miRTarBase - #MIRT456687


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pre-miRNA Information
pre-miRNA hsa-mir-4481   
Genomic Coordinates chr10: 12653138 - 12653197
Description Homo sapiens miR-4481 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4481
Sequence 1| GGAGUGGGCUGGUGGUU |17
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1299710636 5 dbSNP
rs1433739601 12 dbSNP
rs1266754238 14 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol LDB1   
Synonyms CLIM-2, CLIM2, LDB-1, NLI
Description LIM domain binding 1
Transcript NM_001113407   
Other Transcripts NM_003893   
Expression
Putative miRNA Targets on LDB1
3'UTR of LDB1
(miRNA target sites are highlighted)		 
>LDB1|NM_001113407|3'UTR
   1 AAGGCCCTGCTGTGGCCACCCAGTGCTCTGCCTACCTGCCCCACCCCTCACAGCCCCAGGGAGCAGAAGACAGAATGAAG
  81 AGACTGAGCATCTAAAATGGGCAGCCTCCATCCACCCGCTTCAGGGAGGAACTGGACTCTCTGGGGGCAGGTGCCAAGAT
 161 TTGCCCCCCCAGTGGCCCTGGGCTGGGCCTGGCCTCTACAGAGCCTTTTAGGGGGAGGGGGTACTCATGTGGATGCCTAC
 241 TTGGAACCTGGGCCTCTGAGACATGTCCTGACCACCCCCCAGGGCATTTGCCTCCATCTTCACCCCAGATTGTGGGTTTC
 321 CCATCCCCCTGACTTTACCCCTTTCAAGCCTGGGGTTGTCTATACCCACAGCCCTTAGGGACTTAAAGTTACGGGGCTTC
 401 GTTGAATGCTCCTTCCCCTAGGCAGCTGGTAATAGAGGGGTAAAGCTCTGGGCCCCTCCTCCCTGCTGCCACTTATCCCA
 481 GCTCCAAGTTTTTTTAAAAATAATATTATTAAAAATGTAAGTTAAAAAAAAAATCACTCATGTCCCCCCCTCTTCCCCCT
 561 ATTAAAAGTCCAGCTACCTCCCTACTCTTGGCAGATGGGGGCCTAGGGCCTAGGTGGGGGTGAGAGTGGGGGAGGGAGGT
 641 GTGCATACCATTTTATATGGTGTGAGAGCTTCAGACCAAGGAGACATTTCACCATCTCTCCCCCTTTCCTCTGGGGTGAC
 721 TGCAGTTGAGGAAAGCATGCCATGGGGTAGGGGGACATTGGTGGCCACATTTTGGTGACAGACCCCTGCTGTTGTCTCTG
 801 TGTCCCCATTCTCTGGACTCTGGCCTGCCCTCCTAGTGCTTGTGACTCCCTCTCTTCCAGCCCCACCCCCATGGTATGTA
 881 TATTCCTTACAAGTCCTCCACAAGAGCAGCTGTCTAGGATGCGGGGAGGGGAGGCTCCTTCCCTTAGGGAGCGTGGAGAG
 961 AAGGGAGCAGCCTTGTTGCTGTATTTTTGGTTTTGTTTCAGTTGGGCAGGCATGGGATGGGAGAGGGGCTCAGCCACTTT
1041 CCTCCAGAATCTTCCCTCAGCCCCTCCAACTGCATATGTAATCCTACTCTGTCCTTCATAGAGGGGAAGGAGCCACAGAT
1121 GACATCCCAGTTCTAAGCCCACCAGGGAGGAACAGGCCTCTGTCCCCATAGGTGAGGTAGAGGTAGAGGGTCTTCACCTG
1201 CCAGTATCCCCTGCCGCTCCTTCCTCACAGAAGGAAGGAGGAGGAGGCAGCCGGGATCCTCGGCTCTGCCAGGGTGCAGC
1281 CAGGAGCAGGGTTTCACGCAGCTGGTCCAGCTCTGTGGCTTTGCTGCCTTTTCCTGTGGCCAGTCCCAGGAAGTGCTAAC
1361 ACCACCTCTCTCCCCACTCTTCCCTCTGGATTCTGGGGTCCCCCACACCGTATTTCCTCCACTCCAGCTGCCACTTTTGG
1441 AAGGGTATTGAGTCAGGAGCTGAGGGAAGGGGTGAGGAAGGTGGACATCCCATCCCAACTGTAATGCCTTTTTTTTTTTT
1521 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGGCCATTTGAGTCATGTATGGTACCAATCAATAAAGAGACTTTTCGGT
1601 TAAAAAAAAAAAAAAAAA
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' uuGGUG----GUCGGGUGAGg 5'
            ||||    |  ||||||| 
Target 5' caCCACCTCTCTCCCCACTCt 3'
 1360 - 1380 145.00 -20.90
2 
miRNA  3' uuGGUGGUCGGGUGAGg 5'
            |:|||  ||:|||| 
Target 5' agCTACCTCCCTACTCt 3'
 572 - 588 139.00 -19.30
