miRTarBase - #MIRT484229


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pre-miRNA Information
pre-miRNA hsa-mir-3942   
Genomic Coordinates chr15: 35372256 - 35372364
Description Homo sapiens miR-3942 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3942-3p
Sequence 65| UUUCAGAUAACAGUAUUACAU |85
Evidence Experimental
Experiments Illumina
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 5 15 - 35372296 29233923 MiREDiBase
A-to-I 10 15 - 35372291 23291724, 29233923 MiREDiBase
A-to-I 18 15 - 35372283 23291724, 29233923 MiREDiBase
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN1674243 19 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1043666670 6 dbSNP
rs1264147291 18 dbSNP
rs1223363654 20 dbSNP
Putative Targets

Gene Information
Gene Symbol CLDN1   
Synonyms CLD1, ILVASC, SEMP1
Description claudin 1
Transcript NM_021101   
Expression
Putative miRNA Targets on CLDN1
3'UTR of CLDN1
(miRNA target sites are highlighted)		 
>CLDN1|NM_021101|3'UTR
   1 CACAGAGGCAAAAGGAGAAAATCATGTTGAAACAAACCGAAAATGGACATTGAGATACTATCATTAACATTAGGACCTTA
  81 GAATTTTGGGTATTGTAATCTGAAGTATGGTATTACAAAACAAACAAACAAACAAAAAACCCATGTGTTAAAATACTCAG
 161 TGCTAAACATGGCTTAATCTTATTTTATCTTCTTTCCTCAATATAGGAGGGAAGATTTTTCCATTTGTATTACTGCTTCC
 241 CATTGAGTAATCATACTCAACTGGGGGAAGGGGTGCTCCTTAAATATATATAGATATGTATATATACATGTTTTTCTATT
 321 AAAAATAGACAGTAAAATACTATTCTCATTATGTTGATACTAGCATACTTAAAATATCTCTAAAATAGGTAAATGTATTT
 401 AATTCCATATTGATGAAGATGTTTATTGGTATATTTTCTTTTTCGTCTATATATACATATGTAACAGTCAAATATCATTT
 481 ACTCTTCTTCATTAGCTTTGGGTGCCTTTGCCACAAGACCTAGCCTAATTTACCAAGGATGAATTCTTTCAATTCTTCAT
 561 GCGTGCCCTTTTCATATACTTATTTTATTTTTTACCATAATCTTATAGCACTTGCATCGTTATTAAGCCCTTATTTGTTT
 641 TGTGTTTCATTGGTCTCTATCTCCTGAATCTAACACATTTCATAGCCTACATTTTAGTTTCTAAAGCCAAGAAGAATTTA
 721 TTACAAATCAGAACTTTGGAGGCAAATCTTTCTGCATGACCAAAGTGATAAATTCCTGTTGACCTTCCCACACAATCCCT
 801 GTACTCTGACCCATAGCACTCTTGTTTGCTTTGAAAATATTTGTCCAATTGAGTAGCTGCATGCTGTTCCCCCAGGTGTT
 881 GTAACACAACTTTATTGATTGAATTTTTAAGCTACTTATTCATAGTTTTATATCCCCCTAAACTACCTTTTTGTTCCCCA
 961 TTCCTTAATTGTATTGTTTTCCCAAGTGTAATTATCATGCGTTTTATATCTTCCTAATAAGGTGTGGTCTGTTTGTCTGA
1041 ACAAAGTGCTAGACTTTCTGGAGTGATAATCTGGTGACAAATATTCTCTCTGTAGCTGTAAGCAAGTCACTTAATCTTTC
1121 TACCTCTTTTTTCTATCTGCCAAATTGAGATAATGATACTTAACCAGTTAGAAGAGGTAGTGTGAATATTAATTAGTTTA
1201 TATTACTCTCATTCTTTGAACATGAACTATGCCTATGTAGTGTCTTTATTTGCTCAGCTGGCTGAGACACTGAAGAAGTC
1281 ACTGAACAAAACCTACACACGTACCTTCATGTGATTCACTGCCTTCCTCTCTCTACCAGTCTATTTCCACTGAACAAAAC
1361 CTACACACATACCTTCATGTGGTTCAGTGCCTTCCTCTCTCTACCAGTCTATTTCCACTGAACAAAACCTACGCACATAC
1441 CTTCATGTGGCTCAGTGCCTTCCTCTCTCTACCAGTCTATTTCCATTCTTTCAGCTGTGTCTGACATGTTTGTGCTCTGT
1521 TCCATTTTAACAACTGCTCTTACTTTTCCAGTCTGTACAGAATGCTATTTCACTTGAGCAAGATGATGTAATGGAAAGGG
1601 TGTTGGCATTGGTGTCTGGAGACCTGGATTTGAGTCTTGGTGCTATCAATCACCGTCTGTGTTTGAGCAAGGCATTTGGC
1681 TGCTGTAAGCTTATTGCTTCATCTGTAAGCGGTGGTTTGTAATTCCTGATCTTCCCACCTCACAGTGATGTTGTGGGGAT
1761 CCAGTGAGATAGAATACATGTAAGTGTGGTTTTGTAATTTAAAAAGTGCTATACTAAGGGAAAGAATTGAGGAATTAACT
1841 GCATACGTTTTGGTGTTGCTTTTCAAATGTTTGAAAACAAAAAAAATGTTAAGAAATGGGTTTCTTGCCTTAACCAGTCT
1921 CTCAAGTGATGAGACAGTGAAGTAAAATTGAGTGCACTAAACAAATAAGATTCTGAGGAAGTCTTATCTTCTGCAGTGAG
