17:653150-655857	chr17:653150-655372	chr17:655858-656098	chr17:655373-655501			8.96
K	jcn_only_AA	CUFF.1037	chr8	+	chr8:71564130-71564769	chr8:71564130-71564745		chr8:71564746-71564769	chr8:71564769-71564770		7.89
N	intron_retention	CUFF.728	chr22	-	chr22:51018232-51018402				chr22:51018231-51018232;chr22:51018402-51018403		96.48
K	cassette	CUFF.114	chr10	-	chr10:73892940-73921295	chr10:73892940-73912626;chr10:73912747-73921295		chr10:73912627-73912746			92.25
K	alternative_first_exon	CUFF.1010	chr7	+	chr7:129019591-129028896	chr7:129028782-129028896	chr7:129019479-129019590	chr7:129028640-129028781			27.68
K	alternative_acceptor	CUFF.36	chr1	+	chr1:110212194-110213935	chr1:110212194-110213908		chr1:110213909-110213935	chr1:110213935-110213936		38.24
K	intron_retention	CUFF.812	chr4	-	chr4:2932878-2933281				chr4:2932877-2932878;chr4:2933281-2933282		90.34
N	alternative_acceptor	CUFF.497	chr18	-	chr18:67614007-67614596	chr18:67614306-67614596		chr18:67614007-67614305	chr18:67614006-67614007		70.31
N	cassette	CUFF.269	chr14	+	chr14:58956959-58965500	chr14:58956959-58958861;chr14:58958994-58965500		chr14:58958862-58958993			86.15
K	jcn_only_AA	CUFF.225	chr12	+	chr12:53854928-53856276	chr12:53854928-53856264		chr12:53856265-53856276	chr12:53856276-53856277		56.37
K	intron_retention	CUFF.747	chr3	-	chr3:38049655-38049725				chr3:38049654-38049655;chr3:38049725-38049726		15.91
N	alternative_last_exon	CUFF.417	chr17	-	chr17:1616190-1617149,chr17:1616199-1617149;chr17:1615694-1617149	chr17:1615941-1617149,chr17:1616350-1617149	chr17:1614805-1615693	chr17:1615696-1615940			12.55
N	jcn_only_AD	CUFF.551	chr19	+	chr19:45251386-45254483	chr19:45252304-45254483		chr19:45251386-45252303	chr19:45251385-45251386		77.78
K	intron_retention	CUFF.36	chr1	+	chr1:110211123-110211546				chr1:110211122-110211123;chr1:110211546-110211547		6.53
K	intron_retention	CUFF.741	chr3	-	chr3:33437773-33438236				chr3:33437772-33437773;chr3:33438236-33438237		41.00
N	jcn_only_AA	CUFF.119	chr10	-	chr10:79396274-79397022;chr10:79163782-79397022	chr10:79396328-79397022		chr10:79163782-79396273;chr10:79396274-79396327	chr10:79163781-79163782;chr10:79396273-79396274		13.79
K	intron_retention	CUFF.205	chr12	+	chr12:11709019-11709869				chr12:11709018-11709019;chr12:11709869-11709870		7.55
K	jcn_only_AA	CUFF.208	chr12	+	chr12:21200152-21207512	chr12:21200152-21201645					61.54
K	alternative_acceptor	CUFF.943	chr6	-	chr6:116988076-116989728	chr6:116988371-116989728		chr6:116988076-116988370	chr6:116988075-116988076		67.50
N	alternative_donor	CUFF.155	chr11	+	chr11:36383732-36415395;chr11:36322621-36415395	chr11:36398255-36415395		chr11:36322621-36383731;chr11:36383732-36398254	chr11:36322620-36322621;chr11:36383731-36383732		30.00
N	jcn_only_AD	CUFF.436	chr17	+	chr17:29687722-29701030	chr17:29694297-29701030		chr17:29687722-29694296	chr17:29687721-29687722		19.23
N	jcn_only_AD		chr15	+	chr15:24811948-24814929;chr15:24813711-24814929	chr15:24813330-24814929					20.00
N	alternative_last_exon		chr10	+	chr10:6270182-6271071;chr10:6270182-6274857	chr10:6270182-6273225	chr10:6274858-6277593	chr10:6273226-6273328			76.60
K	coord_cassette	CUFF.467	chr17	-	chr17:76994046-77001453	chr17:76994046-76994229;chr17:76994369-76996181;chr17:76996353-77001453		chr17:76994230-76994368;chr17:76996182-76996352			51.98
K	cassette	CUFF.94	chr10	+	chr10:18280233-18284584	chr10:18280233-18282109;chr10:18282221-18284584		chr10:18282110-18282220			96.08
K	alternative_donor	CUFF.1024	chr8	+	chr8:7123432-7124095	chr8:7123438-7124095		chr8:7123432-7123437	chr8:7123431-7123432	chr8:7124096-7125058;chr8:7123323-7123431	83.33
K	jcn_only_AD	CUFF.330	chr15	+	chr15:64445539-64445850	chr15:64445586-64445850		chr15:64445539-64445585	chr15:64445538-64445539		16.67
N	alternative_donor	CUFF.325	chr15	+	chr15:57384090-57458599;chr15:57401516-57458599;chr15:57422171-57458599	chr15:57426699-57458599		chr15:57384090-57401515;chr15:57401516-57422170;chr15:57422171-57426698	chr15:57384089-57384090;chr15:57401515-57401516;chr15:57422170-57422171		0.00
K	cassette	CUFF.1096	chr9	+	chr9:125027218-125033142	chr9:125027218-125027740;chr9:125027825-125033142		chr9:125027741-125027824			14.58
N	cassette	CUFF.426	chr17	-	chr17:15584268-15586349;chr17:15584537-15586349	chr17:15584537-15586167,chr17:15584268-15586167;chr17:15586266-15586349		chr17:15586168-15586265			68.61
K	coord_cassette	CUFF.927	chr6	-	chr6:39856832-39864972	chr6:39856832-39859081;chr6:39859156-39859398;chr6:39859540-39864972		chr6:39859082-39859155;chr6:39859399-39859539			34.78
K	intron_retention	CUFF.919	chr6	-	chr6:31939503-31939705				chr6:31939502-31939503;chr6:31939705-31939706		85.38
K	cassette	CUFF.394	chr16	+	chr16:31383992-31388119	chr16:31383992-31384569;chr16:31384712-31388119		chr16:31384570-31384711			61.54
N	jcn_only_AD	CUFF.739	chr3	+	chr3:28357915-28360999;chr3:28358351-28360999	chr3:28360371-28360999		chr3:28357915-28358350;chr3:28358351-28360370	chr3:28357914-28357915;chr3:28358350-28358351		5.74
N	intron_retention		chr1	+	chr1:200860531-200867519				chr1:200860530-200860531;chr1:200867519-200867520		61.90
K	alternative_donor	CUFF.36	chr1	+	chr1:110211106-110211546	chr1:110211123-110211546		chr1:110211106-110211122	chr1:110211105-110211106		91.43
N	coord_cassette	CUFF.317	chr15	-	chr15:45464277-45467416	chr15:45464277-45464344;chr15:45464517-45465773;chr15:45465915-45467416		chr15:45464345-45464516;chr15:45465774-45465914			75.00
K	intron_retention	CUFF.371	chr16	+	chr16:2202887-2202989				chr16:2202886-2202887;chr16:2202989-2202990		19.40
N	coord_cassette	CUFF.354	chr15	+	chr15:91341568-91352366	chr15:91341568-91346750;chr15:91346951-91347396;chr15:91347590-91352366		chr15:91346751-91346950;chr15:91347397-91347589			94.94
N	alternative_acceptor	CUFF.1101	chr9	-	chr9:131484854-131486272	chr9:131485019-131486272		chr9:131484854-131485018	chr9:131484853-131484854		12.79
K	alternative_last_exon	CUFF.211	chr12	-	chr12:25652931-25656671;chr12:25650729-25656671;chr12:25562365-25656671;chr12:25655973-25656671	chr12:25629395-25656671	chr12:25650631-25650728;chr12:25562143-25562364;chr12:25655879-25655972	chr12:25628947-25629394			84.04
N	alternative_donor	CUFF.971,CUFF.999	chr7	-	chr7:102608565-102665509	chr7:102608565-102613596		chr7:102613597-102665509	chr7:102665509-102665510		0.00
N	alternative_donor	CUFF.531	chr19	+	chr19:17611442-17615263;chr19:17611686-17615263	chr19:17612229-17615263		chr19:17611442-17611685;chr19:17611686-17612228	chr19:17611441-17611442;chr19:17611685-17611686		14.00
N	cassette	CUFF.1087	chr9	-	chr9:107651477-107690215	chr9:107651477-107665894;chr9:107666053-107690215		chr9:107665895-107666052			74.07
K	intron_retention	CUFF.476	chr17	+	chr17:80442807-80446096				chr17:80442806-80442807;chr17:80446096-80446097		84.34
N	alternative_acceptor	CUFF.802	chr3	+	chr3:186790736-186791946	chr3:186790736-186791192		chr3:186791193-186791946	chr3:186791946-186791947		5.88
N	jcn_only_AD	CUFF.225	chr12	+	chr12:53846760-53848509;chr12:53846161-53848509;chr12:53837558-53848509	chr12:53847068-53848509		chr12:53837558-53846160;chr12:53846161-53846759;chr12:53846760-53847067	chr12:53837557-53837558;chr12:53846160-53846161;chr12:53846759-53846760		24.58
N	intron_retention		chr19	+	chr19:17448457-17448816				chr19:17448456-17448457;chr19:17448816-17448817		65.18
N	intron_retention		chr17	-	chr17:650523-650784				chr17:650522-650523;chr17:650784-650785		96.09
N	alternative_acceptor	CUFF.276	chr14	-	chr14:71200060-71201102	chr14:71200516-71201102		chr14:71200060-71200515	chr14:71200059-71200060		44.44
K	intron_retention		chr4	-	chr4:83816001-83816844				chr4:83816000-83816001;chr4:83816844-83816845		96.58
K	jcn_only_AA	CUFF.506,CUFF.531	chr19	+	chr19:17598339-17599816	chr19:17598339-17599656					88.75
N	cassette	CUFF.418	chr17	+	chr17:1937137-1939822	chr17:1937137-1939263;chr17:1939386-1939822		chr17:1939264-1939385			90.70
K	jcn_only_AA	CUFF.432,CUFF.476	chr17	+	chr17:25970647-25972886	chr17:25970647-25972339					60.53
N	intron_retention		chr7	+	chr7:150831656-150835229				chr7:150831655-150831656;chr7:150835229-150835230		28.00
K	cassette	CUFF.524	chr19	-	chr19:14876617-14877789	chr19:14876617-14877046;chr19:14877194-14877789		chr19:14877047-14877193			19.75
N	jcn_only_AA	CUFF.976	chr7	+	chr7:129015768-129019481	chr7:129015768-129019478		chr7:129019479-129019481	chr7:129019481-129019482		89.66
N	intron_retention		chr12	-	chr12:120156622-120158282				chr12:120156621-120156622;chr12:120158282-120158283		16.13
N	jcn_only_AA		chr14	+	chr14:76201633-76203908;chr14:76201633-76211437	chr14:76201633-76210719					75.00
K	alternative_first_exon	CUFF.79	chr1	+	chr1:224371121-224377278;chr1:224363650-224377278	chr1:224371534-224377278	chr1:224370860-224371120;chr1:224363458-224363649	chr1:224371312-224371533			52.60
K	alternative_acceptor	CUFF.1097	chr9	-	chr9:125616861-125617462	chr9:125616895-125617462		chr9:125616861-125616894	chr9:125616860-125616861		46.88
N	jcn_only_AD	CUFF.1066	chr9	-	chr9:15188131-15189701	chr9:15188131-15189571		chr9:15189572-15189701	chr9:15189701-15189702		67.16
N	jcn_only_AD	CUFF.1115	chrX	-	chrX:13801641-13803740	chrX:13801641-13801897		chrX:13801898-13803740	chrX:13803740-13803741		7.45
K	intron_retention	CUFF.473	chr17	-	chr17:79894738-79895133				chr17:79894737-79894738;chr17:79895133-79895134	chr17:79894624-79894737;chr17:79895134-79895264	47.19
K	cassette	CUFF.561	chr19	-	chr19:51534178-51537235	chr19:51534178-51535131;chr19:51535392-51537235		chr19:51535132-51535391			16.33
N	jcn_only_AD	CUFF.598	chr2	+	chr2:38150511-38156404	chr2:38152569-38156404		chr2:38150511-38152568	chr2:38150510-38150511		50.00
N	jcn_only_AD	CUFF.673	chr2	+	chr2:242610821-242611605;chr2:242610841-242611605	chr2:242610857-242611605		chr2:242610821-242610840;chr2:242610841-242610856	chr2:242610820-242610821;chr2:242610840-242610841		3.30
K	cassette	CUFF.33	chr1	-	chr1:103975719-104068017	chr1:103975719-104011963;chr1:104012013-104068017		chr1:104011964-104012012			27.59
K	jcn_only_AD	CUFF.1040	chr8	+	chr8:75263557-75272371	chr8:75263702-75272371		chr8:75263557-75263701	chr8:75263556-75263557		63.64
N	alternative_donor	CUFF.143	chr11	+	chr11:2798263-2799205	chr11:2799044-2799205		chr11:2798263-2799043	chr11:2798262-2798263		7.41
K	intron_retention	CUFF.184	chr11	-	chr11:118923542-118924832				chr11:118923541-118923542;chr11:118924832-118924833		9.82
N	alternative_donor		chr5	-	chr5:64887330-64887698	chr5:64887330-64887669		chr5:64887670-64887698	chr5:64887698-64887699		88.64
N	jcn_only_AA	CUFF.1004	chr7	-	chr7:111161506-111201906	chr7:111172642-111201906		chr7:111161506-111172641	chr7:111161505-111161506		7.22
N	jcn_only_AD	CUFF.611	chr2	-	chr2:73215478-73226077	chr2:73215478-73221974		chr2:73221975-73226077	chr2:73226077-73226078		2.16
K	cassette	CUFF.584	chr2	-	chr2:11593925-11597304	chr2:11593925-11595467;chr2:11595601-11597304		chr2:11595468-11595600			25.19
N	alternative_acceptor	CUFF.418	chr17	+	chr17:80416385-80417867	chr17:80416385-80417150		chr17:80417151-80417867	chr17:80417867-80417868		17.39
N	jcn_only_AD	CUFF.923	chr6	+	chr6:34434048-34494019;chr6:34482846-34494019	chr6:34452922-34494019		chr6:34434048-34452921;chr6:34452922-34482845	chr6:34434047-34434048;chr6:34452921-34452922		14.71
N	intron_retention		chr19	+	chr19:17448474-17448816				chr19:17448473-17448474;chr19:17448816-17448817		52.42
N	alternative_first_exon		chr1	-	chr1:156939836-156946774	chr1:156939836-156941488	chr1:156946775-156946846	chr1:156941489-156941710			96.00
N	cassette	CUFF.377	chr16	-	chr16:4458253-4466459	chr16:4458253-4462356;chr16:4462432-4466459		chr16:4462357-4462431			96.39
N	alternative_acceptor	CUFF.155,CUFF.163	chr11	+	chr11:64000087-64000175	chr11:64000087-64000172		chr11:64000173-64000175	chr11:64000175-64000176		2.35
K	jcn_only_AD	CUFF.47	chr1	-	chr1:151158427-151162599	chr1:151158427-151162480		chr1:151162481-151162599	chr1:151162599-151162600		81.58
N	intron_retention		chr17	+	chr17:6352728-6353681				chr17:6352727-6352728;chr17:6353681-6353682		83.33
N	alternative_acceptor	CUFF.83	chr1	+	chr1:245222761-245245384	chr1:245222761-245238875		chr1:245238876-245245384	chr1:245245384-245245385		0.00
K	intron_retention	CUFF.163	chr11	+	chr11:64001453-64001544				chr11:64001452-64001453;chr11:64001544-64001545		7.49
K	cassette	CUFF.1040	chr8	+	chr8:75262814-75272371	chr8:75262814-75263508;chr8:75263702-75272371		chr8:75263509-75263701			43.02
N	jcn_only_AD	CUFF.325	chr15	+	chr15:57384090-57458599;chr15:57426699-57458599;chr15:57422171-57458599	chr15:57401516-57458599		chr15:57384090-57401515;chr15:57401516-57422170;chr15:57422171-57426698	chr15:57384089-57384090;chr15:57401515-57401516;chr15:57422170-57422171		8.74
K	intron_retention	CUFF.404	chr16	-	chr16:67970007-67970117				chr16:67970006-67970007;chr16:67970117-67970118	chr16:67969866-67970006;chr16:67970118-67970215	43.75
K	coord_cassette	CUFF.412	chr16	+	chr16:77756515-77775478	chr16:77756515-77759327;chr16:77759482-77769724;chr16:77769884-77775478		chr16:77759328-77759481;chr16:77769725-77769883			72.88
N	coord_cassette	CUFF.385	chr16	+	chr16:19613046-19621643	chr16:19613046-19619499;chr16:19619597-19620295;chr16:19620344-19621643		chr16:19619500-19619596;chr16:19620296-19620343			84.05
K	intron_retention		chr11	+	chr11:118402587-118402864				chr11:118402586-118402587;chr11:118402864-118402865	chr11:118401663-118402586;chr11:118402865-118403176	20.40
K	intron_retention	CUFF.1098	chr9	-	chr9:130929444-130931354				chr9:130929443-130929444;chr9:130931354-130931355		64.29
N	cassette	CUFF.671	chr2	-	chr2:242439697-242447420	chr2:242439697-242440154;chr2:242440212-242447420		chr2:242440155-242440211			92.64
K	cassette	CUFF.1018	chr7	-	chr7:156526952-156549086	chr7:156526952-156529186;chr7:156529310-156549086		chr7:156529187-156529309			9.27
K	alternative_last_exon	CUFF.254	chr13	-	chr13:101129697-101132514	chr13:101132018-101132514	chr13:101129583-101129696	chr13:101131714-101132017			90.00
N	jcn_only_AD	CUFF.530	chr19	+	chr19:17447967-17448682	chr19:17448474-17448682		chr19:17447967-17448473	chr19:17447966-17447967		65.33
K	intron_retention	CUFF.802	chr3	+	chr3:186769135-186790636				chr3:186769134-186769135;chr3:186790636-186790637		12.75
N	alternative_acceptor	CUFF.716	chr22	+	chr22:29694886-29695223	chr22:29694886-29695184		chr22:29695185-29695223	chr22:29695223-29695224		6.67
K	cassette	CUFF.1110	chrX	+	chrX:1419520-1424338	chrX:1419520-1422815;chrX:1422913-1424338		chrX:1422816-1422912			71.58
K	cassette	CUFF.837	chr4	+	chr4:77172974-77184856	chr4:77172974-77177330;chr4:77177677-77184856		chr4:77177331-77177676			5.36
K	intron_retention	CUFF.476	chr17	+	chr17:80436795-80438957				chr17:80436794-80436795;chr17:80438957-80438958		10.34
K	cassette	CUFF.556	chr19	-	chr19:49318399-49335922	chr19:49318399-49334924;chr19:49335017-49335922		chr19:49334925-49335016			93.14
N	intron_retention	CUFF.975	chr7	+	chr7:44247798-44248005				chr7:44247797-44247798;chr7:44248005-44248006		71.11
N	alternative_acceptor	CUFF.787	chr3	+	chr3:133419898-133472438	chr3:133419898-133426336		chr3:133426337-133472438	chr3:133472438-133472439		4.55
K	intron_retention	CUFF.36	chr1	+	chr1:110212686-110212796				chr1:110212685-110212686;chr1:110212796-110212797		69.05
N	alternative_acceptor	CUFF.780	chr3	-	chr3:125032501-125042152	chr3:125033898-125042152		chr3:125032501-125033897	chr3:125032500-125032501		0.00
K	alternative_first_exon	CUFF.1040	chr8	+	chr8:75233824-75272371;chr8:75233481-75272371	chr8:75263557-75272371,chr8:75263702-75272371	chr8:75233365-75233480	chr8:75263509-75263556			16.33
K	cassette	CUFF.795	chr3	-	chr3:155520381-155523927	chr3:155520381-155523385;chr3:155523513-155523927		chr3:155523386-155523512			42.11
K	intron_retention	CUFF.138	chr11	+	chr11:830338-830620				chr11:830337-830338;chr11:830620-830621	chr11:830250-830337;chr11:830621-830713	37.18
N	coord_cassette	CUFF.509	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			79.45
K	alternative_last_exon	CUFF.535	chr19	-	chr19:21627226-21637184	chr19:21636580-21637184	chr19:21627043-21627225	chr19:21636352-21636579			89.81
K	mutually_exclusive	CUFF.640	chr2	-	chr2:166714915-166721493,chr2:166721588-166727306	chr2:166714915-166719453,chr2:166719576-166727306	chr2:166721494-166721587	chr2:166719454-166719575			50.00
K	jcn_only_AD	CUFF.160	chr11	+	chr11:61588941-61593754	chr11:61593610-61593754				chr11:61593755-61594081	36.49
N	coord_cassette	CUFF.816	chr4	-	chr4:3945100-3949816	chr4:3945100-3948495;chr4:3948645-3949468;chr4:3949735-3949816		chr4:3948496-3948644;chr4:3949469-3949734			73.03
N	jcn_only_AA	CUFF.417	chr17	-	chr17:1615941-1617149	chr17:1616350-1617149		chr17:1615941-1616349	chr17:1615940-1615941		93.44
N	jcn_only_AA	CUFF.872,CUFF.894	chr5	+	chr5:139915124-139916973	chr5:139915124-139916922		chr5:139916923-139916973	chr5:139916973-139916974	chr5:139914947-139915123;chr5:139916974-139917174	10.00
N	intron_retention		chr7	+	chr7:73098135-73105245				chr7:73098134-73098135;chr7:73105245-73105246		66.67
N	jcn_only_AD	CUFF.848	chr4	+	chr4:120381976-120382871	chr4:120381983-120382871		chr4:120381976-120381982	chr4:120381975-120381976		81.12
K	intron_retention	CUFF.673	chr2	+	chr2:242610821-242611605				chr2:242610820-242610821;chr2:242611605-242611606		26.32
K	cassette	CUFF.1092	chr9	-	chr9:123538505-123550046	chr9:123538505-123540628;chr9:123540824-123550046		chr9:123540629-123540823		chr9:123538371-123538504	66.67
N	alternative_first_exon	CUFF.752	chr3	-	chr3:49349088-49362134;chr3:49349088-49351303	chr3:49349088-49355741	chr3:49362135-49362196;chr3:49351304-49351556	chr3:49355742-49356244			13.13
K	jcn_only_AD	CUFF.628	chr2	+	chr2:101565943-101584742	chr2:101582229-101584742					7.09
N	jcn_only_AA	CUFF.165,CUFF.168	chr11	+	chr11:65479751-65479849	chr11:65479751-65479820		chr11:65479821-65479849	chr11:65479849-65479850		37.50
