>THRA|NM_199334|3'UTR
   1 AGCCTCAGGCGGCCAGAGGGTGTGCGGAGCTGGTGGGGAGGAGCCTGGAGAGAAGGGGCAGAGCTGGGGGCTGAGGGAGA
  81 CCCCCCCACACCCCTTCTCTCCTTCCTCTCGTCCTTGGATAGATTCAGCTCCCACACACACACCCGCACTGCCCAGGTCC
 161 CTCCTCAGACCTCCAGCCCTGGGACAGGGCAAACAACTGAACTTGCTATGGAAAGGACAGTGTGGGAGGCTGGGGGAGCT
 241 GTGTCCTGCAGTTCCCAGGACCCCATCCTCTCAGAAGGTAGGGGAAGGGCGGGAGGATTGAGAAGGGACAAGCCACCTTG
 321 ACCGTAGGGGAAGGAGGAATGTGGGCTGGGGGAAGATGCCCTCAACTCACCCCCTACACACACATGAGAGAGAGCCCCCA
 401 CCCAGTTCCTTGGCCTAGGTCTCCCCTCCAGGCTGAGGGCCTCTCTACTTCCCCAGATGCCTGGGTGCAAAGAACGGCTT
 481 GGCTTGGCTCCTCCTCTGGAGGTTAAAATTTATAGTCATTCTAACTGCACTTTGGAAACCAAGCAAGGGGAGAAGACAAA
 561 TGAAGAAAAACTAGACAGAGAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' auGAACAUUGCCUCUCGUGauc 5' |||| |:||| || || Target 5' aaCTTGCTATGGAAAGGACagt 3'	200 - 221	100.00	-15.90
2	miRNA 3' auGAACAUUGCCUCUCGUGAUc 5' || ||:: | :|||| ||: Target 5' agCTGGTGGGGAGGAGC-CTGg 3'	28 - 48	96.00	-17.20
3	miRNA 3' augaacauugccucUCGUGAUc 5' ||| ||: Target 5' ctcctcagacctccAGCCCTGg 3'	161 - 182	92.00	-5.60

Mutant ID	Mutant Position	Mutant Source
COSN18433617	26	COSMIC
COSN25751677	81	COSMIC
COSN18740598	88	COSMIC
COSN31563520	92	COSMIC
COSN30161297	100	COSMIC
COSN24143100	109	COSMIC
COSN24147151	160	COSMIC
COSN25688124	325	COSMIC
COSN26645619	434	COSMIC
COSN24480189	452	COSMIC
COSN26600290	477	COSMIC
COSN30173611	562	COSMIC
COSN30542628	581	COSMIC
COSN7166307	628	COSMIC
COSN8836272	675	COSMIC
COSN29818526	1119	COSMIC
COSN21112526	1149	COSMIC
COSN20854218	1369	COSMIC
COSN31923177	1805	COSMIC
COSN27297336	1816	COSMIC
COSN27390759	1816	COSMIC
COSN15041771	1956	COSMIC
COSN6103669	2190	COSMIC
COSN14818457	2931	COSMIC
COSN16141928	3269	COSMIC
COSN5839798	3362	COSMIC
COSN30464584	3428	COSMIC
COSN13718647	3443	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs746462735	2	dbSNP
rs1186894783	5	dbSNP
rs1488074925	7	dbSNP
rs751770131	7	dbSNP
rs768780514	11	dbSNP
rs950849781	11	dbSNP
rs762110365	12	dbSNP
rs1273915276	14	dbSNP
rs370332354	16	dbSNP
rs1232721736	17	dbSNP
rs1024957536	18	dbSNP
rs776696601	20	dbSNP
rs750768397	25	dbSNP
rs756484201	26	dbSNP
rs780560106	27	dbSNP
rs754336049	30	dbSNP
rs199737729	33	dbSNP
rs1383112953	34	dbSNP
rs1186162087	36	dbSNP
rs778409334	44	dbSNP
rs778414590	49	dbSNP
rs1442694183	60	dbSNP
rs1221770645	69	dbSNP
rs972019147	71	dbSNP
rs1425686102	81	dbSNP
rs981726905	81	dbSNP
rs12939700	83	dbSNP
rs1432352022	87	dbSNP
rs1265039571	88	dbSNP
rs925728210	89	dbSNP
rs1253625927	94	dbSNP
rs1474258886	95	dbSNP
rs958902521	103	dbSNP
rs771376452	107	dbSNP
rs1456544945	108	dbSNP
rs1185114174	111	dbSNP
rs757674823	112	dbSNP
rs774649624	124	dbSNP
rs1311938502	132	dbSNP
rs914353613	135	dbSNP
rs945792644	143	dbSNP
rs759786898	146	dbSNP
rs913096029	147	dbSNP
rs1398058748	158	dbSNP
rs778280657	160	dbSNP
rs933806982	160	dbSNP
rs368427838	164	dbSNP
rs1173497253	165	dbSNP
rs912231213	177	dbSNP
rs1375664405	196	dbSNP
rs1175283203	197	dbSNP
rs1051039924	207	dbSNP
rs1392296161	210	dbSNP
rs1454598792	212	dbSNP
rs772217524	225	dbSNP
rs1395902566	230	dbSNP