3 
miRNA  3' uugguggUCGGGUGAGg 5'
                 | ||:|||| 
Target 5' atatgtaATCCTACTCt 3'
 1074 - 1090 126.00 -10.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30174837 139 COSMIC
COSN1111299 163 COSMIC
COSN31490459 194 COSMIC
COSN26638239 204 COSMIC
COSN30161053 345 COSMIC
COSN22831225 442 COSMIC
COSN31487753 484 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1173066282 1 dbSNP
rs748728287 4 dbSNP
rs774992937 7 dbSNP
rs1359012603 9 dbSNP
rs1430697150 10 dbSNP
rs1160899482 15 dbSNP
rs754615555 17 dbSNP
rs769351249 19 dbSNP
rs747510199 20 dbSNP
rs778179030 21 dbSNP
rs918409341 23 dbSNP
rs758764022 24 dbSNP
rs982329536 26 dbSNP
rs1391119154 28 dbSNP
rs1199619608 29 dbSNP
rs1487790592 30 dbSNP
rs748481424 32 dbSNP
rs1300975601 36 dbSNP
rs1218565893 38 dbSNP
rs918556264 39 dbSNP
rs779153664 40 dbSNP
rs1259554709 42 dbSNP
rs1315602071 43 dbSNP
rs916613562 46 dbSNP
rs1231012719 51 dbSNP
rs1273742656 54 dbSNP
rs1489399124 63 dbSNP
rs990943519 66 dbSNP
rs1266471203 81 dbSNP
rs1428858299 89 dbSNP
rs748837507 90 dbSNP
rs1196200878 94 dbSNP
rs1324042489 95 dbSNP
rs1032374101 102 dbSNP
rs978323216 103 dbSNP
rs1223646235 111 dbSNP
rs941446620 112 dbSNP
rs576827591 117 dbSNP
rs980664854 118 dbSNP
rs967343787 122 dbSNP
rs1030593770 124 dbSNP
rs1293439549 127 dbSNP
rs971565483 128 dbSNP
rs117578835 131 dbSNP
rs1279765211 134 dbSNP
rs900670055 139 dbSNP
rs1293314569 140 dbSNP
rs1365151316 143 dbSNP
rs539807955 143 dbSNP
rs1017974860 147 dbSNP
rs989043076 148 dbSNP
rs866499325 164 dbSNP
rs888099283 165 dbSNP
rs1486103298 167 dbSNP
rs572790384 169 dbSNP
rs929663050 170 dbSNP
rs1362056887 171 dbSNP
rs1422104756 171 dbSNP
rs1164777466 177 dbSNP
rs1346295064 181 dbSNP
rs372243555 189 dbSNP
rs1158266588 190 dbSNP
rs897029948 191 dbSNP
rs1421920965 199 dbSNP
rs1296692328 200 dbSNP
rs1358255766 203 dbSNP
rs1399063822 204 dbSNP
rs1419503604 206 dbSNP
rs999968495 211 dbSNP
rs554492610 212 dbSNP
rs949240005 218 dbSNP
rs1017324290 219 dbSNP
rs1283561933 221 dbSNP
rs1487829130 226 dbSNP
rs1211920338 227 dbSNP
rs1196968492 229 dbSNP
rs916452825 248 dbSNP
rs1048117339 254 dbSNP
rs990891271 260 dbSNP
rs1442033438 261 dbSNP
rs936764923 262 dbSNP
rs114758555 264 dbSNP
rs1380116269 275 dbSNP
rs1435717115 277 dbSNP
rs143162156 278 dbSNP
rs941479065 280 dbSNP
rs1377586532 282 dbSNP
rs966741724 283 dbSNP
rs1306950218 284 dbSNP
rs1352799023 292 dbSNP
rs1802361 293 dbSNP
rs79377741 296 dbSNP
rs1281016784 301 dbSNP
rs950269895 303 dbSNP
rs1209529225 306 dbSNP
rs1233570567 307 dbSNP
rs1459118598 308 dbSNP
rs1177385200 311 dbSNP
rs1238089619 315 dbSNP
rs1259545540 317 dbSNP
rs976399197 320 dbSNP
rs1174608997 321 dbSNP
rs1358969102 325 dbSNP
rs917413781 329 dbSNP
rs965233086 332 dbSNP
rs1017756320 336 dbSNP
rs34145152 342 dbSNP
rs1400443535 346 dbSNP