N	intron_retention		chr14	-	chr14:59941245-59942586				chr14:59941244-59941245;chr14:59942586-59942587		32.73
N	jcn_only_AD	CUFF.1113,CUFF.1135	chrX	-	chrX:106184863-106185205	chrX:106184863-106185167		chrX:106185168-106185205	chrX:106185205-106185206		33.33
K	cassette	CUFF.183	chr11	-	chr11:118532219-118532598	chr11:118532219-118532345;chr11:118532439-118532598		chr11:118532346-118532438			81.25
N	jcn_only_AD	CUFF.647	chr2	-	chr2:175809672-175816891	chr2:175809672-175809897		chr2:175809898-175816891	chr2:175816891-175816892		40.35
K	cassette	CUFF.969	chr7	+	chr7:30793555-30818047	chr7:30793555-30805960;chr7:30806178-30818047		chr7:30805961-30806177			30.00
K	intron_retention	CUFF.555	chr19	-	chr19:49300591-49302931				chr19:49300590-49300591;chr19:49302931-49302932		3.00
K	intron_retention	CUFF.418	chr17	+	chr17:1945170-1945898				chr17:1945169-1945170;chr17:1945898-1945899		11.90
N	alternative_donor	CUFF.182	chr11	+	chr11:118402242-118402489;chr11:118401950-118402489	chr11:118402317-118402489		chr11:118401950-118402241;chr11:118402242-118402316	chr11:118401949-118401950;chr11:118402241-118402242	chr11:118402490-118402586;chr11:118401663-118401949	11.42
N	alternative_acceptor	CUFF.481	chr18	+	chr18:11999187-12009881	chr18:11999187-12008331		chr18:12008332-12009881	chr18:12009881-12009882		2.07
N	jcn_only_AD	CUFF.2	chr1	+	chr1:1982141-1986879	chr1:1982452-1986879		chr1:1982141-1982451	chr1:1982140-1982141		56.69
K	alternative_donor	CUFF.686	chr20	+	chr20:33104267-33114072	chr20:33104682-33114072		chr20:33104267-33104681	chr20:33104266-33104267		47.34
K	intron_retention	CUFF.377	chr16	-	chr16:4411471-4411985				chr16:4411470-4411471;chr16:4411985-4411986		50.00
N	alternative_donor	CUFF.531	chr19	+	chr19:17608274-17611086	chr19:17610764-17611086		chr19:17608274-17610763	chr19:17608273-17608274		11.19
K	alternative_last_exon	CUFF.1018	chr7	-	chr7:156476858-156516805	chr7:156480886-156516805	chr7:156474523-156476857	chr7:156480711-156480885			87.50
K	cassette	CUFF.463	chr17	-	chr17:66279265-66287226	chr17:66279265-66281685;chr17:66281784-66287226		chr17:66281686-66281783			54.55
K	jcn_only_AA	CUFF.166	chr11	-	chr11:67766776-67766988	chr11:67766846-67766988		chr11:67766776-67766845	chr11:67766775-67766776		18.10
K	cassette	CUFF.52	chr1	-	chr1:156438813-156446803	chr1:156438813-156444899;chr1:156445030-156446803		chr1:156444900-156445029			31.25
K	coord_cassette	CUFF.412	chr16	+	chr16:77759482-77775478	chr16:77759482-77769724;chr16:77769884-77770546;chr16:77770641-77775478		chr16:77769725-77769883;chr16:77770547-77770640			57.58
N	jcn_only_AA	CUFF.298	chr14	-	chr14:104201417-104204030	chr14:104202540-104204030		chr14:104201417-104202539	chr14:104201416-104201417		18.39
N	jcn_only_AA		chr2	-	chr2:242440263-242440892;chr2:242440335-242440892	chr2:242440493-242440892					44.78
N	intron_retention	CUFF.1125	chrX	-	chrX:53569501-53570801				chrX:53569500-53569501;chrX:53570801-53570802		68.97
N	cassette	CUFF.310	chr15	+	chr15:40565878-40568127	chr15:40565878-40566342;chr15:40566478-40568127		chr15:40566343-40566477			93.88
K	alternative_first_exon	CUFF.247	chr13	+	chr13:31192194-31195900	chr13:31195377-31195900	chr13:31191830-31192193	chr13:31195315-31195376			13.33
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		94.96
K	intron_retention	CUFF.1096	chr9	+	chr9:125047567-125048058				chr9:125047566-125047567;chr9:125048058-125048059		24.46
K	jcn_only_AD	CUFF.136	chr11	-	chr11:407569-407851	chr11:407569-407816		chr11:407817-407851	chr11:407851-407852		92.91
N	cassette	CUFF.316	chr15	-	chr15:44859791-44864880	chr15:44859791-44862722;chr15:44862857-44864880		chr15:44862723-44862856			67.65
K	intron_retention	CUFF.457	chr17	+	chr17:61562428-61562596				chr17:61562427-61562428;chr17:61562596-61562597		15.66
N	cassette	CUFF.265	chr14	+	chr14:50247494-50249259	chr14:50247494-50249087;chr14:50249176-50249259		chr14:50249088-50249175			90.08
N	jcn_only_AD	CUFF.352	chr15	-	chr15:44884637-44888257	chr15:44884637-44887456		chr15:44887457-44888257	chr15:44888257-44888258		80.65
K	alternative_first_exon	CUFF.392	chr16	-	chr16:28515372-28523148	chr16:28515372-28518101	chr16:28523149-28523458	chr16:28518102-28518155			16.13
N	alternative_acceptor		chr7	+	chr7:91730371-91732000	chr7:91730371-91731907		chr7:91731908-91732000	chr7:91732000-91732001		47.87
K	intron_retention		chr22	+	chr22:45244941-45255610				chr22:45244940-45244941;chr22:45255610-45255611		9.00
K	jcn_only_AD	CUFF.528	chr19	-	chr19:16593597-16594740	chr19:16593597-16594572		chr19:16594573-16594740	chr19:16594740-16594741		83.33
K	alternative_first_exon	CUFF.1001	chr7	+	chr7:107220747-107221203;chr7:107221091-107221203	chr7:107220812-107221203	chr7:107220422-107220746;chr7:107220910-107221090	chr7:107220751-107220811			3.37
N	cassette	CUFF.182	chr11	+	chr11:118403177-118404571;chr11:118403177-118404134	chr11:118403177-118403631;chr11:118403923-118404571,chr11:118403923-118404134		chr11:118403632-118403922		chr11:118402865-118403176;chr11:118404572-118404602	91.86
N	intron_retention		chr12	-	chr12:48276558-48298737				chr12:48276557-48276558;chr12:48298737-48298738		50.00
K	jcn_only_AD	CUFF.395	chr16	+	chr16:56370773-56388777	chr16:56385450-56388777					87.93
K	cassette	CUFF.797	chr3	-	chr3:165504100-165547304	chr3:165504100-165545773;chr3:165545858-165547304		chr3:165545774-165545857			21.43
N	jcn_only_AD	CUFF.136	chr11	-	chr11:410028-417324;chr11:410028-414822	chr11:410028-417293		chr11:414823-417293;chr11:417294-417324	chr11:417293-417294;chr11:417324-417325		8.92
N	alternative_acceptor	CUFF.785,CUFF.787	chr3	+	chr3:133100006-133109023	chr3:133100006-133105267		chr3:133105268-133109023	chr3:133109023-133109024		21.74
N	coord_cassette	CUFF.816	chr4	-	chr4:3945100-3954837	chr4:3945100-3948495;chr4:3948645-3949468;chr4:3949735-3949816;chr4:3949948-3954837		chr4:3948496-3948644;chr4:3949469-3949734;chr4:3949817-3949947			63.93
K	cassette	CUFF.30	chr1	-	chr1:85724406-85725040	chr1:85724406-85724617;chr1:85724745-85725040		chr1:85724618-85724744			22.50
K	intron_retention	CUFF.179	chr11	+	chr11:115267610-115267986				chr11:115267609-115267610;chr11:115267986-115267987		21.05
K	cassette	CUFF.146	chr11	+	chr11:3405515-3422988	chr11:3405515-3418346;chr11:3418637-3422988		chr11:3418347-3418636			84.44
K	intron_retention		chr2	+	chr2:160599765-160602280				chr2:160599764-160599765;chr2:160602280-160602281		90.16
K	intron_retention	CUFF.557	chr19	+	chr19:50309511-50309937				chr19:50309510-50309511;chr19:50309937-50309938		50.65
K	cassette	CUFF.823	chr4	+	chr4:20555592-20568884	chr4:20555592-20555930;chr4:20555964-20568884		chr4:20555931-20555963			10.75
N	jcn_only_AA		chr3	-	chr3:107578109-107586157	chr3:107585601-107586157					82.35
K	intron_retention	CUFF.640	chr2	-	chr2:166727531-166731188				chr2:166727530-166727531;chr2:166731188-166731189		29.41
N	jcn_only_AD	CUFF.663	chr2	+	chr2:220094681-220094949;chr2:220094703-220094949	chr2:220094623-220094949		chr2:220094623-220094680;chr2:220094681-220094702	chr2:220094622-220094623;chr2:220094680-220094681		90.85
N	intron_retention		chr2	+	chr2:220095073-220096649				chr2:220095072-220095073;chr2:220096649-220096650		51.95
K	alternative_last_exon	CUFF.296	chr14	+	chr14:103187422-103188523	chr14:103187422-103187656	chr14:103188524-103188753	chr14:103187657-103187963			49.46
N	cassette	CUFF.36	chr1	+	chr1:110214005-110217368	chr1:110214005-110214094;chr1:110214206-110217368		chr1:110214095-110214205			93.75
K	cassette	CUFF.970	chr7	+	chr7:34724297-34867012;chr7:34818178-34867012	chr7:34724297-34851381,chr7:34818178-34851381;chr7:34851476-34867012		chr7:34851382-34851475			59.40
N	alternative_acceptor	CUFF.553	chr19	-	chr19:49116565-49117964	chr19:49117885-49117964		chr19:49116565-49117884	chr19:49116564-49116565		2.90
K	coord_cassette	CUFF.841	chr4	+	chr4:81105210-81117505	chr4:81105210-81112625;chr4:81112724-81115266;chr4:81115394-81117505		chr4:81112626-81112723;chr4:81115267-81115393			75.68
N	intron_retention		chr2	-	chr2:110920710-110922096				chr2:110920709-110920710;chr2:110922096-110922097		60.00
K	intron_retention	CUFF.918	chr6	+	chr6:31936574-31936647				chr6:31936573-31936574;chr6:31936647-31936648		9.85
N	intron_retention		chr7	+	chr7:75045695-75045764				chr7:75045694-75045695;chr7:75045764-75045765		90.12
K	cassette	CUFF.1099	chr9	+	chr9:131008783-131009653	chr9:131008783-131009215;chr9:131009403-131009653		chr9:131009216-131009402			28.57
K	intron_retention	CUFF.998	chr7	-	chr7:102234690-102234938				chr7:102234689-102234690;chr7:102234938-102234939		45.00
K	jcn_only_AD	CUFF.920	chr6	+	chr6:32125498-32130344	chr6:32125702-32130344					58.33
N	alternative_donor		chr18	-	chr18:67614769-67623849;chr18:67614769-67623990	chr18:67614769-67628827		chr18:67623850-67623990;chr18:67623991-67628827	chr18:67623990-67623991;chr18:67628827-67628828		81.82
N	intron_retention		chr22	+	chr22:29683124-29688125				chr22:29683123-29683124;chr22:29688125-29688126		16.67
K	alternative_first_exon	CUFF.276	chr14	-	chr14:71216799-71227718	chr14:71216799-71219654	chr14:71227719-71227899	chr14:71219655-71219753			66.67
K	intron_retention		chr4	-	chr4:6382822-6383503				chr4:6382821-6382822;chr4:6383503-6383504		22.22
N	jcn_only_AA	CUFF.919	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		18.45
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		19.08
K	alternative_acceptor	CUFF.1029,CUFF.1047	chr8	+	chr8:98817693-98827555	chr8:98817693-98827531		chr8:98827532-98827555	chr8:98827555-98827556		29.73
K	intron_retention	CUFF.785	chr3	+	chr3:126133023-126135158				chr3:126133022-126133023;chr3:126135158-126135159		69.81
K	intron_retention	CUFF.1001	chr7	+	chr7:107234551-107236311				chr7:107234550-107234551;chr7:107236311-107236312		4.43
K	alternative_first_exon	CUFF.1109	chr9	+	chr9:139780732-139793164;chr9:139780994-139793164;chr9:139784995-139793164	chr9:139777163-139793164	chr9:139780437-139780731;chr9:139780897-139780993;chr9:139784801-139784994	chr9:139777119-139777162			7.20
N	alternative_acceptor	CUFF.737	chr3	-	chr3:27329235-27332752	chr3:27332246-27332752		chr3:27329235-27332245	chr3:27329234-27329235		1.35
N	alternative_acceptor	CUFF.971	chr7	-	chr7:37256301-37262219	chr7:37257362-37262219		chr7:37256301-37257361	chr7:37256300-37256301		4.00
K	intron_retention	CUFF.426	chr17	-	chr17:15586686-15587509				chr17:15586685-15586686;chr17:15587509-15587510		57.14
K	jcn_only_AA	CUFF.363,CUFF.407	chr16	+	chr16:105550-105793	chr16:105550-105776		chr16:105777-105793	chr16:105793-105794		79.41
K	jcn_only_AA	CUFF.59	chr1	-	chr1:161970129-161976086	chr1:161970132-161976086		chr1:161970129-161970131	chr1:161970128-161970129		42.86
N	jcn_only_AA		chr1	+	chr1:70820892-70832009;chr1:70820892-70831828	chr1:70820892-70832126		chr1:70831829-70832009;chr1:70832010-70832126	chr1:70832009-70832010;chr1:70832126-70832127		63.44
N	alternative_acceptor	CUFF.212	chr12	+	chr12:26205930-26208211	chr12:26205930-26208168		chr12:26208169-26208211	chr12:26208211-26208212		9.04
K	jcn_only_AA	CUFF.834	chr4	-	chr4:70513414-70518905	chr4:70513417-70518905		chr4:70513414-70513416	chr4:70513413-70513414		57.69
N	cassette	CUFF.1072	chr9	+	chr9:35396935-35397631	chr9:35396935-35397163;chr9:35397308-35397631		chr9:35397164-35397307			42.86
K	intron_retention	CUFF.460	chr17	+	chr17:61908296-61908379				chr17:61908295-61908296;chr17:61908379-61908380		67.39
N	jcn_only_AD	CUFF.984	chr7	+	chr7:75040010-75040690	chr7:75040118-75040690		chr7:75040010-75040117	chr7:75040009-75040010		85.37
K	intron_retention	CUFF.417	chr17	-	chr17:1615941-1617149				chr17:1615940-1615941;chr17:1617149-1617150		98.16
N	intron_retention		chr1	+	chr1:2005369-2066700				chr1:2005368-2005369;chr1:2066700-2066701		40.74
K	intron_retention	CUFF.919	chr6	-	chr6:31937802-31937885				chr6:31937801-31937802;chr6:31937885-31937886		1.18
K	alternative_first_exon	CUFF.55,CUFF.6	chr1	-	chr1:158581180-158582606	chr1:158581180-158581575	chr1:158582607-158582751	chr1:158581576-158581672			0.55
K	cassette	CUFF.1040	chr8	+	chr8:75262814-75272371	chr8:75262814-75263508;chr8:75263557-75272371		chr8:75263509-75263556			31.94
K	alternative_donor	CUFF.618	chr2	-	chr2:86386795-86389098	chr2:86386795-86389074		chr2:86389075-86389098	chr2:86389098-86389099		17.52
N	cassette	CUFF.547	chr19	-	chr19:41939579-41945378	chr19:41939579-41944122;chr19:41944320-41945378		chr19:41944123-41944319			81.40
K	intron_retention	CUFF.728	chr22	-	chr22:51009722-51009803				chr22:51009721-51009722;chr22:51009803-51009804		6.06
N	coord_cassette	CUFF.775	chr3	-	chr3:120360541-120365819	chr3:120360541-120363165;chr3:120363291-120365113;chr3:120365214-120365819		chr3:120363166-120363290;chr3:120365114-120365213			92.45
N	intron_retention		chr22	-	chr22:51015023-51015285				chr22:51015022-51015023;chr22:51015285-51015286		80.00
K	intron_retention	CUFF.661	chr2	+	chr2:219231824-219232152				chr2:219231823-219231824;chr2:219232152-219232153		48.84
N	cassette	CUFF.136	chr11	-	chr11:408207-409867	chr11:408207-408893;chr11:409102-409867		chr11:408894-409101			73.04
K	alternative_donor	CUFF.658	chr2	-	chr2:207953306-207988497;chr2:207953306-207988699	chr2:207953306-207989067		chr2:207988498-207988699;chr2:207988700-207989067	chr2:207988699-207988700;chr2:207989067-207989068		46.02
N	alternative_acceptor	CUFF.224	chr12	-	chr12:53471046-53473094	chr12:53471956-53473094		chr12:53471046-53471955	chr12:53471045-53471046		2.78
K	jcn_only_AD	CUFF.435	chr17	+	chr17:29490395-29508439	chr17:29497016-29508439					34.38
K	intron_retention		chr2	-	chr2:61761039-61761692				chr2:61761038-61761039;chr2:61761692-61761693		91.57
N	jcn_only_AD	CUFF.56	chr1	+	chr1:160137203-160141040	chr1:160137220-160141040		chr1:160137203-160137219	chr1:160137202-160137203		83.33
N	alternative_donor	CUFF.751	chr3	-	chr3:46982556-47017842;chr3:46982556-47018126	chr3:46982556-47007473		chr3:47007474-47017842;chr3:47017843-47018126	chr3:47017842-47017843;chr3:47018126-47018127		2.19
K	cassette	CUFF.920	chr6	+	chr6:32121414-32122363	chr6:32121414-32121972;chr6:32122024-32122363		chr6:32121973-32122023			10.48
N	jcn_only_AD	CUFF.739	chr3	+	chr3:28357915-28360999;chr3:28360371-28360999	chr3:28358351-28360999		chr3:28357915-28358350;chr3:28358351-28360370	chr3:28357914-28357915;chr3:28358350-28358351		5.74
K	intron_retention	CUFF.350	chr15	-	chr15:84869961-84871621				chr15:84869960-84869961;chr15:84871621-84871622		25.84
K	jcn_only_AA	CUFF.961	chr7	+	chr7:6630107-6631333	chr7:6630107-6631276		chr7:6631277-6631333	chr7:6631333-6631334		45.00
N	jcn_only_AD	CUFF.1066	chr9	-	chr9:15226011-15267911	chr9:15226011-15232229		chr9:15232230-15267911	chr9:15267911-15267912		40.28
N	coord_cassette	CUFF.726	chr22	+	chr22:47158746-47189397	chr22:47158746-47188416;chr22:47188474-47188564;chr22:47188660-47189397		chr22:47188417-47188473;chr22:47188565-47188659			92.45
N	jcn_only_AD	CUFF.743	chr3	-	chr3:33592888-33600798	chr3:33592888-33600616		chr3:33600617-33600798	chr3:33600798-33600799		10.64
N	alternative_donor	CUFF.1004	chr7	-	chr7:111161506-111201906	chr7:111161506-111172573		chr7:111172574-111201906	chr7:111201906-111201907		0.00
N	jcn_only_AA		chr14	+	chr14:76201633-76211437;chr14:76201633-76210719	chr14:76201633-76203908					8.65
N	alternative_donor	CUFF.572	chr2	-	chr2:242872-247537;chr2:242872-244626	chr2:242872-243502		chr2:243503-244626;chr2:244627-247537	chr2:244626-244627;chr2:247537-247538		2.78
N	cassette	CUFF.167	chr11	+	chr11:67786725-67788953	chr11:67786725-67787183;chr11:67787266-67788953		chr11:67787184-67787265			92.50
N	coord_cassette	CUFF.509	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			10.42
N	alternative_first_exon		chr16	-	chr16:4463406-4464307,chr16:4463406-4465715,chr16:4463406-4465766;chr16:4463406-4466785	chr16:4463406-4466459	chr16:4466786-4466962	chr16:4466460-4466665			74.40
N	cassette	CUFF.209	chr12	-	chr12:22610096-22612425	chr12:22610096-22611417;chr12:22611520-22612425		chr12:22611418-22611519			87.13
K	alternative_first_exon	CUFF.626	chr2	+	chr2:99232810-99234630	chr2:99232997-99234630	chr2:99232609-99232809	chr2:99232856-99232996			82.35
K	intron_retention	CUFF.1098	chr9	-	chr9:130929444-130931330				chr9:130929443-130929444;chr9:130931330-130931331		15.94
N	cassette	CUFF.274	chr14	-	chr14:69585948-69619660	chr14:69585948-69588933;chr14:69589078-69619660		chr14:69588934-69589077			68.75
K	alternative_last_exon	CUFF.693	chr21	+	chr21:15664069-15678016	chr21:15664069-15671758	chr21:15678017-15678163	chr21:15671759-15673789		chr21:15663891-15664068	73.68
N	jcn_only_AD	CUFF.598	chr2	+	chr2:38224658-38231133	chr2:38230170-38231133		chr2:38224658-38230169	chr2:38224657-38224658		6.04
K	intron_retention	CUFF.202	chr12	-	chr12:7090345-7090971				chr12:7090344-7090345;chr12:7090971-7090972		4.47
K	alternative_first_exon	CUFF.112	chr10	+	chr10:70679738-70695761	chr10:70694675-70695761	chr10:70679573-70679737	chr10:70694555-70694674			34.21
N	jcn_only_AA		chr12	+	chr12:26205536-26208211	chr12:26205536-26208168		chr12:26208169-26208211	chr12:26208211-26208212		28.95
K	cassette	CUFF.716	chr22	+	chr22:29669854-29674018	chr22:29669854-29670256;chr22:29670272-29674018		chr22:29670257-29670271			26.64
N	alternative_acceptor	CUFF.769	chr3	+	chr3:119196296-119198897;chr3:119196296-119197180	chr3:119196296-119198754		chr3:119197181-119198754;chr3:119198755-119198897	chr3:119198754-119198755;chr3:119198897-119198898		49.40
K	alternative_donor	CUFF.472	chr17	-	chr17:79479387-79479759	chr17:79479387-79479640		chr17:79479641-79479759	chr17:79479759-79479760		20.66
K	coord_cassette	CUFF.476	chr17	+	chr17:80426773-80436675	chr17:80426773-80430439;chr17:80430575-80436446;chr17:80436544-80436675		chr17:80430440-80430574;chr17:80436447-80436543			66.91
N	alternative_acceptor	CUFF.427	chr17	+	chr17:15603483-15604465	chr17:15603483-15603586		chr17:15603587-15604465	chr17:15604465-15604466		4.76
N	jcn_only_AD	CUFF.743,CUFF.796	chr3	-	chr3:33614847-33617660	chr3:33614847-33615964		chr3:33615965-33617660	chr3:33617660-33617661		5.78
