ID	Duplex structure	Position	Score	MFE
1	miRNA 3' aacaGGUGAAGAAGGACG-GGAc 5' |||| :|| |||| ||| Target 5' gtagCCACACTTTGCTGCTCCTg 3'	173 - 195	130.00	-21.10
2	miRNA 3' aacaggugaagaagGACGGGAc 5' ||||:|| Target 5' gccccggatccgggCTGCTCTc 3'	32 - 53	124.00	-14.90
3	miRNA 3' aacaggugaagaagGACGGGAc 5' |||||:| Target 5' ccgagaggcacacaCTGCCTTc 3'	813 - 834	124.00	-10.10

Mutant ID	Mutant Position	Mutant Source
COSN26998603	15	COSMIC
COSN31500898	35	COSMIC
COSN31534558	39	COSMIC
COSN30494572	71	COSMIC
COSN26998604	77	COSMIC
COSN31597882	96	COSMIC
COSN1730551	121	COSMIC
COSN30132382	124	COSMIC
COSN31511556	134	COSMIC
COSN23172482	604	COSMIC
COSN9324766	1065	COSMIC
COSN25176143	2069	COSMIC
COSN6549579	2127	COSMIC
COSN31596438	2525	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs749976361	2	dbSNP
rs1016386714	3	dbSNP
rs758373361	5	dbSNP
rs1463875758	6	dbSNP
rs780146376	8	dbSNP
rs1271380336	9	dbSNP
rs746744924	12	dbSNP
rs1480876568	15	dbSNP
rs1312129004	16	dbSNP
rs754791215	18	dbSNP
rs1371340376	19	dbSNP
rs954959409	27	dbSNP
rs780919473	36	dbSNP
rs551172891	37	dbSNP
rs193292443	38	dbSNP
rs773289409	42	dbSNP
rs749397566	43	dbSNP
rs74971146	44	dbSNP
rs369271117	47	dbSNP
rs143573501	49	dbSNP
rs151010010	50	dbSNP
rs1170356497	55	dbSNP
rs1429889201	57	dbSNP
rs925751143	58	dbSNP
rs934479027	59	dbSNP
rs1052972314	63	dbSNP
rs1256343995	70	dbSNP
rs544493456	72	dbSNP
rs1342622243	73	dbSNP
rs949978032	80	dbSNP
rs1204246689	84	dbSNP
rs184257817	96	dbSNP
rs1207887047	98	dbSNP
rs531010426	103	dbSNP
rs1273989084	109	dbSNP
rs1183628632	116	dbSNP
rs1323733737	119	dbSNP
rs545186233	124	dbSNP
rs188180262	125	dbSNP
rs1376671671	129	dbSNP
rs907773131	130	dbSNP
rs140885589	131	dbSNP
rs191495764	134	dbSNP
rs1423396801	140	dbSNP
rs1161919606	148	dbSNP
rs973091010	150	dbSNP
rs552029953	151	dbSNP
rs564093563	154	dbSNP
rs1368710864	156	dbSNP
rs1163610173	157	dbSNP
rs150077642	165	dbSNP
rs184008004	166	dbSNP
rs931740179	169	dbSNP
rs1185041894	170	dbSNP
rs333646	175	dbSNP
rs912747797	181	dbSNP
rs1251639021	191	dbSNP
rs1194178638	194	dbSNP
rs994047668	195	dbSNP
rs775132437	196	dbSNP
rs1026488855	199	dbSNP
rs1244293359	200	dbSNP
rs1332495005	205	dbSNP
rs1289998828	207	dbSNP
rs1450841675	208	dbSNP
rs954908849	209	dbSNP
rs1302877064	210	dbSNP
rs1009146100	213	dbSNP
rs1388063664	215	dbSNP
rs1390792182	224	dbSNP
rs1292659007	227	dbSNP
rs536550023	228	dbSNP
rs944179534	252	dbSNP
rs188692979	253	dbSNP
rs925666905	258	dbSNP
rs1180255767	260	dbSNP
rs1435019430	272	dbSNP