rs1006575777 353 dbSNP
rs1329302802 358 dbSNP
rs925636764 362 dbSNP
rs1436941832 365 dbSNP
rs1276355103 366 dbSNP
rs978436011 367 dbSNP
rs1218901282 368 dbSNP
rs1258942301 373 dbSNP
rs964351840 378 dbSNP
rs952440053 379 dbSNP
rs1290636907 380 dbSNP
rs1196761984 382 dbSNP
rs1257982146 390 dbSNP
rs574089862 392 dbSNP
rs994199301 393 dbSNP
rs1345118459 396 dbSNP
rs571605136 398 dbSNP
rs185558205 400 dbSNP
rs896858469 401 dbSNP
rs1190339395 407 dbSNP
rs1423880532 408 dbSNP
rs2815396 410 dbSNP
rs765666467 411 dbSNP
rs1167839943 416 dbSNP
rs1399501809 419 dbSNP
rs1405931549 432 dbSNP
rs41307072 437 dbSNP
rs1347968429 438 dbSNP
rs763155390 442 dbSNP
rs1435474763 450 dbSNP
rs1390682180 457 dbSNP
rs1342534965 458 dbSNP
rs1046399 459 dbSNP
rs894956166 461 dbSNP
rs549725758 466 dbSNP
rs1037554882 476 dbSNP
rs1451451911 477 dbSNP
rs531212121 478 dbSNP
rs1429641650 479 dbSNP
rs1478577059 480 dbSNP
rs1054943332 481 dbSNP
rs1472836773 488 dbSNP
rs576463003 489 dbSNP
rs764211090 495 dbSNP
rs1044906418 496 dbSNP
rs1411456537 496 dbSNP
rs563886218 496 dbSNP
rs1042495756 501 dbSNP
rs945365507 503 dbSNP
rs1341216653 505 dbSNP
rs923329774 506 dbSNP
rs1282958154 511 dbSNP
rs1356188156 512 dbSNP
rs1241372223 522 dbSNP
rs1053266435 524 dbSNP
rs976725764 527 dbSNP
rs1260590470 534 dbSNP
rs200777935 534 dbSNP
rs551974437 534 dbSNP
rs934785690 534 dbSNP
rs965012767 535 dbSNP
rs1465765471 537 dbSNP
rs1188941793 539 dbSNP
rs978971210 543 dbSNP
rs1443875838 544 dbSNP
rs910821915 547 dbSNP
rs1417629168 548 dbSNP
rs1397868841 549 dbSNP
rs763098128 550 dbSNP
rs1256859599 551 dbSNP
rs1448233955 552 dbSNP
rs1235652567 553 dbSNP
rs3210585 554 dbSNP
rs1324867519 555 dbSNP
rs1352033345 557 dbSNP
rs532245658 558 dbSNP
rs1259784619 561 dbSNP
rs1345233763 571 dbSNP
rs1201698634 587 dbSNP
rs1435830126 592 dbSNP
rs1367272727 593 dbSNP
rs987668756 594 dbSNP
rs1334603723 601 dbSNP
rs1239923485 605 dbSNP
rs1437608480 608 dbSNP
rs1180742610 609 dbSNP
rs954469873 610 dbSNP
rs1362281661 616 dbSNP
rs1406517157 621 dbSNP
rs1401641124 625 dbSNP
rs564873538 627 dbSNP
rs993966883 628 dbSNP
rs961321614 629 dbSNP
rs540322292 632 dbSNP
rs993305300 638 dbSNP
rs1333167723 644 dbSNP
rs1372098987 649 dbSNP
rs1253881777 652 dbSNP
rs1322296394 655 dbSNP
rs963141367 657 dbSNP
rs1259919494 662 dbSNP
rs1456356926 668 dbSNP
rs1195035332 674 dbSNP
rs1024667805 681 dbSNP
rs1170553313 684 dbSNP
rs572781710 688 dbSNP
rs1013689459 690 dbSNP
rs1197093449 692 dbSNP
rs1428784767 702 dbSNP
rs1478189449 703 dbSNP
rs560531318 708 dbSNP
rs1172851604 710 dbSNP
rs1450785213 713 dbSNP
rs1250500505 736 dbSNP
rs895037544 744 dbSNP
rs559695353 757 dbSNP
rs375614675 761 dbSNP
rs1461965611 764 dbSNP
rs1294597746 765 dbSNP
rs539956976 769 dbSNP
rs1000659705 774 dbSNP
rs903725928 783 dbSNP
rs1042855942 784 dbSNP
