>WSB1|NM_015626|3'UTR
   1 AAGATTCTGCCTTCCCTAGTAGTAGGGACTGACAGAATACACTTAACACAAACCTCAAGCTTTACTGACTTCAATTATCT
  81 GTTTTTAAAGACGTAGAAGATTTATTTAATTTGATATGTTCTTGTACTGCATTTTGATCAGTTGAGCTTTTAAAATATTA
 161 TTTATAGACAATAGAAGTATTTCTGAACATATCAAATATAAATTTTTTTAAAGATCTAACTGTGAAAACATACATACCTG
 241 TACATATTTAGATATAAGCTGCTATATGTTGAATGGACCCTTTTGCTTTTCTGATTTTTAGTTCTGACATGTATATATTG
 321 CTTCAGTAGAGCCACAATATGTATCTTTGCTGTAAAGTGCAAGGAAATTTTAAATTCTGGGACACTGAGTTAGATGGTAA
 401 ATACTGACTTACGAAAGTTGAATTGGGTGAGGCGGGCAAATCACCTGAGGTCAGCAGTTTGAGACTAGCCTGGCAAACAT
 481 GATGAAACCCTGTCTCTACTAAAAATACAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCTAGCT
 561 ACTTGGGAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGGTGGAGGTTGCAGTAAGCCAAGATCACACCACTGCACTC
 641 CAACCTGGACAACAGAGCGAGACTCCATCTCAAAAAAAAAAAAAAATTGTGTTGCCTCATACGAAATGTATTTGGTTTTG
 721 TTGGAGAGTGTCAGACTGATCTGGAAGTGAAACACAGTTTATGTACAGGGAAAAGGATTTTATTATCCTTAGGAATGTCA
 801 TCCAAGACGTAGAGCTTGAATGTGACGTTATTTAAAAACAACAACAAAGAAGGCAGAGCCAGGATATAACTAGAAAAAGG
 881 ATGTCTTTTTTTTTTTTTTTACTCCCCCTCTAAACACTGCTGCTGCCTTAATTTTAGAAAGCAGCTTACTAGTTTACCCT
 961 TGTGGTATAAAGTATTATAAATTGTTGTGAATTTGAAGAATCCGTCTACTGTATTATTGCTAAATATTTTGTTTATACTA
1041 AGGGACAATTATTTTAAGACCATGGATTTAAAAAAAAAAAAAAAAACTCTGTTTCTGCAGGGGATGATATTGGTGAGTTG
1121 CCAAAGAAGCAATACAGCATATCTGCTTTTGCCTTCTGTTGTTTATCTTACCTGCAGATATTAAGAATGTATGCATTATG
1201 TAAAATGCTCAATTATATATTTTTGTTGAGTTTTTTAATTAAAGACTTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1281 AAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' guuUGUGGUAACAGUGUGAGGu 5' |||||| | :|||||| Target 5' atcACACCACT---GCACTCCa 3'	624 - 642	144.00	-18.50
2	miRNA 3' guUUGUGGUAACAGUGUGAGGu 5' :||| || | | ||||| Target 5' tgGACAACAGAGCGAGACTCCa 3'	646 - 667	124.00	-12.70
3	miRNA 3' guUUGUGGUAACAGUGUGAGgu 5' :||| || |||||: Target 5' ctGACAGAAT----ACACTTaa 3'	29 - 46	110.00	-6.00

Mutant ID	Mutant Position	Mutant Source
COSN30187965	6	COSMIC
COSN20079112	9	COSMIC
COSN30496959	14	COSMIC
COSN30712823	41	COSMIC
COSN31542875	79	COSMIC
COSN32053262	80	COSMIC
COSN13707338	93	COSMIC
COSN20078742	94	COSMIC
COSN31525134	122	COSMIC
COSN16724367	156	COSMIC
COSN30154469	167	COSMIC
COSN31549346	206	COSMIC
COSN1194769	214	COSMIC
COSN30159681	214	COSMIC
COSN23730480	462	COSMIC
COSN23140367	523	COSMIC
COSN28676227	687	COSMIC
COSN29764227	687	COSMIC
COSN22806172	688	COSMIC
COSN31546105	764	COSMIC
COSN30543883	769	COSMIC
COSN20113714	901	COSMIC
COSN20113715	901	COSMIC
COSN31523334	983	COSMIC
COSN31519480	999	COSMIC
COSN20113716	1087	COSMIC
COSN26574997	1113	COSMIC
COSN26572693	1152	COSMIC
COSN26635826	1178	COSMIC
COSN25410477	1218	COSMIC
COSN21468794	1458	COSMIC
COSN22707890	1589	COSMIC
COSN25166784	1618	COSMIC
COSN22255243	1666	COSMIC
COSN7162717	1691	COSMIC
COSN32152732	2133	COSMIC
COSN14438739	2203	COSMIC
COSN25995409	2545	COSMIC
