>CDKL1|NM_004196|3'UTR
   1 AGGAGCTAGGAGACATGATTTTAAAAAAGGAATCAATAGATGCTTTGAAGAAAATAAAACTTATACAGTTGATTGAAAAC
  81 AATTACAATGTTGAAAACACACCAGGAGAAAACATAAGCAAGAAACTGGGAGGCCAACTGGCAAGATATGAAGGGAAATT
 161 CCAGATCCAGTCTTCCATGCTTGATGATGGTGTCCAGAAAAGAAAAAACCTGTTTGGAGTTGCACTTGTATTTCAGTTTA
 241 TGTAAGTAGCCGAACTTATGGACAGAATATGAACTGTCCCATACCTCTGGCAAAACTAGATGATATCAAAAAGATTTATG
 321 CTTCAGTTGTACCACATGCCACACAAGAAAAATGAACCACAAAATGCCCATATATATTTCCTCGGATCTCTGTTGCCTGA
 401 GTCCTATCTCCTGCCTCTCAGATTGTTTCAGCATCATATTTAAGATAGTTCTATTTCTTGAAATCAAAATGTTTAAAATC
 481 CCAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ccUGAGAUGUCUGUGUGGa 5' |: :|: | ||||||| Target 5' caATGTTGAAAACACACCa 3'	86 - 104	149.00	-9.60
2	miRNA 3' ccUGAGAUGUCUGUGUGGa 5' ::| ||| |||::|| Target 5' caGTTGTAC-CACATGCCa 3'	324 - 341	116.00	-6.00
3	miRNA 3' ccUGAGAUGUCUGUGUGGa 5' ||| | | ||:||| Target 5' gaACTGTCC---CATACCt 3'	271 - 286	105.00	-9.10

Mutant ID	Mutant Position	Mutant Source
COSN28194886	9	COSMIC
COSN31599035	59	COSMIC
COSN28880184	125	COSMIC
COSN29445183	407	COSMIC
COSN25820325	515	COSMIC
COSN14616568	562	COSMIC
COSN15923997	898	COSMIC
COSN18832679	1014	COSMIC
COSN22906502	1230	COSMIC
COSN19380124	1845	COSMIC
COSN23143851	1846	COSMIC
COSN16032048	2442	COSMIC
COSN23106493	2579	COSMIC
COSN17253021	2746	COSMIC
COSN16087008	2795	COSMIC
COSN8660129	2946	COSMIC
COSN23455468	3441	COSMIC
COSN29576720	3790	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs771893011	9	dbSNP
rs542797096	10	dbSNP
rs12882930	13	dbSNP
rs1293121725	14	dbSNP
rs778999738	16	dbSNP
rs1319867738	22	dbSNP
rs1351740953	23	dbSNP
rs766762864	24	dbSNP
rs1228287153	29	dbSNP
rs1326905149	29	dbSNP
rs8007971	31	dbSNP
rs763096694	36	dbSNP
rs557128887	37	dbSNP
rs755838967	39	dbSNP
rs543808565	47	dbSNP
rs990105860	55	dbSNP
rs1366297546	56	dbSNP
rs936025486	59	dbSNP
rs1207159969	64	dbSNP
rs925209933	64	dbSNP
rs1300859468	83	dbSNP
rs981067034	86	dbSNP
rs969351142	88	dbSNP
rs1025189849	101	dbSNP
rs1194711562	102	dbSNP
rs1365851823	108	dbSNP
rs1157820942	109	dbSNP
rs992013919	112	dbSNP
rs951104011	119	dbSNP
rs1419539687	121	dbSNP
rs868184608	122	dbSNP
rs1385590543	123	dbSNP
rs931694306	131	dbSNP
rs1332100847	136	dbSNP
rs112748297	138	dbSNP
rs1294157986	143	dbSNP
rs1337170849	147	dbSNP
rs1159748532	148	dbSNP
rs750661392	149	dbSNP
rs1351829462	153	dbSNP
rs976270135	156	dbSNP
rs1277081132	161	dbSNP
rs1485085643	166	dbSNP
rs1266897376	176	dbSNP
rs1259224297	185	dbSNP
rs898194100	190	dbSNP
rs1364225570	191	dbSNP
rs1455149078	193	dbSNP
rs577923499	199	dbSNP
rs1170791253	202	dbSNP
rs908102462	207	dbSNP
rs1262830716	212	dbSNP
rs985227587	213	dbSNP
rs1017954085	217	dbSNP
rs1007531638	223	dbSNP
rs1203741875	224	dbSNP
rs952036361	225	dbSNP
rs891382035	231	dbSNP
rs1408297285	234	dbSNP
