pre-miRNA Information
pre-miRNA hsa-mir-4747   
Genomic Coordinates chr19: 4932687 - 4932740
Description Homo sapiens miR-4747 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4747-5p
Sequence 1| AGGGAAGGAGGCUUGGUCUUAG |22
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs560927363 4 dbSNP
rs1471226927 10 dbSNP
rs763137545 12 dbSNP
rs767337154 15 dbSNP
rs775298039 16 dbSNP
rs760472311 19 dbSNP
rs1207950315 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol RARA   
Synonyms NR1B1, RAR
Description retinoic acid receptor alpha
Transcript NM_000964   
Other Transcripts NM_001024809 , NM_001145301 , NM_001145302   
Expression
Putative miRNA Targets on RARA
3'UTR of RARA
(miRNA target sites are highlighted)
>RARA|NM_000964|3'UTR
   1 CCGCCCACGCCACATGGACACAGCCCTCGCCCTCCGCCCCGGCTTTTCTCTGCCTTTCTACCGACCATGTGACCCCGCAC
  81 CAGCCCTGCCCCCACCTGCCCTCCCGGGCAGTACTGGGGACCTTCCCTGGGGGACGGGGAGGGAGGAGGCAGCGACTCCT
 161 TGGACAGAGGCCTGGGCCCTCAGTGGACTGCCTGCTCCCACAGCCTGGGCTGACGTCAGAGGCCGAGGCCAGGAACTGAG
 241 TGAGGCCCCTGGTCCTGGGTCTCAGGATGGGTCCTGGGGGCCTCGTGTTCATCAAGACACCCCTCTGCCCAGCTCACCAC
 321 ATCTTCATCACCAGCAAACGCCAGGACTTGGCTCCCCCATCCTCAGAACTCACAAGCCATTGCTCCCCAGCTGGGGAACC
 401 TCAACCTCCCCCCTGCCTCGGTTGGTGACAGAGGGGGTGGGACAGGGGCGGGGGGTTCCCCCTGTACATACCCTGCCATA
 481 CCAACCCCAGGTATTAATTCTCGCTGGTTTTGTTTTTATTTTAATTTTTTTGTTTTGATTTTTTTAATAAGAATTTTCAT
 561 TTTAAGCACATTTATACTGAAGGAATTTGTGCTGTGTATTGGGGGGAGCTGGATCCAGAGCTGGAGGGGGTGGGTCCGGG
 641 GGAGGGAGTGGCTCGGAAGGGGCCCCCACTCTCCTTTCATGTCCCTGTGCCCCCCAGTTCTCCTCCTCAGCCTTTTCCTC
 721 CTCAGTTTTCTCTTTAAAACTGTGAAGTACTAACTTTCCAAGGCCTGCCTTCCCCTCCCTCCCACTGGAGAAGCCGCCAG
 801 CCCCTTTCTCCCTCTGCCTGACCACTGGGTGTGGACGGTGTGGGGCAGCCCTGAAAGGACAGGCTCCTGGCCTTGGCACT
 881 TGCCTGCACCCACCATGAGGCATGGAGCAGGGCAGAGCAAGGGCCCCGGGACAGAGTTTTCCCAGACCTGGCTCCTCGGC
 961 AGAGCTGCCTCCCGTCAGGGCCCACATCATCTAGGCTCCCCAGCCCCCACTGTGAAGGGGCTGGCCAGGGGCCCGAGCTG
1041 CCCCCACCCCCGGCCTCAGCCACCAGCACCCCCATAGGGCCCCCAGACACCACACACATGCGCGTGCGCACACACACAAA
1121 CACACACACACTGGACAGTAGATGGGCCGACACACACTTGGCCCGAGTTCCTCCATTTCCCTGGCCTGCCCCCCACCCCC
1201 AACCTGTCCCACCCCCGTGCCCCCTCCTTACCCCGCAGGACGGGCCTACAGGGGGGTCTCCCCTCACCCCTGCACCCCCA
1281 GCTGGGGGAGCTGGCTCTGCCCCGACCTCCTTCACCAGGGGTTGGGGCCCCTTCCCCTGGAGCCCGTGGGTGCACCTGTT
1361 ACTGTTGGGCTTTCCACTGAGATCTACTGGATAAAGAATAAAGTTCTATTTATTCTAAAAAAAAAAAAAAAAAA
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' gauucuGGUU-CGGA-GGAAGGGa 5'
                |||| |||| ||||||| 
Target 5' aactttCCAAGGCCTGCCTTCCCc 3'
752 - 775 164.00 -23.60
2
miRNA  3' gaUUCUGGUUCGGAGGAAGGGa 5'
            ::|:::::| | ||||||| 
Target 5' caGGGGTTGGGGCCCCTTCCCc 3'
1316 - 1337 156.00 -21.00
3
miRNA  3' gaUUCUGGUUCGGAGGAAGGGa 5'
            |: ||:::|   ||||||| 
Target 5' gcAGTACTGGG-GACCTTCCCt 3'
108 - 128 147.00 -17.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN24294758 37 COSMIC
COSN30119298 42 COSMIC
COSN1196555 119 COSMIC
COSN30131309 137 COSMIC
COSN15618744 142 COSMIC
COSN24306216 225 COSMIC
COSN31513035 285 COSMIC
COSN13719008 286 COSMIC
COSN15618651 301 COSMIC
COSN31595431 307 COSMIC
COSN15618736 316 COSMIC
COSN7166379 340 COSMIC
COSN23508190 363 COSMIC
COSN23520798 363 COSMIC
COSN18002832 433 COSMIC
COSN26634870 438 COSMIC
COSN18003368 450 COSMIC
COSN21016684 581 COSMIC
COSN28774800 656 COSMIC
COSN20905262 821 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs2229773 3 dbSNP
rs769793497 4 dbSNP
rs1218513818 5 dbSNP
rs912991920 7 dbSNP
rs996352460 9 dbSNP
rs576294738 10 dbSNP
