pre-miRNA Information
pre-miRNA hsa-mir-3689a   
Genomic Coordinates chr9: 134849487 - 134849564
Description Homo sapiens miR-3689a stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3689a-5p
Sequence 10| UGUGAUAUCAUGGUUCCUGGGA |31
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs866098973 7 dbSNP
rs1203092136 8 dbSNP
rs1275806724 10 dbSNP
rs1264215348 13 dbSNP
rs1203436967 16 dbSNP
rs1170643534 22 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol ZBTB39   
Synonyms ZNF922
Description zinc finger and BTB domain containing 39
Transcript NM_014830   
Expression
Putative miRNA Targets on ZBTB39
3'UTR of ZBTB39
(miRNA target sites are highlighted)
>ZBTB39|NM_014830|3'UTR
   1 CTGGGTCCCGGCAGAGCCACGGGGAGCTCCCAAGCAGCAGCCAGGATGCTGATATCTAAGAGGTGTTGGTCCCTCCCCAG
  81 CTGAAGTTATAATTTTGCCTTGGTAGGAATTCTGTTCTGTGTTGTGTTTAAAGAAGAAAAGAAGAAGAAATAGCACATAA
 161 GCTGTTACTGTTGTTGAGAAGCAACAGCCCTATCACATTTACCTCCATACCTGTTCTTGCCCATGCAGGGCTATGTTTTT
 241 CATTCTTTTGAGGCTGGTTTTGGGATCTAGTCAAGCAGTTGGTGTCCACTAGACCCCCTTCCCCAGCCTCTCTAGTTTTA
 321 GTTTACTGATAGGTTTTATGCTGCTAAGAATCCAACCAACAGCCTCACTTAACAGAGGAGGTAAAGGGAGGTTTTCACTG
 401 TGGGTGTTACTGCAGGCCTCCAACTGGGATGACCAGCAATGAGAAAGATTTTGGGAATGTGATCATTCAGAAAAGACAGG
 481 TCAGCAGGGCAGTCCCCTCAGGTTCCAGCCCTCAGCAGGGACAAGACATCAGGGATGTTGGTGTCTGCTTATCTACAGCC
 561 CTAATCTGCTGATTGAACAGTGAAAATCTTTTGGCAGCTAGATCCATACTAGGCACAGAGCTTTCTATTTAGGTCAGAAA
 641 GCTTTGGGATGAACCCCTGCCAGCCAGAAGGGGTGTCCTGCAGTGCCACCAGAAGTGGCAGCCTGGATGGACAGGAGAGG
 721 TTTCTCTTTTCTCCTCATTTCCAAAGAAACAGGATTTTATGGAGTGATGGCCCGGGACGTCCGGCCTTCTGTGGGGCAGA
 801 GAGGATAGGGAACCACTTTGATATAGTCATCTGTTTTGGCCACTTCTGTTGGCCATGAGTGTCTTGGTGGAGAGGTGGGG
 881 ATGTATCTGACAGCAGCAGCCTTGCCTTAATTTATATCTGGTCTCCCGTCCAGAAGTGTTTGGCCCGTGGTGTAGATGAG
 961 CTGACTCCATGAAGTGGTGGAGTGGCAGACCGCGAGCCCTTCAGGATTAAAGGGACCTGAGTAACTGGTGGTGTGTAGCA
1041 GGGTGTGCGTTCTGACTGTCTGTCCTAGTCGGGTAACCTGTTTACTTTGTGCTAACAGTGCCGGAGCTTTGTCAGCTCAC
1121 CTTTGACCTGCTGGAATTTATCCTGATCTGTCGTTGCCATCACCTCCAGGGGGCGCTATTGGATGGCAGCTGGTTCAGGC
1201 CCTCCGTGGGTGGCTGCAGAGTGTGCCGGCACAGCCCACGCAGCTGGTTAGCTCCACTCTTACTTGGTTTTCTAAGGGGC
1281 TTTGCCCAAAGAAGTCTTGAGGGATAGGGCCCTCGATCTTGCATACTTGTGAGGTGCCACCTCAGTAGCTCATACTACCT
1361 CACCCTGCTCAGGTGAGCTCTGGGAGTCCCTGGCCTCAGCCCTGGCACTGCCCCTGGTGGGATTCAGCAACACCCCGGGC
1441 TGTTTCACAAGCAAGTGGTTTTCATTAACTCACAAAGCCTTTTTGGACATTAATATTTATTTATTTTTGTTTTTGTATAC
1521 ACATTACCCAGCATCTCTTTTGTATAAGAGACTTTAGGAAAATGAGTTTCTCCCCAGCAAGTAGCCATATTCCAGAGAAC
1601 AGCCTTGACCAGAGATGTGGAGAACCAGGGGTATAACTAAGGGAAGACATGTCAAGCCCTTAAGCAAATTCTTCTTCTCC
1681 AGATTGTCTCTAGCATAATAAACCCAGGGAACACTTTAGGCCATGGGTGTATGTTCTATAAAGTTCGGGACAGTTAAATT
1761 CCAGGCCTTTCATCCCCCTTCCTTCCTGTGATGGAGTAGATTGGGGACAGGGTTGAGGGGAACAAGTGACATGAATGACC
1841 TATTTGCACAGTTTGGAAGCCTCCTGTCTTTATTTATATTGAGATGTCAGACAAACCAAAGCTCCATCCTTGTTGGACCT
1921 GCTGCTTCTCCCCAGCCCTGAACTGATAAAGCCTCAGAGTTGGAGTGCCTGGCTCTCTGGTGGGGTGACCATTAGATGAA
2001 GGGACTTGTACAGTGGCCAGTTTAAAGGTCCACCTTTGACCATCTAAACCCACCTTGTTCAGTGTCCTCTGAGGACATCC
2081 TCATCAGGAAAGCAGTGTTGAGACTCTTCATTGCTGACTGGCTTCTCCCTTTCTTACTCACACTGACCATTAGAATTTAA
2161 GAAGGAAATGTGTAACAGACTACAGTCAAGTGTCTGCTACATTTTCAAGCATGAGCAATCCCTCCCAGACTGTTGGTGAG
2241 GACTGATTTTTGAAATGCTGGTGTGAGAGAGGTGGTAATTACAGGAACCAGCCGAGTGGCTGAGAGCAGATAAATGTGCT
2321 GGAGAAACCTTTTTCCTTAACAGAGGGCATCATGGATGCTGGGTGGTCTGTGTACTTAACCTGAAACTGTGAAGTTTTCC
2401 CTTTTTGCCAGTAAACCAAAAAGCAGATCCTTGAAACTTGGCCCTTGAAACACGAAACAGAAAACTGCATCCCCTGATCC
2481 CCCGGGGGCTGATCAGATTGATCAGGGTGGCTCAGTTGGTCCCAGTCAGATACGTCATAGGATCAGTAGCTCATGAGATT
2561 TGTTGACCAAACCCTCTCCCTGTTGGTGACCCCTGTATTCACACCTGAACTTCCCGTTTCCCCCCACCCCACCAAAGTCA
2641 TGTCTGCTTCCTCTGCCTCCAGCTCACCCTCTTCTGAATGGTTTTGCTTGAAACACTATATTGTGGCAGAGGGCACCCTG
