>UBE2N|NM_003348|3'UTR
   1 ATTGATACGATCATCAAGTGTGCATCACTTCTCCTGTTCTGCCAAGACTTCCTCCTCTTTGTTTGCATTTAATGGACACA
  81 GTCTTAGAAACATTACAGAATAAAAAAGCCCAGACATCTTCAGTCCTTTGGTGATTAAATGCACATTAGCAAATCTATGT
 161 CTTGTCCTGATTCACTGTCATAAAGCATGAGCAGAGGCTAGAAGTATCATCTGGATTGTTGTGAAACGTTTAAAAGCAGT
 241 GGCCCCTCCCTGCTTTTATTCATTTCCCCCATCCTGGTTTAAGTATAAAGCACTGTGAATGAAGGTAGTTGTCAGGTTAG
 321 CTGCAGGGGTGTGGGTGTTTTTATTTTATTTTATTTTATTTTATTTTTGAGGGGGGAGGTAGTTTAATTTTATGGGCTCC
 401 TTTCCCCCTTTTTTGGTGATCTAATTGCATTGGTTAAAAGCAGCTAACCAGGTCTTTAGAATATGCTCTAGCCAAGTCTA
 481 ACTTTATTTAGACGCTGTAGATGGACAAGCTTGATTGTTGGAACCAAAATGGGAACATTAAACAAACATCACAGCCCTCA
 561 CTAATAACATTGCTGTCAAGTGTAGATTCCCCCCTTCAAAAAAAGCTTGTGACCATTTTGTATGGCTTGTCTGGAAACTT
 641 CTGTAAATCTTATGTTTTAGTAAAATATTTTTTGTTATTCTACTTTGCCTTTGTACAGTTTATTTTACTGTGTTTATTTC
 721 ATTTTCCCAATTTGACAATCGTATTTTAAAATTGAAACTGATGGAACATTCTTTCTTGGTCTTCACCATCTGACAAATTG
 801 AATGGCAAGAGGTGGATTTTGCCAGTTTCTTTTCACTGATGCAGATTTGTGTTAAGATAGTACTGAATGGAGTATTTATA
 881 AACTGGCCCTGAGCATGCATAAAGCATCAGTATCTGACCTTTTTTTAACCTTCTAGGAATTTGAAATAAATGTGTTTGTG
 961 TTGTCTGATTAGATGATCATTGGTGTCTTGCCACAATGTTTAAAAATTACTGTACAGGAAAGTCACAGCAAAGATAGCAG
1041 TTGTGACTGACATGTAGGACTTTCACAGTTGTGCCACATTTTTGCCTAAAATTTGGGTTATGACATTTTTCTTGGTTCTT
1121 ATCTGAAAATTTCATCTGTAACCTTTCATGTGTGTTAAGAAACACTGATCTGATCATTTGGGATTTGCTGAGGCATTTGT
1201 GAGTCTTCCTTATAAACCTGATGAGCAGATCTCAACTATCTAGCTTGTGTGTCATCAGAAAGGTTTATCCCTTTGAGAGT
1281 ATCAAGTCCTCAGTTAATGATTCTTGCTTTCATCCCTCCAGTATTTGCTGTGGGAGCTCGTTTTATTCTTTAATTTGGAA
1361 TTCAGTAATTTTTCTTCTTTATTGACGAATTCCTCCCCTCACAAAACTGTTCTTTCCCACCTCTCTCCATATCTAATTCC
1441 TGATTCTTGTTATTTTTAAGTCATAAATGTAGCCAGTCATAAATACATAAATGTTAACCTTCGGGTTGCAACCTTGTCTC
1521 TTGCAGTTTAAGGTAATGGATATTGTAGCCCATTTGAATTTTCTTCACTCTTATTCTCGTAATTCTGGAGTTTCTTCAGA
1601 TTGTGGTGTATTTTATTGTGCTCCTATGTAAGATGAAGAATTAACTATTAAAATTACATTTTCAACATACAAAAGCTTTT
1681 GATGACTGGTAACTGGTATCCTTCCAAATAAATGCATTGCTTGGTAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' agauuGUGGUGUCACACCAAAc 5' | :|| | |||||| | Target 5' agtttCTTCAGATTGTGGTGTa 3'	1589 - 1610	125.00	-8.52
2	miRNA 3' agauuguggugucacACCAAAc 5' |||||| Target 5' tcatttcccccatccTGGTTTa 3'	260 - 281	120.00	-6.00
3	miRNA 3' agaUUGUGGUGUCACACCAAAc 5' ||:: || : |||| || Target 5' ttgAATGGCAAGAGGTGGATTt 3'	798 - 819	119.00	-8.30

Mutant ID	Mutant Position	Mutant Source
COSN14597999	8	COSMIC
COSN30168962	98	COSMIC
COSN13425395	112	COSMIC
COSN30135612	124	COSMIC
COSN31587474	155	COSMIC
COSN31542526	175	COSMIC
COSN30167639	261	COSMIC
COSN26668359	274	COSMIC
COSN31541001	336	COSMIC
COSN30110984	338	COSMIC
COSN19551831	339	COSMIC
COSN30121942	358	COSMIC
COSN31516059	361	COSMIC
COSN26571233	363	COSMIC
COSN26644277	395	COSMIC
COSN30173291	452	COSMIC
COSN31520845	459	COSMIC
COSN31595919	567	COSMIC
COSN31595916	597	COSMIC
COSN31567464	646	COSMIC
COSN31524063	661	COSMIC
COSN26668073	667	COSMIC
COSN19325056	761	COSMIC
COSN31585348	829	COSMIC
COSN32058588	926	COSMIC
COSN26635705	929	COSMIC
COSN17131960	1244	COSMIC
COSN32088587	1395	COSMIC
COSN1594182	1903	COSMIC
COSN32088586	2121	COSMIC
COSN5871208	3035	COSMIC
COSN16579714	3110	COSMIC
COSN23189726	3792	COSMIC
COSN23189328	3794	COSMIC
COSN1594180	3839	COSMIC
COSN20731842	4112	COSMIC
COSN29550798	4155	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs146107137	1	dbSNP
rs1389279986	7	dbSNP
rs745829441	8	dbSNP
rs752340935	8	dbSNP
rs1370831800	9	dbSNP
rs767429440	10	dbSNP
rs773664444	17	dbSNP
rs993437560	20	dbSNP
rs759405179	21	dbSNP
rs1228428281	33	dbSNP
rs1311489773	34	dbSNP
rs370542398	35	dbSNP
rs201199367	36	dbSNP
rs770631026	36	dbSNP
rs1163596627	37	dbSNP
rs766399603	41	dbSNP
rs1464822382	43	dbSNP