rs1268877692 14 dbSNP
rs1415918839 16 dbSNP
rs1216078635 20 dbSNP
rs1340514647 21 dbSNP
rs761900323 22 dbSNP
rs1195498519 24 dbSNP
rs773450052 25 dbSNP
rs1345963982 27 dbSNP
rs760854493 29 dbSNP
rs1442009995 30 dbSNP
rs1403855464 31 dbSNP
rs1160274962 32 dbSNP
rs1363778498 36 dbSNP
rs1452226981 37 dbSNP
rs1453066635 37 dbSNP
rs543619460 38 dbSNP
rs1391573099 40 dbSNP
rs143781383 41 dbSNP
rs1324214059 42 dbSNP
rs755468217 49 dbSNP
rs1245951322 53 dbSNP
rs1242113889 54 dbSNP
rs1307400442 55 dbSNP
rs1490534269 57 dbSNP
rs1014561656 61 dbSNP
rs1316073084 63 dbSNP
rs942595144 64 dbSNP
rs1267079537 70 dbSNP
rs1334927229 74 dbSNP
rs752624786 77 dbSNP
rs898329126 78 dbSNP
rs1458801440 81 dbSNP
rs1178182679 84 dbSNP
rs1250297316 85 dbSNP
rs937175558 88 dbSNP
rs1167545061 90 dbSNP
rs2229772 92 dbSNP
rs1434567249 93 dbSNP
rs758015735 94 dbSNP
rs1303294811 95 dbSNP
rs1162849705 96 dbSNP
rs1402780163 99 dbSNP
rs1443242076 101 dbSNP
rs1297771819 105 dbSNP
rs1465186545 106 dbSNP
rs746653550 106 dbSNP
rs902493348 107 dbSNP
rs1389390755 109 dbSNP
rs886541517 111 dbSNP
rs1314852792 112 dbSNP
rs1335382530 113 dbSNP
rs944978084 115 dbSNP
rs1270699584 116 dbSNP
rs11544351 117 dbSNP
rs1319335890 120 dbSNP
rs1204807576 127 dbSNP
rs1253258181 128 dbSNP
rs1040611474 129 dbSNP
rs1250357259 129 dbSNP
rs1479866236 130 dbSNP
rs1259480776 131 dbSNP
rs900698133 131 dbSNP
rs1258886004 132 dbSNP
rs545072314 136 dbSNP
rs781040511 137 dbSNP
rs1049327018 138 dbSNP
rs1425897280 140 dbSNP
rs559919766 147 dbSNP
rs527302805 148 dbSNP
rs139482076 154 dbSNP
rs971030813 155 dbSNP
rs190879195 156 dbSNP
rs183204850 165 dbSNP
rs1415985752 167 dbSNP
rs777091819 167 dbSNP
rs1414127097 168 dbSNP
rs1192214145 170 dbSNP
rs1291309695 172 dbSNP
rs1341849237 175 dbSNP
rs990000894 177 dbSNP
rs1466815683 178 dbSNP
rs1294476555 180 dbSNP
rs1305378222 187 dbSNP
rs1020019209 188 dbSNP
rs1281531752 193 dbSNP
rs1485519616 195 dbSNP
rs760945393 202 dbSNP
rs1265887506 208 dbSNP
rs1475819362 210 dbSNP
rs571460851 211 dbSNP
rs776997866 215 dbSNP
rs538792963 216 dbSNP
rs765801130 225 dbSNP
rs547849750 226 dbSNP
rs375417623 227 dbSNP
rs1041061563 229 dbSNP
rs1310999063 231 dbSNP
rs763607614 232 dbSNP
rs1430888467 234 dbSNP
rs1287751391 241 dbSNP
rs910877927 242 dbSNP
rs1311466587 245 dbSNP
rs1236069721 246 dbSNP
rs942416670 249 dbSNP
rs1342647334 250 dbSNP
rs747078113 253 dbSNP
rs1303609560 255 dbSNP
rs1347608817 260 dbSNP
rs1219519747 265 dbSNP
rs763649611 275 dbSNP
rs1288859011 282 dbSNP
rs1448063021 283 dbSNP
rs149687193 285 dbSNP
rs536667337 286 dbSNP
rs1489478177 289 dbSNP
rs929787594 291 dbSNP
rs1375817881 292 dbSNP
rs1194519323 294 dbSNP
rs1157889024 296 dbSNP
rs1394636080 300 dbSNP
rs1046893372 301 dbSNP
rs1171498463 302 dbSNP
rs1417479246 306 dbSNP
rs1410120485 311 dbSNP
rs1401249149 316 dbSNP
rs1159125240 317 dbSNP
rs896348666 322 dbSNP
rs796618173 326 dbSNP
rs1485793914 327 dbSNP
rs1422758765 330 dbSNP
rs1253511298 331 dbSNP
rs950160714 331 dbSNP
rs1342935550 338 dbSNP
rs1045853471 339 dbSNP
rs780727297 340 dbSNP
rs1326245886 341 dbSNP
rs1369767626 342 dbSNP
rs115635151 346 dbSNP
rs1281609017 348 dbSNP
rs1351706275 352 dbSNP
rs1351805231 354 dbSNP
rs1239816973 356 dbSNP
rs117770216 359 dbSNP
rs1310734574 362 dbSNP
rs537346006 367 dbSNP
rs1323586993 372 dbSNP
rs1214395224 377 dbSNP
rs1421843278 378 dbSNP
rs1297282717 379 dbSNP
rs1252673102 382 dbSNP
rs1036098452 386 dbSNP
rs1010379239 388 dbSNP