rs555111691	235	dbSNP
rs558063583	236	dbSNP
rs1456476314	242	dbSNP
rs911100415	244	dbSNP
rs1378848657	251	dbSNP
rs1196840638	264	dbSNP
rs371637594	266	dbSNP
rs1483219281	270	dbSNP
rs1254563399	279	dbSNP
rs1213463554	284	dbSNP
rs1324350280	285	dbSNP
rs568425990	291	dbSNP
rs376283259	292	dbSNP
rs1039404169	293	dbSNP
rs899673023	305	dbSNP
rs1297300207	312	dbSNP
rs1336965874	317	dbSNP
rs560924224	324	dbSNP
rs1395312981	325	dbSNP
rs1399970844	329	dbSNP
rs1314724535	331	dbSNP
rs1049119835	344	dbSNP
rs775674059	345	dbSNP
rs994954924	351	dbSNP
rs1291377003	353	dbSNP
rs1047826883	356	dbSNP
rs887832708	361	dbSNP
rs1423387375	370	dbSNP
rs1036739729	371	dbSNP
rs886626328	373	dbSNP
rs1003536722	376	dbSNP
rs1444905942	378	dbSNP
rs1214662958	384	dbSNP
rs368966849	385	dbSNP
rs115187810	391	dbSNP
rs1196401758	396	dbSNP
rs1243415096	400	dbSNP
rs778705627	401	dbSNP
rs1416314969	404	dbSNP
rs1295016890	405	dbSNP
rs1415358600	406	dbSNP
rs1472797613	409	dbSNP
rs760874028	410	dbSNP
rs1399108568	422	dbSNP
rs1001791298	424	dbSNP
rs1021822211	426	dbSNP
rs772402529	427	dbSNP
rs1297822927	430	dbSNP
rs1167667348	432	dbSNP
rs534177123	440	dbSNP
rs967078665	445	dbSNP
rs764048334	446	dbSNP
rs1360862115	453	dbSNP
rs1449155014	460	dbSNP
rs957023879	467	dbSNP
rs988542456	471	dbSNP
rs1310912642	477	dbSNP
rs1353599022	480	dbSNP
rs35100224	484	dbSNP
rs1448734320	490	dbSNP
rs1233763726	494	dbSNP
rs1285405388	509	dbSNP
rs1317227538	511	dbSNP
rs1276308404	512	dbSNP
rs955221008	514	dbSNP
rs987004528	534	dbSNP
rs1326860252	543	dbSNP
rs1319197820	544	dbSNP
rs912205501	545	dbSNP
rs564957022	548	dbSNP
rs1462090062	558	dbSNP
rs975715974	559	dbSNP
rs921206484	567	dbSNP
rs931240877	571	dbSNP
rs532129093	575	dbSNP
rs1048190515	577	dbSNP
rs546852493	577	dbSNP
rs547394224	577	dbSNP
rs73983006	578	dbSNP
rs1456979432	589	dbSNP
rs1270776287	594	dbSNP
rs1036490220	596	dbSNP
rs1355485018	596	dbSNP
rs907182108	600	dbSNP
rs1219242744	601	dbSNP
rs1002905473	605	dbSNP
rs116932128	606	dbSNP
rs894707648	609	dbSNP
rs1011839803	612	dbSNP
rs1021766740	612	dbSNP
rs1412156459	618	dbSNP
rs930609911	622	dbSNP
rs1239212695	624	dbSNP
rs1453037172	624	dbSNP
rs1468678056	626	dbSNP
rs1047857783	631	dbSNP
rs1396497985	635	dbSNP
rs34982445	653	dbSNP
rs1158181623	656	dbSNP
rs780426227	660	dbSNP
rs879707667	661	dbSNP
rs886491975	665	dbSNP
rs950248913	666	dbSNP
rs1206463716	667	dbSNP
rs1019383787	668	dbSNP
rs1421791339	669	dbSNP
rs965404266	673	dbSNP
rs1235338854	675	dbSNP
rs1171494981	678	dbSNP
rs1376188639	680	dbSNP
rs1401265091	681	dbSNP
rs1355622532	686	dbSNP
rs1334152371	689	dbSNP
rs548550672	690	dbSNP
rs920946330	691	dbSNP
rs1173835262	701	dbSNP
rs952597983	711	dbSNP
rs1178422661	715	dbSNP
rs1333419667	722	dbSNP
rs1470247057	723	dbSNP
rs1236809514	733	dbSNP
rs747192217	734	dbSNP
rs1445388430	737	dbSNP
rs1486505901	738	dbSNP
rs1280807621	742	dbSNP
rs1211797515	745	dbSNP
rs34826591	746	dbSNP
rs1378617036	747	dbSNP
rs148185106	759	dbSNP
rs908381673	760	dbSNP
rs1413509027	773	dbSNP
rs1357707169	776	dbSNP
rs70964667	788	dbSNP
