>SRP9|NM_001130440|3'UTR
   1 ATAGCAGAGACTACAGTGTTTGGTGTATAAAACAGACCAAGCTCAAGATGTAAAGAAGATTGAGAAATTCCACAGTCAAC
  81 TAATGCGACTTATGGTAGCCAAGGAAGCCCGCAATGTTACCATGGAAACTGAGTGAATGGTTTGAAATGAAGACTTTGTC
 161 GTGTACTTAGGAAGTAAATATCTTTTGAATTAGAGAAAGTGTTGGGACAGAAAGTACTTTATGTAACTAAGTGGGCTGTT
 241 CAGAAGCTTAGAGGTCATTTTTTGTAATTTTCTTTTTAATTACTTTAGAGAGCTAGGGATGCAAATGTTTTCAGTTAGAA
 321 AGCCTTTATTTACTTTTGGAAATTGAACAAGAAATGCATCTGTCTTAGAAACTGGAGATTATTTGATGTTAGGTAAAACA
 401 TGTAATTGTTTCTCTGGCAAATTTGTATCAGTAATTTGAAAATGAGATATTAGGAAAAACCAATTCTTCTTAAATTTAGT
 481 TCATCTTTCTTTAAAAGAACATTAAATGTAACCATTTTGTCAGATCCATGTATTTTGGAGCATAAAATGTATGCTGTTGT
 561 GACCAATAAATATAAAATATGGTAATTGGAATTAACTCCACACCATAGTATGCATTGTTATACATACTGTGTACCTAATT
 641 ATGTATAGCAGTGTAGTCTCAATTATATCTGAAAGTAATTGTGACTAACAAGTATGCTTTGCCTTATTTCCACATTTAAA
 721 CTACCTGTTAATATAAGGGATTTGTAGTATCAGCTTGTTGAGCAATGACTTTGAATCTAGTTTTCAGTGATCAGAAGCAG
 801 CAGTTATTTGAGTGTATGAATGGAATGATGATCACTGTGCTATAATGTACTGAAACCACCATATTACAGAAATATTTACT
 881 ACATATTTTCCATCTGTAGTTTCTCAGAAGGGCTATGGATTAGTTTGAACTGTCAAATCCTTGCATACTTCTGTGACACC
 961 CCTGCCCATTTTCTGTCTTTAATTAACCAAGGTGTTAGGTGTGACTGTCACAACTGTTATGTTTTCCAGTAAACTAGAAG
1041 TACGATATTTGATAATTATATTTGTATTTCACCACCTAAATGTAATGTTGATTCCTCAAGAATGAAATGAAGGCACTACA
1121 TTGAAATATGTTTTGTATAAATTTGTCATGTTGAACAGCATTTTAGCATGGTAAGTTCCCTTAGCTATATGAATTTTGGC
1201 ATGTTTCAGAGAGATCAGTAAATAAAATATTAGATAAAATATAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' aaaGAGGAGGGUAGAAGGUGUg 5' ||:: ||: :||||||| Target 5' atgCTTTGCCTTATTTCCACAt 3'	694 - 715	155.00	-15.90
2	miRNA 3' aaagaggaggguagAAGGUGUg 5' ||||||| Target 5' agaagattgagaaaTTCCACAg 3'	54 - 75	140.00	-7.70
3	miRNA 3' aaAGAGGA-GGGUAGAAGGUGug 5' |:| || | :||:|||||: Target 5' taTTTACTACATATTTTCCATct 3'	873 - 895	128.00	-10.60

Mutant ID	Mutant Position	Mutant Source
COSN31785124	29	COSMIC
COSN30586575	56	COSMIC
COSN20045870	61	COSMIC
COSN1434039	71	COSMIC
COSN30599509	75	COSMIC
COSN16215711	601	COSMIC
COSN21311313	638	COSMIC
COSN145890	1399	COSMIC
COSN29529006	1882	COSMIC
COSM8985655	2105	COSMIC
COSN26634976	2144	COSMIC
COSN6025311	2239	COSMIC
COSM7893471	2277	COSMIC
COSM8966625	2293	COSMIC
COSM3484218	2310	COSMIC
COSM6124903	2311	COSMIC
COSM7572858	2312	COSMIC
COSM4730039	2316	COSMIC
COSM8195425	2341	COSMIC
COSM8193794	2350	COSMIC
COSM904660	2365	COSMIC
COSM138279	2379	COSMIC
COSM7634973	2383	COSMIC
COSM4852493	2388	COSMIC
COSN30529595	2428	COSMIC
COSN31602743	2429	COSMIC
COSN30173085	2431	COSMIC
COSN30169340	2504	COSMIC
COSN30120537	2623	COSMIC
COSN16211609	3298	COSMIC
COSN1434040	3366	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1461758875	2	dbSNP
rs1173564787	7	dbSNP
rs1404941578	9	dbSNP
rs1413315596	20	dbSNP
