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 RRM2   
Synonyms R2, RR2, RR2M
Description ribonucleotide reductase regulatory subunit M2
Transcript NM_001034   
Other Transcripts NM_001165931   
Expression
Putative miRNA Targets on RRM2
3'UTR of RRM2
(miRNA target sites are highlighted)
>RRM2|NM_001034|3'UTR
   1 ATGAACTGAAGATGTGCCCTTACTTGGCTGATTTTTTTTTTCCATCTCATAAGAAAAATCAGCTGAAGTGTTACCAACTA
  81 GCCACACCATGAATTGTCCGTAATGTTCATTAACAGCATCTTTAAAACTGTGTAGCTACCTCACAACCAGTCCTGTCTGT
 161 TTATAGTGCTGGTAGTATCACCTTTTGCCAGAAGGCCTGGCTGGCTGTGACTTACCATAGCAGTGACAATGGCAGTCTTG
 241 GCTTTAAAGTGAGGGGTGACCCTTTAGTGAGCTTAGCACAGCGGGATTAAACAGTCCTTTAACCAGCACAGCCAGTTAAA
 321 AGATGCAGCCTCACTGCTTCAACGCAGATTTTAATGTTTACTTAAATATAAACCTGGCACTTTACAAACAAATAAACATT
 401 GTTTGTACTCACAAGGCGATAATAGCTTGATTTATTTGGTTTCTACACCAAATACATTCTCCTGACCACTAATGGGAGCC
 481 AATTCACAATTCACTAAGTGACTAAAGTAAGTTAAACTTGTGTAGACTAAGCATGTAATTTTTAAGTTTTATTTTAATGA
 561 ATTAAAATATTTGTTAACCAACTTTAAAGTCAGTCCTGTGTATACCTAGATATTAGTCAGTTGGTGCCAGATAGAAGACA
 641 GGTTGTGTTTTTATCCTGTGGCTTGTGTAGTGTCCTGGGATTCTCTGCCCCCTCTGAGTAGAGTGTTGTGGGATAAAGGA
 721 ATCTCTCAGGGCAAGGAGCTTCTTAAGTTAAATCACTAGAAATTTAGGGGTGATCTGGGCCTTCATATGTGTGAGAAGCC
 801 GTTTCATTTTATTTCTCACTGTATTTTCCTCAACGTCTGGTTGATGAGAAAAAATTCTTGAAGAGTTTTCATATGTGGGA
 881 GCTAAGGTAGTATTGTAAAATTTCAAGTCATCCTTAAACAAAATGATCCACCTAAGATCTTGCCCCTGTTAAGTGGTGAA
 961 ATCAACTAGAGGTGGTTCCTACAAGTTGTTCATTCTAGTTTTGTTTGGTGTAAGTAGGTTGTGTGAGTTAATTCATTTAT
1041 ATTTACTATGTCTGTTAAATCAGAAATTTTTTATTATCTATGTTCTTCTAGATTTTACCTGTAGTTCATACTTCAGTCAC
1121 CCAGTGTCTTATTCTGGCATTGTCTAAATCTGAGCATTGTCTAGGGGGATCTTAAACTTTAGTAGGAAACCATGAGCTGT
1201 TAATACAGTTTCCATTCAAATATTAATTTCAGAATGAAACATAATTTTTTTTTTTTTTTTTGAGATGGAGTCTCGCTCTG
1281 TTGCCCAGGCTGGAGTGCAGTGGCGCGATTTTGGCTCACTGTAACCTCCATCTCCTGGGTTCAAGCAATTCTCCTGTCTC
1361 AGCCTCCCTAGTAGCTGGGACTGCAGGTATGTGCTACCACACCTGGCTAATTTTTGTATTTTTAGTAGAGATGGAGTTTC
1441 ACCATATTGGTCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCACCCACCTCGGCCTCCCAAAGTGCTGGGATTGCA
1521 GGCGTGATAAACAAATATTCTTAATAGGGCTACTTTGAATTAATCTGCCTTTATGTTTGGGAGAAGAAAGCTGAGACATT
1601 GCATGAAAGATGATGAGAGATAAATGTTGATCTTTTGGCCCCATTTGTTAATTGTATTCAGTATTTGAACGTCGTCCTGT
1681 TTATTGTTAGTTTTCTTCATCATTTATTGTATAGACAATTTTTAAATCTCTGTAATATGATACATTTTCCTATCTTTTAA
1761 GTTATTGTTACCTAAAGTTAATCCAGATTATATGGTCCTTATATGTGTACAACATTAAAATGAAAGGCTTTGTCTTGCAT
1841 TGTGAGGTACAGGCGGAAGTTGGAATCAGGTTTTAGGATTCTGTCTCTCATTAGCTGAATAATGTGAGGATTAACTTCTG
1921 CCAGCTCAGACCATTTCCTAATCAGTTGAAAGGGAAACAAGTATTTCAGTCTCAAAATTGAATAATGCACAAGTCTTAAG
2001 TGATTAAAATAAAACTGTTCTTATGTCAGTTTCAAAAAAAAAAAAAAAAAA