rs1467285408 392 dbSNP
rs1362018364 396 dbSNP
rs1180698819 399 dbSNP
rs1234417399 400 dbSNP
rs1470356606 401 dbSNP
rs749208030 403 dbSNP
rs1457137436 408 dbSNP
rs906899862 408 dbSNP
rs367819767 409 dbSNP
rs1462612582 412 dbSNP
rs1164977847 413 dbSNP
rs1393330615 416 dbSNP
rs1459578506 417 dbSNP
rs1264349989 420 dbSNP
rs558760636 420 dbSNP
rs370334154 421 dbSNP
rs1336739652 430 dbSNP
rs1263756007 432 dbSNP
rs1441852006 433 dbSNP
rs1278365886 435 dbSNP
rs200674161 438 dbSNP
rs895638454 439 dbSNP
rs1277516327 440 dbSNP
rs375909325 442 dbSNP
rs368586881 443 dbSNP
rs748455062 444 dbSNP
rs1332705034 445 dbSNP
rs1197788587 448 dbSNP
rs771137228 449 dbSNP
rs1021431675 450 dbSNP
rs770479738 450 dbSNP
rs553845872 451 dbSNP
rs1180802486 452 dbSNP
rs1231150271 456 dbSNP
rs759880021 457 dbSNP
rs770262951 458 dbSNP
rs1170557747 460 dbSNP
rs1477157944 462 dbSNP
rs978176612 465 dbSNP
rs1194428851 466 dbSNP
rs973727791 468 dbSNP
rs1316873402 470 dbSNP
rs371896486 471 dbSNP
rs1265552284 472 dbSNP
rs919814609 473 dbSNP
rs1169290360 479 dbSNP
rs924020692 481 dbSNP
rs1396763673 488 dbSNP
rs763553004 489 dbSNP
rs764517107 492 dbSNP
rs1377609340 493 dbSNP
rs917739191 496 dbSNP
rs949281130 497 dbSNP
rs1353648993 498 dbSNP
rs751026996 503 dbSNP
rs761257563 504 dbSNP
rs1338955090 505 dbSNP
rs1195047212 509 dbSNP
rs1272252093 510 dbSNP
rs921895799 513 dbSNP
rs1486504153 514 dbSNP
rs1211529399 520 dbSNP
rs1256637453 521 dbSNP
rs1421613564 524 dbSNP
rs1399265154 525 dbSNP
rs932266587 525 dbSNP
rs767090750 536 dbSNP
rs1373343359 539 dbSNP
rs185566558 546 dbSNP
rs909407267 554 dbSNP
rs1438825362 567 dbSNP
rs1397287004 568 dbSNP
rs1376095323 569 dbSNP
rs940829014 574 dbSNP
rs755818342 577 dbSNP
rs1054471070 578 dbSNP
rs1189444000 595 dbSNP
rs1409291266 597 dbSNP
rs1176861849 600 dbSNP
rs542645312 600 dbSNP
rs1159214379 601 dbSNP
rs1251179447 603 dbSNP
rs1342571242 607 dbSNP
rs1390241533 622 dbSNP
rs1234557946 623 dbSNP
rs1306376049 626 dbSNP
rs1352621189 626 dbSNP
rs1443756744 629 dbSNP
rs906952343 631 dbSNP
rs1005477260 632 dbSNP
rs1374011886 636 dbSNP
rs1017343402 638 dbSNP
rs1401859204 639 dbSNP
rs1156838342 644 dbSNP
rs938394698 645 dbSNP
rs1396960355 651 dbSNP
rs1186727644 653 dbSNP
rs1055476590 654 dbSNP
rs894108589 655 dbSNP
rs893168663 656 dbSNP
rs1010472655 667 dbSNP
rs961408278 669 dbSNP
rs1487724655 682 dbSNP
rs1228050037 688 dbSNP
rs1283468712 690 dbSNP
rs1042008053 691 dbSNP
rs375581332 694 dbSNP
rs879179749 697 dbSNP
rs879892460 700 dbSNP
rs1483568351 704 dbSNP
rs891256751 707 dbSNP
rs1008400522 710 dbSNP
rs1212721441 716 dbSNP
rs1019368378 718 dbSNP
rs1018420528 719 dbSNP
rs779503010 724 dbSNP
rs1415802786 725 dbSNP
rs1028132667 726 dbSNP
rs1482498874 726 dbSNP
rs963777542 731 dbSNP
rs1182478659 734 dbSNP
rs1402707510 735 dbSNP
rs777254933 755 dbSNP
rs1462993411 764 dbSNP
rs759983760 768 dbSNP
rs1413455286 769 dbSNP
rs190326404 780 dbSNP
rs1419960520 782 dbSNP
rs995245706 787 dbSNP
rs1188332863 796 dbSNP
rs1477391770 797 dbSNP
rs1240183761 799 dbSNP
rs1217472055 804 dbSNP
rs1430953012 810 dbSNP
rs1026591491 812 dbSNP
rs951092162 825 dbSNP
rs983096131 829 dbSNP
rs917848162 837 dbSNP
rs1333261535 838 dbSNP
rs985072239 841 dbSNP
rs970927352 844 dbSNP
rs980646195 851 dbSNP
rs927339170 854 dbSNP
rs1346020333 862 dbSNP
rs1322914419 864 dbSNP
rs1467040215 872 dbSNP
rs937394322 884 dbSNP
rs1054566833 885 dbSNP
rs1396546946 888 dbSNP
rs1165524077 896 dbSNP
rs940882740 905 dbSNP