rs1215580167	25	dbSNP
rs1347675726	27	dbSNP
rs954567908	30	dbSNP
rs1354348240	32	dbSNP
rs1297234345	37	dbSNP
rs1400082947	37	dbSNP
rs1442385014	42	dbSNP
rs912655731	49	dbSNP
rs987704594	49	dbSNP
rs775149032	56	dbSNP
rs1015617381	57	dbSNP
rs1258010934	58	dbSNP
rs897125653	61	dbSNP
rs543491041	63	dbSNP
rs73125801	64	dbSNP
rs538840969	70	dbSNP
rs1254042717	73	dbSNP
rs554372429	82	dbSNP
rs970248559	84	dbSNP
rs1257035571	90	dbSNP
rs1235910876	97	dbSNP
rs980275838	106	dbSNP
rs1315498832	111	dbSNP
rs1041973509	113	dbSNP
rs903441540	115	dbSNP
rs1192138356	120	dbSNP
rs1261751368	128	dbSNP
rs1036244390	129	dbSNP
rs1480495611	142	dbSNP
rs1178081983	146	dbSNP
rs1003074943	149	dbSNP
rs1057474634	158	dbSNP
rs1413558048	171	dbSNP
rs959829387	176	dbSNP
rs988932149	184	dbSNP
rs1376004943	200	dbSNP
rs1304499155	204	dbSNP
rs1451444517	206	dbSNP
rs1344355624	207	dbSNP
rs1375547542	211	dbSNP
rs912899971	213	dbSNP
rs11583055	217	dbSNP
rs1414419849	222	dbSNP
rs1185909282	228	dbSNP
rs748260898	232	dbSNP
rs1013055394	236	dbSNP
rs1257562136	238	dbSNP
rs921836924	246	dbSNP
rs1016010418	248	dbSNP
rs1485123052	250	dbSNP
rs931833095	256	dbSNP
rs181736239	261	dbSNP
rs186942034	264	dbSNP
rs1051625310	265	dbSNP
rs911687140	268	dbSNP
rs576062616	269	dbSNP
rs1397998597	279	dbSNP
rs1297542719	280	dbSNP
rs543492724	286	dbSNP
rs1037080124	288	dbSNP
rs137942871	289	dbSNP
rs577105440	292	dbSNP
rs779246128	293	dbSNP
rs540986984	294	dbSNP
rs559461405	295	dbSNP
rs367620301	296	dbSNP
rs1048705628	299	dbSNP
rs529856393	302	dbSNP
rs11583073	303	dbSNP
rs10915876	308	dbSNP
rs1427288763	316	dbSNP
rs1215034522	321	dbSNP
rs960444451	329	dbSNP
rs947428234	330	dbSNP
rs1189624413	331	dbSNP
rs1466518835	332	dbSNP
rs746432865	337	dbSNP
rs772610823	338	dbSNP
rs143721962	341	dbSNP
rs747125102	342	dbSNP
rs938891411	346	dbSNP
rs1224563502	347	dbSNP
rs1057315721	354	dbSNP
rs968382667	360	dbSNP
rs796066848	362	dbSNP
rs188665232	363	dbSNP
rs1324193266	368	dbSNP
rs1386440908	377	dbSNP
rs1432179913	380	dbSNP
rs898908492	382	dbSNP
rs527882745	388	dbSNP
rs181292252	389	dbSNP
rs1373065650	393	dbSNP
rs987761997	394	dbSNP
rs1451766458	404	dbSNP
rs759971991	410	dbSNP
rs1025947315	414	dbSNP
rs1451855697	414	dbSNP
rs1417660425	420	dbSNP
rs1193589046	421	dbSNP
rs1157881453	423	dbSNP
rs1366081625	427	dbSNP
rs1426544658	428	dbSNP
rs1295345788	433	dbSNP
rs1302449138	435	dbSNP
rs954669341	439	dbSNP
rs1331913678	448	dbSNP
rs1325754971	450	dbSNP
rs11581798	452	dbSNP
rs547790988	453	dbSNP
rs1369991367	457	dbSNP
rs1386358597	460	dbSNP
rs1308017072	462	dbSNP
rs768573805	474	dbSNP
rs566225686	475	dbSNP
rs1173411268	487	dbSNP
rs1017508198	490	dbSNP
rs1379069414	502	dbSNP
rs918662377	508	dbSNP
rs1251931109	509	dbSNP