COSN8342825	2883	COSMIC
COSN6100948	3207	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs753475794	8	dbSNP
rs1228143306	9	dbSNP
rs555569936	10	dbSNP
rs1252317565	15	dbSNP
rs1168290219	17	dbSNP
rs754780784	17	dbSNP
rs1478642610	18	dbSNP
rs781033703	18	dbSNP
rs748114651	21	dbSNP
rs201870860	23	dbSNP
rs764890411	26	dbSNP
rs1388250638	33	dbSNP
rs1448585755	34	dbSNP
rs373703943	36	dbSNP
rs139016589	38	dbSNP
rs747145899	42	dbSNP
rs1161706471	43	dbSNP
rs757267111	44	dbSNP
rs769304638	45	dbSNP
rs777196772	45	dbSNP
rs781394200	50	dbSNP
rs1328446200	53	dbSNP
rs1264857415	56	dbSNP
rs1466970737	57	dbSNP
rs1318986987	65	dbSNP
rs1195313572	67	dbSNP
rs1008603737	75	dbSNP
rs559673655	93	dbSNP
rs533178921	94	dbSNP
rs1175148016	96	dbSNP
rs1390835194	99	dbSNP
rs78397567	103	dbSNP
rs564213739	105	dbSNP
rs1333571786	113	dbSNP
rs781115269	115	dbSNP
rs1467014445	116	dbSNP
rs1400830594	120	dbSNP
rs997096593	122	dbSNP
rs1471810256	125	dbSNP
rs1370109279	130	dbSNP
rs1419165016	132	dbSNP
rs1417930766	141	dbSNP
rs531682168	142	dbSNP
rs188833941	143	dbSNP
rs1393000298	146	dbSNP
rs9867	147	dbSNP
rs968977514	154	dbSNP
rs1000171764	156	dbSNP
rs1272989699	156	dbSNP
rs1031685946	158	dbSNP
rs956071111	167	dbSNP
rs1238462147	172	dbSNP
rs1440210878	174	dbSNP
rs993354928	187	dbSNP
rs1281506188	189	dbSNP
rs1370527030	191	dbSNP
rs764450095	193	dbSNP
rs1403337584	195	dbSNP
rs970317638	200	dbSNP
rs1163727157	203	dbSNP
rs979976553	205	dbSNP
rs557177989	216	dbSNP
rs56916727	216	dbSNP
rs930569361	221	dbSNP
rs1439994401	227	dbSNP
rs1251973857	230	dbSNP
rs1197206602	232	dbSNP
rs1453644910	234	dbSNP
rs1268694254	236	dbSNP
rs983038572	237	dbSNP
rs1352112214	238	dbSNP
rs528962084	239	dbSNP
rs1273534503	248	dbSNP
rs1240953275	253	dbSNP
rs1347451302	254	dbSNP
rs907584734	256	dbSNP
rs1332554127	257	dbSNP
rs113920041	274	dbSNP
rs547196622	275	dbSNP
rs1381618547	277	dbSNP
rs565624661	279	dbSNP
rs539053472	284	dbSNP
rs1234310155	294	dbSNP
rs1470193249	302	dbSNP
rs1358540571	306	dbSNP
rs1159993035	309	dbSNP
rs557782269	310	dbSNP
rs1040557608	312	dbSNP
rs1416301231	318	dbSNP
rs901322539	321	dbSNP
rs1478794485	327	dbSNP
rs932788867	338	dbSNP
rs547034345	346	dbSNP
rs1192918702	353	dbSNP
rs1049940697	360	dbSNP
rs1265908715	364	dbSNP
rs1217448034	365	dbSNP
rs1476450444	378	dbSNP
rs1166292081	386	dbSNP
rs1485360818	392	dbSNP
rs904744200	394	dbSNP
rs1423289394	403	dbSNP
rs1000453720	406	dbSNP
rs1275290825	407	dbSNP
rs114916240	413	dbSNP
rs1355382006	415	dbSNP
rs1299917193	418	dbSNP
rs1400104308	419	dbSNP
rs1434806907	434	dbSNP
rs1447365491	435	dbSNP
rs11550665	439	dbSNP
rs1415883468	443	dbSNP
rs140641463	448	dbSNP
rs1014320938	458	dbSNP
rs1477005729	466	dbSNP
rs1426452841	468	dbSNP
rs201598775	471	dbSNP
rs1234986111	476	dbSNP
rs1293841211	480	dbSNP
rs1338487588	482	dbSNP