rs1336761253	247	dbSNP
rs1034325117	248	dbSNP
rs980183050	249	dbSNP
rs765504080	251	dbSNP
rs558912178	252	dbSNP
rs1210986921	267	dbSNP
rs538961631	272	dbSNP
rs1481779241	274	dbSNP
rs946255713	282	dbSNP
rs1250758413	291	dbSNP
rs1177785917	296	dbSNP
rs11570887	297	dbSNP
rs1196428920	301	dbSNP
rs1054496495	307	dbSNP
rs1394405619	309	dbSNP
rs776926308	330	dbSNP
rs1454612837	335	dbSNP
rs1311005519	336	dbSNP
rs1175420696	339	dbSNP
rs1234594732	343	dbSNP
rs1013416986	347	dbSNP
rs1280771369	353	dbSNP
rs1406313705	361	dbSNP
rs936099381	363	dbSNP
rs927262216	371	dbSNP
rs763749420	374	dbSNP
rs11570888	384	dbSNP
rs182242520	392	dbSNP
rs1235745146	401	dbSNP
rs1306269341	406	dbSNP
rs1339507338	414	dbSNP
rs1226034851	417	dbSNP
rs567360601	421	dbSNP
rs1380241704	429	dbSNP
rs1386904910	430	dbSNP
rs1207851328	435	dbSNP
rs1252203463	438	dbSNP
rs1468743290	443	dbSNP
rs1289323280	445	dbSNP
rs372928491	457	dbSNP
rs917875740	459	dbSNP
rs1427167452	483	dbSNP
rs1178678595	485	dbSNP
rs1480839841	487	dbSNP
rs1373864165	498	dbSNP
rs1050017454	511	dbSNP
rs768426280	513	dbSNP
rs1324119895	528	dbSNP
rs991989657	529	dbSNP
rs1394293897	530	dbSNP
rs760689008	558	dbSNP
rs1191310820	565	dbSNP
rs1025386502	567	dbSNP
rs901592214	570	dbSNP
rs1295598355	574	dbSNP
rs1040967764	580	dbSNP
rs11157736	584	dbSNP
rs908009868	586	dbSNP
rs1049356787	587	dbSNP
rs1200279415	591	dbSNP
rs11570889	594	dbSNP
rs1246147766	602	dbSNP
rs1186018242	605	dbSNP
rs1485466147	605	dbSNP
rs1262590053	609	dbSNP
rs571130201	614	dbSNP
rs1430378432	621	dbSNP
rs369372965	622	dbSNP
rs927284637	627	dbSNP
rs1018320451	630	dbSNP
rs1167503199	634	dbSNP
rs1441961720	637	dbSNP
rs1430713519	657	dbSNP
rs971510688	664	dbSNP
rs550941276	671	dbSNP
rs891367517	672	dbSNP
rs1031212607	675	dbSNP
rs745713757	680	dbSNP
rs1323627996	685	dbSNP
rs1281814198	690	dbSNP
rs1316107454	695	dbSNP
rs1277132085	696	dbSNP
rs1010345442	711	dbSNP
rs1262389070	715	dbSNP
rs891935664	724	dbSNP
rs1486920592	726	dbSNP
rs967928949	731	dbSNP
rs528794941	735	dbSNP
rs995778163	739	dbSNP
rs377068350	745	dbSNP
rs1400454524	749	dbSNP
rs936048334	758	dbSNP
rs1347412048	762	dbSNP
rs905954345	765	dbSNP
rs1311671877	766	dbSNP
rs1040134845	767	dbSNP
rs1375694319	777	dbSNP
rs1416306115	813	dbSNP
rs1395312927	820	dbSNP
rs1005019234	830	dbSNP
rs1044784352	834	dbSNP
rs1224112508	837	dbSNP
rs1309093152	839	dbSNP
rs1208827182	844	dbSNP
rs1279775153	845	dbSNP
rs1049227253	849	dbSNP
rs1486035805	849	dbSNP
rs1470306547	851	dbSNP
rs1231369786	858	dbSNP
rs1399688050	859	dbSNP
rs950119252	861	dbSNP
rs559609082	866	dbSNP
rs927529019	872	dbSNP
rs1453054459	875	dbSNP
rs1056424617	886	dbSNP
rs1044440533	888	dbSNP
rs950067848	890	dbSNP
rs1187265907	891	dbSNP
rs1326501472	901	dbSNP
rs750113113	904	dbSNP
rs1443179759	913	dbSNP