rs1309038103	524	dbSNP
rs1206626089	527	dbSNP
rs1360781293	527	dbSNP
rs989270044	528	dbSNP
rs1224450129	532	dbSNP
rs1346853402	538	dbSNP
rs536842259	542	dbSNP
rs551924695	553	dbSNP
rs1237127797	557	dbSNP
rs775932214	558	dbSNP
rs368431566	559	dbSNP
rs977393404	560	dbSNP
rs1195975308	565	dbSNP
rs1374190228	565	dbSNP
rs924580859	566	dbSNP
rs762053466	569	dbSNP
rs761319266	570	dbSNP
rs1472075866	574	dbSNP
rs916163518	574	dbSNP
rs1183729620	575	dbSNP
rs1473931213	577	dbSNP
rs554704562	595	dbSNP
rs569809060	598	dbSNP
rs1475915626	599	dbSNP
rs12031296	601	dbSNP
rs1057503621	603	dbSNP
rs758554320	618	dbSNP
rs929016249	618	dbSNP
rs1047440985	624	dbSNP
rs1230376589	626	dbSNP
rs1446305153	628	dbSNP
rs1392165287	642	dbSNP
rs1162600877	649	dbSNP
rs1342738734	653	dbSNP
rs890146482	654	dbSNP
rs1456988894	655	dbSNP
rs116045473	657	dbSNP
rs1160916300	658	dbSNP
rs1010345260	662	dbSNP
rs576775513	665	dbSNP
rs1017977449	669	dbSNP
rs1181887530	670	dbSNP
rs900406790	672	dbSNP
rs1240219415	674	dbSNP
rs1187714111	675	dbSNP
rs551056731	687	dbSNP
rs1465175015	688	dbSNP
rs1248954765	690	dbSNP
rs1010700568	693	dbSNP
rs541277036	694	dbSNP
rs1289279906	697	dbSNP
rs1020013613	704	dbSNP
rs1359089942	706	dbSNP
rs549790246	709	dbSNP
rs80078182	713	dbSNP
rs999876032	722	dbSNP
rs1322192986	724	dbSNP
rs369886882	725	dbSNP
rs1383993660	729	dbSNP
rs1348899518	730	dbSNP
rs148691302	743	dbSNP
rs1164869731	753	dbSNP
rs1230488910	754	dbSNP
rs561029374	758	dbSNP
rs953124511	759	dbSNP
rs1167882319	768	dbSNP
rs116335664	769	dbSNP
rs781692460	779	dbSNP
rs1249643118	781	dbSNP
rs1487628698	790	dbSNP
rs1246283723	792	dbSNP
rs1019271941	794	dbSNP
rs543574069	797	dbSNP
rs1227482425	805	dbSNP
rs1259508177	807	dbSNP
rs1271551508	811	dbSNP
rs1228283167	813	dbSNP
rs1456159825	820	dbSNP
rs961933555	820	dbSNP
rs1197637032	822	dbSNP
rs1243453349	824	dbSNP
rs1293741464	825	dbSNP
rs1438072993	833	dbSNP
rs916157314	834	dbSNP
rs1307399510	847	dbSNP
rs1484128466	848	dbSNP
rs748091852	851	dbSNP
rs973586563	852	dbSNP
rs753708789	853	dbSNP
rs1429088724	863	dbSNP
rs929446754	870	dbSNP
rs1191959116	872	dbSNP
rs931393545	873	dbSNP
rs4653677	874	dbSNP
rs1204473735	875	dbSNP
rs927355832	877	dbSNP
rs1483670830	880	dbSNP
rs778526184	882	dbSNP
rs1277322246	883	dbSNP
rs557939779	892	dbSNP
rs548023650	893	dbSNP
rs1038661920	903	dbSNP
rs1301595862	903	dbSNP
rs900418926	904	dbSNP
rs1370667044	913	dbSNP
rs77233296	920	dbSNP
rs1409837998	921	dbSNP
rs1043612753	923	dbSNP
rs116110999	929	dbSNP
rs946280815	933	dbSNP
rs1450610531	938	dbSNP
rs1041883540	944	dbSNP
rs904667383	945	dbSNP
rs1301504021	947	dbSNP
rs1181568321	949	dbSNP
rs999905841	953	dbSNP
rs1254680464	955	dbSNP
rs1180594673	961	dbSNP
