>USP42|NM_032172|3'UTR
   1 AAACTCAGCCTCAAAACAAAAAATTCACTAGTTATGATTCAACGCGTTCAACAGAAGCCATCCCCAGCCCAGCTTAAATT
  81 ATAAAGATAGACAATAACTCTGTTCCAATCTGCGTGGTGCTTCTTTAGTAAATACTGTACAGATTTTACCATGGAGAACT
 161 TTTTTTTTAGTTTTTACCTTTTCTTAATTACCCTTATTCCGAATGGACGAACACTTTCTACCACTGCTGACCATTGTAAA
 241 ATACCGTGTATATAAATCCCATTGAAATAATGCCCTGGAATAGAACATCTCAAATGCTGCTTAATTACAGACTCAGGTCG
 321 ATTACTTGTATTTCATGTAATGTTCCTCCAAGTTAGACATCTGGTGCAAGACCAACCGGGAGACCATGGAATTGTCAAAA
 401 GTACAAACTGACAGTGTGTATATTTAATTTAAAGACTTATTTAAAAACTCACAAGCTCTCACCTAGACTTTGGAGAGCAG
 481 TCTGTTTTCTGTAATGTCTGATACTAGAAACTAATTTGCTTATTTTAGTTGTATTCAAGATTTGAAGATGTATTTTATAG
 561 ACAAGTTCTGTTTTTGAACTTTGTGGAACTGTTCCAATCAATCAATTTCCCAGTTATGATGAGTATTTACATTATGAATG
 641 TATAACCCAGACATGATTTGTAAAGCCGACAGTATGTTTCTATTACACAACACTTTTTGATACAGCGTCTCTTGTCTTCA
 721 CTGATACTGGAGTCTCCGTTGTCTGCTTGGTCCCTTCGAGTTTCTAGTTACAGACACAATCATACTGTGATTTTATTTTT
 801 AATATGGATATGCTATCAAACTGTGATACACTTATAATTCACTGGTCCTGCATCAGGAGATGGAGTGGGGAAAACTGTAT
 881 TTAATACAGTTTGTATCTGAATAATCTGTATGGTTTATACAGTTTGTGTTGTTCAGAGATGTTTAAAGTTTGATCTTTGT
 961 TTTTCTAAAGATTAAAAAAGCACTTGCCCCACTGTAAATATACAGCATGTAAAATTTCTATAGTATATAAATGGCAGCAA
1041 ATCACAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uuccucGUUCCGCCGUAGAGa 5' ::| | ||:|||| Target 5' acttttTGATACAGCGTCTCt 3'	692 - 712	127.00	-10.80
2	miRNA 3' uuccucguuccgccGUAGAGa 5' |||||| Target 5' gccctggaatagaaCATCTCa 3'	272 - 292	120.00	-7.90
3	miRNA 3' uuccucGUUCCGC-------CGUAGAGa 5' ||:| || |:||:|| Target 5' cagactCAGGTCGATTACTTGTATTTCa 3'	308 - 335	111.00	-7.71

Mutant ID	Mutant Position	Mutant Source
COSN30106801	18	COSMIC
COSN30648993	24	COSMIC
COSN16934580	27	COSMIC
COSN24695802	90	COSMIC
COSN30741259	100	COSMIC
COSN1351960	132	COSMIC
COSN28765228	169	COSMIC
COSN28650070	178	COSMIC
COSN26530960	203	COSMIC
COSN29321259	913	COSMIC
COSN29316434	921	COSMIC
COSN31489332	1096	COSMIC
COSN31489176	1102	COSMIC
COSN31489362	1162	COSMIC
COSN26640046	1174	COSMIC
COSN5660969	1283	COSMIC
COSN28651268	1312	COSMIC
COSN26552056	1334	COSMIC
COSN31555559	1334	COSMIC
COSN31484775	1376	COSMIC
COSN31488540	1569	COSMIC
COSN26603449	1580	COSMIC
COSN31573157	1831	COSMIC
COSN25231589	1885	COSMIC
COSN31484806	1909	COSMIC
COSN26677921	2056	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs748819055	6	dbSNP
rs754526590	8	dbSNP
rs778725705	11	dbSNP
rs747735804	12	dbSNP
rs1369975345	18	dbSNP
