pre-miRNA Information
pre-miRNA hsa-mir-3160-1   
Genomic Coordinates chr11: 46451805 - 46451889
Description Homo sapiens miR-3160-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA hsa-mir-3160-2   
Genomic Coordinates chr11: 46451807 - 46451887
Description Homo sapiens miR-3160-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3160-3p
Sequence 54| AGAGCUGAGACUAGAAAGCCCA |75
Evidence Experimental
Experiments Illumina
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN30582333 1 COSMIC
COSN1535547 3 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1396368683 1 dbSNP
rs1162409303 2 dbSNP
rs1404378453 12 dbSNP
rs1171960732 14 dbSNP
rs1324633375 16 dbSNP
rs1187765019 16 dbSNP
rs1300058326 19 dbSNP
rs1432898407 21 dbSNP
rs1011279103 22 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol MRPS14   
Synonyms DJ262D12.2, HSMRPS14, MRP-S14, S14mt
Description mitochondrial ribosomal protein S14
Transcript NM_022100   
Expression
Putative miRNA Targets on MRPS14
3'UTR of MRPS14
(miRNA target sites are highlighted)
>MRPS14|NM_022100|3'UTR
   1 ATGAGCTCCAGAACCTATTGAGCTTGCAGGGAAGCCAAGCTTGCAGTTCCAGCAAGCAAAGATTTTTTTTAATAGACCAA
  81 ACCCTAATCTCTACAGGGGCCCAGTACAGTTGTTTGGCCTACCTGATGCTATCTCTAAACTACTTTTAAAATGAAGACAT
 161 TTGGGTGTTTCATGTCAGTGAATTATCTTTTCTCTTGGACTTAACAAACATACTGTTCCCATACATAGTACAAAGAGTAG
 241 CATAATAAATATTTTCTGTGAATGTTTTTTATACCCTCCTTTTAAGTTTAATCTTTTAGTAACATATAGGGGTTTTTGTA
 321 TTAAGAGCATTATTTCATAAAATGCTATCTTATACATAATCCAACTAATTGACATGTAGCTCATGTATGGCAGTTTGTAA
 401 TCCTGGACTAGCTTTGCTGACCTGCAGAGCTCCCCTTAACTATTATTGTTAGATAAACAGATTGGATAGCAAGGCTGCTG
 481 TTCTGGATTATCTAATGCTCCACTTCTTCTTGTGATGGCTGAACAAAAGAACCACTAAGTGTTTTCTTGTCCATCCTTAA
 561 GGGACTTTAAAACAAATTATGCCTCTTTAAGTCCTTGAAAGTCTCCATCTAAAGAGGAAAAGTTTGTTGGAACAGTATAT
 641 ATTCCCTATTTTTATGTTTATTTAATCCATAACAGAAATGAGTAAGGGTAGCACAAAGTTCTCATTCAGTAACTCAACAG
 721 TGTGATCATCAGCCCAGTGATAAAAATATACATACTGAATGGAAGTACCTACTTAACATCAGGAAAATATTCCTGGAGAA
 801 CTTAATAAATCAGGAGGTGAGGGGTGAGATTTTTTTCTGCACACAGAGGGAACAAAAGCACAAAGAAGCAAAGGCACTCT
 881 GTAGCATCAGAGAACCACAGTCACTTCAGTAGATCAGAAATATGAAGCACAAGACAAGGCCCGTATTGTGGAGGATCTCA
 961 CAAATCATGTGAAGGAATTAAGACTGACATACCAGGTATTACAGAGTTTTAAGCACAGGAATGACATCATCAGTTTGTAA
1041 TACAGGTAAGTGACAGCTGTGTGGCAGATGGCCATGAGAGGAAAAAGCTACAGGCAAGACAACCAGTTAGGAGGATGTCT
1121 TAGTTGTTGAGGAAGATGAAGGCCTGAACTAACATTGTGGTATTAGTAGAGGAGAGAGGACAGATTTTTAAAGTTTTAGG
1201 AAAGAAAATTGGGCAAGACTTACAAGACTGATTATATCTAAGAGGTAAAGATGGTTCTCTGGGTTCCTGATAAAAGTGTC
1281 TAGATAGATGGTAGAGGGCAATTCCAAGAGGGCAACTCCAAGATAGAAAATTTGGAAAAAGAACAAATTTAGGGGAAACA
1361 GAAGATAAGCGAGTTCAGGTTCCAGTCATGCGGTGTTGGAGATGCCTGTGTCATCTGATGAAGACTAGTACGCAGCTGGA
1441 TAGCAGAGTCCGAAACTCAGGTGGAGGTGAAGTTATGAGGGAATTATCACAATCTAGTTTGGATTCATATTTCTTAAATA