rs1366530013	46	dbSNP
rs761995234	51	dbSNP
rs1207328284	52	dbSNP
rs1239750713	54	dbSNP
rs1483578765	60	dbSNP
rs1181367964	61	dbSNP
rs111847364	66	dbSNP
rs529954161	67	dbSNP
rs1366062945	73	dbSNP
rs1174333243	75	dbSNP
rs1412503860	80	dbSNP
rs1456529723	86	dbSNP
rs1037987947	98	dbSNP
rs1433030549	102	dbSNP
rs1006170751	114	dbSNP
rs189963688	116	dbSNP
rs1050296265	137	dbSNP
rs1201917556	140	dbSNP
rs1411324645	147	dbSNP
rs539238615	155	dbSNP
rs185386395	157	dbSNP
rs922985274	166	dbSNP
rs1281268838	173	dbSNP
rs535250425	173	dbSNP
rs566129028	179	dbSNP
rs1262481605	201	dbSNP
rs1235844834	207	dbSNP
rs1230787558	209	dbSNP
rs1183106479	213	dbSNP
rs1251404386	220	dbSNP
rs1472105010	221	dbSNP
rs1175283486	222	dbSNP
rs1311430321	227	dbSNP
rs1301510198	228	dbSNP
rs1406342839	229	dbSNP
rs1431132205	232	dbSNP
rs1308187617	238	dbSNP
rs552851496	240	dbSNP
rs35415779	241	dbSNP
rs1277039769	243	dbSNP
rs1296969542	246	dbSNP
rs748287246	247	dbSNP
rs532669106	249	dbSNP
rs1387766821	250	dbSNP
rs1344358811	252	dbSNP
rs990138033	260	dbSNP
rs563744475	263	dbSNP
rs958341008	270	dbSNP
rs1179392522	271	dbSNP
rs34704075	271	dbSNP
rs1465830698	285	dbSNP
rs1248287675	291	dbSNP
rs569001583	314	dbSNP
rs151131121	316	dbSNP
rs143190704	326	dbSNP
rs1024977575	335	dbSNP
rs993552151	343	dbSNP
rs1350784201	357	dbSNP
rs752099432	361	dbSNP
rs1016305658	363	dbSNP
rs1050782137	368	dbSNP
rs527860095	368	dbSNP
rs889067850	368	dbSNP
rs1337667779	369	dbSNP
rs1211911114	372	dbSNP
rs149103079	374	dbSNP
rs1041482012	375	dbSNP
rs1251043101	381	dbSNP
rs192648563	385	dbSNP
rs1198707574	386	dbSNP
rs1188606718	393	dbSNP
rs1482899684	394	dbSNP
rs945820305	396	dbSNP
rs1474153517	407	dbSNP
rs1164601206	413	dbSNP
rs766501094	417	dbSNP
rs1414073632	423	dbSNP
rs1256330205	428	dbSNP
rs1225122228	431	dbSNP
rs34880795	435	dbSNP
rs1405079248	451	dbSNP
rs1315621205	452	dbSNP
rs892777876	453	dbSNP
rs531682798	457	dbSNP
rs1319951143	459	dbSNP
rs1218708349	461	dbSNP
rs1378351426	466	dbSNP
rs1803750	468	dbSNP
rs775252659	480	dbSNP
rs937016882	486	dbSNP
rs750431906	488	dbSNP
rs374372794	493	dbSNP
rs1232449423	494	dbSNP
rs1271080583	500	dbSNP
rs1466180633	510	dbSNP
rs1209223282	516	dbSNP
rs559254453	520	dbSNP
rs1395914977	528	dbSNP
rs1403539918	529	dbSNP
rs1339036548	538	dbSNP
rs1189036952	547	dbSNP
rs1237684465	557	dbSNP
rs546081642	561	dbSNP
rs1399830817	563	dbSNP
rs980993732	565	dbSNP
rs949522478	572	dbSNP
rs1158985226	573	dbSNP
rs1366741942	584	dbSNP
rs918117990	589	dbSNP
rs1335006563	593	dbSNP
rs972119708	599	dbSNP
rs1423107685	612	dbSNP
rs1330899197	620	dbSNP
rs643636	621	dbSNP
rs1228785824	622	dbSNP
rs564455412	624	dbSNP
rs1260015459	625	dbSNP
rs981137159	629	dbSNP
rs577167836	632	dbSNP
rs1278765489	636	dbSNP
rs1185290052	642	dbSNP
rs1485129152	642	dbSNP
rs1456330320	643	dbSNP
rs574299	648	dbSNP
rs1253568622	653	dbSNP
rs1256996929	654	dbSNP
rs643258	660	dbSNP
rs1181978097	662	dbSNP
rs643247	667	dbSNP
rs1196068163	679	dbSNP
rs188599636	682	dbSNP
rs775200382	687	dbSNP
rs951282311	689	dbSNP
rs537489429	691	dbSNP
rs1432973044	693	dbSNP
rs995289759	693	dbSNP
rs1351353654	694	dbSNP
rs1410196231	694	dbSNP
rs1281852483	700	dbSNP
rs1243444310	702	dbSNP
rs1333879695	705	dbSNP
rs953520363	706	dbSNP
rs1341576716	709	dbSNP
rs1256543588	718	dbSNP
rs1317863191	721	dbSNP
rs898371950	738	dbSNP
rs1346473328	740	dbSNP
rs1208114625	741	dbSNP
rs1028873880	742	dbSNP
rs1483215655	751	dbSNP
rs1195558263	752	dbSNP
rs997440336	767	dbSNP
rs901675509	771	dbSNP
rs1444986310	777	dbSNP
rs1020154888	778	dbSNP
rs1452595653	781	dbSNP
rs1010390085	794	dbSNP
rs183521994	796	dbSNP
rs1297375302	798	dbSNP
rs1394009324	804	dbSNP