2001 TATGGCCCGATGCTTTCTGTGGCTAAACAGATGTAATGGGAAGAAATAAAAGCCTACGTGTTGGTAAATCCAACAGCAAG
2081 GGAGATTTTTGAATCATAATAACTCATAAGGTGCTATCTGTTCAGTGATGCCCTCAGAGCTCTTGCTGTTAGCTGGCAGC
2161 TGACGCTGCTAGGATAGTTAGTTTGGAAATGGTACTTCATAATAAACTACACAAGGAAAGTCAGCCACTGTGTCTTATGA
2241 GGAATTGGACCTAATAAATTTTAGTGTGCCTTCCAAACCTGAGAATATATGCTTTTGGAAGTTAAAATTTAAATGGCTTT
2321 TGCCACATACATAGATCTTCATGATGTGTGAGTGTAATTCCATGTGGATATCAGTTACCAAACATTACAAAAAAATTTTA
2401 TGGCCCAAAATGACCAACGAAATTGTTACAATAGAATTTATCCAATTTTGATCTTTTTATATTCTTCTACCACACCTGGA
2481 AACAGACCAATAGACATTTTGGGGTTTTATAATAGGAATTTGTATAAAGCATTACTCTTTTTCAATAAATTGTTTTTTAA
2561 TTTAAAAAAAGGATTA
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' uacaUUAUGACAAUAGACUUu 5'
              ::||:||| ||||||| 
Target 5' tttgGGTATTGTAATCTGAAg 3'
 85 - 105 165.00 -14.80
2 
miRNA  3' uaCAUUAUGAC-AAUAGACUUu 5'
            ||::| ||| ||:|||||| 
Target 5' gtGTGGT-CTGTTTGTCTGAAc 3'
 1022 - 1042 150.00 -15.60
3 
miRNA  3' uaCAUU---AUGAC-AA-UAGACUUu 5'
            ||||   ||:|| || ||||| | 
Target 5' ctGTAAGCTTATTGCTTCATCTGTAa 3'
 1683 - 1708 131.00 -7.22
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
1183502 102 ClinVar
COSN30458177 14 COSMIC
COSN30523128 15 COSMIC
COSN30465408 23 COSMIC
COSN14053778 39 COSMIC
COSN30149673 46 COSMIC
COSN30535017 51 COSMIC
COSN30157951 64 COSMIC
COSN20692288 84 COSMIC
COSN30477824 89 COSMIC
COSN30482014 90 COSMIC
COSN18728150 102 COSMIC
COSN30464751 110 COSMIC
COSN30502673 128 COSMIC
COSN31581090 131 COSMIC
COSN31574034 153 COSMIC
COSN31581945 206 COSMIC
COSN22712743 283 COSMIC
COSN30059320 346 COSMIC
COSN32057649 466 COSMIC
COSN29289755 547 COSMIC
COSN6759040 640 COSMIC
COSN7841710 833 COSMIC
COSN217000 943 COSMIC
COSN8488893 1103 COSMIC
COSN31529183 1131 COSMIC
COSN28676341 1173 COSMIC
COSN31609702 1354 COSMIC
COSN28646655 1423 COSMIC
COSN8488892 1472 COSMIC
COSN31594044 1493 COSMIC
COSN26555023 1543 COSMIC
COSN31550207 1564 COSMIC
COSN6759039 1775 COSMIC
COSN24928505 2166 COSMIC
COSN1937876 2202 COSMIC
COSN9717246 2289 COSMIC
COSN17181981 2365 COSMIC
COSN22373769 2426 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs768210136 3 dbSNP
rs1428021005 4 dbSNP
rs762573398 4 dbSNP
rs1431490740 5 dbSNP
rs188286992 7 dbSNP
rs779794586 9 dbSNP
rs1025986404 10 dbSNP
rs187348147 11 dbSNP
rs867085422 13 dbSNP
rs1283653368 15 dbSNP
rs750042291 19 dbSNP
rs779158499 23 dbSNP
rs1344102568 26 dbSNP
rs754463416 37 dbSNP
rs756313619 38 dbSNP
rs752689978 39 dbSNP
rs1484916726 43 dbSNP
rs1239321827 46 dbSNP
rs1204499468 48 dbSNP
rs767597561 50 dbSNP
rs569479829 58 dbSNP
rs1487574469 59 dbSNP
rs1046299923 60 dbSNP
rs1436470959 61 dbSNP
rs879036750 67 dbSNP
rs1013196797 68 dbSNP
rs894721788 72 dbSNP
rs1393270320 78 dbSNP
rs1420604531 89 dbSNP
rs757057660 90 dbSNP
rs3172404 102 dbSNP
rs927246180 108 dbSNP
rs3172403 110 dbSNP
rs764055541 112 dbSNP
rs963935269 114 dbSNP
rs1330486625 115 dbSNP
rs935946324 133 dbSNP
rs1419169610 137 dbSNP
rs1281124732 139 dbSNP
rs1239025198 140 dbSNP
rs1350935437 140 dbSNP
rs924695882 140 dbSNP
rs1016540628 160 dbSNP
rs1360912996 163 dbSNP
rs1222624877 169 dbSNP
rs1268585735 179 dbSNP
rs1175148153 197 dbSNP
rs1482248470 198 dbSNP