1521 TGTATGACAACTTACCAACTGGAATGTTCTAGCTAATATCTCAACTTAGAATCCATCTCACTACCAATGGGCAAACACTT
1601 GTGTTCTAAAGTTACTTGCAAGTAGTTTATACTGCCAACTTGATATATATACATGCTATAGTTTGAACATTTTGTGTACT
1681 TCCAAAATTCACATTAAAATCTAATCCACAAAAAAAAAAAAAAAAA
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' acccgaaAGAUCAG-AGUCGAGa 5'
                 | |: || ||||| | 
Target 5' tcaacagTGTGATCATCAGCCCa 3'
714 - 736 115.00 -5.52
2
miRNA  3' acccgaAAGAUC------AGAGUCGAGa 5'
                ||||||      ||||| ||: 
Target 5' ggaatgTTCTAGCTAATATCTCAACTTa 3'
1541 - 1568 114.00 -10.20
3
miRNA  3' acccgaaaGAUCA-GAGUCGAga 5'
                  ||||| | |||||  
Target 5' gatgaagaCTAGTACGCAGCTgg 3'
1417 - 1439 110.00 -12.10
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30457394 9 COSMIC
COSN1414007 22 COSMIC
COSN30143139 35 COSMIC
COSN30154278 93 COSMIC
COSN31534470 123 COSMIC
COSN31598500 164 COSMIC
COSN31479755 171 COSMIC
COSN30129989 213 COSMIC
COSN31487262 219 COSMIC
COSN31569292 221 COSMIC
COSN31609261 249 COSMIC
COSN31481782 256 COSMIC
COSN31547942 340 COSMIC
COSN31516556 358 COSMIC
COSN30538380 417 COSMIC
COSN20090408 444 COSMIC
COSN20095601 446 COSMIC
COSN26356203 842 COSMIC
COSN30382410 892 COSMIC
COSN32083295 1023 COSMIC
COSN1414005 1086 COSMIC
COSN16167138 1129 COSMIC
COSN20787548 1176 COSMIC
COSN7185210 1385 COSMIC
COSN16366661 1495 COSMIC
COSN6009157 1659 COSMIC
COSN30391687 1665 COSMIC
rs16847706 598 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1236566723 4 dbSNP
rs201569223 5 dbSNP
rs757033224 8 dbSNP
rs1325409777 11 dbSNP
rs1438875458 14 dbSNP
rs777197099 15 dbSNP
rs201209223 18 dbSNP
rs754256677 21 dbSNP
rs1199859379 32 dbSNP
rs1379407781 34 dbSNP
rs766887314 37 dbSNP
rs760964289 45 dbSNP
rs1353224840 46 dbSNP
rs368671197 49 dbSNP
rs772487730 49 dbSNP
rs759901081 51 dbSNP
rs998264656 52 dbSNP
rs3850 61 dbSNP
rs1172333870 62 dbSNP
rs867472764 65 dbSNP
rs981852978 71 dbSNP
rs1390421151 73 dbSNP
rs1018224726 78 dbSNP
rs1007136313 84 dbSNP
rs571798056 89 dbSNP
rs551878350 98 dbSNP
rs1021038900 105 dbSNP
rs1053930540 107 dbSNP
rs958233460 108 dbSNP
rs115356343 109 dbSNP
rs902656741 118 dbSNP
rs1417535035 120 dbSNP
rs1210611841 122 dbSNP
rs562504684 125 dbSNP
rs1251393023 131 dbSNP
rs1046594246 132 dbSNP
rs1431483226 133 dbSNP
rs889098940 136 dbSNP
rs1052212413 141 dbSNP
rs997576511 145 dbSNP
rs549264196 149 dbSNP
rs529221385 151 dbSNP
rs897915777 156 dbSNP
rs1293721739 158 dbSNP
rs1036489435 159 dbSNP
rs1402539339 165 dbSNP
rs949150719 170 dbSNP
rs1282026254 171 dbSNP
rs1058741 172 dbSNP
rs1054791326 173 dbSNP
rs909747789 174 dbSNP
rs185719379 185 dbSNP
rs1222087014 187 dbSNP