rs1447905007	18	dbSNP
rs772024867	22	dbSNP
rs772834644	25	dbSNP
rs746798598	28	dbSNP
rs770838446	29	dbSNP
rs201085042	31	dbSNP
rs1458244037	32	dbSNP
rs988732100	34	dbSNP
rs1208274481	36	dbSNP
rs1471925079	36	dbSNP
rs1489708274	43	dbSNP
rs369863349	45	dbSNP
rs764093779	49	dbSNP
rs749488498	50	dbSNP
rs775587133	50	dbSNP
rs1469630237	51	dbSNP
rs117177787	53	dbSNP
rs1266440417	55	dbSNP
rs943626278	57	dbSNP
rs1392360996	65	dbSNP
rs1303559943	77	dbSNP
rs7783538	79	dbSNP
rs1358590057	90	dbSNP
rs187290777	91	dbSNP
rs1407124241	96	dbSNP
rs549061604	100	dbSNP
rs567063970	101	dbSNP
rs917804558	102	dbSNP
rs1216397933	103	dbSNP
rs929436482	103	dbSNP
rs115618671	109	dbSNP
rs1217990017	112	dbSNP
rs1344844228	113	dbSNP
rs553104752	115	dbSNP
rs879065251	116	dbSNP
rs1273746989	117	dbSNP
rs1230375919	118	dbSNP
rs1332494492	119	dbSNP
rs1036690572	120	dbSNP
rs1399218618	121	dbSNP
rs1301534985	127	dbSNP
rs896863094	129	dbSNP
rs1372741104	130	dbSNP
rs1401333652	133	dbSNP
rs1170915194	135	dbSNP
rs1467610626	136	dbSNP
rs1430309219	158	dbSNP
rs949812441	161	dbSNP
rs371140550	165	dbSNP
rs539509271	165	dbSNP
rs1286073491	167	dbSNP
rs59486546	169	dbSNP
rs999869914	170	dbSNP
rs1346476785	173	dbSNP
rs1217629218	175	dbSNP
rs10246266	178	dbSNP
rs1279868774	179	dbSNP
rs145418957	195	dbSNP
rs1321811771	200	dbSNP
rs1332092921	202	dbSNP
rs575574982	203	dbSNP
rs773675337	204	dbSNP
rs542700070	205	dbSNP
rs1464276747	207	dbSNP
rs1425991415	209	dbSNP
rs1472657060	215	dbSNP
rs1236282886	218	dbSNP
rs1205585269	219	dbSNP
rs1462317754	222	dbSNP
rs1010479727	224	dbSNP
rs1468529888	225	dbSNP
rs763497389	229	dbSNP
rs765670169	231	dbSNP
rs1183529529	239	dbSNP
rs987549056	240	dbSNP
rs1414554119	241	dbSNP
rs766755385	244	dbSNP
rs965031404	245	dbSNP
rs1450137767	246	dbSNP
rs968714456	250	dbSNP
rs1383369457	259	dbSNP
rs1330791917	262	dbSNP
rs973441827	263	dbSNP
rs920822059	264	dbSNP
rs878986736	266	dbSNP
rs1165297255	268	dbSNP
rs1445780280	271	dbSNP
rs546812626	272	dbSNP
rs368815194	277	dbSNP
rs191739123	282	dbSNP
rs573332510	283	dbSNP
rs958838054	289	dbSNP
rs991024048	290	dbSNP
rs949781877	298	dbSNP
rs917767748	303	dbSNP
rs927069489	306	dbSNP
rs949278517	309	dbSNP
rs540730573	313	dbSNP
rs1308405454	323	dbSNP
rs1303958687	324	dbSNP
rs1054145165	326	dbSNP
rs891686437	328	dbSNP
rs972666731	329	dbSNP
rs1244561538	333	dbSNP
rs1010137441	335	dbSNP
rs1325966644	336	dbSNP
