pre-miRNA Information
pre-miRNA hsa-mir-3689d-1   
Genomic Coordinates chr9: 134849609 - 134849682
Description Homo sapiens miR-3689d-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA hsa-mir-3689d-2   
Genomic Coordinates chr9: 134850277 - 134850356
Description Homo sapiens miR-3689d-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3689d
Sequence 2| GGGAGGUGUGAUCUCACACUCG |23
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs551722268 8 dbSNP
rs143142996 8 dbSNP
rs1236297052 12 dbSNP
rs573148947 14 dbSNP
rs1210004979 14 dbSNP
rs1217460444 14 dbSNP
rs762590109 18 dbSNP
rs574332265 18 dbSNP
rs1164353021 21 dbSNP
rs963741171 21 dbSNP
rs1177416877 22 dbSNP
rs765777344 22 dbSNP
Putative Targets

Gene Information
Gene Symbol FNDC3B   
Synonyms FAD104, PRO4979, YVTM2421
Description fibronectin type III domain containing 3B
Transcript NM_001135095   
Other Transcripts NM_022763   
Expression
Putative miRNA Targets on FNDC3B
3'UTR of FNDC3B
(miRNA target sites are highlighted)
>FNDC3B|NM_001135095|3'UTR
   1 ACCCAACAAAACTAGAGGTATGAATTAATGCTACACATTTTAATACACACATTTATTCAGATACTCCCCTTTTTAAAGCC
  81 CTTTTGTTTTTTGATTTATATACTCTGTTTTACAGATTTAGCTAGAAAAAAAATGTCAGTGTTTTGGTGCACCTTTTTGA
 161 AATGCAAAACTAGGAAAAGGTTAAACTGGATTTTTTTTTTTAAAAAAAAGAAAAAAAAAGAAGAAAAGTATACCAGATAC
 241 CAAAAGCTAGCTTTCTTATGTTTTCCTTTAAATTTTCAGATTTACCTTCATTCTGTTTTCACTGATGTCTTTTGCAAGCC
 321 TTTGATTTTTTTTTTTTTGTTACAGTTTAGTAATTTATATTCACCAGTCACTTCATATGTCTTGAACATCTGTATCTGTA
 401 AACATGAATCACCGTGTGTGTACTTACAGGGCTAGGATTTCAGTGTTGTCAGAGTATTACCACACAGCAACAGCAACATA
 481 CAGAAGATATGTTCACTCAGATAAGACTGCCCTAAACAACCATTTTGTCACTCAGTTATTTAACTGTGTTTAGCTCATTT
 561 AAATCAAAATGTGTACTTTAATCTAAAATGTTTTAATAATCTGTATTTCTTATAATTTTAACACTATGAGCTGCCTGTAT
 641 AAGAAATCAAGTAACCAGAATGCACCTATAAATTATGGAGCATTGTAGATTTTACCACATCAATTCATAGCAGTAACTTT
 721 AAGAGGGCATTGTGCAATAGTTAGTTGTTTTCTTGTTCAGCTATTTTAAAGGCTGCTTTAACTTGTTTGTTTGTCTTTGT
 801 ATATAACTACTTCTAATCTAATCACTAGAGTTATTATATTCTGTTATGTTTGACCAGAATTATATGACAAGAACTGGTGA
 881 CAGTTTAGTGCCTCTGCCCATTGTCCATGATTTACACTAATTGTGAGCAGTCTTCTTATGTGTCAGCTCATTATTTTTGA
 961 AACATTTGCCTTTAGGCTGTTCTTTGAGGTATCAATGAAGTGATTGAATTTCAATACCTTAATTCAGTGCACATAATACT
1041 AATGTAACAGCAGATGAAAATTGATAAAACCCAAAAGAGAGTCATCTAAATTTGTAGTTCCTATTTCTGTGGGTTTGCCT
1121 GGCCATGGTTGGAGAGGGAATGGTGTTTGATGGTAAACACAGGGTGTTTGGGGATCAAGGAGCCTAGATTCTCTCCCTGG
1201 ATCTGTCACTAACTTGCTGCGTGACCTGAACACGTCACTTTACCTCTCTGTGCCTCAGTTTTCCCATGCATGAAAAATAA
1281 AATAAAATAAAACGGGGATTCTAATGTTTGTAAGTGCTTTGAGATCTTTGACCAACAGGTGCTATTGGAGTGCAAAGTGT
1361 TACTCTTACGTGTTTATTTTGAGTCATGAGATAATCAATTTTAACCCAAAGTCATTGGATTATTTATATGAAGTCCATAA
1441 TGTTCGAGTACCTCAGGGACATTTAAGAGTTGGAGGTGCAAATATATTCCAAAAGGGTGCAACAGACACAGTGTATCCCC
1521 CTGCTTCTGTTTTTGTATATTTTTGCTACTTGGTTTTTCTTGATCATAGCTATTTTGTGCTTGATCTTTATTGTCTAAGA
1601 TGCAGTATCCTGTACTAGCTTATAATATTCCCATACCAAAGTCATGGGGAAACAAACATTATTTTGTTTTTGGTTTATTT
1681 ATACTATATTCTGCATACAGTACTTTAAATGCCAATTACAGTGCAATCTTTATTTATTGTAAAATTTTTTAAGTGTACTT
1761 ATGTACTAATTTTCCCTTGTAGCATGTTATATTTTTGTGTTTTATACTTTTGTAATTTTAGGTCAGTCTTGTTCCTTGGC
1841 AACATCTGTAGTATTATTAATCTTCTGACATTTTCTTATGTTTTTAAAAAGATAAGAGCATCTAGTGCATTAAATGCCAA
1921 AAAAAAAATACATTATCAGTGATTGAAACGTTTACATGTACCCAAAAACCATAATCATCTCTTGGAAGAAAATGCTGAGA
2001 TCAATGAATTATTCTGTGTGCCTATATTGACGTAGTGAGTACTAGAGAGTTCTGTATTTTATTATTGACTATAATAATTA
2081 GTTTAATTAGCTTTGCAAACTGATGGCATCAAGGTAAATATATTTTTGCCAAAGTTCTGGCCTTCCAAAACTCACCCCCT
2161 TATTTAAATGTGTGCTATGACCCACTATGACCACAGCATCTGCATTTTCTAAAAAATTCCATGCAGGTGTTTTGGGGAGA
2241 GGTATTTTTTAAGCAATGAAAATTCAACTGAGTACAAAGCCCCCTCTTGGGGGGTTGGGGAAGTCTCTTTTTTGAAACAC
2321 TTCAGAACTGCTGCTATAAAGAAATTCTCTAATTGGTTGAATTTTTTTTTTAAGTAAATAGTACTTTAGGCCAAAATTTA
2401 TATGAATATTTGATCTTCTTGAGATTTTCATACTATCATTTAACCACCAGGAAGCTGAAGTGTGTGAAGTACAAAGCTGA
2481 CAGCACTTTATTTTATTGCTCTCCATTATTTGGTATTCATTATATTCCTTCAGTCAGAAAATTATTACTCTCTATGGCAC
2561 TGTTTTTTATCACAAATATGTATATGTGATATTGATATATAACTATATATATTGCCATCACACACGAACAATAAAATAAA
2641 GTGTTCTATTAACCTGATCTCTTTGCCCTTTTGCTATGTGAGGAGTGAATGAGTGGCCTTCTGATGCTCTGACTCTTCTC
2721 TGTATGTCAAACTCATCCCTGGCACAAGAAATTCCAGTCATGTGAAGCAAACTGCCCTTTGTCCTCAAAGAAATTGTTGA
2801 AAAAGAAAACTTTTTAAAGAGATTTTTTGCATATTCTCTGCCTTGTTCTTATCAACTTGAAATGTTGGCATTTTCTAACC
2881 TTGTTTTGTTGGCTACAATAATTCAGTATTCATGTCAAAATTGAGAAGTGCCCTAATTGAATGTGTTTGAATGTTATCCT
2961 TGCACAATTCTTTAAATTGAAAGATAAAATGTTTTACCTCACTGTTGGACATACATTCCAAGCTTTTCAACTCTAGGAGA
3041 AAAAGAAAATCATGTTTTCCTGTATTGTAAATTTTAGACTATTTCATATACATTGTATTAAAACTGCCATATCAATTTTA
3121 ATGTATAGATTTTGCAAATATTATGCTATATGTAATACCTAACTGTATCTGTAGTGTATATGTAATATATTTATGCCCAA
3201 TAAATGTTTTAATTCTTTCTGACTTAAAAAAAAAAAAAAA
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1
miRNA  3' gcUCACACUCUAGUGUGGAGGg 5'
            | | | ||||: :||||:| 
Target 5' aaATTTTCAGATT-TACCTTCa 3'
270 - 290 127.00 -11.10
2
miRNA  3' gcUCACACUCUAGUGUGGAGGg 5'
            |||||   : ::|||||:: 
Target 5' tcAGTGTTTTGGTGCACCTTTt 3'
136 - 157 124.00 -14.70
3
miRNA  3' gcUCACACUCUAGUGUGGAGgg 5'