rs1388333684	812	dbSNP
rs1301818958	824	dbSNP
rs1332488009	825	dbSNP
rs145013241	827	dbSNP
rs1231429819	834	dbSNP
rs896577894	836	dbSNP
rs1342404382	842	dbSNP
rs1226176788	847	dbSNP
rs1249289674	849	dbSNP
rs1489632128	856	dbSNP
rs1056447913	858	dbSNP
rs936984491	862	dbSNP
rs191289755	863	dbSNP
rs1467579007	868	dbSNP
rs781377469	870	dbSNP
rs1015547804	875	dbSNP
rs935355938	880	dbSNP
rs924176621	881	dbSNP
rs1428021707	882	dbSNP
rs1168555904	887	dbSNP
rs1370426242	897	dbSNP
rs1385784446	904	dbSNP
rs1045283813	907	dbSNP
rs1185391672	908	dbSNP
rs1293959350	908	dbSNP
rs1044035727	909	dbSNP
rs918067059	910	dbSNP
rs1322491577	914	dbSNP
rs1237291844	927	dbSNP
rs1269197237	927	dbSNP
rs114331208	929	dbSNP
rs922056584	932	dbSNP
rs1323200872	942	dbSNP
rs1245983395	949	dbSNP
rs1287365044	952	dbSNP
rs975328759	953	dbSNP
rs759459616	964	dbSNP
rs774419854	970	dbSNP
rs1249228111	978	dbSNP
rs1359582510	988	dbSNP
rs909272929	992	dbSNP
rs1238545266	996	dbSNP
rs912323645	998	dbSNP
rs953369961	1007	dbSNP
rs1165346065	1034	dbSNP
rs986469696	1035	dbSNP
rs558839499	1037	dbSNP
rs1459706037	1044	dbSNP
rs1161198192	1048	dbSNP
rs78184142	1051	dbSNP
rs1310365367	1055	dbSNP
rs1429397206	1063	dbSNP
rs1025511821	1070	dbSNP
rs1444834429	1075	dbSNP
rs774675020	1087	dbSNP
rs975980729	1094	dbSNP
rs1396301649	1097	dbSNP
rs1292322110	1100	dbSNP
rs570059090	1104	dbSNP
rs1353913309	1105	dbSNP
rs774045155	1114	dbSNP
rs1329549460	1115	dbSNP
rs114629734	1121	dbSNP
rs80282991	1122	dbSNP
rs1483631330	1123	dbSNP
rs1367584684	1141	dbSNP
rs1023440363	1147	dbSNP
rs1187441634	1149	dbSNP
rs1156957472	1150	dbSNP
rs1417709355	1152	dbSNP
rs1379626573	1154	dbSNP
rs892962554	1156	dbSNP
rs1408620580	1166	dbSNP
rs1012514607	1169	dbSNP
rs1158913263	1172	dbSNP
rs896552636	1173	dbSNP
rs187564458	1176	dbSNP
rs1360344132	1196	dbSNP
rs1244590851	1208	dbSNP
rs1035545857	1213	dbSNP
rs1197785715	1213	dbSNP
rs1373257853	1215	dbSNP
rs1490417586	1215	dbSNP
rs183827081	1219	dbSNP
rs1213834576	1227	dbSNP
rs528127135	1229	dbSNP
rs902555972	1231	dbSNP
rs193299810	1238	dbSNP
rs1343366470	1240	dbSNP
rs896711640	1242	dbSNP
rs1224308076	1253	dbSNP
rs1484182783	1270	dbSNP
rs769381081	1281	dbSNP
rs1233299956	1285	dbSNP
rs946921871	1291	dbSNP
rs1427215765	1295	dbSNP
rs940829461	1300	dbSNP
rs900772792	1316	dbSNP
rs1431316135	1321	dbSNP
rs1049136610	1323	dbSNP
rs1296353232	1335	dbSNP
rs1354246049	1336	dbSNP
rs1399537171	1337	dbSNP
rs1039183740	1340	dbSNP
rs149938511	1351	dbSNP
rs912304247	1358	dbSNP
rs976052785	1368	dbSNP
rs1301426417	1374	dbSNP
rs1344566420	1376	dbSNP
rs986992035	1377	dbSNP
rs1272565377	1379	dbSNP
rs1436971192	1380	dbSNP
rs532344393	1380	dbSNP
rs1202207215	1381	dbSNP
rs929728596	1382	dbSNP
rs918217588	1386	dbSNP
rs747803618	1387	dbSNP
rs1392662282	1389	dbSNP
rs1430994947	1396	dbSNP
rs1190863530	1401	dbSNP
rs1168097422	1403	dbSNP
rs1487714710	1406	dbSNP
rs113958401	1407	dbSNP
rs1218625559	1408	dbSNP
rs962581386	1416	dbSNP
rs1441218776	1417	dbSNP
rs1023999516	1418	dbSNP
rs1033299625	1423	dbSNP
rs1224520086	1424	dbSNP
rs1001272032	1425	dbSNP
rs1269774205	1426	dbSNP
rs1276610487	1429	dbSNP
rs990658485	1431	dbSNP
rs118054246	1446	dbSNP
rs1218055432	1446	dbSNP
rs960857649	1447	dbSNP
rs1335256284	1449	dbSNP
rs1251100883	1453	dbSNP
rs1465823415	1455	dbSNP
rs1193342030	1463	dbSNP
rs781476188	1465	dbSNP
rs11107016	1472	dbSNP
rs1024018851	1484	dbSNP
rs1165350898	1492	dbSNP
rs554640828	1502	dbSNP
rs1013849220	1503	dbSNP
rs999571951	1505	dbSNP
rs1391496123	1511	dbSNP
rs560751043	1513	dbSNP
rs1432757746	1514	dbSNP
rs1324900438	1518	dbSNP
rs1450402630	1519	dbSNP
rs1357361730	1525	dbSNP
rs1022281111	1529	dbSNP