rs1343842879	338	dbSNP
rs559560480	339	dbSNP
rs533177313	342	dbSNP
rs551636315	350	dbSNP
rs1435879635	351	dbSNP
rs930936906	355	dbSNP
rs1212083849	364	dbSNP
rs1238011032	369	dbSNP
rs1224499129	371	dbSNP
rs1490446397	372	dbSNP
rs1285296202	376	dbSNP
rs1214351205	380	dbSNP
rs964843263	382	dbSNP
rs1285060334	383	dbSNP
rs1048077619	385	dbSNP
rs1460843906	386	dbSNP
rs1181803458	389	dbSNP
rs889493674	391	dbSNP
rs1296668218	395	dbSNP
rs182471448	397	dbSNP
rs369402298	401	dbSNP
rs540017149	401	dbSNP
rs1346261167	402	dbSNP
rs528450165	403	dbSNP
rs760312724	409	dbSNP
rs1416548680	411	dbSNP
rs759252037	414	dbSNP
rs1201121457	415	dbSNP
rs1480678206	418	dbSNP
rs530519056	419	dbSNP
rs1191166967	420	dbSNP
rs1486819804	422	dbSNP
rs1261193902	426	dbSNP
rs1010426993	428	dbSNP
rs1209553171	431	dbSNP
rs1027685033	432	dbSNP
rs548662206	434	dbSNP
rs566927212	435	dbSNP
rs983744837	436	dbSNP
rs917510815	438	dbSNP
rs534385981	439	dbSNP
rs927008947	440	dbSNP
rs980277592	440	dbSNP
rs763671686	443	dbSNP
rs1000131064	444	dbSNP
rs1403264100	446	dbSNP
rs546308346	447	dbSNP
rs758188911	448	dbSNP
rs767141836	450	dbSNP
rs1422407391	453	dbSNP
rs1168311121	457	dbSNP
rs1430045818	458	dbSNP
rs1859546	464	dbSNP
rs1220705611	465	dbSNP
rs992964629	466	dbSNP
rs538892894	469	dbSNP
rs557631931	470	dbSNP
rs1204335186	474	dbSNP
rs1457512023	476	dbSNP
rs1025209476	485	dbSNP
rs1230138718	490	dbSNP
rs1322710517	494	dbSNP
rs1050930351	495	dbSNP
rs891049215	495	dbSNP
rs114172066	497	dbSNP
rs1465418739	499	dbSNP
rs370606288	500	dbSNP
rs918483917	501	dbSNP
rs931220306	502	dbSNP
rs994966573	505	dbSNP
rs1373424010	510	dbSNP
rs554953244	512	dbSNP
rs142289927	513	dbSNP
rs1192130884	516	dbSNP
rs1386974209	516	dbSNP
rs1184337973	525	dbSNP
rs1457354818	530	dbSNP
rs1236641727	534	dbSNP
rs1429113630	536	dbSNP
rs1481045387	540	dbSNP
rs1265238973	543	dbSNP
rs1219760916	544	dbSNP
rs1362259953	544	dbSNP
rs1468636202	547	dbSNP
rs886675	548	dbSNP
rs942442483	555	dbSNP
rs1375499491	561	dbSNP
rs1040824424	562	dbSNP
rs901337796	563	dbSNP
rs1392774705	564	dbSNP
rs1317070244	565	dbSNP
rs1396711998	567	dbSNP
rs1292760353	570	dbSNP
rs1324297630	572	dbSNP
rs1004896450	575	dbSNP
rs1283613004	581	dbSNP
rs532462789	583	dbSNP
rs1221560921	586	dbSNP
rs1269975821	587	dbSNP
rs367760197	595	dbSNP
rs1266890370	599	dbSNP
rs371139737	600	dbSNP
rs551058924	602	dbSNP
rs1282322001	604	dbSNP
rs1258460911	607	dbSNP
