>FAM83H|NM_198488|3'UTR
   1 GTCTTCTGGCCTGGCAACCCAGGCCAGGGTGCCCGCATCGCTGCCCCGGTCATCCAGAAGCCCCGCGGAACAGAGAGCCC
  81 TGCTCATGTGCTTGAGCAGCGGCTGTCAGGCCACGGCCGCTTGGGGCTTGGCTGAGTGCGCCAGACCTCGGCTCCACTGG
 161 AGGCTCACCTGGCAGCTGCCGTCTCTGCCCCCTGGCCTCCCCAACGCTGGGGCTGCACCCCTCGCCACCAGTGCCTTTCT
 241 CCCCTCAGCACCTTCATCTCTGCACCGTCAGCCTTGCGTGGCGCAGCGTCTGGCTCCGCCATCTCTTTGTGCCTCAGTCC
 321 CCCCCGCCCCCTTTATTTTTTTGAGACCTAGGGCTGGAGTGCAGTTGAGCGGTCTGGGCTCACTGCAACCTCTGCCTCCC
 401 GGGTTCCAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGATGTATGCTACCACGCCCAGGTAGTTTTTG
 481 TATTTTTAGTAGAGACAGGGTTTCACTATGTTGGCCAGGCTGGTCTCCAACTCCTGGCCTCAAATGATCAGCCCGCTTCA
 561 GCCTCCCAAAGTGGGGGGATTACAGGCGTGAGCCTTGCACCCCGCTAAGTCCCCTATCCTCTTGCAAGGGTCTCGCCTCT
 641 GTGCCTCAATTCCTCATTCTCTGGGCCCTTCTCCTCCTCAGGGCCTCCTGTTCTCAGGGCCTCCCCCCTCCCCGCTCCCT
 721 CCCTCTCTCAAGGTCTCCTCCTTCCCTCCCCCCCCCGTCTCCCCCCTCCCCCGCCTGGGCTTCACTTCCTTTCCTACTTG
 801 GATTCTCCTGCTCGCTGCCTCCCAGCATCTTTTTTGGAGGCCCGTCTCTTGCTGTGGGGAAGACTGGGCTGGCTGCGGGC
 881 AGTTTGCAAGGGGTGGGTGGGGCGGGGGGGGGAGCTGGACCAGAAGATGCCCCTTGGAGTGGCAAGGAAGCTGGACAGGG
 961 CAGGCCTCTGGGGACGGGACACAGGGAAGCCCGAAGGGGCGCCTTGGCCAGGTCTGCCATCTCCTCCAGCGAGGCTCTGG
1041 CCAGCACTGGGTGAGAGTGGGGAGGGGGCACTGGCCTTTGCAGCACAGTAAAACATGGTCCAGACAACCTGTGGCCCCGG
1121 CCTCATGAGCACCCCCTGCACAGGCCCGGCCCAAGCCAGGCGCTAGAAGGGCTGGTTGTGGAGTGCTTATCCTTGACAGG
1201 TATGGGGCCAGGTGAGGGCAGGGGACAAGGTGCAGCTGAGGCCGAGCCCAACTAGGTCCTGGGCACCCCTGCAGGTGGGA
1281 GTGGTCCTTGTCCTCCTGGTATCCAGCAGACACCCCCCTCTCCCCACCAGCCCCATTCTCAGGTCCTTTCCTCTTTGTCA
1361 CCAACACCAAGAATCTGTCCAGGGTTCTTGGCTTATCTTTTATCTCTTTTCACTCCTAGAGAGGAATTGCAATTGACTCA
1441 GAATGACACATTTTGGCACCACGTGTGTAGAAAGCCCCCACTGTTAGATGATAGCCTCGTGAAATTCATGTTTCTGTATT
1521 CTCCTATTTCTTTTCAAAAACTAATTTTTTTTTTAGTGTAATAAATCCTAAGAGGGAACTGATTTAAGAAACAAGGCCGC
1601 CAAACAAAGGCAGCAGTTCCGACTCCAGCAGCTGGGAAAGGAAGGAAAGTGACCCCACTTTCACTCCTGCACAGCCCACT
1681 GGTTACCAAAACCACCGTGCAAGTCGGGATGACAGCAGGGACTTCTGGCCAGGTGGGAAAGGTGCCTGGAAGCGGGATGC
1761 GCCTGTGCGTCTCTTGGCCATGATGTTCTTGTGGGCATGTTATTCTTGGTGCTGCCTGGGGTGTTGCTGAGCGGACAGGC
1841 TCTCCAGCTGGAGTCCATGGAGAGGCCAGAGGCTGGCGGCCCTGCCTGGGCCTTCGGAGCCTCCTGCCTGCACCCTCCAC
1921 CTCTTCTAAACCATGATGTGGCACATTTTGGTGTTAATAAAACACAACACACAAAGTAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ggggguaaCGAUGUCGGCGGACa 5' || ||:|||||:|| Target 5' gctgtcagGCCACGGCCGCTTGg 3'	102 - 124	147.00	-24.30
2	miRNA 3' gggGGUAACGAUGUCGGCGGACa 5' ::||| :|: ||:||||| Target 5' atgTTATTCTTGGTGCTGCCTGg 3'	1797 - 1819	144.00	-16.30