rs1271173588	1535	dbSNP
rs541521284	1542	dbSNP
rs747313702	1549	dbSNP
rs900740259	1550	dbSNP
rs1283014122	1551	dbSNP
rs969325727	1552	dbSNP
rs1335772388	1573	dbSNP
rs1444792848	1574	dbSNP
rs1039727152	1575	dbSNP
rs1189539208	1576	dbSNP
rs780540143	1578	dbSNP
rs887934578	1579	dbSNP
rs1475056002	1581	dbSNP
rs11558878	1585	dbSNP
rs944887804	1586	dbSNP
rs572411507	1591	dbSNP
rs1049725137	1602	dbSNP
rs1487937514	1608	dbSNP
rs890578321	1616	dbSNP
rs1168147949	1617	dbSNP
rs1047891216	1625	dbSNP
rs1286326689	1626	dbSNP
rs1419551982	1627	dbSNP
rs1313664556	1638	dbSNP
rs1375124053	1642	dbSNP
rs559003295	1645	dbSNP
rs929697564	1664	dbSNP
rs918355264	1675	dbSNP
rs538872467	1691	dbSNP
rs1037984345	1695	dbSNP
rs1278888657	1698	dbSNP
rs1347869385	1707	dbSNP
rs913271760	1709	dbSNP
rs988743387	1714	dbSNP
rs146590886	1715	dbSNP
rs1209168147	1723	dbSNP
rs1253171839	1729	dbSNP
rs1420058982	1730	dbSNP
rs758865407	1733	dbSNP
rs1362595015	1736	dbSNP
rs991184369	1737	dbSNP
rs960659832	1746	dbSNP
rs980311447	1749	dbSNP
rs927754344	1753	dbSNP
rs1433156902	1766	dbSNP
rs1023969542	1767	dbSNP
rs1391788988	1773	dbSNP
rs1013966690	1774	dbSNP
rs542501784	1776	dbSNP
rs1333956925	1788	dbSNP
rs1235807588	1792	dbSNP
rs1303587666	1797	dbSNP
rs1275124090	1800	dbSNP
rs961020349	1804	dbSNP
rs541889672	1810	dbSNP
rs750529008	1812	dbSNP
rs1481138224	1814	dbSNP
rs12822459	1817	dbSNP
rs12821957	1818	dbSNP
rs1470273668	1820	dbSNP
rs1314382624	1822	dbSNP
rs1252389937	1846	dbSNP
rs144241861	1847	dbSNP
rs1005123193	1849	dbSNP
rs866951735	1854	dbSNP
rs879626874	1860	dbSNP
rs1462283956	1861	dbSNP
rs12821933	1866	dbSNP
rs777369545	1878	dbSNP
rs1167146883	1881	dbSNP
rs1022416923	1883	dbSNP
rs765280850	1891	dbSNP
rs1326509659	1892	dbSNP
rs1369564741	1893	dbSNP
rs1027924667	1895	dbSNP
rs1297252134	1902	dbSNP
rs139525168	1903	dbSNP
rs757463960	1906	dbSNP
rs1250038150	1907	dbSNP
rs1017604502	1910	dbSNP
rs1461139492	1912	dbSNP
rs150815057	1922	dbSNP
rs1214792062	1925	dbSNP
rs890725403	1929	dbSNP
rs1467154334	1930	dbSNP
rs1188405939	1932	dbSNP
rs1171884325	1940	dbSNP
rs1047863360	1956	dbSNP
rs751647245	1964	dbSNP
rs188291931	1969	dbSNP
rs891778242	1970	dbSNP
rs1184799283	1972	dbSNP
rs376669439	1976	dbSNP
rs1459388799	1977	dbSNP
rs896899259	1979	dbSNP
rs565684259	1986	dbSNP
rs1381246284	1989	dbSNP
rs1293002746	1998	dbSNP
rs1236688017	2003	dbSNP
rs372751723	2008	dbSNP
rs1481048126	2015	dbSNP
rs1273082571	2018	dbSNP
rs1253361532	2027	dbSNP
rs941034156	2028	dbSNP
rs925837624	2029	dbSNP
rs1203544880	2035	dbSNP
rs979988286	2038	dbSNP
rs916193374	2040	dbSNP
rs1476054692	2048	dbSNP
rs1188443957	2049	dbSNP
rs1321239987	2053	dbSNP
rs1422046842	2053	dbSNP
rs1054808413	2061	dbSNP
rs1345198378	2062	dbSNP
rs1452469222	2066	dbSNP
rs1295908545	2068	dbSNP
rs1376951001	2078	dbSNP
rs917114159	2086	dbSNP
rs1293131946	2089	dbSNP
rs754088165	2090	dbSNP
rs1354098082	2098	dbSNP
rs1225914587	2101	dbSNP
rs1308340890	2103	dbSNP
rs552227686	2105	dbSNP
rs1361546883	2107	dbSNP
rs1237041316	2112	dbSNP
rs1306729514	2112	dbSNP
rs765267798	2114	dbSNP
rs532383319	2121	dbSNP
rs1373597406	2122	dbSNP
rs575215399	2126	dbSNP
rs1211317218	2128	dbSNP
rs1299562971	2129	dbSNP
rs1482156094	2133	dbSNP
rs141586817	2134	dbSNP
rs1408656544	2135	dbSNP
rs1417977801	2136	dbSNP
rs1156346245	2140	dbSNP
rs966568382	2143	dbSNP
rs984169399	2155	dbSNP
rs952415133	2181	dbSNP
rs1028291309	2189	dbSNP
rs996466790	2190	dbSNP
rs900671191	2196	dbSNP
rs1019148809	2199	dbSNP
rs915326339	2212	dbSNP
rs1008971207	2213	dbSNP
rs1348706162	2221	dbSNP
rs1252890543	2227	dbSNP
rs112504286	2228	dbSNP
rs1278499398	2238	dbSNP
rs891843075	2239	dbSNP
rs1053224969	2242	dbSNP