rs374829972 786 dbSNP
rs1203784207 802 dbSNP
rs1265960227 805 dbSNP
rs1202492586 811 dbSNP
rs1337710667 813 dbSNP
rs905896526 816 dbSNP
rs945508979 818 dbSNP
rs771488010 820 dbSNP
rs1250905570 822 dbSNP
rs923245243 827 dbSNP
rs1196088102 830 dbSNP
rs1421626099 832 dbSNP
rs1427989124 834 dbSNP
rs1014783029 835 dbSNP
rs1040350894 852 dbSNP
rs943378007 854 dbSNP
rs753758737 855 dbSNP
rs542528787 858 dbSNP
rs1364600219 859 dbSNP
rs575169560 861 dbSNP
rs1400284162 864 dbSNP
rs1299621888 866 dbSNP
rs1359341661 870 dbSNP
rs1213414279 871 dbSNP
rs1313347654 872 dbSNP
rs1323387124 874 dbSNP
rs1242367448 878 dbSNP
rs556741733 885 dbSNP
rs192603473 886 dbSNP
rs1219151188 889 dbSNP
rs147322651 890 dbSNP
rs574156174 892 dbSNP
rs904658947 895 dbSNP
rs1451791607 896 dbSNP
rs1043363809 900 dbSNP
rs1182455695 901 dbSNP
rs1258916482 902 dbSNP
rs943631329 909 dbSNP
rs930805256 916 dbSNP
rs1340953586 918 dbSNP
rs773859560 919 dbSNP
rs972877922 921 dbSNP
rs553238059 922 dbSNP
rs1302864212 923 dbSNP
rs1025160516 925 dbSNP
rs991806685 928 dbSNP
rs959027292 935 dbSNP
rs1431153719 937 dbSNP
rs1382815258 941 dbSNP
rs1162331574 942 dbSNP
rs1284157617 946 dbSNP
rs1444583488 946 dbSNP
rs1369493032 947 dbSNP
rs1033591692 951 dbSNP
rs765518895 952 dbSNP
rs1250150055 953 dbSNP
rs1239307653 957 dbSNP
rs535096074 964 dbSNP
rs1441932634 965 dbSNP
rs1000816999 967 dbSNP
rs759798224 970 dbSNP
rs567694093 971 dbSNP
rs1009832386 972 dbSNP
rs901898040 973 dbSNP
rs969319075 975 dbSNP
rs1360453498 979 dbSNP
rs1467762424 989 dbSNP
rs1025282802 990 dbSNP
rs1377462957 993 dbSNP
rs1448758190 998 dbSNP
rs1356987731 1006 dbSNP
rs1285818054 1007 dbSNP
rs1014274917 1017 dbSNP
rs1040867111 1022 dbSNP
rs777021175 1025 dbSNP
rs1220077142 1026 dbSNP
rs1303673251 1027 dbSNP
rs943370841 1037 dbSNP
rs1259300356 1044 dbSNP
rs895764753 1048 dbSNP
rs1031769327 1049 dbSNP
rs889150029 1051 dbSNP
rs1478557346 1056 dbSNP
rs1191470122 1057 dbSNP
rs1426761314 1058 dbSNP
rs1411308509 1064 dbSNP
rs374009232 1069 dbSNP
rs537760608 1074 dbSNP
rs1467167078 1076 dbSNP
rs1326736708 1081 dbSNP
rs1353780888 1087 dbSNP
rs1363274617 1094 dbSNP
rs371465750 1098 dbSNP
rs1276846374 1101 dbSNP
rs930920970 1104 dbSNP
rs570314709 1120 dbSNP
rs58159715 1133 dbSNP
rs1343826347 1142 dbSNP
rs1223003162 1157 dbSNP
rs1278967923 1164 dbSNP
rs904732435 1166 dbSNP
rs1043230807 1167 dbSNP
rs1452563068 1168 dbSNP
rs1224152466 1171 dbSNP
rs1248128391 1174 dbSNP
rs1489692115 1188 dbSNP
rs1294260128 1196 dbSNP
rs943649627 1197 dbSNP
rs889389827 1204 dbSNP
rs1418638199 1208 dbSNP
rs919530077 1213 dbSNP
rs933007933 1215 dbSNP
rs554754877 1216 dbSNP
rs771426356 1233 dbSNP
rs971825315 1233 dbSNP
rs1473710392 1237 dbSNP
rs1342511860 1242 dbSNP
rs941764081 1248 dbSNP
rs1244557139 1252 dbSNP
rs909078715 1253 dbSNP
rs1230410776 1255 dbSNP