rs1235030441 201 dbSNP
rs983618275 204 dbSNP
rs950895964 219 dbSNP
rs934054048 229 dbSNP
rs1030512767 231 dbSNP
rs1163917844 233 dbSNP
rs923159836 235 dbSNP
rs1403597156 246 dbSNP
rs976314624 250 dbSNP
rs997231047 251 dbSNP
rs1043747 261 dbSNP
rs1017660910 262 dbSNP
rs910431961 271 dbSNP
rs1245998446 280 dbSNP
rs1232548346 286 dbSNP
rs1317595962 289 dbSNP
rs1356255054 293 dbSNP
rs544541711 295 dbSNP
rs1208623535 300 dbSNP
rs1309363432 308 dbSNP
rs1275529018 309 dbSNP
rs1458459843 314 dbSNP
rs1000567677 319 dbSNP
rs984430624 323 dbSNP
rs1236518463 331 dbSNP
rs951687352 333 dbSNP
rs1188322758 337 dbSNP
rs1368006107 338 dbSNP
rs530539535 339 dbSNP
rs1350145995 349 dbSNP
rs1169525630 353 dbSNP
rs1400978150 354 dbSNP
rs903749590 358 dbSNP
rs993284435 368 dbSNP
rs1329060307 371 dbSNP
rs1313257894 374 dbSNP
rs1396317729 380 dbSNP
rs55724972 389 dbSNP
rs1009346138 394 dbSNP
rs542885479 407 dbSNP
rs766453486 416 dbSNP
rs1056229854 420 dbSNP
rs1453807229 428 dbSNP
rs1256629679 430 dbSNP
rs140567409 431 dbSNP
rs1201291865 437 dbSNP
rs1365051715 438 dbSNP
rs1255761429 440 dbSNP
rs1156372733 444 dbSNP
rs183996446 445 dbSNP
rs35558331 448 dbSNP
rs9842576 448 dbSNP
rs9825098 449 dbSNP
rs200685867 450 dbSNP
rs386669503 450 dbSNP
rs1486865543 454 dbSNP
rs1168267891 457 dbSNP
rs576923171 460 dbSNP
rs1200410029 461 dbSNP
rs1466213090 464 dbSNP
rs9825088 466 dbSNP
rs903159020 475 dbSNP
rs1042100138 489 dbSNP
rs934126933 491 dbSNP
rs55945457 502 dbSNP
rs950947770 505 dbSNP
rs1328744739 510 dbSNP
rs1294154809 526 dbSNP
rs1234837794 544 dbSNP
rs567992824 547 dbSNP
rs1343153647 555 dbSNP
rs923412514 562 dbSNP
rs976262715 563 dbSNP
rs964805596 565 dbSNP
rs1387093606 567 dbSNP
rs1191482671 568 dbSNP
rs1270992317 579 dbSNP
rs1433518511 583 dbSNP
rs73056495 586 dbSNP
rs1000935262 596 dbSNP
rs535449802 597 dbSNP
rs760627434 598 dbSNP
rs1158686898 605 dbSNP
rs1166651017 606 dbSNP
rs1024434247 609 dbSNP
rs1370365302 613 dbSNP
rs775497434 616 dbSNP
rs991677972 618 dbSNP
rs573986269 619 dbSNP
rs1187335735 626 dbSNP
rs1286798967 627 dbSNP
rs146819132 629 dbSNP
rs896425596 630 dbSNP
rs1264552125 635 dbSNP
rs1267076642 636 dbSNP
rs1488775772 638 dbSNP
rs1190400772 640 dbSNP
rs1265092365 643 dbSNP
rs769145693 650 dbSNP
rs546735284 653 dbSNP
rs1206841626 658 dbSNP
rs533586709 662 dbSNP
rs1379331718 666 dbSNP
rs1417245082 671 dbSNP
rs1464506849 675 dbSNP
rs1352109152 676 dbSNP
rs1458925296 683 dbSNP
rs1056196455 690 dbSNP
rs1033278038 691 dbSNP
rs1365993050 705 dbSNP
rs749814941 714 dbSNP
rs780769636 732 dbSNP
rs755668498 733 dbSNP
rs865960266 734 dbSNP
rs1000481420 739 dbSNP
rs903430312 740 dbSNP
rs557383916 742 dbSNP
rs1237981239 747 dbSNP
rs1315013113 757 dbSNP
rs998556618 760 dbSNP
rs191911854 762 dbSNP
rs531266099 764 dbSNP
rs901266659 769 dbSNP
rs1263631536 787 dbSNP
rs1458893495 788 dbSNP
rs1199040520 790 dbSNP
rs1354566245 795 dbSNP
rs1040165029 796 dbSNP
rs1183090465 800 dbSNP
rs1413940198 805 dbSNP
rs1424883763 810 dbSNP
rs537588696 814 dbSNP
rs1348679950 820 dbSNP
rs1344601886 824 dbSNP
rs562359831 827 dbSNP
rs1399824296 837 dbSNP
rs1444935273 843 dbSNP
rs1328111172 844 dbSNP
rs942117392 846 dbSNP