3	miRNA 3' ggGGGUA-A----CGAUGUCGGCGGACa 5' |||:| | || | ||||||| Target 5' ccCCCGTCTCCCCCCT-CCCCCGCCTGg 3'	752 - 778	142.00	-23.54

Mutant ID	Mutant Position	Mutant Source
COSN24593044	23	COSMIC
COSN30474809	27	COSMIC
COSN26975923	41	COSMIC
COSN16433863	43	COSMIC
COSN31505897	101	COSMIC
COSN30121657	139	COSMIC
COSN21800662	181	COSMIC
COSN22845816	450	COSMIC
COSN19492711	464	COSMIC
COSN17038225	567	COSMIC
COSN31963018	603	COSMIC
COSN31484523	634	COSMIC
COSN28671985	635	COSMIC
COSN31595106	664	COSMIC
COSN31532161	680	COSMIC
COSN30542652	703	COSMIC
COSN30543113	704	COSMIC
COSN22056908	822	COSMIC
COSN23018265	912	COSMIC
COSN27431395	912	COSMIC
COSN1361522	1010	COSMIC
COSN14879593	1158	COSMIC
COSN20105953	1460	COSMIC
COSN1361520	1555	COSMIC
COSN8074108	1626	COSMIC
COSN22046256	1630	COSMIC
COSN18954599	1730	COSMIC
COSN15919858	1763	COSMIC
COSN8074107	1825	COSMIC
COSN9258105	1839	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs782531719	3	dbSNP
rs782442697	4	dbSNP
rs1282087412	11	dbSNP
rs369336871	17	dbSNP
rs782200237	19	dbSNP
rs1016065346	22	dbSNP
rs782613374	23	dbSNP
rs782616158	26	dbSNP
rs1188394095	27	dbSNP
rs782464887	30	dbSNP
rs1258480942	32	dbSNP
rs781874617	32	dbSNP
rs782515617	33	dbSNP
rs781856557	34	dbSNP
rs376024869	35	dbSNP
rs985857226	40	dbSNP
rs782537108	44	dbSNP
rs374080114	45	dbSNP
rs186583661	47	dbSNP
rs1359194079	49	dbSNP
rs782752121	50	dbSNP
rs997127116	55	dbSNP
rs1419479754	61	dbSNP
rs373210297	63	dbSNP
rs1356955427	64	dbSNP
rs1393972150	65	dbSNP
rs1311605717	66	dbSNP
rs1020954774	67	dbSNP
rs772169734	68	dbSNP
rs1240575336	73	dbSNP
rs1306900761	74	dbSNP
rs538256996	76	dbSNP
rs1352980787	77	dbSNP
rs1211313938	78	dbSNP
rs181812686	78	dbSNP
rs1198896922	79	dbSNP
rs1055946889	86	dbSNP
rs4875045	88	dbSNP
rs1419681996	90	dbSNP
rs1184161046	94	dbSNP
rs538398953	96	dbSNP
rs1439677649	97	dbSNP
rs1174624942	100	dbSNP
rs907272882	103	dbSNP
rs567741107	111	dbSNP
rs1045794761	112	dbSNP
rs1301836789	114	dbSNP
rs782626052	115	dbSNP
rs918556960	119	dbSNP
rs1328756232	120	dbSNP
rs1376030682	121	dbSNP
rs972400362	133	dbSNP
rs1234978447	134	dbSNP
rs1305564713	139	dbSNP
rs1310160862	145	dbSNP
rs941929224	147	dbSNP
rs782497044	149	dbSNP
rs1236480094	150	dbSNP
rs1457397834	152	dbSNP
rs7007656	162	dbSNP
rs985910892	163	dbSNP
rs527984779	166	dbSNP
rs1431733662	170	dbSNP
rs781822439	179	dbSNP
rs1373274199	180	dbSNP
rs1463245504	181	dbSNP
rs782716214	183	dbSNP
rs1398871819	189	dbSNP
rs1030031476	190	dbSNP
rs1327760003	195	dbSNP