N	intron_retention	CUFF.687	chr20	+	chr20:33589889-33589961				chr20:33589888-33589889;chr20:33589961-33589962		12.16
K	intron_retention	CUFF.212	chr12	+	chr12:26221857-26224588				chr12:26221856-26221857;chr12:26224588-26224589		69.23
K	alternative_last_exon	CUFF.766	chr3	-	chr3:108464359-108475354	chr3:108474753-108475354	chr3:108464278-108464358	chr3:108474442-108474752			45.00
N	coord_cassette	CUFF.578	chr2	+	chr2:1168870-1215567	chr2:1168870-1204788;chr2:1204917-1206142;chr2:1206366-1215567		chr2:1204789-1204916;chr2:1206143-1206365			75.00
N	intron_retention		chr3	+	chr3:28283304-28357823				chr3:28283303-28283304;chr3:28357823-28357824		50.00
K	alternative_donor	CUFF.542	chr19	-	chr19:39924059-39924161;chr19:39924059-39924133	chr19:39924059-39924157		chr19:39924134-39924157;chr19:39924158-39924161	chr19:39924157-39924158;chr19:39924161-39924162		1.49
K	intron_retention	CUFF.732	chr3	+	chr3:8787560-8787655				chr3:8787559-8787560;chr3:8787655-8787656		37.50
K	intron_retention	CUFF.350	chr15	-	chr15:84873269-84873351				chr15:84873268-84873269;chr15:84873351-84873352		59.70
N	cassette	CUFF.641	chr2	+	chr2:169659184-169681143	chr2:169659184-169668076;chr2:169668163-169681143		chr2:169668077-169668162			87.18
N	jcn_only_AD	CUFF.358	chr15	+	chr15:97326820-97327382;chr15:97326975-97327382	chr15:97327061-97327382		chr15:97326820-97326974;chr15:97326975-97327060	chr15:97326819-97326820;chr15:97326974-97326975		87.10
N	jcn_only_AA	CUFF.394	chr16	+	chr16:31368423-31368654	chr16:31368423-31368573		chr16:31368574-31368654	chr16:31368654-31368655		20.00
K	alternative_last_exon	CUFF.93	chr10	-	chr10:17636383-17645558	chr10:17641411-17645558	chr10:17636127-17636382	chr10:17641024-17641410			75.44
K	intron_retention	CUFF.511	chr19	-	chr19:6211077-6211308				chr19:6211076-6211077;chr19:6211308-6211309		95.52
K	cassette	CUFF.1133	chrX	-	chrX:100170073-100182958	chrX:100170073-100177781;chrX:100178051-100182958		chrX:100177782-100178050			83.33
K	intron_retention	CUFF.146	chr11	+	chr11:3427841-3428851				chr11:3427840-3427841;chr11:3428851-3428852		85.50
K	intron_retention	CUFF.36	chr1	+	chr1:110212194-110213908				chr1:110212193-110212194;chr1:110213908-110213909		35.80
K	alternative_donor	CUFF.1150	chrX	+	chrX:153238312-153247300	chrX:153238338-153247300		chrX:153238312-153238337	chrX:153238311-153238312	chrX:153247301-153248646;chrX:153237778-153238311	48.00
N	alternative_acceptor	CUFF.325	chr15	+	chr15:57574797-57578354;chr15:57574797-57591423	chr15:57574797-57583026		chr15:57578355-57583026;chr15:57583027-57591423	chr15:57583026-57583027;chr15:57591423-57591424		0.00
K	intron_retention	CUFF.136	chr11	-	chr11:407165-407424				chr11:407164-407165;chr11:407424-407425		31.30
N	alternative_acceptor	CUFF.225	chr12	+	chr12:53865592-53873189	chr12:53865592-53868652		chr12:53868653-53873189	chr12:53873189-53873190		0.77
N	jcn_only_AD	CUFF.271	chr14	-	chr14:59946070-59950526;chr14:59946070-59950207	chr14:59946070-59950397		chr14:59950208-59950397;chr14:59950398-59950526	chr14:59950397-59950398;chr14:59950526-59950527		28.57
N	intron_retention		chr17	+	chr17:61904875-61905188				chr17:61904874-61904875;chr17:61905188-61905189		84.44
K	alternative_last_exon	CUFF.983	chr7	-	chr7:74953399-74982536	chr7:74981241-74982536	chr7:74953243-74953398	chr7:74981057-74981240			18.00
N	jcn_only_AA	CUFF.777	chr3	+	chr3:186714462-186756529	chr3:186714462-186723929		chr3:186723930-186756529	chr3:186756529-186756530		54.05
K	intron_retention	CUFF.671	chr2	-	chr2:242440212-242440892				chr2:242440211-242440212;chr2:242440892-242440893		10.74
K	cassette	CUFF.442	chr17	-	chr17:37599882-37604050	chr17:37599882-37601663;chr17:37601823-37604050		chr17:37601664-37601822			85.19
K	alternative_acceptor	CUFF.193	chr11	-	chr11:124766952-124768293	chr11:124767158-124768293		chr11:124766952-124767157	chr11:124766951-124766952		85.71
K	intron_retention	CUFF.812	chr4	-	chr4:2933664-2933771				chr4:2933663-2933664;chr4:2933771-2933772		68.16
N	intron_retention		chr12	+	chr12:53861628-53862563				chr12:53861627-53861628;chr12:53862563-53862564		17.57
N	jcn_only_AA	CUFF.1002	chr7	-	chr7:107642179-107643293	chr7:107642830-107643293		chr7:107642179-107642829	chr7:107642178-107642179		24.56
N	alternative_acceptor	CUFF.241	chr12	-	chr12:120128257-120135463	chr12:120128260-120135463		chr12:120128257-120128259	chr12:120128256-120128257		78.95
K	alternative_first_exon	CUFF.1027	chr8	-	chr8:22012977-22014508	chr8:22012977-22013849	chr8:22014509-22014602	chr8:22013850-22014425			70.00
N	jcn_only_AA	CUFF.224	chr12	-	chr12:53471046-53473094	chr12:53471956-53473094		chr12:53471046-53471955	chr12:53471045-53471046		10.26
K	intron_retention	CUFF.566	chr19	+	chr19:54656737-54657451				chr19:54656736-54656737;chr19:54657451-54657452		53.23
N	alternative_acceptor	CUFF.856	chr4	-	chr4:162402322-162421167	chr4:162416633-162421167		chr4:162402322-162416632	chr4:162402321-162402322		0.77
K	intron_retention	CUFF.471	chr17	-	chr17:79358833-79358928				chr17:79358832-79358833;chr17:79358928-79358929		2.07
K	cassette	CUFF.785	chr3	+	chr3:126113822-126114784	chr3:126113822-126114167;chr3:126114273-126114784		chr3:126114168-126114272			80.00
K	cassette	CUFF.1130	chrX	+	chrX:78005721-78006706	chrX:78005721-78006226;chrX:78006290-78006706		chrX:78006227-78006289			71.05
N	alternative_acceptor	CUFF.966	chr7	-	chr7:22162140-22165221	chr7:22165040-22165221		chr7:22162140-22165039	chr7:22162139-22162140		25.00
K	intron_retention	CUFF.68	chr1	+	chr1:200882752-200882988				chr1:200882751-200882752;chr1:200882988-200882989		40.00
N	alternative_donor	CUFF.273	chr14	+	chr14:61497242-61503776	chr14:61500832-61503776		chr14:61497242-61500831	chr14:61497241-61497242		3.87
N	alternative_donor	CUFF.976	chr7	+	chr7:54614433-54614639;chr7:54613910-54614639	chr7:54612482-54614639		chr7:54612482-54613909;chr7:54613910-54614432	chr7:54612481-54612482;chr7:54613909-54613910		92.39
K	alternative_first_exon	CUFF.533	chr19	-	chr19:20243397-20261169;chr19:20243397-20351308	chr19:20243397-20349096	chr19:20261170-20261357;chr19:20351309-20351446	chr19:20349097-20349344			70.24
K	mutually_exclusive	CUFF.1004	chr7	-	chr7:110303778-110526648,chr7:110526752-110603555	chr7:110303778-110304879,chr7:110305069-110603555	chr7:110526649-110526751	chr7:110304880-110305068			17.65
K	intron_retention	CUFF.1007	chr7	-	chr7:117398025-117400488				chr7:117398024-117398025;chr7:117400488-117400489		5.51
K	alternative_acceptor	CUFF.617	chr2	-	chr2:79364464-79365092	chr2:79364469-79365092		chr2:79364464-79364468	chr2:79364463-79364464		34.38
K	intron_retention	CUFF.741	chr3	-	chr3:33437773-33438536				chr3:33437772-33437773;chr3:33438536-33438537		65.96
N	jcn_only_AA	CUFF.163	chr11	+	chr11:63999437-63999865;chr11:63999437-64001365;chr11:63999437-63999981	chr11:63999437-63999901					67.50
N	cassette	CUFF.2	chr1	+	chr1:1987002-1990979	chr1:1987002-1987922;chr1:1988013-1990979		chr1:1987923-1988012			92.66
K	alternative_last_exon	CUFF.851	chr4	-	chr4:142241055-142244575	chr4:142242536-142244575	chr4:142240506-142241054	chr4:142242184-142242535			80.77
K	intron_retention	CUFF.693	chr21	+	chr21:15688690-15689793				chr21:15688689-15688690;chr21:15689793-15689794	chr21:15688522-15688689;chr21:15689794-15689956	78.57
K	intron_retention	CUFF.775	chr3	-	chr3:120365214-120365819				chr3:120365213-120365214;chr3:120365819-120365820		7.58
K	jcn_only_AA	CUFF.85	chr1	-	chr1:247323116-247335149	chr1:247323170-247335149		chr1:247323116-247323169	chr1:247323115-247323116		12.50
N	alternative_acceptor	CUFF.722	chr22	+	chr22:37695348-37696193;chr22:37695348-37696947	chr22:37695348-37696110		chr22:37696111-37696193;chr22:37696194-37696947	chr22:37696193-37696194;chr22:37696947-37696948		2.44
K	intron_retention	CUFF.473	chr17	-	chr17:79894738-79895137				chr17:79894737-79894738;chr17:79895137-79895138	chr17:79894624-79894737;chr17:79895138-79895264	46.07
N	jcn_only_AD	CUFF.61	chr1	+	chr1:167301773-167334703	chr1:167326759-167334703		chr1:167301773-167326758	chr1:167301772-167301773		5.53
N	alternative_acceptor	CUFF.97	chr10	-	chr10:27112235-27149675	chr10:27128713-27149675		chr10:27112235-27128712	chr10:27112234-27112235		0.00
N	alternative_donor	CUFF.971	chr7	-	chr7:37382368-37392635;chr7:37382368-37488277;chr7:37382368-37488462;chr7:37382368-37382655	chr7:37382368-37433424		chr7:37382656-37392635;chr7:37392636-37433424;chr7:37433425-37488277;chr7:37488278-37488462	chr7:37392635-37392636;chr7:37433424-37433425;chr7:37488277-37488278;chr7:37488462-37488463		0.00
K	jcn_only_AD	CUFF.219	chr12	-	chr12:50232799-50236636	chr12:50232799-50236168		chr12:50236169-50236636	chr12:50236636-50236637		94.69
K	intron_retention	CUFF.232	chr12	+	chr12:58015211-58015472				chr12:58015210-58015211;chr12:58015472-58015473		12.58
N	alternative_donor		chr6	-	chr6:128313855-128316393;chr6:128313855-128316591	chr6:128313855-128316606		chr6:128316394-128316591;chr6:128316592-128316606	chr6:128316591-128316592;chr6:128316606-128316607		82.50
N	jcn_only_AD		chr7	+	chr7:150831656-150838984	chr7:150837204-150838984		chr7:150831656-150837203	chr7:150831655-150831656		56.25
N	cassette	CUFF.572	chr2	-	chr2:253116-263210;chr2:253116-262630	chr2:253116-260084;chr2:260703-262630,chr2:260703-263210		chr2:260085-260702			67.74
N	alternative_donor	CUFF.490	chr18	+	chr18:55895140-55912658;chr18:55833094-55912658;chr18:55865102-55912658;chr18:55895121-55912658;chr18:55862966-55912658	chr18:55888990-55912658		chr18:55833094-55862965;chr18:55862966-55865101;chr18:55865102-55888989;chr18:55888990-55895120;chr18:55895121-55895139	chr18:55833093-55833094;chr18:55862965-55862966;chr18:55865101-55865102;chr18:55888989-55888990;chr18:55895120-55895121		0.00
K	alternative_acceptor	CUFF.184	chr11	-	chr11:118919916-118920267	chr11:118920083-118920267		chr11:118919916-118920082	chr11:118919915-118919916		80.68
K	intron_retention		chr15	-	chr15:44865019-44865744				chr15:44865018-44865019;chr15:44865744-44865745		46.67
K	alternative_last_exon	CUFF.1142	chrX	+	chrX:133632715-133654511	chrX:133632715-133634059	chrX:133654512-133654641	chrX:133634060-133634750			33.33
K	intron_retention	CUFF.1136	chrX	+	chrX:107381115-107393381				chrX:107381114-107381115;chrX:107393381-107393382		45.08
K	intron_retention	CUFF.1014	chr7	+	chr7:148990584-148990841				chr7:148990583-148990584;chr7:148990841-148990842		90.48
K	intron_retention	CUFF.330	chr15	+	chr15:64447103-64447305				chr15:64447102-64447103;chr15:64447305-64447306		84.21
K	intron_retention	CUFF.316	chr15	-	chr15:44889142-44890462				chr15:44889141-44889142;chr15:44890462-44890463		16.33
N	alternative_acceptor		chr19	+	chr19:17448474-17448682;chr19:17448474-17448707	chr19:17448474-17448816		chr19:17448683-17448707;chr19:17448708-17448816	chr19:17448707-17448708;chr19:17448816-17448817		44.36
K	intron_retention	CUFF.708	chr22	+	chr22:21058329-21058475				chr22:21058328-21058329;chr22:21058475-21058476		35.78
N	intron_retention		chr11	+	chr11:119056951-119057187				chr11:119056950-119056951;chr11:119057187-119057188		84.51
K	intron_retention	CUFF.504	chr19	+	chr19:1438892-1440024				chr19:1438891-1438892;chr19:1440024-1440025		28.81
N	jcn_only_AD	CUFF.787	chr3	+	chr3:132757280-132764745	chr3:132760700-132764745		chr3:132757280-132760699	chr3:132757279-132757280		5.88
K	intron_retention	CUFF.486	chr18	-	chr18:44424803-44426669				chr18:44424802-44424803;chr18:44426669-44426670		34.57
N	jcn_only_AA	CUFF.338	chr15	-	chr15:77577421-77578764;chr15:77577398-77578764	chr15:77474383-77578764					1.79
N	alternative_acceptor	CUFF.566	chr19	+	chr19:54657578-54657680;chr19:54657578-54658995	chr19:54657578-54659046		chr19:54657681-54658995;chr19:54658996-54659046	chr19:54658995-54658996;chr19:54659046-54659047		18.18
K	coord_cassette	CUFF.1014	chr7	+	chr7:148984868-148987028	chr7:148984868-148985521;chr7:148986549-148986638;chr7:148986818-148987028		chr7:148985522-148986548;chr7:148986639-148986817			57.45
K	alternative_donor	CUFF.124	chr10	+	chr10:96961943-96966964	chr10:96961953-96966964		chr10:96961943-96961952	chr10:96961942-96961943		73.68
K	intron_retention	CUFF.755	chr3	+	chr3:51748138-51749077				chr3:51748137-51748138;chr3:51749077-51749078		94.86
N	intron_retention	CUFF.165	chr11	+	chr11:65479751-65479820				chr11:65479750-65479751;chr11:65479820-65479821		92.25
K	alternative_last_exon	CUFF.578,CUFF.637	chr2	+	chr2:139326797-139331421	chr2:139326797-139328337	chr2:139331422-139332028	chr2:139328338-139328736			41.18
K	intron_retention	CUFF.671	chr2	-	chr2:242435950-242437030				chr2:242435949-242435950;chr2:242437030-242437031		8.28
N	alternative_donor	CUFF.475	chr17	-	chr17:79993940-79994057;chr17:79993940-79994066	chr17:79993940-79994022		chr17:79994023-79994057;chr17:79994058-79994066	chr17:79994057-79994058;chr17:79994066-79994067		12.22
N	jcn_only_AA		chr19	+	chr19:17450409-17451915	chr19:17450409-17451852		chr19:17451853-17451915	chr19:17451915-17451916		85.23
K	mutually_exclusive	CUFF.145	chr11	+	chr11:3239790-3241456,chr11:3241590-3242799	chr11:3239790-3240929,chr11:3241019-3242799	chr11:3241457-3241589	chr11:3240930-3241018		chr11:3239562-3239789;chr11:3242800-3244361	52.63
K	cassette	CUFF.401	chr16	+	chr16:66613796-66620899	chr16:66613796-66613928;chr16:66614088-66620899		chr16:66613929-66614087			91.11
N	jcn_only_AD	CUFF.230	chr12	-	chr12:56709027-56709690;chr12:56709027-56709500	chr12:56709027-56709604		chr12:56709501-56709604;chr12:56709605-56709690	chr12:56709604-56709605;chr12:56709690-56709691		63.39
K	cassette	CUFF.467	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			71.86
K	jcn_only_AA	CUFF.850	chr4	+	chr4:130701255-130724146	chr4:130701255-130710066					67.31
K	alternative_first_exon	CUFF.829	chr4	-	chr4:56496628-56502710	chr4:56496628-56502247	chr4:56502711-56502960	chr4:56502248-56502530			88.67
K	intron_retention	CUFF.152	chr11	-	chr11:10827572-10828856				chr11:10827571-10827572;chr11:10828856-10828857		84.46
N	alternative_acceptor	CUFF.377	chr16	-	chr16:4412133-4445289	chr16:4438633-4445289		chr16:4412133-4438632	chr16:4412132-4412133		50.00
K	jcn_only_AA	CUFF.171	chr11	-	chr11:75522582-75524647	chr11:75522615-75524647		chr11:75522582-75522614	chr11:75522581-75522582		14.00
N	coord_cassette	CUFF.936	chr6	+	chr6:90326377-90331640	chr6:90326377-90326592;chr6:90326676-90327672;chr6:90327751-90331640		chr6:90326593-90326675;chr6:90327673-90327750			45.78
N	cassette	CUFF.77	chr1	-	chr1:213181809-213188954	chr1:213181809-213184549;chr1:213184801-213188954		chr1:213184550-213184800			86.79
K	jcn_only_AA	CUFF.688	chr20	-	chr20:34246905-34252800	chr20:34246937-34252800		chr20:34246905-34246936	chr20:34246904-34246905		63.64
K	intron_retention	CUFF.192	chr11	+	chr11:124078396-124078521				chr11:124078395-124078396;chr11:124078521-124078522	chr11:124077890-124078395;chr11:124078522-124078819	34.78
N	cassette	CUFF.1098	chr9	-	chr9:130943079-130952607	chr9:130943079-130947825;chr9:130948056-130952607		chr9:130947826-130948055			94.00
N	cassette	CUFF.490	chr18	+	chr18:56001125-56010137	chr18:56001125-56008909;chr18:56009030-56010137		chr18:56008910-56009029			16.10
N	jcn_only_AA	CUFF.929	chr6	-	chr6:43480837-43481096	chr6:43480939-43481096		chr6:43480837-43480938	chr6:43480836-43480837		95.22
K	intron_retention	CUFF.189	chr11	-	chr11:119291089-119291578				chr11:119291088-119291089;chr11:119291578-119291579		70.00
K	intron_retention		chr18	-	chr18:44483597-44486189				chr18:44483596-44483597;chr18:44486189-44486190		51.28
N	jcn_only_AD	CUFF.271	chr14	-	chr14:59946070-59950397;chr14:59946070-59950207	chr14:59946070-59950526		chr14:59950208-59950397;chr14:59950398-59950526	chr14:59950397-59950398;chr14:59950526-59950527		62.05
K	intron_retention	CUFF.542	chr19	-	chr19:39924059-39924157				chr19:39924058-39924059;chr19:39924157-39924158		71.43
K	intron_retention	CUFF.1002	chr7	-	chr7:107599926-107600135				chr7:107599925-107599926;chr7:107600135-107600136		44.44
N	jcn_only_AD		chr9	-	chr9:104293842-104295734	chr9:104293842-104294958		chr9:104294959-104295734	chr9:104295734-104295735		40.00
N	cassette	CUFF.387	chr16	+	chr16:21969921-21972648	chr16:21969921-21970659;chr16:21970877-21972648		chr16:21970660-21970876			72.55
N	cassette	CUFF.1146	chrX	+	chrX:148863659-148867663;chrX:148863691-148867663	chrX:148863691-148867418,chrX:148863659-148867418;chrX:148867506-148867663		chrX:148867419-148867505			25.93
K	jcn_only_AA	CUFF.758	chr3	-	chr3:57569760-57570110;chr3:57569788-57570110	chr3:57569735-57570110		chr3:57569735-57569759;chr3:57569760-57569787	chr3:57569734-57569735;chr3:57569759-57569760		55.24
N	alternative_acceptor	CUFF.230	chr12	-	chr12:56705180-56708634;chr12:56706670-56708634;chr12:56705238-56708634	chr12:56705199-56708634		chr12:56705180-56705198;chr12:56705199-56705237;chr12:56705238-56706669	chr12:56705179-56705180;chr12:56705198-56705199;chr12:56705237-56705238		64.06
N	alternative_acceptor	CUFF.894	chr5	+	chr5:139815843-139818045;chr5:139815843-139818087	chr5:139815843-139818078		chr5:139818046-139818078;chr5:139818079-139818087	chr5:139818078-139818079;chr5:139818087-139818088	chr5:139815689-139815842;chr5:139818088-139818202	42.86
K	alternative_first_exon	CUFF.1027,CUFF.1046	chr8	-	chr8:96081464-96085156	chr8:96081464-96084944	chr8:96085157-96085482	chr8:96084945-96085148			10.34
K	alternative_acceptor	CUFF.475	chr17	-	chr17:79995418-79995506	chr17:79995424-79995506		chr17:79995418-79995423	chr17:79995417-79995418		35.56
N	jcn_only_AA		chr19	-	chr19:6192041-6199486;chr19:6148341-6199486	chr19:6176455-6199486					54.43
N	alternative_acceptor		chr2	+	chr2:109092307-109098165	chr2:109092307-109098152		chr2:109098153-109098165	chr2:109098165-109098166		94.05
N	jcn_only_AD	CUFF.324,CUFF.352	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		10.84