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' tcACTGTAACCTC-CATCTCCt 3'
1316 - 1336 139.00 -11.10
2
miRNA  3' gcucacaCUCUA-GU--GUGGAGgg 5'
                 | ||| ||  ||||||  
Target 5' acctcagGTGATCCACCCACCTCgg 3'
1473 - 1497 129.00 -14.00
3
miRNA  3' gcUCAC-ACUCUAGU-GUGGAGGg 5'
            |||| ||: | :| |||||:: 
Target 5' atAGTGCTGGTAGTATCACCTTTt 3'
163 - 186 128.00 -12.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31485740 28 COSMIC
COSN1220591 42 COSMIC
COSN31613776 42 COSMIC
COSN30153780 49 COSMIC
COSN30518760 49 COSMIC
COSN31576965 51 COSMIC
COSN19312988 83 COSMIC
COSN31543880 101 COSMIC
COSN31583080 117 COSMIC
COSN28750194 135 COSMIC
COSN26677306 160 COSMIC
COSN19660334 181 COSMIC
COSN30120258 197 COSMIC
COSN31523393 299 COSMIC
COSN29192619 322 COSMIC
COSN6149472 348 COSMIC
COSN31488910 444 COSMIC
COSN29549608 451 COSMIC
COSN24013993 695 COSMIC
COSN30031157 786 COSMIC
COSN20096319 1262 COSMIC
COSN21407161 1359 COSMIC
COSN4909415 1519 COSMIC
COSN17376957 1675 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs756637379 2 dbSNP
rs778037879 11 dbSNP
rs749647333 16 dbSNP
rs771373014 17 dbSNP
rs376458388 22 dbSNP
rs371603045 32 dbSNP
rs764059345 32 dbSNP
rs78311808 32 dbSNP
rs756710024 33 dbSNP
rs79162203 33 dbSNP
rs1258460287 35 dbSNP
rs5030757 36 dbSNP
rs1247301601 38 dbSNP
rs1186886752 42 dbSNP
rs772288724 45 dbSNP
rs567302711 50 dbSNP
rs975301006 74 dbSNP
rs535862183 79 dbSNP
rs923485611 83 dbSNP
rs1469556842 86 dbSNP
rs1407301205 89 dbSNP
rs1179201192 94 dbSNP
rs186654277 100 dbSNP
rs151112936 101 dbSNP
rs1191897819 119 dbSNP
rs776799796 129 dbSNP
rs1263346898 131 dbSNP
rs1181385288 139 dbSNP
rs1460656066 140 dbSNP
rs538123832 147 dbSNP
rs978160437 156 dbSNP
rs1337429404 166 dbSNP
rs557947933 173 dbSNP
rs1250803716 178 dbSNP
rs577803252 191 dbSNP
rs1337026883 196 dbSNP
rs1358250641 198 dbSNP
rs1313101479 200 dbSNP
rs1445289424 202 dbSNP
rs1452269056 210 dbSNP
rs534347219 216 dbSNP
rs1383971126 226 dbSNP
rs1339160724 234 dbSNP
rs774957221 239 dbSNP
rs1390135279 244 dbSNP
rs1396354023 251 dbSNP
rs1291010685 256 dbSNP
rs1462000907 267 dbSNP
rs1363006245 270 dbSNP
rs5030759 273 dbSNP
rs1276845424 278 dbSNP
rs1325818883 279 dbSNP
rs1224170599 281 dbSNP
rs1277958451 283 dbSNP
rs1189412402 284 dbSNP
rs1310689264 286 dbSNP
rs936676506 288 dbSNP
rs191054082 306 dbSNP
rs914462632 307 dbSNP
rs1243639203 310 dbSNP
rs574906421 315 dbSNP
rs1341551311 324 dbSNP
rs139954791 344 dbSNP
rs79765591 354 dbSNP
rs1260893939 357 dbSNP
rs948688925 359 dbSNP
rs1317465871 367 dbSNP
rs1044599335 369 dbSNP
rs1335560801 384 dbSNP
rs1330065900 386 dbSNP
rs1393716129 388 dbSNP