rs1365487525	202	dbSNP
rs1385999339	204	dbSNP
rs1296091752	205	dbSNP
rs1308272649	218	dbSNP
rs1220655616	219	dbSNP
rs782055955	220	dbSNP
rs1256428278	221	dbSNP
rs1317308154	223	dbSNP
rs1248957791	224	dbSNP
rs1487823894	235	dbSNP
rs117694773	242	dbSNP
rs79832726	244	dbSNP
rs1430695903	246	dbSNP
rs1168023261	248	dbSNP
rs1422477348	251	dbSNP
rs1461503416	260	dbSNP
rs1166542757	263	dbSNP
rs782134144	265	dbSNP
rs559732101	266	dbSNP
rs562975067	267	dbSNP
rs151038527	277	dbSNP
rs1363748553	278	dbSNP
rs1397934431	281	dbSNP
rs868957944	282	dbSNP
rs574114928	283	dbSNP
rs1340209525	288	dbSNP
rs1233966715	293	dbSNP
rs539801600	298	dbSNP
rs1221422862	299	dbSNP
rs1034545157	300	dbSNP
rs1489437061	307	dbSNP
rs560728487	313	dbSNP
rs1262001869	314	dbSNP
rs373885136	319	dbSNP
rs572000425	320	dbSNP
rs1159665625	324	dbSNP
rs3934951	325	dbSNP
rs1045851593	326	dbSNP
rs1297419375	326	dbSNP
rs1415670560	326	dbSNP
rs1377003713	327	dbSNP
rs569832420	327	dbSNP
rs1227814122	336	dbSNP
rs1308333538	339	dbSNP
rs1356537335	345	dbSNP
rs3934952	347	dbSNP
rs1285799504	348	dbSNP
rs1486219749	350	dbSNP
rs577580467	352	dbSNP
rs1235394182	353	dbSNP
rs1472142274	354	dbSNP
rs1038350685	371	dbSNP
rs116336990	372	dbSNP
rs1395415058	378	dbSNP
rs909122517	379	dbSNP
rs1415983824	381	dbSNP
rs1336339283	389	dbSNP
rs1357709672	390	dbSNP
rs1447370390	399	dbSNP
rs1298867056	400	dbSNP
rs1379718154	404	dbSNP
rs537520255	410	dbSNP
rs1238556321	415	dbSNP
rs778233136	420	dbSNP
rs931815452	422	dbSNP
rs1348973103	427	dbSNP
rs1221295942	431	dbSNP
rs1276067195	432	dbSNP
rs1441550713	433	dbSNP
rs1239510473	435	dbSNP
rs923070806	436	dbSNP
rs1177881323	441	dbSNP
rs190575239	446	dbSNP
rs1478884303	448	dbSNP
rs1170653927	449	dbSNP
rs187281316	455	dbSNP
rs534405820	458	dbSNP
rs1414158365	459	dbSNP
rs1171691017	462	dbSNP
rs1402485531	464	dbSNP
rs912910975	465	dbSNP
rs567125669	468	dbSNP
rs989816207	471	dbSNP
rs1439040233	482	dbSNP
rs1273496283	491	dbSNP
rs1343818074	494	dbSNP
rs1214757516	504	dbSNP
rs1259618388	506	dbSNP
rs957891615	508	dbSNP
rs1197463925	510	dbSNP
rs552127596	523	dbSNP
rs1001746570	525	dbSNP
rs1253533908	530	dbSNP
rs533325758	531	dbSNP
rs1196439921	548	dbSNP
rs1245871243	549	dbSNP
rs1475630098	551	dbSNP
rs1194581561	552	dbSNP
rs115967725	553	dbSNP
rs1464123867	555	dbSNP
rs550981289	556	dbSNP
rs1392059397	560	dbSNP
rs897220386	565	dbSNP
rs1038808404	567	dbSNP
rs1322183592	568	dbSNP
rs1005545737	570	dbSNP
rs1330838633	573	dbSNP
rs887736344	576	dbSNP