rs531673704 907 dbSNP
rs946040993 909 dbSNP
rs1042324785 914 dbSNP
rs1188051301 923 dbSNP
rs1475504093 926 dbSNP
rs891398413 928 dbSNP
rs543728371 929 dbSNP
rs938462875 931 dbSNP
rs1039860139 933 dbSNP
rs1055932138 933 dbSNP
rs900034578 939 dbSNP
rs1385145849 948 dbSNP
rs1216703873 949 dbSNP
rs767236403 958 dbSNP
rs947034304 959 dbSNP
rs1300734669 961 dbSNP
rs1312668582 965 dbSNP
rs1026724030 970 dbSNP
rs1042994491 974 dbSNP
rs1272148768 975 dbSNP
rs1341212838 986 dbSNP
rs1352697880 987 dbSNP
rs951017275 988 dbSNP
rs1003884505 989 dbSNP
rs903112457 990 dbSNP
rs1205341878 999 dbSNP
rs1025287883 1018 dbSNP
rs1455351137 1022 dbSNP
rs1253079231 1030 dbSNP
rs1177473615 1033 dbSNP
rs970681274 1035 dbSNP
rs1019420409 1036 dbSNP
rs1207022177 1041 dbSNP
rs900980699 1046 dbSNP
rs1267479157 1047 dbSNP
rs981123868 1048 dbSNP
rs926424127 1049 dbSNP
rs1232357845 1050 dbSNP
rs957895244 1052 dbSNP
rs1455048578 1053 dbSNP
rs1029481902 1056 dbSNP
rs953442125 1058 dbSNP
rs1442899126 1064 dbSNP
rs1358345319 1070 dbSNP
rs1310914518 1071 dbSNP
rs984790988 1074 dbSNP
rs1395323263 1075 dbSNP
rs1429512093 1077 dbSNP
rs1157477773 1080 dbSNP
rs1416824427 1081 dbSNP
rs1409581494 1082 dbSNP
rs564963890 1083 dbSNP
rs1481281437 1084 dbSNP
rs1257257337 1085 dbSNP
rs1209190755 1086 dbSNP
rs1486746683 1089 dbSNP
rs1356470107 1092 dbSNP
rs1456615899 1093 dbSNP
rs1292971147 1097 dbSNP
rs532360714 1102 dbSNP
rs914664083 1103 dbSNP
rs115248059 1104 dbSNP
rs1224265917 1105 dbSNP
rs74396306 1107 dbSNP
rs182891484 1108 dbSNP
rs1042945479 1109 dbSNP
rs376581605 1109 dbSNP
rs536023561 1109 dbSNP
rs756956672 1111 dbSNP
rs1159283814 1114 dbSNP
rs552625476 1116 dbSNP
rs548225262 1118 dbSNP
rs1485053351 1120 dbSNP
rs368001358 1120 dbSNP
rs900889212 1120 dbSNP
rs1262498999 1121 dbSNP
rs1216608171 1122 dbSNP
rs931488222 1124 dbSNP
rs1048093137 1126 dbSNP
rs886877284 1127 dbSNP
rs1265457479 1128 dbSNP
rs1355835354 1135 dbSNP
rs1469425073 1137 dbSNP
rs1186200454 1138 dbSNP
rs1004254627 1142 dbSNP
rs1246717505 1143 dbSNP
rs1024628341 1147 dbSNP
rs906213466 1149 dbSNP
rs1432568681 1150 dbSNP
rs1456994063 1152 dbSNP
rs1289390152 1153 dbSNP
rs1391696249 1159 dbSNP
rs1006424345 1162 dbSNP
rs1163369813 1162 dbSNP
rs1002123136 1165 dbSNP
rs1033606247 1166 dbSNP
rs957820351 1171 dbSNP
rs1264153383 1173 dbSNP
rs537376620 1177 dbSNP
rs71355453 1179 dbSNP
rs1164358142 1186 dbSNP
rs1350473000 1189 dbSNP
rs1468065763 1189 dbSNP
rs1271407731 1191 dbSNP
rs1335469478 1193 dbSNP
rs993468523 1193 dbSNP
rs1250487103 1195 dbSNP
rs1463071335 1195 dbSNP
rs994235000 1196 dbSNP
rs1036108068 1199 dbSNP
rs1387780571 1200 dbSNP
rs1029782241 1202 dbSNP
rs1439764304 1203 dbSNP
rs1368133821 1204 dbSNP
rs1271668773 1206 dbSNP
rs1376720478 1207 dbSNP
rs1443664785 1208 dbSNP
rs955455575 1212 dbSNP
rs1214749012 1217 dbSNP
rs1312985292 1218 dbSNP
rs1336575330 1220 dbSNP
rs1206263878 1226 dbSNP
rs1266981711 1227 dbSNP
rs1464807208 1229 dbSNP
rs1454046024 1234 dbSNP
rs1251217457 1235 dbSNP
rs1195586830 1236 dbSNP
rs960112620 1242 dbSNP
rs1244135669 1243 dbSNP
rs1341177280 1246 dbSNP
rs991980308 1250 dbSNP
rs1233103302 1251 dbSNP
rs558844389 1253 dbSNP
rs1021691518 1259 dbSNP
rs1332142830 1270 dbSNP
rs1328734663 1271 dbSNP
rs1390218284 1274 dbSNP
rs967475958 1276 dbSNP
rs1309093964 1285 dbSNP
rs1476337359 1287 dbSNP
rs1434270487 1288 dbSNP
rs978587040 1293 dbSNP
rs924506038 1294 dbSNP
rs934589288 1295 dbSNP
rs1156983890 1298 dbSNP