rs904746624	611	dbSNP
rs1336026126	613	dbSNP
rs1222589737	616	dbSNP
rs1300140921	617	dbSNP
rs577888454	624	dbSNP
rs1402938851	625	dbSNP
rs1347160393	626	dbSNP
rs1056193327	628	dbSNP
rs186811376	630	dbSNP
rs544917457	634	dbSNP
rs1268551032	637	dbSNP
rs989953605	638	dbSNP
rs894498930	653	dbSNP
rs1184914206	654	dbSNP
rs945680598	655	dbSNP
rs986448032	661	dbSNP
rs1319320980	670	dbSNP
rs572200118	672	dbSNP
rs74541050	672	dbSNP
rs760491665	672	dbSNP
rs536487611	678	dbSNP
rs1264438135	680	dbSNP
rs1206427246	686	dbSNP
rs1350755079	692	dbSNP
rs1255124561	694	dbSNP
rs1221311434	709	dbSNP
rs1406684907	718	dbSNP
rs1024364657	721	dbSNP
rs962139293	724	dbSNP
rs993961703	734	dbSNP
rs1283708335	737	dbSNP
rs1399119874	749	dbSNP
rs1025489497	753	dbSNP
rs530671281	756	dbSNP
rs542930244	761	dbSNP
rs560517172	762	dbSNP
rs750366607	763	dbSNP
rs1174281029	764	dbSNP
rs1290040102	767	dbSNP
rs528112306	768	dbSNP
rs931143502	773	dbSNP
rs963775594	777	dbSNP
rs546269639	780	dbSNP
rs1474619107	782	dbSNP
rs571058266	784	dbSNP
rs886538009	788	dbSNP
rs922335370	789	dbSNP
rs1358575550	790	dbSNP
rs1246920969	794	dbSNP
rs532727835	798	dbSNP
rs907439651	810	dbSNP
rs1217832713	816	dbSNP
rs550852770	821	dbSNP
rs926160081	824	dbSNP
rs936230280	825	dbSNP
rs1228069210	826	dbSNP
rs1339743723	828	dbSNP
rs1334814874	830	dbSNP
rs1454619614	831	dbSNP
rs1330918891	837	dbSNP
rs1407178922	837	dbSNP
rs1251761821	838	dbSNP
rs1056078034	839	dbSNP
rs1180306827	840	dbSNP
rs990731521	841	dbSNP
rs894730442	845	dbSNP
rs1472772283	846	dbSNP
rs1473512114	849	dbSNP
rs1181255989	865	dbSNP
rs1163710856	867	dbSNP
rs1020003141	868	dbSNP
rs1014230359	870	dbSNP
rs569434808	873	dbSNP
rs377566217	882	dbSNP
rs536513775	883	dbSNP
rs1309621236	890	dbSNP
rs897878167	893	dbSNP
rs555316611	894	dbSNP
rs1025479441	895	dbSNP
rs1390688237	897	dbSNP
rs566854995	909	dbSNP
rs376081299	910	dbSNP
rs1005870125	912	dbSNP
rs1440312722	920	dbSNP
rs534211649	924	dbSNP
rs931134316	925	dbSNP
rs1246758778	927	dbSNP
rs368831707	930	dbSNP
rs559089237	931	dbSNP
rs1047353811	933	dbSNP
rs886501948	934	dbSNP
rs1230974072	935	dbSNP
rs550944641	936	dbSNP
rs1182321366	941	dbSNP
rs940782898	944	dbSNP
rs1339165795	945	dbSNP
rs1045752893	946	dbSNP
rs577228740	947	dbSNP
rs1194545653	948	dbSNP
rs111773054	959	dbSNP
rs56943349	959	dbSNP
rs745603542	959	dbSNP
rs869226982	959	dbSNP
rs1022060938	965	dbSNP