rs1268140733	273	dbSNP
rs35016834	275	dbSNP
rs902743353	275	dbSNP
rs34996885	279	dbSNP
rs35128921	282	dbSNP
rs879373795	289	dbSNP
rs1209255372	290	dbSNP
rs566993699	309	dbSNP
rs1467315209	313	dbSNP
rs138680008	319	dbSNP
rs1209148494	330	dbSNP
rs1227372032	336	dbSNP
rs1053801886	337	dbSNP
rs1277747156	338	dbSNP
rs1235326543	341	dbSNP
rs895111125	344	dbSNP
rs763598511	356	dbSNP
rs1025035993	357	dbSNP
rs927242178	359	dbSNP
rs937980959	360	dbSNP
rs1388321721	369	dbSNP
rs1210740053	382	dbSNP
rs1037724658	385	dbSNP
rs776149390	386	dbSNP
rs114553150	396	dbSNP
rs993605421	401	dbSNP
rs1047877424	402	dbSNP
rs1015296167	405	dbSNP
rs890626395	408	dbSNP
rs765748037	411	dbSNP
rs963317594	412	dbSNP
rs973694372	414	dbSNP
rs1255296067	416	dbSNP
rs1231466045	417	dbSNP
rs1297931746	426	dbSNP
rs921604674	438	dbSNP
rs1188269325	439	dbSNP
rs1316687736	440	dbSNP
rs1417851300	442	dbSNP
rs1258013736	444	dbSNP
rs1032683110	449	dbSNP
rs114640667	450	dbSNP
rs761643423	455	dbSNP
rs1172483879	456	dbSNP
rs146952600	458	dbSNP
rs1392099836	459	dbSNP
rs911627529	459	dbSNP
rs1449110748	462	dbSNP
rs1240512230	464	dbSNP
rs944231711	471	dbSNP
rs917017832	475	dbSNP
rs1042556230	476	dbSNP
rs1359151791	478	dbSNP
rs759044594	479	dbSNP
rs1467767400	482	dbSNP
rs1322032236	487	dbSNP
rs1388858316	490	dbSNP
rs199909189	492	dbSNP
rs556607964	492	dbSNP
rs979918295	492	dbSNP
rs1433948700	493	dbSNP
rs1450691021	502	dbSNP
rs72812079	502	dbSNP
rs542195351	503	dbSNP
rs1054424905	509	dbSNP
rs201100645	513	dbSNP
rs1413456326	514	dbSNP
rs895163634	516	dbSNP
rs73978317	518	dbSNP
rs1300499409	520	dbSNP
rs1012241988	523	dbSNP
rs146153275	524	dbSNP
rs560287949	526	dbSNP
rs543300366	527	dbSNP
rs2884904	528	dbSNP
rs138050930	529	dbSNP
rs1473028204	536	dbSNP
rs3191897	537	dbSNP
rs3191899	538	dbSNP
rs777075672	545	dbSNP
rs773161316	553	dbSNP
rs1047825301	557	dbSNP
rs1005158356	559	dbSNP
rs1270116210	560	dbSNP
rs1252398790	563	dbSNP
rs1465480733	566	dbSNP
rs1208349129	573	dbSNP
rs1014767774	582	dbSNP
rs1435543329	585	dbSNP
rs890575790	592	dbSNP
rs1228528702	595	dbSNP
rs1357560125	599	dbSNP
rs898954544	600	dbSNP
rs994781841	601	dbSNP
rs1028837165	602	dbSNP
rs563999283	603	dbSNP
rs1479199315	604	dbSNP
rs1309119734	610	dbSNP
rs1192202037	619	dbSNP
rs1425040889	623	dbSNP
rs1352809818	627	dbSNP
rs1479757110	633	dbSNP
rs1039239049	645	dbSNP
rs1388741010	646	dbSNP
rs1162534038	655	dbSNP
rs9737	656	dbSNP
rs987077732	657	dbSNP
rs1018686903	658	dbSNP
rs1468213558	661	dbSNP
rs1247930952	662	dbSNP