rs547741370	578	dbSNP
rs1050309087	582	dbSNP
rs931869458	583	dbSNP
rs923124808	587	dbSNP
rs529367106	588	dbSNP
rs1207934632	592	dbSNP
rs945812563	593	dbSNP
rs912972644	595	dbSNP
rs180929340	603	dbSNP
rs529317285	604	dbSNP
rs957028226	607	dbSNP
rs1193003572	608	dbSNP
rs1369093139	611	dbSNP
rs1473831169	614	dbSNP
rs1161918835	615	dbSNP
rs1390651773	618	dbSNP
rs926910981	621	dbSNP
rs1300484937	632	dbSNP
rs980364158	633	dbSNP
rs4072459	635	dbSNP
rs1024502259	638	dbSNP
rs188170434	639	dbSNP
rs1283518434	642	dbSNP
rs1351380399	644	dbSNP
rs1218495513	645	dbSNP
rs1283675922	649	dbSNP
rs1487858864	653	dbSNP
rs994334363	665	dbSNP
rs1216107243	666	dbSNP
rs184183760	673	dbSNP
rs1185596787	680	dbSNP
rs1368387851	683	dbSNP
rs1440891558	685	dbSNP
rs1161005496	688	dbSNP
rs1378799988	690	dbSNP
rs1017019338	698	dbSNP
rs1419492310	700	dbSNP
rs1302997242	701	dbSNP
rs1403987476	703	dbSNP
rs1006012490	705	dbSNP
rs1393773840	705	dbSNP
rs889793831	706	dbSNP
rs1242181580	707	dbSNP
rs1307025316	708	dbSNP
rs1233714269	709	dbSNP
rs1352640844	709	dbSNP
rs1256806213	711	dbSNP
rs1049691750	713	dbSNP
rs1458288376	714	dbSNP
rs1180988917	718	dbSNP
rs1236886064	723	dbSNP
rs1439464287	736	dbSNP
rs1177318903	737	dbSNP
rs996071041	738	dbSNP
rs1464269665	740	dbSNP
rs1171673888	741	dbSNP
rs1400334910	746	dbSNP
rs1448376344	747	dbSNP
rs1329143159	749	dbSNP
rs1376158649	750	dbSNP
rs1231271751	752	dbSNP
rs1387123519	752	dbSNP
rs1200673144	753	dbSNP
rs1192110719	754	dbSNP
rs1256697205	754	dbSNP
rs868907209	755	dbSNP
rs1423903946	756	dbSNP
rs1431826825	756	dbSNP
rs1466730432	757	dbSNP
rs1167989988	758	dbSNP
rs1399430782	762	dbSNP
rs1458309759	763	dbSNP
rs1386012817	764	dbSNP
rs1220517253	765	dbSNP
rs1222302426	765	dbSNP
rs1222894838	765	dbSNP
rs1263440233	765	dbSNP
rs1267773048	765	dbSNP
rs1276426443	765	dbSNP
rs1282876454	765	dbSNP
rs1307028418	765	dbSNP
rs1341422624	765	dbSNP
rs1423902513	765	dbSNP
rs1478627872	765	dbSNP
rs1487673551	765	dbSNP
rs1166748173	766	dbSNP
rs1298630638	766	dbSNP
rs1348118649	766	dbSNP
rs202215510	766	dbSNP
rs1361374322	768	dbSNP
rs1276571926	769	dbSNP
rs1402039831	769	dbSNP
rs1361295470	773	dbSNP
rs1228971323	775	dbSNP
rs1315431577	775	dbSNP
rs1320502487	778	dbSNP
rs1245677495	779	dbSNP
rs1287240755	780	dbSNP
rs1213931839	781	dbSNP
rs1489487645	781	dbSNP
rs797034015	781	dbSNP
rs1411499431	782	dbSNP
rs1443975241	785	dbSNP
rs1159209590	786	dbSNP
rs1040642248	788	dbSNP
rs1417648046	791	dbSNP
rs945898334	792	dbSNP
rs891583681	796	dbSNP