            | |||  ||  ::|||||  
Target 5' atAATGTTCGA--GTACCTCag 3'
1437 - 1456 116.00 -12.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30478032 69 COSMIC
COSN30153143 75 COSMIC
COSN26575956 134 COSMIC
COSN31551359 134 COSMIC
COSN28821506 200 COSMIC
COSN20099380 201 COSMIC
COSN31562903 202 COSMIC
COSN20099381 220 COSMIC
COSN1271970 222 COSMIC
COSN20099385 339 COSMIC
COSN28650617 638 COSMIC
COSN24455293 796 COSMIC
COSN30164501 853 COSMIC
COSN23025758 1035 COSMIC
COSN30161828 1389 COSMIC
COSN31523876 1394 COSMIC
COSN31571122 1428 COSMIC
COSN26555596 1497 COSMIC
COSN20090942 1537 COSMIC
COSN26566654 1613 COSMIC
COSN31522571 1745 COSMIC
COSN14843807 1789 COSMIC
COSN31549020 1802 COSMIC
COSN29310888 1811 COSMIC
COSN26561925 1827 COSMIC
COSN31546999 1907 COSMIC
COSN29080302 1929 COSMIC
COSN23510476 1931 COSMIC
COSN31566579 1960 COSMIC
COSN31609973 2015 COSMIC
COSN19465224 2119 COSMIC
COSN20099390 2193 COSMIC
COSN31513542 2291 COSMIC
COSN6753583 2324 COSMIC
COSN20099394 2372 COSMIC
COSN28198259 2372 COSMIC
COSN8488690 2400 COSMIC
COSN23455831 2403 COSMIC
COSN505754 2429 COSMIC
COSN23455832 2436 COSMIC
COSN19656227 2441 COSMIC
COSN7835432 2448 COSMIC
COSN31545003 2543 COSMIC
COSN31569655 2551 COSMIC
COSN31515036 2565 COSMIC
COSN31544293 2569 COSMIC
COSN32062616 2647 COSMIC
COSN9763910 2793 COSMIC
COSN30175277 2913 COSMIC
COSN25012546 3015 COSMIC
COSN9763911 3018 COSMIC
COSN9763912 3106 COSMIC
COSN22622455 3121 COSMIC
COSN21057667 3124 COSMIC
COSN26671610 3177 COSMIC
COSN26556759 3183 COSMIC
COSN31516433 3216 COSMIC
COSN21518547 3290 COSMIC
COSN31813351 3466 COSMIC
COSN7626742 3591 COSMIC
COSN23423859 3706 COSMIC
COSN22570899 4059 COSMIC
COSN5527978 4095 COSMIC
COSN9533748 4165 COSMIC
rs12897 638 GWAS
rs35263143 3868 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs569866127 3 dbSNP
rs1287834881 7 dbSNP
rs1446118450 8 dbSNP
rs753138278 12 dbSNP
rs1224621305 13 dbSNP
rs761098167 15 dbSNP
rs764504222 16 dbSNP
rs372496204 21 dbSNP
rs757470424 25 dbSNP
rs1335953520 28 dbSNP
rs199589869 30 dbSNP
rs1274647293 31 dbSNP
rs1386211672 35 dbSNP
rs763652046 36 dbSNP
rs758509093 37 dbSNP
rs953684281 38 dbSNP
rs1481545554 43 dbSNP
rs764825957 45 dbSNP
rs1199722242 49 dbSNP
rs1255132174 51 dbSNP
rs1445179421 59 dbSNP
rs1006006614 61 dbSNP
rs985194977 67 dbSNP
rs1036119556 68 dbSNP
rs1191195094 74 dbSNP
rs776095342 79 dbSNP
rs761491758 92 dbSNP
rs965190400 99 dbSNP
rs997606712 101 dbSNP
rs1475743490 102 dbSNP
rs1428863690 103 dbSNP
rs1263645577 116 dbSNP
rs555628513 125 dbSNP
rs1353469320 126 dbSNP
rs535706239 126 dbSNP
rs918412070 135 dbSNP
rs147227232 136 dbSNP
rs1164569842 140 dbSNP
rs1347294799 144 dbSNP
rs1384929968 145 dbSNP
rs1273580172 151 dbSNP
rs535991129 158 dbSNP
rs1327363568 160 dbSNP
rs1300290170 166 dbSNP
rs1381013721 168 dbSNP
rs1387457504 174 dbSNP
rs77031651 176 dbSNP
rs758067591 181 dbSNP
rs1171905320 191 dbSNP
rs1313117769 191 dbSNP
rs927294194 191 dbSNP
rs1462453703 195 dbSNP
rs1391745269 199 dbSNP
rs1451208760 199 dbSNP
rs796993938 199 dbSNP
rs1184517307 200 dbSNP
rs1247630691 200 dbSNP
rs201950296 200 dbSNP
rs572453554 200 dbSNP
rs879363297 200 dbSNP
rs1276643831 201 dbSNP
rs1306751073 201 dbSNP
rs6794474 201 dbSNP
rs1277128665 202 dbSNP
rs1483514555 202 dbSNP
rs494572 202 dbSNP
rs1226665569 203 dbSNP
rs1255584847 203 dbSNP
rs1315303446 207 dbSNP
rs1364995960 207 dbSNP
rs200602393 210 dbSNP
rs1062949 211 dbSNP
rs1166707893 211 dbSNP
rs1491062232 211 dbSNP
rs149535531 211 dbSNP
rs60867657 211 dbSNP
rs937303091 213 dbSNP
rs1385683584 214 dbSNP
rs1361103618 215 dbSNP
rs1246494369 217 dbSNP
rs1259915755 218 dbSNP
rs1235764753 219 dbSNP
rs1491055825 219 dbSNP
rs397971488 220 dbSNP
rs1062950 221 dbSNP
rs1206828031 224 dbSNP
rs1438839354 225 dbSNP
rs1057240882 230 dbSNP
rs1203718774 231 dbSNP
rs1341858291 234 dbSNP
rs1292987098 239 dbSNP
rs953443221 240 dbSNP
rs1353824617 250 dbSNP
rs1283028251 256 dbSNP
rs576689780 259 dbSNP
rs1007463996 260 dbSNP
rs1306070852 261 dbSNP
rs1032170451 274 dbSNP
rs1365914833 295 dbSNP
rs140278594 303 dbSNP
rs1407231358 308 dbSNP
rs946117070 314 dbSNP
rs1162950868 315 dbSNP
rs1180588379 326 dbSNP
rs1472957427 326 dbSNP
rs57003017 326 dbSNP
rs63693860 326 dbSNP
rs869163409 326 dbSNP
rs78631136 328 dbSNP
rs1241571387 333 dbSNP
rs1041930013 334 dbSNP
rs1247587033 336 dbSNP
rs1224254531 339 dbSNP
rs1450299683 339 dbSNP
rs201998495 340 dbSNP
rs1363584038 342 dbSNP
rs1451998647 343 dbSNP
rs1160816389 345 dbSNP
rs78674234 346 dbSNP
rs1386254959 347 dbSNP
rs1468864292 349 dbSNP
rs1334083632 354 dbSNP
rs1384607955 357 dbSNP
rs1452910942 358 dbSNP
rs1305764751 359 dbSNP
rs763823131 364 dbSNP
rs1333780645 368 dbSNP
rs1240857260 371 dbSNP
rs987895329 372 dbSNP
rs796776633 374 dbSNP
rs529436513 375 dbSNP
rs495702 376 dbSNP
rs981866353 379 dbSNP
rs1458011275 391 dbSNP
rs1390874921 408 dbSNP
rs1203163981 414 dbSNP
rs1472516646 414 dbSNP
rs1029177214 415 dbSNP