rs1313873063	795	dbSNP
rs1231652505	797	dbSNP
rs1343055439	797	dbSNP
rs1160895572	802	dbSNP
rs1400751608	806	dbSNP
rs1412483886	811	dbSNP
rs939893472	815	dbSNP
rs141373347	816	dbSNP
rs1192664537	837	dbSNP
rs570897472	840	dbSNP
rs1484804038	842	dbSNP
rs1344754373	843	dbSNP
rs1201466776	854	dbSNP
rs1218264498	856	dbSNP
rs1317555796	868	dbSNP
rs928709920	874	dbSNP
rs938785160	875	dbSNP
rs1055766532	880	dbSNP
rs1294497928	881	dbSNP
rs1360361934	883	dbSNP
rs894486722	890	dbSNP
rs1281329314	891	dbSNP
rs1393021247	894	dbSNP
rs906024632	901	dbSNP
rs1462626384	905	dbSNP
rs1002223830	906	dbSNP
rs1418468756	910	dbSNP
rs1169940289	913	dbSNP
rs750174429	917	dbSNP
rs150793078	920	dbSNP
rs1009828466	930	dbSNP
rs1019999142	931	dbSNP
rs955083467	941	dbSNP
rs1211880677	944	dbSNP
rs986562813	959	dbSNP
rs1376792382	960	dbSNP
rs1018556606	967	dbSNP
rs1055115350	970	dbSNP
rs1298201225	972	dbSNP
rs34316313	975	dbSNP
rs963897771	977	dbSNP
rs974417188	978	dbSNP
rs552935381	979	dbSNP
rs919815084	991	dbSNP
rs1027938847	998	dbSNP
rs1394245843	1000	dbSNP
rs1394634065	1006	dbSNP
rs1297502078	1021	dbSNP
rs1460429069	1028	dbSNP
rs952420899	1034	dbSNP
rs867154359	1041	dbSNP
rs1432439024	1042	dbSNP
rs1394677367	1051	dbSNP
rs1192026393	1057	dbSNP
rs1455612254	1058	dbSNP
rs983985600	1064	dbSNP
rs1331413325	1067	dbSNP
rs1479946006	1069	dbSNP
rs1253667753	1078	dbSNP
rs139166758	1084	dbSNP
rs376140898	1085	dbSNP
rs927791897	1087	dbSNP
rs557588986	1088	dbSNP
rs115194007	1108	dbSNP
rs1371036262	1108	dbSNP
rs772839450	1110	dbSNP
rs915909098	1119	dbSNP
rs1298725412	1121	dbSNP
rs1433829496	1123	dbSNP
rs1045803926	1127	dbSNP
rs1373425681	1128	dbSNP
rs906050464	1133	dbSNP
rs1277010242	1134	dbSNP
rs937501116	1143	dbSNP
rs1181167598	1146	dbSNP
rs1417467530	1152	dbSNP
rs1316567924	1158	dbSNP
rs1054646803	1160	dbSNP
rs1485527068	1164	dbSNP
rs893355717	1166	dbSNP
rs112022341	1167	dbSNP
rs78527468	1167	dbSNP
rs1348163990	1172	dbSNP
rs934925129	1188	dbSNP
rs546348914	1192	dbSNP
rs1009860955	1194	dbSNP
rs1318237590	1198	dbSNP
rs1307566664	1200	dbSNP
rs1019945071	1201	dbSNP
rs890782635	1203	dbSNP
rs1414113354	1207	dbSNP
rs1353267377	1216	dbSNP
rs754560240	1220	dbSNP
rs1041178968	1222	dbSNP
rs1415237288	1232	dbSNP
rs1403167539	1239	dbSNP
rs1158264035	1246	dbSNP
rs901373405	1251	dbSNP
rs12948025	1252	dbSNP
rs576856054	1255	dbSNP
rs1208232834	1257	dbSNP
rs964236657	1258	dbSNP
rs973901470	1262	dbSNP
rs1255772071	1269	dbSNP
rs541167885	1272	dbSNP
rs1200698826	1277	dbSNP
rs1260564897	1280	dbSNP
rs951315769	1284	dbSNP
rs1371178851	1288	dbSNP
rs559387285	1291	dbSNP
rs1477431226	1297	dbSNP
rs982688187	1298	dbSNP
rs1232532891	1300	dbSNP
rs1332582040	1312	dbSNP
rs907904989	1316	dbSNP
rs749824312	1319	dbSNP
rs981951173	1320	dbSNP
rs1317856131	1321	dbSNP
rs1380768672	1323	dbSNP
rs1387162875	1324	dbSNP
rs1015695650	1332	dbSNP
rs1461053331	1340	dbSNP
rs1425077792	1352	dbSNP
rs1167783431	1357	dbSNP
rs1473304965	1364	dbSNP
rs529668174	1368	dbSNP
rs541856351	1369	dbSNP
rs1448371723	1370	dbSNP
rs937513154	1371	dbSNP
rs1390961260	1373	dbSNP