rs374760568	798	dbSNP
rs1304713458	801	dbSNP
rs1452498299	813	dbSNP
rs1310646349	814	dbSNP
rs1356213094	815	dbSNP
rs1054218555	821	dbSNP
rs935708931	822	dbSNP
rs1312454907	823	dbSNP
rs1211575476	827	dbSNP
rs1235198957	828	dbSNP
rs926966074	830	dbSNP
rs1460505328	831	dbSNP
rs1179117454	840	dbSNP
rs1239949040	844	dbSNP
rs1437591787	844	dbSNP
rs1157841622	847	dbSNP
rs1407503994	848	dbSNP
rs1415298726	849	dbSNP
rs979746953	851	dbSNP
rs544958346	852	dbSNP
rs1332625607	858	dbSNP
rs1379836117	860	dbSNP
rs372042860	863	dbSNP
rs973353721	864	dbSNP
rs961572363	867	dbSNP
rs1276087076	868	dbSNP
rs1017487706	870	dbSNP
rs1198803612	874	dbSNP
rs1259904640	884	dbSNP
rs1456427468	885	dbSNP
rs1180785992	892	dbSNP
rs1247029467	898	dbSNP
rs984238528	899	dbSNP
rs1478900590	904	dbSNP
rs1193065258	906	dbSNP
rs1427542061	909	dbSNP
rs1469343855	910	dbSNP
rs868920513	911	dbSNP
rs113442489	912	dbSNP
rs1328795261	913	dbSNP
rs1350776092	913	dbSNP
rs1373510214	914	dbSNP
rs797031480	914	dbSNP
rs1293268863	915	dbSNP
rs954109077	916	dbSNP
rs1315565049	917	dbSNP
rs368411791	918	dbSNP
rs1453108822	921	dbSNP
rs1219179261	923	dbSNP
rs570614778	924	dbSNP
rs1480253425	925	dbSNP
rs1194689932	934	dbSNP
rs142782941	941	dbSNP
rs1474473505	943	dbSNP
rs901807227	949	dbSNP
rs1018866311	952	dbSNP
rs1167777283	956	dbSNP
rs1392169364	960	dbSNP
rs1407427242	961	dbSNP
rs1301741176	966	dbSNP
rs1364537379	975	dbSNP
rs1400188163	984	dbSNP
rs1010534077	985	dbSNP
rs891638792	986	dbSNP
rs1284692712	988	dbSNP
rs555881866	992	dbSNP
rs935761312	993	dbSNP
rs191638389	1002	dbSNP
rs1488505669	1003	dbSNP
rs1217543420	1007	dbSNP
rs1044118347	1008	dbSNP
rs1265619758	1009	dbSNP
rs1445352156	1010	dbSNP
rs1192642797	1011	dbSNP
rs1369534316	1022	dbSNP
rs949700312	1034	dbSNP
rs573735817	1036	dbSNP
rs1474082478	1040	dbSNP
rs1162259141	1042	dbSNP
rs555508392	1045	dbSNP
rs1384950181	1050	dbSNP
rs1420711564	1056	dbSNP
rs1160079643	1060	dbSNP
rs916865397	1060	dbSNP
rs1381140825	1067	dbSNP
rs1334289177	1074	dbSNP
rs6558385	1081	dbSNP
rs940239581	1086	dbSNP
rs1354063849	1104	dbSNP
rs1242139961	1113	dbSNP
rs1288414872	1119	dbSNP
rs1348874235	1128	dbSNP
rs910073536	1129	dbSNP
rs1256905770	1132	dbSNP
rs984239380	1139	dbSNP
rs1444222674	1140	dbSNP
rs954159510	1143	dbSNP
rs1028359434	1147	dbSNP
rs1440684356	1148	dbSNP
rs368934812	1154	dbSNP
rs558366618	1157	dbSNP
rs7463064	1158	dbSNP
rs1452553254	1167	dbSNP
rs1172817789	1168	dbSNP
rs1403642100	1169	dbSNP
rs1467776681	1171	dbSNP