rs1212656031	488	dbSNP
rs145810370	493	dbSNP
rs1438095376	497	dbSNP
rs1209749693	500	dbSNP
rs1254689944	501	dbSNP
rs1486375467	506	dbSNP
rs1189254825	507	dbSNP
rs1197784941	509	dbSNP
rs1219214952	509	dbSNP
rs1279833665	509	dbSNP
rs1315779670	509	dbSNP
rs780575361	509	dbSNP
rs565426179	511	dbSNP
rs1281978307	521	dbSNP
rs1340699455	523	dbSNP
rs1474615596	523	dbSNP
rs1170059739	533	dbSNP
rs970178093	533	dbSNP
rs1420702741	534	dbSNP
rs1037851251	538	dbSNP
rs542669188	550	dbSNP
rs1183685609	553	dbSNP
rs1473128972	581	dbSNP
rs1232543244	586	dbSNP
rs751122469	590	dbSNP
rs1377289847	598	dbSNP
rs1459233229	602	dbSNP
rs1415535600	604	dbSNP
rs1199021107	609	dbSNP
rs1027446964	611	dbSNP
rs748907037	616	dbSNP
rs878966575	617	dbSNP
rs919433262	619	dbSNP
rs148106079	623	dbSNP
rs983365667	624	dbSNP
rs1379206203	634	dbSNP
rs907536550	641	dbSNP
rs1444180757	642	dbSNP
rs1378652695	646	dbSNP
rs944395281	650	dbSNP
rs975792256	652	dbSNP
rs1348652248	653	dbSNP
rs545068050	654	dbSNP
rs7218634	659	dbSNP
rs192619120	660	dbSNP
rs1156925544	664	dbSNP
rs1441837233	666	dbSNP
rs931760385	670	dbSNP
rs1277822871	671	dbSNP
rs1346623901	672	dbSNP
rs1488010514	672	dbSNP
rs757458208	672	dbSNP
rs1349416675	677	dbSNP
rs1284775547	679	dbSNP
rs1237312478	680	dbSNP
rs904734112	684	dbSNP
rs1309448617	685	dbSNP
rs1060618	687	dbSNP
rs374285747	687	dbSNP
rs1053388453	688	dbSNP
rs1284159646	689	dbSNP
rs1445731491	691	dbSNP
rs1296432665	697	dbSNP
rs892069384	698	dbSNP
rs1421516739	699	dbSNP
rs1381180394	704	dbSNP
rs1195986752	705	dbSNP
rs1014640515	708	dbSNP
rs1024317498	709	dbSNP
rs183704519	711	dbSNP
rs1262314713	712	dbSNP
rs1001665217	719	dbSNP
rs1488962531	722	dbSNP
rs1286315374	730	dbSNP
rs1232128852	735	dbSNP
rs1027436933	748	dbSNP
rs561837141	749	dbSNP
rs1220117970	752	dbSNP
rs1340453646	756	dbSNP
rs541369304	763	dbSNP
rs1361300595	764	dbSNP
rs1014771797	768	dbSNP
rs188465642	784	dbSNP
rs1464795412	785	dbSNP
rs966002696	786	dbSNP
rs1177986355	789	dbSNP
rs1435383279	792	dbSNP
rs976122946	796	dbSNP
rs565635594	803	dbSNP
rs533076334	804	dbSNP
rs1478744161	809	dbSNP
rs191750845	810	dbSNP
rs1199374242	812	dbSNP
rs184810588	817	dbSNP
rs1257321606	823	dbSNP
rs979211815	827	dbSNP
rs150610699	828	dbSNP
rs1256533278	830	dbSNP
rs1221050939	831	dbSNP
rs936129412	832	dbSNP
rs533210726	837	dbSNP
rs564266140	837	dbSNP
rs1046143074	846	dbSNP
rs905896830	846	dbSNP
rs950332343	846	dbSNP
rs1001559434	852	dbSNP
rs1049159131	863	dbSNP
rs777720952	867	dbSNP
rs1271600991	878	dbSNP
rs1186228892	879	dbSNP
rs1004644680	880	dbSNP
rs1257858709	881	dbSNP
rs139356758	885	dbSNP
rs1183869407	886	dbSNP
rs1200902355	886	dbSNP
rs1319235597	886	dbSNP
rs878882322	886	dbSNP
rs1265306482	896	dbSNP
rs1345443693	898	dbSNP
rs1014719446	901	dbSNP
rs1234594089	901	dbSNP
rs1259584786	902	dbSNP
rs1347933496	903	dbSNP