rs909135746 187 dbSNP
rs1267456212 194 dbSNP
rs983336848 200 dbSNP
rs1222025255 202 dbSNP
rs1236278951 211 dbSNP
rs1489324187 213 dbSNP
rs749585486 220 dbSNP
rs1192096804 223 dbSNP
rs1419473683 228 dbSNP
rs1349448786 231 dbSNP
rs950633746 233 dbSNP
rs923118632 238 dbSNP
rs1410762907 258 dbSNP
rs17302346 262 dbSNP
rs141657779 273 dbSNP
rs982185800 276 dbSNP
rs746205995 284 dbSNP
rs1360553702 292 dbSNP
rs1401363378 292 dbSNP
rs1287019515 297 dbSNP
rs984627 299 dbSNP
rs1018275382 311 dbSNP
rs1414371020 320 dbSNP
rs540782935 325 dbSNP
rs1174342755 327 dbSNP
rs1451763727 329 dbSNP
rs1245456823 341 dbSNP
rs1006854825 345 dbSNP
rs181451752 347 dbSNP
rs1183144648 349 dbSNP
rs1214627826 373 dbSNP
rs1473733480 374 dbSNP
rs1483831806 375 dbSNP
rs1255097059 383 dbSNP
rs576229787 384 dbSNP
rs1032942610 385 dbSNP
rs1032576094 387 dbSNP
rs1442880560 389 dbSNP
rs556525027 397 dbSNP
rs147983480 406 dbSNP
rs116067602 414 dbSNP
rs1327883188 419 dbSNP
rs1268279918 432 dbSNP
rs1344091793 434 dbSNP
rs1030294311 435 dbSNP
rs1304534677 439 dbSNP
rs554423838 442 dbSNP
rs757093473 443 dbSNP
rs1013789364 446 dbSNP
rs1282766623 456 dbSNP
rs1310257470 460 dbSNP
rs1447790910 460 dbSNP
rs534207291 462 dbSNP
rs1356191232 465 dbSNP
rs1341554652 467 dbSNP
rs1222295797 469 dbSNP
rs1015005532 481 dbSNP
rs1006335560 483 dbSNP
rs1312881651 501 dbSNP
rs1433597331 502 dbSNP
rs1387991199 504 dbSNP
rs1160050630 505 dbSNP
rs1458994947 507 dbSNP
rs1179731898 509 dbSNP
rs1411921822 512 dbSNP
rs1441081460 519 dbSNP
rs1162389699 521 dbSNP
rs894897125 532 dbSNP
rs1406541895 539 dbSNP
rs1048708448 550 dbSNP
rs1178102058 552 dbSNP
rs1054845701 553 dbSNP
rs905105421 565 dbSNP
rs571635113 580 dbSNP
rs1378843910 581 dbSNP
rs74317897 590 dbSNP
rs1248075731 593 dbSNP
rs1210107839 594 dbSNP
rs16847706 598 dbSNP
rs913593851 601 dbSNP
rs987826335 609 dbSNP
rs936438885 611 dbSNP
rs925441349 622 dbSNP
rs1201975656 626 dbSNP
rs1231991587 626 dbSNP
rs569333132 629 dbSNP
rs12741561 632 dbSNP
rs1426607179 635 dbSNP
rs1480031019 644 dbSNP
rs12754912 646 dbSNP
rs1171337793 648 dbSNP
rs929233454 649 dbSNP
rs1408050233 650 dbSNP
rs953612834 653 dbSNP
rs12741553 660 dbSNP
rs1286391727 662 dbSNP
rs1350756711 669 dbSNP
rs1438692021 672 dbSNP
rs1030993541 681 dbSNP
rs1226799313 683 dbSNP
rs1344996912 696 dbSNP
rs923138976 704 dbSNP
rs1280700228 711 dbSNP
rs1337816159 713 dbSNP
rs975943950 715 dbSNP
rs964867976 733 dbSNP
rs12737197 741 dbSNP
rs12741401 750 dbSNP
rs1271832545 759 dbSNP
rs777277961 760 dbSNP
rs1321242157 763 dbSNP
rs12741397 767 dbSNP
rs1224257642 777 dbSNP
rs12741387 786 dbSNP
rs12741386 787 dbSNP
rs1266102201 790 dbSNP
rs376554326 798 dbSNP
rs12755758 813 dbSNP