rs888972581 847 dbSNP
rs1295332372 848 dbSNP
rs1319927924 849 dbSNP
rs1433624314 859 dbSNP
rs909173639 860 dbSNP
rs1257260630 861 dbSNP
rs1456149362 862 dbSNP
rs547587328 866 dbSNP
rs1048867859 871 dbSNP
rs1047780804 875 dbSNP
rs930595627 876 dbSNP
rs80187925 877 dbSNP
rs1179614761 879 dbSNP
rs923548186 895 dbSNP
rs1327391338 896 dbSNP
rs976639063 899 dbSNP
rs1171830383 905 dbSNP
rs971758486 909 dbSNP
rs964944430 913 dbSNP
rs1403216274 915 dbSNP
rs1360002043 916 dbSNP
rs1447328089 921 dbSNP
rs1301222341 922 dbSNP
rs949716104 923 dbSNP
rs1400609669 925 dbSNP
rs1277318434 934 dbSNP
rs1315769785 935 dbSNP
rs1220743340 940 dbSNP
rs917017288 946 dbSNP
rs528044643 948 dbSNP
rs780870918 949 dbSNP
rs1207384165 956 dbSNP
rs991211876 960 dbSNP
rs958423594 967 dbSNP
rs1195100757 969 dbSNP
rs1263111897 973 dbSNP
rs1163028685 986 dbSNP
rs559409931 987 dbSNP
rs1392504021 1000 dbSNP
rs756892944 1001 dbSNP
rs1020553308 1005 dbSNP
rs967660751 1006 dbSNP
rs1362600210 1007 dbSNP
rs1400703967 1008 dbSNP
rs987778952 1014 dbSNP
rs1297433785 1021 dbSNP
rs1338375942 1022 dbSNP
rs1438285547 1031 dbSNP
rs1275271997 1039 dbSNP
rs1366427854 1042 dbSNP
rs1217183285 1045 dbSNP
rs1287520185 1047 dbSNP
rs1353723862 1055 dbSNP
rs960598930 1058 dbSNP
rs1445825488 1063 dbSNP
rs1201423914 1068 dbSNP
rs1247726235 1070 dbSNP
rs1477815019 1071 dbSNP
rs545547199 1083 dbSNP
rs576989981 1091 dbSNP
rs1382406517 1095 dbSNP
rs1253677236 1096 dbSNP
rs1420341393 1096 dbSNP
rs1382662837 1106 dbSNP
rs1020923618 1115 dbSNP
rs1323960357 1115 dbSNP
rs1349142804 1116 dbSNP
rs1450074825 1123 dbSNP
rs759103047 1126 dbSNP
rs751322968 1127 dbSNP
rs904991617 1131 dbSNP
rs1196100194 1137 dbSNP
rs1341215905 1139 dbSNP
rs1272334048 1140 dbSNP
rs1227602177 1141 dbSNP
rs1306508045 1145 dbSNP
rs1017182976 1147 dbSNP
rs1349158695 1148 dbSNP
rs373667236 1156 dbSNP
rs563365443 1158 dbSNP
rs1018258540 1165 dbSNP
rs17500920 1173 dbSNP
rs1212242623 1174 dbSNP
rs1240206360 1178 dbSNP
rs1330090831 1180 dbSNP
rs888523041 1191 dbSNP
rs1048921073 1194 dbSNP
rs1362198693 1196 dbSNP
rs1473727148 1208 dbSNP
rs1060679 1210 dbSNP
rs1389968170 1218 dbSNP
rs897748287 1223 dbSNP
rs1167160295 1224 dbSNP
rs554441770 1230 dbSNP
rs949763598 1235 dbSNP
rs535461690 1238 dbSNP
rs902095646 1240 dbSNP
rs916922738 1251 dbSNP
rs1040662036 1254 dbSNP
rs1244889542 1271 dbSNP
rs991148061 1274 dbSNP
rs1356286152 1295 dbSNP
rs752627313 1300 dbSNP
rs910679190 1304 dbSNP
rs1458379112 1314 dbSNP
rs1198313710 1317 dbSNP
rs1248696684 1319 dbSNP
rs1246278373 1323 dbSNP
rs141031294 1325 dbSNP
rs1367801517 1327 dbSNP
rs553451964 1335 dbSNP
rs937114841 1335 dbSNP
rs541748212 1336 dbSNP
rs539575032 1340 dbSNP
rs570907298 1343 dbSNP
rs1172552176 1352 dbSNP
rs374835236 1361 dbSNP
rs1464920969 1363 dbSNP
rs946440631 1365 dbSNP
rs531676990 1372 dbSNP
rs1396056054 1377 dbSNP
rs1332983370 1378 dbSNP
rs1355346760 1382 dbSNP
rs913682386 1383 dbSNP
rs1280473170 1387 dbSNP
rs1348488488 1390 dbSNP
rs1282401899 1394 dbSNP
rs1216910438 1396 dbSNP
rs868767231 1409 dbSNP
rs1343717926 1410 dbSNP
rs1249791099 1417 dbSNP
rs1060680 1423 dbSNP
rs761824021 1428 dbSNP
rs1348282568 1429 dbSNP
rs187505682 1432 dbSNP