rs1261318080 425 dbSNP
rs1462878682 427 dbSNP
rs545438281 428 dbSNP
rs1477224799 431 dbSNP
rs1006475871 441 dbSNP
rs937616300 443 dbSNP
rs1208917653 447 dbSNP
rs1019230015 449 dbSNP
rs1250016074 451 dbSNP
rs1265627434 463 dbSNP
rs77763588 471 dbSNP
rs376604677 472 dbSNP
rs1217446589 480 dbSNP
rs781474732 482 dbSNP
rs551110464 485 dbSNP
rs1366616137 488 dbSNP
rs1056047813 490 dbSNP
rs562147819 499 dbSNP
rs748210423 502 dbSNP
rs972875244 518 dbSNP
rs188353908 534 dbSNP
rs952627148 536 dbSNP
rs370713200 538 dbSNP
rs984076761 541 dbSNP
rs1413284795 547 dbSNP
rs1036505730 554 dbSNP
rs572766565 557 dbSNP
rs1450886733 558 dbSNP
rs897598713 613 dbSNP
rs1245805968 616 dbSNP
rs927158385 624 dbSNP
rs997257982 627 dbSNP
rs12897 638 dbSNP
rs1207873561 645 dbSNP
rs1311538098 647 dbSNP
rs888780028 659 dbSNP
rs1407662935 664 dbSNP
rs1230319531 666 dbSNP
rs917253195 677 dbSNP
rs1295636166 679 dbSNP
rs1297272408 683 dbSNP
rs1007928608 685 dbSNP
rs1434705088 691 dbSNP
rs946179933 698 dbSNP
rs549287101 700 dbSNP
rs1304689452 707 dbSNP
rs1446383448 720 dbSNP
rs1359112835 726 dbSNP
rs1032222779 727 dbSNP
rs957914236 733 dbSNP
rs1169848976 736 dbSNP
rs1432014234 738 dbSNP
rs776808646 748 dbSNP
rs749677085 751 dbSNP
rs1392958291 757 dbSNP
rs771134806 760 dbSNP
rs144227067 764 dbSNP
rs967888791 765 dbSNP
rs534812659 768 dbSNP
rs138175940 783 dbSNP
rs1221611206 787 dbSNP
rs368294033 791 dbSNP
rs1207254687 805 dbSNP
rs1339773611 810 dbSNP
rs1325777337 811 dbSNP
rs1210850638 812 dbSNP
rs1251001715 820 dbSNP
rs1314875451 823 dbSNP
rs372705358 824 dbSNP
rs1479764031 826 dbSNP
rs1197977017 831 dbSNP
rs1009099497 835 dbSNP
rs1412281415 848 dbSNP
rs1369045742 850 dbSNP
rs1252974957 851 dbSNP
rs928658774 856 dbSNP
rs1458043750 858 dbSNP
rs546736508 866 dbSNP
rs1369824492 877 dbSNP
rs1490269414 884 dbSNP
rs1019261316 887 dbSNP
rs1422695456 888 dbSNP
rs1412126345 892 dbSNP
rs958728851 900 dbSNP
rs1482048076 906 dbSNP
rs1197906641 913 dbSNP
rs774764478 920 dbSNP
rs1210230309 926 dbSNP
rs145495952 928 dbSNP
rs1219697542 931 dbSNP
rs909479438 931 dbSNP
rs993947149 940 dbSNP
rs1025794484 947 dbSNP
rs1230732524 960 dbSNP
rs1349189453 965 dbSNP
rs1306986821 974 dbSNP
rs942237639 978 dbSNP
rs1457113839 983 dbSNP
rs1045838 984 dbSNP
rs1036557157 996 dbSNP
rs539896207 998 dbSNP
rs1371960581 1002 dbSNP
rs1471538171 1005 dbSNP
rs1411135903 1006 dbSNP
rs1005355919 1007 dbSNP
rs1371030520 1015 dbSNP
rs148853408 1018 dbSNP
rs34159360 1022 dbSNP
rs1208240925 1032 dbSNP
rs868024766 1033 dbSNP
rs1268777287 1040 dbSNP
rs933100642 1041 dbSNP
rs992727252 1049 dbSNP
rs1051520440 1056 dbSNP
rs1260614876 1057 dbSNP
rs114365249 1062 dbSNP
rs967757992 1070 dbSNP
rs977535457 1082 dbSNP
rs1439616035 1083 dbSNP
rs943057136 1084 dbSNP
rs746410961 1094 dbSNP
rs925996148 1100 dbSNP
rs1402814885 1112 dbSNP
rs1053355634 1120 dbSNP
rs1050590719 1122 dbSNP
rs142379863 1129 dbSNP
rs910700623 1140 dbSNP
rs555639241 1141 dbSNP
rs1009419717 1142 dbSNP
rs1020770902 1144 dbSNP
rs1197913015 1146 dbSNP
rs1449909513 1160 dbSNP
rs1248875663 1162 dbSNP
rs1219929974 1164 dbSNP
rs1463581475 1165 dbSNP
rs772535557 1178 dbSNP
rs1003406371 1179 dbSNP
rs1201484576 1181 dbSNP
rs1347753867 1193 dbSNP
rs944987820 1194 dbSNP
rs73880159 1221 dbSNP
rs959015725 1222 dbSNP
rs541240150 1228 dbSNP
rs1299319772 1232 dbSNP
rs181122449 1234 dbSNP
rs577691839 1235 dbSNP
rs545072222 1239 dbSNP
rs1397642582 1243 dbSNP
rs1173006001 1249 dbSNP
rs888230064 1249 dbSNP
rs963653685 1271 dbSNP
rs1034209048 1274 dbSNP
rs563174242 1279 dbSNP
rs778738890 1288 dbSNP
rs530513388 1289 dbSNP
rs548950095 1294 dbSNP
rs1014196934 1295 dbSNP
rs919459448 1298 dbSNP
rs1259048105 1308 dbSNP
rs1429710044 1325 dbSNP
rs933506900 1334 dbSNP
rs1024601231 1337 dbSNP
rs1444252976 1340 dbSNP
rs1254684668 1344 dbSNP
rs761261012 1345 dbSNP
rs977858671 1346 dbSNP
rs1483575316 1370 dbSNP
rs16845423 1371 dbSNP
rs1225681002 1372 dbSNP
rs528362440 1373 dbSNP
rs1338348591 1395 dbSNP
rs1284216782 1407 dbSNP
rs1246345250 1410 dbSNP
rs1338232086 1416 dbSNP
rs772670713 1419 dbSNP
rs1410379901 1423 dbSNP
rs986164887 1437 dbSNP
rs1372131188 1438 dbSNP
rs1305955762 1439 dbSNP
rs910735006 1446 dbSNP
rs1053407131 1447 dbSNP
rs893458879 1449 dbSNP
rs919469257 1468 dbSNP
rs929568809 1474 dbSNP
rs1187801081 1481 dbSNP
rs945328561 1485 dbSNP
rs1047209450 1489 dbSNP
rs186364845 1500 dbSNP
rs888103146 1511 dbSNP
rs1005336345 1517 dbSNP
rs1288435180 1528 dbSNP
rs1211315865 1536 dbSNP
rs1359971425 1538 dbSNP
rs1042302922 1540 dbSNP
rs906401645 1549 dbSNP
rs1228856368 1551 dbSNP
rs894314797 1559 dbSNP
rs1352266599 1567 dbSNP
rs1286439932 1569 dbSNP
rs1014060982 1573 dbSNP
rs1298646275 1574 dbSNP
rs1003394001 1580 dbSNP
rs1350296728 1584 dbSNP
rs1033909740 1586 dbSNP
rs79552239 1587 dbSNP
rs1407321292 1591 dbSNP
rs1392330671 1593 dbSNP
rs543862644 1601 dbSNP
rs1164310694 1603 dbSNP
rs1012994205 1606 dbSNP
rs903137834 1607 dbSNP