rs1245432462	919	dbSNP
rs1204892502	920	dbSNP
rs190414195	923	dbSNP
rs1368720761	927	dbSNP
rs1233559338	931	dbSNP
rs1304023826	940	dbSNP
rs988913837	945	dbSNP
rs1220968538	959	dbSNP
rs1271185806	979	dbSNP
rs1271651554	981	dbSNP
rs770657030	982	dbSNP
rs1437392239	985	dbSNP
rs1193616064	986	dbSNP
rs956284476	992	dbSNP
rs374148585	996	dbSNP
rs1467414850	1003	dbSNP
rs1270475146	1004	dbSNP
rs923808933	1006	dbSNP
rs1455212623	1008	dbSNP
rs1165615802	1010	dbSNP
rs1244905714	1010	dbSNP
rs1392069305	1012	dbSNP
rs1410129530	1012	dbSNP
rs200113966	1012	dbSNP
rs1438708609	1014	dbSNP
rs372955511	1014	dbSNP
rs979231066	1014	dbSNP
rs1215448434	1016	dbSNP
rs1338809227	1016	dbSNP
rs911011222	1016	dbSNP
rs985510326	1017	dbSNP
rs1317025030	1018	dbSNP
rs1453319098	1019	dbSNP
rs1028851883	1020	dbSNP
rs1376137070	1020	dbSNP
rs1190419562	1022	dbSNP
rs996018477	1022	dbSNP
rs1326929043	1023	dbSNP
rs965756233	1027	dbSNP
rs1397408094	1028	dbSNP
rs1162894487	1029	dbSNP
rs1423083376	1030	dbSNP
rs1387492227	1032	dbSNP
rs1415142326	1032	dbSNP
rs1460755834	1033	dbSNP
rs1184644025	1034	dbSNP
rs1439586968	1035	dbSNP
rs1231744019	1036	dbSNP
rs1165294003	1038	dbSNP
rs1317556116	1038	dbSNP
rs1333082075	1038	dbSNP
rs1385670136	1038	dbSNP
rs1396612969	1038	dbSNP
rs1398937841	1038	dbSNP
rs1474643095	1038	dbSNP
rs199949248	1038	dbSNP
rs57657571	1038	dbSNP
rs67088222	1038	dbSNP
rs766292540	1038	dbSNP
rs1188203326	1039	dbSNP
rs947652275	1046	dbSNP
rs1370041471	1052	dbSNP
rs1157977931	1055	dbSNP
rs1468382589	1055	dbSNP
rs748724834	1058	dbSNP
rs538356115	1059	dbSNP
rs1273187489	1061	dbSNP
rs1373888904	1062	dbSNP
rs1221322602	1064	dbSNP
rs1294135487	1069	dbSNP
rs1356948111	1071	dbSNP
rs745362476	1074	dbSNP
rs1237271321	1075	dbSNP
rs1279517079	1085	dbSNP
rs1351942088	1092	dbSNP
rs1218180137	1104	dbSNP
rs886181735	1110	dbSNP
rs1029295259	1118	dbSNP
rs774075938	1120	dbSNP
rs202215405	1122	dbSNP
rs1293645782	1123	dbSNP
rs1180774087	1125	dbSNP
rs1010420489	1127	dbSNP
rs1246525790	1129	dbSNP
rs200006894	1131	dbSNP
rs75961992	1133	dbSNP
rs554012447	1135	dbSNP
rs796368991	1135	dbSNP
rs569227431	1136	dbSNP
rs151281958	1138	dbSNP
rs1243037987	1144	dbSNP
rs905940893	1145	dbSNP
rs1301839600	1146	dbSNP
rs1346589288	1146	dbSNP
rs398118192	1146	dbSNP
rs71118871	1146	dbSNP
rs1336458731	1148	dbSNP
rs867853946	1148	dbSNP
rs1323081708	1149	dbSNP
rs1014658841	1150	dbSNP
rs1403309034	1150	dbSNP
rs111875032	1153	dbSNP
rs994987256	1154	dbSNP
rs1386850816	1155	dbSNP
rs1302693756	1158	dbSNP
rs1305246442	1164	dbSNP
rs1047780672	1166	dbSNP
rs201607613	1168	dbSNP
rs4901013	1174	dbSNP
rs918516817	1180	dbSNP
rs1192834515	1184	dbSNP
rs1269640541	1192	dbSNP
rs578028045	1193	dbSNP
rs1426779698	1199	dbSNP
rs941225416	1204	dbSNP
rs1470857425	1206	dbSNP