rs12755757 814 dbSNP
rs758206594 815 dbSNP
rs752267182 817 dbSNP
rs1348287507 818 dbSNP
rs1474303020 825 dbSNP
rs1167174271 827 dbSNP
rs1414280028 828 dbSNP
rs764606677 836 dbSNP
rs887859748 837 dbSNP
rs1365008920 840 dbSNP
rs1034476731 843 dbSNP
rs1400728870 845 dbSNP
rs1300578355 846 dbSNP
rs1032290430 855 dbSNP
rs1325262711 858 dbSNP
rs549266604 871 dbSNP
rs529072500 881 dbSNP
rs966985055 882 dbSNP
rs1025606300 899 dbSNP
rs1166530658 900 dbSNP
rs1448774415 904 dbSNP
rs1390736061 905 dbSNP
rs1013760008 910 dbSNP
rs371275903 912 dbSNP
rs1216773313 913 dbSNP
rs141447109 914 dbSNP
rs1221840409 915 dbSNP
rs949321482 922 dbSNP
rs892103086 923 dbSNP
rs1292443155 931 dbSNP
rs1446268799 932 dbSNP
rs1161883196 940 dbSNP
rs1420381150 942 dbSNP
rs189807999 943 dbSNP
rs760661639 956 dbSNP
rs12741068 960 dbSNP
rs1005962675 963 dbSNP
rs936386605 968 dbSNP
rs1400585729 969 dbSNP
rs762322918 973 dbSNP
rs1047390329 976 dbSNP
rs1342603721 994 dbSNP
rs774851238 997 dbSNP
rs1450975325 1004 dbSNP
rs1342019903 1006 dbSNP
rs1312443549 1007 dbSNP
rs12062145 1015 dbSNP
rs1240423419 1017 dbSNP
rs1261907343 1021 dbSNP
rs932130351 1023 dbSNP
rs923489068 1024 dbSNP
rs1230626018 1033 dbSNP
rs767326513 1035 dbSNP
rs1040666576 1037 dbSNP
rs138464982 1040 dbSNP
rs369008639 1043 dbSNP
rs367698240 1046 dbSNP
rs1440491839 1047 dbSNP
rs1437423116 1052 dbSNP
rs910368370 1061 dbSNP
rs563553841 1063 dbSNP
rs376704515 1069 dbSNP
rs1305901675 1070 dbSNP
rs1453194817 1072 dbSNP
rs1173647208 1075 dbSNP
rs1409015261 1078 dbSNP
rs1468559041 1079 dbSNP
rs879661964 1080 dbSNP
rs1401494344 1082 dbSNP
rs563689313 1085 dbSNP
rs1446996331 1090 dbSNP
rs1308752154 1091 dbSNP
rs543799703 1098 dbSNP
rs145829491 1101 dbSNP
rs561801809 1111 dbSNP
rs1275368051 1119 dbSNP
rs1431433196 1125 dbSNP
rs978117573 1126 dbSNP
rs1191317015 1137 dbSNP
rs1458071703 1145 dbSNP
rs542887739 1162 dbSNP
rs1249201020 1163 dbSNP
rs140657937 1164 dbSNP
rs1418563296 1165 dbSNP
rs554189835 1166 dbSNP
rs1482939324 1167 dbSNP
rs1275867259 1169 dbSNP
rs969603286 1170 dbSNP
rs1176360283 1171 dbSNP
rs146833893 1173 dbSNP
rs1424734609 1174 dbSNP
rs1463899509 1178 dbSNP
rs1311000952 1181 dbSNP
rs754870054 1182 dbSNP
rs1393971527 1193 dbSNP
rs865836836 1193 dbSNP
rs1219913593 1195 dbSNP
rs578076888 1197 dbSNP
rs558223289 1200 dbSNP
rs185303434 1209 dbSNP
rs1286689328 1214 dbSNP
rs1346874182 1219 dbSNP
rs1033841986 1224 dbSNP
rs892385803 1225 dbSNP
rs1052341684 1227 dbSNP
rs1318307830 1231 dbSNP
rs1000933412 1234 dbSNP
rs903548296 1234 dbSNP
rs1050583726 1237 dbSNP
rs931760673 1238 dbSNP
rs1271075708 1241 dbSNP
rs1489888072 1247 dbSNP
rs1006016480 1250 dbSNP
rs887531907 1252 dbSNP
rs1168698710 1257 dbSNP