rs1294383257 1609 dbSNP
rs1176025446 1613 dbSNP
rs766149466 1618 dbSNP
rs1033455151 1620 dbSNP
rs1200500318 1626 dbSNP
rs1466859819 1633 dbSNP
rs1271918363 1637 dbSNP
rs1215706450 1640 dbSNP
rs539584977 1654 dbSNP
rs1486577153 1655 dbSNP
rs986199072 1674 dbSNP
rs1017605379 1677 dbSNP
rs1188601271 1681 dbSNP
rs1223200077 1682 dbSNP
rs1367986748 1683 dbSNP
rs1276434479 1684 dbSNP
rs1438795304 1693 dbSNP
rs751349657 1694 dbSNP
rs972019605 1696 dbSNP
rs966190203 1701 dbSNP
rs551844174 1710 dbSNP
rs1457832776 1720 dbSNP
rs1442371449 1721 dbSNP
rs1185256442 1722 dbSNP
rs1157491905 1729 dbSNP
rs976691103 1729 dbSNP
rs1026574585 1732 dbSNP
rs919433018 1733 dbSNP
rs1426231134 1739 dbSNP
rs1174689407 1740 dbSNP
rs1453023476 1741 dbSNP
rs929573888 1742 dbSNP
rs1188848177 1746 dbSNP
rs985049771 1748 dbSNP
rs1239886065 1753 dbSNP
rs955099085 1754 dbSNP
rs1346852222 1761 dbSNP
rs759589386 1761 dbSNP
rs1312710296 1763 dbSNP
rs987674891 1764 dbSNP
rs1458921422 1770 dbSNP
rs1302924577 1783 dbSNP
rs1321271258 1785 dbSNP
rs1367392516 1787 dbSNP
rs1287194541 1791 dbSNP
rs909553608 1806 dbSNP
rs569762758 1807 dbSNP
rs1433210949 1808 dbSNP
rs940964407 1808 dbSNP
rs1382378318 1812 dbSNP
rs1450712622 1814 dbSNP
rs1394909689 1825 dbSNP
rs367625695 1833 dbSNP
rs1055558079 1835 dbSNP
rs2431 1843 dbSNP
rs1185445214 1845 dbSNP
rs989180246 1846 dbSNP
rs914945695 1849 dbSNP
rs1483324728 1853 dbSNP
rs1282810806 1859 dbSNP
rs1239131671 1861 dbSNP
rs1208691260 1866 dbSNP
rs1319222458 1880 dbSNP
rs1275125102 1889 dbSNP
rs1229327690 1890 dbSNP
rs1208863623 1905 dbSNP
rs949778744 1907 dbSNP
rs1459753960 1915 dbSNP
rs945045078 1916 dbSNP
rs1045997246 1917 dbSNP
rs1205180636 1918 dbSNP
rs1214054806 1919 dbSNP
rs1413499975 1919 dbSNP
rs542085075 1919 dbSNP
rs1237645584 1920 dbSNP
rs79690588 1929 dbSNP
rs1375181759 1930 dbSNP
rs1309027404 1931 dbSNP
rs529280097 1938 dbSNP
rs752848609 1939 dbSNP
rs999190109 1942 dbSNP
rs1423860408 1944 dbSNP
rs1415357097 1949 dbSNP
rs779771121 1950 dbSNP
rs1054997597 1951 dbSNP
rs1361222594 1954 dbSNP
rs191834441 1957 dbSNP
rs754074715 1958 dbSNP
rs1207014044 1972 dbSNP
rs893141642 1980 dbSNP
rs1249803657 1987 dbSNP
rs1204148479 2001 dbSNP
rs367876626 2005 dbSNP
rs1013046081 2009 dbSNP
rs1355403605 2011 dbSNP
rs1289591035 2012 dbSNP
rs1037792934 2015 dbSNP
rs140685843 2019 dbSNP
rs1297231606 2020 dbSNP
rs1026930144 2021 dbSNP
rs950885539 2022 dbSNP
rs183576272 2025 dbSNP
rs993525312 2027 dbSNP
rs1278127344 2028 dbSNP
rs187279398 2032 dbSNP
rs955006114 2033 dbSNP
rs1417057182 2044 dbSNP
rs1249580158 2046 dbSNP
rs1176795593 2047 dbSNP
rs1488933655 2049 dbSNP
rs1275070839 2050 dbSNP
rs1211889012 2055 dbSNP
rs938234861 2063 dbSNP
rs145883648 2070 dbSNP
rs915562110 2070 dbSNP
rs949868076 2072 dbSNP
rs1017803618 2075 dbSNP
rs1283131034 2084 dbSNP
rs1323554457 2087 dbSNP
rs1045456237 2093 dbSNP
rs575367804 2097 dbSNP
rs964844298 2102 dbSNP
rs989566519 2105 dbSNP
rs914998011 2114 dbSNP
rs903033085 2118 dbSNP
rs966412097 2118 dbSNP
rs1388792037 2124 dbSNP
rs746201774 2141 dbSNP
rs1320831049 2145 dbSNP
rs934473730 2147 dbSNP
rs760083322 2155 dbSNP
rs542657611 2156 dbSNP
rs772588443 2171 dbSNP
rs939319539 2185 dbSNP
rs34229028 2191 dbSNP
rs397830498 2191 dbSNP
rs1007429162 2192 dbSNP
rs1039036089 2194 dbSNP
rs1207338593 2197 dbSNP
rs1055450018 2204 dbSNP
rs1260712589 2206 dbSNP
rs1234387135 2217 dbSNP
rs998023634 2228 dbSNP
rs1300773475 2233 dbSNP
rs542611079 2235 dbSNP
rs1233133314 2237 dbSNP
rs1483220793 2237 dbSNP
rs1365234573 2240 dbSNP
rs1319724449 2243 dbSNP
rs1380403009 2246 dbSNP
rs1198615624 2250 dbSNP
rs1384151809 2272 dbSNP
rs1427058339 2281 dbSNP
rs1393094784 2282 dbSNP
rs1026376282 2287 dbSNP
rs1297533394 2289 dbSNP
rs1454024425 2289 dbSNP
rs375890117 2291 dbSNP
rs1195398140 2295 dbSNP
rs1445418117 2295 dbSNP
rs1261598117 2296 dbSNP
rs1201576151 2298 dbSNP
rs950955354 2306 dbSNP
rs1426205210 2308 dbSNP
rs1233027476 2309 dbSNP
rs1006420787 2310 dbSNP
rs916463105 2331 dbSNP
rs941182279 2334 dbSNP
rs1038180364 2336 dbSNP
rs1224612217 2337 dbSNP
rs539946445 2337 dbSNP
rs1016436203 2343 dbSNP
rs1416567658 2344 dbSNP
rs899266039 2349 dbSNP
rs993970495 2354 dbSNP
rs991056653 2356 dbSNP
rs1397476535 2357 dbSNP
rs915591669 2360 dbSNP
rs11359449 2362 dbSNP
rs1372596703 2362 dbSNP
rs397991666 2362 dbSNP
rs200656607 2363 dbSNP
rs1047751312 2366 dbSNP
rs971061951 2370 dbSNP
rs376093950 2372 dbSNP
rs190777580 2381 dbSNP
rs1009189747 2382 dbSNP
rs1483626695 2389 dbSNP
rs1274641518 2399 dbSNP
rs780478960 2404 dbSNP
rs1017812229 2407 dbSNP
rs1193766332 2413 dbSNP
rs1338121786 2428 dbSNP
rs964896004 2429 dbSNP
rs747659289 2431 dbSNP
rs528426139 2432 dbSNP
rs540508063 2433 dbSNP
rs966463123 2446 dbSNP
rs769357443 2463 dbSNP
rs138490632 2473 dbSNP
rs1331074223 2482 dbSNP
rs141181816 2506 dbSNP
rs10989 2509 dbSNP
rs1165768173 2513 dbSNP
rs990466726 2516 dbSNP
rs550457278 2523 dbSNP
rs941234544 2543 dbSNP