rs558669534	2262	dbSNP
rs148804133	2266	dbSNP
rs1480306240	2270	dbSNP
rs1488292467	2279	dbSNP
rs1269651610	2289	dbSNP
rs904530589	2297	dbSNP
rs1254267591	2300	dbSNP
rs1454333360	2301	dbSNP
rs1044283229	2306	dbSNP
rs1422645037	2307	dbSNP
rs948677931	2325	dbSNP
rs964830671	2326	dbSNP
rs1017992115	2336	dbSNP
rs34934936	2337	dbSNP
rs1445139573	2341	dbSNP
rs1008917360	2344	dbSNP
rs1490804726	2345	dbSNP
rs1283874319	2355	dbSNP
rs529971319	2357	dbSNP
rs1238016716	2358	dbSNP
rs992593157	2362	dbSNP
rs1273276538	2363	dbSNP
rs939888679	2366	dbSNP
rs908249715	2370	dbSNP
rs1217074414	2376	dbSNP
rs759389384	2386	dbSNP
rs12816436	2387	dbSNP
rs1406304096	2390	dbSNP
rs1026555533	2394	dbSNP
rs1028030879	2398	dbSNP
rs1476225100	2404	dbSNP
rs1186760007	2405	dbSNP
rs1288838255	2414	dbSNP
rs993620527	2416	dbSNP
rs974975724	2419	dbSNP
rs144380439	2420	dbSNP
rs1167672748	2433	dbSNP
rs1395916956	2438	dbSNP
rs964989310	2442	dbSNP
rs12311641	2446	dbSNP
rs144039269	2447	dbSNP
rs1430266003	2450	dbSNP
rs1431680590	2458	dbSNP
rs894909517	2459	dbSNP
rs1339549730	2460	dbSNP
rs956233154	2464	dbSNP
rs772888229	2468	dbSNP
rs576250034	2474	dbSNP
rs1208717545	2479	dbSNP
rs1000319837	2481	dbSNP
rs1448228123	2486	dbSNP
rs1260901850	2488	dbSNP
rs1241182563	2490	dbSNP
rs1190562351	2494	dbSNP
rs1419203716	2495	dbSNP
rs1475200299	2508	dbSNP
rs904519543	2528	dbSNP
rs1044398634	2534	dbSNP
rs769341783	2535	dbSNP
rs73216891	2539	dbSNP
rs781688702	2540	dbSNP
rs1262200627	2545	dbSNP
rs1042367453	2547	dbSNP
rs536556825	2562	dbSNP
rs1314558083	2565	dbSNP
rs544677099	2575	dbSNP
rs1243893513	2578	dbSNP
rs1283600542	2582	dbSNP
rs1352155080	2583	dbSNP
rs989339912	2588	dbSNP
rs1224781623	2591	dbSNP
rs1223904399	2596	dbSNP
rs1337838622	2597	dbSNP
rs1294261537	2608	dbSNP
rs768124096	2609	dbSNP
rs910662656	2611	dbSNP
rs987866196	2614	dbSNP
rs1185993437	2618	dbSNP
rs1048619051	2619	dbSNP
rs931103287	2622	dbSNP
rs1158107558	2623	dbSNP
rs1469666954	2626	dbSNP
rs1436758511	2628	dbSNP
rs1313724869	2633	dbSNP
rs554444239	2642	dbSNP
rs1375796465	2645	dbSNP
rs1395262899	2650	dbSNP
rs747403274	2652	dbSNP
rs1337509019	2655	dbSNP
rs1026523160	2658	dbSNP
rs975044703	2660	dbSNP
rs972250553	2683	dbSNP
rs1178909535	2694	dbSNP
rs965058387	2695	dbSNP
rs1199145312	2696	dbSNP
rs1253245338	2698	dbSNP
rs963606874	2702	dbSNP
rs1178587686	2703	dbSNP
rs1016359703	2709	dbSNP
rs1455666833	2714	dbSNP
rs1013105543	2718	dbSNP
rs1372533036	2721	dbSNP
rs1465333943	2730	dbSNP
rs1170665941	2731	dbSNP
rs1398525140	2732	dbSNP
rs1385488789	2733	dbSNP
rs138475858	2738	dbSNP
rs894872868	2739	dbSNP
rs1410404974	2744	dbSNP
rs1330596926	2746	dbSNP
rs1193995930	2747	dbSNP
rs956396113	2765	dbSNP
rs1303657295	2773	dbSNP
rs1330188310	2779	dbSNP
rs1231518284	2789	dbSNP
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rs1340509639	2806	dbSNP
rs1033467673	2809	dbSNP
rs1198529099	2819	dbSNP
rs1256742675	2822	dbSNP
rs1469861537	2824	dbSNP
rs1263838947	2831	dbSNP
rs1031877732	2839	dbSNP
rs7484994	2856	dbSNP
rs1431717062	2865	dbSNP
rs565656414	2875	dbSNP
rs1195615848	2880	dbSNP
rs1374513495	2883	dbSNP
rs1181519729	2884	dbSNP
rs374007839	2890	dbSNP
rs1003615392	2895	dbSNP
rs552319175	2896	dbSNP
rs1263353179	2902	dbSNP
rs780350346	2903	dbSNP
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rs1315714776	2910	dbSNP
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rs1250202916	2922	dbSNP
rs1389408600	2930	dbSNP
rs1384651300	2931	dbSNP
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rs1227540544	2937	dbSNP
rs1327345512	2939	dbSNP
rs1054007963	2941	dbSNP
rs1328698988	2943	dbSNP
rs943246927	2946	dbSNP
rs910619514	2953	dbSNP