rs184981434	1379	dbSNP
rs1388199129	1380	dbSNP
rs982447065	1383	dbSNP
rs1466789909	1387	dbSNP
rs530738696	1404	dbSNP
rs1214282077	1407	dbSNP
rs914737804	1425	dbSNP
rs959230912	1426	dbSNP
rs1225436980	1435	dbSNP
rs946334235	1437	dbSNP
rs1041937313	1440	dbSNP
rs1279408771	1450	dbSNP
rs890809231	1459	dbSNP
rs1298691250	1463	dbSNP
rs1440219669	1464	dbSNP
rs916023499	1471	dbSNP
rs1328454938	1473	dbSNP
rs1264978191	1477	dbSNP
rs1488918019	1483	dbSNP
rs1211882302	1486	dbSNP
rs1007867086	1492	dbSNP
rs541673080	1497	dbSNP
rs552329977	1498	dbSNP
rs924608656	1501	dbSNP
rs570592218	1504	dbSNP
rs1041734141	1512	dbSNP
rs922777324	1512	dbSNP
rs1275567117	1513	dbSNP
rs1233867854	1514	dbSNP
rs1425682775	1518	dbSNP
rs995255953	1523	dbSNP
rs1305720632	1525	dbSNP
rs1437361361	1531	dbSNP
rs1335672209	1534	dbSNP
rs1327491752	1538	dbSNP
rs1026854367	1542	dbSNP
rs1163430073	1543	dbSNP
rs528558919	1544	dbSNP
rs951181832	1545	dbSNP
rs1004157188	1560	dbSNP
rs546639723	1562	dbSNP
rs932850260	1567	dbSNP
rs1024875852	1575	dbSNP
rs774024495	1583	dbSNP
rs1358963765	1585	dbSNP
rs1049898534	1595	dbSNP
rs1256556501	1604	dbSNP
rs561823108	1605	dbSNP
rs927372127	1606	dbSNP
rs958857591	1612	dbSNP
rs1394853866	1617	dbSNP
rs990183405	1620	dbSNP
rs568223027	1629	dbSNP
rs1445017506	1630	dbSNP
rs1351425911	1632	dbSNP
rs535422607	1633	dbSNP
rs1312660215	1638	dbSNP
rs1413397919	1646	dbSNP
rs1376885593	1647	dbSNP
rs1176403767	1654	dbSNP
rs1399587955	1658	dbSNP
rs1312035433	1659	dbSNP
rs1322410019	1660	dbSNP
rs1472879034	1662	dbSNP
rs1185512015	1666	dbSNP
rs1247187258	1666	dbSNP
rs1005263574	1667	dbSNP
rs1211124996	1670	dbSNP
rs557096463	1671	dbSNP
rs1282265502	1673	dbSNP
rs12949322	1674	dbSNP
rs1230706907	1676	dbSNP
rs12949331	1679	dbSNP
rs1217024823	1680	dbSNP
rs1293279656	1694	dbSNP
rs914769079	1695	dbSNP
rs1003457929	1708	dbSNP
rs527585620	1721	dbSNP
rs1303013328	1725	dbSNP
rs1429603757	1727	dbSNP
rs1482205863	1741	dbSNP
rs1035370212	1742	dbSNP
rs942228433	1747	dbSNP
rs946198681	1748	dbSNP
rs1181238745	1753	dbSNP
rs1041968607	1754	dbSNP
rs959178467	1762	dbSNP
rs1162754258	1770	dbSNP
rs12949650	1770	dbSNP
rs912781764	1773	dbSNP
rs1182607683	1775	dbSNP
rs1190799504	1776	dbSNP
rs1192230691	1776	dbSNP
rs1236861333	1776	dbSNP
rs1252459856	1776	dbSNP
rs1266603608	1776	dbSNP
rs1323753950	1776	dbSNP
rs1350186872	1776	dbSNP
rs1408061573	1776	dbSNP
rs1417613520	1776	dbSNP
rs1435150160	1776	dbSNP
rs1450126057	1776	dbSNP
rs1459393589	1776	dbSNP
rs1475212023	1776	dbSNP
rs1489749979	1776	dbSNP
rs368963847	1776	dbSNP
rs71152640	1776	dbSNP
rs774422377	1776	dbSNP
rs775335532	1776	dbSNP
rs943707005	1781	dbSNP
rs1022155390	1782	dbSNP
rs1176308967	1783	dbSNP
rs1379303177	1790	dbSNP
rs1419973644	1792	dbSNP
rs1276283281	1796	dbSNP
rs1228710905	1803	dbSNP
rs1159606609	1804	dbSNP
rs1369538703	1804	dbSNP
rs1388076961	1804	dbSNP
rs1297591787	1805	dbSNP
rs915854623	1805	dbSNP
rs1362871884	1807	dbSNP
rs1170669572	1808	dbSNP
rs1464950871	1808	dbSNP
rs147494815	1809	dbSNP
rs979262816	1809	dbSNP
rs1346699723	1811	dbSNP