N	mutually_exclusive	CUFF.162	chr11	+	chr11:63672516-63675731,chr11:63675777-63676348	chr11:63672516-63673559,chr11:63673587-63676348	chr11:63675732-63675776	chr11:63673560-63673586			35.71
N	alternative_donor	CUFF.161	chr11	-	chr11:410028-417324;chr11:410028-417293	chr11:410028-414822		chr11:414823-417293;chr11:417294-417324	chr11:417293-417294;chr11:417324-417325		70.79
N	jcn_only_AA		chr14	+	chr14:76349246-76368484	chr14:76349246-76353042					6.58
K	alternative_last_exon	CUFF.1054	chr8	+	chr8:118541049-118552121	chr8:118541049-118542961	chr8:118552122-118552599	chr8:118542962-118543066			27.78
K	alternative_first_exon	CUFF.912	chr6	+	chr6:28109808-28112108	chr6:28110042-28112108	chr6:28109624-28109807	chr6:28109938-28110041			64.71
N	alternative_donor	CUFF.271	chr14	-	chr14:59939809-59942586;chr14:59939809-59941445	chr14:59939809-59941156		chr14:59941157-59941445;chr14:59941446-59942586	chr14:59941445-59941446;chr14:59942586-59942587		7.81
K	alternative_acceptor	CUFF.223	chr12	-	chr12:52993087-52994810	chr12:52993194-52994810		chr12:52993087-52993193	chr12:52993086-52993087		65.00
N	intron_retention		chr11	-	chr11:10830291-10830428				chr11:10830290-10830291;chr11:10830428-10830429		78.63
N	jcn_only_AA		chr17	+	chr17:61555460-61557129;chr17:61555460-61556367	chr17:61555460-61556171		chr17:61556172-61556367;chr17:61556368-61557129	chr17:61556367-61556368;chr17:61557129-61557130		13.11
N	alternative_acceptor	CUFF.848	chr4	+	chr4:120434126-120449894	chr4:120434126-120440643		chr4:120440644-120449894	chr4:120449894-120449895		0.00
K	intron_retention	CUFF.673	chr2	+	chr2:242607637-242607954				chr2:242607636-242607637;chr2:242607954-242607955		4.41
K	intron_retention	CUFF.739	chr3	+	chr3:28357915-28360999				chr3:28357914-28357915;chr3:28360999-28361000		42.78
N	alternative_acceptor	CUFF.426	chr17	-	chr17:15581036-15584178;chr17:15580997-15584178	chr17:15557746-15584178		chr17:15557746-15580996;chr17:15580997-15581035	chr17:15557745-15557746;chr17:15580996-15580997		90.91
N	cassette	CUFF.269	chr14	+	chr14:59006855-59014498	chr14:59006855-59010600;chr14:59010686-59014498		chr14:59010601-59010685			4.48
K	coord_cassette	CUFF.90	chr10	+	chr10:6263491-6265920	chr10:6263491-6263603;chr10:6263709-6264817;chr10:6264948-6265920		chr10:6263604-6263708;chr10:6264818-6264947			96.63
N	jcn_only_AD	CUFF.306	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		5.13
N	jcn_only_AD		chr17	-	chr17:1615694-1617149	chr17:1615694-1616996		chr17:1616997-1617149	chr17:1617149-1617150		37.50
K	intron_retention	CUFF.946	chr6	-	chr6:133055526-133055618				chr6:133055525-133055526;chr6:133055618-133055619		23.08
N	intron_retention		chr18	+	chr18:56001125-56008269				chr18:56001124-56001125;chr18:56008269-56008270		63.38
N	alternative_acceptor		chr1	-	chr1:113471975-113497897	chr1:113472657-113497897		chr1:113471975-113472656	chr1:113471974-113471975		16.67
N	jcn_only_AD	CUFF.209	chr12	-	chr12:22627826-22631246	chr12:22627826-22630195		chr12:22630196-22631246	chr12:22631246-22631247		15.84
K	alternative_last_exon	CUFF.211	chr12	-	chr12:25652931-25656671;chr12:25650729-25656671;chr12:25629395-25656671;chr12:25562365-25656671	chr12:25655973-25656671	chr12:25650631-25650728;chr12:25628947-25629394;chr12:25562143-25562364	chr12:25655879-25655972			3.19
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55713251-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55816802-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		3.52
N	alternative_donor	CUFF.276,CUFF.286	chr14	-	chr14:71200060-71201102	chr14:71200060-71200473		chr14:71200474-71201102	chr14:71201102-71201103		41.18
K	cassette	CUFF.112	chr10	+	chr10:70661228-70666466	chr10:70661228-70666039;chr10:70666094-70666466		chr10:70666040-70666093			71.43
N	alternative_donor	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55713251-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55713021-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		3.42
N	alternative_acceptor	CUFF.910	chr6	-	chr6:5144497-5216850;chr6:5138974-5216850;chr6:5187215-5216850	chr6:5113652-5216850		chr6:5113652-5138973;chr6:5138974-5144496;chr6:5144497-5187214	chr6:5113651-5113652;chr6:5138973-5138974;chr6:5144496-5144497		100.00
N	jcn_only_AD	CUFF.286	chr14	-	chr14:81893557-81902664	chr14:81893557-81902431		chr14:81902432-81902664	chr14:81902664-81902665	chr14:81893446-81893556	47.06
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		87.50
N	coord_cassette	CUFF.102	chr10	+	chr10:35437420-35495822	chr10:35437420-35467816;chr10:35467915-35468061;chr10:35468205-35495822		chr10:35467817-35467914;chr10:35468062-35468204			83.23
N	alternative_donor		chr17	-	chr17:1615694-1617149	chr17:1615694-1616996		chr17:1616997-1617149	chr17:1617149-1617150		80.00
K	alternative_first_exon	CUFF.1060	chr8	+	chr8:143915706-143921831	chr8:143916285-143921831	chr8:143915663-143915705	chr8:143916136-143916284			84.21
K	alternative_donor	CUFF.173	chr11	-	chr11:94705358-94706452	chr11:94705358-94706436		chr11:94706437-94706452	chr11:94706452-94706453		55.00
N	alternative_donor	CUFF.631	chr2	+	chr2:109085541-109086106	chr2:109085789-109086106		chr2:109085541-109085788	chr2:109085540-109085541		42.11
N	intron_retention		chr6	+	chr6:112375365-112375537				chr6:112375364-112375365;chr6:112375537-112375538		60.34
K	alternative_last_exon	CUFF.7	chr1	+	chr1:15753781-15755088	chr1:15753781-15754393	chr1:15755089-15756936	chr1:15754394-15754505			40.00
K	jcn_only_AD	CUFF.765	chr3	-	chr3:107595034-107595301	chr3:107595034-107595281		chr3:107595282-107595301	chr3:107595301-107595302		71.13
K	alternative_first_exon	CUFF.734	chr3	+	chr3:19989014-19992297	chr3:19989356-19992297	chr3:19988497-19989013	chr3:19989257-19989355			4.58
K	intron_retention	CUFF.1101	chr9	-	chr9:131483548-131483703				chr9:131483547-131483548;chr9:131483703-131483704		7.35
K	intron_retention	CUFF.187	chr11	+	chr11:119056220-119056630				chr11:119056219-119056220;chr11:119056630-119056631		13.08
N	cassette	CUFF.209	chr12	-	chr12:22610096-22612425	chr12:22610096-22611417;chr12:22611490-22612425		chr12:22611418-22611489			81.69
N	cassette	CUFF.152	chr11	-	chr11:10828433-10829823;chr11:10828433-10830251	chr11:10828433-10828801;chr11:10828929-10829823,chr11:10828929-10830251		chr11:10828802-10828928			69.88
N	alternative_donor	CUFF.1098	chr9	-	chr9:130929444-130929817;chr9:130929444-130931330	chr9:130929444-130931354		chr9:130929818-130931330;chr9:130931331-130931354	chr9:130931330-130931331;chr9:130931354-130931355		14.29
N	alternative_acceptor	CUFF.230	chr12	-	chr12:56705180-56708634;chr12:56706670-56708634;chr12:56705199-56708634	chr12:56705238-56708634		chr12:56705180-56705198;chr12:56705199-56705237;chr12:56705238-56706669	chr12:56705179-56705180;chr12:56705198-56705199;chr12:56705237-56705238		9.38
K	coord_cassette	CUFF.946	chr6	-	chr6:133046119-133055391	chr6:133046119-133047860;chr6:133047978-133049879;chr6:133050119-133055391		chr6:133047861-133047977;chr6:133049880-133050118			53.57
N	jcn_only_AA		chr22	+	chr22:29683124-29688125	chr22:29683124-29684594					79.17
N	intron_retention	CUFF.473	chr17	-	chr17:79894738-79895103				chr17:79894737-79894738;chr17:79895103-79895104	chr17:79894624-79894737;chr17:79895104-79895264	89.58
N	jcn_only_AD	CUFF.506	chr19	+	chr19:4323144-4323344;chr19:4323235-4323344	chr19:4323211-4323344		chr19:4323144-4323210;chr19:4323211-4323234	chr19:4323143-4323144;chr19:4323210-4323211		59.84
N	jcn_only_AD	CUFF.551	chr19	+	chr19:45254638-45259488	chr19:45258732-45259488		chr19:45254638-45258731	chr19:45254637-45254638		47.62
N	alternative_acceptor	CUFF.519	chr19	+	chr19:11468416-11470146;chr19:11468416-11470282	chr19:11468416-11470207		chr19:11470147-11470207;chr19:11470208-11470282	chr19:11470207-11470208;chr19:11470282-11470283		50.48
N	intron_retention		chr3	+	chr3:51749200-51750033				chr3:51749199-51749200;chr3:51750033-51750034		80.00
K	intron_retention	CUFF.93	chr10	-	chr10:17645648-17645724				chr10:17645647-17645648;chr10:17645724-17645725		36.62
K	alternative_donor	CUFF.146	chr11	+	chr11:3427841-3428851	chr11:3427946-3428851		chr11:3427841-3427945	chr11:3427840-3427841		77.91
N	alternative_donor	CUFF.708	chr22	+	chr22:21058040-21058255;chr22:21058172-21058255	chr22:21057981-21058255		chr22:21057981-21058039;chr22:21058040-21058171	chr22:21057980-21057981;chr22:21058039-21058040		29.93
K	intron_retention	CUFF.663	chr2	+	chr2:220099011-220099547				chr2:220099010-220099011;chr2:220099547-220099548		41.07
N	jcn_only_AD		chr3	-	chr3:27394411-27410521;chr3:27394411-27410715	chr3:27394411-27409013					15.38
K	intron_retention	CUFF.929	chr6	-	chr6:43480613-43480806				chr6:43480612-43480613;chr6:43480806-43480807		7.58
K	alternative_first_exon	CUFF.879,CUFF.899	chr5	-	chr5:148756589-148783670	chr5:148756589-148758767	chr5:148783671-148783861	chr5:148758768-148758905			64.86
N	cassette	CUFF.681	chr20	-	chr20:29965243-29978225	chr20:29965243-29966154;chr20:29966195-29978225		chr20:29966155-29966194			60.00
N	mutually_exclusive	CUFF.611	chr2	-	chr2:73172229-73195576,chr2:73195663-73215386	chr2:73172229-73188259,chr2:73188378-73215386	chr2:73195577-73195662	chr2:73188260-73188377			81.16
K	intron_retention	CUFF.604	chr2	-	chr2:61725928-61725999				chr2:61725927-61725928;chr2:61725999-61726000		34.88
K	alternative_acceptor	CUFF.550,CUFF.566	chr19	+	chr19:44768529-44770350	chr19:44768529-44770307		chr19:44770308-44770350	chr19:44770350-44770351		7.34
K	alternative_donor	CUFF.4	chr1	+	chr1:11082299-11083249	chr1:11082308-11083249		chr1:11082299-11082307	chr1:11082298-11082299		66.67
N	jcn_only_AD	CUFF.928	chr6	-	chr6:41491964-41513826	chr6:41491964-41513737		chr6:41513738-41513826	chr6:41513826-41513827		95.14
N	alternative_acceptor	CUFF.884	chr5	-	chr5:82969369-83016607	chr5:82971157-83016607		chr5:82969369-82971156	chr5:82969368-82969369		66.67
K	intron_retention	CUFF.180	chr11	+	chr11:117072658-117073717				chr11:117072657-117072658;chr11:117073717-117073718		62.50
N	cassette	CUFF.269	chr14	+	chr14:58979346-59014498	chr14:58979346-59006788;chr14:59006855-59014498		chr14:59006789-59006854			89.47
K	cassette	CUFF.394	chr16	+	chr16:31374696-31382404	chr16:31374696-31381301;chr16:31381420-31382404		chr16:31381302-31381419			25.00
N	cassette	CUFF.946	chr6	-	chr6:133046119-133049879;chr6:133046119-133055391	chr6:133046119-133047860;chr6:133047978-133049879,chr6:133047978-133055391		chr6:133047861-133047977			58.70
K	alternative_donor	CUFF.550	chr19	+	chr19:44764362-44768466;chr19:44764092-44768466	chr19:44764156-44768466		chr19:44764092-44764155;chr19:44764156-44764361	chr19:44764091-44764092;chr19:44764155-44764156		38.64
N	jcn_only_AA		chr16	+	chr16:19592976-19612985;chr16:19592976-19598714	chr16:19592976-19603111					51.67
K	intron_retention	CUFF.542	chr19	-	chr19:39924059-39924133				chr19:39924058-39924059;chr19:39924133-39924134		18.54
K	alternative_first_exon	CUFF.256	chr13	+	chr13:103525694-103527656	chr13:103527209-103527656	chr13:103525609-103525693	chr13:103527006-103527208			82.50
K	intron_retention	CUFF.460	chr17	+	chr17:61904884-61907492				chr17:61904883-61904884;chr17:61907492-61907493		82.65
N	alternative_acceptor	CUFF.809	chr4	+	chr4:661796-663837	chr4:661796-663834		chr4:663835-663837	chr4:663837-663838		69.23
K	jcn_only_AA	CUFF.382	chr16	+	chr16:14020614-14021978	chr16:14020614-14021884		chr16:14021885-14021978	chr16:14021978-14021979		40.48
N	alternative_donor	CUFF.663	chr2	+	chr2:220095128-220096649;chr2:220095073-220096649	chr2:220094623-220096649		chr2:220094623-220095072;chr2:220095073-220095127	chr2:220094622-220094623;chr2:220095072-220095073		31.78
N	jcn_only_AA	CUFF.193	chr11	-	chr11:124767529-124767621;chr11:124767158-124767621	chr11:124766952-124767621		chr11:124766952-124767157;chr11:124767158-124767528	chr11:124766951-124766952;chr11:124767157-124767158		8.00
K	cassette	CUFF.526	chr19	+	chr19:16186983-16197232	chr19:16186983-16192722;chr19:16192857-16197232		chr19:16192723-16192856			38.18
K	cassette	CUFF.442	chr17	-	chr17:37595447-37596875	chr17:37595447-37596638;chr17:37596772-37596875		chr17:37596639-37596771			66.67
K	coord_cassette	CUFF.681	chr20	-	chr20:29965243-29978225	chr20:29965243-29966154;chr20:29966195-29976125;chr20:29976163-29978225		chr20:29966155-29966194;chr20:29976126-29976162			62.96
N	mutually_exclusive	CUFF.265	chr14	+	chr14:50247041-50249087,chr14:50249176-50249259	chr14:50247041-50247420,chr14:50247494-50249259	chr14:50249088-50249175	chr14:50247421-50247493			71.43
N	jcn_only_AA	CUFF.954	chr6	+	chr6:161471012-161491639	chr6:161471012-161488230		chr6:161488231-161491639	chr6:161491639-161491640	chr6:161469648-161471011;chr6:161491640-161491882	8.00
K	jcn_only_AD	CUFF.138	chr11	+	chr11:827319-828259	chr11:827460-828259		chr11:827319-827459	chr11:827318-827319	chr11:828260-828772;chr11:827215-827318	56.25
K	intron_retention	CUFF.576	chr2	-	chr2:676239-676573				chr2:676238-676239;chr2:676573-676574		51.85
K	alternative_last_exon	CUFF.352	chr15	-	chr15:90380955-90414706	chr15:90408926-90414706	chr15:90380847-90380954	chr15:90408831-90408925			13.02
K	cassette	CUFF.150	chr11	-	chr11:8483457-8494709	chr11:8483457-8486255;chr11:8486370-8494709		chr11:8486256-8486369			78.95
N	intron_retention		chr7	+	chr7:75040010-75044162				chr7:75040009-75040010;chr7:75044162-75044163		69.57
K	intron_retention	CUFF.663	chr2	+	chr2:220098156-220098436				chr2:220098155-220098156;chr2:220098436-220098437		37.60
N	jcn_only_AA	CUFF.428	chr17	+	chr17:61560051-61560820	chr17:61560051-61560389					65.62
K	cassette	CUFF.653	chr2	+	chr2:200472851-200493786	chr2:200472851-200489254;chr2:200489320-200493786		chr2:200489255-200489319			85.90
N	alternative_donor	CUFF.966	chr7	-	chr7:22206767-22232984	chr7:22206767-22231146		chr7:22231147-22232984	chr7:22232984-22232985		19.23
K	intron_retention	CUFF.673	chr2	+	chr2:242590527-242592926				chr2:242590526-242590527;chr2:242592926-242592927		72.73
K	cassette	CUFF.218	chr12	-	chr12:49334972-49351092	chr12:49334972-49335350;chr12:49335361-49351092		chr12:49335351-49335360			55.07
N	alternative_first_exon	CUFF.663	chr2	+	chr2:220095073-220096981;chr2:220095128-220096981	chr2:220096763-220096981	chr2:220094404-220095127	chr2:220096560-220096762			49.76
K	intron_retention	CUFF.1118	chrX	-	chrX:19932545-19933056				chrX:19932544-19932545;chrX:19933056-19933057		36.36
N	cassette	CUFF.426	chr17	-	chr17:15546131-15584178;chr17:15555261-15580489;chr17:15546131-15580489	chr17:15546131-15562115,chr17:15555261-15562115;chr17:15562191-15580489,chr17:15562191-15584178		chr17:15562116-15562190			68.36
N	jcn_only_AD	CUFF.12,CUFF.53	chr1	-	chr1:156918291-156921364	chr1:156918291-156918364		chr1:156918365-156921364	chr1:156921364-156921365		53.33
N	cassette	CUFF.752	chr3	-	chr3:49348171-49362134	chr3:49348171-49348946;chr3:49349088-49362134		chr3:49348947-49349087			94.52
N	alternative_acceptor	CUFF.504	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		4.98
K	jcn_only_AD	CUFF.542	chr19	-	chr19:39924402-39926297	chr19:39924402-39926246		chr19:39926247-39926297	chr19:39926297-39926298		51.48
N	alternative_acceptor	CUFF.581	chr2	-	chr2:4009394-4021134;chr2:4015879-4021134;chr2:4020693-4021134;chr2:4009485-4021134	chr2:4020665-4021134		chr2:4009394-4009484;chr2:4009485-4015878;chr2:4015879-4020664;chr2:4020665-4020692	chr2:4009393-4009394;chr2:4009484-4009485;chr2:4015878-4015879;chr2:4020664-4020665		6.45
N	cassette	CUFF.966	chr7	-	chr7:22357657-22396448	chr7:22357657-22395596;chr7:22396231-22396448		chr7:22395597-22396230			91.67
K	alternative_donor	CUFF.147	chr11	-	chr11:5685404-5686885	chr11:5685404-5686398		chr11:5686399-5686885	chr11:5686885-5686886		38.20
N	alternative_donor		chr15	+	chr15:57211105-57212089	chr15:57211427-57212089		chr15:57211105-57211426	chr15:57211104-57211105		20.41
N	jcn_only_AA	CUFF.743	chr3	-	chr3:33614847-33617660	chr3:33615989-33617660		chr3:33614847-33615988	chr3:33614846-33614847		4.93
N	alternative_first_exon	CUFF.752	chr3	-	chr3:49349088-49355741;chr3:49349088-49351303	chr3:49349088-49362134	chr3:49355742-49356244;chr3:49351304-49351556	chr3:49362135-49362196			2.02
K	intron_retention	CUFF.543	chr19	+	chr19:40486054-40486192				chr19:40486053-40486054;chr19:40486192-40486193		51.35
N	intron_retention		chr19	+	chr19:1439826-1440017				chr19:1439825-1439826;chr19:1440017-1440018		33.33
K	intron_retention	CUFF.921	chr6	+	chr6:32823983-32825781				chr6:32823982-32823983;chr6:32825781-32825782		7.14
N	jcn_only_AA		chr10	-	chr10:78637649-78644746	chr10:78637652-78644746		chr10:78637649-78637651	chr10:78637648-78637649		40.00
N	intron_retention		chr1	+	chr1:160146353-160147308				chr1:160146352-160146353;chr1:160147308-160147309		88.15
K	alternative_donor	CUFF.177	chr11	-	chr11:104915386-104916017	chr11:104915386-104915917		chr11:104915918-104916017	chr11:104916017-104916018		35.00
N	alternative_donor	CUFF.802	chr3	+	chr3:186660216-186681572;chr3:186648624-186681572;chr3:186648928-186681572;chr3:186666727-186681572	chr3:186649184-186681572		chr3:186648624-186648927;chr3:186648928-186649183;chr3:186649184-186660215;chr3:186660216-186666726	chr3:186648623-186648624;chr3:186648927-186648928;chr3:186649183-186649184;chr3:186660215-186660216		1.29
K	alternative_donor	CUFF.239	chr12	-	chr12:113599803-113600736	chr12:113599803-113600700		chr12:113600701-113600736	chr12:113600736-113600737		11.56
N	intron_retention		chr19	+	chr19:17448386-17448816				chr19:17448385-17448386;chr19:17448816-17448817		80.49
K	alternative_donor	CUFF.516	chr19	-	chr19:10207250-10213243	chr19:10207250-10213227		chr19:10213228-10213243	chr19:10213243-10213244		14.29
N	jcn_only_AD	CUFF.606	chr2	-	chr2:68374700-68384505;chr2:68374700-68384058	chr2:68374700-68384392		chr2:68384059-68384392;chr2:68384393-68384505	chr2:68384392-68384393;chr2:68384505-68384506		64.62
N	cassette	CUFF.1002	chr7	-	chr7:107576102-107577537	chr7:107576102-107576723;chr7:107576819-107577537		chr7:107576724-107576818			22.22