rs1035107033 1433 dbSNP
rs73056492 1434 dbSNP
rs548858468 1441 dbSNP
rs913504666 1446 dbSNP
rs1378981002 1447 dbSNP
rs1466266498 1451 dbSNP
rs528104875 1459 dbSNP
rs1171478966 1464 dbSNP
rs1373150176 1465 dbSNP
rs750500005 1469 dbSNP
rs969729195 1474 dbSNP
rs1300511271 1482 dbSNP
rs112003034 1484 dbSNP
rs965646029 1496 dbSNP
rs552129283 1499 dbSNP
rs771444714 1501 dbSNP
rs1159269098 1507 dbSNP
rs1018264010 1512 dbSNP
rs115942418 1522 dbSNP
rs867722426 1523 dbSNP
rs1026441623 1524 dbSNP
rs993487954 1531 dbSNP
rs1181118305 1536 dbSNP
rs994691969 1539 dbSNP
rs796319336 1548 dbSNP
rs563037223 1549 dbSNP
rs543263047 1553 dbSNP
rs1014614374 1554 dbSNP
rs1440953588 1565 dbSNP
rs1207967349 1576 dbSNP
rs1158780844 1583 dbSNP
rs1361703415 1588 dbSNP
rs1453762257 1598 dbSNP
rs1287475779 1606 dbSNP
rs1393256761 1607 dbSNP
rs9290928 1609 dbSNP
rs1302904071 1614 dbSNP
rs1040778139 1621 dbSNP
rs943608281 1622 dbSNP
rs1284313931 1625 dbSNP
rs1242377717 1629 dbSNP
rs536130243 1633 dbSNP
rs1225033748 1639 dbSNP
rs774707225 1646 dbSNP
rs1213623986 1647 dbSNP
rs560861908 1654 dbSNP
rs184636197 1655 dbSNP
rs1212866913 1659 dbSNP
rs913649741 1659 dbSNP
rs987816604 1663 dbSNP
rs572279616 1672 dbSNP
rs1042804522 1676 dbSNP
rs1178714662 1678 dbSNP
rs945798423 1679 dbSNP
rs1379220194 1680 dbSNP
rs1416809093 1685 dbSNP
rs1026054059 1694 dbSNP
rs913419343 1700 dbSNP
rs1305057099 1709 dbSNP
rs769136120 1710 dbSNP
rs966052875 1711 dbSNP
rs1325708762 1712 dbSNP
rs1359134823 1714 dbSNP
rs927629103 1719 dbSNP
rs980859378 1724 dbSNP
rs969322077 1726 dbSNP
rs763465126 1727 dbSNP
rs1449362085 1728 dbSNP
rs1458900592 1730 dbSNP
rs983954171 1731 dbSNP
rs1372623019 1738 dbSNP
rs1386645944 1742 dbSNP
rs1222143947 1744 dbSNP
rs1314721045 1749 dbSNP
rs1322276468 1757 dbSNP
rs1232425638 1761 dbSNP
rs951229372 1770 dbSNP
rs776114979 1777 dbSNP
rs566962095 1778 dbSNP
rs553123863 1780 dbSNP
rs1198825428 1782 dbSNP
rs778253632 1788 dbSNP
rs373294864 1792 dbSNP
rs993540342 1794 dbSNP
rs966133426 1796 dbSNP
rs1479350182 1799 dbSNP
rs9283658 1801 dbSNP
rs1475843282 1803 dbSNP
rs370486149 1806 dbSNP
rs1008000747 1807 dbSNP
rs193237150 1808 dbSNP
rs748678818 1812 dbSNP
rs1475386567 1813 dbSNP
rs1415673977 1815 dbSNP
rs557442731 1820 dbSNP
rs889356918 1821 dbSNP
rs1472422110 1831 dbSNP
rs1171567364 1839 dbSNP
rs1354194073 1845 dbSNP
rs372422384 1846 dbSNP
rs537649799 1847 dbSNP
rs1209991196 1853 dbSNP
rs1414160997 1857 dbSNP
rs1291381942 1858 dbSNP
rs1319655177 1859 dbSNP
rs141698326 1873 dbSNP
rs2204226 1878 dbSNP
rs1305457397 1886 dbSNP
rs1052571222 1887 dbSNP
rs1189866467 1887 dbSNP
rs1211579022 1887 dbSNP
rs939075245 1889 dbSNP
rs376618305 1901 dbSNP
rs1015212979 1914 dbSNP
rs927734617 1915 dbSNP
rs1044720476 1917 dbSNP
rs1419043346 1917 dbSNP
rs947752704 1918 dbSNP
rs1359759407 1922 dbSNP
rs770562815 1923 dbSNP
rs548923113 1927 dbSNP
rs866930475 1931 dbSNP
rs909794865 1935 dbSNP
rs984002836 1936 dbSNP
rs951278047 1940 dbSNP
rs1055693599 1943 dbSNP
rs866394380 1952 dbSNP
rs142724314 1954 dbSNP
rs1271292974 1955 dbSNP
rs1269420687 1957 dbSNP
rs113521179 1962 dbSNP
rs1895708 1963 dbSNP
rs549649926 1965 dbSNP
rs1019470353 1978 dbSNP