rs1029158386	963	dbSNP
rs566127590	973	dbSNP
rs1008967343	980	dbSNP
rs1326653359	984	dbSNP
rs1353769287	987	dbSNP
rs1267081216	996	dbSNP
rs1018887725	1000	dbSNP
rs1279474811	1006	dbSNP
rs961967423	1007	dbSNP
rs548837852	1012	dbSNP
rs1395406130	1014	dbSNP
rs1027491305	1023	dbSNP
rs1379753308	1024	dbSNP
rs1304375098	1030	dbSNP
rs1451285454	1030	dbSNP
rs920827599	1032	dbSNP
rs1158702127	1039	dbSNP
rs950900774	1052	dbSNP
rs1414251422	1053	dbSNP
rs1263397188	1064	dbSNP
rs951855596	1094	dbSNP
rs1257401007	1104	dbSNP
rs1207717983	1118	dbSNP
rs372497870	1125	dbSNP
rs1236751011	1126	dbSNP
rs1486121913	1128	dbSNP
rs984237211	1129	dbSNP
rs927355582	1143	dbSNP
rs1247070531	1149	dbSNP
rs1463818342	1149	dbSNP
rs911636675	1171	dbSNP
rs1330708787	1172	dbSNP
rs185154024	1184	dbSNP
rs1039126817	1194	dbSNP
rs1265379290	1199	dbSNP
rs1177835137	1203	dbSNP
rs993253833	1211	dbSNP
rs917231108	1221	dbSNP
rs369165638	1222	dbSNP
rs1314755526	1230	dbSNP
rs1170129048	1239	dbSNP
rs946311715	1242	dbSNP
rs1364158923	1243	dbSNP
rs1320202727	1251	dbSNP
rs1436121229	1252	dbSNP
rs1041914400	1253	dbSNP
rs551993172	1256	dbSNP
rs1457456472	1258	dbSNP
rs1369611562	1260	dbSNP
rs946368896	1264	dbSNP
rs1174384838	1277	dbSNP
rs1448095397	1278	dbSNP
rs189917122	1282	dbSNP
rs1050215471	1297	dbSNP
rs1465979843	1298	dbSNP
rs1264755475	1302	dbSNP
rs1208786230	1306	dbSNP
rs1488520053	1308	dbSNP
rs902432913	1311	dbSNP
rs1226055988	1315	dbSNP
rs1341313432	1322	dbSNP
rs888844283	1332	dbSNP
rs181990958	1334	dbSNP
rs1008624764	1335	dbSNP
rs553222638	1336	dbSNP
rs897456724	1345	dbSNP
rs80234619	1350	dbSNP
rs573068399	1359	dbSNP
rs747071826	1370	dbSNP
rs1391512544	1371	dbSNP
rs1304974062	1381	dbSNP
rs1398825086	1383	dbSNP
rs556708946	1384	dbSNP
rs951886534	1386	dbSNP
rs1002426753	1390	dbSNP
rs1023458121	1391	dbSNP
rs1369279164	1394	dbSNP
rs1033492340	1395	dbSNP
rs970068852	1397	dbSNP
rs1268854621	1408	dbSNP
rs1277572106	1410	dbSNP
rs1482704252	1412	dbSNP
rs187289407	1412	dbSNP
rs543858633	1424	dbSNP
rs950910692	1427	dbSNP
rs917252158	1431	dbSNP
rs1218643072	1442	dbSNP
rs1349946318	1446	dbSNP
rs1408024640	1446	dbSNP
rs35284825	1446	dbSNP
rs984025552	1448	dbSNP
rs1487947065	1449	dbSNP
rs1412060485	1452	dbSNP
rs1193041158	1466	dbSNP
rs1053378556	1467	dbSNP
rs1162627596	1468	dbSNP
rs912038785	1469	dbSNP
rs967350875	1471	dbSNP
rs966198770	1472	dbSNP
rs1471963039	1475	dbSNP
rs1252540514	1479	dbSNP
rs1184245107	1480	dbSNP
rs1440573170	1481	dbSNP
rs977678235	1487	dbSNP
rs565239051	1488	dbSNP
rs1346006514	1495	dbSNP
rs1265210242	1496	dbSNP
rs1189697112	1500	dbSNP
rs1349944055	1501	dbSNP
rs1289588897	1504	dbSNP
rs1424845608	1506	dbSNP
rs1440717849	1514	dbSNP
rs1445006212	1515	dbSNP