rs1192806704	1207	dbSNP
rs1424544095	1208	dbSNP
rs1232975014	1209	dbSNP
rs1163146121	1211	dbSNP
rs1394414410	1218	dbSNP
rs564505576	1220	dbSNP
rs1458920040	1223	dbSNP
rs1295799541	1224	dbSNP
rs1198128425	1225	dbSNP
rs910948066	1233	dbSNP
rs985196153	1236	dbSNP
rs1270669584	1238	dbSNP
rs541424618	1253	dbSNP
rs955317422	1257	dbSNP
rs1446217857	1258	dbSNP
rs1160054125	1260	dbSNP
rs1272377965	1267	dbSNP
rs895824407	1268	dbSNP
rs1223731449	1270	dbSNP
rs1282015150	1272	dbSNP
rs1258869491	1275	dbSNP
rs922230856	1279	dbSNP
rs988443846	1283	dbSNP
rs1204591122	1293	dbSNP
rs573218419	1296	dbSNP
rs1264176946	1297	dbSNP
rs8021046	1302	dbSNP
rs1238079785	1309	dbSNP
rs780341941	1313	dbSNP
rs926020103	1314	dbSNP
rs375896930	1321	dbSNP
rs536457676	1327	dbSNP
rs1347609921	1337	dbSNP
rs1303999941	1338	dbSNP
rs534246896	1349	dbSNP
rs1343834953	1358	dbSNP
rs1361877889	1359	dbSNP
rs1412613568	1365	dbSNP
rs148299214	1366	dbSNP
rs1000754583	1368	dbSNP
rs185084056	1371	dbSNP
rs1425134897	1385	dbSNP
rs567058818	1406	dbSNP
rs758750911	1417	dbSNP
rs1479177215	1420	dbSNP
rs1286906987	1432	dbSNP
rs1489311732	1435	dbSNP
rs1430887362	1442	dbSNP
rs1257054058	1453	dbSNP
rs1483798790	1462	dbSNP
rs750857908	1463	dbSNP
rs1023569179	1473	dbSNP
rs571305184	1483	dbSNP
rs1014319124	1485	dbSNP
rs974692541	1491	dbSNP
rs1381667651	1493	dbSNP
rs181889950	1495	dbSNP
rs1311917449	1499	dbSNP
rs1359339792	1501	dbSNP
rs1449957985	1506	dbSNP
rs1018648529	1509	dbSNP
rs983521840	1511	dbSNP
rs534274269	1512	dbSNP
rs950471627	1514	dbSNP
rs143261043	1520	dbSNP
rs1240873062	1530	dbSNP
rs1311331257	1531	dbSNP
rs1447507274	1533	dbSNP
rs765417733	1538	dbSNP
rs1232123647	1540	dbSNP
rs993533789	1548	dbSNP
rs897053712	1566	dbSNP
rs1312928392	1574	dbSNP
rs1212494296	1575	dbSNP
rs1231591124	1577	dbSNP
rs768859766	1580	dbSNP
rs941285937	1584	dbSNP
rs1179869473	1593	dbSNP
rs1240515404	1597	dbSNP
rs1452065535	1599	dbSNP
rs906049427	1610	dbSNP
rs1415879572	1611	dbSNP
rs1425449844	1611	dbSNP
rs1023105654	1614	dbSNP
rs8020274	1615	dbSNP
rs1447222880	1624	dbSNP
rs896053863	1625	dbSNP
rs1050028012	1626	dbSNP
rs1274393938	1629	dbSNP
rs1368387553	1630	dbSNP
rs933721127	1637	dbSNP
rs1272259695	1641	dbSNP
rs753816190	1643	dbSNP
rs988433895	1645	dbSNP
rs1317711270	1653	dbSNP
rs1199620726	1669	dbSNP
rs934351819	1673	dbSNP
rs780513950	1676	dbSNP
rs1198759815	1701	dbSNP
rs1246853842	1707	dbSNP
rs188625823	1716	dbSNP
rs1432015796	1717	dbSNP
rs1405917297	1721	dbSNP
rs1418296451	1722	dbSNP
rs1465978123	1723	dbSNP
rs6572658	1724	dbSNP
rs1460914227	1738	dbSNP
rs932696483	1740	dbSNP
rs1331801232	1748	dbSNP
rs1467737488	1754	dbSNP
rs1438641114	1759	dbSNP
rs1268668873	1761	dbSNP
rs1340040976	1775	dbSNP
rs760469130	1778	dbSNP
rs550331177	1785	dbSNP
rs371625175	1787	dbSNP