rs372912480	1172	dbSNP
rs1377634281	1173	dbSNP
rs1448695038	1174	dbSNP
rs1304657419	1175	dbSNP
rs1021343916	1180	dbSNP
rs1238542101	1181	dbSNP
rs1256827080	1182	dbSNP
rs550691665	1190	dbSNP
rs1201912156	1191	dbSNP
rs1263036619	1191	dbSNP
rs1458636526	1192	dbSNP
rs1010173277	1193	dbSNP
rs891689707	1194	dbSNP
rs1418872359	1195	dbSNP
rs782448446	1205	dbSNP
rs1379073564	1210	dbSNP
rs1479164144	1229	dbSNP
rs1032874327	1239	dbSNP
rs1000022408	1253	dbSNP
rs76774993	1254	dbSNP
rs113822375	1255	dbSNP
rs1400909687	1256	dbSNP
rs1467087935	1257	dbSNP
rs1296405742	1261	dbSNP
rs1395433444	1263	dbSNP
rs568187015	1272	dbSNP
rs1302241746	1273	dbSNP
rs1013980970	1281	dbSNP
rs1221729549	1282	dbSNP
rs35820987	1286	dbSNP
rs566623327	1287	dbSNP
rs546703221	1288	dbSNP
rs1207165177	1295	dbSNP
rs1250130033	1303	dbSNP
rs1480506667	1307	dbSNP
rs1210874823	1308	dbSNP
rs60220695	1313	dbSNP
rs1489745423	1316	dbSNP
rs940312379	1318	dbSNP
rs910113974	1324	dbSNP
rs1048581249	1328	dbSNP
rs1168152977	1329	dbSNP
rs1372500965	1329	dbSNP
rs1458198843	1336	dbSNP
rs1295109119	1338	dbSNP
rs932823910	1343	dbSNP
rs921398105	1344	dbSNP
rs1341133975	1348	dbSNP
rs976817483	1350	dbSNP
rs965819104	1351	dbSNP
rs1294039863	1360	dbSNP
rs782686268	1361	dbSNP
rs913928406	1371	dbSNP
rs988535122	1372	dbSNP
rs1489968418	1377	dbSNP
rs1221208808	1381	dbSNP
rs1263465231	1383	dbSNP
rs1486560845	1385	dbSNP
rs559892298	1386	dbSNP
rs1032927086	1394	dbSNP
rs1260915998	1400	dbSNP
rs1424281288	1402	dbSNP
rs1000077692	1407	dbSNP
rs969889902	1412	dbSNP
rs1423771028	1414	dbSNP
rs1163168622	1421	dbSNP
rs1361475560	1421	dbSNP
rs1432947110	1423	dbSNP
rs1022777042	1425	dbSNP
rs145855625	1429	dbSNP
rs7831666	1431	dbSNP
rs782760253	1433	dbSNP
rs1317797946	1437	dbSNP
rs868959549	1442	dbSNP
rs1245791003	1444	dbSNP
rs1286271067	1453	dbSNP
rs11437950	1465	dbSNP
rs74542934	1465	dbSNP
rs1213247405	1469	dbSNP
rs1004280831	1471	dbSNP
rs1259576744	1472	dbSNP
rs888078539	1473	dbSNP
rs1185273700	1474	dbSNP
rs1241273269	1484	dbSNP
rs1048634813	1488	dbSNP
rs533064576	1491	dbSNP
rs921450378	1492	dbSNP
rs1179073287	1497	dbSNP
rs1408948578	1507	dbSNP
rs1402628444	1508	dbSNP
rs1157223865	1514	dbSNP
rs1344624857	1524	dbSNP
rs782105386	1533	dbSNP
rs1466625220	1536	dbSNP
rs868949018	1537	dbSNP
rs539799055	1540	dbSNP
rs1381300127	1541	dbSNP
rs1452349693	1546	dbSNP
rs1310396154	1551	dbSNP
rs1376009039	1554	dbSNP
rs1221656661	1556	dbSNP
rs1283120339	1565	dbSNP
rs1312259649	1565	dbSNP
rs1205078493	1570	dbSNP