K	intron_retention	CUFF.557	chr19	+	chr19:50305857-50306205				chr19:50305856-50305857;chr19:50306205-50306206		2.78
K	alternative_acceptor	CUFF.187	chr11	+	chr11:119056220-119056633;chr11:119056220-119056630	chr11:119056220-119056557		chr11:119056558-119056630;chr11:119056631-119056633	chr11:119056630-119056631;chr11:119056633-119056634		3.16
K	cassette	CUFF.998	chr7	-	chr7:102228218-102230605	chr7:102228218-102228680;chr7:102228893-102230605		chr7:102228681-102228892			57.58
K	alternative_donor	CUFF.920	chr6	+	chr6:32122024-32122363;chr6:32122182-32122363	chr6:32122172-32122363		chr6:32122024-32122171;chr6:32122172-32122181	chr6:32122023-32122024;chr6:32122171-32122172		8.62
N	alternative_donor	CUFF.28	chr1	+	chr1:70820795-70832126;chr1:70820892-70832126;chr1:70820791-70832126	chr1:70832012-70832126		chr1:70820791-70820794;chr1:70820795-70820891;chr1:70820892-70832011	chr1:70820790-70820791;chr1:70820794-70820795;chr1:70820891-70820892		0.81
N	jcn_only_AA	CUFF.2	chr1	+	chr1:2106753-2116021	chr1:2106753-2113270		chr1:2113271-2116021	chr1:2116021-2116022		3.36
K	cassette	CUFF.904	chr5	-	chr5:178032384-178039416	chr5:178032384-178035376;chr5:178035460-178039416		chr5:178035377-178035459			55.38
N	jcn_only_AA	CUFF.49	chr1	-	chr1:153925846-153930820	chr1:153927643-153930820					33.33
N	cassette	CUFF.211	chr12	-	chr12:25679890-25801427	chr12:25679890-25699307;chr12:25699489-25801427		chr12:25699308-25699488			93.24
K	cassette	CUFF.765	chr3	-	chr3:107595034-107596159	chr3:107595034-107595301;chr3:107595379-107596159		chr3:107595302-107595378			37.24
K	intron_retention	CUFF.261	chr14	-	chr14:24683602-24683697				chr14:24683601-24683602;chr14:24683697-24683698		50.00
K	intron_retention	CUFF.83	chr1	+	chr1:245133101-245180543				chr1:245133100-245133101;chr1:245180543-245180544		21.92
N	alternative_donor	CUFF.189	chr11	-	chr11:2192001-2192926	chr11:2192001-2192914		chr11:2192915-2192926	chr11:2192926-2192927		22.73
N	cassette	CUFF.1033	chr8	-	chr8:56652778-56663522;chr8:56652778-56657619	chr8:56652778-56656039;chr8:56656180-56663522,chr8:56656180-56657619		chr8:56656040-56656179			36.72
N	jcn_only_AA	CUFF.385	chr16	+	chr16:19663413-19680481	chr16:19663413-19663676		chr16:19663677-19680481	chr16:19680481-19680482		36.89
N	alternative_donor	CUFF.849	chr4	+	chr4:124582989-124750249	chr4:124695531-124750249		chr4:124582989-124695530	chr4:124582988-124582989		0.00
K	cassette	CUFF.524	chr19	-	chr19:14865940-14867049	chr19:14865940-14866465;chr19:14866657-14867049		chr19:14866466-14866656			35.29
N	jcn_only_AD	CUFF.1033	chr8	-	chr8:56676540-56685785;chr8:56676540-56685827	chr8:56676540-56685534		chr8:56685535-56685785;chr8:56685786-56685827	chr8:56685785-56685786;chr8:56685827-56685828		6.19
K	intron_retention	CUFF.720	chr22	-	chr22:30741180-30742300				chr22:30741179-30741180;chr22:30742300-30742301		47.06
K	cassette	CUFF.524	chr19	-	chr19:14854597-14857707	chr19:14854597-14857043;chr19:14857136-14857707		chr19:14857044-14857135			81.51
N	intron_retention		chr12	+	chr12:69237613-69237713				chr12:69237612-69237613;chr12:69237713-69237714		71.21
K	intron_retention	CUFF.920	chr6	+	chr6:32122182-32122363				chr6:32122181-32122182;chr6:32122363-32122364		2.68
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55816802-55833019;chr18:55711941-55833019;chr18:55758860-55833019;chr18:55713021-55833019;chr18:55712848-55833019;chr18:55714743-55833019;chr18:55816792-55833019;chr18:55722109-55833019	chr18:55713251-55833019		chr18:55711941-55712847;chr18:55712848-55713020;chr18:55713021-55713250;chr18:55713251-55714742;chr18:55714743-55722108;chr18:55722109-55758859;chr18:55758860-55816791;chr18:55816792-55816801	chr18:55711940-55711941;chr18:55712847-55712848;chr18:55713020-55713021;chr18:55713250-55713251;chr18:55714742-55714743;chr18:55722108-55722109;chr18:55758859-55758860;chr18:55816791-55816792		4.23
N	alternative_donor	CUFF.663	chr2	+	chr2:220094681-220094949;chr2:220094623-220094949	chr2:220094703-220094949		chr2:220094623-220094680;chr2:220094681-220094702	chr2:220094622-220094623;chr2:220094680-220094681		9.50
K	alternative_first_exon	CUFF.1099	chr9	+	chr9:131002276-131004510	chr9:131003327-131004510	chr9:131002264-131002275	chr9:131003053-131003326			26.51
N	alternative_donor		chr5	-	chr5:64906871-64907583	chr5:64906871-64907429		chr5:64907430-64907583	chr5:64907583-64907584		90.36
N	jcn_only_AD	CUFF.989	chr7	+	chr7:91732141-91739435	chr7:91737948-91739435					88.33
K	alternative_first_exon	CUFF.953	chr6	-	chr6:151757690-151765600;chr6:151757690-151773150	chr6:151757690-151766442	chr6:151765601-151765760;chr6:151773151-151773335	chr6:151766443-151767007			57.14
N	intron_retention		chr16	+	chr16:3117417-3118180				chr16:3117416-3117417;chr16:3118180-3118181		80.00
N	alternative_last_exon	CUFF.1066	chr9	-	chr9:15214248-15249915	chr9:15249686-15249915	chr9:15214137-15214247	chr9:15248942-15249685			99.49
N	jcn_only_AA	CUFF.751	chr3	-	chr3:46982556-47017842	chr3:47007620-47017842		chr3:46982556-47007619	chr3:46982555-46982556		4.76
N	jcn_only_AD	CUFF.460	chr17	+	chr17:61904884-61907492	chr17:61907310-61907492		chr17:61904884-61907309	chr17:61904883-61904884		73.85
K	alternative_first_exon	CUFF.168	chr11	+	chr11:67818400-67820446	chr11:67819909-67820446	chr11:67818207-67818399	chr11:67819552-67819908			50.00
N	alternative_first_exon	CUFF.271	chr14	-	chr14:75152364-75179635	chr14:75152364-75158743	chr14:75179636-75179896	chr14:75158744-75159031		chr14:75152303-75152363	90.75
K	intron_retention	CUFF.728	chr22	-	chr22:51015067-51015285				chr22:51015066-51015067;chr22:51015285-51015286		62.10
K	coord_cassette	CUFF.231	chr12	+	chr12:57853985-57858455	chr12:57853985-57857447;chr12:57857575-57857781;chr12:57857875-57858455		chr12:57857448-57857574;chr12:57857782-57857874			31.03
N	alternative_acceptor	CUFF.385	chr16	+	chr16:19576273-19580745	chr16:19576273-19580565		chr16:19580566-19580745	chr16:19580745-19580746		11.67
K	jcn_only_AD	CUFF.333	chr15	-	chr15:66786891-66787667	chr15:66786891-66787240		chr15:66787241-66787667	chr15:66787667-66787668		22.98
N	alternative_acceptor	CUFF.720	chr22	-	chr22:30735169-30752718	chr22:30749062-30752718		chr22:30735169-30749061	chr22:30735168-30735169		62.50
N	alternative_donor	CUFF.809	chr4	+	chr4:661731-663834	chr4:661796-663834		chr4:661731-661795	chr4:661730-661731		13.75
K	intron_retention	CUFF.363	chr16	+	chr16:105883-106538				chr16:105882-105883;chr16:106538-106539		22.22
N	intron_retention		chr11	+	chr11:118402587-118403004				chr11:118402586-118402587;chr11:118403004-118403005	chr11:118401663-118402586;chr11:118403005-118403176	95.08
K	alternative_first_exon	CUFF.782	chr3	-	chr3:125787090-125789043,chr3:125787090-125791995,chr3:125787090-125802718;chr3:125787090-125797816;chr3:125787090-125802935,chr3:125787090-125802896	chr3:125787090-125802771	chr3:125797817-125797915;chr3:125802936-125803219	chr3:125802772-125802870			1.93
K	coord_cassette	CUFF.467	chr17	-	chr17:76994046-77005745	chr17:76994046-76994229;chr17:76994369-76996181;chr17:76996353-77005745		chr17:76994230-76994368;chr17:76996182-76996352			81.55
K	coord_cassette	CUFF.555	chr19	-	chr19:49303555-49314240	chr19:49303555-49309773;chr19:49309975-49310256;chr19:49310332-49314240		chr19:49309774-49309974;chr19:49310257-49310331			59.95
K	cassette	CUFF.1153	chrY	+	chrY:20893684-20894740	chrY:20893684-20894044;chrY:20894159-20894740		chrY:20894045-20894158			37.23
N	jcn_only_AA	CUFF.1016	chr7	+	chr7:150825772-150831486	chr7:150825772-150828158		chr7:150828159-150831486	chr7:150831486-150831487		12.13
N	jcn_only_AD	CUFF.877	chr5	-	chr5:54577344-54579030	chr5:54577344-54578943		chr5:54578944-54579030	chr5:54579030-54579031		29.41
K	jcn_only_AA	CUFF.683,CUFF.689	chr20	+	chr20:30132839-30136831	chr20:30132839-30136767		chr20:30136768-30136831	chr20:30136831-30136832	chr20:30132750-30132838;chr20:30136832-30136917	1.31
N	jcn_only_AA		chr11	+	chr11:118404845-118404983	chr11:118404845-118404980		chr11:118404981-118404983	chr11:118404983-118404984	chr11:118404744-118404844;chr11:118404984-118405070	77.07
K	alternative_acceptor	CUFF.758	chr3	-	chr3:57569760-57570110;chr3:57569735-57570110	chr3:57569788-57570110		chr3:57569735-57569759;chr3:57569760-57569787	chr3:57569734-57569735;chr3:57569759-57569760		24.39
N	cassette	CUFF.140	chr11	-	chr11:2191102-2192914;chr11:2191102-2192926	chr11:2191102-2191919;chr11:2192001-2192914,chr11:2192001-2192926		chr11:2191920-2192000			58.62
N	alternative_acceptor	CUFF.739	chr3	+	chr3:28357915-28358243;chr3:28357915-28360222	chr3:28357915-28360999		chr3:28358244-28360222;chr3:28360223-28360999	chr3:28360222-28360223;chr3:28360999-28361000		94.69
K	alternative_acceptor	CUFF.29,CUFF.73	chr1	+	chr1:207277776-207286345	chr1:207277776-207286243		chr1:207286244-207286345	chr1:207286345-207286346		31.37
N	alternative_donor	CUFF.1151	chrX	+	chrX:153607898-153608049	chrX:153607927-153608049		chrX:153607898-153607926	chrX:153607897-153607898		71.88
K	alternative_last_exon	CUFF.945	chr6	-	chr6:128384671-128385902;chr6:128330411-128385902,chr6:128330414-128385902	chr6:128383570-128385902	chr6:128330275-128330410	chr6:128383127-128383569			58.24
N	intron_retention		chr1	+	chr1:145584837-145585355				chr1:145584836-145584837;chr1:145585355-145585356		28.57
K	intron_retention	CUFF.193	chr11	-	chr11:124757110-124757253				chr11:124757109-124757110;chr11:124757253-124757254		3.70
N	jcn_only_AD		chr7	-	chr7:37954056-37966281	chr7:37954056-37955694		chr7:37955695-37966281	chr7:37966281-37966282		80.77
K	alternative_first_exon	CUFF.594	chr2	-	chr2:31428366-31449393	chr2:31428366-31440321	chr2:31449394-31449517	chr2:31440322-31440411			10.00
N	jcn_only_AD	CUFF.579	chr2	+	chr2:3447663-3461391;chr2:3461001-3461391	chr2:3453249-3461391		chr2:3447663-3453248;chr2:3453249-3461000	chr2:3447662-3447663;chr2:3453248-3453249		15.81
K	cassette	CUFF.451	chr17	-	chr17:47302494-47304008	chr17:47302494-47303017;chr17:47303140-47304008		chr17:47303018-47303139			11.51
N	alternative_acceptor	CUFF.332	chr15	-	chr15:66645294-66678987	chr15:66672279-66678987		chr15:66645294-66672278	chr15:66645293-66645294		0.00
K	intron_retention	CUFF.506	chr19	+	chr19:4310594-4311838				chr19:4310593-4310594;chr19:4311838-4311839		23.28
N	jcn_only_AA		chr11	+	chr11:118402587-118403124;chr11:118402587-118402811;chr11:118402587-118403004	chr11:118402587-118402960				chr11:118401663-118402586	15.79
N	jcn_only_AD	CUFF.271	chr14	-	chr14:59939809-59942586;chr14:59939809-59941445	chr14:59939809-59941156		chr14:59941157-59941445;chr14:59941446-59942586	chr14:59941445-59941446;chr14:59942586-59942587		13.11
N	alternative_donor	CUFF.292	chr14	+	chr14:92915504-92920243;chr14:92915561-92920243	chr14:92918991-92920243		chr14:92915504-92915560;chr14:92915561-92918990	chr14:92915503-92915504;chr14:92915560-92915561		34.38
K	intron_retention	CUFF.407	chr16	+	chr16:70395414-70398445				chr16:70395413-70395414;chr16:70398445-70398446		46.48
N	coord_cassette	CUFF.234	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			62.96
K	cassette	CUFF.110	chr10	-	chr10:69571422-69583071	chr10:69571422-69575797;chr10:69575892-69583071		chr10:69575798-69575891		chr10:69571282-69571421;chr10:69583072-69583150	29.51
N	jcn_only_AD		chr20	+	chr20:30135410-30136479	chr20:30135496-30136479					48.00
N	jcn_only_AA	CUFF.1080	chr9	-	chr9:86506417-86514575	chr9:86513864-86514575		chr9:86506417-86513863	chr9:86506416-86506417		50.00
K	alternative_first_exon	CUFF.238	chr12	+	chr12:111809875-111840941	chr12:111834678-111840941	chr12:111809773-111809874	chr12:111834583-111834677			70.00
N	alternative_acceptor	CUFF.269	chr14	+	chr14:58899176-58906787;chr14:58899176-58909423	chr14:58899176-58899829		chr14:58899830-58906787;chr14:58906788-58909423	chr14:58906787-58906788;chr14:58909423-58909424		0.00
N	jcn_only_AD	CUFF.160	chr11	+	chr11:61560501-61593503	chr11:61583899-61593503		chr11:61560501-61583898	chr11:61560500-61560501		56.25
N	alternative_acceptor	CUFF.1004	chr7	-	chr7:111161506-111201906	chr7:111172642-111201906		chr7:111161506-111172641	chr7:111161505-111161506		0.00
N	jcn_only_AA	CUFF.418	chr17	+	chr17:80416707-80417875	chr17:80416707-80417867		chr17:80417868-80417875	chr17:80417875-80417876		96.22
K	cassette	CUFF.317	chr15	-	chr15:45464517-45467416	chr15:45464517-45465773;chr15:45465915-45467416		chr15:45465774-45465914			23.53
N	alternative_donor	CUFF.97	chr10	-	chr10:27112235-27149675	chr10:27112235-27128661		chr10:27128662-27149675	chr10:27149675-27149676		0.00
K	jcn_only_AA	CUFF.1037	chr8	+	chr8:71521069-71564047	chr8:71521069-71543339					50.00
N	alternative_donor	CUFF.504	chr19	+	chr19:1438892-1440017	chr19:1439826-1440017		chr19:1438892-1439825	chr19:1438891-1438892		7.32
N	intron_retention		chr2	+	chr2:220094681-220094949				chr2:220094680-220094681;chr2:220094949-220094950		84.72
K	intron_retention	CUFF.115	chr10	-	chr10:74094376-74095537				chr10:74094375-74094376;chr10:74095537-74095538		59.09
K	alternative_first_exon	CUFF.299	chr14	+	chr14:105046341-105052751	chr14:105047963-105052751	chr14:105046021-105046340	chr14:105047866-105047962			6.25
K	intron_retention	CUFF.189	chr11	-	chr11:119290231-119290760				chr11:119290230-119290231;chr11:119290760-119290761		2.06
K	cassette	CUFF.793	chr3	-	chr3:141713984-141724282	chr3:141713984-141719093;chr3:141719197-141724282		chr3:141719094-141719196			10.03
N	alternative_donor	CUFF.490	chr18	+	chr18:55833094-55912658;chr18:55865102-55912658;chr18:55895121-55912658;chr18:55862966-55912658;chr18:55888990-55912658	chr18:55895140-55912658		chr18:55833094-55862965;chr18:55862966-55865101;chr18:55865102-55888989;chr18:55888990-55895120;chr18:55895121-55895139	chr18:55833093-55833094;chr18:55862965-55862966;chr18:55865101-55865102;chr18:55888989-55888990;chr18:55895120-55895121		0.00
N	jcn_only_AD	CUFF.1052	chr8	+	chr8:107738538-107749747;chr8:107738486-107749747	chr8:107726214-107749747		chr8:107726214-107738485;chr8:107738486-107738537	chr8:107726213-107726214;chr8:107738485-107738486		76.32
K	alternative_first_exon	CUFF.66	chr1	-	chr1:174124836-174129054	chr1:174124836-174128024	chr1:174129055-174129237	chr1:174128025-174128419			51.34
N	cassette	CUFF.572	chr2	-	chr2:263373-264781	chr2:263373-263563;chr2:263763-264781		chr2:263564-263762			57.14
N	jcn_only_AD	CUFF.119	chr10	-	chr10:78637649-78647048	chr10:78637649-78644746		chr10:78644747-78647048	chr10:78647048-78647049		84.00
N	alternative_donor	CUFF.790	chr3	+	chr3:133407209-133419725	chr3:133418468-133419725		chr3:133407209-133418467	chr3:133407208-133407209		0.00
K	intron_retention	CUFF.160	chr11	+	chr11:61615757-61624482				chr11:61615756-61615757;chr11:61624482-61624483	chr11:61615631-61615756;chr11:61624483-61624543	5.41
N	mutually_exclusive	CUFF.639	chr2	+	chr2:160599765-160604315,chr2:160605415-160608912	chr2:160599765-160602280,chr2:160602449-160608912	chr2:160604316-160605414	chr2:160602281-160602448			37.75
K	intron_retention	CUFF.1048	chr8	-	chr8:99055004-99057054				chr8:99055003-99055004;chr8:99057054-99057055		68.25
N	intron_retention		chr17	-	chr17:79994890-79995506				chr17:79994889-79994890;chr17:79995506-79995507		93.26
N	alternative_acceptor	CUFF.765	chr3	-	chr3:107567966-107572719;chr3:107569199-107572719	chr3:107568819-107572719		chr3:107567966-107568818;chr3:107568819-107569198	chr3:107567965-107567966;chr3:107568818-107568819		8.11
N	jcn_only_AA		chr4	+	chr4:130821810-130849722	chr4:130821810-130829788		chr4:130829789-130849722	chr4:130849722-130849723		79.41
K	alternative_first_exon	CUFF.1142	chrX	+	chrX:133594369-133607388	chrX:133594566-133607388	chrX:133594183-133594368	chrX:133594385-133594565			75.00
N	cassette	CUFF.1096	chr9	+	chr9:125047567-125054027	chr9:125047567-125048317;chr9:125048446-125054027		chr9:125048318-125048445			33.53
K	jcn_only_AD	CUFF.858	chr4	+	chr4:186253868-186260532	chr4:186253914-186260532		chr4:186253868-186253913	chr4:186253867-186253868		95.71
N	alternative_acceptor		chr1	+	chr1:70820892-70832009;chr1:70820892-70831828	chr1:70820892-70832126		chr1:70831829-70832009;chr1:70832010-70832126	chr1:70832009-70832010;chr1:70832126-70832127		78.67
K	intron_retention	CUFF.903	chr5	+	chr5:177631742-177631815				chr5:177631741-177631742;chr5:177631815-177631816		30.88
K	jcn_only_AD	CUFF.152	chr11	-	chr11:10819429-10823840	chr11:10819429-10820538					39.75
N	jcn_only_AA	CUFF.212	chr12	+	chr12:13366510-13369377	chr12:13366510-13366614		chr12:13366615-13369377	chr12:13369377-13369378		89.47
N	intron_retention		chr17	-	chr17:56082403-56082758				chr17:56082402-56082403;chr17:56082758-56082759		94.46
N	jcn_only_AD	CUFF.476	chr17	+	chr17:80417949-80422162	chr17:80418200-80422162		chr17:80417949-80418199	chr17:80417948-80417949		4.21
K	intron_retention	CUFF.693	chr21	+	chr21:15660868-15663606				chr21:15660867-15660868;chr21:15663606-15663607	chr21:15660725-15660867;chr21:15663607-15664068	54.55
K	alternative_acceptor	CUFF.519	chr19	+	chr19:11467653-11468335	chr19:11467653-11468294		chr19:11468295-11468335	chr19:11468335-11468336		60.47
N	jcn_only_AD	CUFF.1039	chr8	+	chr8:74891097-74893389;chr8:74891111-74893389	chr8:74891407-74893389					46.43
N	alternative_first_exon	CUFF.310	chr15	+	chr15:40531337-40545378,chr15:40545216-40545378,chr15:40544465-40545378;chr15:40532883-40545378;chr15:40509869-40545378	chr15:40544893-40545378	chr15:40532681-40532882;chr15:40509629-40509868	chr15:40544751-40544892			10.77
K	alternative_acceptor	CUFF.59	chr1	-	chr1:161970129-161976086	chr1:161970132-161976086		chr1:161970129-161970131	chr1:161970128-161970129		27.27
N	intron_retention	CUFF.984	chr7	+	chr7:75042211-75043917				chr7:75042210-75042211;chr7:75043917-75043918		77.78
N	cassette	CUFF.152	chr11	-	chr11:10822635-10823595	chr11:10822635-10823207;chr11:10823322-10823595		chr11:10823208-10823321			52.38
N	jcn_only_AA	CUFF.119	chr10	-	chr10:79396328-79397022;chr10:79396274-79397022	chr10:79163782-79397022		chr10:79163782-79396273;chr10:79396274-79396327	chr10:79163781-79163782;chr10:79396273-79396274		46.55