rs1221582990	664	dbSNP
rs1251699997	668	dbSNP
rs752886197	669	dbSNP
rs1212238046	680	dbSNP
rs333645	681	dbSNP
rs528826456	685	dbSNP
rs1223711956	693	dbSNP
rs1365343656	697	dbSNP
rs1276705449	701	dbSNP
rs1009884222	704	dbSNP
rs1370559470	709	dbSNP
rs1023979437	713	dbSNP
rs1290218802	713	dbSNP
rs370619509	713	dbSNP
rs538613429	719	dbSNP
rs971138387	720	dbSNP
rs1158367288	722	dbSNP
rs1329947712	729	dbSNP
rs1227922562	735	dbSNP
rs149402951	739	dbSNP
rs1427092282	740	dbSNP
rs1191294711	742	dbSNP
rs1250809787	752	dbSNP
rs745657009	752	dbSNP
rs187149469	753	dbSNP
rs989778530	769	dbSNP
rs867022924	771	dbSNP
rs916817553	785	dbSNP
rs1215446792	790	dbSNP
rs974016017	793	dbSNP
rs948076046	797	dbSNP
rs1246525679	798	dbSNP
rs1281299119	799	dbSNP
rs1489984926	801	dbSNP
rs1219938875	802	dbSNP
rs1370297769	807	dbSNP
rs772054319	811	dbSNP
rs3867592	812	dbSNP
rs867456347	813	dbSNP
rs906498609	815	dbSNP
rs1471976648	816	dbSNP
rs190330955	820	dbSNP
rs1176680093	825	dbSNP
rs1433607647	826	dbSNP
rs1170156447	827	dbSNP
rs1036829964	828	dbSNP
rs1039188192	831	dbSNP
rs1186331191	837	dbSNP
rs1485084430	840	dbSNP
rs899010651	841	dbSNP
rs936187694	848	dbSNP
rs144787394	853	dbSNP
rs1028889297	856	dbSNP
rs558570420	858	dbSNP
rs1009833084	859	dbSNP
rs527851118	860	dbSNP
rs1018570261	867	dbSNP
rs1295059750	873	dbSNP
rs552293213	885	dbSNP
rs1381035092	888	dbSNP
rs906926484	891	dbSNP
rs1001232458	895	dbSNP
rs1349864190	897	dbSNP
rs1034554045	898	dbSNP
rs962557567	900	dbSNP
rs776155007	905	dbSNP
rs546605561	910	dbSNP
rs1229109361	916	dbSNP
rs1427178782	924	dbSNP
rs538348454	929	dbSNP
rs1033164603	934	dbSNP
rs763193585	939	dbSNP
rs951296178	940	dbSNP
rs148575084	942	dbSNP
rs958255537	943	dbSNP
rs1207823357	944	dbSNP
rs989645547	947	dbSNP
rs911906031	949	dbSNP
rs1207406420	951	dbSNP
rs1480989939	952	dbSNP
rs1251014544	953	dbSNP
rs916868533	955	dbSNP
rs944726624	962	dbSNP
rs568511260	964	dbSNP
rs982321744	969	dbSNP
rs1313177791	970	dbSNP
rs769568340	973	dbSNP
rs1353519109	974	dbSNP
rs940658204	978	dbSNP
rs1395138364	989	dbSNP
rs1409947127	989	dbSNP
rs1472883463	990	dbSNP
rs1296149872	992	dbSNP
rs974834658	999	dbSNP
rs751039530	1000	dbSNP
rs1036475770	1003	dbSNP
rs899225788	1004	dbSNP
rs1369847629	1006	dbSNP
rs1249896942	1010	dbSNP
rs930531236	1011	dbSNP
rs564745850	1012	dbSNP
rs1212861525	1015	dbSNP
rs1332385321	1018	dbSNP
rs913446547	1019	dbSNP
rs1239662483	1021	dbSNP
rs1335035711	1025	dbSNP
rs1304233906	1026	dbSNP
rs1387964549	1036	dbSNP
rs1326862557	1038	dbSNP