rs1302788936	1813	dbSNP
rs1234758597	1815	dbSNP
rs1380599451	1815	dbSNP
rs1312308985	1816	dbSNP
rs1352025132	1816	dbSNP
rs569510844	1816	dbSNP
rs866336653	1817	dbSNP
rs1048155237	1818	dbSNP
rs1376405583	1819	dbSNP
rs1241174618	1821	dbSNP
rs1287840498	1822	dbSNP
rs1310220268	1823	dbSNP
rs956259890	1824	dbSNP
rs1158943333	1826	dbSNP
rs1209269840	1831	dbSNP
rs1256506261	1832	dbSNP
rs1484235845	1836	dbSNP
rs1183336665	1838	dbSNP
rs886959679	1849	dbSNP
rs922829043	1856	dbSNP
rs1201857999	1859	dbSNP
rs1004018325	1860	dbSNP
rs1259647248	1862	dbSNP
rs1236332488	1863	dbSNP
rs1237086493	1864	dbSNP
rs539777998	1868	dbSNP
rs1180159749	1869	dbSNP
rs558320970	1880	dbSNP
rs1410545906	1881	dbSNP
rs573523975	1882	dbSNP
rs1332378047	1884	dbSNP
rs1398019450	1885	dbSNP
rs1002528184	1890	dbSNP
rs1175880290	1890	dbSNP
rs1455764334	1892	dbSNP
rs540832710	1896	dbSNP
rs1360218847	1900	dbSNP
rs941108475	1900	dbSNP
rs1475063991	1902	dbSNP
rs1367113216	1904	dbSNP
rs1471268765	1905	dbSNP
rs1037226461	1911	dbSNP
rs1260691024	1914	dbSNP
rs896798157	1915	dbSNP
rs1003647826	1922	dbSNP
rs1268635860	1926	dbSNP
rs779256151	1927	dbSNP
rs553064764	1928	dbSNP
rs1311761314	1929	dbSNP
rs1365831881	1932	dbSNP
rs1218427434	1943	dbSNP
rs895040781	1944	dbSNP
rs1341289359	1947	dbSNP
rs574602037	1948	dbSNP
rs1367465682	1950	dbSNP
rs1321760535	1957	dbSNP
rs772421279	1960	dbSNP
rs1461378952	1965	dbSNP
rs1388948330	1970	dbSNP
rs958683477	1970	dbSNP
rs1022102818	1971	dbSNP
rs967907037	1979	dbSNP
rs775729152	1980	dbSNP
rs541782192	1981	dbSNP
rs563167753	1982	dbSNP
rs1449781387	1983	dbSNP
rs1457827403	1984	dbSNP
rs375264607	1999	dbSNP
rs956162724	1999	dbSNP
rs977133961	1999	dbSNP
rs1250919932	2000	dbSNP
rs922610437	2004	dbSNP
rs1344322377	2007	dbSNP
rs759140923	2010	dbSNP
rs1244616226	2011	dbSNP
rs760786831	2013	dbSNP
rs1440355487	2015	dbSNP
rs1329828334	2023	dbSNP
rs1487976727	2033	dbSNP
rs1190953996	2037	dbSNP
rs954263938	2038	dbSNP
rs1387660465	2042	dbSNP
rs1481680085	2043	dbSNP
rs189784039	2076	dbSNP
rs912720334	2077	dbSNP
rs944337754	2079	dbSNP
rs1390465344	2083	dbSNP
rs1172470329	2087	dbSNP
rs1476778707	2089	dbSNP
rs1248361281	2098	dbSNP
rs976059754	2111	dbSNP
rs1348331999	2115	dbSNP
rs920965352	2118	dbSNP
rs1249352243	2123	dbSNP
rs930944804	2132	dbSNP
rs1293848014	2136	dbSNP
rs918300636	2140	dbSNP
rs1369505507	2141	dbSNP
rs1216653028	2142	dbSNP
rs1342993936	2144	dbSNP
rs1277469941	2147	dbSNP
rs879450006	2150	dbSNP
rs1219900762	2156	dbSNP
rs1048186972	2164	dbSNP
rs768799957	2165	dbSNP
rs1056494119	2166	dbSNP
rs886822465	2173	dbSNP
rs894820236	2174	dbSNP
rs947942941	2177	dbSNP
rs545822875	2178	dbSNP
rs1469572157	2187	dbSNP
rs1490946169	2188	dbSNP
rs1192027084	2192	dbSNP
rs75248071	2197	dbSNP
rs1483290799	2207	dbSNP
rs903676776	2209	dbSNP
rs1209725269	2210	dbSNP
rs1046264315	2211	dbSNP
rs564111107	2212	dbSNP
rs1280844761	2216	dbSNP
rs1169706376	2222	dbSNP
rs1411749075	2226	dbSNP
rs528227503	2227	dbSNP
rs1165757432	2228	dbSNP
rs1367146129	2229	dbSNP
rs1351510796	2235	dbSNP
rs1445359889	2239	dbSNP