rs1007555213 1982 dbSNP
rs1462138648 1987 dbSNP
rs369243908 1988 dbSNP
rs1489583410 1999 dbSNP
rs114147627 2003 dbSNP
rs1162412062 2004 dbSNP
rs532134169 2007 dbSNP
rs569417807 2008 dbSNP
rs1364722 2009 dbSNP
rs1190465558 2010 dbSNP
rs529858937 2017 dbSNP
rs1453820218 2018 dbSNP
rs1447077102 2029 dbSNP
rs912977616 2037 dbSNP
rs1401283129 2048 dbSNP
rs1317355084 2052 dbSNP
rs892733030 2054 dbSNP
rs372112021 2057 dbSNP
rs148820783 2058 dbSNP
rs1275031476 2059 dbSNP
rs559483779 2060 dbSNP
rs1231407051 2064 dbSNP
rs1310862144 2083 dbSNP
rs1045253419 2086 dbSNP
rs1224772520 2096 dbSNP
rs1489254925 2109 dbSNP
rs1263329567 2114 dbSNP
rs911486747 2120 dbSNP
rs1224270604 2125 dbSNP
rs985651739 2131 dbSNP
rs1219738713 2132 dbSNP
rs1191826089 2133 dbSNP
rs947838516 2144 dbSNP
rs1321530290 2153 dbSNP
rs1382307385 2157 dbSNP
rs909497786 2158 dbSNP
rs931545453 2163 dbSNP
rs1405741387 2164 dbSNP
rs1048108251 2165 dbSNP
rs541201242 2171 dbSNP
rs1326384047 2173 dbSNP
rs929847541 2181 dbSNP
rs1393234416 2190 dbSNP
rs918534528 2195 dbSNP
rs976563192 2200 dbSNP
rs1296965860 2202 dbSNP
rs1335767491 2210 dbSNP
rs943907580 2211 dbSNP
rs1279441142 2218 dbSNP
rs8798 2229 dbSNP
rs145437848 2230 dbSNP
rs1369923695 2232 dbSNP
rs1292003684 2237 dbSNP
rs986585525 2238 dbSNP
rs1334426356 2244 dbSNP
rs1211993563 2254 dbSNP
rs1265149849 2257 dbSNP
rs1435438272 2264 dbSNP
rs1438427103 2268 dbSNP
rs953507257 2269 dbSNP
rs1231077190 2278 dbSNP
rs1473758331 2283 dbSNP
rs1354916333 2286 dbSNP
rs1165369495 2290 dbSNP
rs1416827950 2295 dbSNP
rs1459684850 2301 dbSNP
rs188642984 2309 dbSNP
rs144213816 2312 dbSNP
rs386669502 2312 dbSNP
rs956936615 2313 dbSNP
rs199760214 2314 dbSNP
rs529185975 2328 dbSNP
rs140366759 2335 dbSNP
rs184148681 2336 dbSNP
rs1055140027 2350 dbSNP
rs1434401189 2351 dbSNP
rs1334506000 2360 dbSNP
rs1264780071 2364 dbSNP
rs1034167860 2382 dbSNP
rs1355145527 2383 dbSNP
rs1001481709 2387 dbSNP
rs904433539 2394 dbSNP
rs1340377422 2395 dbSNP
rs1021749427 2396 dbSNP
rs1190297423 2396 dbSNP
rs1003707903 2397 dbSNP
rs906662029 2400 dbSNP
rs1023806601 2413 dbSNP
rs1012384626 2418 dbSNP
rs891547457 2419 dbSNP
rs147172504 2422 dbSNP
rs1048076359 2425 dbSNP
rs944228324 2426 dbSNP
rs533913719 2429 dbSNP
rs555236911 2431 dbSNP
rs1049869894 2441 dbSNP
rs931597668 2447 dbSNP
rs1340647346 2451 dbSNP
rs929651211 2456 dbSNP
rs897071750 2458 dbSNP
rs1274564963 2459 dbSNP
rs535211743 2463 dbSNP
rs1227039316 2469 dbSNP
rs377072835 2469 dbSNP
rs1314051738 2471 dbSNP
rs1268646183 2473 dbSNP
rs1350097497 2475 dbSNP
rs1211717512 2476 dbSNP
rs943976857 2486 dbSNP
rs1299401336 2487 dbSNP
rs911023397 2493 dbSNP
rs1262239720 2495 dbSNP
rs1386401954 2496 dbSNP
rs566294009 2497 dbSNP
rs1351377677 2502 dbSNP
rs1309617573 2509 dbSNP
rs8298 2514 dbSNP
rs144803280 2517 dbSNP
rs1313441639 2525 dbSNP
rs918015526 2529 dbSNP
rs915351292 2534 dbSNP
rs989439885 2535 dbSNP
rs956741085 2547 dbSNP
rs1375410236 2553 dbSNP
rs1030970682 2558 dbSNP
rs1386055366 2559 dbSNP
rs1382045504 2564 dbSNP
rs1034218671 2571 dbSNP
rs1316434838 2571 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 GSM1462573. RNA binding protein: AGO2. Condition:TZM-bl BaL ...