rs1342361269	1039	dbSNP
rs1324773836	1041	dbSNP
rs1448928971	1048	dbSNP
rs1461290642	1058	dbSNP
rs201562447	1059	dbSNP
rs1162073103	1060	dbSNP
rs1193237672	1061	dbSNP
rs1253922500	1061	dbSNP
rs1434931879	1061	dbSNP
rs1454778588	1061	dbSNP
rs1467015091	1061	dbSNP
rs368956121	1061	dbSNP
rs535066980	1061	dbSNP
rs58985331	1061	dbSNP
rs751531884	1061	dbSNP
rs879559913	1061	dbSNP
rs1051540	1062	dbSNP
rs116120219	1063	dbSNP
rs143003304	1064	dbSNP
rs1275828867	1065	dbSNP
rs1339257927	1066	dbSNP
rs1194589095	1067	dbSNP
rs77706863	1078	dbSNP
rs888912242	1080	dbSNP
rs1442483909	1083	dbSNP
rs1045996666	1084	dbSNP
rs1008790286	1085	dbSNP
rs1040241432	1088	dbSNP
rs1186303973	1089	dbSNP
rs1240844935	1090	dbSNP
rs1450993328	1092	dbSNP
rs1188908669	1104	dbSNP
rs553810119	1107	dbSNP
rs1383090129	1114	dbSNP
rs998910225	1119	dbSNP
rs1384903609	1124	dbSNP
rs182488829	1129	dbSNP
rs1389329020	1132	dbSNP
rs1395752348	1132	dbSNP
rs1467684967	1132	dbSNP
rs957341616	1133	dbSNP
rs1193656747	1135	dbSNP
rs1446189015	1137	dbSNP
rs1001180088	1138	dbSNP
rs1202107238	1138	dbSNP
rs1012638953	1159	dbSNP
rs1023812219	1161	dbSNP
rs1055536399	1173	dbSNP
rs969521219	1177	dbSNP
rs982372342	1178	dbSNP
rs1228674847	1186	dbSNP
rs186347782	1189	dbSNP
rs1316912679	1196	dbSNP
rs76131008	1199	dbSNP
rs1312384153	1201	dbSNP
rs1025902681	1204	dbSNP
rs189567791	1210	dbSNP
rs74343380	1214	dbSNP
rs1474997613	1220	dbSNP
rs564013627	1228	dbSNP
rs142016250	1230	dbSNP
rs1298707432	1237	dbSNP
rs1475499599	1240	dbSNP
rs1019564620	1244	dbSNP
rs1208130807	1245	dbSNP
rs1483737846	1250	dbSNP
rs966019808	1251	dbSNP
rs541039741	1253	dbSNP
rs1336977505	1256	dbSNP
rs150608020	1259	dbSNP
rs944531736	1260	dbSNP
rs1277116759	1261	dbSNP
rs957687395	1263	dbSNP
rs1040318360	1273	dbSNP
rs1346370652	1274	dbSNP
rs903096977	1275	dbSNP
rs990300274	1278	dbSNP
rs1356349035	1280	dbSNP
rs1260730120	1287	dbSNP
rs1465941268	1288	dbSNP
rs527994495	1289	dbSNP
rs1054538290	1290	dbSNP
rs1475385641	1291	dbSNP
rs1426516813	1292	dbSNP
rs199937460	1293	dbSNP
rs1378111983	1295	dbSNP
rs1477670590	1296	dbSNP
rs1175754061	1298	dbSNP
rs1045943251	1318	dbSNP
rs1180378623	1325	dbSNP
rs760040971	1336	dbSNP
rs1291519601	1337	dbSNP
rs1458962820	1341	dbSNP
rs892764295	1349	dbSNP
rs1273181313	1352	dbSNP
rs1012689000	1354	dbSNP
rs1384608646	1355	dbSNP
rs936994630	1360	dbSNP
rs1055888402	1361	dbSNP
rs898206321	1367	dbSNP
rs333644	1368	dbSNP
rs1393455471	1371	dbSNP
rs538611371	1371	dbSNP
rs1408572016	1372	dbSNP
rs1223471293	1377	dbSNP