rs181708929 1262 dbSNP
rs940876141 1263 dbSNP
rs555812615 1271 dbSNP
rs1461129692 1276 dbSNP
rs1163863319 1284 dbSNP
rs751389074 1285 dbSNP
rs1309664406 1289 dbSNP
rs1366861186 1290 dbSNP
rs1402612567 1291 dbSNP
rs1026449025 1298 dbSNP
rs529227563 1301 dbSNP
rs1302456458 1304 dbSNP
rs1464463212 1308 dbSNP
rs565005930 1313 dbSNP
rs769805366 1318 dbSNP
rs1293102265 1320 dbSNP
rs952129288 1322 dbSNP
rs745940097 1339 dbSNP
rs927329892 1344 dbSNP
rs901483122 1345 dbSNP
rs1221934209 1347 dbSNP
rs1182161426 1350 dbSNP
rs1040316838 1354 dbSNP
rs1487105142 1356 dbSNP
rs1180987264 1363 dbSNP
rs1185311339 1363 dbSNP
rs781451557 1364 dbSNP
rs1424801190 1365 dbSNP
rs943275882 1370 dbSNP
rs1024730133 1378 dbSNP
rs888982302 1383 dbSNP
rs757469357 1386 dbSNP
rs1013363901 1388 dbSNP
rs189399109 1391 dbSNP
rs1453181983 1392 dbSNP
rs566617733 1393 dbSNP
rs1482537261 1396 dbSNP
rs1245540859 1397 dbSNP
rs1237445175 1402 dbSNP
rs546500884 1408 dbSNP
rs1210826528 1413 dbSNP
rs1260705774 1416 dbSNP
rs1483775244 1424 dbSNP
rs1185882592 1428 dbSNP
rs184567372 1431 dbSNP
rs1266379679 1432 dbSNP
rs945414082 1445 dbSNP
rs1442331633 1446 dbSNP
rs80331520 1451 dbSNP
rs992446661 1452 dbSNP
rs1330135950 1458 dbSNP
rs959611250 1471 dbSNP
rs1156808483 1476 dbSNP
rs752534293 1480 dbSNP
rs34838911 1484 dbSNP
rs1394103534 1491 dbSNP
rs901587150 1492 dbSNP
rs550190540 1493 dbSNP
rs1403666856 1496 dbSNP
rs1452139791 1502 dbSNP
rs191307922 1507 dbSNP
rs940822401 1508 dbSNP
rs1450193745 1514 dbSNP
rs1385798230 1516 dbSNP
rs1306908910 1518 dbSNP
rs984967427 1523 dbSNP
rs1324812756 1524 dbSNP
rs1157828948 1530 dbSNP
rs908071877 1538 dbSNP
rs1261602139 1540 dbSNP
rs1049750155 1545 dbSNP
rs952282691 1549 dbSNP
rs1233145919 1551 dbSNP
rs1174908816 1556 dbSNP
rs1481328090 1556 dbSNP
rs1406629712 1558 dbSNP
rs1413750456 1559 dbSNP
rs1178540159 1562 dbSNP
rs149801718 1565 dbSNP
rs927247549 1568 dbSNP
rs1329777120 1569 dbSNP
rs1356563164 1575 dbSNP
rs776589717 1577 dbSNP
rs971837552 1582 dbSNP
rs1198688207 1586 dbSNP
rs1225844800 1595 dbSNP
rs1182938360 1601 dbSNP
rs988877906 1608 dbSNP
rs1275562575 1615 dbSNP
rs1439138490 1628 dbSNP
rs956524285 1632 dbSNP
rs965770774 1638 dbSNP
rs1019018079 1639 dbSNP
rs1202036776 1640 dbSNP
rs1250379802 1642 dbSNP
rs1490382486 1643 dbSNP
rs375410934 1646 dbSNP
rs540875759 1649 dbSNP
rs541880383 1652 dbSNP
rs967992491 1658 dbSNP
rs889034384 1659 dbSNP
rs1029361141 1662 dbSNP
rs545206633 1663 dbSNP
rs529466614 1664 dbSNP
rs560627676 1669 dbSNP
rs1301818697 1675 dbSNP
rs1345363745 1676 dbSNP
rs1432131128 1685 dbSNP
rs1272242701 1688 dbSNP
rs1262713945 1696 dbSNP
rs1337893773 1696 dbSNP
rs764189230 1700 dbSNP