rs1293078218 390 dbSNP
rs1423781056 394 dbSNP
rs534766369 398 dbSNP
rs1412401959 399 dbSNP
rs1047516544 409 dbSNP
rs545306582 410 dbSNP
rs1164662966 411 dbSNP
rs1468346086 417 dbSNP
rs1160832307 418 dbSNP
rs886230373 425 dbSNP
rs1005880515 429 dbSNP
rs144948625 434 dbSNP
rs1266824581 438 dbSNP
rs185874295 440 dbSNP
rs1490540373 442 dbSNP
rs996458906 444 dbSNP
rs1296935277 454 dbSNP
rs1347974724 456 dbSNP
rs1203621237 459 dbSNP
rs1406036418 460 dbSNP
rs1350404867 463 dbSNP
rs1280566860 467 dbSNP
rs1274351714 470 dbSNP
rs1241783878 480 dbSNP
rs1344219650 485 dbSNP
rs1342880009 490 dbSNP
rs1403746254 495 dbSNP
rs1030887637 502 dbSNP
rs547511857 503 dbSNP
rs1398648410 506 dbSNP
rs1383937331 512 dbSNP
rs1225756566 518 dbSNP
rs1473468129 519 dbSNP
rs1427053162 521 dbSNP
rs1198617243 529 dbSNP
rs867120429 532 dbSNP
rs1248599398 536 dbSNP
rs764106357 539 dbSNP
rs1285189270 544 dbSNP
rs1446688886 567 dbSNP
rs769909116 570 dbSNP
rs62129883 582 dbSNP
rs1321884767 594 dbSNP
rs1215667504 597 dbSNP
rs1224730997 606 dbSNP
rs1283557335 615 dbSNP
rs1345578234 617 dbSNP
rs1490823017 624 dbSNP
rs1031041610 632 dbSNP
rs10178011 646 dbSNP
rs201630221 666 dbSNP
rs1318588616 668 dbSNP
rs1458564138 677 dbSNP
rs549536921 678 dbSNP
rs1403643218 679 dbSNP
rs943264042 681 dbSNP
rs989423360 688 dbSNP
rs916604481 692 dbSNP
rs569278922 698 dbSNP
rs1475146749 699 dbSNP
rs1178627643 700 dbSNP
rs948615515 710 dbSNP
rs753857774 722 dbSNP
rs538183732 724 dbSNP
rs1367784495 725 dbSNP
rs868538774 726 dbSNP
rs928421140 733 dbSNP
rs938494630 739 dbSNP
rs551639029 756 dbSNP
rs886174658 766 dbSNP
rs1338195360 769 dbSNP
rs1270345626 773 dbSNP
rs941782920 776 dbSNP
rs114571498 779 dbSNP
rs1335896650 784 dbSNP
rs1444426961 801 dbSNP
rs900179009 802 dbSNP
rs1168269247 816 dbSNP
rs1409395441 818 dbSNP
rs534137052 830 dbSNP
rs1030584011 835 dbSNP
rs554292811 836 dbSNP
rs1384965126 840 dbSNP
rs192510398 847 dbSNP
rs1184546204 849 dbSNP
rs1484455676 849 dbSNP
rs536716140 855 dbSNP
rs556628299 860 dbSNP
rs1306809175 862 dbSNP
rs183195414 869 dbSNP
rs1281803697 874 dbSNP
rs34279704 877 dbSNP
rs999636218 890 dbSNP
rs5030760 894 dbSNP
rs766063643 916 dbSNP
rs958091335 920 dbSNP
rs545368074 927 dbSNP
rs1356877981 932 dbSNP
rs558883655 953 dbSNP
rs1289036676 954 dbSNP
rs1449420205 957 dbSNP
rs989538564 966 dbSNP
rs1206052309 970 dbSNP
rs1024025574 976 dbSNP
rs969421525 980 dbSNP
rs1438710470 992 dbSNP
rs1309978425 996 dbSNP
rs186091130 1002 dbSNP
rs1176327484 1004 dbSNP
rs1345067162 1011 dbSNP
rs1387548261 1020 dbSNP
rs1384789112 1022 dbSNP
rs1473323766 1024 dbSNP
rs1163227912 1025 dbSNP