rs1207354124	905	dbSNP
rs1374936066	906	dbSNP
rs1285649648	907	dbSNP
rs372481485	908	dbSNP
rs966318260	911	dbSNP
rs534892978	913	dbSNP
rs997484766	914	dbSNP
rs1029070124	917	dbSNP
rs1456305383	918	dbSNP
rs1181399561	924	dbSNP
rs1219570157	926	dbSNP
rs553576225	931	dbSNP
rs1362075156	948	dbSNP
rs1235919780	955	dbSNP
rs1180907379	966	dbSNP
rs1471232339	966	dbSNP
rs140924028	969	dbSNP
rs1208630963	970	dbSNP
rs578016055	975	dbSNP
rs979108957	982	dbSNP
rs924993519	984	dbSNP
rs1385629359	987	dbSNP
rs1351786652	988	dbSNP
rs956448736	998	dbSNP
rs753701114	1004	dbSNP
rs543499120	1005	dbSNP
rs539155612	1006	dbSNP
rs1322609495	1007	dbSNP
rs1385072473	1012	dbSNP
rs1441106822	1022	dbSNP
rs1305874713	1024	dbSNP
rs1392783498	1032	dbSNP
rs988938948	1041	dbSNP
rs1418492784	1045	dbSNP
rs190061572	1047	dbSNP
rs138745604	1049	dbSNP
rs1377462557	1056	dbSNP
rs1334819714	1062	dbSNP
rs1232025647	1063	dbSNP
rs950339494	1064	dbSNP
rs1275395313	1069	dbSNP
rs1046008997	1070	dbSNP
rs1288223473	1070	dbSNP
rs1453847841	1070	dbSNP
rs750489113	1070	dbSNP
rs927268896	1071	dbSNP
rs1274092962	1080	dbSNP
rs1230722162	1081	dbSNP
rs1347329560	1082	dbSNP
rs937320431	1083	dbSNP
rs1248764489	1085	dbSNP
rs1358131616	1086	dbSNP
rs1299463767	1087	dbSNP
rs1400977199	1087	dbSNP
rs1400998950	1087	dbSNP
rs1171189578	1088	dbSNP
rs1430637573	1090	dbSNP
rs1193632810	1092	dbSNP
rs56688826	1095	dbSNP
rs1265510473	1096	dbSNP
rs887829414	1099	dbSNP
rs1417273228	1101	dbSNP
rs1266085689	1104	dbSNP
rs1276688664	1107	dbSNP
rs1004927780	1114	dbSNP
rs1474814951	1121	dbSNP
rs1325362143	1124	dbSNP
rs1036604146	1130	dbSNP
rs1217981753	1132	dbSNP
rs1338331726	1133	dbSNP
rs1430736612	1138	dbSNP
rs1339538971	1140	dbSNP
rs1331735588	1142	dbSNP
rs901711746	1144	dbSNP
rs757282808	1151	dbSNP
rs1419691245	1157	dbSNP
rs143728649	1159	dbSNP
rs1464570859	1162	dbSNP
rs1489539513	1164	dbSNP
rs1028884958	1168	dbSNP
rs1187193197	1175	dbSNP
rs1472488455	1176	dbSNP
rs1235971002	1179	dbSNP
rs1189937960	1191	dbSNP
rs1461919449	1201	dbSNP
rs1243601230	1203	dbSNP
rs1393934225	1204	dbSNP
rs1197766726	1205	dbSNP
rs889043632	1206	dbSNP
rs1274978288	1207	dbSNP
rs187250475	1217	dbSNP
rs1355097179	1218	dbSNP
rs1281890347	1220	dbSNP
rs1328892039	1220	dbSNP
rs1454305221	1223	dbSNP
rs1383051223	1226	dbSNP
rs1000497727	1235	dbSNP
rs1331111839	1235	dbSNP
rs1354306090	1236	dbSNP
rs1231926629	1245	dbSNP
rs1295715228	1246	dbSNP
rs1356826265	1246	dbSNP
rs1032012137	1251	dbSNP
rs113216584	1251	dbSNP
rs1171679521	1251	dbSNP
rs564015544	1251	dbSNP
rs59031980	1251	dbSNP
rs879199057	1251	dbSNP
rs540847753	1252	dbSNP
rs147206852	1260	dbSNP
rs1020858124	1261	dbSNP
rs1052471980	1263	dbSNP
rs532854560	1264	dbSNP
rs772172687	1266	dbSNP
rs1308030084	1268	dbSNP
rs1256811744	1282	dbSNP
rs1484742041	1289	dbSNP
rs1376052584	1297	dbSNP
rs1185700109	1300	dbSNP