rs879584498 1258 dbSNP
rs980642910 1261 dbSNP
rs969603185 1262 dbSNP
rs917638525 1266 dbSNP
rs1024893288 1273 dbSNP
rs1263440274 1275 dbSNP
rs1448241736 1278 dbSNP
rs747575629 1280 dbSNP
rs537700032 1286 dbSNP
rs1241465379 1288 dbSNP
rs959017360 1297 dbSNP
rs533408571 1298 dbSNP
rs1383219631 1301 dbSNP
rs1423749106 1304 dbSNP
rs998963805 1307 dbSNP
rs979323316 1311 dbSNP
rs11191217 1313 dbSNP
rs1380635665 1318 dbSNP
rs1207377178 1326 dbSNP
rs1021691463 1332 dbSNP
rs967933164 1342 dbSNP
rs1021303347 1343 dbSNP
rs1313551235 1346 dbSNP
rs1382583400 1351 dbSNP
rs1282236830 1353 dbSNP
rs1436645256 1369 dbSNP
rs868035580 1370 dbSNP
rs1007747235 1373 dbSNP
rs1202978636 1375 dbSNP
rs12412487 1379 dbSNP
rs889245496 1381 dbSNP
rs1052056725 1384 dbSNP
rs12246649 1386 dbSNP
rs12246646 1393 dbSNP
rs1241130618 1403 dbSNP
rs1443783583 1406 dbSNP
rs144145554 1409 dbSNP
rs546415735 1410 dbSNP
rs1403089114 1413 dbSNP
rs1035971275 1418 dbSNP
rs1335336586 1420 dbSNP
rs1306896672 1421 dbSNP
rs1019021758 1422 dbSNP
rs941672070 1426 dbSNP
rs908983830 1431 dbSNP
rs1045173655 1432 dbSNP
rs1160390124 1440 dbSNP
rs947919690 1444 dbSNP
rs1345125222 1445 dbSNP
rs1204942510 1450 dbSNP
rs186479511 1454 dbSNP
rs1199170981 1460 dbSNP
rs1460777838 1460 dbSNP
rs889098215 1474 dbSNP
rs1252455815 1475 dbSNP
rs1049028796 1485 dbSNP
rs1214454191 1488 dbSNP
rs1181434764 1491 dbSNP
rs956591788 1494 dbSNP
rs1481464203 1497 dbSNP
rs930659672 1497 dbSNP
rs538913542 1498 dbSNP
rs977434163 1499 dbSNP
rs1248558130 1500 dbSNP
rs11191216 1505 dbSNP
rs1191049729 1506 dbSNP
rs369822550 1507 dbSNP
rs1268610060 1508 dbSNP
rs898045755 1509 dbSNP
rs1327768424 1512 dbSNP
rs1210429344 1536 dbSNP
rs1321134329 1539 dbSNP
rs1037026247 1551 dbSNP
rs1164148714 1552 dbSNP
rs1173177475 1552 dbSNP
rs1188315349 1552 dbSNP
rs1194950420 1552 dbSNP
rs1197493458 1552 dbSNP
rs1219248005 1552 dbSNP
rs1220606638 1552 dbSNP
rs1224843316 1552 dbSNP
rs1226456536 1552 dbSNP
rs1260286796 1552 dbSNP
rs1265865513 1552 dbSNP
rs1268374947 1552 dbSNP
rs1280866916 1552 dbSNP
rs1297645221 1552 dbSNP
rs1300898978 1552 dbSNP
rs1305656342 1552 dbSNP
rs1322174379 1552 dbSNP
rs1331284391 1552 dbSNP
rs1339093769 1552 dbSNP
rs1367824333 1552 dbSNP
rs1371776250 1552 dbSNP
rs1400019425 1552 dbSNP
rs1406432339 1552 dbSNP
rs1428492809 1552 dbSNP
rs1428760918 1552 dbSNP
rs1461823585 1552 dbSNP
rs1478179838 1552 dbSNP
rs1488659173 1552 dbSNP
rs1490889241 1552 dbSNP
rs558516308 1552 dbSNP
rs560592963 1552 dbSNP
rs566913040 1552 dbSNP
rs754354454 1552 dbSNP
rs764008788 1552 dbSNP
rs769387128 1552 dbSNP
rs773661555 1552 dbSNP
rs1188816611 1557 dbSNP
rs950240749 1567 dbSNP
rs1423117835 1570 dbSNP
rs71471232 1574 dbSNP
rs1161300323 1581 dbSNP
rs767988852 1594 dbSNP
rs1346638217 1597 dbSNP
rs917437689 1598 dbSNP
rs1267924634 1600 dbSNP