rs1222108254	966	dbSNP
rs1183660508	968	dbSNP
rs386709807	969	dbSNP
rs1180868185	970	dbSNP
rs200284815	970	dbSNP
rs1375845781	971	dbSNP
rs1242066960	974	dbSNP
rs1280334854	974	dbSNP
rs1001942632	976	dbSNP
rs1344017121	981	dbSNP
rs10590782	982	dbSNP
rs867731742	982	dbSNP
rs1425858912	988	dbSNP
rs967095220	995	dbSNP
rs1034573290	997	dbSNP
rs1157771113	999	dbSNP
rs977182333	1012	dbSNP
rs1373382524	1014	dbSNP
rs926110020	1017	dbSNP
rs936152802	1023	dbSNP
rs1266530117	1029	dbSNP
rs1056382902	1030	dbSNP
rs73675859	1033	dbSNP
rs950355870	1034	dbSNP
rs1019327328	1035	dbSNP
rs1045753119	1038	dbSNP
rs1223135130	1041	dbSNP
rs897866783	1045	dbSNP
rs556851328	1050	dbSNP
rs1049203321	1051	dbSNP
rs963714570	1052	dbSNP
rs887872779	1053	dbSNP
rs575412043	1054	dbSNP
rs71531360	1055	dbSNP
rs542500281	1056	dbSNP
rs1225673363	1057	dbSNP
rs1426725580	1061	dbSNP
rs1178376908	1063	dbSNP
rs71531361	1065	dbSNP
rs1258202050	1068	dbSNP
rs750728748	1069	dbSNP
rs982621198	1073	dbSNP
rs560880058	1075	dbSNP
rs528075408	1077	dbSNP
rs372364231	1078	dbSNP
rs940751856	1081	dbSNP
rs191273045	1082	dbSNP
rs928711790	1083	dbSNP
rs998094821	1085	dbSNP
rs1029283601	1087	dbSNP
rs1265197611	1087	dbSNP
rs1224572100	1089	dbSNP
rs1459607257	1098	dbSNP
rs967044487	1105	dbSNP
rs977067947	1106	dbSNP
rs768755241	1107	dbSNP
rs1012276618	1108	dbSNP
rs957348139	1114	dbSNP
rs1466416805	1115	dbSNP
rs1431249487	1116	dbSNP
rs991637488	1119	dbSNP
rs1353709222	1120	dbSNP
rs1041866973	1123	dbSNP
rs903322110	1128	dbSNP
rs1420094036	1131	dbSNP
rs185759664	1141	dbSNP
rs1442832414	1142	dbSNP
rs1204551698	1144	dbSNP
rs1458861511	1144	dbSNP
rs1289571030	1146	dbSNP
rs916098263	1146	dbSNP
rs1361513984	1147	dbSNP
rs950327313	1150	dbSNP
rs1314942965	1152	dbSNP
rs190285232	1154	dbSNP
rs1008360426	1156	dbSNP
rs1379932828	1162	dbSNP
rs981713255	1170	dbSNP
rs1396260281	1172	dbSNP
rs1372097343	1175	dbSNP
rs550670477	1176	dbSNP
rs1463300855	1181	dbSNP
rs1303781626	1182	dbSNP
rs929264686	1184	dbSNP
rs569316048	1189	dbSNP
rs1422599974	1190	dbSNP
rs1049109323	1197	dbSNP
rs1223385877	1198	dbSNP
rs887829715	1201	dbSNP
rs943458470	1203	dbSNP
rs964155318	1204	dbSNP
rs1248653748	1205	dbSNP
rs1418756618	1205	dbSNP
rs530351761	1209	dbSNP
rs1179371149	1212	dbSNP
rs779831321	1213	dbSNP
rs996504861	1217	dbSNP
rs140634673	1218	dbSNP
rs1331889542	1221	dbSNP
rs1027092466	1225	dbSNP
rs567216778	1231	dbSNP
rs1304385369	1239	dbSNP