rs993414089	1788	dbSNP
rs960106602	1803	dbSNP
rs775553128	1821	dbSNP
rs911781991	1826	dbSNP
rs1212991075	1827	dbSNP
rs983167415	1834	dbSNP
rs993481571	1841	dbSNP
rs899133892	1845	dbSNP
rs11570890	1846	dbSNP
rs1163791905	1846	dbSNP
rs1415444410	1846	dbSNP
rs1005427939	1854	dbSNP
rs1316239274	1855	dbSNP
rs969786995	1855	dbSNP
rs889708145	1865	dbSNP
rs74515247	1876	dbSNP
rs1023172010	1880	dbSNP
rs191859028	1881	dbSNP
rs568297214	1883	dbSNP
rs1354011186	1885	dbSNP
rs1032350591	1891	dbSNP
rs111342310	1898	dbSNP
rs1359003865	1901	dbSNP
rs1052830030	1906	dbSNP
rs1284767831	1909	dbSNP
rs1263807608	1913	dbSNP
rs1218394512	1919	dbSNP
rs1254895384	1921	dbSNP
rs904533277	1923	dbSNP
rs934425534	1925	dbSNP
rs572432387	1952	dbSNP
rs1370133972	1955	dbSNP
rs1043005692	1961	dbSNP
rs996922119	1968	dbSNP
rs899926500	1969	dbSNP
rs186664292	1974	dbSNP
rs978839147	1978	dbSNP
rs1275396128	1992	dbSNP
rs944526190	1993	dbSNP
rs1335209966	1994	dbSNP
rs1215453531	2005	dbSNP
rs1048126814	2009	dbSNP
rs911700857	2009	dbSNP
rs774336171	2010	dbSNP
rs1382538931	2013	dbSNP
rs1313495130	2014	dbSNP
rs929168361	2021	dbSNP
rs1353823600	2030	dbSNP
rs1455027952	2030	dbSNP
rs920291915	2034	dbSNP
rs973062852	2034	dbSNP
rs969818012	2045	dbSNP
rs184390218	2046	dbSNP
rs1352348333	2066	dbSNP
rs992560122	2067	dbSNP
rs1440434829	2069	dbSNP
rs573858786	2073	dbSNP
rs1376149154	2076	dbSNP
rs556912667	2077	dbSNP
rs1430126850	2084	dbSNP
rs993011774	2086	dbSNP
rs569747738	2092	dbSNP
rs537241531	2096	dbSNP
rs960221216	2097	dbSNP
rs1026495568	2102	dbSNP
rs1331267806	2103	dbSNP
rs577364232	2107	dbSNP
rs1378248950	2116	dbSNP
rs972117712	2120	dbSNP
rs750496634	2121	dbSNP
rs550272080	2123	dbSNP
rs963457635	2123	dbSNP
rs1181578742	2132	dbSNP
rs1016230666	2134	dbSNP
rs1243747859	2135	dbSNP
rs1233603730	2148	dbSNP
rs1257381629	2158	dbSNP
rs1176679518	2170	dbSNP
rs1197703945	2172	dbSNP
rs899945479	2174	dbSNP
rs1458994890	2176	dbSNP
rs1479700253	2182	dbSNP
rs1234777342	2186	dbSNP
rs866918211	2187	dbSNP
rs1265445625	2188	dbSNP
rs770442036	2191	dbSNP
rs112533600	2195	dbSNP
rs1359053914	2196	dbSNP
rs1379524189	2197	dbSNP
rs749001770	2198	dbSNP
rs757380688	2199	dbSNP
rs1401455562	2205	dbSNP
rs1008289575	2209	dbSNP
rs1248707539	2210	dbSNP
rs1292285257	2211	dbSNP
rs1389458573	2214	dbSNP
rs890288823	2217	dbSNP
rs111985271	2225	dbSNP
rs929247002	2226	dbSNP
rs1306928664	2227	dbSNP
rs920491986	2231	dbSNP
rs1337905642	2240	dbSNP
rs60103816	2240	dbSNP
rs894481777	2240	dbSNP
rs1319735511	2249	dbSNP
rs193207924	2251	dbSNP
rs915554707	2262	dbSNP
rs1488201944	2265	dbSNP
rs900985995	2273	dbSNP
rs1269767209	2287	dbSNP
rs959780789	2310	dbSNP
rs565307234	2313	dbSNP
rs548940735	2317	dbSNP
rs1424873103	2324	dbSNP
rs1478999566	2326	dbSNP
rs769361970	2329	dbSNP
rs116849769	2331	dbSNP