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

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 GSM1462573
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl BaL
Location of target site ENST00000295522.3 | 3UTR | UUUUGGGUAUUGUAAU
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
116 hsa-miR-3942-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT093395 TMA16 translation machinery associated 16 homolog 2 2
MIRT134018 SDE2 SDE2 telomere maintenance homolog 2 2
MIRT194942 TNRC6A trinucleotide repeat containing 6A 2 2
MIRT265807 NOTCH2 notch 2 2 2
MIRT287615 NPEPPS aminopeptidase puromycin sensitive 2 2
MIRT444196 SESN3 sestrin 3 2 2
MIRT444480 UBN2 ubinuclein 2 2 2
MIRT446589 FBXO40 F-box protein 40 2 2
MIRT450501 ALPK3 alpha kinase 3 2 2
MIRT455182 AGTRAP angiotensin II receptor associated protein 2 2
MIRT455446 EPB41L4B erythrocyte membrane protein band 4.1 like 4B 2 2
MIRT456385 KLHL12 kelch like family member 12 2 2
MIRT460303 FLCN folliculin 2 2
MIRT461247 COX10 COX10, heme A:farnesyltransferase cytochrome c oxidase assembly factor 2 6
MIRT467948 SLC16A1 solute carrier family 16 member 1 2 2
MIRT468007 SIX4 SIX homeobox 4 2 2
MIRT468211 SGK1 serum/glucocorticoid regulated kinase 1 2 2
MIRT470635 POM121C POM121 transmembrane nucleoporin C 2 2
MIRT471785 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT473557 MATR3 matrin 3 2 2
MIRT475415 ICK intestinal cell kinase 2 2
MIRT476265 GNAL G protein subunit alpha L 2 6
MIRT477135 FAM107B family with sequence similarity 107 member B 2 6
MIRT478433 DAZAP2 DAZ associated protein 2 2 2
MIRT479050 CNOT6L CCR4-NOT transcription complex subunit 6 like 2 8
MIRT480872 BDNF-AS BDNF antisense RNA 2 2
MIRT484229 CLDN1 claudin 1 2 2
MIRT485055 SUCO SUN domain containing ossification factor 2 2
MIRT489871 MPLKIP M-phase specific PLK1 interacting protein 2 2
MIRT492411 SCARB2 scavenger receptor class B member 2 2 2
MIRT499682 KCTD2 potassium channel tetramerization domain containing 2 2 4
MIRT505969 RAB11FIP1 RAB11 family interacting protein 1 2 4
MIRT507708 CNIH cornichon family AMPA receptor auxiliary protein 1 2 4
MIRT511878 GID4 GID complex subunit 4 homolog 2 6
MIRT513411 RTP4 receptor transporter protein 4 2 2
MIRT519873 ZFP30 ZFP30 zinc finger protein 2 4
MIRT520703 TMCO1 transmembrane and coiled-coil domains 1 2 2
MIRT522890 KCNN3 potassium calcium-activated channel subfamily N member 3 2 6
MIRT523781 FAM63B MINDY lysine 48 deubiquitinase 2 2 2
MIRT523950 DYNLT1 dynein light chain Tctex-type 1 2 4
MIRT526894 ATP6V0E2 ATPase H+ transporting V0 subunit e2 2 2
MIRT529167 CCDC25 coiled-coil domain containing 25 2 2
MIRT529703 ZBTB49 zinc finger and BTB domain containing 49 2 2
MIRT530359 PCSK1 proprotein convertase subtilisin/kexin type 1 2 2
MIRT530595 C7orf33 chromosome 7 open reading frame 33 2 4
MIRT531528 CCT6A chaperonin containing TCP1 subunit 6A 2 2
MIRT531992 BARD1 BRCA1 associated RING domain 1 2 2
MIRT539547 AAK1 AP2 associated kinase 1 2 2
MIRT547757 KATNAL1 katanin catalytic subunit A1 like 1 2 2
MIRT549059 CAMSAP1 calmodulin regulated spectrin associated protein 1 2 2
MIRT549836 ECHDC1 ethylmalonyl-CoA decarboxylase 1 2 2
MIRT552698 YWHAH tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein eta 2 2
MIRT554318 SH3GLB1 SH3 domain containing GRB2 like, endophilin B1 2 2
MIRT556358 MAF MAF bZIP transcription factor 2 2
MIRT557772 FRS2 fibroblast growth factor receptor substrate 2 2 2
MIRT558795 CHEK2 checkpoint kinase 2 2 2
MIRT561367 UBXN2B UBX domain protein 2B 2 2