rs1339153820	1516	dbSNP
rs936196989	1528	dbSNP
rs1051051905	1535	dbSNP
rs974544746	1538	dbSNP
rs1160872878	1549	dbSNP
rs921684820	1550	dbSNP
rs910687020	1551	dbSNP
rs1407902937	1555	dbSNP
rs1156506966	1557	dbSNP
rs548401730	1565	dbSNP
rs946421296	1567	dbSNP
rs1471788414	1570	dbSNP
rs1043342543	1571	dbSNP
rs1188058855	1571	dbSNP
rs944456026	1583	dbSNP
rs1040119402	1596	dbSNP
rs1351122430	1597	dbSNP
rs1328679351	1598	dbSNP
rs897528440	1601	dbSNP
rs993148170	1604	dbSNP
rs1049027957	1605	dbSNP
rs887710593	1606	dbSNP
rs192084481	1610	dbSNP
rs1033939555	1614	dbSNP
rs1433914567	1617	dbSNP
rs1388868713	1618	dbSNP
rs753555111	1620	dbSNP
rs1403076009	1631	dbSNP
rs960532533	1634	dbSNP
rs541109605	1636	dbSNP
rs1290596030	1637	dbSNP
rs1024338069	1639	dbSNP
rs1219583610	1651	dbSNP
rs1246318643	1652	dbSNP
rs560074433	1654	dbSNP
rs896349949	1660	dbSNP
rs967380533	1667	dbSNP
rs977375300	1668	dbSNP
rs1218095022	1675	dbSNP
rs117078233	1678	dbSNP
rs994846390	1684	dbSNP
rs537328301	1688	dbSNP
rs563828867	1689	dbSNP
rs1362138123	1692	dbSNP
rs986359797	1697	dbSNP
rs531127322	1698	dbSNP
rs1005105118	1707	dbSNP
rs944884601	1710	dbSNP
rs1486430623	1712	dbSNP
rs552245583	1715	dbSNP
rs111255620	1720	dbSNP
rs918989388	1724	dbSNP
rs929013060	1725	dbSNP
rs74323976	1726	dbSNP
rs887406107	1737	dbSNP
rs546305534	1738	dbSNP
rs1449819743	1741	dbSNP
rs1420538325	1742	dbSNP
rs1188497053	1747	dbSNP
rs937930206	1754	dbSNP
rs567739468	1756	dbSNP
rs150777864	1758	dbSNP
rs1013408593	1761	dbSNP
rs1246567962	1762	dbSNP
rs1024367500	1771	dbSNP
rs1204947740	1773	dbSNP
rs903295923	1781	dbSNP
rs1274752499	1787	dbSNP
rs1217127991	1791	dbSNP
rs998868074	1803	dbSNP
rs1274958240	1817	dbSNP
rs867054125	1824	dbSNP
rs1354219927	1826	dbSNP
rs1226648158	1835	dbSNP
rs917824119	1847	dbSNP
rs1032976174	1850	dbSNP
rs1289327280	1852	dbSNP
rs1458373155	1854	dbSNP
rs957390442	1861	dbSNP
rs556847760	1863	dbSNP
rs1236689259	1864	dbSNP
rs1413013953	1869	dbSNP
rs1457616933	1872	dbSNP
rs1200292847	1873	dbSNP
rs1481442935	1873	dbSNP
rs201423099	1873	dbSNP
rs575048415	1874	dbSNP
rs1239694710	1875	dbSNP
rs571062790	1878	dbSNP
rs966632439	1882	dbSNP
rs1472136489	1883	dbSNP
rs976264193	1886	dbSNP
rs886468853	1894	dbSNP
rs1005291155	1896	dbSNP
rs1019229044	1898	dbSNP
rs1162116831	1902	dbSNP
rs1326452272	1904	dbSNP
rs1423743885	1907	dbSNP
rs1444796659	1912	dbSNP
rs919394853	1920	dbSNP
rs902062046	1931	dbSNP
rs1410367608	1934	dbSNP
rs1375395767	1940	dbSNP
rs576784099	1947	dbSNP
rs984501955	1951	dbSNP
rs750770423	1958	dbSNP
rs1358846059	1961	dbSNP
rs77581122	1962	dbSNP
rs1055481968	1963	dbSNP
rs1158432409	1972	dbSNP
rs1399208890	1973	dbSNP
rs896386047	1974	dbSNP
rs1253223503	1980	dbSNP