rs752741764	1379	dbSNP
rs756394860	1389	dbSNP
rs1248132147	1390	dbSNP
rs1330588975	1394	dbSNP
rs1003694354	1401	dbSNP
rs1252776254	1407	dbSNP
rs1259749527	1417	dbSNP
rs1212142174	1422	dbSNP
rs1046883683	1425	dbSNP
rs1285520532	1426	dbSNP
rs1223340654	1428	dbSNP
rs1348590392	1435	dbSNP
rs78286208	1441	dbSNP
rs1441900795	1443	dbSNP
rs1267836372	1451	dbSNP
rs1008090935	1456	dbSNP
rs1197203107	1470	dbSNP
rs962598216	1475	dbSNP
rs1345765160	1476	dbSNP
rs1019512406	1477	dbSNP
rs1253958952	1488	dbSNP
rs1398513653	1490	dbSNP
rs1396346278	1494	dbSNP
rs1173648694	1495	dbSNP
rs753997889	1496	dbSNP
rs920592803	1501	dbSNP
rs531835111	1502	dbSNP
rs952021007	1503	dbSNP
rs1243241387	1507	dbSNP
rs1487043241	1507	dbSNP
rs1363416053	1510	dbSNP
rs1445410902	1511	dbSNP
rs957427942	1514	dbSNP
rs1451925211	1526	dbSNP
rs1282582050	1530	dbSNP
rs986209110	1530	dbSNP
rs750878624	1539	dbSNP
rs1165321219	1548	dbSNP
rs1235060653	1554	dbSNP
rs990636511	1555	dbSNP
rs910620559	1556	dbSNP
rs1216151047	1558	dbSNP
rs1362391299	1565	dbSNP
rs967506366	1576	dbSNP
rs550334370	1578	dbSNP
rs1428565312	1580	dbSNP
rs143627389	1580	dbSNP
rs182225574	1594	dbSNP
rs1409884307	1596	dbSNP
rs1433510026	1604	dbSNP
rs928868261	1611	dbSNP
rs1172049083	1613	dbSNP
rs1305704688	1622	dbSNP
rs1314725237	1625	dbSNP
rs1430734190	1633	dbSNP
rs1420655236	1634	dbSNP
rs937594729	1637	dbSNP
rs554153925	1640	dbSNP
rs1040602924	1647	dbSNP
rs991138056	1652	dbSNP
rs756630109	1656	dbSNP
rs1278534075	1658	dbSNP
rs565796153	1658	dbSNP
rs1358443573	1662	dbSNP
rs1220059510	1670	dbSNP
rs924435284	1671	dbSNP
rs1294588907	1673	dbSNP
rs931036036	1675	dbSNP
rs1357316013	1679	dbSNP
rs934577278	1680	dbSNP
rs1413683074	1684	dbSNP
rs1483369804	1686	dbSNP
rs1177804378	1688	dbSNP
rs372833565	1691	dbSNP
rs1170214792	1694	dbSNP
rs886867884	1700	dbSNP
rs758128910	1702	dbSNP
rs1040901990	1703	dbSNP
rs1386173212	1711	dbSNP
rs899713989	1717	dbSNP
rs1178954032	1726	dbSNP
rs185278396	1727	dbSNP
rs948355288	1730	dbSNP
rs376279128	1733	dbSNP
rs1044191819	1734	dbSNP
rs777385616	1739	dbSNP
rs1336641096	1744	dbSNP
rs1273807644	1749	dbSNP
rs1011606569	1753	dbSNP
rs906947251	1756	dbSNP
rs779856005	1757	dbSNP
rs1391414502	1760	dbSNP
rs1430989256	1761	dbSNP
rs1296060703	1768	dbSNP
rs575866726	1774	dbSNP
rs1445115185	1776	dbSNP
rs543091394	1778	dbSNP
rs897952534	1779	dbSNP
rs746940389	1786	dbSNP
rs1301502205	1790	dbSNP
rs1370560208	1790	dbSNP
rs768609944	1791	dbSNP
rs1419727733	1795	dbSNP
rs1250132934	1804	dbSNP
rs555013486	1805	dbSNP