rs977933436 1301 dbSNP
rs912562575 1302 dbSNP
rs571021564 1304 dbSNP
rs944072489 1305 dbSNP
rs1357428081 1306 dbSNP
rs975601880 1307 dbSNP
rs932371142 1309 dbSNP
rs1211208827 1316 dbSNP
rs756042544 1317 dbSNP
rs1349305124 1322 dbSNP
rs921521555 1324 dbSNP
rs1303266933 1331 dbSNP
rs931457226 1332 dbSNP
rs1277324085 1337 dbSNP
rs1048558052 1343 dbSNP
rs1356945117 1346 dbSNP
rs140111856 1347 dbSNP
rs1289316364 1348 dbSNP
rs888227881 1356 dbSNP
rs1374065880 1358 dbSNP
rs1314976403 1361 dbSNP
rs1415311451 1363 dbSNP
rs575638278 1364 dbSNP
rs1006371526 1374 dbSNP
rs1412647871 1385 dbSNP
rs1286949863 1388 dbSNP
rs1474086717 1394 dbSNP
rs1259413399 1397 dbSNP
rs1037887162 1404 dbSNP
rs1446139949 1411 dbSNP
rs898046509 1415 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' gauucugguucGGAGGAAGGGa 5'
                     ||||| |||| 
Target 5' -------uuccCCUCCCUCCCa 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 GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_001145302 | 3UTR | GGGGCCCCUUCCCCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_001145302 | 3UTR | CUGGGGGACGGGGAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_001145302 | 3UTR | CUGGGGGACGGGGAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_001145302 | 3UTR | GGGGCCCCUUCCCCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_001145302 | 3UTR | CUGGGGGACGGGGAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_001145302 | 3UTR | CUGGGGGACGGGGAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000425707.3 | 3UTR | UUCCCCUCCCUCCCACUG
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
215 hsa-miR-4747-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT061689 BTG2 BTG anti-proliferation factor 2 2 2
MIRT062834 BCL7A BCL tumor suppressor 7A 2 2
MIRT079371 CCDC137 coiled-coil domain containing 137 2 2
MIRT081190 MIDN midnolin 2 4
MIRT081724 ZNF507 zinc finger protein 507 2 2
MIRT110565 ZMYND11 zinc finger MYND-type containing 11 2 2
MIRT133724 SKI SKI proto-oncogene 2 4
MIRT146689 MINK1 misshapen like kinase 1 2 2
MIRT150676 SLC27A1 solute carrier family 27 member 1 2 2
MIRT159196 NRBP1 nuclear receptor binding protein 1 2 2
MIRT180865 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT190659 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT196111 MPRIP myosin phosphatase Rho interacting protein 2 2
MIRT232390 SP1 Sp1 transcription factor 2 2
MIRT331070 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 4
MIRT338632 SHMT2 serine hydroxymethyltransferase 2 2 2
MIRT407441 CTDSP1 CTD small phosphatase 1 2 2
MIRT444276 NKX6-1 NK6 homeobox 1 2 2
MIRT444834 PDE6D phosphodiesterase 6D 2 2
MIRT445452 EXT1 exostosin glycosyltransferase 1 2 2
MIRT445644 NPY4R neuropeptide Y receptor Y4 2 2
MIRT446157 RPL12 ribosomal protein L12 2 2
MIRT446608 HIP1 huntingtin interacting protein 1 2 2
MIRT447108 CLPX caseinolytic mitochondrial matrix peptidase chaperone subunit 2 2
MIRT449314 MRO maestro 2 2
MIRT450305 DRAXIN dorsal inhibitory axon guidance protein 2 2
MIRT451245 ZNF444 zinc finger protein 444 2 2
MIRT451714 OLR1 oxidized low density lipoprotein receptor 1 2 2
MIRT451908 ILK integrin linked kinase 2 2
MIRT452183 KIAA1456 KIAA1456 2 2
MIRT452610 REPIN1 replication initiator 1 2 2
MIRT453422 GLG1 golgi glycoprotein 1 2 2
MIRT454006 ALKBH5 alkB homolog 5, RNA demethylase 2 2
MIRT455072 ARHGAP39 Rho GTPase activating protein 39 2 2
MIRT455319 TTLL9 tubulin tyrosine ligase like 9 2 2