rs1457995401	2332	dbSNP
rs1294721975	2334	dbSNP
rs1358044328	2341	dbSNP
rs1042723858	2355	dbSNP
rs948432133	2359	dbSNP
rs916150066	2364	dbSNP
rs964411244	2365	dbSNP
rs921287373	2368	dbSNP
rs1322205655	2370	dbSNP
rs1019572564	2372	dbSNP
rs1267346470	2377	dbSNP
rs1158330741	2378	dbSNP
rs1417345841	2382	dbSNP
rs1487347097	2393	dbSNP
rs1216236793	2398	dbSNP
rs1264098671	2409	dbSNP
rs1489477057	2411	dbSNP
rs1180438317	2412	dbSNP
rs1057496981	2418	dbSNP
rs1008736823	2420	dbSNP
rs887196560	2421	dbSNP
rs1026175725	2437	dbSNP
rs1183030894	2438	dbSNP
rs1378013444	2439	dbSNP
rs938931891	2447	dbSNP
rs1418502976	2449	dbSNP
rs1490245503	2451	dbSNP
rs149136376	2452	dbSNP
rs1225108207	2453	dbSNP
rs898968724	2457	dbSNP
rs550151473	2459	dbSNP
rs1302098060	2460	dbSNP
rs1037638148	2461	dbSNP
rs972232373	2464	dbSNP
rs533519564	2465	dbSNP
rs1351615008	2467	dbSNP
rs1239430986	2469	dbSNP
rs146766928	2475	dbSNP
rs948578095	2478	dbSNP
rs963448267	2479	dbSNP
rs1056789840	2482	dbSNP
rs1260611322	2486	dbSNP
rs938471446	2489	dbSNP
rs1237303528	2490	dbSNP
rs924368414	2494	dbSNP
rs909327541	2495	dbSNP
rs1236818459	2513	dbSNP
rs986130881	2515	dbSNP
rs1228543097	2522	dbSNP
rs370797512	2524	dbSNP
rs547880729	2528	dbSNP
rs1381605027	2544	dbSNP
rs1412445239	2547	dbSNP
rs1174910792	2549	dbSNP
rs548413212	2555	dbSNP
rs1467336343	2560	dbSNP
rs1329232444	2565	dbSNP
rs1406499168	2572	dbSNP
rs1376008404	2574	dbSNP
rs1391214908	2577	dbSNP
rs1288120716	2582	dbSNP
rs111657658	2583	dbSNP
rs1365527477	2584	dbSNP
rs1159980248	2590	dbSNP
rs1205930092	2591	dbSNP
rs1313161269	2591	dbSNP
rs1480157612	2592	dbSNP
rs1457749841	2593	dbSNP
rs1179781450	2594	dbSNP
rs1239535015	2598	dbSNP
rs1427376821	2603	dbSNP
rs1201903815	2604	dbSNP
rs1434076692	2605	dbSNP
rs1261443444	2607	dbSNP
rs1203796679	2609	dbSNP
rs1476748774	2613	dbSNP
rs1190286368	2614	dbSNP
rs1168209288	2615	dbSNP
rs1225560948	2615	dbSNP
rs1274521568	2615	dbSNP
rs1275653392	2615	dbSNP
rs1333275551	2615	dbSNP
rs1356408390	2615	dbSNP
rs1399243002	2615	dbSNP
rs1434316386	2615	dbSNP
rs1434717973	2615	dbSNP
rs1466111086	2615	dbSNP
rs1491189908	2615	dbSNP
rs555068519	2615	dbSNP
rs750138701	2615	dbSNP
rs758016227	2615	dbSNP
rs761957738	2615	dbSNP
rs773565273	2615	dbSNP
rs1220135069	2616	dbSNP
rs1491533985	2616	dbSNP
rs1246946185	2617	dbSNP
rs1490752154	2622	dbSNP
rs1191016379	2628	dbSNP
rs1422736563	2630	dbSNP
rs1478016699	2632	dbSNP
rs1172743043	2635	dbSNP
rs1411488555	2637	dbSNP
rs914719946	2638	dbSNP
rs188961144	2642	dbSNP
rs372205602	2648	dbSNP
rs374510361	2651	dbSNP
rs1340312624	2656	dbSNP
rs1219557622	2660	dbSNP
rs144862473	2666	dbSNP
rs1354800819	2673	dbSNP
rs1228228715	2675	dbSNP
rs1290014146	2679	dbSNP
rs904271608	2680	dbSNP
rs1360966383	2681	dbSNP
rs1280914743	2690	dbSNP