rs1259617209	1307	dbSNP
rs1436481857	1307	dbSNP
rs140620135	1309	dbSNP
rs1169545874	1313	dbSNP
rs1348635329	1314	dbSNP
rs1305047350	1317	dbSNP
rs189271279	1318	dbSNP
rs1425334260	1319	dbSNP
rs780187618	1332	dbSNP
rs1157134406	1336	dbSNP
rs1441743513	1340	dbSNP
rs1463163983	1364	dbSNP
rs35722010	1392	dbSNP
rs1168843446	1393	dbSNP
rs937603375	1394	dbSNP
rs562900450	1406	dbSNP
rs1244838506	1413	dbSNP
rs116221117	1419	dbSNP
rs868184803	1420	dbSNP
rs1315315967	1422	dbSNP
rs1284664084	1423	dbSNP
rs1356712295	1425	dbSNP
rs1214055003	1426	dbSNP
rs867154115	1433	dbSNP
rs1308233372	1434	dbSNP
rs1218950385	1435	dbSNP
rs1366119301	1438	dbSNP
rs1382177215	1439	dbSNP
rs1360026795	1440	dbSNP
rs1293828348	1444	dbSNP
rs566852908	1452	dbSNP
rs1455589020	1465	dbSNP
rs901656685	1467	dbSNP
rs933138731	1468	dbSNP
rs1413663495	1474	dbSNP
rs1427144320	1493	dbSNP
rs1328564885	1511	dbSNP
rs1480706827	1515	dbSNP
rs1050691520	1523	dbSNP
rs768995853	1542	dbSNP
rs888993629	1556	dbSNP
rs548606574	1564	dbSNP
rs777120706	1567	dbSNP
rs1260882685	1578	dbSNP
rs763913632	1592	dbSNP
rs1279957927	1599	dbSNP
rs1224732851	1620	dbSNP
rs1032002532	1630	dbSNP
rs1276394804	1633	dbSNP
rs762197795	1637	dbSNP
rs1009711887	1653	dbSNP
rs181981877	1654	dbSNP
rs879025765	1655	dbSNP
rs535358876	1660	dbSNP
rs1470296604	1675	dbSNP
rs1422762966	1677	dbSNP
rs1282358291	1705	dbSNP
rs1167711901	1708	dbSNP
rs1429734331	1712	dbSNP
rs534159448	1718	dbSNP
rs1483509981	1723	dbSNP
rs59999068	1727	dbSNP
rs1259322312	1728	dbSNP
rs1245417427	1731	dbSNP
rs563250660	1743	dbSNP
rs1488582313	1749	dbSNP
rs958947132	1750	dbSNP
rs1188800737	1752	dbSNP
rs1229736670	1758	dbSNP
rs773613131	1762	dbSNP
rs571828071	1764	dbSNP
rs1394580538	1779	dbSNP
rs1432301474	1782	dbSNP
rs1385248560	1786	dbSNP
rs1338473661	1788	dbSNP
rs940720689	1789	dbSNP
rs754022713	1792	dbSNP
rs1296430005	1796	dbSNP
rs1463433029	1803	dbSNP
rs1373212579	1808	dbSNP
rs1174917565	1811	dbSNP
rs144561041	1813	dbSNP
rs933401938	1822	dbSNP
rs557495602	1824	dbSNP
rs888985241	1828	dbSNP
rs575669588	1829	dbSNP
rs1453589090	1833	dbSNP
rs936557865	1836	dbSNP
rs1364503075	1841	dbSNP
rs1436369778	1842	dbSNP
rs759075161	1847	dbSNP
rs1053726150	1850	dbSNP
rs1242624968	1852	dbSNP
rs1302918712	1865	dbSNP
rs892406364	1870	dbSNP
rs1009207472	1873	dbSNP
rs185076341	1896	dbSNP
rs1393124911	1899	dbSNP
rs535975161	1900	dbSNP
rs189739729	1901	dbSNP
rs1002402247	1908	dbSNP
rs1367073436	1909	dbSNP
rs1163886093	1922	dbSNP
rs1438664874	1924	dbSNP
rs1316419811	1925	dbSNP
rs115380329	1928	dbSNP
rs866473286	1929	dbSNP
rs183054267	1932	dbSNP
rs1209173914	1933	dbSNP
rs1220394453	1943	dbSNP
rs1490847449	1946	dbSNP
rs1016449599	1953	dbSNP
rs962275321	1960	dbSNP
rs1252169862	1962	dbSNP
rs1348792063	1964	dbSNP
rs1452137299	1972	dbSNP
rs972049758	1996	dbSNP