rs1425857127 1050 dbSNP
rs1389243321 1053 dbSNP
rs190501818 1054 dbSNP
rs1470827314 1059 dbSNP
rs115318989 1074 dbSNP
rs928564013 1077 dbSNP
rs182776618 1081 dbSNP
rs578112183 1083 dbSNP
rs983263669 1085 dbSNP
rs1384781580 1089 dbSNP
rs907724615 1091 dbSNP
rs1350986799 1094 dbSNP
rs941729931 1098 dbSNP
rs1403118820 1099 dbSNP
rs1294335161 1104 dbSNP
rs775895379 1108 dbSNP
rs763139689 1115 dbSNP
rs1459694456 1117 dbSNP
rs749562845 1118 dbSNP
rs1283344483 1119 dbSNP
rs557816054 1121 dbSNP
rs1158890795 1126 dbSNP
rs537779131 1127 dbSNP
rs1401684000 1149 dbSNP
rs1414774756 1151 dbSNP
rs1354195765 1155 dbSNP
rs921556741 1169 dbSNP
rs1216202657 1170 dbSNP
rs1191388237 1183 dbSNP
rs1489278811 1190 dbSNP
rs931662559 1195 dbSNP
rs1051900862 1196 dbSNP
rs529769226 1198 dbSNP
rs200259620 1200 dbSNP
rs1269866533 1205 dbSNP
rs1196438457 1224 dbSNP
rs188323526 1229 dbSNP
rs1221682177 1230 dbSNP
rs562974254 1237 dbSNP
rs1302129685 1239 dbSNP
rs1388711150 1242 dbSNP
rs999752248 1243 dbSNP
rs1174906670 1245 dbSNP
rs1469794405 1245 dbSNP
rs34217469 1245 dbSNP
rs397732775 1245 dbSNP
rs1052524331 1246 dbSNP
rs1176102799 1250 dbSNP
rs1367025328 1258 dbSNP
rs76515542 1262 dbSNP
rs1368812454 1263 dbSNP
rs1458661866 1264 dbSNP
rs531969479 1271 dbSNP
rs1010908271 1273 dbSNP
rs1322786699 1275 dbSNP
rs1256549645 1276 dbSNP
rs571350098 1279 dbSNP
rs537185523 1284 dbSNP
rs557670968 1286 dbSNP
rs192657663 1289 dbSNP
rs1403223403 1291 dbSNP
rs182957125 1305 dbSNP
rs547688813 1306 dbSNP
rs187569312 1307 dbSNP
rs1335186484 1308 dbSNP
rs1003534411 1320 dbSNP
rs1403469692 1337 dbSNP
rs1486764240 1337 dbSNP
rs1338415452 1340 dbSNP
rs1305122528 1346 dbSNP
rs1467069531 1349 dbSNP
rs1370907241 1351 dbSNP
rs1167556947 1358 dbSNP
rs191269083 1364 dbSNP
rs557271849 1370 dbSNP
rs1035453135 1371 dbSNP
rs1316814582 1382 dbSNP
rs1460724229 1384 dbSNP
rs959919500 1389 dbSNP
rs1202115023 1390 dbSNP
rs1479697743 1391 dbSNP
rs983377685 1399 dbSNP
rs907675195 1407 dbSNP
rs963209913 1408 dbSNP
rs1313212042 1410 dbSNP
rs1345294125 1412 dbSNP
rs1138727 1417 dbSNP
rs1138728 1419 dbSNP
rs1341447993 1424 dbSNP
rs1390224534 1443 dbSNP
rs556689737 1445 dbSNP
rs1254596658 1447 dbSNP
rs570106471 1455 dbSNP
rs1449083925 1457 dbSNP
rs1429865865 1459 dbSNP
rs1195093344 1464 dbSNP
rs868811318 1468 dbSNP
rs1472306690 1478 dbSNP
rs539045567 1481 dbSNP
rs768854661 1490 dbSNP
rs1378217749 1491 dbSNP
rs1205895334 1494 dbSNP
rs1465735805 1496 dbSNP
rs1171036798 1499 dbSNP
rs1222111205 1519 dbSNP
rs1051414332 1520 dbSNP
rs774481698 1524 dbSNP
rs1237478567 1525 dbSNP
rs1293717473 1529 dbSNP
rs1401596289 1529 dbSNP