rs768936408 2558 dbSNP
rs973926216 2561 dbSNP
rs1048182503 2563 dbSNP
rs544541490 2595 dbSNP
rs1221413788 2596 dbSNP
rs1290214708 2604 dbSNP
rs1215010075 2606 dbSNP
rs1332077218 2608 dbSNP
rs929440960 2619 dbSNP
rs762565898 2624 dbSNP
rs890504476 2626 dbSNP
rs1352524513 2627 dbSNP
rs1277558181 2629 dbSNP
rs1490815095 2632 dbSNP
rs1335386676 2644 dbSNP
rs1201171470 2649 dbSNP
rs1247361397 2654 dbSNP
rs1392435901 2658 dbSNP
rs1475087201 2659 dbSNP
rs750097205 2662 dbSNP
rs944709555 2693 dbSNP
rs1038980657 2695 dbSNP
rs1253203118 2698 dbSNP
rs770589572 2705 dbSNP
rs781357470 2706 dbSNP
rs1392212796 2707 dbSNP
rs1466712029 2713 dbSNP
rs150195379 2719 dbSNP
rs1022454750 2724 dbSNP
rs1216326456 2728 dbSNP
rs759358191 2731 dbSNP
rs1282141903 2756 dbSNP
rs1364315081 2765 dbSNP
rs1236804688 2787 dbSNP
rs1304413341 2787 dbSNP
rs1345503189 2787 dbSNP
rs1389026153 2789 dbSNP
rs564783837 2816 dbSNP
rs567306046 2819 dbSNP
rs550161093 2822 dbSNP
rs1325359378 2823 dbSNP
rs1293431669 2830 dbSNP
rs1175083142 2832 dbSNP
rs1452190844 2837 dbSNP
rs924269008 2839 dbSNP
rs955840249 2856 dbSNP
rs900124607 2861 dbSNP
rs914422495 2865 dbSNP
rs1299408996 2869 dbSNP
rs1365437633 2870 dbSNP
rs943184283 2876 dbSNP
rs1038933105 2887 dbSNP
rs1346015090 2889 dbSNP
rs923246187 2897 dbSNP
rs183327428 2898 dbSNP
rs1364228368 2899 dbSNP
rs570084166 2941 dbSNP
rs1430681538 2956 dbSNP
rs769859628 2957 dbSNP
rs1315196984 2958 dbSNP
rs1047744420 2960 dbSNP
rs553623690 2968 dbSNP
rs536125386 2986 dbSNP
rs1037764808 2990 dbSNP
rs918461044 2992 dbSNP
rs1185823525 2996 dbSNP
rs929799510 3006 dbSNP
rs986615485 3008 dbSNP
rs1185515920 3012 dbSNP
rs186485491 3014 dbSNP
rs539229960 3015 dbSNP
rs527543233 3016 dbSNP
rs944792963 3018 dbSNP
rs1250186106 3022 dbSNP
rs374081276 3032 dbSNP
rs769392154 3034 dbSNP
rs906824234 3039 dbSNP
rs900504998 3053 dbSNP
rs1449664533 3059 dbSNP
rs1172675720 3060 dbSNP
rs191284948 3063 dbSNP
rs1356644300 3064 dbSNP
rs1000168297 3071 dbSNP
rs1031367066 3073 dbSNP
rs947010688 3079 dbSNP
rs1459713935 3086 dbSNP
rs955871574 3089 dbSNP
rs549723588 3096 dbSNP
rs575435457 3100 dbSNP
rs1352199177 3106 dbSNP
rs1043958795 3109 dbSNP
rs542724779 3114 dbSNP
rs1461564553 3124 dbSNP
rs902731765 3128 dbSNP
rs1162763323 3129 dbSNP
rs1398494237 3149 dbSNP
rs1321949913 3151 dbSNP
rs1000115810 3158 dbSNP
rs1389002997 3164 dbSNP
rs1035171738 3166 dbSNP
rs1312375886 3189 dbSNP
rs1021292624 3190 dbSNP
rs896247553 3193 dbSNP
rs1011990330 3194 dbSNP
rs1335596373 3195 dbSNP
rs1278921182 3211 dbSNP
rs1023339307 3212 dbSNP
rs964420710 3213 dbSNP
rs1321457597 3216 dbSNP
rs1308170474 3218 dbSNP
rs1206968968 3220 dbSNP
rs1270087155 3222 dbSNP
rs1370711775 3226 dbSNP
rs1297321903 3229 dbSNP
rs1440972099 3231 dbSNP
rs554643285 3240 dbSNP
rs1203282464 3250 dbSNP
rs973693885 3256 dbSNP
rs1161003484 3260 dbSNP
rs201107538 3260 dbSNP
rs763000468 3260 dbSNP
rs766221963 3260 dbSNP
rs923076733 3260 dbSNP
rs933279576 3263 dbSNP
rs183254820 3265 dbSNP
rs1178313573 3278 dbSNP
rs753666789 3278 dbSNP
rs1188645424 3282 dbSNP
rs1254996991 3282 dbSNP
rs1468932553 3282 dbSNP
rs11359824 3286 dbSNP
rs1241623246 3286 dbSNP
rs1308011646 3286 dbSNP
rs878903810 3286 dbSNP
rs1234607266 3287 dbSNP
rs1363778355 3289 dbSNP
rs1428634298 3290 dbSNP
rs1323321755 3291 dbSNP
rs1471891592 3299 dbSNP
rs1160833632 3301 dbSNP
rs201555132 3302 dbSNP
rs1468779935 3303 dbSNP
rs1334312932 3306 dbSNP
rs1403855892 3307 dbSNP
rs1158233055 3312 dbSNP
rs1454875072 3315 dbSNP
rs907888078 3319 dbSNP
rs188128881 3320 dbSNP
rs1327922946 3322 dbSNP
rs1333975907 3323 dbSNP
rs1037796395 3325 dbSNP
rs1288840891 3328 dbSNP
rs1329953689 3337 dbSNP
rs1300888206 3339 dbSNP
rs1349583312 3339 dbSNP
rs1222937660 3343 dbSNP
rs534944971 3344 dbSNP
rs1297576451 3345 dbSNP
rs565188162 3346 dbSNP
rs532267205 3351 dbSNP
rs1377502419 3353 dbSNP
rs13088414 3354 dbSNP
rs1171081371 3359 dbSNP
rs1373746204 3364 dbSNP
rs760685462 3364 dbSNP
rs1482242021 3373 dbSNP
rs1184988296 3374 dbSNP
rs948117477 3395 dbSNP
rs371944983 3400 dbSNP
rs1413279777 3409 dbSNP
rs1277720502 3412 dbSNP
rs1479842982 3415 dbSNP
rs1173306997 3419 dbSNP
rs1339429844 3421 dbSNP
rs1379065237 3423 dbSNP
rs1252559379 3425 dbSNP
rs1466226697 3429 dbSNP
rs1046583869 3431 dbSNP
rs138756518 3432 dbSNP
rs1353386223 3433 dbSNP
rs996224364 3436 dbSNP
rs193083828 3437 dbSNP
rs1395673279 3440 dbSNP
rs1411374494 3441 dbSNP
rs1169707402 3442 dbSNP
rs530945729 3444 dbSNP
rs1423497043 3445 dbSNP
rs1344766470 3446 dbSNP
rs1255888259 3447 dbSNP
rs1404466888 3449 dbSNP
rs1273717130 3450 dbSNP
rs1345253878 3450 dbSNP
rs3057949 3450 dbSNP
rs369829269 3450 dbSNP
rs386398552 3450 dbSNP
rs878979515 3466 dbSNP
rs1209769755 3467 dbSNP
rs1280044520 3468 dbSNP
rs1314236923 3470 dbSNP
rs1234250663 3471 dbSNP
rs1250913240 3474 dbSNP
rs1340510114 3479 dbSNP
rs1207694801 3481 dbSNP
rs549056451 3487 dbSNP
rs149375909 3488 dbSNP
rs1331174040 3494 dbSNP