rs1224939098	2697	dbSNP
rs1043224449	2700	dbSNP
rs1012679398	2706	dbSNP
rs894106936	2710	dbSNP
rs1331365041	2715	dbSNP
rs1056818197	2721	dbSNP
rs938879605	2724	dbSNP
rs1195007838	2727	dbSNP
rs74332015	2738	dbSNP
rs11295551	2740	dbSNP
rs1235502360	2740	dbSNP
rs1491098235	2740	dbSNP
rs398025028	2740	dbSNP
rs572873116	2740	dbSNP
rs75453465	2740	dbSNP
rs764149606	2741	dbSNP
rs772342450	2741	dbSNP
rs112635475	2744	dbSNP
rs1339042643	2745	dbSNP
rs1321145039	2747	dbSNP
rs1469321269	2754	dbSNP
rs1297245421	2756	dbSNP
rs1025746323	2769	dbSNP
rs561658214	2780	dbSNP
rs527304439	2788	dbSNP
rs541892416	2800	dbSNP
rs942215581	2806	dbSNP
rs1206498631	2807	dbSNP
rs1276328166	2807	dbSNP
rs1441620272	2813	dbSNP
rs543261777	2814	dbSNP
rs995565469	2822	dbSNP
rs564929194	2823	dbSNP
rs909285868	2834	dbSNP
rs1446552750	2842	dbSNP
rs1176802859	2853	dbSNP
rs986592054	2856	dbSNP
rs1379741991	2860	dbSNP
rs953507223	2864	dbSNP
rs780536449	2865	dbSNP
rs1400586712	2866	dbSNP
rs976063492	2870	dbSNP
rs965258981	2871	dbSNP
rs577383734	2874	dbSNP
rs1031591509	2875	dbSNP
rs998629236	2878	dbSNP
rs1460407016	2883	dbSNP
rs894392468	2886	dbSNP
rs1240817291	2887	dbSNP
rs1272660207	2889	dbSNP
rs1344039760	2890	dbSNP
rs1057227404	2901	dbSNP
rs938349177	2921	dbSNP
rs544753631	2926	dbSNP
rs183619492	2927	dbSNP
rs190630091	2929	dbSNP
rs1345266074	2938	dbSNP
rs1041467649	2943	dbSNP
rs559076357	2944	dbSNP
rs1419730626	2955	dbSNP
rs1184262992	2957	dbSNP
rs1376065402	2962	dbSNP
rs1021475314	2965	dbSNP
rs1013040610	2967	dbSNP
rs139269206	2971	dbSNP
rs1224882151	2976	dbSNP
rs7147718	2978	dbSNP
rs1035345911	2983	dbSNP
rs1002577828	2988	dbSNP
rs182427567	2989	dbSNP
rs1330098390	2994	dbSNP
rs376139589	3000	dbSNP
rs942305227	3010	dbSNP
rs1315831772	3011	dbSNP
rs1217994279	3022	dbSNP
rs1258562964	3023	dbSNP
rs987429763	3031	dbSNP
rs1415173777	3037	dbSNP
rs1197587020	3039	dbSNP
rs1265336486	3040	dbSNP
rs887903807	3041	dbSNP
rs951431635	3045	dbSNP
rs1050633508	3047	dbSNP
rs1431981628	3051	dbSNP
rs932029352	3052	dbSNP
rs1477013308	3053	dbSNP
rs757351447	3057	dbSNP
rs570254769	3068	dbSNP
rs923385045	3070	dbSNP
rs1170599342	3073	dbSNP
rs1166378223	3076	dbSNP
rs1202545954	3087	dbSNP
rs1374100339	3100	dbSNP
rs1463091530	3103	dbSNP
rs918550915	3110	dbSNP
rs1389346742	3122	dbSNP
rs556778791	3134	dbSNP
rs1463805594	3139	dbSNP
rs112928084	3142	dbSNP
rs935371315	3144	dbSNP
rs924520852	3152	dbSNP
rs112774313	3156	dbSNP
rs1188951694	3161	dbSNP
rs1309241484	3166	dbSNP
rs1442499898	3166	dbSNP
rs1012736151	3172	dbSNP
rs958904500	3180	dbSNP
rs1035626910	3181	dbSNP
rs1355718009	3185	dbSNP
rs1003182439	3187	dbSNP
rs540056987	3188	dbSNP
rs1041332092	3199	dbSNP
rs1487531763	3199	dbSNP
rs968684652	3202	dbSNP
rs1430849400	3207	dbSNP
rs1163288988	3209	dbSNP
rs112034799	3213	dbSNP