rs1420237740	1980	dbSNP
rs369458890	1985	dbSNP
rs1335978169	1988	dbSNP
rs1338620851	1989	dbSNP
rs1205156710	1999	dbSNP
rs1463220610	2004	dbSNP
rs1447274681	2011	dbSNP
rs949304178	2019	dbSNP
rs1252302795	2034	dbSNP
rs1226370268	2038	dbSNP
rs1256406109	2042	dbSNP
rs1227600354	2049	dbSNP
rs1347005162	2051	dbSNP
rs756105017	2052	dbSNP
rs1279531194	2064	dbSNP
rs770354270	2065	dbSNP
rs1218922481	2067	dbSNP
rs1175423841	2068	dbSNP
rs956437804	2071	dbSNP
rs992225506	2072	dbSNP
rs1259870860	2080	dbSNP
rs1428183632	2083	dbSNP
rs1199999854	2084	dbSNP
rs1319994389	2087	dbSNP
rs1379792841	2091	dbSNP
rs1477324655	2096	dbSNP
rs1454354640	2097	dbSNP
rs1042216379	2098	dbSNP
rs1361746357	2102	dbSNP
rs902321679	2109	dbSNP
rs1299533413	2111	dbSNP
rs1163286283	2123	dbSNP
rs1382281183	2128	dbSNP
rs779983991	2129	dbSNP
rs748965866	2131	dbSNP
rs144331314	2143	dbSNP
rs1231826690	2144	dbSNP
rs1302527537	2146	dbSNP
rs1178368558	2150	dbSNP
rs1373681664	2154	dbSNP
rs1033048788	2156	dbSNP
rs1354364857	2163	dbSNP
rs947925439	2170	dbSNP
rs980616108	2171	dbSNP
rs773823606	2172	dbSNP
rs1263674473	2173	dbSNP
rs112101541	2183	dbSNP
rs775337368	2183	dbSNP
rs763628790	2188	dbSNP
rs1017997005	2189	dbSNP
rs966330399	2190	dbSNP
rs775689467	2192	dbSNP
rs541396846	2194	dbSNP
rs1422429144	2206	dbSNP
rs1466291421	2212	dbSNP
rs940711428	2214	dbSNP
rs1399814537	2216	dbSNP
rs747881191	2225	dbSNP
rs771675451	2229	dbSNP
rs1210735715	2232	dbSNP
rs772923137	2235	dbSNP
rs760106713	2237	dbSNP
rs373334091	2238	dbSNP
rs1193425673	2239	dbSNP
rs765780699	2242	dbSNP
rs1442125283	2249	dbSNP
rs763179593	2250	dbSNP
rs769777605	2253	dbSNP
rs1452600120	2258	dbSNP
rs1408330135	2263	dbSNP
rs1490499662	2277	dbSNP
rs1293696790	2280	dbSNP
rs1202809228	2289	dbSNP
rs1392460130	2295	dbSNP
rs764569734	2305	dbSNP
rs751702134	2312	dbSNP
rs1297955504	2323	dbSNP
rs559757893	2335	dbSNP
rs767574296	2337	dbSNP
rs1304956608	2338	dbSNP
rs1369006728	2341	dbSNP
rs1228440656	2346	dbSNP
rs1328352425	2346	dbSNP
rs1221405987	2348	dbSNP
rs750448224	2361	dbSNP
rs372066327	2363	dbSNP
rs199511703	2365	dbSNP
rs756194834	2366	dbSNP
rs779811715	2367	dbSNP
rs201568819	2369	dbSNP
rs1050624407	2374	dbSNP
rs1274839826	2377	dbSNP
rs149323412	2379	dbSNP
rs1463231190	2383	dbSNP
rs542491478	2384	dbSNP
rs773215789	2384	dbSNP
rs1459471727	2385	dbSNP
rs754704124	2389	dbSNP
rs1250437719	2390	dbSNP
rs778806792	2393	dbSNP
rs1164902991	2394	dbSNP
rs1030783572	2395	dbSNP
rs747749485	2402	dbSNP
rs200262058	2415	dbSNP
rs373834174	2416	dbSNP
rs146544886	2418	dbSNP
rs1448727975	2419	dbSNP
rs770587978	2420	dbSNP
rs1372549827	2422	dbSNP
rs1393379920	2424	dbSNP
rs1223058749	2425	dbSNP
rs1324359802	2432	dbSNP
rs775840400	2433	dbSNP