rs982734994	1239	dbSNP
rs998042467	1242	dbSNP
rs1350890440	1243	dbSNP
rs1485337547	1252	dbSNP
rs746793140	1253	dbSNP
rs1270702422	1262	dbSNP
rs113567702	1263	dbSNP
rs970513722	1266	dbSNP
rs998434637	1271	dbSNP
rs1362341771	1293	dbSNP
rs1161543866	1295	dbSNP
rs1473000913	1296	dbSNP
rs1268640608	1297	dbSNP
rs1427087716	1306	dbSNP
rs981953961	1307	dbSNP
rs776618352	1308	dbSNP
rs1033097611	1309	dbSNP
rs193182710	1312	dbSNP
rs748664352	1315	dbSNP
rs1209965800	1319	dbSNP
rs937452383	1324	dbSNP
rs1344695220	1336	dbSNP
rs1055791520	1337	dbSNP
rs570846912	1345	dbSNP
rs1240761865	1347	dbSNP
rs796342852	1351	dbSNP
rs1329362899	1355	dbSNP
rs537918421	1356	dbSNP
rs1366538335	1368	dbSNP
rs1347376399	1369	dbSNP
rs1324117893	1378	dbSNP
rs145445036	1381	dbSNP
rs947413997	1386	dbSNP
rs1290644095	1390	dbSNP
rs755178406	1391	dbSNP
rs1476988311	1392	dbSNP
rs903460577	1396	dbSNP
rs1481609561	1405	dbSNP
rs781420515	1405	dbSNP
rs1378775890	1412	dbSNP
rs971586033	1416	dbSNP
rs575326198	1419	dbSNP
rs1445720711	1423	dbSNP
rs536091458	1426	dbSNP
rs919486679	1435	dbSNP
rs1224892188	1439	dbSNP
rs1307004887	1440	dbSNP
rs1315825446	1441	dbSNP
rs1201600926	1447	dbSNP
rs1236371168	1449	dbSNP
rs1293454507	1451	dbSNP
rs899565324	1456	dbSNP
rs1221444152	1459	dbSNP
rs1226616583	1463	dbSNP
rs1324562665	1464	dbSNP
rs929548143	1466	dbSNP
rs1435863202	1468	dbSNP
rs1405689769	1469	dbSNP
rs984777110	1470	dbSNP
rs1471198604	1475	dbSNP
rs1266594040	1476	dbSNP
rs1167652712	1478	dbSNP
rs1474732457	1482	dbSNP
rs1026646542	1483	dbSNP
rs997032008	1483	dbSNP
rs1449533829	1487	dbSNP
rs554435551	1488	dbSNP
rs1177729914	1492	dbSNP
rs1443724254	1496	dbSNP
rs572758903	1497	dbSNP
rs1417440615	1498	dbSNP
rs770483825	1498	dbSNP
rs1039554586	1502	dbSNP
rs1229301802	1503	dbSNP
rs1003888833	1504	dbSNP
rs1312930551	1507	dbSNP
rs1454803679	1508	dbSNP
rs923392359	1516	dbSNP
rs1386068112	1520	dbSNP
rs1328653318	1521	dbSNP
rs1015489959	1525	dbSNP
rs540137631	1533	dbSNP
rs970651009	1541	dbSNP
rs933800751	1555	dbSNP
rs780642812	1556	dbSNP
rs564695754	1559	dbSNP
rs981922879	1560	dbSNP
rs1033965389	1562	dbSNP
rs1356645054	1566	dbSNP
rs576785161	1568	dbSNP
rs1253973746	1572	dbSNP
rs1205789054	1573	dbSNP
rs1358582700	1574	dbSNP
rs769840226	1575	dbSNP
rs1230073329	1576	dbSNP
rs1357386109	1577	dbSNP
rs1443488665	1578	dbSNP
rs1298125754	1579	dbSNP
rs1279177840	1583	dbSNP