rs1342361792	3218	dbSNP
rs1165086705	3225	dbSNP
rs571030844	3239	dbSNP
rs1343921475	3244	dbSNP
rs991368460	3245	dbSNP
rs1358187332	3260	dbSNP
rs1399187606	3262	dbSNP
rs1275048918	3270	dbSNP
rs1245061829	3279	dbSNP
rs1363814850	3295	dbSNP
rs1015516833	3297	dbSNP
rs958682282	3298	dbSNP
rs1128692	3301	dbSNP
rs111446193	3302	dbSNP
rs1382133686	3303	dbSNP
rs146476824	3304	dbSNP
rs897461690	3305	dbSNP
rs111453906	3306	dbSNP
rs568533881	3307	dbSNP
rs754102433	3311	dbSNP
rs1487046309	3331	dbSNP
rs1045886	3345	dbSNP
rs548340695	3350	dbSNP
rs1255987026	3355	dbSNP
rs1444745117	3359	dbSNP
rs113730157	3360	dbSNP
rs1302906800	3368	dbSNP
rs1423144277	3369	dbSNP
rs764277812	3370	dbSNP
rs962813004	3374	dbSNP
rs1302225018	3376	dbSNP
rs916656890	3380	dbSNP
rs991284507	3385	dbSNP
rs958585568	3386	dbSNP
rs1035893462	3389	dbSNP
rs1362688224	3391	dbSNP
rs531685296	3394	dbSNP
rs10133342	3408	dbSNP
rs967259457	3413	dbSNP
rs1019948226	3416	dbSNP
rs1221390593	3417	dbSNP
rs901931561	3418	dbSNP
rs1489800882	3425	dbSNP
rs1040468111	3430	dbSNP
rs1235892838	3451	dbSNP
rs1011183128	3454	dbSNP
rs1177432632	3459	dbSNP
rs935423541	3462	dbSNP
rs923922559	3464	dbSNP
rs78401946	3478	dbSNP
rs1406505940	3492	dbSNP
rs767539716	3494	dbSNP
rs113426815	3497	dbSNP
rs914520579	3513	dbSNP
rs1230367757	3515	dbSNP
rs1398217707	3517	dbSNP
rs1441481550	3528	dbSNP
rs370472521	3537	dbSNP
rs930248502	3543	dbSNP
rs958562038	3548	dbSNP
rs533034731	3549	dbSNP
rs1283086532	3553	dbSNP
rs1324702345	3555	dbSNP
rs117513134	3558	dbSNP
rs540815766	3566	dbSNP
rs571854789	3572	dbSNP
rs941357376	3574	dbSNP
rs1324679168	3578	dbSNP
rs1014569812	3580	dbSNP
rs1005913800	3581	dbSNP
rs916546588	3584	dbSNP
rs952376492	3593	dbSNP
rs762552673	3595	dbSNP
rs1029284314	3599	dbSNP
rs377567904	3603	dbSNP
rs1190266274	3604	dbSNP
rs990925167	3610	dbSNP
rs1156291527	3615	dbSNP
rs1481262137	3616	dbSNP
rs1473297135	3617	dbSNP
rs939397964	3619	dbSNP
rs1409472053	3630	dbSNP
rs996738145	3632	dbSNP
rs1171279794	3668	dbSNP
rs1356321464	3669	dbSNP
rs149907445	3675	dbSNP
rs981679991	3679	dbSNP
rs1040540375	3682	dbSNP
rs1020170437	3692	dbSNP
rs1276880825	3695	dbSNP
rs1339365084	3701	dbSNP
rs1215637187	3703	dbSNP
rs1248207509	3718	dbSNP
rs1319388791	3723	dbSNP
rs1221295614	3741	dbSNP
rs999539524	3750	dbSNP
rs190157058	3752	dbSNP
rs1222113873	3753	dbSNP
rs1490788357	3753	dbSNP
rs374964333	3753	dbSNP
rs1241279211	3754	dbSNP
rs1446339548	3755	dbSNP
rs575960805	3760	dbSNP
rs1421759714	3763	dbSNP
rs990001495	3766	dbSNP
rs116425757	3767	dbSNP
rs1366375237	3769	dbSNP
rs1426761731	3772	dbSNP
rs375971812	3773	dbSNP
rs1326206443	3775	dbSNP
rs1432181924	3776	dbSNP
rs868384611	3791	dbSNP
rs1272373778	3796	dbSNP
rs1376348420	3797	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.