2721 GGATACCTGGTAGAAGGTATTCATTTTATTTTGCATTTTTAATTGTTTTGACTTTCTGTTCATTTGATTTTGTTGCTCCC
2801 TCTCTCCTGGAACCTAGTTTACTACTCTCTTCTGTGTTACTCTGAAGTTCTGTTTAAGCCTTGAACATCCTCTTCTCCCA
2881 TTTTCTTGGTATGTACTCAGGACCAGCTACATCATTTGTGGAGCCCTCTTATTCATAAATTATTAAAAATTTCAAGGTGG
2961 TGGTCATAGAGCATTAAACCAAATATGAGGCCATTCCCAACTTGTTTTCCGAGGGGAAAATGGTAATACTTGTGTGGCAC
3041 CCGGGGTTAAACAGCAGAGGCTCCATGTGGCCAGAGGCAGAGATTAGTATCCTGGCACTCCAGTGACCCACTGGGTGACT
3121 CACTGATGCCACAGCACCCGCTAGGAAGCTCTGCTGAACCTTAGTATTTGGTCCTAAATTTTATGACTCCATGGAGTTCC
3201 CGTAGTCCATGGCTAGTTAGGAAGAAAGGAGGTGGGATAAGGGTCAGGCCCAGGTGACCCCTAAGAACCAGGAGATGGGT
3281 AAAAGTTTTTTTTTATATTCTGCTTTTCTGATCTGTGAGTACCTGTTTGTCTCCAGGCCAAACCTTTGGGCTTAAATATC
3361 TTTTTCCTAGACAGGTTTTTGCTAGTGTTGAATTTTCTTCTTCCTCTGGCCTCCTTCTGTGCCCCTTTCCCCAAGCCCAA
3441 GACTGCTTAACTTCCAAAGCAAATTCTAGATAGACACTGTATTTATTGGTATGGGAGTGGGCTCTATGGGGTGGTCTGCA
3521 CCCATCTGGGACTCTTTTCCCTAAATCCTGCACCAAATGAGTCAGGAGGCAGGGTGCACAGCATTAGTTTCAATGTGGTT
3601 ATGCATCATAAGCTTAACATCAGAATGAAAATGAAACTCGATTTTGATGTTTCTTTAAAACCCTTCCCCTGTCCAATCCA
3681 CTCGCCGCCCCCACCTTGAATAGCTAAAGTCTCTTATGAAACAGAGAAGAGTTGTTGACGTCTAACTCCTTCCATTAAAT
3761 TAATAAGTACTGACCTCCTAATATTTAAGTGTTTACTATCTATTGCTGTAAAGTTTTGTATATTTTGTAAACTTTTTTCC
3841 CCAAATAGTAGATGTCTAAAATCATTGTACATCTGATTCTTTTATATTCCATTGTTCAGCACAAAGTGTGGTTTTTATTT
3921 AGAATAAAAAAAGAAATTTGAAATGAAAAAAAAAAAAAAAAAAA
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' agGGUCCUUGGUACUAUAGugu 5'
            ||||||  | |||||||   
Target 5' agCCAGGATGC-TGATATCtaa 3'
39 - 59 131.00 -16.70
2
miRNA  3' agggUCCUUGGUACUAUAGUGu 5'
              || ||| :   |||||| 
Target 5' gagaAGCAACAGCCCTATCACa 3'
176 - 197 122.00 -9.70
3
miRNA  3' aggGUCCUUGGUACUAUAGUgu 5'
             ||||:| || || ||||  
Target 5' cagCAGGGA-CAAGACATCAgg 3'
513 - 533 118.00 -14.00
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31502277 22 COSMIC
COSN28858946 24 COSMIC
COSN30449651 56 COSMIC
COSN31528543 136 COSMIC
COSN31588831 142 COSMIC
COSN31515724 153 COSMIC
COSN8586445 303 COSMIC
COSN31533096 411 COSMIC
COSN26595822 437 COSMIC
COSN26507752 582 COSMIC
COSN31570429 588 COSMIC
COSN5717518 941 COSMIC
COSN1577529 1353 COSMIC
COSN8586444 1446 COSMIC
COSN23306299 1458 COSMIC
COSN22449323 1751 COSMIC
COSN31485628 2294 COSMIC
COSN5186256 2343 COSMIC
COSN31524569 2386 COSMIC
COSN5324427 2556 COSMIC
COSN5324426 2698 COSMIC
COSN30380658 3139 COSMIC
COSN29258925 3148 COSMIC
COSN31546423 3721 COSMIC
COSN30543381 3778 COSMIC
COSN31609607 3810 COSMIC
COSN28706427 3899 COSMIC
rs3741578 1928 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs746180673 6 dbSNP
rs746425596 6 dbSNP
rs779464915 7 dbSNP
rs757650522 8 dbSNP
rs375243744 9 dbSNP
rs756351932 10 dbSNP
rs371275827 11 dbSNP
rs745554871 16 dbSNP
rs767625415 20 dbSNP
rs373470484 21 dbSNP
rs1279916389 27 dbSNP
rs1317077482 37 dbSNP
rs751533887 45 dbSNP
rs1300044941 53 dbSNP
rs1342559942 58 dbSNP
rs1231720395 72 dbSNP
rs1272552971 73 dbSNP
rs1384543011 78 dbSNP
rs1223946091 85 dbSNP
rs1372475353 86 dbSNP
rs1259454550 87 dbSNP
rs1326529070 89 dbSNP
rs1485854504 98 dbSNP
rs1217740181 105 dbSNP
rs1007342707 107 dbSNP
rs1186793691 150 dbSNP
rs1386199491 150 dbSNP
rs903779804 152 dbSNP
rs553748257 157 dbSNP
rs190579314 159 dbSNP
rs1455598924 164 dbSNP
rs1009200569 168 dbSNP
rs1156368729 168 dbSNP
rs1364567156 177 dbSNP
rs1373399196 183 dbSNP
rs1413102517 187 dbSNP
rs1283806550 193 dbSNP
rs1380255628 194 dbSNP
rs892102525 201 dbSNP
rs1175568707 219 dbSNP
rs1056113776 223 dbSNP
rs35425462 223 dbSNP
rs149139001 228 dbSNP
rs186722479 230 dbSNP
rs537023454 232 dbSNP
rs1045298213 233 dbSNP
rs941471287 257 dbSNP
rs905028974 263 dbSNP
rs1194817842 267 dbSNP
rs1464834291 276 dbSNP