rs34298383 3501 dbSNP
rs35643627 3504 dbSNP
rs1031649525 3505 dbSNP
rs369658030 3513 dbSNP
rs951298175 3517 dbSNP
rs1169330429 3518 dbSNP
rs1011165019 3521 dbSNP
rs1387890943 3522 dbSNP
rs1431438160 3525 dbSNP
rs546634567 3526 dbSNP
rs1176452111 3530 dbSNP
rs1456897141 3535 dbSNP
rs36122113 3536 dbSNP
rs1467072217 3537 dbSNP
rs185292163 3539 dbSNP
rs1224098519 3540 dbSNP
rs1456327435 3541 dbSNP
rs35691237 3541 dbSNP
rs1295151602 3542 dbSNP
rs1238285894 3548 dbSNP
rs966135483 3549 dbSNP
rs1443275053 3551 dbSNP
rs1348642948 3552 dbSNP
rs974796903 3553 dbSNP
rs1401632044 3557 dbSNP
rs1387629506 3562 dbSNP
rs921983254 3569 dbSNP
rs538933002 3574 dbSNP
rs1043680741 3575 dbSNP
rs1295166169 3580 dbSNP
rs1395362171 3582 dbSNP
rs1030176770 3587 dbSNP
rs190332889 3588 dbSNP
rs35978207 3591 dbSNP
rs9859248 3593 dbSNP
rs1448476946 3594 dbSNP
rs1359084519 3597 dbSNP
rs1057063455 3598 dbSNP
rs536396015 3603 dbSNP
rs896644285 3605 dbSNP
rs1012042584 3606 dbSNP
rs34911026 3609 dbSNP
rs555705383 3609 dbSNP
rs1044836885 3610 dbSNP
rs13093263 3612 dbSNP
rs1245863783 3614 dbSNP
rs907749998 3615 dbSNP
rs1189053321 3616 dbSNP
rs898211795 3619 dbSNP
rs1384389014 3622 dbSNP
rs995183980 3624 dbSNP
rs375942021 3625 dbSNP
rs369113301 3629 dbSNP
rs951406060 3636 dbSNP
rs578206437 3637 dbSNP
rs1476359412 3638 dbSNP
rs1261013284 3641 dbSNP
rs1019907545 3649 dbSNP
rs963851011 3650 dbSNP
rs575660396 3654 dbSNP
rs922033922 3659 dbSNP
rs1046890839 3660 dbSNP
rs1310482086 3664 dbSNP
rs1298533433 3666 dbSNP
rs558234795 3667 dbSNP
rs1215297394 3668 dbSNP
rs138096295 3669 dbSNP
rs1226921330 3671 dbSNP
rs1315481031 3674 dbSNP
rs1322823609 3676 dbSNP
rs192412494 3677 dbSNP
rs1214524541 3679 dbSNP
rs562382700 3680 dbSNP
rs574289781 3686 dbSNP
rs541574286 3687 dbSNP
rs561875942 3690 dbSNP
rs532902283 3691 dbSNP
rs1056714935 3694 dbSNP
rs184955622 3695 dbSNP
rs948207773 3696 dbSNP
rs546991440 3705 dbSNP
rs1237182310 3711 dbSNP
rs1205268288 3716 dbSNP
rs1459180540 3718 dbSNP
rs143655199 3723 dbSNP
rs1414510304 3724 dbSNP
rs1418420875 3725 dbSNP
rs761514676 3729 dbSNP
rs386668285 3730 dbSNP
rs1285080 3731 dbSNP
rs995234993 3732 dbSNP
rs55765148 3733 dbSNP
rs188105403 3734 dbSNP
rs1014758210 3735 dbSNP
rs142040862 3736 dbSNP
rs916598494 3740 dbSNP
rs1358766388 3758 dbSNP
rs566578359 3764 dbSNP
rs1162423349 3769 dbSNP
rs761259994 3771 dbSNP
rs116369853 3776 dbSNP
rs1228326346 3777 dbSNP
rs1459113158 3796 dbSNP
rs550322130 3797 dbSNP
rs1021397223 3800 dbSNP
rs1469294539 3805 dbSNP
rs1330637205 3810 dbSNP
rs1219785013 3813 dbSNP
rs1228430274 3816 dbSNP
rs1321548701 3817 dbSNP
rs181070980 3819 dbSNP
rs979532774 3820 dbSNP
rs1373932929 3821 dbSNP
rs750345151 3822 dbSNP
rs1441085573 3828 dbSNP
rs956734502 3828 dbSNP
rs1212046760 3835 dbSNP
rs1460667005 3838 dbSNP
rs992531989 3842 dbSNP
rs946981040 3843 dbSNP
rs1237842728 3855 dbSNP
rs35263143 3868 dbSNP
rs1452787791 3869 dbSNP
rs1160018789 3871 dbSNP
rs62281182 3872 dbSNP
rs1378761580 3875 dbSNP
rs1473634438 3877 dbSNP
rs1178096812 3885 dbSNP
rs1454796145 3886 dbSNP
rs1159969087 3887 dbSNP
rs372992375 3892 dbSNP
rs1424794125 3895 dbSNP
rs1412975830 3900 dbSNP
rs1285079 3902 dbSNP
rs1218270797 3903 dbSNP
rs920085857 3904 dbSNP
rs1284911426 3925 dbSNP
rs1234350847 3936 dbSNP
rs1332336647 3945 dbSNP
rs551641854 3957 dbSNP
rs113697834 3963 dbSNP
rs374155850 3970 dbSNP
rs1455156596 3978 dbSNP
rs1046817028 3979 dbSNP
rs886827599 3990 dbSNP
rs1409959848 3993 dbSNP
rs1299793110 3997 dbSNP
rs1273722362 4001 dbSNP
rs1342524840 4006 dbSNP
rs943731341 4008 dbSNP
rs1435368002 4017 dbSNP
rs1379480613 4019 dbSNP
rs1197295645 4028 dbSNP
rs1433133324 4029 dbSNP
rs560059556 4037 dbSNP
rs1278825567 4050 dbSNP
rs1196254937 4051 dbSNP
rs80028714 4064 dbSNP
rs1041086315 4065 dbSNP
rs1487538569 4067 dbSNP
rs1371342005 4070 dbSNP
rs1261951426 4078 dbSNP
rs543628977 4079 dbSNP
rs1211192333 4095 dbSNP
rs1341231314 4097 dbSNP
rs773999095 4098 dbSNP
rs1253752702 4100 dbSNP
rs573313747 4104 dbSNP
rs540356641 4105 dbSNP
rs557082875 4108 dbSNP
rs1280061106 4109 dbSNP
rs1483333623 4110 dbSNP
rs1183070349 4112 dbSNP
rs904361299 4114 dbSNP
rs1246207809 4123 dbSNP
rs565323689 4133 dbSNP
rs532550081 4134 dbSNP
rs1404376771 4136 dbSNP
rs117004117 4138 dbSNP
rs1465668495 4139 dbSNP
rs1424936204 4141 dbSNP
rs1023520872 4146 dbSNP
rs1443773528 4146 dbSNP
rs751660814 4146 dbSNP
rs777671166 4146 dbSNP
rs969424937 4146 dbSNP
rs1253723950 4153 dbSNP
rs1199359058 4158 dbSNP
rs1480701720 4164 dbSNP
rs982556701 4173 dbSNP
rs1216757154 4176 dbSNP
rs1317002954 4178 dbSNP
rs956975057 4185 dbSNP
rs1246796760 4187 dbSNP
rs957034573 4190 dbSNP
rs988211597 4191 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' gcucacacUCUAGUGUGGAGGg 5'
                  || || ||||||| 
Target 5' ------caAGCUC-CACCUCCc 3'
1 - 15
Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- 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.