rs891836587	2240	dbSNP
rs1334228657	2250	dbSNP
rs998290987	2252	dbSNP
rs546402537	2262	dbSNP
rs1002155824	2263	dbSNP
rs879294007	2268	dbSNP
rs894498514	2269	dbSNP
rs963003991	2270	dbSNP
rs1239501021	2273	dbSNP
rs1011503087	2277	dbSNP
rs918766018	2288	dbSNP
rs939064047	2289	dbSNP
rs991941896	2292	dbSNP
rs568185136	2294	dbSNP
rs1211157965	2296	dbSNP
rs139979507	2298	dbSNP
rs1228476801	2300	dbSNP
rs1330164287	2300	dbSNP
rs1289628492	2302	dbSNP
rs1227018583	2304	dbSNP
rs1021668444	2311	dbSNP
rs1284478891	2312	dbSNP
rs761811160	2318	dbSNP
rs977901452	2321	dbSNP
rs1019811669	2322	dbSNP
rs1457716985	2324	dbSNP
rs947731217	2327	dbSNP
rs759869118	2329	dbSNP
rs550936134	2330	dbSNP
rs965913142	2331	dbSNP
rs903745008	2345	dbSNP
rs765206526	2348	dbSNP
rs1182686169	2353	dbSNP
rs975710617	2359	dbSNP
rs921488585	2365	dbSNP
rs1052665579	2374	dbSNP
rs901713196	2375	dbSNP
rs998676117	2381	dbSNP
rs1029727799	2382	dbSNP
rs113211153	2391	dbSNP
rs889769303	2394	dbSNP
rs930973436	2397	dbSNP
rs983746633	2398	dbSNP
rs1299162253	2408	dbSNP
rs963246316	2421	dbSNP
rs1182587008	2428	dbSNP
rs1291766080	2431	dbSNP
rs1387277671	2435	dbSNP
rs1418152918	2445	dbSNP
rs569196339	2449	dbSNP
rs973016142	2452	dbSNP
rs1438287074	2453	dbSNP
rs540122368	2453	dbSNP
rs908203594	2455	dbSNP
rs1429361669	2462	dbSNP
rs960943078	2462	dbSNP
rs939783524	2464	dbSNP
rs1046558793	2467	dbSNP
rs145404278	2469	dbSNP
rs937818929	2471	dbSNP
rs866052322	2477	dbSNP
rs1190017233	2478	dbSNP
rs1448119837	2486	dbSNP
rs1316590570	2493	dbSNP
rs1374177227	2494	dbSNP
rs969145977	2509	dbSNP
rs567181742	2511	dbSNP
rs893686377	2519	dbSNP
rs1276385103	2520	dbSNP
rs1239009381	2531	dbSNP
rs1311125562	2532	dbSNP
rs1299056145	2535	dbSNP
rs1220876287	2541	dbSNP
rs1010777119	2548	dbSNP
rs1351855607	2549	dbSNP
rs924982867	2555	dbSNP
rs1407836180	2558	dbSNP
rs534356415	2561	dbSNP
rs903179433	2562	dbSNP
rs935240271	2564	dbSNP
rs1442388389	2567	dbSNP
rs1210878247	2572	dbSNP
rs998974901	2573	dbSNP
rs1020095631	2575	dbSNP
rs919533614	2576	dbSNP
rs965589727	2579	dbSNP
rs1181875267	2581	dbSNP
rs975953594	2590	dbSNP
rs923081476	2591	dbSNP
rs1028580022	2592	dbSNP
rs1178258348	2593	dbSNP
rs952978491	2595	dbSNP
rs556020357	2597	dbSNP
rs1312693219	2598	dbSNP
rs1287688406	2601	dbSNP
rs908233753	2606	dbSNP
rs931238747	2607	dbSNP
rs961315053	2607	dbSNP
rs1352134793	2608	dbSNP
rs981901956	2614	dbSNP
rs1471030467	2615	dbSNP
rs1038741600	2627	dbSNP
rs1170662325	2628	dbSNP
rs927674120	2634	dbSNP
rs929631921	2637	dbSNP
rs1401841375	2639	dbSNP
rs1055409297	2641	dbSNP
rs138640083	2641	dbSNP
rs1050692390	2642	dbSNP
rs3744805	2646	dbSNP
rs1006603522	2648	dbSNP
rs903212405	2649	dbSNP
rs1039866460	2651	dbSNP
rs1471791719	2653	dbSNP
rs1397546058	2654	dbSNP
rs999235608	2655	dbSNP
rs961262494	2656	dbSNP
rs535232805	2661	dbSNP
rs1013739213	2662	dbSNP
rs1023812074	2663	dbSNP
rs1446232631	2663	dbSNP
rs1267369830	2668	dbSNP
rs969093544	2674	dbSNP
rs979211945	2679	dbSNP
rs1268513328	2682	dbSNP
rs1243881345	2688	dbSNP
rs1041144520	2690	dbSNP
rs1241582359	2692	dbSNP