MIRT455357 KDM5C lysine demethylase 5C 2 2
MIRT455589 TAF12 TATA-box binding protein associated factor 12 2 2
MIRT455711 EIF4EBP2 eukaryotic translation initiation factor 4E binding protein 2 2 2
MIRT455860 TMEM254 transmembrane protein 254 2 2
MIRT455919 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 2
MIRT455946 CYP4A22 cytochrome P450 family 4 subfamily A member 22 2 2
MIRT456935 LRP10 LDL receptor related protein 10 2 2
MIRT457223 AP3D1 adaptor related protein complex 3 delta 1 subunit 2 2
MIRT457431 NOL10 nucleolar protein 10 2 2
MIRT457470 SLC35F6 solute carrier family 35 member F6 2 2
MIRT457907 ZNF212 zinc finger protein 212 2 2
MIRT458046 TSEN54 tRNA splicing endonuclease subunit 54 2 2
MIRT458073 RNLS renalase, FAD dependent amine oxidase 2 2
MIRT458234 NXPH3 neurexophilin 3 2 2
MIRT458307 TNFAIP8L3 TNF alpha induced protein 8 like 3 2 2
MIRT458378 ITM2C integral membrane protein 2C 2 2
MIRT458967 ZNF436 zinc finger protein 436 2 2
MIRT459099 CYP4A11 cytochrome P450 family 4 subfamily A member 11 2 2
MIRT459446 TMEM37 transmembrane protein 37 2 2
MIRT459671 VPS37C VPS37C, ESCRT-I subunit 2 2
MIRT460727 ASXL3 additional sex combs like 3, transcriptional regulator 2 2
MIRT460744 SRP14 signal recognition particle 14 2 2
MIRT461531 C14orf1 ergosterol biosynthesis 28 homolog 2 2
MIRT461752 DDX11 DEAD/H-box helicase 11 2 2
MIRT461837 F2RL3 F2R like thrombin or trypsin receptor 3 2 2
MIRT462019 RIF1 replication timing regulatory factor 1 2 2
MIRT462631 PHF5A PHD finger protein 5A 2 2
MIRT462772 ZNF8 zinc finger protein 8 2 2
MIRT463032 ZNF689 zinc finger protein 689 2 2
MIRT463886 WNT7B Wnt family member 7B 2 2
MIRT463995 WDTC1 WD and tetratricopeptide repeats 1 2 2
MIRT464371 URM1 ubiquitin related modifier 1 2 2
MIRT465342 TPM3 tropomyosin 3 2 4
MIRT465515 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT465602 TNRC6A trinucleotide repeat containing 6A 2 2
MIRT465697 TNPO2 transportin 2 2 10
MIRT466988 SSRP1 structure specific recognition protein 1 2 4
MIRT467630 SLC7A5 solute carrier family 7 member 5 2 2
MIRT468132 SH3PXD2A SH3 and PX domains 2A 2 2
MIRT468322 SF3B3 splicing factor 3b subunit 3 2 2
MIRT468502 SESN2 sestrin 2 2 2
MIRT468881 RREB1 ras responsive element binding protein 1 2 2
MIRT469322 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 2 2
MIRT469562 RARA retinoic acid receptor alpha 2 2
MIRT469898 PTRF caveolae associated protein 1 2 2
MIRT470045 PTGFRN prostaglandin F2 receptor inhibitor 2 2
MIRT470068 PTGES2 prostaglandin E synthase 2 2 2
MIRT470238 PRRC2A proline rich coiled-coil 2A 2 2
MIRT470390 PPP1R16B protein phosphatase 1 regulatory subunit 16B 2 2
MIRT470500 PPP1R11 protein phosphatase 1 regulatory inhibitor subunit 11 2 2
MIRT470689 POLR2D RNA polymerase II subunit D 2 2
MIRT470704 POGK pogo transposable element derived with KRAB domain 2 2
MIRT471083 PIK3C2B phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta 2 2
MIRT472482 NACC2 NACC family member 2 2 2
MIRT473583 MAT2A methionine adenosyltransferase 2A 2 2
MIRT474554 KLHDC3 kelch domain containing 3 2 2
MIRT474651 KLF13 Kruppel like factor 13 2 2
MIRT474843 KHSRP KH-type splicing regulatory protein 2 2
MIRT474934 KCTD15 potassium channel tetramerization domain containing 15 2 2
MIRT475573 HNRNPC heterogeneous nuclear ribonucleoprotein C (C1/C2) 2 2
MIRT476045 GRSF1 G-rich RNA sequence binding factor 1 2 2
MIRT476080 GRB2 growth factor receptor bound protein 2 2 2