rs1381640062 1603 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' uugguggucGGGUGAGg 5'
                   ||||||| 
Target 5' ------cucCCCACUCu 3'
 		1 - 11
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 ENST00000361198.5 | 3UTR | CUCCCCACUCUUCCCUCUG
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
84 hsa-miR-4481 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT100715 TJAP1 tight junction associated protein 1 2 2
MIRT183589 ZC3H11A zinc finger CCCH-type containing 11A 2 2
MIRT338033 DAZAP2 DAZ associated protein 2 2 4
MIRT395796 SPCS3 signal peptidase complex subunit 3 2 2
MIRT443947 LRIT3 leucine rich repeat, Ig-like and transmembrane domains 3 2 2
MIRT450580 HIST1H2BG histone cluster 1 H2B family member g 2 6
MIRT451617 MEIS3P1 Meis homeobox 3 pseudogene 1 2 2
MIRT452331 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 2
MIRT453279 EFTUD2 elongation factor Tu GTP binding domain containing 2 2 2
MIRT455212 GNL1 G protein nucleolar 1 (putative) 2 2
MIRT455470 LYPLA2 lysophospholipase II 2 2
MIRT456503 PFKFB2 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 2 2
MIRT456687 LDB1 LIM domain binding 1 2 2
MIRT456915 DDA1 DET1 and DDB1 associated 1 2 2
MIRT457603 IDS iduronate 2-sulfatase 2 2
MIRT457848 RNASEH2B ribonuclease H2 subunit B 2 4
MIRT458455 RPRM reprimo, TP53 dependent G2 arrest mediator homolog 2 2
MIRT460179 UNK unkempt family zinc finger 2 6
MIRT461465 SLC19A3 solute carrier family 19 member 3 2 2
MIRT464739 UBE2Q1 ubiquitin conjugating enzyme E2 Q1 2 2
MIRT465279 TRIM28 tripartite motif containing 28 2 2
MIRT468450 SETD1B SET domain containing 1B 2 2
MIRT468620 SUMO1 small ubiquitin-like modifier 1 2 6
MIRT469152 RNF121 ring finger protein 121 2 2
MIRT470073 PTGES2 prostaglandin E synthase 2 2 2
MIRT470172 PSMD11 proteasome 26S subunit, non-ATPase 11 2 4
MIRT473156 MLLT1 MLLT1, super elongation complex subunit 2 2
MIRT474308 LAMC1 laminin subunit gamma 1 2 2
MIRT474782 KIAA0895L KIAA0895 like 2 2
MIRT476484 GATAD2A GATA zinc finger domain containing 2A 2 2
MIRT477613 EFNA3 ephrin A3 2 2
MIRT479525 CDCA4 cell division cycle associated 4 2 2
MIRT479973 CARD10 caspase recruitment domain family member 10 2 2
MIRT480410 C19orf47 chromosome 19 open reading frame 47 2 2
MIRT480426 C17orf85 nuclear cap binding subunit 3 2 2
MIRT483573 SYT2 synaptotagmin 2 2 2
MIRT483664 QSOX2 quiescin sulfhydryl oxidase 2 2 4
MIRT484532 POLD3 DNA polymerase delta 3, accessory subunit 2 2
MIRT484616 SIX3 SIX homeobox 3 2 6
MIRT485897 ZFP36 ZFP36 ring finger protein 2 2
MIRT486505 MYH11 myosin heavy chain 11 2 2
MIRT487505 GRK5 G protein-coupled receptor kinase 5 2 2
MIRT488852 UBTF upstream binding transcription factor, RNA polymerase I 2 2
MIRT489464 MSC musculin 2 2
MIRT491170 LRP3 LDL receptor related protein 3 2 2