rs1484059765 277 dbSNP
rs1260170893 278 dbSNP
rs1207233088 279 dbSNP
rs1045192154 284 dbSNP
rs1255070418 286 dbSNP
rs1231568985 289 dbSNP
rs1038477257 293 dbSNP
rs910144747 296 dbSNP
rs570150348 300 dbSNP
rs1433866893 304 dbSNP
rs983006408 307 dbSNP
rs181264510 310 dbSNP
rs930013968 312 dbSNP
rs1296453479 321 dbSNP
rs987763957 325 dbSNP
rs529115780 332 dbSNP
rs1324612505 341 dbSNP
rs1241035096 344 dbSNP
rs1312090174 345 dbSNP
rs1320090968 356 dbSNP
rs1218986479 357 dbSNP
rs1279812292 363 dbSNP
rs1313546026 369 dbSNP
rs1202009660 371 dbSNP
rs1236976358 372 dbSNP
rs922619685 390 dbSNP
rs767454265 391 dbSNP
rs1382594471 393 dbSNP
rs979654430 394 dbSNP
rs953645737 401 dbSNP
rs1029174390 413 dbSNP
rs964514029 423 dbSNP
rs1427010809 426 dbSNP
rs71461305 427 dbSNP
rs985932629 434 dbSNP
rs751561471 440 dbSNP
rs1397034614 442 dbSNP
rs1399926027 444 dbSNP
rs1022186739 455 dbSNP
rs966137442 458 dbSNP
rs546533286 467 dbSNP
rs147659818 476 dbSNP
rs1004881552 478 dbSNP
rs1275744316 481 dbSNP
rs1347601269 485 dbSNP
rs1213242664 502 dbSNP
rs564008488 505 dbSNP
rs768702734 506 dbSNP
rs1199926168 507 dbSNP
rs1035133691 510 dbSNP
rs36041955 512 dbSNP
rs545796170 524 dbSNP
rs537659691 530 dbSNP
rs1450892383 548 dbSNP
rs1199503312 549 dbSNP
rs1248443597 559 dbSNP
rs1474300860 560 dbSNP
rs1026865527 568 dbSNP
rs763161498 570 dbSNP
rs1371826784 572 dbSNP
rs1423152778 573 dbSNP
rs530407399 588 dbSNP
rs199866126 591 dbSNP
rs1392383104 601 dbSNP
rs995455115 606 dbSNP
rs904997464 607 dbSNP
rs1255824535 608 dbSNP
rs866982657 618 dbSNP
rs1044893924 620 dbSNP
rs904943650 627 dbSNP
rs1044803983 631 dbSNP
rs1220090177 636 dbSNP
rs1005738501 649 dbSNP
rs888594680 650 dbSNP
rs1486440933 654 dbSNP
rs1209984030 656 dbSNP
rs1291896500 664 dbSNP
rs1445259838 672 dbSNP
rs1215559887 675 dbSNP
rs1052143769 680 dbSNP
rs934958269 681 dbSNP
rs924966227 686 dbSNP
rs762236041 689 dbSNP
rs930251097 693 dbSNP
rs1189511140 695 dbSNP
rs1163953179 701 dbSNP
rs1226985596 707 dbSNP
rs922874902 708 dbSNP
rs1399495898 709 dbSNP
rs1297897787 710 dbSNP
rs1361584266 713 dbSNP
rs922203310 714 dbSNP
rs1291052187 722 dbSNP
rs1271892610 725 dbSNP
rs541556554 727 dbSNP
rs966647044 729 dbSNP
rs942681088 731 dbSNP
rs1239345565 736 dbSNP
rs1489141030 737 dbSNP
rs983541015 737 dbSNP
rs911317930 739 dbSNP
rs978791469 743 dbSNP
rs769855975 744 dbSNP
rs575125408 747 dbSNP
rs1254306178 765 dbSNP
rs915104317 768 dbSNP
rs987983094 770 dbSNP
rs762833182 773 dbSNP
rs1188280557 774 dbSNP
rs1377474848 774 dbSNP
rs1438316379 776 dbSNP
rs1034905543 778 dbSNP
rs1381543031 779 dbSNP
rs1003628490 781 dbSNP
rs746106842 782 dbSNP
rs1400989066 783 dbSNP
rs1396279123 793 dbSNP
rs1409479163 795 dbSNP
rs1023409826 800 dbSNP
rs1333492621 801 dbSNP
rs56305333 802 dbSNP
rs1355820770 807 dbSNP
rs1231780280 813 dbSNP
rs189663534 815 dbSNP
rs61939634 816 dbSNP
rs1047298205 819 dbSNP
rs3741577 823 dbSNP
rs1258597395 825 dbSNP
rs1186250025 829 dbSNP
rs1456494583 835 dbSNP
rs2840074 844 dbSNP
rs559260060 846 dbSNP
rs1239297272 848 dbSNP
rs1442109479 851 dbSNP
rs372290071 859 dbSNP
rs1024005971 870 dbSNP
rs1013384789 871 dbSNP
rs537488152 879 dbSNP
rs1397757648 881 dbSNP
rs754398 885 dbSNP
rs1331502645 893 dbSNP
rs1378962666 895 dbSNP
rs745354132 901 dbSNP
rs1196370717 907 dbSNP
rs1052109714 922 dbSNP
rs1355557717 927 dbSNP
rs942712936 928 dbSNP
rs375555711 931 dbSNP
rs1234883819 937 dbSNP
rs1258829781 945 dbSNP
rs77579238 946 dbSNP
rs536341433 947 dbSNP
rs1434116109 951 dbSNP
rs1441659450 956 dbSNP
rs565798882 966 dbSNP
rs1330955190 971 dbSNP
rs879631340 982 dbSNP
rs1043379359 991 dbSNP
rs1201516494 992 dbSNP
rs1464802705 993 dbSNP
rs1411082521 994 dbSNP