rs1054265939 1702 dbSNP
rs1273533873 1712 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' acccgaaagaUCAGAGUCGAGa 5'
                    | ||||||||| 
Target 5' -------cacAAUCUCAGCUCa 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]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions Prostate Tissue
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 SRX1760628. RNA binding protein: AGO2. Condition:AGO-CLIP-LAPC4_B PAR-CLIP data was present in SRX1760630. RNA binding protein: AGO2. Condition:AGO-CLIP-22RV1_A ...

- Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al., 2016, Neoplasia (New York, N.Y.).

Article - Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al.
- Neoplasia (New York, N.Y.), 2016
MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.
LinkOut: [PMID: 27292025]
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 ENST00000476371.1 | 3UTR | CACAAUCUCAGCUCACUGCAACCUCUGCCUCCCG
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
Click to see details
118 hsa-miR-3160-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT066658 DYRK2 dual specificity tyrosine phosphorylation regulated kinase 2 2 2
MIRT075318 SF3B3 splicing factor 3b subunit 3 2 4
MIRT077083 EIF1 eukaryotic translation initiation factor 1 2 2
MIRT100381 HSPA1B heat shock protein family A (Hsp70) member 1B 2 6
MIRT135259 TMBIM6 transmembrane BAX inhibitor motif containing 6 2 4
MIRT184913 ZNF268 zinc finger protein 268 2 2
MIRT218862 CDKN1A cyclin dependent kinase inhibitor 1A 2 2
MIRT446580 FPR2 formyl peptide receptor 2 2 2
MIRT448834 FGD4 FYVE, RhoGEF and PH domain containing 4 2 2
MIRT449455 RNF13 ring finger protein 13 2 2
MIRT452284 CARD8 caspase recruitment domain family member 8 2 2
MIRT452628 FAM162A family with sequence similarity 162 member A 2 2
MIRT453454 GLG1 golgi glycoprotein 1 2 2
MIRT454188 AP1S3 adaptor related protein complex 1 sigma 3 subunit 2 6
MIRT454434 GTF2F1 general transcription factor IIF subunit 1 2 2
MIRT454575 NT5DC3 5'-nucleotidase domain containing 3 2 2
MIRT455555 TRAF1 TNF receptor associated factor 1 2 6
MIRT455841 MPL MPL proto-oncogene, thrombopoietin receptor 2 6
MIRT455969 BCAS4 breast carcinoma amplified sequence 4 2 4
MIRT456805 SIGLEC14 sialic acid binding Ig like lectin 14 2 2
MIRT457320 DUSP19 dual specificity phosphatase 19 2 2
MIRT457366 POFUT2 protein O-fucosyltransferase 2 2 2
MIRT457684 ZNF587 zinc finger protein 587 2 2
MIRT458158 LYRM4 LYR motif containing 4 2 6
MIRT458641 SGPP2 sphingosine-1-phosphate phosphatase 2 2 2
MIRT459134 FADS6 fatty acid desaturase 6 2 2
MIRT459153 NARF nuclear prelamin A recognition factor 2 4
MIRT460460 NOM1 nucleolar protein with MIF4G domain 1 2 4