MIRT561673 RAPGEF2 Rap guanine nucleotide exchange factor 2 2 2
MIRT567898 CSNK1A1 casein kinase 1 alpha 1 2 2
MIRT568456 ARPP19 cAMP regulated phosphoprotein 19 2 2
MIRT568838 NBPF12 NBPF member 12 2 2
MIRT568846 VPS53 VPS53, GARP complex subunit 2 2
MIRT568856 NBPF1 NBPF member 1 2 2
MIRT568888 NBPF15 NBPF member 15 2 2
MIRT569331 CDC5L cell division cycle 5 like 2 2
MIRT569388 NBPF11 NBPF member 11 2 2
MIRT569398 NBPF14 NBPF member 14 2 2
MIRT569644 NBPF10 NBPF member 10 2 2
MIRT571582 TROVE2 TROVE domain family member 2 2 2
MIRT573027 NBPF3 NBPF member 3 2 2
MIRT573293 UFM1 ubiquitin fold modifier 1 2 2
MIRT608814 SEPT6 septin 6 2 6
MIRT609046 BACH2 BTB domain and CNC homolog 2 2 6
MIRT609517 RAB3IP RAB3A interacting protein 2 2
MIRT611861 SRRM4 serine/arginine repetitive matrix 4 2 2
MIRT612174 EMC3 ER membrane protein complex subunit 3 2 2
MIRT612714 NR2F6 nuclear receptor subfamily 2 group F member 6 2 4
MIRT613305 ARL6IP6 ADP ribosylation factor like GTPase 6 interacting protein 6 2 4
MIRT616357 SH3TC2 SH3 domain and tetratricopeptide repeats 2 2 2
MIRT632424 SHOC2 SHOC2, leucine rich repeat scaffold protein 2 2
MIRT636005 SAMD15 sterile alpha motif domain containing 15 2 2
MIRT636534 FAM126B family with sequence similarity 126 member B 2 2
MIRT637275 FGFR1OP FGFR1 oncogene partner 2 2
MIRT639131 ZNF726 zinc finger protein 726 2 2
MIRT641257 C8orf46 chromosome 8 open reading frame 46 2 2
MIRT642930 KRTAP5-9 keratin associated protein 5-9 2 2
MIRT644018 NUCB1 nucleobindin 1 2 2
MIRT645021 MAGEB4 MAGE family member B4 2 2
MIRT646790 EVC2 EvC ciliary complex subunit 2 2 2
MIRT647338 RPH3AL rabphilin 3A like (without C2 domains) 2 2
MIRT647975 PDE12 phosphodiesterase 12 2 2
MIRT650610 NEK4 NIMA related kinase 4 2 2
MIRT651052 ZNF579 zinc finger protein 579 2 2
MIRT651593 WDFY2 WD repeat and FYVE domain containing 2 2 2
MIRT652785 TCEANC2 transcription elongation factor A N-terminal and central domain containing 2 2 2
MIRT656450 MAPK6 mitogen-activated protein kinase 6 2 2
MIRT660086 BTD biotinidase 2 2
MIRT661398 OLR1 oxidized low density lipoprotein receptor 1 2 2
MIRT661759 MICA MHC class I polypeptide-related sequence A 2 2
MIRT666402 SH3D19 SH3 domain containing 19 2 2
MIRT668362 FGD4 FYVE, RhoGEF and PH domain containing 4 2 2
MIRT668895 CREG2 cellular repressor of E1A stimulated genes 2 2 2
MIRT669329 BSND barttin CLCNK type accessory beta subunit 2 2
MIRT672369 PDPK1 3-phosphoinositide dependent protein kinase 1 2 2
MIRT686261 YTHDF1 YTH N6-methyladenosine RNA binding protein 1 2 2
MIRT695571 ASB16 ankyrin repeat and SOCS box containing 16 2 2
MIRT701959 MINK1 misshapen like kinase 1 2 2
MIRT702322 KMT2A lysine methyltransferase 2A 2 2
MIRT705209 BRWD1 bromodomain and WD repeat domain containing 1 2 2
MIRT713949 KCTD6 potassium channel tetramerization domain containing 6 2 2
MIRT717082 EBF4 early B-cell factor 4 2 2
MIRT717896 COPS8 COP9 signalosome subunit 8 2 2
MIRT721043 TRIM67 tripartite motif containing 67 2 2
MIRT722194 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT722782 ACADSB acyl-CoA dehydrogenase, short/branched chain 2 2
MIRT725412 HNRNPU heterogeneous nuclear ribonucleoprotein U 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3942-3p Osimertinib 71496458 NSC779217 approved resistant Low Non-Small Cell Lung Cancer tissue
hsa-miR-3942-3p Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-3942-3p Neoadjuvant chemotherapy resistant tissue (breast cancer)

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