rs1381634255	1808	dbSNP
rs1469696150	1809	dbSNP
rs573414998	1812	dbSNP
rs1212769464	1813	dbSNP
rs1017677701	1819	dbSNP
rs139651881	1820	dbSNP
rs1315807930	1822	dbSNP
rs1342735449	1822	dbSNP
rs1236054461	1823	dbSNP
rs1306702807	1823	dbSNP
rs1371186478	1825	dbSNP
rs1327027371	1828	dbSNP
rs992150680	1833	dbSNP
rs920216105	1835	dbSNP
rs757062502	1837	dbSNP
rs1454436093	1839	dbSNP
rs1250772209	1844	dbSNP
rs1479697155	1845	dbSNP
rs1202290655	1846	dbSNP
rs930942688	1855	dbSNP
rs1243953552	1857	dbSNP
rs559303049	1864	dbSNP
rs1192825711	1865	dbSNP
rs1182092940	1876	dbSNP
rs1263849215	1876	dbSNP
rs1205633216	1886	dbSNP
rs769375393	1886	dbSNP
rs1283263263	1896	dbSNP
rs796203180	1903	dbSNP
rs1429569878	1905	dbSNP
rs572647751	1907	dbSNP
rs1040848703	1909	dbSNP
rs1302213973	1909	dbSNP
rs899661154	1910	dbSNP
rs1298456179	1911	dbSNP
rs546518540	1919	dbSNP
rs1384793172	1922	dbSNP
rs1467100601	1927	dbSNP
rs1436610743	1932	dbSNP
rs934482001	1937	dbSNP
rs7219458	1941	dbSNP
rs1374598029	1949	dbSNP
rs1193546147	1951	dbSNP
rs1427877255	1955	dbSNP
rs1260870164	1957	dbSNP
rs566406871	1960	dbSNP
rs948406763	1961	dbSNP
rs1020245645	1964	dbSNP
rs550419782	1965	dbSNP
rs1253453620	1972	dbSNP
rs1228563691	1973	dbSNP
rs1340475977	1977	dbSNP
rs1276821086	1985	dbSNP
rs1416770588	1988	dbSNP
rs903243572	1990	dbSNP
rs1333519318	1991	dbSNP
rs1293315801	1996	dbSNP
rs1044075415	1998	dbSNP
rs959111799	1999	dbSNP
rs1013096004	2000	dbSNP
rs1189978824	2001	dbSNP
rs906831219	2010	dbSNP
rs938432009	2016	dbSNP
rs1027624681	2017	dbSNP
rs1256212638	2023	dbSNP
rs1036758052	2024	dbSNP
rs1460990732	2030	dbSNP
rs771222875	2031	dbSNP
rs993664341	2038	dbSNP
rs1273212891	2043	dbSNP
rs190289968	2043	dbSNP
rs1202026845	2048	dbSNP
rs1196796164	2053	dbSNP
rs1027904413	2054	dbSNP
rs557335550	2054	dbSNP
rs562130140	2061	dbSNP
rs1007732054	2063	dbSNP
rs1017561524	2065	dbSNP
rs908198768	2066	dbSNP
rs1283705449	2068	dbSNP
rs183389220	2071	dbSNP
rs976586700	2072	dbSNP
rs1445861867	2073	dbSNP
rs547429506	2081	dbSNP
rs1053646020	2082	dbSNP
rs1461899236	2083	dbSNP
rs1417031155	2087	dbSNP
rs1160978170	2088	dbSNP
rs569935421	2091	dbSNP
rs1233165220	2093	dbSNP
rs768200030	2096	dbSNP
rs1042322131	2102	dbSNP
rs149919406	2114	dbSNP
rs989996042	2115	dbSNP
rs1215898982	2116	dbSNP
rs774758096	2123	dbSNP
rs1289763317	2125	dbSNP
rs948623572	2128	dbSNP
rs1226720262	2134	dbSNP
rs759999237	2144	dbSNP
rs1280419269	2154	dbSNP
rs1239713025	2155	dbSNP
rs1374865067	2157	dbSNP
rs979975765	2159	dbSNP