MIRT460974 STK17B serine/threonine kinase 17b 2 2
MIRT461439 ACSBG1 acyl-CoA synthetase bubblegum family member 1 2 2
MIRT461507 NEDD4L neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase 2 2
MIRT462490 GSR glutathione-disulfide reductase 2 2
MIRT462638 PHF5A PHD finger protein 5A 2 2
MIRT463279 ZFX zinc finger protein, X-linked 2 2
MIRT463360 ZFAND4 zinc finger AN1-type containing 4 2 2
MIRT465777 TMOD3 tropomodulin 3 2 2
MIRT466143 TMEM120B transmembrane protein 120B 2 2
MIRT468401 SETD3 SET domain containing 3 2 2
MIRT468998 RNPS1 RNA binding protein with serine rich domain 1 2 2
MIRT471574 PARD6B par-6 family cell polarity regulator beta 2 2
MIRT472108 NME2 NME/NM23 nucleoside diphosphate kinase 2 2 2
MIRT472125 NME1-NME2 NME1-NME2 readthrough 2 2
MIRT473020 MRPS14 mitochondrial ribosomal protein S14 2 2
MIRT473083 MORN4 MORN repeat containing 4 2 2
MIRT475598 HMGB2 high mobility group box 2 2 4
MIRT475937 GXYLT2 glucoside xylosyltransferase 2 2 8
MIRT476117 GPR157 G protein-coupled receptor 157 2 2
MIRT476406 GDE1 glycerophosphodiester phosphodiesterase 1 2 2
MIRT478003 DNAL1 dynein axonemal light chain 1 2 2
MIRT487969 IQSEC2 IQ motif and Sec7 domain 2 2 2
MIRT489418 TUBB2A tubulin beta 2A class IIa 2 2
MIRT491522 IL10RA interleukin 10 receptor subunit alpha 2 2
MIRT492673 PLEC plectin 2 2
MIRT493545 ICOSLG inducible T-cell costimulator ligand 2 2
MIRT513085 USP9X ubiquitin specific peptidase 9, X-linked 2 2
MIRT514009 CECR2 CECR2, histone acetyl-lysine reader 2 4
MIRT516683 ZNF860 zinc finger protein 860 2 2
MIRT518392 ZNF250 zinc finger protein 250 2 2
MIRT522683 LUZP1 leucine zipper protein 1 2 6
MIRT524488 CEP97 centrosomal protein 97 2 2
MIRT527457 CLEC12B C-type lectin domain family 12 member B 2 2
MIRT527705 IL17REL interleukin 17 receptor E like 2 2
MIRT531647 C19orf52 translocase of inner mitochondrial membrane 29 2 2
MIRT532381 UMPS uridine monophosphate synthetase 2 2
MIRT532588 MTHFD1 methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1 2 2
MIRT533555 TPM4 tropomyosin 4 2 2
MIRT548371 ENTPD5 ectonucleoside triphosphate diphosphohydrolase 5 2 4
MIRT550250 PVR poliovirus receptor 2 2
MIRT552555 ZFP36L2 ZFP36 ring finger protein like 2 2 4
MIRT554113 SMARCE1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 2 2
MIRT554131 SMARCA5 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 2 2
MIRT561344 ZBTB18 zinc finger and BTB domain containing 18 2 2
MIRT561638 RUNX3 runt related transcription factor 3 2 2
MIRT566497 PBX2P1 PBX homeobox 2 pseudogene 1 2 2
MIRT570583 OTUD7B OTU deubiquitinase 7B 2 2
MIRT572731 MCTS1 MCTS1, re-initiation and release factor 2 2