rs1394348505 996 dbSNP
rs947507831 1005 dbSNP
rs1455982500 1007 dbSNP
rs931680807 1013 dbSNP
rs922200748 1020 dbSNP
rs1388272299 1021 dbSNP
rs1276097051 1028 dbSNP
rs546396258 1031 dbSNP
rs1041034294 1035 dbSNP
rs988383583 1041 dbSNP
rs944818065 1048 dbSNP
rs1219555121 1049 dbSNP
rs534472461 1052 dbSNP
rs1418946877 1058 dbSNP
rs3044224 1065 dbSNP
rs5798399 1065 dbSNP
rs5798400 1065 dbSNP
rs956533108 1070 dbSNP
rs1234180414 1071 dbSNP
rs920702660 1073 dbSNP
rs927885073 1083 dbSNP
rs1421506490 1085 dbSNP
rs982029534 1088 dbSNP
rs980117127 1089 dbSNP
rs570445496 1096 dbSNP
rs552163243 1102 dbSNP
rs1359676661 1103 dbSNP
rs145342003 1103 dbSNP
rs1400448824 1106 dbSNP
rs1299028647 1107 dbSNP
rs1364400232 1113 dbSNP
rs1226659043 1117 dbSNP
rs1312130247 1118 dbSNP
rs1023337638 1121 dbSNP
rs1322811594 1123 dbSNP
rs1247636616 1127 dbSNP
rs1284573728 1144 dbSNP
rs1488163917 1145 dbSNP
rs753187078 1146 dbSNP
rs761316893 1147 dbSNP
rs776412740 1152 dbSNP
rs1482083498 1153 dbSNP
rs1180732106 1156 dbSNP
rs1267191972 1161 dbSNP
rs994754910 1164 dbSNP
rs1425424735 1166 dbSNP
rs1013936778 1167 dbSNP
rs960499980 1168 dbSNP
rs1420052244 1172 dbSNP
rs1160288421 1174 dbSNP
rs61939633 1174 dbSNP
rs1347138354 1175 dbSNP
rs1030778855 1183 dbSNP
rs141675944 1184 dbSNP
rs779455325 1192 dbSNP
rs1442989175 1197 dbSNP
rs1370274055 1205 dbSNP
rs1020182189 1206 dbSNP
rs1454708156 1225 dbSNP
rs1007124760 1226 dbSNP
rs890028999 1227 dbSNP
rs147902554 1228 dbSNP
rs1158830355 1239 dbSNP
rs1398638074 1245 dbSNP
rs1237751955 1253 dbSNP
rs900169705 1261 dbSNP
rs1409683593 1275 dbSNP
rs1176287400 1279 dbSNP
rs1043077739 1308 dbSNP
rs1440265372 1312 dbSNP
rs1040608591 1314 dbSNP
rs1422807854 1324 dbSNP
rs1175614932 1338 dbSNP
rs769629418 1343 dbSNP
rs1360003827 1344 dbSNP
rs1453304438 1348 dbSNP
rs755612094 1357 dbSNP
rs1376759241 1358 dbSNP
rs947350856 1359 dbSNP
rs1281578554 1364 dbSNP
rs891889853 1366 dbSNP
rs1219078368 1369 dbSNP
rs374288686 1376 dbSNP
rs1247254452 1377 dbSNP
rs930830994 1379 dbSNP
rs1325308143 1380 dbSNP
rs920654496 1384 dbSNP
rs529817375 1387 dbSNP
rs1445544937 1390 dbSNP
rs980594396 1397 dbSNP
rs948722754 1400 dbSNP
rs1244973675 1403 dbSNP
rs1053182668 1405 dbSNP
rs1191603148 1413 dbSNP
rs1224501034 1416 dbSNP
rs1244594734 1416 dbSNP
rs1426072109 1421 dbSNP
rs917251334 1430 dbSNP
rs1347263790 1433 dbSNP
rs1301324319 1435 dbSNP
rs935179891 1436 dbSNP
rs565891317 1437 dbSNP
rs139842449 1438 dbSNP
rs1288709483 1445 dbSNP
rs1429094166 1448 dbSNP
rs992871318 1467 dbSNP
rs1275836751 1471 dbSNP
rs1346963655 1488 dbSNP
rs1216420247 1489 dbSNP
rs1276959932 1499 dbSNP
rs982342408 1505 dbSNP
rs1347281407 1509 dbSNP
rs947988706 1510 dbSNP
rs916459877 1514 dbSNP
rs1030915085 1517 dbSNP
rs983793953 1538 dbSNP
rs952327758 1544 dbSNP
rs1450983902 1572 dbSNP
rs1025832189 1573 dbSNP
rs972531779 1574 dbSNP
rs559462674 1584 dbSNP
rs965486754 1585 dbSNP
rs1022007037 1587 dbSNP
rs541660821 1592 dbSNP
rs1454687211 1600 dbSNP
rs1418677936 1601 dbSNP
rs1184656433 1610 dbSNP
rs1478171698 1611 dbSNP
rs1486742762 1614 dbSNP
rs1412200909 1620 dbSNP
rs1405325753 1628 dbSNP
rs1242428540 1630 dbSNP
rs745462468 1631 dbSNP
rs142961533 1636 dbSNP
rs780853687 1639 dbSNP
rs1278336022 1657 dbSNP
rs1021798884 1670 dbSNP
rs1011547405 1671 dbSNP
rs577498150 1674 dbSNP
rs891772350 1679 dbSNP
rs1355469630 1683 dbSNP
rs1053513157 1684 dbSNP
rs1293932838 1694 dbSNP
rs1019016400 1695 dbSNP
rs1213260354 1712 dbSNP
rs1262717560 1713 dbSNP
rs938810460 1717 dbSNP
rs1447822373 1726 dbSNP
rs1195369678 1729 dbSNP
rs545418452 1738 dbSNP
rs1008593266 1740 dbSNP
rs1472725672 1743 dbSNP
rs543757674 1746 dbSNP
rs1048014763 1747 dbSNP