rs186453776	1997	dbSNP
rs1418058058	1998	dbSNP
rs1403000352	2004	dbSNP
rs1346893477	2005	dbSNP
rs954808937	2016	dbSNP
rs1418776532	2019	dbSNP
rs1382256266	2021	dbSNP
rs1160660660	2022	dbSNP
rs1454596428	2023	dbSNP
rs763790134	2026	dbSNP
rs1377580606	2036	dbSNP
rs986648537	2053	dbSNP
rs1481701966	2055	dbSNP
rs1269763216	2058	dbSNP
rs1157555403	2059	dbSNP
rs577769251	2062	dbSNP
rs1347509392	2064	dbSNP
rs910368964	2071	dbSNP
rs1286554741	2075	dbSNP
rs1206692930	2077	dbSNP
rs1351190340	2079	dbSNP
rs1455877535	2091	dbSNP
rs936465934	2102	dbSNP
rs1221685409	2114	dbSNP
rs1325580180	2124	dbSNP
rs1053632586	2128	dbSNP
rs148424031	2132	dbSNP
rs1325595895	2142	dbSNP
rs1319829283	2143	dbSNP
rs1382417274	2155	dbSNP
rs563032862	2164	dbSNP
rs1046063039	2165	dbSNP
rs1430526290	2166	dbSNP
rs1294355680	2169	dbSNP
rs906228120	2172	dbSNP
rs191686601	2174	dbSNP
rs1054827855	2176	dbSNP
rs888217496	2179	dbSNP
rs1442059803	2185	dbSNP
rs1242363179	2186	dbSNP
rs757276532	2189	dbSNP
rs1325600224	2192	dbSNP
rs1228960820	2194	dbSNP
rs1263642839	2201	dbSNP
rs757027790	2207	dbSNP
rs778872422	2214	dbSNP
rs1271401704	2217	dbSNP
rs1227776553	2223	dbSNP
rs746546249	2228	dbSNP
rs1030318736	2232	dbSNP
rs1246988621	2233	dbSNP
rs1480010043	2234	dbSNP
rs1407500829	2235	dbSNP
rs1175025771	2237	dbSNP
rs1409559774	2250	dbSNP
rs1473183235	2263	dbSNP
rs548724181	2266	dbSNP
rs1416069863	2272	dbSNP
rs986148264	2275	dbSNP
rs1463398521	2276	dbSNP
rs1383551086	2285	dbSNP
rs548550420	2285	dbSNP
rs796397737	2286	dbSNP
rs910610093	2286	dbSNP
rs958117927	2293	dbSNP
rs12938646	2299	dbSNP
rs1324413234	2300	dbSNP
rs1354215807	2303	dbSNP
rs1274512646	2307	dbSNP
rs989273989	2307	dbSNP
rs1195800279	2308	dbSNP
rs913776949	2318	dbSNP
rs1440318165	2320	dbSNP
rs945306226	2321	dbSNP
rs1351185803	2326	dbSNP
rs1279331050	2330	dbSNP
rs758418688	2331	dbSNP
rs1356730618	2341	dbSNP
rs1329629734	2351	dbSNP
rs1424054677	2356	dbSNP
rs1410294490	2360	dbSNP
rs780167149	2361	dbSNP
rs560587180	2365	dbSNP
rs528747545	2366	dbSNP
rs1332403620	2377	dbSNP
rs565699342	2383	dbSNP
rs1176351248	2385	dbSNP
rs1468535649	2398	dbSNP
rs937653635	2407	dbSNP
rs1204628326	2412	dbSNP
rs1490057642	2422	dbSNP
rs1054735660	2429	dbSNP
rs1224338491	2433	dbSNP
rs1359690381	2438	dbSNP
rs1290124998	2441	dbSNP
rs547296082	2442	dbSNP
rs571704494	2443	dbSNP
rs941150714	2449	dbSNP
rs1483106105	2455	dbSNP
rs1343766994	2456	dbSNP
rs1187846756	2457	dbSNP
rs1300404183	2462	dbSNP
rs1037824232	2464	dbSNP
rs1256105044	2476	dbSNP
rs1425547103	2478	dbSNP
rs1476377791	2485	dbSNP
rs1344761043	2486	dbSNP
rs898016032	2490	dbSNP
rs535783539	2491	dbSNP
rs1030977648	2492	dbSNP
rs1419286991	2493	dbSNP
rs1266220004	2494	dbSNP
rs1408356484	2498	dbSNP
rs1490413240	2499	dbSNP
rs890725690	2502	dbSNP
rs1007531963	2503	dbSNP
rs1319161096	2508	dbSNP
rs1017620896	2523	dbSNP