LinkOut: [PMID: 23592263]
CLIP-seq Support 1 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000336824.4 | 3UTR | CAAGCUCCACCUCCCGGGUUCAUGCCAUUCUCCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
231 hsa-miR-3689d Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059166 TXNIP thioredoxin interacting protein 2 4
MIRT080699 KIAA1468 KIAA1468 2 2
MIRT218770 CDKN1A cyclin dependent kinase inhibitor 1A 2 2
MIRT278059 KHNYN KH and NYN domain containing 2 2
MIRT345933 EIF4A1 eukaryotic translation initiation factor 4A1 2 2
MIRT366238 VMA21 VMA21, vacuolar ATPase assembly factor 2 2
MIRT449689 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT451149 C19orf53 chromosome 19 open reading frame 53 2 2
MIRT451266 NDUFA11 NADH:ubiquinone oxidoreductase subunit A11 2 2
MIRT451375 C19orf43 telomerase RNA component interacting RNase 2 2
MIRT451570 CIAPIN1 cytokine induced apoptosis inhibitor 1 2 2
MIRT451585 HIRIP3 HIRA interacting protein 3 2 2
MIRT451614 MEIS3P1 Meis homeobox 3 pseudogene 1 2 2
MIRT451763 ZNF611 zinc finger protein 611 2 6
MIRT452383 LY6E lymphocyte antigen 6 family member E 2 4
MIRT452573 ZFP69B ZFP69 zinc finger protein B 2 2
MIRT452735 PTGES3L prostaglandin E synthase 3 like 2 6
MIRT452867 LAX1 lymphocyte transmembrane adaptor 1 2 2
MIRT452975 CABP4 calcium binding protein 4 2 2
MIRT453215 CERS1 ceramide synthase 1 2 2
MIRT453259 PARP11 poly(ADP-ribose) polymerase family member 11 2 2
MIRT453449 GLG1 golgi glycoprotein 1 2 2
MIRT453479 PITPNM3 PITPNM family member 3 2 2
MIRT453663 CD207 CD207 molecule 2 6
MIRT453724 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 2 2
MIRT453760 RANGAP1 Ran GTPase activating protein 1 2 2
MIRT454181 AP1S3 adaptor related protein complex 1 sigma 3 subunit 2 6
MIRT454330 PPARA peroxisome proliferator activated receptor alpha 2 2
MIRT454338 CDKL1 cyclin dependent kinase like 1 2 2
MIRT454427 GTF2F1 general transcription factor IIF subunit 1 2 2
MIRT454665 FBXL18 F-box and leucine rich repeat protein 18 2 2
MIRT454825 POLR2J3 RNA polymerase II subunit J3 2 2
MIRT455130 TBC1D25 TBC1 domain family member 25 2 2
MIRT455166 SUV39H1 suppressor of variegation 3-9 homolog 1 2 2
MIRT455416 RXRB retinoid X receptor beta 2 2
MIRT455668 GLO1 glyoxalase I 2 2
MIRT455999 CYP2C19 cytochrome P450 family 2 subfamily C member 19 2 2
MIRT456446 TMEM81 transmembrane protein 81 2 2
MIRT456642 NOS1AP nitric oxide synthase 1 adaptor protein 2 2
MIRT456728 TMEM239 transmembrane protein 239 2 2
MIRT457131 ASPH aspartate beta-hydroxylase 2 2
MIRT457157 MXRA7 matrix remodeling associated 7 2 2
MIRT457358 POFUT2 protein O-fucosyltransferase 2 2 2
MIRT457458 UNC119B unc-119 lipid binding chaperone B 2 2
MIRT457619 UPK3BL uroplakin 3B like 1 2 2
MIRT457692 ZNF587 zinc finger protein 587 2 2
MIRT457727 SMOX spermine oxidase 2 2
MIRT457788 VWA1 von Willebrand factor A domain containing 1 2 2
MIRT457875 THEM6 thioesterase superfamily member 6 2 4
MIRT457909 ZNF212 zinc finger protein 212 2 2
MIRT458395 ABCF1 ATP binding cassette subfamily F member 1 2 2
MIRT458496 MARVELD2 MARVEL domain containing 2 2 2
MIRT458544 CYP2B6 cytochrome P450 family 2 subfamily B member 6 2 2
MIRT458577 TCOF1 treacle ribosome biogenesis factor 1 2 2
MIRT458732 CES2 carboxylesterase 2 2 2
MIRT458814 ZNF843 zinc finger protein 843 2 2
MIRT458931 SAMD4B sterile alpha motif domain containing 4B 2 2
MIRT459341 ZNF17 zinc finger protein 17 2 2
MIRT459365 MPLKIP M-phase specific PLK1 interacting protein 2 6
MIRT459572 NLGN2 neuroligin 2 2 2
MIRT460015 DTX3L deltex E3 ubiquitin ligase 3L 2 4
MIRT460144 ASB16 ankyrin repeat and SOCS box containing 16 2 2
MIRT460653 IGFBP4 insulin like growth factor binding protein 4 2 2
MIRT460798 VPS33A VPS33A, CORVET/HOPS core subunit 2 2
MIRT461058 KCNK6 potassium two pore domain channel subfamily K member 6 2 4
MIRT461458 SLC19A3 solute carrier family 19 member 3 2 2
MIRT461572 SCO1 SCO1, cytochrome c oxidase assembly protein 2 4
MIRT461927 TNFSF14 TNF superfamily member 14 2 2
MIRT461953 C3 complement C3 2 2
MIRT462278 KRR1 KRR1, small subunit processome component homolog 2 2
MIRT462744 EFNB1 ephrin B1 2 2
MIRT463136 ZNF451 zinc finger protein 451 2 4
MIRT463566 ZBTB39 zinc finger and BTB domain containing 39 2 6
MIRT463866 WNT7B Wnt family member 7B 2 2
MIRT464326 UST uronyl 2-sulfotransferase 2 2
MIRT464796 UBE2F ubiquitin conjugating enzyme E2 F (putative) 2 2
MIRT465034 TTC39C tetratricopeptide repeat domain 39C 2 2
MIRT466207 TMED10 transmembrane p24 trafficking protein 10 2 2
MIRT467007 SSBP2 single stranded DNA binding protein 2 2 2
MIRT467029 SRSF1 serine and arginine rich splicing factor 1 2 4
MIRT468001 SKI SKI proto-oncogene 2 2
MIRT468031 SIKE1 suppressor of IKBKE 1 2 6
MIRT468575 SERBP1 SERPINE1 mRNA binding protein 1 2 6
MIRT468834 RRM2 ribonucleotide reductase regulatory subunit M2 2 2
MIRT468970 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT469450 REL REL proto-oncogene, NF-kB subunit 2 6
MIRT470888 PLXND1 plexin D1 2 2
MIRT470953 PKM pyruvate kinase, muscle 2 2
MIRT471828 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT472590 NACC1 nucleus accumbens associated 1 2 2
MIRT472805 MTMR12 myotubularin related protein 12 2 2
MIRT472818 MTMR10 myotubularin related protein 10 2 6
MIRT472914 MSN moesin 2 2
MIRT474558 KLHDC3 kelch domain containing 3 2 2
MIRT474716 KIF13A kinesin family member 13A 2 6
MIRT475279 TOR1AIP2 torsin 1A interacting protein 2 2 2
MIRT475300 IFNLR1 interferon lambda receptor 1 2 2
MIRT475759 HDLBP high density lipoprotein binding protein 2 2
MIRT475786 HDGF heparin binding growth factor 2 2
MIRT475933 GXYLT2 glucoside xylosyltransferase 2 2 8
MIRT476212 GNS glucosamine (N-acetyl)-6-sulfatase 2 2
MIRT476238 GNPNAT1 glucosamine-phosphate N-acetyltransferase 1 2 4
MIRT476799 FNDC3B fibronectin type III domain containing 3B 2 2
MIRT477988 DNAL1 dynein axonemal light chain 1 2 2
MIRT478317 DDN dendrin 2 2
MIRT479257 CHSY1 chondroitin sulfate synthase 1 2 2
MIRT479344 CEP97 centrosomal protein 97 2 2
MIRT479522 CDCA4 cell division cycle associated 4 2 2
MIRT479906 CCDC117 coiled-coil domain containing 117 2 6
MIRT481147 AVL9 AVL9 cell migration associated 2 6
MIRT481735 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT482089 ALG8 ALG8, alpha-1,3-glucosyltransferase 2 2
MIRT482389 AEN apoptosis enhancing nuclease 2 2
MIRT483093 TFPI tissue factor pathway inhibitor 2 2
MIRT484246 ANK1 ankyrin 1 2 2
MIRT484342 EPN1 epsin 1 2 4