rs947832754 1756 dbSNP
rs930757451 1759 dbSNP
rs899345366 1761 dbSNP
rs916511736 1765 dbSNP
rs1383562454 1767 dbSNP
rs1331558197 1768 dbSNP
rs984012824 1772 dbSNP
rs931198807 1777 dbSNP
rs1448206348 1778 dbSNP
rs1317034871 1786 dbSNP
rs79481211 1788 dbSNP
rs918286861 1790 dbSNP
rs111364260 1791 dbSNP
rs965196804 1792 dbSNP
rs1286516038 1793 dbSNP
rs180712560 1794 dbSNP
rs770526504 1797 dbSNP
rs1276847703 1798 dbSNP
rs536604216 1801 dbSNP
rs934696476 1803 dbSNP
rs572232542 1809 dbSNP
rs564463602 1815 dbSNP
rs1420050509 1820 dbSNP
rs977982065 1822 dbSNP
rs1178338155 1825 dbSNP
rs1364749005 1835 dbSNP
rs1186922350 1841 dbSNP
rs1455727855 1846 dbSNP
rs1170439730 1863 dbSNP
rs1401103592 1866 dbSNP
rs1021851432 1876 dbSNP
rs1414520260 1877 dbSNP
rs1475031808 1878 dbSNP
rs1255703099 1879 dbSNP
rs1445963151 1888 dbSNP
rs1011807711 1896 dbSNP
rs1190283678 1906 dbSNP
rs2371717 1909 dbSNP
rs868691367 1911 dbSNP
rs1250777736 1918 dbSNP
rs1254455749 1919 dbSNP
rs1203103113 1924 dbSNP
rs1309775259 1927 dbSNP
rs3741578 1928 dbSNP
rs867246627 1935 dbSNP
rs1456779251 1938 dbSNP
rs189401199 1941 dbSNP
rs1198554900 1948 dbSNP
rs974635058 1954 dbSNP
rs1353902182 1957 dbSNP
rs1197257987 1958 dbSNP
rs964799721 1967 dbSNP
rs148406515 1975 dbSNP
rs1177886430 1978 dbSNP
rs1008532592 1979 dbSNP
rs1464703749 1989 dbSNP
rs536951423 1990 dbSNP
rs754298876 1991 dbSNP
rs1398602302 1992 dbSNP
rs1384845475 2013 dbSNP
rs1372057118 2030 dbSNP
rs1300364086 2034 dbSNP
rs1330672378 2056 dbSNP
rs1044467124 2060 dbSNP
rs1285492516 2066 dbSNP
rs1026541564 2072 dbSNP
rs1218134871 2073 dbSNP
rs1252381680 2079 dbSNP
rs995098595 2082 dbSNP
rs899443100 2088 dbSNP
rs1267113099 2106 dbSNP
rs1490395216 2109 dbSNP
rs1463498407 2110 dbSNP
rs569892254 2116 dbSNP
rs1477193839 2129 dbSNP
rs1170598582 2136 dbSNP
rs1012104310 2141 dbSNP
rs1456329208 2142 dbSNP
rs75839214 2144 dbSNP
rs1365945888 2147 dbSNP
rs1048244405 2151 dbSNP
rs1305153936 2169 dbSNP
rs529686579 2172 dbSNP
rs1214010149 2179 dbSNP
rs1057154905 2182 dbSNP
rs1309710500 2185 dbSNP
rs1243272546 2187 dbSNP
rs931277913 2193 dbSNP
rs1360614503 2198 dbSNP
rs1225239737 2199 dbSNP
rs1419678840 2200 dbSNP
rs1260565368 2204 dbSNP
rs1487772804 2211 dbSNP
rs918496777 2216 dbSNP
rs924633788 2218 dbSNP
rs1036702812 2225 dbSNP
rs765269298 2227 dbSNP
rs1249989246 2230 dbSNP
rs912327614 2231 dbSNP
rs1426290211 2232 dbSNP
rs946615279 2241 dbSNP
rs915188116 2252 dbSNP
rs1175520099 2256 dbSNP
rs1430284657 2263 dbSNP
rs146192242 2265 dbSNP
rs547498315 2267 dbSNP
rs1289464795 2277 dbSNP
rs1481933088 2279 dbSNP
rs985154060 2282 dbSNP
rs532794405 2290 dbSNP
rs565332999 2293 dbSNP
rs914772480 2294 dbSNP
rs184615286 2297 dbSNP
rs1275377487 2312 dbSNP
rs987235974 2327 dbSNP
rs1216046351 2328 dbSNP
rs1262191157 2332 dbSNP
rs117244087 2333 dbSNP
rs780335841 2335 dbSNP
rs1180821922 2336 dbSNP
rs560648474 2342 dbSNP
rs956358130 2346 dbSNP
rs1025970408 2347 dbSNP
rs1176475402 2348 dbSNP
rs370577820 2363 dbSNP
rs1401133494 2377 dbSNP
rs1315931466 2380 dbSNP
rs1304295491 2385 dbSNP
rs994528281 2398 dbSNP
rs1336190812 2400 dbSNP
rs1407433024 2401 dbSNP
rs35483007 2407 dbSNP
rs1455062553 2410 dbSNP
rs963962032 2411 dbSNP
rs1373044682 2417 dbSNP
rs1373382257 2422 dbSNP
rs1013468598 2423 dbSNP
rs1202439609 2429 dbSNP
rs1263222959 2437 dbSNP
rs1325150714 2438 dbSNP
rs3803018 2440 dbSNP
rs141505148 2442 dbSNP
rs1022952107 2451 dbSNP
rs373231284 2452 dbSNP
rs1013033289 2453 dbSNP
rs1410363397 2460 dbSNP
rs1431658192 2466 dbSNP
rs1175746619 2467 dbSNP
rs887853471 2473 dbSNP
rs1157126217 2474 dbSNP
rs572094297 2475 dbSNP
rs915136520 2476 dbSNP
rs192230482 2483 dbSNP
rs553891555 2484 dbSNP