K	alternative_first_exon	CUFF.1117	chrX	+	chrX:15699171-15706783;chrX:15693696-15706783;chrX:15693902-15706783;chrX:15699311-15706783	chrX:15693092-15706783	chrX:15693624-15693695;chrX:15693813-15693901;chrX:15699124-15699310	chrX:15692971-15693091			29.09
N	alternative_donor	CUFF.152	chr11	-	chr11:10828929-10829080;chr11:10828929-10829720	chr11:10828929-10829291		chr11:10829081-10829291;chr11:10829292-10829720	chr11:10829291-10829292;chr11:10829720-10829721		54.05
N	jcn_only_AD	CUFF.509,CUFF.555	chr19	-	chr19:6047516-6148241;chr19:6047516-6110403;chr19:6047516-6057172;chr19:6047516-6072015	chr19:6047516-6049146		chr19:6049147-6057172;chr19:6057173-6072015;chr19:6072016-6110403;chr19:6110404-6148241	chr19:6057172-6057173;chr19:6072015-6072016;chr19:6110403-6110404;chr19:6148241-6148242		11.80
K	alternative_first_exon	CUFF.611	chr2	-	chr2:73285726-73286222,chr2:73285726-73298168,chr2:73285726-73302708;chr2:73285726-73286136;chr2:73285726-73297588	chr2:73285726-73298732	chr2:73286137-73286312;chr2:73297589-73298469	chr2:73298733-73298921			23.28
K	jcn_only_AA	CUFF.101	chr10	-	chr10:35349853-35351887	chr10:35349897-35351887		chr10:35349853-35349896	chr10:35349852-35349853		84.88
N	jcn_only_AA	CUFF.1081	chr9	-	chr9:86924630-86928273	chr9:86925503-86928273		chr9:86924630-86925502	chr9:86924629-86924630		78.57
K	coord_cassette	CUFF.172	chr11	-	chr11:77885630-77899618	chr11:77885630-77887933;chr11:77888032-77888784;chr11:77889032-77899618		chr11:77887934-77888031;chr11:77888785-77889031			97.40
N	alternative_donor	CUFF.657	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		10.00
N	jcn_only_AD	CUFF.595	chr2	+	chr2:33487889-33488360	chr2:33487892-33488360		chr2:33487889-33487891	chr2:33487888-33487889		9.68
K	intron_retention	CUFF.1018	chr7	-	chr7:156589187-156619298				chr7:156589186-156589187;chr7:156619298-156619299		19.84
K	cassette	CUFF.133	chr10	+	chr10:124186548-124189139	chr10:124186548-124187791;chr10:124187833-124189139		chr10:124187792-124187832			96.24
N	alternative_donor	CUFF.325	chr15	+	chr15:57565461-57574642	chr15:57573991-57574642		chr15:57565461-57573990	chr15:57565460-57565461		0.00
K	mutually_exclusive	CUFF.478	chr18	+	chr18:163454-178932,chr18:179038-180235	chr18:163454-166786,chr18:166820-180235	chr18:178933-179037	chr18:166787-166819			26.32
K	jcn_only_AD	CUFF.674,CUFF.688	chr20	-	chr20:1517957-1532516	chr20:1517957-1532336		chr20:1532337-1532516	chr20:1532516-1532517		78.43
K	cassette	CUFF.696	chr21	-	chr21:30909707-30927372	chr21:30909707-30910118;chr21:30910206-30927372		chr21:30910119-30910205			44.26
N	alternative_donor	CUFF.708	chr22	+	chr22:21058329-21058475	chr22:21058345-21058475		chr22:21058329-21058344	chr22:21058328-21058329		30.21
N	alternative_donor	CUFF.374	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		40.00
N	alternative_donor	CUFF.457	chr17	+	chr17:61571021-61571282;chr17:61567390-61571282	chr17:61568730-61571282		chr17:61567390-61568729;chr17:61568730-61571020	chr17:61567389-61567390;chr17:61568729-61568730		4.17
N	cassette	CUFF.611	chr2	-	chr2:73195663-73215386	chr2:73195663-73198698;chr2:73198815-73215386		chr2:73198699-73198814			66.00
K	mutually_exclusive	CUFF.618	chr2	-	chr2:86393768-86398330,chr2:86398505-86400772	chr2:86393768-86397871,chr2:86397965-86400772	chr2:86398331-86398504	chr2:86397872-86397964			90.00
N	coord_cassette	CUFF.102	chr10	+	chr10:35416122-35495822	chr10:35416122-35467816;chr10:35467915-35468061;chr10:35468205-35495822		chr10:35467817-35467914;chr10:35468062-35468204			75.59
K	intron_retention	CUFF.232	chr12	+	chr12:58019471-58019780				chr12:58019470-58019471;chr12:58019780-58019781		87.50
N	jcn_only_AA	CUFF.171	chr11	-	chr11:75514771-75522468;chr11:75520420-75522468	chr11:75514563-75522468		chr11:75514563-75514770;chr11:75514771-75520419	chr11:75514562-75514563;chr11:75514770-75514771		46.43
K	jcn_only_AA	CUFF.575	chr2	-	chr2:280150-283110	chr2:280153-283110		chr2:280150-280152	chr2:280149-280150		6.65
K	alternative_last_exon	CUFF.697	chr21	-	chr21:39471433-39492400;chr21:39325309-39492400	chr21:39427076-39492400	chr21:39325124-39325308	chr21:39426217-39427075			85.98
N	alternative_donor	CUFF.182	chr11	+	chr11:118402242-118402489;chr11:118402317-118402489	chr11:118401950-118402489		chr11:118401950-118402241;chr11:118402242-118402316	chr11:118401949-118401950;chr11:118402241-118402242	chr11:118402490-118402586;chr11:118401663-118401949	73.86
N	alternative_donor	CUFF.473	chr17	-	chr17:79894070-79898625;chr17:79894070-79894623	chr17:79894070-79900171		chr17:79894624-79898625;chr17:79898626-79900171	chr17:79898625-79898626;chr17:79900171-79900172	chr17:79893999-79894069	31.58
K	cassette	CUFF.974	chr7	-	chr7:38766589-38768141	chr7:38766589-38767940;chr7:38768035-38768141		chr7:38767941-38768034			70.93
N	alternative_donor	CUFF.352	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		0.00
K	intron_retention	CUFF.49	chr1	-	chr1:153924143-153924493				chr1:153924142-153924143;chr1:153924493-153924494		72.73
K	coord_cassette	CUFF.980	chr7	+	chr7:73101231-73106925	chr7:73101231-73101328;chr7:73101426-73105245;chr7:73105343-73106925		chr7:73101329-73101425;chr7:73105246-73105342			25.37
K	alternative_acceptor	CUFF.988	chr7	-	chr7:86541488-86542256	chr7:86541562-86542256		chr7:86541488-86541561	chr7:86541487-86541488		88.89
N	jcn_only_AA	CUFF.147	chr11	-	chr11:5687504-5699433	chr11:5691178-5699433		chr11:5687504-5691177	chr11:5687503-5687504		81.58
N	jcn_only_AD		chr3	-	chr3:124951499-124953143	chr3:124951499-124951952					57.14
N	alternative_acceptor	CUFF.519	chr19	+	chr19:11468416-11470146;chr19:11468416-11470207	chr19:11468416-11470282		chr19:11470147-11470207;chr19:11470208-11470282	chr19:11470207-11470208;chr19:11470282-11470283		45.71
K	coord_cassette	CUFF.148	chr11	-	chr11:6622006-6624633	chr11:6622006-6622155;chr11:6622833-6623081;chr11:6623495-6624633		chr11:6622156-6622832;chr11:6623082-6623494			88.00
K	alternative_first_exon	CUFF.428	chr17	+	chr17:17380580-17394592	chr17:17388748-17394592	chr17:17380229-17380579	chr17:17388614-17388747			55.56
N	coord_cassette	CUFF.760	chr3	-	chr3:71743093-71759562	chr3:71743093-71745610;chr3:71745672-71748764;chr3:71748860-71759562		chr3:71745611-71745671;chr3:71748765-71748859			95.14
N	jcn_only_AA	CUFF.473	chr17	-	chr17:79893021-79893998	chr17:79893393-79893998		chr17:79893021-79893392	chr17:79893020-79893021	chr17:79893999-79894069;chr17:79892802-79893020	85.16
N	intron_retention		chr16	-	chr16:4463406-4465766				chr16:4463405-4463406;chr16:4465766-4465767		78.79
K	intron_retention	CUFF.1098	chr9	-	chr9:130943094-130947825				chr9:130943093-130943094;chr9:130947825-130947826		2.23
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		39.39
K	cassette	CUFF.235	chr12	+	chr12:72083485-72090215	chr12:72083485-72084118;chr12:72084211-72090215		chr12:72084119-72084210			60.00
K	intron_retention	CUFF.235	chr12	+	chr12:72094806-72097756				chr12:72094805-72094806;chr12:72097756-72097757		23.08
N	cassette	CUFF.566	chr19	+	chr19:54656737-54657233	chr19:54656737-54656917;chr19:54657131-54657233		chr19:54656918-54657130			50.00
N	coord_cassette	CUFF.150	chr11	-	chr11:8486370-8615629	chr11:8486370-8494709;chr11:8494824-8496227;chr11:8496364-8502080;chr11:8502162-8615629		chr11:8494710-8494823;chr11:8496228-8496363;chr11:8502081-8502161			92.86
N	jcn_only_AD		chr17	+	chr17:61560051-61560820	chr17:61560535-61560820					64.52
K	alternative_first_exon	CUFF.953	chr6	-	chr6:151757690-151765600;chr6:151757690-151766442	chr6:151757690-151773150	chr6:151765601-151765760;chr6:151766443-151767007	chr6:151773151-151773335			24.49
K	intron_retention	CUFF.910	chr6	-	chr6:5104185-5108785				chr6:5104184-5104185;chr6:5108785-5108786		78.85
N	coord_cassette	CUFF.306	chr15	+	chr15:29131425-29213842	chr15:29131425-29139019;chr15:29139191-29140665;chr15:29140756-29213842		chr15:29139020-29139190;chr15:29140666-29140755			85.29
N	coord_cassette	CUFF.473	chr17	-	chr17:79891253-79892801	chr17:79891253-79892201;chr17:79892366-79892528;chr17:79892622-79892801		chr17:79892202-79892365;chr17:79892529-79892621		chr17:79891183-79891252;chr17:79892802-79893023	86.43
N	cassette	CUFF.147	chr11	-	chr11:5686913-5688918	chr11:5686913-5687210;chr11:5687312-5688918		chr11:5687211-5687311			94.74
N	alternative_acceptor	CUFF.138,CUFF.179	chr11	+	chr11:827460-828259	chr11:827460-828229		chr11:828230-828259	chr11:828259-828260	chr11:827215-827459;chr11:828260-828772	73.53
N	cassette	CUFF.611	chr2	-	chr2:73268061-73297588	chr2:73268061-73285656;chr2:73285726-73297588		chr2:73285657-73285725			97.24
K	jcn_only_AD	CUFF.920	chr6	+	chr6:32122024-32122363;chr6:32122182-32122363	chr6:32122172-32122363		chr6:32122024-32122171;chr6:32122172-32122181	chr6:32122023-32122024;chr6:32122171-32122172		6.90
N	jcn_only_AA	CUFF.566	chr19	+	chr19:10381903-10394804	chr19:10381903-10385440		chr19:10385441-10394804	chr19:10394804-10394805		67.86
N	alternative_acceptor	CUFF.572	chr2	-	chr2:253116-260084	chr2:256691-260084		chr2:253116-256690	chr2:253115-253116		42.86
K	intron_retention	CUFF.338	chr15	-	chr15:77470366-77471131				chr15:77470365-77470366;chr15:77471131-77471132		12.50
N	alternative_acceptor	CUFF.303	chr15	+	chr15:24825478-24869114	chr15:24825478-24832713		chr15:24832714-24869114	chr15:24869114-24869115		0.00
N	intron_retention		chr14	+	chr14:76201633-76211437				chr14:76201632-76201633;chr14:76211437-76211438		26.09
N	alternative_donor	CUFF.752	chr3	-	chr3:49330032-49331839	chr3:49330032-49330978		chr3:49330979-49331839	chr3:49331839-49331840		11.43
K	intron_retention		chr9	-	chr9:130941184-130941351				chr9:130941183-130941184;chr9:130941351-130941352		69.08
K	alternative_acceptor	CUFF.101	chr10	-	chr10:35349853-35351887	chr10:35349897-35351887		chr10:35349853-35349896	chr10:35349852-35349853		75.00
K	coord_cassette	CUFF.225	chr12	+	chr12:53856352-53861004	chr12:53856352-53858543;chr12:53858637-53859715;chr12:53859758-53861004		chr12:53858544-53858636;chr12:53859716-53859757			77.23
K	alternative_acceptor	CUFF.1121	chrX	+	chrX:45184847-45192754	chrX:45184847-45192518		chrX:45192519-45192754	chrX:45192754-45192755		54.29
K	intron_retention	CUFF.980	chr7	+	chr7:73106977-73111934				chr7:73106976-73106977;chr7:73111934-73111935		12.94
K	coord_cassette	CUFF.270	chr14	+	chr14:59295274-59360860	chr14:59295274-59355515;chr14:59355641-59357041;chr14:59357239-59360860		chr14:59355516-59355640;chr14:59357042-59357238			5.62
K	alternative_last_exon	CUFF.391	chr16	-	chr16:25098045-25114671;chr16:25097094-25114671	chr16:25112007-25114671	chr16:25097561-25098044;chr16:25096913-25097093	chr16:25111790-25112006			50.00
N	jcn_only_AA		chr1	+	chr1:200860531-200867519	chr1:200860531-200867434		chr1:200867435-200867519	chr1:200867519-200867520		84.91
K	cassette	CUFF.1033	chr8	-	chr8:56668971-56676494	chr8:56668971-56675193;chr8:56675588-56676494		chr8:56675194-56675587			74.22
N	alternative_acceptor	CUFF.879	chr5	-	chr5:60224787-60240758	chr5:60227976-60240758		chr5:60224787-60227975	chr5:60224786-60224787		0.00
N	jcn_only_AD	CUFF.941	chr6	+	chr6:112558118-112604255	chr6:112600441-112604255		chr6:112558118-112600440	chr6:112558117-112558118		20.00
N	alternative_acceptor	CUFF.363	chr16	+	chr16:89789592-89789686	chr16:89789592-89789667		chr16:89789668-89789686	chr16:89789686-89789687		87.04
N	alternative_donor		chr1	+	chr1:70820791-70831828	chr1:70820892-70831828		chr1:70820791-70820891	chr1:70820790-70820791		67.50
N	intron_retention		chr1	-	chr1:153924081-153930874				chr1:153924080-153924081;chr1:153930874-153930875		90.00
N	jcn_only_AA	CUFF.595	chr2	+	chr2:1251216-1263141	chr2:1251216-1260176					38.89
N	alternative_donor	CUFF.225	chr12	+	chr12:53846760-53848509;chr12:53846161-53848509;chr12:53847068-53848509	chr12:53837558-53848509		chr12:53837558-53846160;chr12:53846161-53846759;chr12:53846760-53847067	chr12:53837557-53837558;chr12:53846160-53846161;chr12:53846759-53846760		40.00
N	jcn_only_AA		chr17	+	chr17:61905570-61907211	chr17:61905570-61906853					92.62
N	jcn_only_AA	CUFF.504	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		1.03
K	coord_cassette	CUFF.486	chr18	-	chr18:44471018-44497284	chr18:44471018-44473393;chr18:44473495-44483489;chr18:44483599-44497284		chr18:44473394-44473494;chr18:44483490-44483598			21.95
N	alternative_donor	CUFF.1000	chr7	+	chr7:107204192-107205032;chr7:107204505-107205032;chr7:107204693-107205032	chr7:107204655-107205032		chr7:107204192-107204504;chr7:107204505-107204654;chr7:107204655-107204692	chr7:107204191-107204192;chr7:107204504-107204505;chr7:107204654-107204655		35.09
N	alternative_first_exon		chr19	-	chr19:49311494-49314240	chr19:49311494-49314065	chr19:49314241-49314381	chr19:49314066-49314194			61.29
N	alternative_acceptor	CUFF.460	chr17	+	chr17:61904884-61907492	chr17:61904884-61904979		chr17:61904980-61907492	chr17:61907492-61907493		59.52
K	alternative_first_exon	CUFF.133	chr10	+	chr10:124151889-124152696;chr10:124134323-124152696	chr10:124134364-124152696	chr10:124151819-124151888;chr10:124134212-124134322	chr10:124134325-124134363			0.18
N	jcn_only_AD	CUFF.237	chr12	-	chr12:7086688-7087582	chr12:7086688-7086759		chr12:7086760-7087582	chr12:7087582-7087583		28.00
N	coord_cassette	CUFF.426	chr17	-	chr17:15546131-15584178	chr17:15546131-15562115;chr17:15562191-15580489;chr17:15580595-15584178		chr17:15562116-15562190;chr17:15580490-15580594			20.63
N	jcn_only_AA	CUFF.1016,CUFF.994	chr7	+	chr7:150815432-150815591	chr7:150815432-150815560		chr7:150815561-150815591	chr7:150815591-150815592		5.83
K	cassette	CUFF.4	chr1	+	chr1:11074023-11076900	chr1:11074023-11075580;chr1:11075704-11076900		chr1:11075581-11075703			3.74
K	cassette	CUFF.291	chr14	-	chr14:92195824-92246919	chr14:92195824-92245318;chr14:92245415-92246919		chr14:92245319-92245414		chr14:92195745-92195823;chr14:92246920-92247139	88.37
N	jcn_only_AA		chr17	+	chr17:61904875-61905033;chr17:61904875-61905210;chr17:61904875-61905478;chr17:61904875-61905497	chr17:61904875-61905188					5.26
N	alternative_donor	CUFF.155	chr11	+	chr11:36383732-36415395;chr11:36398255-36415395	chr11:36322621-36415395		chr11:36322621-36383731;chr11:36383732-36398254	chr11:36322620-36322621;chr11:36383731-36383732		70.00
N	alternative_donor	CUFF.550	chr19	+	chr19:44771115-44777051	chr19:44771298-44777051		chr19:44771115-44771297	chr19:44771114-44771115		21.21
K	alternative_acceptor	CUFF.1000	chr7	+	chr7:107215756-107216853	chr7:107215756-107216810		chr7:107216811-107216853	chr7:107216853-107216854		89.66
N	cassette	CUFF.464	chr17	+	chr17:66509120-66511534;chr17:66508284-66511534	chr17:66509120-66511127,chr17:66508284-66511127;chr17:66511261-66511534		chr17:66511128-66511260			7.96
N	alternative_donor	CUFF.728	chr22	-	chr22:51016364-51016977;chr22:51016364-51016814	chr22:51016364-51016512		chr22:51016513-51016814;chr22:51016815-51016977	chr22:51016814-51016815;chr22:51016977-51016978		1.37
N	jcn_only_AA	CUFF.633	chr2	-	chr2:110920710-110922264	chr2:110920713-110922264		chr2:110920710-110920712	chr2:110920709-110920710		59.09
K	intron_retention	CUFF.50	chr1	+	chr1:155182359-155182484				chr1:155182358-155182359;chr1:155182484-155182485		23.28
K	intron_retention	CUFF.891	chr5	+	chr5:134191018-134193046				chr5:134191017-134191018;chr5:134193046-134193047		95.24
N	jcn_only_AA	CUFF.1052	chr8	+	chr8:107593480-107691437	chr8:107593480-107617009		chr8:107617010-107691437	chr8:107691437-107691438		18.12
N	alternative_donor	CUFF.490	chr18	+	chr18:56024485-56031499	chr18:56027291-56031499		chr18:56024485-56027290	chr18:56024484-56024485		2.46
N	jcn_only_AD	CUFF.761	chr3	-	chr3:73450161-73453298	chr3:73450161-73450919		chr3:73450920-73453298	chr3:73453298-73453299		11.69
K	alternative_first_exon	CUFF.123	chr10	+	chr10:94833592-94834064	chr10:94833881-94834064	chr10:94833232-94833591	chr10:94833592-94833880			88.89
N	jcn_only_AD	CUFF.951	chr6	+	chr6:144904737-144999541;chr6:144898425-144999541	chr6:144981412-144999541		chr6:144898425-144904736;chr6:144904737-144981411	chr6:144898424-144898425;chr6:144904736-144904737		15.79
N	jcn_only_AA	CUFF.83	chr1	+	chr1:245222761-245245384	chr1:245222761-245238875		chr1:245238876-245245384	chr1:245245384-245245385		4.28
N	alternative_donor	CUFF.476	chr17	+	chr17:80417949-80422162	chr17:80418200-80422162		chr17:80417949-80418199	chr17:80417948-80417949		5.13
K	cassette	CUFF.587	chr2	-	chr2:23598556-23599654	chr2:23598556-23599108;chr2:23599201-23599654		chr2:23599109-23599200			93.75
K	jcn_only_AA	CUFF.404	chr16	-	chr16:67968575-67968699	chr16:67968598-67968699		chr16:67968575-67968597	chr16:67968574-67968575	chr16:67968700-67968851;chr16:67968307-67968574	75.73
K	intron_retention	CUFF.812	chr4	-	chr4:2933391-2933551				chr4:2933390-2933391;chr4:2933551-2933552		82.32
K	cassette	CUFF.13	chr1	-	chr1:27436269-27480473	chr1:27436269-27440316;chr1:27440778-27480473		chr1:27440317-27440777			71.43
K	jcn_only_AA	CUFF.1131	chrX	-	chrX:85219058-85302487	chrX:85282562-85302487					87.50
K	alternative_first_exon	CUFF.659	chr2	-	chr2:211085527-211089910	chr2:211085527-211089038	chr2:211089911-211090215	chr2:211089039-211089649			82.35
N	cassette	CUFF.945	chr6	-	chr6:128326390-128330274	chr6:128326390-128327170;chr6:128327201-128330274		chr6:128327171-128327200			51.79
K	intron_retention	CUFF.464	chr17	+	chr17:66526143-66526417				chr17:66526142-66526143;chr17:66526417-66526418		24.18
K	alternative_last_exon	CUFF.887	chr5	-	chr5:127396337-127396835;chr5:127302621-127396835;chr5:127359991-127396835	chr5:127292614-127396835	chr5:127301504-127302620;chr5:127359827-127359990	chr5:127292496-127292613			37.33
N	alternative_acceptor		chr17	+	chr17:60783831-60784792;chr17:60783831-60803388	chr17:60783831-60813446		chr17:60784793-60803388;chr17:60803389-60813446	chr17:60803388-60803389;chr17:60813446-60813447		100.00