rs1007550735	2529	dbSNP
rs142582561	2530	dbSNP
rs551703938	2534	dbSNP
rs556875955	2539	dbSNP
rs1312163478	2540	dbSNP
rs1361550349	2541	dbSNP
rs781238224	2544	dbSNP
rs1353543178	2545	dbSNP
rs1450159514	2549	dbSNP
rs569352422	2550	dbSNP
rs1361019011	2553	dbSNP
rs1469240855	2560	dbSNP
rs1212379560	2561	dbSNP
rs1178006314	2568	dbSNP
rs1418142876	2571	dbSNP
rs369093943	2577	dbSNP
rs1486642287	2578	dbSNP
rs981988491	2579	dbSNP
rs927844283	2580	dbSNP
rs1460394052	2585	dbSNP
rs554967507	2587	dbSNP
rs76638724	2588	dbSNP
rs1224636106	2598	dbSNP
rs990441045	2603	dbSNP
rs748494900	2606	dbSNP
rs755916224	2607	dbSNP
rs1444593216	2621	dbSNP
rs909584967	2622	dbSNP
rs941100252	2630	dbSNP
rs1188858576	2631	dbSNP
rs1241828999	2636	dbSNP
rs1320986121	2642	dbSNP
rs1323735160	2645	dbSNP
rs1451594022	2646	dbSNP
rs1403846722	2648	dbSNP
rs1036764978	2650	dbSNP
rs1474663055	2651	dbSNP
rs1188497004	2652	dbSNP
rs896920013	2655	dbSNP
rs150929996	2658	dbSNP
rs1434164772	2675	dbSNP
rs1171797395	2684	dbSNP
rs1377387676	2687	dbSNP
rs1390358024	2694	dbSNP
rs1051945564	2695	dbSNP
rs773701541	2696	dbSNP
rs1245317337	2699	dbSNP
rs1201597924	2700	dbSNP
rs140750382	2701	dbSNP
rs553239348	2702	dbSNP
rs1017611168	2704	dbSNP
rs1334762882	2706	dbSNP
rs10603203	2720	dbSNP
rs759516351	2720	dbSNP
rs1010979696	2721	dbSNP
rs1428462425	2722	dbSNP
rs1380364656	2725	dbSNP
rs773879550	2729	dbSNP
rs1021435486	2735	dbSNP
rs1395617622	2736	dbSNP
rs966834874	2744	dbSNP
rs1370609805	2745	dbSNP
rs1365410247	2747	dbSNP
rs1233150964	2749	dbSNP
rs1162577103	2751	dbSNP
rs1300541347	2752	dbSNP
rs149585017	2755	dbSNP
rs1387537561	2759	dbSNP
rs1201512684	2763	dbSNP
rs1419008254	2767	dbSNP
rs1248987568	2776	dbSNP
rs771691789	2778	dbSNP
rs982321529	2781	dbSNP
rs1291094166	2791	dbSNP
rs1220628773	2794	dbSNP
rs1361849826	2797	dbSNP
rs775202896	2798	dbSNP
rs1245166116	2799	dbSNP
rs1445603525	2803	dbSNP
rs959272329	2804	dbSNP
rs116793488	2805	dbSNP
rs544798347	2816	dbSNP
rs760370589	2824	dbSNP
rs1422375634	2825	dbSNP
rs941005650	2835	dbSNP
rs183360874	2838	dbSNP
rs1164228720	2845	dbSNP
rs1453437066	2855	dbSNP
rs745340607	2863	dbSNP
rs1362402883	2866	dbSNP
rs1478430511	2870	dbSNP
rs763853274	2871	dbSNP
rs972438534	2874	dbSNP
rs918297295	2878	dbSNP
rs1407221068	2879	dbSNP
rs933759052	2882	dbSNP
rs1197294770	2883	dbSNP
rs1398903649	2885	dbSNP
rs1322250696	2887	dbSNP
rs879113158	2894	dbSNP
rs1389108002	2900	dbSNP
rs1439631406	2904	dbSNP
rs3751921	2921	dbSNP
rs912098940	2938	dbSNP
rs866678567	2942	dbSNP
rs1329712824	2943	dbSNP
rs1282092890	2951	dbSNP
rs143174011	2954	dbSNP
rs1233387089	2955	dbSNP
rs764959798	2959	dbSNP
rs1039328656	2962	dbSNP
rs560521467	2967	dbSNP
rs894082655	2968	dbSNP
rs553074762	2971	dbSNP
rs528094240	2973	dbSNP
rs1174413113	2975	dbSNP
rs749614240	2986	dbSNP
rs1378240476	2997	dbSNP