rs1443313479 2486 dbSNP
rs564680129 2505 dbSNP
rs545014037 2506 dbSNP
rs1222549571 2511 dbSNP
rs138624564 2533 dbSNP
rs1325031123 2534 dbSNP
rs1216326284 2540 dbSNP
rs1272183361 2545 dbSNP
rs1438336799 2553 dbSNP
rs987329360 2567 dbSNP
rs1210789147 2571 dbSNP
rs578012298 2573 dbSNP
rs145966735 2579 dbSNP
rs919048048 2580 dbSNP
rs1430329867 2581 dbSNP
rs35732313 2581 dbSNP
rs1481453667 2589 dbSNP
rs912254788 2592 dbSNP
rs1392152244 2594 dbSNP
rs1419346426 2603 dbSNP
rs1049372918 2607 dbSNP
rs932438829 2608 dbSNP
rs1348477548 2610 dbSNP
rs773579215 2615 dbSNP
rs963083366 2620 dbSNP
rs1303373752 2623 dbSNP
rs1232075843 2624 dbSNP
rs772431121 2625 dbSNP
rs1013187191 2626 dbSNP
rs1023600231 2626 dbSNP
rs1326385847 2629 dbSNP
rs1381458106 2630 dbSNP
rs1216275719 2640 dbSNP
rs1287698550 2648 dbSNP
rs1382460417 2660 dbSNP
rs1223028295 2665 dbSNP
rs1269802139 2669 dbSNP
rs1287335896 2688 dbSNP
rs990339489 2693 dbSNP
rs956371289 2698 dbSNP
rs537216322 2699 dbSNP
rs1475811058 2706 dbSNP
rs1170115366 2708 dbSNP
rs1412348435 2712 dbSNP
rs1424407063 2716 dbSNP
rs1164619702 2717 dbSNP
rs1417513798 2718 dbSNP
rs1035807413 2719 dbSNP
rs982123115 2722 dbSNP
rs149512436 2739 dbSNP
rs1381964855 2752 dbSNP
rs748635213 2756 dbSNP
rs1023004496 2760 dbSNP
rs1361797732 2770 dbSNP
rs1203592912 2775 dbSNP
rs762001241 2776 dbSNP
rs1283875395 2778 dbSNP
rs1397455401 2784 dbSNP
rs1195489450 2787 dbSNP
rs1200150424 2795 dbSNP
rs1444564745 2796 dbSNP
rs1184547182 2799 dbSNP
rs751562312 2800 dbSNP
rs188372281 2810 dbSNP
rs1468965898 2816 dbSNP
rs185103428 2821 dbSNP
rs536286814 2827 dbSNP
rs995366002 2829 dbSNP
rs1039332611 2831 dbSNP
rs1206592457 2832 dbSNP
rs1331632728 2836 dbSNP
rs755629121 2848 dbSNP
rs943284628 2856 dbSNP
rs1317137089 2863 dbSNP
rs1374342335 2868 dbSNP
rs1488412610 2870 dbSNP
rs1238145270 2872 dbSNP
rs1015410314 2874 dbSNP
rs138009345 2877 dbSNP
rs891036070 2880 dbSNP
rs745358474 2891 dbSNP
rs1461218598 2897 dbSNP
rs1204837498 2908 dbSNP
rs547561304 2909 dbSNP
rs1226520117 2911 dbSNP
rs1417694951 2912 dbSNP
rs1049426175 2913 dbSNP
rs1324479680 2921 dbSNP
rs1363954854 2945 dbSNP
rs1470977903 2949 dbSNP
rs932283096 2955 dbSNP
rs892897807 2959 dbSNP
rs1469906072 2961 dbSNP
rs61939632 2964 dbSNP
rs918974711 2969 dbSNP
rs973178093 2972 dbSNP
rs941670016 2985 dbSNP
rs1336534165 2993 dbSNP
rs934406478 2993 dbSNP
rs1281667482 2994 dbSNP
rs1322869115 2995 dbSNP
rs1224269758 3000 dbSNP
rs571278869 3003 dbSNP
rs1432976248 3004 dbSNP
rs915593812 3010 dbSNP
rs550120531 3011 dbSNP
rs1439970721 3015 dbSNP
rs1196798224 3017 dbSNP
rs756978089 3022 dbSNP
rs924801616 3026 dbSNP
rs981623894 3027 dbSNP
rs1035945750 3029 dbSNP
rs192731683 3032 dbSNP
rs775370007 3033 dbSNP
rs1461445920 3037 dbSNP
rs967529163 3041 dbSNP
rs751201446 3042 dbSNP
rs916125061 3043 dbSNP
rs1011673702 3045 dbSNP
rs899942036 3052 dbSNP
rs769645912 3055 dbSNP
rs1018255467 3059 dbSNP
rs991494680 3065 dbSNP
rs1405565886 3072 dbSNP
rs764005049 3082 dbSNP
rs1285313433 3084 dbSNP
rs1306220442 3091 dbSNP
rs1008270966 3092 dbSNP
rs1252448044 3096 dbSNP
rs890370156 3107 dbSNP
rs1220794127 3131 dbSNP
rs1267661815 3137 dbSNP
rs1490412171 3138 dbSNP
rs561462255 3139 dbSNP
rs542907159 3140 dbSNP
rs951997379 3144 dbSNP
rs1193765147 3150 dbSNP
rs1374785599 3153 dbSNP
rs1422458744 3164 dbSNP
rs1027760066 3165 dbSNP
rs1389597814 3173 dbSNP
rs972582701 3199 dbSNP
rs188138210 3201 dbSNP
rs879718077 3202 dbSNP
rs1015879077 3209 dbSNP
rs1037829659 3216 dbSNP
rs1381790354 3223 dbSNP
rs752622422 3232 dbSNP
rs1367989132 3233 dbSNP
rs1244154891 3234 dbSNP
rs1291542636 3253 dbSNP
rs1359643874 3254 dbSNP
rs1337363271 3258 dbSNP
rs941776793 3277 dbSNP