rs1314984963	2435	dbSNP
rs1353768294	2436	dbSNP
rs763557687	2436	dbSNP
rs1232961331	2437	dbSNP
rs1259103636	2439	dbSNP
rs1285207266	2440	dbSNP
rs1408543970	2441	dbSNP
rs762997219	2442	dbSNP
rs564184875	2445	dbSNP
rs1477562432	2450	dbSNP
rs1159070011	2453	dbSNP
rs1393478774	2455	dbSNP
rs1399664312	2461	dbSNP
rs1175257553	2464	dbSNP
rs980710832	2466	dbSNP
rs919821682	2472	dbSNP
rs1156230911	2475	dbSNP
rs1417850357	2476	dbSNP
rs952561616	2479	dbSNP
rs763426878	2490	dbSNP
rs982580175	2493	dbSNP
rs1440482508	2495	dbSNP
rs528145770	2497	dbSNP
rs1296359536	2511	dbSNP
rs1254408703	2513	dbSNP
rs1384356115	2522	dbSNP
rs1387528814	2526	dbSNP
rs1265113526	2527	dbSNP
rs1226599185	2534	dbSNP
rs1350647923	2539	dbSNP
rs546304542	2541	dbSNP
rs188550487	2548	dbSNP
rs552802646	2554	dbSNP
rs1336416203	2558	dbSNP
rs1310533082	2559	dbSNP
rs141268331	2564	dbSNP
rs1318015849	2577	dbSNP
rs572884237	2578	dbSNP
rs1050676068	2579	dbSNP
rs1160215808	2584	dbSNP
rs904104097	2587	dbSNP
rs1384384800	2591	dbSNP
rs1488539155	2592	dbSNP
rs11555998	2598	dbSNP
rs12043546	2603	dbSNP
rs1445494977	2609	dbSNP
rs760326459	2615	dbSNP
rs892234183	2619	dbSNP
rs1013721944	2625	dbSNP
rs1024711799	2627	dbSNP
rs776768304	2635	dbSNP
rs1001866036	2654	dbSNP
rs1247108429	2655	dbSNP
rs1381956875	2662	dbSNP
rs1294943613	2666	dbSNP
rs1437678476	2668	dbSNP
rs1429493022	2672	dbSNP
rs1345289098	2673	dbSNP
rs1158010410	2679	dbSNP
rs1026912834	2680	dbSNP
rs1403566019	2681	dbSNP
rs1364836450	2688	dbSNP
rs550458988	2715	dbSNP
rs11555109	2718	dbSNP
rs1426281523	2718	dbSNP
rs1387386255	2723	dbSNP
rs1363255246	2724	dbSNP
rs1475174546	2731	dbSNP
rs548849676	2738	dbSNP
rs34812122	2745	dbSNP
rs1242777878	2746	dbSNP
rs1195362211	2749	dbSNP
rs1450413261	2755	dbSNP
rs982657151	2774	dbSNP
rs908345629	2785	dbSNP
rs568854373	2804	dbSNP
rs965228913	2810	dbSNP
rs11555110	2814	dbSNP
rs923379120	2819	dbSNP
rs1433648823	2824	dbSNP
rs1379576946	2828	dbSNP
rs1238560206	2831	dbSNP
rs932019674	2832	dbSNP
rs1322895823	2835	dbSNP
rs986058716	2836	dbSNP
rs1246347683	2837	dbSNP
rs189915800	2838	dbSNP
rs1420429268	2839	dbSNP
rs1169771746	2841	dbSNP
rs936900198	2848	dbSNP
rs1479496421	2850	dbSNP
rs35170135	2852	dbSNP
rs1333630735	2854	dbSNP
rs557698639	2856	dbSNP
rs768789753	2861	dbSNP
rs182555497	2863	dbSNP
rs1239733797	2867	dbSNP
rs11555121	2868	dbSNP
rs1456296501	2876	dbSNP
rs1274638346	2877	dbSNP
rs1373941933	2885	dbSNP
rs534778115	2893	dbSNP
rs1416846137	2910	dbSNP
rs748425084	2924	dbSNP
rs34451510	2926	dbSNP
rs949558756	2933	dbSNP
rs1297412511	2939	dbSNP
rs1442629738	2944	dbSNP
rs1355406524	2945	dbSNP
rs1331120176	2946	dbSNP
rs1425551096	2952	dbSNP
rs1166980657	2956	dbSNP
rs1428694916	2966	dbSNP