MIRT476440 GBA2 glucosylceramidase beta 2 2 2
MIRT476764 FOSL2 FOS like 2, AP-1 transcription factor subunit 2 2
MIRT478785 CRTC2 CREB regulated transcription coactivator 2 2 2
MIRT479287 CHAC1 ChaC glutathione specific gamma-glutamylcyclotransferase 1 2 2
MIRT479505 CDH6 cadherin 6 2 2
MIRT479732 CCND1 cyclin D1 2 6
MIRT480352 C5orf24 chromosome 5 open reading frame 24 2 2
MIRT480407 C19orf47 chromosome 19 open reading frame 47 2 2
MIRT480859 BHLHB9 basic helix-loop-helix family member b9 2 2
MIRT481445 ARRB2 arrestin beta 2 2 2
MIRT481732 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT481824 AP2M1 adaptor related protein complex 2 mu 1 subunit 2 2
MIRT482566 ABHD2 abhydrolase domain containing 2 2 2
MIRT482607 ABHD14B abhydrolase domain containing 14B 2 2
MIRT483144 SYCE1L synaptonemal complex central element protein 1 like 2 2
MIRT483214 APOA1 apolipoprotein A1 2 6
MIRT483878 TGIF1 TGFB induced factor homeobox 1 2 2
MIRT483917 SPSB1 splA/ryanodine receptor domain and SOCS box containing 1 2 2
MIRT483939 LENG8 leukocyte receptor cluster member 8 2 4
MIRT484420 SNX19 sorting nexin 19 2 2
MIRT484489 SLC9A1 solute carrier family 9 member A1 2 2
MIRT484612 SIX3 SIX homeobox 3 2 6
MIRT484705 RNF11 ring finger protein 11 2 2
MIRT485107 SHISA6 shisa family member 6 2 2
MIRT485354 MYO1C myosin IC 2 4
MIRT485609 FOSL1 FOS like 1, AP-1 transcription factor subunit 2 4
MIRT487311 GLTSCR1 BRD4 interacting chromatin remodeling complex associated protein 2 2
MIRT487417 CACNB1 calcium voltage-gated channel auxiliary subunit beta 1 2 2
MIRT487695 CDK14 cyclin dependent kinase 14 2 2
MIRT487791 GPR20 G protein-coupled receptor 20 2 4
MIRT488042 PABPC1L2B poly(A) binding protein cytoplasmic 1 like 2B 2 2
MIRT488058 PABPC1L2A poly(A) binding protein cytoplasmic 1 like 2A 2 2
MIRT488237 DNLZ DNL-type zinc finger 2 4
MIRT488764 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT489401 TUBB2A tubulin beta 2A class IIa 2 2
MIRT489777 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT490099 FN3K fructosamine 3 kinase 2 2
MIRT490290 ISL2 ISL LIM homeobox 2 2 2
MIRT490378 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT491329 GFER growth factor, augmenter of liver regeneration 2 2
MIRT491435 MSX2 msh homeobox 2 2 2
MIRT491769 ZNF385A zinc finger protein 385A 2 2
MIRT491922 WNK2 WNK lysine deficient protein kinase 2 2 2
MIRT491983 UNK unkempt family zinc finger 2 2
MIRT492228 SLC48A1 solute carrier family 48 member 1 2 2
MIRT492404 SDK1 sidekick cell adhesion molecule 1 2 2
MIRT492767 PDGFB platelet derived growth factor subunit B 2 2
MIRT492966 NCS1 neuronal calcium sensor 1 2 2
MIRT493295 LLGL2 LLGL2, scribble cell polarity complex component 2 2
MIRT493650 HDLBP high density lipoprotein binding protein 2 2
MIRT493913 FAM127B retrotransposon Gag like 8A 2 4
MIRT495601 NKX2-5 NK2 homeobox 5 2 2
MIRT496875 AHCYL2 adenosylhomocysteinase like 2 2 2
MIRT498514 MYH14 myosin heavy chain 14 2 2
MIRT499178 RBPJL recombination signal binding protein for immunoglobulin kappa J region like 2 2
MIRT502143 KIF5B kinesin family member 5B 2 8
MIRT502692 CSNK1G1 casein kinase 1 gamma 1 2 4
MIRT508460 HOXB6 homeobox B6 2 4
MIRT510430 ZNF207 zinc finger protein 207 2 6
MIRT511837 GPATCH8 G-patch domain containing 8 2 4
MIRT512368 CPM carboxypeptidase M 2 2
MIRT512506 BTBD19 BTB domain containing 19 2 2
MIRT513065 ANKRD45 ankyrin repeat domain 45 2 2