rs1263686662 3278 dbSNP
rs891047247 3279 dbSNP
rs1028164645 3285 dbSNP
rs996483978 3286 dbSNP
rs57143727 3288 dbSNP
rs1167169485 3293 dbSNP
rs1054113540 3295 dbSNP
rs967488456 3295 dbSNP
rs977648554 3295 dbSNP
rs1391418056 3297 dbSNP
rs990744650 3302 dbSNP
rs1315024393 3308 dbSNP
rs1383947117 3313 dbSNP
rs964156601 3319 dbSNP
rs1304391926 3322 dbSNP
rs934438244 3326 dbSNP
rs902929551 3331 dbSNP
rs765204112 3339 dbSNP
rs950162964 3343 dbSNP
rs916178836 3354 dbSNP
rs1018808823 3356 dbSNP
rs140411943 3361 dbSNP
rs1175282046 3383 dbSNP
rs557722353 3390 dbSNP
rs1394937261 3395 dbSNP
rs61583191 3397 dbSNP
rs556592922 3407 dbSNP
rs1418752778 3409 dbSNP
rs1159860112 3410 dbSNP
rs1414244436 3412 dbSNP
rs1468333714 3416 dbSNP
rs920622187 3430 dbSNP
rs1336641697 3439 dbSNP
rs1407541088 3457 dbSNP
rs1030229614 3467 dbSNP
rs1296845578 3473 dbSNP
rs1170094663 3481 dbSNP
rs972084167 3481 dbSNP
rs1223974171 3487 dbSNP
rs962479594 3493 dbSNP
rs1320791060 3494 dbSNP
rs897764980 3496 dbSNP
rs1263621442 3503 dbSNP
rs543280396 3506 dbSNP
rs1202128925 3507 dbSNP
rs576169867 3514 dbSNP
rs182372141 3524 dbSNP
rs576216580 3530 dbSNP
rs776695677 3536 dbSNP
rs938312382 3544 dbSNP
rs1416678501 3557 dbSNP
rs1252622023 3561 dbSNP
rs1199120911 3563 dbSNP
rs1169021350 3565 dbSNP
rs928315117 3569 dbSNP
rs1041392486 3570 dbSNP
rs766386290 3574 dbSNP
rs1271026174 3586 dbSNP
rs1343273453 3588 dbSNP
rs565932650 3593 dbSNP
rs553809733 3602 dbSNP
rs1283402153 3603 dbSNP
rs914845189 3608 dbSNP
rs1212714152 3609 dbSNP
rs58230480 3621 dbSNP
rs964568291 3636 dbSNP
rs1276962281 3639 dbSNP
rs760907239 3640 dbSNP
rs1334014145 3641 dbSNP
rs986899933 3646 dbSNP
rs1479073112 3648 dbSNP
rs1185284541 3649 dbSNP
rs1419500902 3658 dbSNP
rs955330737 3661 dbSNP
rs1025638392 3670 dbSNP
rs1423629098 3670 dbSNP
rs1333953528 3671 dbSNP
rs998491959 3671 dbSNP
rs773385242 3681 dbSNP
rs138906929 3683 dbSNP
rs1324298106 3684 dbSNP
rs373082915 3686 dbSNP
rs545728944 3687 dbSNP
rs1230253951 3693 dbSNP
rs894670064 3700 dbSNP
rs538098909 3706 dbSNP
rs930917167 3716 dbSNP
rs920854326 3717 dbSNP
rs1290947460 3722 dbSNP
rs753183942 3722 dbSNP
rs1453390407 3723 dbSNP
rs567846843 3726 dbSNP
rs1213752837 3728 dbSNP
rs894304603 3728 dbSNP
rs1179246474 3732 dbSNP
rs1055449304 3736 dbSNP
rs1002563611 3739 dbSNP
rs549121865 3740 dbSNP
rs1163822722 3742 dbSNP
rs1392503365 3744 dbSNP
rs866386338 3751 dbSNP
rs371129944 3757 dbSNP
rs527989990 3763 dbSNP
rs1215313869 3769 dbSNP
rs147048620 3793 dbSNP
rs189761622 3800 dbSNP
rs1334662985 3803 dbSNP
rs1381768366 3806 dbSNP
rs1246517293 3808 dbSNP
rs188033858 3810 dbSNP
rs748523771 3818 dbSNP
rs1222105563 3820 dbSNP
rs1283678098 3823 dbSNP
rs953447491 3832 dbSNP
rs911392682 3836 dbSNP
rs1211091026 3838 dbSNP
rs142772507 3839 dbSNP
rs781627879 3843 dbSNP
rs183341835 3846 dbSNP
rs1370864551 3847 dbSNP
rs975212701 3850 dbSNP
rs1468306698 3862 dbSNP
rs544683094 3864 dbSNP
rs1412027262 3866 dbSNP
rs918714773 3867 dbSNP
rs576203904 3871 dbSNP
rs972723744 3877 dbSNP
rs1405280317 3879 dbSNP
rs963042597 3884 dbSNP
rs1335971829 3897 dbSNP
rs1016145559 3904 dbSNP
rs1032893968 3905 dbSNP
rs985132956 3910 dbSNP
rs998939682 3911 dbSNP
rs1279229747 3918 dbSNP
rs867639512 3920 dbSNP
rs575125218 3924 dbSNP
rs192068913 3927 dbSNP
rs1230372174 3933 dbSNP
rs1261750819 3933 dbSNP
rs1323454159 3933 dbSNP
rs958677440 3933 dbSNP
rs1258679924 3935 dbSNP
rs1436474026 3936 dbSNP
rs1180645663 3937 dbSNP
rs1252168247 3938 dbSNP
rs1034124805 3943 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
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 GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection ...

- Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' aggguccuugguacuAUAGUGu 5'
                         |||||| 
Target 5' ------------cccUAUCACa 3'
1 - 10
Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 9880.0
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 GSM1065670. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' aggguccuugguacuAUAGUGu 5'
                         |||||| 
Target 5' ------------cccUAUCACa 3'
1 - 10
Article - Memczak S; Jens M; Elefsinioti A; Torti F; et al.
- Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
Experimental Support 3 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.

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 4 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 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 GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000300101.2 | 3UTR | CCCUAUCACAUUUACCUCCAUACCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1065670
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / 4-thiouridine, 3_ML_LG
Location of target site ENST00000300101.2 | 3UTR | CCCUAUCACAUUUACCUCCAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000300101.2 | 3UTR | CAACAGCCCUAUCACAUUUACCUCCAUACCUG
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
45 hsa-miR-3689a-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT112230 MDM4 MDM4, p53 regulator 2 2
MIRT188656 FAM76A family with sequence similarity 76 member A 2 2
MIRT200911 ZNF264 zinc finger protein 264 2 4
MIRT210595 KBTBD8 kelch repeat and BTB domain containing 8 2 6
MIRT299207 CSRNP3 cysteine and serine rich nuclear protein 3 2 2
MIRT317524 SLC39A7 solute carrier family 39 member 7 2 2
MIRT355849 SGMS2 sphingomyelin synthase 2 2 4
MIRT443052 THRB thyroid hormone receptor beta 2 2
MIRT446631 SDC3 syndecan 3 2 2
MIRT449409 TRIM5 tripartite motif containing 5 2 2
MIRT463561 ZBTB39 zinc finger and BTB domain containing 39 2 6
MIRT465704 TNFAIP1 TNF alpha induced protein 1 2 2
MIRT472688 MYCBP MYC binding protein 2 4
MIRT493287 LNPEP leucyl and cystinyl aminopeptidase 2 2
MIRT499338 RAB25 RAB25, member RAS oncogene family 2 2
MIRT501723 OVOL1 ovo like transcriptional repressor 1 2 2
MIRT507977 BCL2L13 BCL2 like 13 2 4
MIRT511811 HDGF heparin binding growth factor 2 6
MIRT516711 PIK3CG phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma 2 4
MIRT527853 SMOC1 SPARC related modular calcium binding 1 2 2
MIRT531286 SLC7A7 solute carrier family 7 member 7 2 2
MIRT531894 INVS inversin 2 8
MIRT536807 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 2 2
MIRT537807 EFNB2 ephrin B2 2 4
MIRT544335 LPGAT1 lysophosphatidylglycerol acyltransferase 1 2 2
MIRT547142 PGM3 phosphoglucomutase 3 2 2
MIRT547429 MED4 mediator complex subunit 4 2 2
MIRT563354 ZNF181 zinc finger protein 181 2 2
MIRT564849 ZBED3 zinc finger BED-type containing 3 2 2
MIRT566426 PIGA phosphatidylinositol glycan anchor biosynthesis class A 2 2
MIRT572512 KIAA0232 KIAA0232 2 2
MIRT574682 HNRNPA3 heterogeneous nuclear ribonucleoprotein A3 2 2
MIRT608820 ONECUT3 one cut homeobox 3 2 6
MIRT608886 CLIC6 chloride intracellular channel 6 2 2
MIRT608959 GIMAP1 GTPase, IMAP family member 1 2 4
MIRT609012 HPS3 HPS3, biogenesis of lysosomal organelles complex 2 subunit 1 2 2
MIRT641431 SCUBE3 signal peptide, CUB domain and EGF like domain containing 3 2 2
MIRT661841 ZNF587B zinc finger protein 587B 2 2
MIRT690651 RPF2 ribosome production factor 2 homolog 2 2
MIRT704619 CLIP1 CAP-Gly domain containing linker protein 1 2 2
MIRT708714 PTPLAD2 3-hydroxyacyl-CoA dehydratase 4 1 1
MIRT710663 CSTF2T cleavage stimulation factor subunit 2 tau variant 2 2
MIRT711260 TPCN2 two pore segment channel 2 2 2
MIRT714649 FSTL1 follistatin like 1 2 2
MIRT718518 COL19A1 collagen type XIX alpha 1 chain 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-3689a Dabrafenib 44462760 NSC764134 approved sensitive cell line (A375)
hsa-miR-3689a-5p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-3689a-5p Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-3689a-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)

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