rs1046608686	2972	dbSNP
rs1177193972	2978	dbSNP
rs1481719120	2979	dbSNP
rs1406398689	2983	dbSNP
rs1366810074	2988	dbSNP
rs1461056900	2989	dbSNP
rs1171693209	2994	dbSNP
rs1201399411	3000	dbSNP
rs770107548	3001	dbSNP
rs1444987943	3002	dbSNP
rs1224759401	3007	dbSNP
rs553503989	3008	dbSNP
rs1315104287	3009	dbSNP
rs561122883	3016	dbSNP
rs574881344	3020	dbSNP
rs1375278155	3026	dbSNP
rs1334766046	3044	dbSNP
rs1309881907	3045	dbSNP
rs542282668	3049	dbSNP
rs759395838	3052	dbSNP
rs35944562	3058	dbSNP
rs1218813738	3069	dbSNP
rs11555113	3072	dbSNP
rs145846119	3082	dbSNP
rs1470979370	3087	dbSNP
rs1344018012	3088	dbSNP
rs575875403	3097	dbSNP
rs1315718236	3102	dbSNP
rs1203548228	3107	dbSNP
rs1004566561	3109	dbSNP
rs1182088510	3115	dbSNP
rs1443649802	3116	dbSNP
rs1015493673	3119	dbSNP
rs965628686	3129	dbSNP
rs1256425319	3130	dbSNP
rs976606849	3132	dbSNP
rs1216421214	3137	dbSNP
rs1318615559	3138	dbSNP
rs1484159852	3143	dbSNP
rs1180047613	3144	dbSNP
rs367776098	3148	dbSNP
rs1030379928	3149	dbSNP
rs1315991606	3151	dbSNP
rs1474933582	3153	dbSNP
rs1359969905	3154	dbSNP
rs953422866	3160	dbSNP
rs564488154	3165	dbSNP
rs528693463	3170	dbSNP
rs1347409012	3183	dbSNP
rs1162113714	3185	dbSNP
rs1194538115	3187	dbSNP
rs1424386124	3188	dbSNP
rs1385548600	3196	dbSNP
rs1426044564	3198	dbSNP
rs1426301770	3200	dbSNP
rs1260475840	3203	dbSNP
rs1186548921	3207	dbSNP
rs186531623	3212	dbSNP
rs1221558364	3213	dbSNP
rs925258189	3217	dbSNP
rs1170119187	3222	dbSNP
rs1360116250	3232	dbSNP
rs1467995186	3233	dbSNP
rs763186007	3233	dbSNP
rs1301633445	3240	dbSNP
rs1355441374	3243	dbSNP
rs1382821989	3253	dbSNP
rs1342976160	3262	dbSNP
rs1301828049	3265	dbSNP
rs936659853	3268	dbSNP
rs1279610906	3272	dbSNP
rs191367978	3275	dbSNP
rs914154173	3286	dbSNP
rs1372121323	3292	dbSNP
rs1170583774	3296	dbSNP
rs1429770358	3296	dbSNP
rs1050033	3298	dbSNP
rs1046521507	3299	dbSNP
rs184461856	3300	dbSNP
rs1490473481	3323	dbSNP
rs569113425	3326	dbSNP
rs1270817819	3333	dbSNP
rs14113	3337	dbSNP
rs904962972	3352	dbSNP
rs1207871967	3358	dbSNP
rs1279495839	3371	dbSNP
rs1250939399	3378	dbSNP
rs937716994	3380	dbSNP
rs1320074368	3384	dbSNP
rs374816734	3390	dbSNP
rs1048161968	3398	dbSNP
rs1346643362	3400	dbSNP
rs1326005270	3404	dbSNP
rs368167273	3410	dbSNP
rs1488614975	3411	dbSNP
rs1217418955	3423	dbSNP
rs1298382842	3426	dbSNP
rs775502611	3431	dbSNP
rs1463149081	3442	dbSNP
rs888136607	3453	dbSNP
rs1175031629	3457	dbSNP
rs751888908	3466	dbSNP
rs1480733255	3467	dbSNP
rs1474512576	3474	dbSNP
rs1431318561	3477	dbSNP
rs1179446289	3481	dbSNP
rs1003880984	3488	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.

- Genes & development, 2013

When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.