rs1371932538	1588	dbSNP
rs1440551198	1604	dbSNP
rs1389153954	1608	dbSNP
rs1337909326	1610	dbSNP
rs1364205071	1620	dbSNP
rs185110158	1620	dbSNP
rs914671307	1624	dbSNP
rs749794022	1626	dbSNP
rs1414141924	1627	dbSNP
rs558552064	1628	dbSNP
rs771349535	1631	dbSNP
rs1289256813	1641	dbSNP
rs924850084	1644	dbSNP
rs998761822	1645	dbSNP
rs1054125109	1651	dbSNP
rs111947274	1656	dbSNP
rs557895405	1656	dbSNP
rs576914083	1656	dbSNP
rs753342582	1656	dbSNP
rs892815339	1656	dbSNP
rs1205089652	1658	dbSNP
rs1012654974	1659	dbSNP
rs1222298277	1661	dbSNP
rs1232199653	1662	dbSNP
rs562630718	1662	dbSNP
rs146475124	1663	dbSNP
rs971155476	1667	dbSNP
rs1305474695	1671	dbSNP
rs1438069480	1673	dbSNP
rs573188154	1673	dbSNP
rs1015291884	1679	dbSNP
rs1243891316	1685	dbSNP
rs1398627236	1686	dbSNP
rs759841484	1688	dbSNP
rs1026492467	1692	dbSNP
rs1003501274	1695	dbSNP
rs1422031945	1697	dbSNP
rs1192858614	1701	dbSNP
rs1478284181	1703	dbSNP
rs1241622828	1705	dbSNP
rs1213675270	1709	dbSNP
rs1466449743	1710	dbSNP
rs1410908293	1715	dbSNP
rs1203493833	1716	dbSNP
rs1321847212	1719	dbSNP
rs1303773013	1722	dbSNP
rs866851272	1723	dbSNP
rs1361812344	1728	dbSNP
rs1269119980	1729	dbSNP
rs1432236933	1729	dbSNP
rs556267933	1730	dbSNP
rs959434336	1731	dbSNP
rs766687557	1732	dbSNP
rs1468906755	1733	dbSNP
rs909198728	1735	dbSNP
rs1353258936	1740	dbSNP
rs1177912110	1743	dbSNP
rs1415006527	1744	dbSNP
rs1022105901	1750	dbSNP
rs965103885	1752	dbSNP
rs1184904353	1755	dbSNP
rs1451392035	1755	dbSNP
rs1248950217	1758	dbSNP
rs1471281694	1759	dbSNP
rs1460103497	1761	dbSNP
rs968799683	1768	dbSNP
rs924646783	1769	dbSNP
rs977382055	1769	dbSNP
rs944288727	1771	dbSNP
rs1225633876	1773	dbSNP
rs1366748407	1774	dbSNP
rs754259896	1775	dbSNP
rs1297623965	1776	dbSNP
rs1451494984	1787	dbSNP
rs1382908634	1789	dbSNP
rs1304410018	1795	dbSNP
rs776392661	1799	dbSNP
rs1166635142	1800	dbSNP
rs1431477385	1801	dbSNP
rs1390880297	1803	dbSNP
rs112979258	1805	dbSNP
rs1282103821	1810	dbSNP
rs1443044590	1813	dbSNP
rs1363691504	1819	dbSNP
rs932782370	1820	dbSNP
rs1048573298	1822	dbSNP
rs796654189	1826	dbSNP
rs1305686597	1831	dbSNP
rs939780342	1831	dbSNP
rs1343442469	1833	dbSNP
rs1274779033	1838	dbSNP
rs1036697121	1839	dbSNP
rs1244567050	1839	dbSNP
rs1263769594	1841	dbSNP
rs1314414203	1851	dbSNP
rs906160635	1852	dbSNP
rs1460944982	1854	dbSNP
rs1372348520	1859	dbSNP
rs755248810	1867	dbSNP
rs879158499	1870	dbSNP