rs1012831406	2955	dbSNP
rs7956793	2962	dbSNP
rs933409404	2966	dbSNP
rs1264880389	2968	dbSNP
rs569870932	2971	dbSNP
rs183804732	2982	dbSNP
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rs1478011009	2990	dbSNP
rs1192715850	2991	dbSNP
rs1421380108	2997	dbSNP
rs1016543739	3000	dbSNP
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rs1165404623	3014	dbSNP
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rs958939392	3022	dbSNP
rs1455956584	3025	dbSNP
rs561052680	3027	dbSNP
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rs1296800545	3033	dbSNP
rs1357771055	3043	dbSNP
rs1234365935	3055	dbSNP
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rs1365144940	3072	dbSNP
rs1241332474	3074	dbSNP
rs1463652449	3081	dbSNP
rs1261496664	3089	dbSNP
rs1488122903	3094	dbSNP
rs1215607003	3099	dbSNP
rs1020609038	3100	dbSNP
rs576856182	3104	dbSNP
rs1182330925	3105	dbSNP
rs1255451908	3108	dbSNP
rs1421511320	3109	dbSNP
rs1160746720	3110	dbSNP
rs1380516533	3117	dbSNP
rs893715556	3120	dbSNP
rs1156461642	3122	dbSNP
rs1053743996	3123	dbSNP
rs558397756	3124	dbSNP
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rs1377669522	3130	dbSNP
rs912263469	3132	dbSNP
rs988125357	3136	dbSNP
rs7968453	3137	dbSNP
rs1238198183	3142	dbSNP
rs1282769654	3149	dbSNP
rs1349761151	3158	dbSNP
rs7953721	3158	dbSNP
rs1185207254	3163	dbSNP
rs142731076	3178	dbSNP
rs1482270034	3182	dbSNP
rs1249456629	3185	dbSNP
rs191048548	3188	dbSNP
rs1022972773	3191	dbSNP
rs1438571678	3193	dbSNP
rs942068999	3197	dbSNP
rs960030887	3200	dbSNP
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rs753736601	3201	dbSNP
rs562633197	3209	dbSNP
rs991713957	3215	dbSNP
rs959219109	3216	dbSNP
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rs1332669739	3223	dbSNP
rs1027332964	3230	dbSNP
rs542860298	3235	dbSNP
rs981624942	3239	dbSNP
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rs970446560	3246	dbSNP
rs117777833	3249	dbSNP
rs1277586612	3250	dbSNP
rs1329839236	3269	dbSNP
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rs1258651606	3276	dbSNP
rs1456911234	3286	dbSNP
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rs1388611133	3289	dbSNP
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rs548367107	3294	dbSNP
rs185792206	3296	dbSNP
rs763050357	3302	dbSNP
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rs1430688157	3305	dbSNP
rs1171985311	3309	dbSNP
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rs1165228655	3310	dbSNP
rs1032427139	3313	dbSNP
rs1464128730	3323	dbSNP
rs979433389	3329	dbSNP
rs112527304	3331	dbSNP
rs1350558010	3331	dbSNP
rs1362834375	3336	dbSNP
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rs1220287719	3338	dbSNP
rs991517163	3347	dbSNP
rs879836802	3351	dbSNP
rs1317292718	3354	dbSNP
rs1196194641	3358	dbSNP
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rs1439222149	3368	dbSNP
rs1220315055	3369	dbSNP
rs138392057	3371	dbSNP
rs997329760	3373	dbSNP
rs1194932221	3377	dbSNP
rs1036198693	3379	dbSNP
rs1221108034	3379	dbSNP
rs1490651879	3380	dbSNP
rs1167746613	3398	dbSNP
rs1294670259	3400	dbSNP
rs1480001568	3402	dbSNP
rs1222392738	3405	dbSNP
rs982781345	3416	dbSNP
rs1321800703	3421	dbSNP
rs558887900	3421	dbSNP
rs897902304	3428	dbSNP
rs558543728	3429	dbSNP
rs1026867808	3439	dbSNP
rs1298641827	3440	dbSNP
rs34241939	3443	dbSNP
rs761386155	3445	dbSNP
rs189893472	3447	dbSNP
rs909179098	3449	dbSNP
rs1056213307	3454	dbSNP
rs150080739	3459	dbSNP
rs549877701	3460	dbSNP
rs558233261	3462	dbSNP
rs185484229	3468	dbSNP
rs1398721306	3470	dbSNP
rs928904371	3478	dbSNP
rs1158931780	3479	dbSNP
rs1470925254	3481	dbSNP
rs981592473	3488	dbSNP
rs1472489149	3492	dbSNP