rs750351716	2998	dbSNP
rs1192824851	3009	dbSNP
rs1445478020	3016	dbSNP
rs1230809001	3022	dbSNP
rs1042401718	3026	dbSNP
rs1210290542	3031	dbSNP
rs1465313422	3035	dbSNP
rs902590389	3036	dbSNP
rs540531055	3041	dbSNP
rs1346561548	3042	dbSNP
rs1274923910	3047	dbSNP
rs1226312930	3051	dbSNP
rs1324265291	3054	dbSNP
rs761172675	3059	dbSNP
rs188767026	3060	dbSNP
rs1452223320	3063	dbSNP
rs766416513	3066	dbSNP
rs561732452	3068	dbSNP
rs1403069926	3081	dbSNP
rs1012052783	3082	dbSNP
rs1471529968	3083	dbSNP
rs532740076	3089	dbSNP
rs1374960529	3093	dbSNP
rs1161300382	3095	dbSNP
rs1016777002	3096	dbSNP
rs1412418410	3107	dbSNP
rs1201771893	3108	dbSNP
rs1444053859	3109	dbSNP
rs1278733358	3119	dbSNP
rs1194672138	3123	dbSNP
rs1047616	3128	dbSNP
rs1228638750	3130	dbSNP
rs1382585050	3131	dbSNP
rs1313351379	3132	dbSNP
rs1162302406	3133	dbSNP
rs1341520798	3140	dbSNP
rs972770878	3142	dbSNP
rs918298347	3157	dbSNP
rs569488018	3158	dbSNP
rs1398697721	3162	dbSNP
rs955292485	3163	dbSNP
rs1424258456	3179	dbSNP
rs1384444720	3188	dbSNP
rs1181464502	3193	dbSNP
rs1473741157	3195	dbSNP
rs1333484591	3197	dbSNP
rs1180501032	3207	dbSNP
rs986597206	3208	dbSNP
rs530189325	3218	dbSNP
rs1289593627	3223	dbSNP
rs1358208448	3227	dbSNP
rs1290049184	3228	dbSNP
rs1334607321	3228	dbSNP
rs139946690	3229	dbSNP
rs1231888938	3236	dbSNP
rs558088699	3242	dbSNP
rs1267434734	3247	dbSNP
rs1380558373	3250	dbSNP
rs1357268040	3254	dbSNP
rs1195446594	3268	dbSNP
rs1440609020	3273	dbSNP
rs544934290	3282	dbSNP
rs1248436755	3299	dbSNP
rs139129682	3320	dbSNP
rs71687011	3320	dbSNP
rs1162472550	3322	dbSNP
rs1039234519	3323	dbSNP
rs1184246836	3324	dbSNP
rs1252497717	3334	dbSNP
rs543660045	3337	dbSNP
rs1468519626	3352	dbSNP
rs1185077189	3358	dbSNP
rs1253358171	3360	dbSNP
rs1182181418	3364	dbSNP
rs1370013151	3370	dbSNP
rs369913033	3381	dbSNP
rs563367978	3382	dbSNP
rs946994569	3396	dbSNP
rs1166981269	3398	dbSNP
rs1284003256	3402	dbSNP
rs1222621235	3403	dbSNP
rs573634708	3412	dbSNP
rs1431174493	3414	dbSNP
rs1222942552	3418	dbSNP
rs1343899741	3420	dbSNP
rs767042785	3420	dbSNP
rs1437447163	3422	dbSNP
rs566710348	3433	dbSNP
rs1317299466	3438	dbSNP
rs1455579102	3444	dbSNP
rs1414040428	3447	dbSNP
rs1159285028	3462	dbSNP
rs748321996	3470	dbSNP
rs1479852188	3471	dbSNP
rs1426549636	3472	dbSNP
rs1192635335	3474	dbSNP
rs369886669	3475	dbSNP
rs1315196246	3476	dbSNP
rs1214010786	3481	dbSNP
rs1341456595	3482	dbSNP
rs1226949757	3486	dbSNP
rs1249900446	3489	dbSNP
rs1344366040	3494	dbSNP
rs1056527875	3495	dbSNP
rs558725525	3497	dbSNP
rs1220044082	3502	dbSNP
rs1012000487	3503	dbSNP
rs756443071	3505	dbSNP
rs1432570192	3507	dbSNP
rs1390534576	3509	dbSNP
rs1321184160	3511	dbSNP
rs191023431	3536	dbSNP
rs559081700	3537	dbSNP
rs1356989804	3554	dbSNP
rs962599609	3557	dbSNP

- 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.