rs1261151986	1571	dbSNP
rs781800171	1578	dbSNP
rs28601778	1583	dbSNP
rs1199230543	1591	dbSNP
rs782700552	1604	dbSNP
rs1468421531	1605	dbSNP
rs1175637817	1606	dbSNP
rs1407622472	1607	dbSNP
rs1480798931	1608	dbSNP
rs1178740063	1609	dbSNP
rs1404037657	1616	dbSNP
rs1469692747	1617	dbSNP
rs1332641991	1620	dbSNP
rs562807857	1625	dbSNP
rs1440547907	1630	dbSNP
rs189799886	1631	dbSNP
rs576142031	1634	dbSNP
rs1280765351	1637	dbSNP
rs1322245415	1649	dbSNP
rs555469709	1651	dbSNP
rs988198586	1658	dbSNP
rs1219105404	1663	dbSNP
rs1275032463	1664	dbSNP
rs958284146	1667	dbSNP
rs1435867044	1673	dbSNP
rs1203636805	1675	dbSNP
rs1232500472	1682	dbSNP
rs1490587129	1691	dbSNP
rs1201885765	1696	dbSNP
rs1427216378	1706	dbSNP
rs185344469	1707	dbSNP
rs1168989792	1708	dbSNP
rs573004447	1715	dbSNP
rs978689666	1716	dbSNP
rs1328649880	1725	dbSNP
rs1366615151	1733	dbSNP
rs1406342903	1735	dbSNP
rs558067126	1740	dbSNP
rs1344252219	1749	dbSNP
rs1218784880	1754	dbSNP
rs369690266	1763	dbSNP
rs1022831095	1765	dbSNP
rs1271848402	1768	dbSNP
rs540066079	1770	dbSNP
rs556174025	1771	dbSNP
rs868975636	1778	dbSNP
rs959853902	1779	dbSNP
rs1361341725	1781	dbSNP
rs1224914030	1783	dbSNP
rs373703340	1785	dbSNP
rs1490203139	1789	dbSNP
rs1194054294	1790	dbSNP
rs557656271	1800	dbSNP
rs1474689257	1804	dbSNP
rs1003931805	1807	dbSNP
rs537764509	1809	dbSNP
rs1426951457	1811	dbSNP
rs1026583582	1813	dbSNP
rs1364640145	1816	dbSNP
rs1382280376	1819	dbSNP
rs1319765719	1822	dbSNP
rs1324207690	1825	dbSNP
rs1429865278	1826	dbSNP
rs1315647383	1829	dbSNP
rs997077867	1837	dbSNP
rs1384716270	1838	dbSNP
rs782116591	1842	dbSNP
rs527909912	1843	dbSNP
rs782338578	1848	dbSNP
rs1205975113	1853	dbSNP
rs1286370653	1858	dbSNP
rs892597368	1867	dbSNP
rs1193017781	1881	dbSNP
rs1244366175	1886	dbSNP
rs1446812676	1887	dbSNP
rs568096260	1888	dbSNP
rs546616966	1900	dbSNP
rs1453964233	1905	dbSNP
rs1159950401	1906	dbSNP
rs936742755	1909	dbSNP
rs925294468	1911	dbSNP
rs782196272	1913	dbSNP
rs79298513	1920	dbSNP
rs1450147354	1923	dbSNP
rs1314056498	1928	dbSNP
rs1336151967	1931	dbSNP
rs1239963563	1933	dbSNP
rs1281497179	1940	dbSNP
rs1348625100	1960	dbSNP
rs551243445	1969	dbSNP
rs948649532	1973	dbSNP
rs140139105	1975	dbSNP
rs562615383	1983	dbSNP
rs1463084077	1984	dbSNP
rs1202363286	1986	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.

- mBio, 2013

UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.

- Genome research, 2016

DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.