rs558946103 1542 dbSNP
rs1298778537 1545 dbSNP
rs879227886 1553 dbSNP
rs11545188 1557 dbSNP
rs935551266 1565 dbSNP
rs761886364 1600 dbSNP
rs184927325 1602 dbSNP
rs1339783024 1604 dbSNP
rs1398004225 1606 dbSNP
rs1451380670 1610 dbSNP
rs1411061886 1615 dbSNP
rs1182814201 1618 dbSNP
rs1284645672 1622 dbSNP
rs1184549612 1640 dbSNP
rs572272890 1641 dbSNP
rs772140952 1655 dbSNP
rs1331170638 1661 dbSNP
rs1232150210 1664 dbSNP
rs541289255 1671 dbSNP
rs1350428304 1672 dbSNP
rs1045671115 1674 dbSNP
rs1261362418 1675 dbSNP
rs905256462 1677 dbSNP
rs1217845952 1681 dbSNP
rs1138729 1684 dbSNP
rs1331272143 1684 dbSNP
rs1325126799 1697 dbSNP
rs1034987931 1710 dbSNP
rs374044024 1716 dbSNP
rs766135373 1717 dbSNP
rs951366002 1718 dbSNP
rs1004763662 1723 dbSNP
rs1487602398 1724 dbSNP
rs1014846857 1727 dbSNP
rs963323051 1728 dbSNP
rs1268231251 1729 dbSNP
rs1464727146 1737 dbSNP
rs761753577 1739 dbSNP
rs1211106202 1746 dbSNP
rs1322089756 1750 dbSNP
rs1432660907 1752 dbSNP
rs1278582773 1753 dbSNP
rs1197090565 1755 dbSNP
rs1218065965 1762 dbSNP
rs1345112949 1772 dbSNP
rs574555188 1779 dbSNP
rs973247082 1784 dbSNP
rs1365727737 1785 dbSNP
rs543162257 1786 dbSNP
rs145863886 1794 dbSNP
rs1321022057 1795 dbSNP
rs987635024 1799 dbSNP
rs1403754242 1804 dbSNP
rs767414325 1809 dbSNP
rs1415046382 1812 dbSNP
rs1417853770 1819 dbSNP
rs1427440420 1829 dbSNP
rs1166359293 1833 dbSNP
rs960282805 1843 dbSNP
rs1449148410 1849 dbSNP
rs934997491 1850 dbSNP
rs1295204849 1855 dbSNP
rs542863601 1856 dbSNP
rs1237340246 1863 dbSNP
rs530846614 1878 dbSNP
rs1280186489 1884 dbSNP
rs1385701584 1884 dbSNP
rs915482402 1886 dbSNP
rs1340971504 1889 dbSNP
rs1020623988 1891 dbSNP
rs1230269719 1896 dbSNP
rs946985020 1904 dbSNP
rs1448743452 1910 dbSNP
rs1298505362 1916 dbSNP
rs966394469 1930 dbSNP
rs532030581 1932 dbSNP
rs1371350459 1933 dbSNP
rs905370078 1934 dbSNP
rs1443154108 1935 dbSNP
rs13389058 1952 dbSNP
rs758777026 1958 dbSNP
rs979573058 1964 dbSNP
rs1182924764 1974 dbSNP
rs939416165 1980 dbSNP
rs1231704031 1984 dbSNP
rs1202345480 1991 dbSNP
rs1482450347 2005 dbSNP
rs1274841412 2012 dbSNP
rs925074527 2021 dbSNP
rs1351957475 2023 dbSNP
rs145536953 2024 dbSNP
rs1225446784 2025 dbSNP
rs1288926804 2028 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' ucACUGUAACCUC-CAUCUCCu 3'
2 - 22
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_001165931 | 3UTR | AUCUCCUGGGUUCAAGCAAUUCUCCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000360566.2 | 3UTR | CUCACUGUAACCUCCAUCUCCUGGGUUCAAG
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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