MIRT496627 TMEM67 transmembrane protein 67 2 2
MIRT497616 ANG angiogenin 2 2
MIRT497766 KIAA0895 KIAA0895 2 2
MIRT499680 MRE11A MRE11 homolog, double strand break repair nuclease 2 6
MIRT499774 SLC29A2 solute carrier family 29 member 2 2 2
MIRT501745 NSD1 nuclear receptor binding SET domain protein 1 2 2
MIRT504995 ZNF652 zinc finger protein 652 2 2
MIRT511664 HIST1H3C histone cluster 1 H3 family member c 2 2
MIRT511690 HIST1H2BO histone cluster 1 H2B family member o 2 4
MIRT511703 HIST1H2BL histone cluster 1 H2B family member l 2 4
MIRT511734 HIST1H2BE histone cluster 1 H2B family member e 2 8
MIRT512858 TBC1D13 TBC1 domain family member 13 2 2
MIRT513444 EMP1 epithelial membrane protein 1 2 6
MIRT515681 TFPI tissue factor pathway inhibitor 2 2
MIRT523529 GLUL glutamate-ammonia ligase 2 2
MIRT525546 PHB2 prohibitin 2 2 4
MIRT526209 SNX24 sorting nexin 24 2 2
MIRT531554 SRD5A1 steroid 5 alpha-reductase 1 2 2
MIRT533764 TMEM135 transmembrane protein 135 2 2
MIRT545582 SNRPA1 small nuclear ribonucleoprotein polypeptide A' 2 2
MIRT552434 ZNF460 zinc finger protein 460 2 2
MIRT561159 BCL2L12 BCL2 like 12 2 2
MIRT562345 EXOSC2 exosome component 2 2 2
MIRT570659 KDM6B lysine demethylase 6B 2 2
MIRT571076 TCHHL1 trichohyalin like 1 2 2
MIRT571330 TPCN2 two pore segment channel 2 2 2
MIRT571603 TOB2 transducer of ERBB2, 2 2 2
MIRT573013 RPP25 ribonuclease P and MRP subunit p25 2 2
MIRT609041 EP300 E1A binding protein p300 2 2
MIRT613398 DNAH17 dynein axonemal heavy chain 17 2 2
MIRT635589 TTC9C tetratricopeptide repeat domain 9C 2 2
MIRT661118 FPR1 formyl peptide receptor 1 2 2
MIRT690103 PNMA2 paraneoplastic Ma antigen 2 2 2
MIRT694972 PLAC8 placenta specific 8 2 2
MIRT695515 ALPI alkaline phosphatase, intestinal 2 2
MIRT695578 ASB16 ankyrin repeat and SOCS box containing 16 2 2
MIRT699570 SIT1 signaling threshold regulating transmembrane adaptor 1 2 2
MIRT701991 MIER3 MIER family member 3 2 2
MIRT725464 GRAP2 GRB2-related adaptor protein 2 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-4 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4481 Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-mir-4481 Androstenedione 6128 NSC9563 sensitive cell line (MCF-7)
hsa-mir-4481 Tamoxifen 2733525 NSC180973 approved resistant cell line (MCF7)
hsa-mir-4481 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-miR-4481 Cisplatin 5460033 NSC119875 approved resistant cell line (CAL-27) (cytosolic RNA)
hsa-miR-4481 Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-4481 Neoadjuvant chemotherapy sensitive tissue (breast cancer)
hsa-miR-4481 Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (100 ng/ml)
hsa-miR-4481 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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