K	intron_retention	CUFF.618	chr2	-	chr2:86398505-86400772				chr2:86398504-86398505;chr2:86400772-86400773		15.56
K	intron_retention	CUFF.940	chr6	+	chr6:112382498-112385966				chr6:112382497-112382498;chr6:112385966-112385967		2.83
N	jcn_only_AA	CUFF.1118	chrX	-	chrX:19948773-19955622	chrX:19954017-19955622		chrX:19948773-19954016	chrX:19948772-19948773		88.24
N	alternative_acceptor	CUFF.119	chr10	-	chr10:78771802-78778770	chr10:78772316-78778770		chr10:78771802-78772315	chr10:78771801-78771802		14.43
K	intron_retention	CUFF.560	chr19	-	chr19:51525921-51526347				chr19:51525920-51525921;chr19:51526347-51526348		64.29
N	intron_retention		chr4	-	chr4:1713655-1713927				chr4:1713654-1713655;chr4:1713927-1713928		91.43
N	alternative_donor	CUFF.489	chr18	-	chr18:47329224-47337765;chr18:47329224-47340051;chr18:47329224-47340186;chr18:47329224-47339838;chr18:47329224-47340101	chr18:47329224-47339094		chr18:47337766-47339094;chr18:47339095-47339838;chr18:47339839-47340051;chr18:47340052-47340101;chr18:47340102-47340186	chr18:47339094-47339095;chr18:47339838-47339839;chr18:47340051-47340052;chr18:47340101-47340102;chr18:47340186-47340187		3.45
K	intron_retention	CUFF.1031	chr8	-	chr8:30657165-30670301				chr8:30657164-30657165;chr8:30670301-30670302		64.66
N	alternative_acceptor	CUFF.1037	chr8	+	chr8:71543526-71558279	chr8:71543526-71544669		chr8:71544670-71558279	chr8:71558279-71558280		0.00
N	coord_cassette	CUFF.18	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			51.14
N	jcn_only_AD	CUFF.765	chr3	-	chr3:107567966-107568669;chr3:107567966-107572719	chr3:107567966-107575926					24.24
N	alternative_donor	CUFF.262,CUFF.278	chr14	-	chr14:31353881-31354618	chr14:31353881-31354173		chr14:31354174-31354618	chr14:31354618-31354619		22.22
N	alternative_donor	CUFF.954	chr6	+	chr6:161455482-161469647	chr6:161469324-161469647		chr6:161455482-161469323	chr6:161455481-161455482	chr6:161469648-161471011;chr6:161455291-161455481	0.00
N	jcn_only_AD	CUFF.708	chr22	+	chr22:21058040-21058255;chr22:21058172-21058255	chr22:21057981-21058255		chr22:21057981-21058039;chr22:21058040-21058171	chr22:21057980-21057981;chr22:21058039-21058040		21.87
N	intron_retention		chr16	+	chr16:3117615-3118180				chr16:3117614-3117615;chr16:3118180-3118181		50.00
K	coord_cassette	CUFF.560	chr19	-	chr19:51526485-51528847	chr19:51526485-51527300;chr19:51527567-51527889;chr19:51528051-51528847		chr19:51527301-51527566;chr19:51527890-51528050			87.37
N	cassette	CUFF.486	chr18	-	chr18:44444212-44497284	chr18:44444212-44470542;chr18:44471018-44497284		chr18:44470543-44471017			90.20
N	alternative_donor	CUFF.796	chr3	-	chr3:156262229-156266593;chr3:156262229-156266693	chr3:156262229-156266654		chr3:156266594-156266654;chr3:156266655-156266693	chr3:156266654-156266655;chr3:156266693-156266694		1.65
K	alternative_acceptor	CUFF.812	chr4	-	chr4:2934137-2934326	chr4:2934240-2934326		chr4:2934137-2934239	chr4:2934136-2934137		96.86
K	jcn_only_AA	CUFF.568	chr19	+	chr19:55255537-55275342	chr19:55255537-55258786					40.00
N	jcn_only_AA	CUFF.189	chr11	-	chr11:119291046-119291578;chr11:119291097-119291578	chr11:119291089-119291578		chr11:119291046-119291088;chr11:119291089-119291096	chr11:119291045-119291046;chr11:119291088-119291089		5.13
N	cassette	CUFF.476	chr17	+	chr17:80417949-80426639	chr17:80417949-80422162;chr17:80422307-80426639		chr17:80422163-80422306			82.22
K	intron_retention	CUFF.173	chr11	-	chr11:94704230-94704538				chr11:94704229-94704230;chr11:94704538-94704539		7.59
K	intron_retention		chr15	-	chr15:83350333-83357487				chr15:83350332-83350333;chr15:83357487-83357488		56.63
K	intron_retention	CUFF.920	chr6	+	chr6:32122024-32122363				chr6:32122023-32122024;chr6:32122363-32122364		80.90
N	jcn_only_AD	CUFF.490	chr18	+	chr18:55912741-55916130	chr18:55914857-55916130		chr18:55912741-55914856	chr18:55912740-55912741		5.17
N	jcn_only_AA	CUFF.1033	chr8	-	chr8:56663717-56668802	chr8:56664106-56668802		chr8:56663717-56664105	chr8:56663716-56663717		3.47
N	jcn_only_AD	CUFF.151	chr11	-	chr11:8941998-8947009	chr11:8941998-8942840		chr11:8942841-8947009	chr11:8947009-8947010		11.11
N	jcn_only_AA	CUFF.714	chr22	+	chr22:45122515-45182336	chr22:45122515-45127609					68.18
N	jcn_only_AD	CUFF.572	chr2	-	chr2:242872-247537;chr2:242872-244626	chr2:242872-243502		chr2:243503-244626;chr2:244627-247537	chr2:244626-244627;chr2:247537-247538		43.06
N	jcn_only_AD	CUFF.531	chr19	+	chr19:17608274-17611086	chr19:17610764-17611086		chr19:17608274-17610763	chr19:17608273-17608274		7.87
K	cassette	CUFF.114	chr10	-	chr10:73862171-73887839;chr10:73857209-73887839	chr10:73862171-73862607,chr10:73857209-73862607;chr10:73862726-73887839		chr10:73862608-73862725			64.86
K	alternative_first_exon	CUFF.939	chr6	+	chr6:111303333-111306208	chr6:111303707-111306208	chr6:111303132-111303332	chr6:111303638-111303706			7.50
N	alternative_donor	CUFF.306	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		94.59
N	intron_retention		chr5	-	chr5:178043950-178045556				chr5:178043949-178043950;chr5:178045556-178045557		96.16
K	intron_retention	CUFF.490	chr18	+	chr18:55989719-55990463				chr18:55989718-55989719;chr18:55990463-55990464		2.13
K	alternative_first_exon	CUFF.879	chr5	-	chr5:60186914-60194102	chr5:60186914-60187863	chr5:60194103-60194227	chr5:60187864-60187955			7.41
N	jcn_only_AA	CUFF.922	chr6	+	chr6:33239900-33240404	chr6:33239900-33240363		chr6:33240364-33240404	chr6:33240404-33240405		3.87
N	alternative_acceptor	CUFF.765	chr3	-	chr3:107572902-107573976;chr3:107572807-107573976	chr3:107573542-107573976		chr3:107572807-107572901;chr3:107572902-107573541	chr3:107572806-107572807;chr3:107572901-107572902		17.39
N	intron_retention	CUFF.709	chr22	-	chr22:21829590-21830280				chr22:21829589-21829590;chr22:21830280-21830281		47.54
N	alternative_last_exon		chr14	+	chr14:77929103-77935419	chr14:77929103-77930940	chr14:77935420-77935912	chr14:77930941-77931029			95.52
K	jcn_only_AD	CUFF.751,CUFF.775	chr3	-	chr3:120389380-120394638	chr3:120389380-120393747					84.03
N	jcn_only_AD	CUFF.1102	chr9	+	chr9:133346903-133352257	chr9:133351777-133352257		chr9:133346903-133351776	chr9:133346902-133346903		23.88
K	intron_retention	CUFF.235	chr12	+	chr12:72094659-72097756				chr12:72094658-72094659;chr12:72097756-72097757		17.86
K	cassette	CUFF.1115	chrX	-	chrX:13803928-13834962	chrX:13803928-13825768;chrX:13825889-13834962		chrX:13825769-13825888			44.12
K	intron_retention	CUFF.542	chr19	-	chr19:39924210-39924304				chr19:39924209-39924210;chr19:39924304-39924305		3.81
K	cassette	CUFF.765	chr3	-	chr3:107595034-107596748	chr3:107595034-107596159;chr3:107596345-107596748		chr3:107596160-107596344			53.68
N	jcn_only_AA	CUFF.230	chr12	-	chr12:56705180-56708634;chr12:56706670-56708634;chr12:56705238-56708634	chr12:56705199-56708634		chr12:56705180-56705198;chr12:56705199-56705237;chr12:56705238-56706669	chr12:56705179-56705180;chr12:56705198-56705199;chr12:56705237-56705238		71.58
K	alternative_last_exon	CUFF.291	chr14	-	chr14:92185823-92191423	chr14:92189534-92191423	chr14:92185762-92185822	chr14:92189365-92189533		chr14:92191424-92191512	86.08
N	alternative_acceptor	CUFF.40	chr1	+	chr1:145575405-145578061	chr1:145575405-145577651		chr1:145577652-145578061	chr1:145578061-145578062		35.29
K	alternative_first_exon	CUFF.766,CUFF.796	chr3	-	chr3:156266793-156271443	chr3:156266793-156269186	chr3:156271444-156271570	chr3:156269187-156269341			43.23
N	alternative_acceptor	CUFF.273	chr14	+	chr14:61512886-61514868;chr14:61512886-61517229	chr14:61512886-61514965		chr14:61514869-61514965;chr14:61514966-61517229	chr14:61514965-61514966;chr14:61517229-61517230		0.00
K	alternative_last_exon	CUFF.33	chr1	-	chr1:103960847-103971908	chr1:103961438-103971908	chr1:103960701-103960846	chr1:103961300-103961437			39.13
N	intron_retention		chr16	-	chr16:57513601-57521157				chr16:57513600-57513601;chr16:57521157-57521158		62.75
N	jcn_only_AD	CUFF.310	chr15	+	chr15:40532297-40532799;chr15:40532004-40532799;chr15:40509869-40532799	chr15:40531337-40532799		chr15:40509869-40531336;chr15:40531337-40532003;chr15:40532004-40532296	chr15:40509868-40509869;chr15:40531336-40531337;chr15:40532003-40532004		65.22
K	alternative_donor	CUFF.473	chr17	-	chr17:79894738-79895137;chr17:79894738-79895055	chr17:79894738-79895133		chr17:79895056-79895133;chr17:79895134-79895137	chr17:79895133-79895134;chr17:79895137-79895138	chr17:79894624-79894737;chr17:79895138-79895264	29.67
N	alternative_donor	CUFF.802	chr3	+	chr3:186756662-186760441	chr3:186759755-186760441		chr3:186756662-186759754	chr3:186756661-186756662		0.71
N	jcn_only_AA		chr11	-	chr11:10821304-10821790	chr11:10821716-10821790		chr11:10821304-10821715	chr11:10821303-10821304		17.14
N	jcn_only_AD	CUFF.374	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		24.00
N	alternative_acceptor	CUFF.417	chr17	-	chr17:1617309-1617664	chr17:1617340-1617664		chr17:1617309-1617339	chr17:1617308-1617309		6.02
N	jcn_only_AA	CUFF.755,CUFF.762	chr3	+	chr3:75500554-75505767	chr3:75500554-75501682		chr3:75501683-75505767	chr3:75505767-75505768		18.60
N	jcn_only_AA	CUFF.377	chr16	-	chr16:4412133-4445289	chr16:4438633-4445289		chr16:4412133-4438632	chr16:4412132-4412133		98.33
K	jcn_only_AA	CUFF.243	chr12	-	chr12:133181418-133182732	chr12:133181605-133182732		chr12:133181418-133181604	chr12:133181417-133181418		37.50
N	alternative_donor	CUFF.940	chr6	+	chr6:112382492-112385957	chr6:112382599-112385957		chr6:112382492-112382598	chr6:112382491-112382492		4.69
K	intron_retention	CUFF.79	chr1	+	chr1:224380221-224380597				chr1:224380220-224380221;chr1:224380597-224380598		48.72
K	alternative_donor	CUFF.726	chr22	+	chr22:47188660-47189397	chr22:47188702-47189397		chr22:47188660-47188701	chr22:47188659-47188660		48.44
K	alternative_acceptor	CUFF.187	chr11	+	chr11:119056220-119056557;chr11:119056220-119056630	chr11:119056220-119056633		chr11:119056558-119056630;chr11:119056631-119056633	chr11:119056630-119056631;chr11:119056633-119056634		72.11
K	cassette	CUFF.201	chr12	+	chr12:4662314-4668022	chr12:4662314-4665518;chr12:4665669-4668022		chr12:4665519-4665668			76.58
K	jcn_only_AA	CUFF.165	chr11	+	chr11:65481320-65482130	chr11:65481320-65481965		chr11:65481966-65482130	chr11:65482130-65482131		91.45
N	jcn_only_AD	CUFF.155	chr11	+	chr11:36397709-36440804	chr11:36424929-36440804		chr11:36397709-36424928	chr11:36397708-36397709		95.05
K	intron_retention	CUFF.387	chr16	+	chr16:21987565-21991867				chr16:21987564-21987565;chr16:21991867-21991868		18.18
N	intron_retention	CUFF.152	chr11	-	chr11:10828929-10829291				chr11:10828928-10828929;chr11:10829291-10829292		34.78
K	intron_retention	CUFF.1050	chr8	+	chr8:103572801-103572988				chr8:103572800-103572801;chr8:103572988-103572989		45.33
N	alternative_acceptor	CUFF.984	chr7	+	chr7:75042211-75044162	chr7:75042211-75043917		chr7:75043918-75044162	chr7:75044162-75044163		83.87
N	alternative_acceptor		chr7	+	chr7:150384176-150389402	chr7:150384176-150386576		chr7:150386577-150389402	chr7:150389402-150389403		28.57
N	jcn_only_AD	CUFF.911	chr6	-	chr6:114289861-114292020	chr6:114289861-114291643		chr6:114291644-114292020	chr6:114292020-114292021		62.50
K	jcn_only_AA	CUFF.414	chr16	-	chr16:87807148-87811473	chr16:87807196-87811473		chr16:87807148-87807195	chr16:87807147-87807148		47.83
K	intron_retention		chr12	+	chr12:58018390-58018506				chr12:58018389-58018390;chr12:58018506-58018507		7.69
N	intron_retention		chrX	-	chrX:46382561-46387784				chrX:46382560-46382561;chrX:46387784-46387785		66.67
N	alternative_donor	CUFF.961	chr7	+	chr7:6641772-6647167	chr7:6642384-6647167		chr7:6641772-6642383	chr7:6641771-6641772		60.61
N	intron_retention	CUFF.187	chr11	+	chr11:119056338-119056557				chr11:119056337-119056338;chr11:119056557-119056558		41.67
K	cassette	CUFF.846	chr4	-	chr4:107847107-108109583	chr4:107847107-108049098;chr4:108049167-108109583		chr4:108049099-108049166			70.97
N	intron_retention	CUFF.557	chr19	+	chr19:50305399-50305790				chr19:50305398-50305399;chr19:50305790-50305791		60.71
K	cassette	CUFF.567	chr19	+	chr19:55085380-55085767	chr19:55085380-55085542;chr19:55085579-55085767		chr19:55085543-55085578			18.92
N	intron_retention	CUFF.473	chr17	-	chr17:79894738-79895068				chr17:79894737-79894738;chr17:79895068-79895069	chr17:79894624-79894737;chr17:79895069-79895264	83.67
N	jcn_only_AD	CUFF.827,CUFF.856	chr4	-	chr4:162463846-162508606	chr4:162463846-162473639		chr4:162473640-162508606	chr4:162508606-162508607		24.65
N	alternative_acceptor		chr10	+	chr10:35485071-35495822	chr10:35485071-35490378		chr10:35490379-35495822	chr10:35495822-35495823		0.00
N	cassette	CUFF.234	chr12	+	chr12:69229765-69233053	chr12:69229765-69230451;chr12:69230530-69233053		chr12:69230452-69230529			85.52
K	coord_cassette	CUFF.440	chr17	-	chr17:34500807-34503839	chr17:34500807-34502089;chr17:34502176-34502338;chr17:34502412-34503839		chr17:34502090-34502175;chr17:34502339-34502411			51.06
N	intron_retention		chr7	+	chr7:75045309-75045380				chr7:75045308-75045309;chr7:75045380-75045381		97.14
N	cassette	CUFF.509	chr19	-	chr19:6010263-6016100	chr19:6010263-6012996;chr19:6013117-6016100		chr19:6012997-6013116			85.94
N	alternative_acceptor	CUFF.352	chr15	-	chr15:90378746-90380846	chr15:90378876-90380846		chr15:90378746-90378875	chr15:90378745-90378746		96.08
N	jcn_only_AD	CUFF.390,CUFF.406	chr16	-	chr16:23505700-23507034;chr16:23505700-23507014	chr16:23505700-23507009		chr16:23507010-23507014;chr16:23507015-23507034	chr16:23507014-23507015;chr16:23507034-23507035	chr16:23505624-23505699;chr16:23507035-23507099	41.50
K	intron_retention	CUFF.628	chr2	+	chr2:101587537-101591264				chr2:101587536-101587537;chr2:101591264-101591265		76.92
N	jcn_only_AD	CUFF.1097,CUFF.1098	chr9	-	chr9:130941184-130941522;chr9:130941184-130941351	chr9:130941184-130941267		chr9:130941268-130941351;chr9:130941352-130941522	chr9:130941351-130941352;chr9:130941522-130941523		27.50
N	jcn_only_AD	CUFF.215,CUFF.230	chr12	-	chr12:56709027-56709604;chr12:56709027-56709690	chr12:56709027-56709500		chr12:56709501-56709604;chr12:56709605-56709690	chr12:56709604-56709605;chr12:56709690-56709691		15.18
K	intron_retention		chr9	+	chr9:43908524-43915359				chr9:43908523-43908524;chr9:43915359-43915360		5.71
N	alternative_acceptor	CUFF.765	chr3	-	chr3:107586273-107591814;chr3:107586425-107591814	chr3:107591328-107591814		chr3:107586273-107586424;chr3:107586425-107591327	chr3:107586272-107586273;chr3:107586424-107586425		0.00
N	mutually_exclusive	CUFF.24	chr1	+	chr1:54360221-54371767,chr1:54371968-54375603	chr1:54360221-54370338,chr1:54370483-54375603	chr1:54371768-54371967	chr1:54370339-54370482			71.70
K	cassette	CUFF.9	chr1	-	chr1:16894526-16899636	chr1:16894526-16895567;chr1:16895732-16899636		chr1:16895568-16895731			98.21
N	alternative_first_exon	CUFF.101,CUFF.106	chr10	-	chr10:46113709-46116227;chr10:46113709-46120030	chr10:46113709-46143741	chr10:46116228-46116411;chr10:46120031-46120085	chr10:46143742-46143982			10.81
K	alternative_donor	CUFF.17	chr1	+	chr1:31769923-31782890	chr1:31769944-31782890		chr1:31769923-31769943	chr1:31769922-31769923		26.32
N	jcn_only_AD	CUFF.90	chr10	+	chr10:6266177-6274857;chr10:6270182-6274857;chr10:6273278-6274857;chr10:6268329-6274857	chr10:6271144-6274857					11.65
K	alternative_donor	CUFF.236	chr12	-	chr12:77260042-77272742	chr12:77260042-77272717		chr12:77272718-77272742	chr12:77272742-77272743		50.00
K	intron_retention	CUFF.526	chr19	+	chr19:16212220-16212869				chr19:16212219-16212220;chr19:16212869-16212870		71.79
K	intron_retention	CUFF.920	chr6	+	chr6:32123756-32125413				chr6:32123755-32123756;chr6:32125413-32125414		4.48
N	jcn_only_AA	CUFF.890	chr5	+	chr5:131658049-131662969	chr5:131658049-131660153		chr5:131660154-131662969	chr5:131662969-131662970		54.55
N	alternative_acceptor		chr11	-	chr11:558980-559346	chr11:559063-559346		chr11:558980-559062	chr11:558979-558980		38.89
N	alternative_donor	CUFF.581	chr2	-	chr2:4009485-4021134	chr2:4009485-4015768		chr2:4015769-4021134	chr2:4021134-4021135		11.58
K	intron_retention	CUFF.382	chr16	+	chr16:14026262-14028048				chr16:14026261-14026262;chr16:14028048-14028049		54.55
N	intron_retention	CUFF.671	chr2	-	chr2:242435950-242436714				chr2:242435949-242435950;chr2:242436714-242436715		82.61
K	intron_retention	CUFF.220	chr12	+	chr12:50357440-50357874				chr12:50357439-50357440;chr12:50357874-50357875	chr12:50357275-50357439;chr12:50357875-50357958	78.26
K	alternative_last_exon	CUFF.683,CUFF.689	chr20	+	chr20:61569606-61572842	chr20:61569606-61569951	chr20:61572843-61572972	chr20:61569952-61570275			96.43
N	alternative_acceptor	CUFF.316	chr15	-	chr15:44878049-44881449	chr15:44880837-44881449		chr15:44878049-44880836	chr15:44878048-44878049		1.72
N	jcn_only_AD		chr15	+	chr15:57211105-57212089	chr15:57211427-57212089		chr15:57211105-57211426	chr15:57211104-57211105		43.07
K	alternative_first_exon	CUFF.1025,CUFF.1031	chr8	-	chr8:10584177-10683661	chr8:10584177-10587705	chr8:10683662-10683754	chr8:10587706-10588022			50.00
K	intron_retention	CUFF.918	chr6	+	chr6:31930576-31930761				chr6:31930575-31930576;chr6:31930761-31930762		9.80
N	coord_cassette	CUFF.234	chr12	+	chr12:69214155-69233053	chr12:69214155-69222550;chr12:69222712-69229608;chr12:69229765-69233053		chr12:69222551-69222711;chr12:69229609-69229764			25.93
K	intron_retention	CUFF.936	chr6	+	chr6:90327751-90331640				chr6:90327750-90327751;chr6:90331640-90331641		13.04
N	cassette	CUFF.272	chr14	-	chr14:60010173-60018072	chr14:60010173-60011880;chr14:60012018-60018072		chr14:60011881-60012017			80.65
K	jcn_only_AA	CUFF.589	chr2	-	chr2:27703994-27706155	chr2:27704128-27706155		chr2:27703994-27704127	chr2:27703993-27703994		77.27
N	alternative_acceptor	CUFF.377	chr16	-	chr16:4445341-4455491	chr16:4447452-4455491		chr16:4445341-4447451	chr16:4445340-4445341		0.46
N	jcn_only_AA	CUFF.663	chr2	+	chr2:220094623-220097211;chr2:220094623-220094949	chr2:220094623-220096649					18.22