MIRT574041 PEX26 peroxisomal biogenesis factor 26 2 2
MIRT575231 Fut1 fucosyltransferase 1 2 2
MIRT606811 BICD2 BICD cargo adaptor 2 2 2
MIRT621016 CLSTN3 calsyntenin 3 2 2
MIRT637852 PDCL3 phosducin like 3 2 2
MIRT640477 ZNF557 zinc finger protein 557 2 2
MIRT642827 LINC00346 long intergenic non-protein coding RNA 346 2 2
MIRT643887 IMP4 IMP4, U3 small nucleolar ribonucleoprotein 2 2
MIRT664874 PCNXL2 pecanex homolog 2 2 2
MIRT680528 PRIM2 DNA primase subunit 2 2 2
MIRT680648 KIAA1456 KIAA1456 2 2
MIRT680807 ZNF578 zinc finger protein 578 2 2
MIRT680921 STX2 syntaxin 2 2 2
MIRT681112 CEP57L1 centrosomal protein 57 like 1 2 2
MIRT681147 INTS7 integrator complex subunit 7 2 2
MIRT681966 TFCP2 transcription factor CP2 2 2
MIRT684316 GTF3C4 general transcription factor IIIC subunit 4 2 2
MIRT684906 GSG2 histone H3 associated protein kinase 2 2
MIRT685499 MED16 mediator complex subunit 16 2 2
MIRT685929 MOCS3 molybdenum cofactor synthesis 3 2 2
MIRT686875 SLC25A32 solute carrier family 25 member 32 2 2
MIRT688204 FNIP1 folliculin interacting protein 1 2 2
MIRT688791 CCNB1 cyclin B1 2 2
MIRT689227 RPS19 ribosomal protein S19 2 2
MIRT690470 ZNF33A zinc finger protein 33A 2 2
MIRT691982 PLCXD1 phosphatidylinositol specific phospholipase C X domain containing 1 2 2
MIRT694006 PPIL4 peptidylprolyl isomerase like 4 2 2
MIRT694529 TRIM72 tripartite motif containing 72 2 2
MIRT695420 ADH5 alcohol dehydrogenase 5 (class III), chi polypeptide 2 2
MIRT695784 HSD17B12 hydroxysteroid 17-beta dehydrogenase 12 2 2
MIRT697799 UBXN2A UBX domain protein 2A 2 2
MIRT698275 TMEM2 transmembrane protein 2 2 2
MIRT698317 TMEM136 transmembrane protein 136 2 2
MIRT699971 RREB1 ras responsive element binding protein 1 2 2
MIRT700717 PNO1 partner of NOB1 homolog 2 2
MIRT701721 MTMR12 myotubularin related protein 12 2 2
MIRT701879 MPLKIP M-phase specific PLK1 interacting protein 2 2
MIRT702959 HIF1A hypoxia inducible factor 1 alpha subunit 2 2
MIRT706178 ZNF716 zinc finger protein 716 2 2
MIRT706463 SPRED1 sprouty related EVH1 domain containing 1 2 2
MIRT718154 TTC33 tetratricopeptide repeat domain 33 2 2
MIRT718711 ANKRD18A ankyrin repeat domain 18A 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3160-3p Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-3160-3p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-3160-3p Osimertinib 71496458 NSC779217 approved resistant cell line (HCC827)
hsa-miR-3160-3p Tripterygium wilfordii Hook F resistant tissue
hsa-miR-3160-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3160-3p Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)

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