rs1383661346	2703	dbSNP
rs1273491655	2711	dbSNP
rs1456124311	2714	dbSNP
rs776854077	2718	dbSNP
rs1159505430	2720	dbSNP
rs1457751116	2723	dbSNP
rs996936331	2727	dbSNP
rs1224697434	2730	dbSNP
rs1028527474	2735	dbSNP
rs1444668959	2739	dbSNP
rs1246898897	2740	dbSNP
rs952841488	2741	dbSNP
rs369942297	2751	dbSNP
rs1015830083	2753	dbSNP
rs961084163	2757	dbSNP
rs1263864031	2758	dbSNP
rs765673452	2762	dbSNP
rs1360180629	2769	dbSNP
rs1433073383	2774	dbSNP
rs1367929531	2783	dbSNP
rs1319607590	2786	dbSNP
rs923182589	2787	dbSNP
rs982149425	2788	dbSNP
rs1164585280	2792	dbSNP
rs1439821024	2793	dbSNP
rs1389242140	2800	dbSNP
rs1166142046	2802	dbSNP
rs927650433	2802	dbSNP
rs148709476	2803	dbSNP
rs1449590465	2804	dbSNP
rs1269217066	2806	dbSNP
rs1223020290	2807	dbSNP
rs1227330444	2807	dbSNP
rs1274240586	2807	dbSNP
rs1490573673	2807	dbSNP
rs990517774	2809	dbSNP
rs1376882766	2810	dbSNP
rs1226242824	2812	dbSNP
rs1478294688	2814	dbSNP
rs915099677	2816	dbSNP
rs946530951	2817	dbSNP
rs1420766357	2818	dbSNP
rs547363534	2819	dbSNP
rs1042300563	2820	dbSNP
rs573053352	2824	dbSNP
rs910391151	2826	dbSNP
rs1398155068	2827	dbSNP
rs934683607	2831	dbSNP
rs1305822503	2832	dbSNP
rs942779444	2835	dbSNP
rs1041481642	2836	dbSNP
rs1396599579	2840	dbSNP
rs1384735516	2841	dbSNP
rs1321939821	2842	dbSNP
rs901163708	2843	dbSNP
rs1286072051	2849	dbSNP
rs1476991627	2859	dbSNP
rs1330884995	2861	dbSNP
rs1199840821	2862	dbSNP
rs1406025067	2862	dbSNP
rs1224454172	2863	dbSNP
rs3834609	2863	dbSNP
rs564002426	2863	dbSNP
rs1049821043	2864	dbSNP
rs1411295669	2864	dbSNP
rs1316664590	2865	dbSNP
rs113962350	2866	dbSNP
rs896701225	2866	dbSNP
rs888635235	2869	dbSNP
rs59275034	2870	dbSNP
rs1471279815	2871	dbSNP
rs1233709360	2876	dbSNP
rs1005694286	2880	dbSNP
rs1186908874	2887	dbSNP
rs1023803797	2891	dbSNP
rs1015861186	2892	dbSNP
rs961888466	2896	dbSNP
rs1204871827	2898	dbSNP
rs1252017693	2904	dbSNP
rs1341678491	2908	dbSNP
rs1266609542	2913	dbSNP
rs1225898221	2919	dbSNP
rs1208319921	2922	dbSNP
rs1266326436	2924	dbSNP
rs3760531	2925	dbSNP
rs1035128731	2926	dbSNP
rs1260934975	2931	dbSNP
rs959052938	2932	dbSNP
rs1477479413	2937	dbSNP
rs1401127698	2938	dbSNP
rs990550194	2940	dbSNP
rs1162921361	2941	dbSNP
rs1021974281	2942	dbSNP
rs1245058593	2942	dbSNP
rs1374324444	2948	dbSNP
rs1184354146	2950	dbSNP
rs956671943	2951	dbSNP
rs1246768856	2952	dbSNP
rs967864879	2953	dbSNP
rs1030411595	2954	dbSNP
rs954592448	2956	dbSNP
rs1226259646	2962	dbSNP
rs1360899090	2966	dbSNP
rs977856563	2967	dbSNP
rs1162298455	2976	dbSNP
rs986043930	2985	dbSNP
rs1290588987	2986	dbSNP
rs377114076	2992	dbSNP
rs1391074030	2993	dbSNP
rs1323078372	2995	dbSNP
rs1403802973	3000	dbSNP
rs903675696	3001	dbSNP
rs941890338	3010	dbSNP
rs1164258807	3012	dbSNP
rs944652371	3017	dbSNP
rs1448991857	3019	dbSNP
rs974549280	3026	dbSNP
rs976010865	3030	dbSNP
rs922614945	3031	dbSNP
rs1339063643	3041	dbSNP
rs932615308	3045	dbSNP
rs1049852985	3048	dbSNP
rs1246499398	3051	dbSNP
rs1399957887	3052	dbSNP
rs930054752	3055	dbSNP
rs1047025235	3060	dbSNP
rs888498407	3068	dbSNP
rs1328281636	3069	dbSNP