rs140684111	3502	dbSNP
rs1426837548	3510	dbSNP
rs760301947	3513	dbSNP
rs1198059794	3528	dbSNP
rs376007359	3535	dbSNP
rs1043312357	3536	dbSNP
rs1158277996	3540	dbSNP
rs1214213750	3544	dbSNP
rs1446964381	3549	dbSNP
rs947665638	3553	dbSNP
rs913652386	3559	dbSNP
rs916069537	3562	dbSNP
rs1446635614	3566	dbSNP
rs752696790	3569	dbSNP
rs1207276703	3570	dbSNP
rs775876619	3572	dbSNP
rs938873660	3574	dbSNP
rs958035788	3583	dbSNP
rs1202590685	3586	dbSNP
rs151019207	3589	dbSNP
rs986221314	3590	dbSNP
rs951402501	3593	dbSNP
rs374364501	3601	dbSNP
rs148721593	3602	dbSNP
rs1440430739	3603	dbSNP
rs1268518858	3607	dbSNP
rs1428469202	3614	dbSNP
rs1344545955	3616	dbSNP
rs1178206390	3620	dbSNP
rs116984700	3621	dbSNP
rs1402297202	3622	dbSNP
rs1417629246	3624	dbSNP
rs1174164641	3626	dbSNP
rs1402660135	3627	dbSNP
rs1413776749	3630	dbSNP
rs1030235900	3645	dbSNP
rs1332154301	3646	dbSNP
rs1378416445	3646	dbSNP
rs1403401312	3649	dbSNP
rs973967297	3655	dbSNP
rs1175326269	3657	dbSNP
rs1235863411	3660	dbSNP
rs1470015839	3663	dbSNP
rs1344756961	3666	dbSNP
rs372449211	3679	dbSNP
rs997300296	3682	dbSNP
rs897622803	3683	dbSNP
rs1014716368	3685	dbSNP
rs564944849	3689	dbSNP
rs1377953637	3691	dbSNP
rs1243260305	3695	dbSNP
rs887877608	3697	dbSNP
rs1277148851	3699	dbSNP
rs963984833	3701	dbSNP
rs1170722018	3704	dbSNP
rs145556071	3705	dbSNP
rs937367402	3706	dbSNP
rs1262729751	3707	dbSNP
rs1204499522	3708	dbSNP
rs1325928398	3711	dbSNP
rs763435930	3713	dbSNP
rs1214117449	3715	dbSNP
rs1388083932	3718	dbSNP
rs1301580623	3719	dbSNP
rs1361176558	3719	dbSNP
rs1270737609	3720	dbSNP
rs531594280	3721	dbSNP
rs1436978526	3722	dbSNP
rs1380243007	3723	dbSNP
rs1280645778	3726	dbSNP
rs1008040260	3727	dbSNP
rs1218578556	3731	dbSNP
rs1452829212	3733	dbSNP
rs1267003698	3734	dbSNP
rs1360555127	3736	dbSNP
rs955393292	3738	dbSNP
rs1408933558	3742	dbSNP
rs1420812240	3744	dbSNP
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rs1170201026	3750	dbSNP
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rs1242842222	3755	dbSNP
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rs1462812602	3757	dbSNP
rs1231458722	3758	dbSNP
rs1203868472	3760	dbSNP
rs1308203723	3761	dbSNP
rs1275233472	3762	dbSNP
rs1905251	3763	dbSNP
rs1164935375	3764	dbSNP
rs1192789500	3764	dbSNP
rs1259632696	3764	dbSNP
rs1264974618	3764	dbSNP
rs1265076977	3764	dbSNP
rs1276885745	3764	dbSNP
rs1287037705	3764	dbSNP
rs1293729775	3764	dbSNP
rs1300374797	3764	dbSNP
rs1323563779	3764	dbSNP
rs1341528478	3764	dbSNP
rs1345286017	3764	dbSNP
rs1354580907	3764	dbSNP
rs1367398716	3764	dbSNP
rs1385445065	3764	dbSNP
rs1389653117	3764	dbSNP
rs1399893769	3764	dbSNP
rs1402250209	3764	dbSNP
rs1422293126	3764	dbSNP
rs1425007929	3764	dbSNP
rs1488512182	3764	dbSNP
rs58309798	3764	dbSNP
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rs1182380608	3765	dbSNP
rs1215677212	3765	dbSNP
rs1254820555	3765	dbSNP
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rs1442266888	3765	dbSNP
rs1484162745	3765	dbSNP
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rs779487801	3771	dbSNP
rs142005285	3772	dbSNP
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rs1419479814	3787	dbSNP
rs1157446222	3793	dbSNP
rs562670465	3796	dbSNP
rs946283504	3798	dbSNP
rs1453179651	3800	dbSNP
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rs1302804804	3804	dbSNP
rs1826592	3811	dbSNP
rs1403937771	3813	dbSNP
rs913369796	3817	dbSNP
rs774019661	3819	dbSNP
rs1380887187	3822	dbSNP
rs990330203	3827	dbSNP
rs1238265934	3828	dbSNP
rs1004265709	3834	dbSNP
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rs936412693	3848	dbSNP
rs925050341	3849	dbSNP