rs1327711054	2161	dbSNP
rs1441305783	2164	dbSNP
rs1349279906	2169	dbSNP
rs928301553	2171	dbSNP
rs1401995054	2174	dbSNP
rs1408085041	2182	dbSNP
rs903191155	2183	dbSNP
rs1002855395	2191	dbSNP
rs539336096	2193	dbSNP
rs1057454951	2205	dbSNP
rs1195947235	2208	dbSNP
rs1345462899	2211	dbSNP
rs938349217	2216	dbSNP
rs537367219	2220	dbSNP
rs1037213471	2222	dbSNP
rs918342618	2223	dbSNP
rs188793375	2228	dbSNP
rs1049227681	2239	dbSNP
rs1215935134	2242	dbSNP
rs192948016	2247	dbSNP
rs1305876974	2250	dbSNP
rs1234807553	2253	dbSNP
rs1007784375	2258	dbSNP
rs1432810568	2264	dbSNP
rs1039232761	2268	dbSNP
rs768063970	2269	dbSNP
rs747786457	2271	dbSNP
rs771500353	2273	dbSNP
rs1270210483	2278	dbSNP
rs965028768	2279	dbSNP
rs997507535	2288	dbSNP
rs1032211792	2289	dbSNP
rs569635735	2298	dbSNP
rs953824667	2304	dbSNP
rs1215451555	2314	dbSNP
rs752831815	2315	dbSNP
rs1012039028	2326	dbSNP
rs1240749678	2328	dbSNP
rs1193107806	2331	dbSNP
rs1487333279	2333	dbSNP
rs1282822548	2342	dbSNP
rs1211881418	2347	dbSNP
rs1311754496	2349	dbSNP
rs1021468556	2354	dbSNP
rs1276278477	2360	dbSNP
rs1216053689	2362	dbSNP
rs915073582	2363	dbSNP
rs969854059	2364	dbSNP
rs1489715483	2366	dbSNP
rs1356800443	2367	dbSNP
rs1200794636	2369	dbSNP
rs1465239794	2383	dbSNP
rs1357033121	2384	dbSNP
rs1411982940	2389	dbSNP
rs980027266	2389	dbSNP
rs34511912	2391	dbSNP
rs533869208	2403	dbSNP
rs145006740	2404	dbSNP
rs972420910	2406	dbSNP
rs918215731	2414	dbSNP
rs1057132565	2416	dbSNP
rs754087702	2428	dbSNP
rs1408201202	2441	dbSNP
rs1399785643	2444	dbSNP
rs1307854902	2446	dbSNP
rs1012994302	2447	dbSNP
rs1216738465	2448	dbSNP
rs1156590182	2450	dbSNP
rs1336776475	2454	dbSNP
rs931080386	2467	dbSNP
rs1054211	2468	dbSNP
rs1048109520	2480	dbSNP
rs35591000	2483	dbSNP
rs909399999	2483	dbSNP
rs943528022	2486	dbSNP
rs757448405	2487	dbSNP
rs1401469427	2490	dbSNP
rs1170325261	2496	dbSNP
rs1464546095	2501	dbSNP
rs1302468953	2507	dbSNP
rs1039283919	2509	dbSNP
rs902089698	2510	dbSNP
rs1165630520	2514	dbSNP
rs1423285566	2516	dbSNP
rs555149551	2519	dbSNP
rs1015825315	2521	dbSNP
rs1179153899	2527	dbSNP
rs1458338350	2527	dbSNP
rs1053131528	2537	dbSNP
rs1403155379	2538	dbSNP
rs1469784225	2541	dbSNP
rs1243487478	2543	dbSNP
rs1265938184	2543	dbSNP
rs1319404202	2548	dbSNP
rs573352401	2551	dbSNP
rs1308774764	2554	dbSNP
rs1224008635	2560	dbSNP
rs1290312206	2560	dbSNP
rs1375641085	2560	dbSNP
rs891750011	2566	dbSNP
rs1397371825	2571	dbSNP
rs1011684547	2580	dbSNP
rs766134963	2581	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.