rs1292118474	3070	dbSNP
rs1242813140	3071	dbSNP
rs896522802	3072	dbSNP
rs1339496326	3083	dbSNP
rs941510805	3088	dbSNP
rs561580614	3091	dbSNP
rs1037238305	3093	dbSNP
rs1283647624	3094	dbSNP
rs1215101389	3098	dbSNP
rs897309000	3102	dbSNP
rs1487897080	3103	dbSNP
rs1272855737	3113	dbSNP
rs1045367495	3114	dbSNP
rs1367657047	3120	dbSNP
rs905349377	3126	dbSNP
rs1187038954	3127	dbSNP
rs529337044	3137	dbSNP
rs1035255276	3141	dbSNP
rs1429613060	3159	dbSNP
rs894818937	3164	dbSNP
rs1189821945	3165	dbSNP
rs1481638091	3170	dbSNP
rs1421528227	3174	dbSNP
rs1011835512	3177	dbSNP
rs1032940911	3184	dbSNP
rs1252541578	3184	dbSNP
rs1204687858	3185	dbSNP
rs1022004969	3186	dbSNP
rs1426213943	3189	dbSNP
rs1276476039	3190	dbSNP
rs1165810737	3194	dbSNP
rs1225066566	3195	dbSNP
rs1345946000	3200	dbSNP
rs1009737887	3203	dbSNP
rs967812667	3204	dbSNP
rs1029944138	3210	dbSNP
rs1299961336	3214	dbSNP
rs1462606571	3215	dbSNP
rs977800958	3216	dbSNP
rs1174950931	3217	dbSNP
rs1471124628	3221	dbSNP
rs1419561896	3222	dbSNP
rs1181984914	3224	dbSNP
rs550842385	3228	dbSNP
rs1252282251	3229	dbSNP
rs1177249187	3233	dbSNP
rs1031279673	3237	dbSNP
rs1254131234	3239	dbSNP
rs1205489150	3240	dbSNP
rs1289982235	3251	dbSNP
rs1323914662	3254	dbSNP
rs370510164	3255	dbSNP
rs965885743	3259	dbSNP
rs1226416233	3262	dbSNP
rs1315317509	3269	dbSNP
rs1309455196	3270	dbSNP
rs1392001222	3272	dbSNP
rs1407559778	3272	dbSNP
rs963278284	3272	dbSNP
rs563003253	3278	dbSNP
rs921842751	3279	dbSNP
rs533134861	3280	dbSNP
rs1461707163	3281	dbSNP
rs983311404	3282	dbSNP
rs1206538602	3299	dbSNP
rs1248480827	3300	dbSNP
rs201886832	3301	dbSNP
rs1486745177	3304	dbSNP
rs932646807	3309	dbSNP
rs985418001	3310	dbSNP
rs1045105795	3312	dbSNP
rs909880395	3314	dbSNP
rs879921405	3315	dbSNP
rs1216306856	3322	dbSNP
rs1320497576	3324	dbSNP
rs1262417259	3332	dbSNP
rs1387597220	3345	dbSNP
rs1289023859	3346	dbSNP
rs1037102093	3349	dbSNP
rs199744223	3352	dbSNP
rs200697396	3353	dbSNP
rs1243244260	3365	dbSNP
rs1009315544	3380	dbSNP
rs892660143	3380	dbSNP
rs1051481979	3387	dbSNP
rs1007151053	3390	dbSNP
rs201812431	3392	dbSNP
rs1209094685	3396	dbSNP
rs551768610	3397	dbSNP
rs200093144	3398	dbSNP
rs1360293738	3401	dbSNP
rs1297422624	3402	dbSNP
rs567142236	3412	dbSNP
rs1328764841	3415	dbSNP
rs1296734429	3417	dbSNP
rs1160378329	3420	dbSNP
rs201099164	3426	dbSNP
rs895363813	3428	dbSNP
rs1026145763	3434	dbSNP
rs1366028921	3443	dbSNP
rs1424670954	3444	dbSNP
rs1369417465	3449	dbSNP
rs201703604	3454	dbSNP
rs1165709653	3461	dbSNP
rs1476351778	3473	dbSNP
rs1373617274	3476	dbSNP
rs1465029102	3477	dbSNP
rs950633891	3478	dbSNP
rs1021948508	3480	dbSNP
rs1302294715	3482	dbSNP
rs1406925389	3483	dbSNP
rs903514551	3488	dbSNP
rs199946991	3494	dbSNP
rs1194221361	3495	dbSNP
rs982852870	3505	dbSNP
rs201132068	3510	dbSNP
rs202167768	3512	dbSNP
rs917980904	3513	dbSNP
rs747714385	3514	dbSNP
rs1232926583	3515	dbSNP
rs771712780	3516	dbSNP
rs1375568543	3531	dbSNP
rs777445843	3532	dbSNP
rs1321616771	3537	dbSNP
rs1030724668	3546	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.