N	alternative_donor	CUFF.436	chr17	+	chr17:29667602-29670026	chr17:29667664-29670026		chr17:29667602-29667663	chr17:29667601-29667602		36.00
N	alternative_donor	CUFF.119,CUFF.134	chr10	-	chr10:78647274-78649208	chr10:78647274-78647552		chr10:78647553-78649208	chr10:78649208-78649209		2.08
K	intron_retention	CUFF.519	chr19	+	chr19:11474512-11474836				chr19:11474511-11474512;chr19:11474836-11474837		72.73
N	jcn_only_AA		chr3	-	chr3:27394411-27410715	chr3:27409054-27410715					14.29
N	jcn_only_AA	CUFF.765	chr3	-	chr3:107586273-107591814;chr3:107586425-107591814	chr3:107591328-107591814		chr3:107586273-107586424;chr3:107586425-107591327	chr3:107586272-107586273;chr3:107586424-107586425		2.88
K	cassette	CUFF.60	chr1	+	chr1:166810326-166818174	chr1:166810326-166816730;chr1:166816830-166818174		chr1:166816731-166816829			47.62
N	jcn_only_AD		chr18	+	chr18:55888990-55895061;chr18:55862966-55895061	chr18:55833094-55895061		chr18:55833094-55862965;chr18:55862966-55888989	chr18:55833093-55833094;chr18:55862965-55862966		47.17
N	jcn_only_AA	CUFF.579,CUFF.631	chr2	+	chr2:109085541-109086106	chr2:109085541-109085755		chr2:109085756-109086106	chr2:109086106-109086107		18.52
K	alternative_last_exon	CUFF.524	chr19	-	chr19:14877922-14883153;chr19:14876383-14883153	chr19:14879747-14883153	chr19:14877790-14877921;chr19:14876336-14876382	chr19:14879520-14879746			51.21
K	alternative_first_exon	CUFF.870	chr5	+	chr5:44809666-44811110	chr5:44810095-44811110	chr5:44808933-44809665	chr5:44809917-44810094			28.57
K	cassette	CUFF.147	chr11	-	chr11:5701469-5706097	chr11:5701469-5705215;chr11:5705370-5706097		chr11:5705216-5705369			20.29
N	alternative_donor	CUFF.363	chr16	+	chr16:105543-105793	chr16:105550-105793		chr16:105543-105549	chr16:105542-105543		45.45
K	alternative_first_exon	CUFF.537	chr19	-	chr19:33968997-33980901;chr19:33968997-33978155	chr19:33968997-33977808	chr19:33978156-33978319	chr19:33977809-33978038			48.17
K	alternative_first_exon	CUFF.751,CUFF.784	chr3	-	chr3:126071791-126076079	chr3:126071791-126072854	chr3:126076080-126076285	chr3:126072855-126073221			92.73
N	jcn_only_AD	CUFF.606	chr2	-	chr2:68374700-68384392;chr2:68374700-68384058	chr2:68374700-68384505		chr2:68384059-68384392;chr2:68384393-68384505	chr2:68384392-68384393;chr2:68384505-68384506		15.38
K	alternative_first_exon	CUFF.971	chr7	-	chr7:37172840-37243713;chr7:37172840-37250990	chr7:37172840-37236705	chr7:37243714-37243905;chr7:37250991-37251122	chr7:37236706-37236877			40.24
K	intron_retention	CUFF.506	chr19	+	chr19:4306210-4323020				chr19:4306209-4306210;chr19:4323020-4323021		49.25
N	intron_retention	CUFF.566	chr19	+	chr19:54657578-54658995				chr19:54657577-54657578;chr19:54658995-54658996		94.79
K	intron_retention	CUFF.918	chr6	+	chr6:31929164-31929323				chr6:31929163-31929164;chr6:31929323-31929324		40.62
K	cassette	CUFF.588	chr2	-	chr2:25174424-25179911	chr2:25174424-25176418;chr2:25176505-25179911		chr2:25176419-25176504			90.41
K	intron_retention	CUFF.292	chr14	+	chr14:92909161-92909743				chr14:92909160-92909161;chr14:92909743-92909744		42.11
N	alternative_donor	CUFF.942	chr6	-	chr6:114283559-114292020;chr6:114283559-114332294	chr6:114283559-114289797		chr6:114289798-114292020;chr6:114292021-114332294	chr6:114292020-114292021;chr6:114332294-114332295		10.00
K	cassette	CUFF.571	chr19	+	chr19:58963072-58965062	chr19:58963072-58963494;chr19:58964150-58965062		chr19:58963495-58964149		chr19:58962971-58963071;chr19:58965063-58965189	28.18
N	jcn_only_AD	CUFF.336	chr15	+	chr15:74754369-74758376;chr15:74754373-74758376	chr15:74754440-74758376		chr15:74754369-74754372;chr15:74754373-74754439	chr15:74754368-74754369;chr15:74754372-74754373		3.51
N	intron_retention		chr22	-	chr22:51011352-51012053				chr22:51011351-51011352;chr22:51012053-51012054		87.35
K	intron_retention	CUFF.60	chr1	+	chr1:166819661-166821821				chr1:166819660-166819661;chr1:166821821-166821822		42.86
K	intron_retention	CUFF.1033	chr8	-	chr8:56663717-56675193				chr8:56663716-56663717;chr8:56675193-56675194		62.50
K	intron_retention	CUFF.774	chr3	+	chr3:119529042-119530385				chr3:119529041-119529042;chr3:119530385-119530386		45.07
K	jcn_only_AD	CUFF.516	chr19	-	chr19:10204296-10204488	chr19:10204296-10204368		chr19:10204369-10204488	chr19:10204488-10204489		78.95
K	jcn_only_AA	CUFF.514,CUFF.564	chr19	+	chr19:7075117-7075686	chr19:7075117-7075665		chr19:7075666-7075686	chr19:7075686-7075687		69.23
K	intron_retention		chr2	+	chr2:220094623-220094949				chr2:220094622-220094623;chr2:220094949-220094950		25.50
K	alternative_acceptor	CUFF.195	chr12	-	chr12:333283-333566	chr12:333296-333566		chr12:333283-333295	chr12:333282-333283		57.45
K	cassette	CUFF.619	chr2	-	chr2:86839398-86847452	chr2:86839398-86842277;chr2:86842381-86847452		chr2:86842278-86842380			71.43
N	alternative_acceptor	CUFF.385	chr16	+	chr16:19663413-19680481	chr16:19663413-19663676		chr16:19663677-19680481	chr16:19680481-19680482		2.99
N	coord_cassette	CUFF.234	chr12	+	chr12:69207409-69214104	chr12:69207409-69208382;chr12:69208470-69210591;chr12:69210726-69214104		chr12:69208383-69208469;chr12:69210592-69210725			8.55
N	jcn_only_AD	CUFF.152	chr11	-	chr11:6632684-6633294	chr11:6632684-6632894					14.58
N	alternative_donor	CUFF.561	chr19	-	chr19:51537897-51538061	chr19:51537897-51538050		chr19:51538051-51538061	chr19:51538061-51538062		2.88
K	intron_retention	CUFF.708	chr22	+	chr22:21058040-21058255				chr22:21058039-21058040;chr22:21058255-21058256		20.50
N	alternative_acceptor		chr8	+	chr8:144373938-144375141	chr8:144373938-144374312		chr8:144374313-144375141	chr8:144375141-144375142		0.00
N	alternative_donor	CUFF.572	chr2	-	chr2:242872-247537;chr2:242872-243502	chr2:242872-244626		chr2:243503-244626;chr2:244627-247537	chr2:244626-244627;chr2:247537-247538		0.00
K	jcn_only_AD	CUFF.272,CUFF.278	chr14	-	chr14:75140815-75142443	chr14:75140815-75142401		chr14:75142402-75142443	chr14:75142443-75142444	chr14:75140737-75140814;chr14:75142444-75142649	46.54
K	alternative_donor	CUFF.524,CUFF.542	chr19	-	chr19:39924059-39924161;chr19:39924059-39924157	chr19:39924059-39924133		chr19:39924134-39924157;chr19:39924158-39924161	chr19:39924157-39924158;chr19:39924161-39924162		13.43
N	alternative_donor	CUFF.728	chr22	-	chr22:51016364-51016512;chr22:51016364-51016977	chr22:51016364-51016814		chr22:51016513-51016814;chr22:51016815-51016977	chr22:51016814-51016815;chr22:51016977-51016978		32.88
K	jcn_only_AA	CUFF.550	chr19	+	chr19:44764092-44768480	chr19:44764092-44768466		chr19:44768467-44768480	chr19:44768480-44768481		9.68
K	jcn_only_AD	CUFF.180	chr11	+	chr11:117070149-117073717	chr11:117070546-117073717		chr11:117070149-117070545	chr11:117070148-117070149		93.84
K	alternative_last_exon	CUFF.626	chr2	+	chr2:99232810-99234630	chr2:99232810-99232894	chr2:99234631-99235077	chr2:99232895-99232996			70.97
N	cassette	CUFF.471	chr17	-	chr17:79354385-79358928;chr17:79354385-79358745	chr17:79354385-79355676;chr17:79355741-79358745,chr17:79355741-79358928		chr17:79355677-79355740			75.61
N	jcn_only_AA	CUFF.833	chr4	-	chr4:69057243-69078079	chr4:69071816-69078079		chr4:69057243-69071815	chr4:69057242-69057243		58.82
N	jcn_only_AA	CUFF.18	chr1	+	chr1:32560573-32566042	chr1:32560573-32561260		chr1:32561261-32566042	chr1:32566042-32566043		3.46
N	alternative_donor	CUFF.333	chr15	-	chr15:66787758-66789979	chr15:66787758-66789827		chr15:66789828-66789979	chr15:66789979-66789980		7.41
N	jcn_only_AD	CUFF.879	chr5	-	chr5:127398193-127418661	chr5:127398193-127418426		chr5:127418427-127418661	chr5:127418661-127418662		39.13
K	intron_retention	CUFF.557	chr19	+	chr19:50305399-50306205				chr19:50305398-50305399;chr19:50306205-50306206		20.83
N	alternative_donor	CUFF.936	chr6	+	chr6:90338943-90340151	chr6:90338958-90340151		chr6:90338943-90338957	chr6:90338942-90338943		38.79
K	cassette	CUFF.203	chr12	+	chr12:9723489-9725598	chr12:9723489-9724056;chr12:9724170-9725598		chr12:9724057-9724169			55.00
N	alternative_acceptor	CUFF.307,CUFF.336	chr15	+	chr15:74771620-74773391	chr15:74771620-74772961		chr15:74772962-74773391	chr15:74773391-74773392		8.33
K	intron_retention	CUFF.404	chr16	-	chr16:67969382-67969484				chr16:67969381-67969382;chr16:67969484-67969485	chr16:67969323-67969381;chr16:67969485-67969600	21.98
N	jcn_only_AA	CUFF.119	chr10	-	chr10:79396328-79397022;chr10:79163782-79397022	chr10:79396274-79397022		chr10:79163782-79396273;chr10:79396274-79396327	chr10:79163781-79163782;chr10:79396273-79396274		39.66
N	alternative_donor	CUFF.606	chr2	-	chr2:68374700-68384505;chr2:68374700-68384058	chr2:68374700-68384392		chr2:68384059-68384392;chr2:68384393-68384505	chr2:68384392-68384393;chr2:68384505-68384506		58.18
K	intron_retention	CUFF.557	chr19	+	chr19:50309035-50309128				chr19:50309034-50309035;chr19:50309128-50309129		20.25
K	alternative_first_exon	CUFF.685	chr20	-	chr20:31115717-31120119;chr20:31115717-31172371	chr20:31115717-31123243	chr20:31172372-31172967	chr20:31123244-31123997			44.83
K	alternative_first_exon	CUFF.497	chr18	-	chr18:67563282-67611719;chr18:67563282-67623990	chr18:67563282-67613969	chr18:67623991-67624477	chr18:67613970-67614305			67.86
K	coord_cassette	CUFF.119	chr10	-	chr10:78729826-78771724	chr10:78729826-78734244;chr10:78734332-78737300;chr10:78737397-78771724		chr10:78734245-78734331;chr10:78737301-78737396			7.14
N	alternative_donor	CUFF.951	chr6	+	chr6:144904737-144999541;chr6:144981412-144999541	chr6:144898425-144999541		chr6:144898425-144904736;chr6:144904737-144981411	chr6:144898424-144898425;chr6:144904736-144904737		83.33
K	intron_retention	CUFF.464	chr17	+	chr17:66519068-66519865				chr17:66519067-66519068;chr17:66519865-66519866		1.59
K	cassette	CUFF.114	chr10	-	chr10:73956748-73963184	chr10:73956748-73958206;chr10:73958424-73963184		chr10:73958207-73958423			8.68
K	intron_retention	CUFF.848	chr4	+	chr4:120381398-120381885				chr4:120381397-120381398;chr4:120381885-120381886		13.24
K	alternative_donor	CUFF.410	chr16	-	chr16:75575354-75576499	chr16:75575354-75576452		chr16:75576453-75576499	chr16:75576499-75576500		20.30
N	intron_retention		chr1	+	chr1:54359960-54360083				chr1:54359959-54359960;chr1:54360083-54360084		94.22
K	cassette	CUFF.218	chr12	-	chr12:49334972-49351092	chr12:49334972-49349880;chr12:49350319-49351092		chr12:49349881-49350318			58.11
K	intron_retention	CUFF.918	chr6	+	chr6:31937198-31937291				chr6:31937197-31937198;chr6:31937291-31937292		31.67
K	jcn_only_AD	CUFF.715	chr22	+	chr22:29469210-29490245	chr22:29469216-29490245		chr22:29469210-29469215	chr22:29469209-29469210		59.09
N	cassette	CUFF.833	chr4	-	chr4:69071816-69083623	chr4:69071816-69078079;chr4:69078196-69083623		chr4:69078080-69078195			84.62
N	alternative_first_exon		chr12	-	chr12:25673010-25679702	chr12:25673010-25679032	chr12:25679703-25679889	chr12:25679033-25679152			95.56
K	cassette	CUFF.647	chr2	-	chr2:175711686-175779785	chr2:175711686-175742567;chr2:175742857-175779785		chr2:175742568-175742856			40.44
K	jcn_only_AA	CUFF.140	chr11	-	chr11:2188716-2189095	chr11:2188747-2189095		chr11:2188716-2188746	chr11:2188715-2188716		22.97
K	jcn_only_AD	CUFF.410	chr16	-	chr16:75575354-75576499	chr16:75575354-75576452		chr16:75576453-75576499	chr16:75576499-75576500		29.91
N	intron_retention		chr22	+	chr22:21057981-21058255				chr22:21057980-21057981;chr22:21058255-21058256		48.43
K	alternative_last_exon	CUFF.1018	chr7	-	chr7:156469378-156471770;chr7:156469319-156471770	chr7:156471045-156471770	chr7:156469080-156469318	chr7:156470400-156471044			51.32
N	alternative_donor	CUFF.390	chr16	-	chr16:23504780-23505623	chr16:23504780-23505619		chr16:23505620-23505623	chr16:23505623-23505624	chr16:23504681-23504779;chr16:23505624-23505699	60.00
K	intron_retention	CUFF.1018	chr7	-	chr7:156472001-156473136				chr7:156472000-156472001;chr7:156473136-156473137		16.67
K	alternative_last_exon	CUFF.391	chr16	-	chr16:25098045-25114671;chr16:25112007-25114671	chr16:25097094-25114671	chr16:25097561-25098044;chr16:25111790-25112006	chr16:25096913-25097093			13.64
N	alternative_acceptor	CUFF.531	chr19	+	chr19:17611442-17615263	chr19:17611442-17611520		chr19:17611521-17615263	chr19:17615263-17615264		8.00
K	cassette	CUFF.691	chr20	-	chr20:61982380-61987326	chr20:61982380-61986847;chr20:61986948-61987326		chr20:61986848-61986947			92.31
K	alternative_donor	CUFF.703	chr21	-	chr21:47556409-47556892;chr21:47556409-47556898	chr21:47556409-47556828		chr21:47556829-47556892;chr21:47556893-47556898	chr21:47556892-47556893;chr21:47556898-47556899		52.94
K	cassette	CUFF.1004	chr7	-	chr7:110303778-110603555	chr7:110303778-110526648;chr7:110526752-110603555		chr7:110526649-110526751			88.05
K	jcn_only_AD	CUFF.920	chr6	+	chr6:32122024-32122363;chr6:32122172-32122363	chr6:32122182-32122363		chr6:32122024-32122171;chr6:32122172-32122181	chr6:32122023-32122024;chr6:32122171-32122172		83.33
N	jcn_only_AA	CUFF.427	chr17	+	chr17:15603483-15604465	chr17:15603483-15603586		chr17:15603587-15604465	chr17:15604465-15604466		16.67
N	alternative_donor	CUFF.271	chr14	-	chr14:59939809-59942586;chr14:59939809-59941156	chr14:59939809-59941445		chr14:59941157-59941445;chr14:59941446-59942586	chr14:59941445-59941446;chr14:59942586-59942587		2.08
N	intron_retention	CUFF.671	chr2	-	chr2:242440212-242440942				chr2:242440211-242440212;chr2:242440942-242440943		81.36
N	jcn_only_AA		chr17	+	chr17:61904875-61905033;chr17:61904875-61905188;chr17:61904875-61905478;chr17:61904875-61905497	chr17:61904875-61905210					18.05
N	mutually_exclusive	CUFF.63	chr1	-	chr1:169696667-169697198,chr1:169697388-169698326	chr1:169696667-169696879,chr1:169697069-169698326	chr1:169697199-169697387	chr1:169696880-169697068			66.67
K	coord_cassette	CUFF.941	chr6	+	chr6:112558118-112627530	chr6:112558118-112604255;chr6:112604395-112604499;chr6:112604730-112627530		chr6:112604256-112604394;chr6:112604500-112604729			92.00
N	jcn_only_AD	CUFF.152,CUFF.176	chr11	-	chr11:10828929-10829720;chr11:10828929-10829291	chr11:10828929-10829080		chr11:10829081-10829291;chr11:10829292-10829720	chr11:10829291-10829292;chr11:10829720-10829721		13.64
K	jcn_only_AD	CUFF.980	chr7	+	chr7:73098135-73100965	chr7:73098232-73100965		chr7:73098135-73098231	chr7:73098134-73098135		23.48
K	intron_retention	CUFF.232	chr12	+	chr12:58017882-58018648				chr12:58017881-58017882;chr12:58018648-58018649		80.39
K	intron_retention	CUFF.475	chr17	-	chr17:79994640-79994734				chr17:79994639-79994640;chr17:79994734-79994735		12.20
N	jcn_only_AD		chr19	-	chr19:33984244-33991843;chr19:33984244-34001933	chr19:33984244-34003498					12.50
K	cassette	CUFF.61	chr1	+	chr1:167353189-167358824	chr1:167353189-167356417;chr1:167356485-167358824		chr1:167356418-167356484			65.35
N	alternative_acceptor		chr2	+	chr2:3464108-3464417;chr2:3464108-3466628	chr2:3464108-3469367		chr2:3464418-3466628;chr2:3466629-3469367	chr2:3466628-3466629;chr2:3469367-3469368		98.68
N	coord_cassette	CUFF.786	chr3	-	chr3:127294109-127294782	chr3:127294109-127294245;chr3:127294349-127294591;chr3:127294653-127294782		chr3:127294246-127294348;chr3:127294592-127294652			94.44
N	intron_retention	CUFF.922	chr6	+	chr6:33239900-33240363				chr6:33239899-33239900;chr6:33240363-33240364		36.36
N	jcn_only_AA	CUFF.1101	chr9	-	chr9:131483760-131483929;chr9:131483810-131483929	chr9:131483782-131483929		chr9:131483760-131483781;chr9:131483782-131483809	chr9:131483759-131483760;chr9:131483781-131483782		92.38
N	jcn_only_AD	CUFF.1004	chr7	-	chr7:110603622-111031893;chr7:110603622-111127293	chr7:110603622-111030626					8.56
K	intron_retention	CUFF.475	chr17	-	chr17:79995418-79995506				chr17:79995417-79995418;chr17:79995506-79995507		36.50
K	cassette	CUFF.432	chr17	+	chr17:25974145-25975861	chr17:25974145-25974295;chr17:25974459-25975861		chr17:25974296-25974458			70.59
N	alternative_donor	CUFF.61	chr1	+	chr1:167301773-167334703	chr1:167326759-167334703		chr1:167301773-167326758	chr1:167301772-167301773		0.00
K	alternative_first_exon	CUFF.936	chr6	+	chr6:90193278-90276552,chr6:90272618-90276552,chr6:90218678-90276552;chr6:90218969-90276552	chr6:90272643-90276552	chr6:90218804-90218968	chr6:90272327-90272642			20.95
N	jcn_only_AA	CUFF.894	chr5	+	chr5:139815843-139818045;chr5:139815843-139818078	chr5:139815843-139818087		chr5:139818046-139818078;chr5:139818079-139818087	chr5:139818078-139818079;chr5:139818087-139818088	chr5:139815689-139815842;chr5:139818088-139818202	34.38
N	alternative_first_exon	CUFF.725	chr22	+	chr22:45181982-45182336,chr22:45173110-45182336;chr22:45131043-45182336;chr22:45148508-45182336;chr22:45122515-45182336	chr22:45162070-45182336	chr22:45130907-45131042;chr22:45148371-45148507;chr22:45122457-45122514	chr22:45161745-45162069			48.96
N	intron_retention		chr8	+	chr8:144356973-144357364				chr8:144356972-144356973;chr8:144357364-144357365		86.61
K	intron_retention	CUFF.589	chr2	-	chr2:27680844-27680992				chr2:27680843-27680844;chr2:27680992-27680993		11.76
K	cassette	CUFF.208	chr12	+	chr12:21229504-21279041	chr12:21229504-21272537;chr12:21272562-21279041		chr12:21272538-21272561		chr12:21229386-21229503;chr12:21279042-21279191	3.81
N	alternative_donor	CUFF.945	chr6	-	chr6:128561296-128563665	chr6:128561296-128562367		chr6:128562368-128563665	chr6:128563665-128563666		10.71
K	alternative_first_exon	CUFF.858	chr4	+	chr4:186125622-186168447	chr4:186131410-186168447	chr4:186125391-186125621	chr4:186131150-186131409			97.83
K	intron_retention	CUFF.1042	chr8	-	chr8:80954904-80956401				chr8:80954903-80954904;chr8:80956401-80956402		4.08
N	jcn_only_AA	CUFF.633	chr2	-	chr2:110920710-110922096	chr2:110920713-110922096		chr2:110920710-110920712	chr2:110920709-110920710		50.00
N	alternative_last_exon	CUFF.676	chr20	-	chr20:3171466-3172410	chr20:3171885-3172410	chr20:3170897-3171465	chr20:3171836-3171884			99.23
N	jcn_only_AD	CUFF.257	chr14	+	chr14:23389408-23392180	chr14:23390330-23392180		chr14:23389408-23390329	chr14:23389407-23389408		77.78