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rs1200058757	3863	dbSNP
rs1423222712	3870	dbSNP
rs1385217192	3871	dbSNP
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rs1438629092	3876	dbSNP
rs1164598136	3877	dbSNP
rs903500703	3882	dbSNP
rs552353174	3900	dbSNP
rs1434138900	3901	dbSNP
rs985802981	3906	dbSNP
rs762685259	3907	dbSNP
rs772533971	3910	dbSNP
rs1175947660	3911	dbSNP
rs7302414	3911	dbSNP
rs1029955645	3915	dbSNP
rs560436207	3921	dbSNP
rs1011884304	3925	dbSNP
rs554825188	3927	dbSNP
rs1219631476	3935	dbSNP
rs975936069	3937	dbSNP
rs777691419	3943	dbSNP
rs1176783522	3944	dbSNP
rs1481084986	3945	dbSNP
rs1234631517	3947	dbSNP
rs1321405480	3951	dbSNP
rs1220379054	3952	dbSNP
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rs1006490057	3967	dbSNP
rs1456953516	3972	dbSNP
rs1201942138	3973	dbSNP
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rs1191047532	3977	dbSNP
rs756442721	3982	dbSNP
rs1427798668	3984	dbSNP
rs769415405	3989	dbSNP
rs887854391	3990	dbSNP
rs938815903	3990	dbSNP
rs1034879850	3999	dbSNP
rs560710418	4000	dbSNP
rs540575470	4001	dbSNP
rs1222780451	4002	dbSNP
rs1373640881	4003	dbSNP
rs1343413003	4005	dbSNP
rs1289659507	4006	dbSNP
rs1278787761	4007	dbSNP
rs1338152390	4015	dbSNP
rs1212331124	4021	dbSNP
rs1291573238	4032	dbSNP
rs1402606132	4033	dbSNP
rs1220383372	4034	dbSNP
rs907164742	4037	dbSNP
rs1045770014	4038	dbSNP
rs1195005904	4041	dbSNP
rs542491259	4043	dbSNP
rs1459911671	4044	dbSNP
rs892074244	4044	dbSNP
rs891122882	4051	dbSNP
rs1054612665	4053	dbSNP
rs1474466677	4057	dbSNP
rs1183734284	4069	dbSNP
rs1414648423	4070	dbSNP
rs1404913018	4071	dbSNP
rs1161933343	4073	dbSNP
rs1363427819	4073	dbSNP
rs936197345	4078	dbSNP
rs181999312	4079	dbSNP
rs986242784	4082	dbSNP
rs1358929315	4084	dbSNP
rs1325851485	4088	dbSNP
rs530410369	4094	dbSNP
rs911102273	4095	dbSNP
rs964057364	4095	dbSNP
rs1244724809	4107	dbSNP
rs1289211593	4108	dbSNP
rs1197322516	4112	dbSNP
rs780051864	4113	dbSNP
rs758277669	4119	dbSNP
rs955233786	4124	dbSNP
rs1284169725	4125	dbSNP
rs961917574	4127	dbSNP
rs77097712	4128	dbSNP
rs763769848	4130	dbSNP
rs1285446049	4132	dbSNP
rs752315682	4133	dbSNP
rs1181953319	4134	dbSNP
rs750114477	4144	dbSNP
rs1489423672	4145	dbSNP
rs1258690920	4150	dbSNP
rs1022021543	4153	dbSNP
rs1382440554	4158	dbSNP
rs1441309308	4158	dbSNP
rs1317111099	4159	dbSNP
rs1289906087	4162	dbSNP
rs1221142751	4163	dbSNP
rs1011830398	4164	dbSNP
rs952010511	4171	dbSNP
rs894820712	4172	dbSNP
rs1359215994	4179	dbSNP
rs1283371817	4184	dbSNP
rs114602467	4185	dbSNP
rs1360518733	4187	dbSNP
rs1001991718	4189	dbSNP
rs556306383	4190	dbSNP
rs536314612	4206	dbSNP
rs138048921	4212	dbSNP
rs1174620368	4213	dbSNP
rs1202647932	4213	dbSNP
rs1024289234	4230	dbSNP
rs1047706321	4232	dbSNP
rs1469492530	4233	dbSNP
rs567350106	4237	dbSNP
rs1010267596	4240	dbSNP
rs1201923495	4243	dbSNP
rs1240245428	4246	dbSNP
rs930171356	4251	dbSNP
rs892041419	4256	dbSNP
rs773794139	4258	dbSNP
rs1038466482	4267	dbSNP
rs1055151330	4268	dbSNP
rs1468454400	4275	dbSNP
rs771483976	4279	dbSNP
rs1000368933	4280	dbSNP
rs1425872274	4283	dbSNP
rs1468824187	4284	dbSNP
rs889916142	4285	dbSNP
rs1334054741	4287	dbSNP
rs1401856338	4293	dbSNP
rs1447016230	4295	dbSNP
rs765249125	4298	dbSNP
rs1334324650	4303	dbSNP
rs1235936551	4305	dbSNP
rs931698895	4305	dbSNP
rs923047920	4306	dbSNP
rs1040002963	4307	dbSNP
rs1486107134	4311	dbSNP
rs933931380	4323	dbSNP
rs544206117	4325	dbSNP
rs1195422522	4330	dbSNP
rs1269801868	4333	dbSNP
rs375458896	4335	dbSNP
rs1195654401	4337	dbSNP
rs1322437866	4342	dbSNP
rs1476625801	4346	dbSNP
rs761603341	4348	dbSNP
rs978306548	4351	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.