MIRT489141 C5orf38 chromosome 5 open reading frame 38 2 2
MIRT489163 MRPL12 mitochondrial ribosomal protein L12 2 4
MIRT489547 SOX11 SRY-box 11 2 4
MIRT489780 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT489799 KRT80 keratin 80 2 6
MIRT490535 KIAA1715 lunapark, ER junction formation factor 2 2
MIRT492198 SOCS1 suppressor of cytokine signaling 1 2 2
MIRT492283 SHISA6 shisa family member 6 2 4
MIRT501059 SMARCAD1 SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 2 4
MIRT501094 SLC5A6 solute carrier family 5 member 6 2 4
MIRT503870 CBS cystathionine-beta-synthase 2 2
MIRT507981 BCL2L13 BCL2 like 13 2 4
MIRT508125 AMD1 adenosylmethionine decarboxylase 1 2 2
MIRT508205 SLC35E1 solute carrier family 35 member E1 2 2
MIRT508385 SPTBN2 spectrin beta, non-erythrocytic 2 2 4
MIRT510308 PDRG1 p53 and DNA damage regulated 1 2 2
MIRT510462 ZDHHC18 zinc finger DHHC-type containing 18 2 2
MIRT512227 ATXN3 ataxin 3 2 8
MIRT512665 STEAP3 STEAP3 metalloreductase 2 2
MIRT514184 PGPEP1 pyroglutamyl-peptidase I 2 2
MIRT515053 EBNA1BP2 EBNA1 binding protein 2 2 2
MIRT515138 ZNF799 zinc finger protein 799 2 4
MIRT515452 ZNF747 zinc finger protein 747 2 2
MIRT515791 COL4A3BP collagen type IV alpha 3 binding protein 2 2
MIRT515905 AGTPBP1 ATP/GTP binding protein 1 2 2
MIRT516129 MRPS16 mitochondrial ribosomal protein S16 2 6
MIRT516679 ZNF860 zinc finger protein 860 2 4
MIRT516750 ZNF100 zinc finger protein 100 2 2
MIRT516971 OR7D2 olfactory receptor family 7 subfamily D member 2 2 2
MIRT517491 NPAP1 nuclear pore associated protein 1 2 2
MIRT517774 PROM2 prominin 2 2 2
MIRT517938 ZNF431 zinc finger protein 431 2 4
MIRT518386 ZNF250 zinc finger protein 250 2 2
MIRT520621 TMEM41B transmembrane protein 41B 2 2
MIRT521028 SLC30A5 solute carrier family 30 member 5 2 2
MIRT521454 RAD51 RAD51 recombinase 2 2
MIRT521564 PTPLB 3-hydroxyacyl-CoA dehydratase 2 1 1
MIRT521581 PTBP2 polypyrimidine tract binding protein 2 2 2
MIRT522263 NKRF NFKB repressing factor 2 2
MIRT522410 MXI1 MAX interactor 1, dimerization protein 2 2
MIRT522543 MED28 mediator complex subunit 28 2 6
MIRT522915 KCNE3 potassium voltage-gated channel subfamily E regulatory subunit 3 2 2
MIRT523029 IGF1 insulin like growth factor 1 2 2
MIRT523854 ESPL1 extra spindle pole bodies like 1, separase 2 4
MIRT524184 DFFA DNA fragmentation factor subunit alpha 2 2
MIRT524520 CDK19 cyclin dependent kinase 19 2 2
MIRT524674 C12orf5 TP53 induced glycolysis regulatory phosphatase 2 2
MIRT530257 ZNF620 zinc finger protein 620 2 2
MIRT540691 BMP3 bone morphogenetic protein 3 2 2
MIRT540976 C17orf85 nuclear cap binding subunit 3 2 2
MIRT545505 NAP1L1 nucleosome assembly protein 1 like 1 2 2
MIRT545631 GGCX gamma-glutamyl carboxylase 2 2
MIRT547358 NAA30 N(alpha)-acetyltransferase 30, NatC catalytic subunit 2 2
MIRT550701 MPL MPL proto-oncogene, thrombopoietin receptor 2 4
MIRT550717 PMPCA peptidase, mitochondrial processing alpha subunit 2 4
MIRT551203 NCR3LG1 natural killer cell cytotoxicity receptor 3 ligand 1 2 2
MIRT553999 SRGAP1 SLIT-ROBO Rho GTPase activating protein 1 2 4
MIRT561081 LLPH LLP homolog, long-term synaptic facilitation 2 2
MIRT563523 TAF8 TATA-box binding protein associated factor 8 2 2
MIRT564463 SLC35E2 solute carrier family 35 member E2 2 2
MIRT565233 TRAF6 TNF receptor associated factor 6 2 2
MIRT566618 NKAP NFKB activating protein 2 2
MIRT569527 AP5Z1 adaptor related protein complex 5 zeta 1 subunit 2 2
MIRT569639 QPCT glutaminyl-peptide cyclotransferase 2 2
MIRT570253 SSPN sarcospan 2 2
MIRT570570 OTUD7B OTU deubiquitinase 7B 2 2
MIRT570621 MTF2 metal response element binding transcription factor 2 2 2
MIRT571098 ISLR2 immunoglobulin superfamily containing leucine rich repeat 2 2 2
MIRT575196 Entpd4 ectonucleoside triphosphate diphosphohydrolase 4 2 2
MIRT575554 Cd99 CD99 antigen 2 2
MIRT575634 Gnl3l guanine nucleotide binding protein-like 3 (nucleolar)-like 2 2
MIRT608267 NOP14 NOP14 nucleolar protein 2 2
MIRT609314 FXYD6 FXYD domain containing ion transport regulator 6 2 2
MIRT627670 RPL28 ribosomal protein L28 2 2
MIRT631185 TSPAN14 tetraspanin 14 2 2
MIRT631964 YIPF5 Yip1 domain family member 5 2 2
MIRT632885 GINM1 glycoprotein integral membrane 1 2 2
MIRT642618 CDKN3 cyclin dependent kinase inhibitor 3 2 2
MIRT645609 TSPAN6 tetraspanin 6 2 2
MIRT662227 PGBD4 piggyBac transposable element derived 4 2 2
MIRT662329 MYLK3 myosin light chain kinase 3 2 2
MIRT662725 LRRC3C leucine rich repeat containing 3C 2 2
MIRT665520 USP14 ubiquitin specific peptidase 14 2 2
MIRT666634 RBMS2 RNA binding motif single stranded interacting protein 2 2 2
MIRT668969 CNBP CCHC-type zinc finger nucleic acid binding protein 2 2
MIRT670925 DESI1 desumoylating isopeptidase 1 2 2
MIRT673939 ZNF500 zinc finger protein 500 2 2
MIRT674675 PLCE1 phospholipase C epsilon 1 2 2
MIRT675230 MAK male germ cell associated kinase 2 2
MIRT680864 MACC1 MACC1, MET transcriptional regulator 2 2
MIRT681047 ZDBF2 zinc finger DBF-type containing 2 2 2
MIRT681105 CEP57L1 centrosomal protein 57 like 1 2 2
MIRT683553 HAVCR1 hepatitis A virus cellular receptor 1 2 2
MIRT684508 C1orf174 chromosome 1 open reading frame 174 2 2
MIRT684812 BRIX1 BRX1, biogenesis of ribosomes 2 2
MIRT685981 CCDC77 coiled-coil domain containing 77 2 2
MIRT686709 TBC1D19 TBC1 domain family member 19 2 2
MIRT686867 SLC25A32 solute carrier family 25 member 32 2 2
MIRT688908 C11orf84 chromosome 11 open reading frame 84 2 2
MIRT691208 KLHL30 kelch like family member 30 2 2
MIRT692298 CNNM3 cyclin and CBS domain divalent metal cation transport mediator 3 2 2
MIRT694380 MTA1 metastasis associated 1 2 2
MIRT696497 COX6B1 cytochrome c oxidase subunit 6B1 2 2
MIRT700686 POLR3D RNA polymerase III subunit D 2 2
MIRT701088 PAPOLG poly(A) polymerase gamma 2 2
MIRT703373 GAPVD1 GTPase activating protein and VPS9 domains 1 2 2
MIRT706189 SAR1B secretion associated Ras related GTPase 1B 2 2
MIRT706648 SMIM19 small integral membrane protein 19 2 2
MIRT709466 KRTAP19-1 keratin associated protein 19-1 2 2
MIRT709699 DMWD DM1 locus, WD repeat containing 2 2
MIRT710693 LYRM4 LYR motif containing 4 2 2
MIRT713457 DNAJC11 DnaJ heat shock protein family (Hsp40) member C11 2 2
MIRT722409 RARS2 arginyl-tRNA synthetase 2, mitochondrial 2 2
MIRT725391 MAP3K9 mitogen-activated protein kinase kinase kinase 9 2 2
MIRT725548 DNMT3A DNA methyltransferase 3 alpha 2 2

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