MIRT513267 SCUBE1 signal peptide, CUB domain and EGF like domain containing 1 2 4
MIRT513575 EVX1 even-skipped homeobox 1 2 2
MIRT515051 EBNA1BP2 EBNA1 binding protein 2 2 2
MIRT515790 COL4A3BP collagen type IV alpha 3 binding protein 2 2
MIRT521657 PRKD3 protein kinase D3 2 2
MIRT522679 LUZP1 leucine zipper protein 1 2 6
MIRT528845 RAB32 RAB32, member RAS oncogene family 2 2
MIRT533569 TOR1AIP1 torsin 1A interacting protein 1 2 2
MIRT543738 DHCR7 7-dehydrocholesterol reductase 2 2
MIRT544295 TSPYL1 TSPY like 1 2 2
MIRT544857 MYH2 myosin heavy chain 2 2 4
MIRT557323 HIATL1 major facilitator superfamily domain containing 14B 2 4
MIRT560522 TMEM98 transmembrane protein 98 2 2
MIRT561565 SLC6A9 solute carrier family 6 member 9 2 2
MIRT562374 ERI2 ERI1 exoribonuclease family member 2 2 2
MIRT565780 SEMA6D semaphorin 6D 2 2
MIRT569548 UNC119B unc-119 lipid binding chaperone B 2 2
MIRT569944 PRRT2 proline rich transmembrane protein 2 2 2
MIRT570016 COL1A2 collagen type I alpha 2 chain 2 2
MIRT572163 CRK CRK proto-oncogene, adaptor protein 2 2
MIRT572322 HSPB6 heat shock protein family B (small) member 6 2 2
MIRT573495 IQSEC3 IQ motif and Sec7 domain 3 2 2
MIRT574139 MARVELD1 MARVEL domain containing 1 2 2
MIRT609449 CCDC149 coiled-coil domain containing 149 2 2
MIRT610619 ARHGAP18 Rho GTPase activating protein 18 2 2
MIRT623355 LZIC leucine zipper and CTNNBIP1 domain containing 2 2
MIRT629854 ACOX1 acyl-CoA oxidase 1 2 2
MIRT630516 CDC73 cell division cycle 73 2 2
MIRT632535 PSMB2 proteasome subunit beta 2 2 2
MIRT633975 SLC35E2 solute carrier family 35 member E2 2 2
MIRT636408 MTHFD2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase 2 2
MIRT641722 LTBR lymphotoxin beta receptor 2 2
MIRT642661 RGS6 regulator of G protein signaling 6 2 2
MIRT649649 MAST3 microtubule associated serine/threonine kinase 3 2 2
MIRT650367 MOCS3 molybdenum cofactor synthesis 3 2 2
MIRT651355 ZBTB40 zinc finger and BTB domain containing 40 2 2
MIRT664840 HUS1 HUS1 checkpoint clamp component 2 2
MIRT667322 MYH9 myosin heavy chain 9 2 2
MIRT670680 SUGT1 SGT1 homolog, MIS12 kinetochore complex assembly cochaperone 2 2
MIRT674922 TRPM6 transient receptor potential cation channel subfamily M member 6 2 2
MIRT675919 CYP51A1 cytochrome P450 family 51 subfamily A member 1 2 2
MIRT676493 GJD3 gap junction protein delta 3 2 2
MIRT680162 ZDHHC20 zinc finger DHHC-type containing 20 2 2
MIRT688008 GSN gelsolin 2 2
MIRT688997 ATP6AP1 ATPase H+ transporting accessory protein 1 2 2
MIRT700337 RAB4A RAB4A, member RAS oncogene family 2 2
MIRT701344 NR4A3 nuclear receptor subfamily 4 group A member 3 2 2
MIRT703519 FKBP15 FK506 binding protein 15 2 2
MIRT703901 EPT1 selenoprotein I 2 2
MIRT705565 ARHGEF18 Rho/Rac guanine nucleotide exchange factor 18 2 2
MIRT709709 DNAJC11 DnaJ heat shock protein family (Hsp40) member C11 2 2
MIRT713108 TMBIM4 transmembrane BAX inhibitor motif containing 4 2 2
MIRT718426 ZNF85 zinc finger protein 85 2 2
MIRT719236 CYSLTR2 cysteinyl leukotriene receptor 2 2 2
MIRT719326 STAC SH3 and cysteine rich domain 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4747 Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-4747-5p Temozolomide 5394 NSC362856 approved sensitive cell line (U251)
hsa-miR-4747-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4747-5p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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