rs1003219326	1876	dbSNP
rs560672191	1877	dbSNP
rs1244029041	1881	dbSNP
rs1302684160	1883	dbSNP
rs1475898686	1885	dbSNP
rs1165757585	1887	dbSNP
rs1418667488	1888	dbSNP
rs1406273174	1889	dbSNP
rs1055424304	1891	dbSNP
rs1483693806	1893	dbSNP
rs1186289903	1896	dbSNP
rs895083141	1897	dbSNP
rs923317857	1898	dbSNP
rs77561123	1904	dbSNP
rs1011139697	1909	dbSNP
rs1487218333	1911	dbSNP
rs575739589	1912	dbSNP
rs1266628000	1923	dbSNP
rs527963094	1923	dbSNP
rs1022159552	1925	dbSNP
rs933412525	1927	dbSNP
rs1177820421	1931	dbSNP
rs144857284	1932	dbSNP
rs998933269	1937	dbSNP
rs1331681147	1938	dbSNP
rs761607977	1939	dbSNP
rs1384937833	1941	dbSNP
rs934576745	1944	dbSNP
rs1392983794	1947	dbSNP
rs1294136039	1949	dbSNP
rs570741606	1953	dbSNP
rs1346579751	1954	dbSNP
rs1453354772	1954	dbSNP
rs1386682831	1955	dbSNP
rs1054809274	1958	dbSNP
rs893067342	1959	dbSNP
rs1429291536	1960	dbSNP
rs1197380578	1972	dbSNP
rs538268480	1977	dbSNP
rs1431092056	1980	dbSNP
rs543239860	1982	dbSNP
rs1044070397	1984	dbSNP
rs1209873994	1984	dbSNP
rs1485363757	1988	dbSNP
rs748287245	1988	dbSNP
rs1210429382	1990	dbSNP
rs1282332265	1991	dbSNP
rs906917941	1991	dbSNP
rs1231002040	1998	dbSNP
rs1338159744	1999	dbSNP
rs1225213147	2001	dbSNP
rs1302116180	2002	dbSNP
rs1363367562	2006	dbSNP
rs965317320	2006	dbSNP
rs1322806447	2007	dbSNP
rs1283884570	2008	dbSNP
rs201039148	2008	dbSNP
rs1405829045	2010	dbSNP
rs1002660898	2011	dbSNP
rs1468058992	2012	dbSNP
rs1378687992	2015	dbSNP
rs1199015361	2017	dbSNP
rs1245593895	2017	dbSNP
rs1448344494	2017	dbSNP
rs1322785575	2021	dbSNP
rs550007416	2028	dbSNP
rs1301962167	2029	dbSNP
rs1190124731	2040	dbSNP
rs775160784	2042	dbSNP
rs1201840142	2043	dbSNP
rs1465028335	2043	dbSNP
rs1026484270	2045	dbSNP
rs1262308177	2048	dbSNP
rs950886085	2054	dbSNP
rs749955992	2056	dbSNP
rs976793532	2059	dbSNP
rs1347094957	2063	dbSNP
rs1256498975	2069	dbSNP
rs1447732872	2070	dbSNP
rs1215350166	2072	dbSNP
rs1363125849	2076	dbSNP
rs1299846967	2078	dbSNP
rs1436121150	2079	dbSNP
rs1332655621	2080	dbSNP
rs760295336	2082	dbSNP
rs1016902642	2087	dbSNP
rs1387805029	2088	dbSNP
rs1481642940	2094	dbSNP
rs1169891745	2100	dbSNP
rs138655151	2102	dbSNP

- Cell, 2010

RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.

- Nature methods, 2011

Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.

- Nature, 2013

Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.