pre-miRNA Information
pre-miRNA hsa-mir-4271   
Genomic Coordinates chr3: 49274120 - 49274186
Description Homo sapiens miR-4271 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4271
Sequence 39| GGGGGAAGAAAAGGUGGGG |57
Evidence Experimental
Experiments SOLiD
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN30481495 1 COSMIC
COSN31532060 5 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs760829741 1 dbSNP
rs1277951968 2 dbSNP
rs189148716 3 dbSNP
rs757021935 4 dbSNP
rs1285201145 6 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TNPO2   
Synonyms IPO3, KPNB2B, TRN2
Description transportin 2
Transcript NM_001136195   
Other Transcripts NM_001136196 , NM_013433   
Expression
Putative miRNA Targets on TNPO2
3'UTR of TNPO2
(miRNA target sites are highlighted)
>TNPO2|NM_001136195|3'UTR
   1 GTGATCATGGAGACTGCCAGGTTTCTGTCTGCGTCGTCGTCGGAGGGATTACTGGGGAGTGCGCTGCATCCGGAAGTCGC
  81 TGTGCCCTGGTTGAGGGGGGTTAGGGAGGAGTGAGTGGGACTCAAATCCAGATGCCTTCCCCGTCCGTCCGTCCGTCCGT
 161 CCATCCGTCCACTTGCCCTCCTGGCAGGTGGGTGGGGCCACCATGCTCATCCTACAAACGGGGAGGTGGGGGGGACTTCT
 241 GGTGGGCAAGGGCCCCTGGGCTCTAATAGGGTCATCTCTGGCAGCCCACTTGGGCCAGCTACGTGGGAGGGAGGAATTAC
 321 ACAGCTGACCGAATCCGGCTTCGGATGAGGTGAGGGAGGAGCAGGTCAGGAGGGGGGCCCTCGTAGGGACGCGTACACTC
 401 ACACGGACACACATGGCCACACGCATGTGCGGGTGCCATAACCGGCGAGGCTGGGCCAGCCGCTCCACCATTTCCCCGAC
 481 TGCATGGAGACAGTAGAATTAGTGAACCCCTGAGTTAACCCGTAAGGCCTTCCGTGTAACCTGCATCTAGAGTTTAAGAA
 561 GCTTCTGCTGTTTTGCCGGAATTGGCGGTGACTGGGGAGGGCTGGGTGGGTGGGGGGCCTCAGGCGGGATCTCGGGGCGG
 641 GGGGAGGAGGATGGTGACCTTGGGAGTCGCCCTGTCAGCACGCACATGCTTGGGACCCACTCCACACACTCCCTGCCAGC
 721 TTTGTTGCAGCCTCAGCTGGTGGTGTCTCCGTCCTTATCCTAGCCTAGCTCGCAGGGTGAGAACCACTGGAGTGGCTGGG
 801 GCTGGCCAGAGGTCACCGTTTCTCCTTCCTGTGTGCTCCAGTGGCTTTTGAAGACACTGGGTTGGGACCTTTTTCCTGAA
 881 GAGAGCTGGGTGTAGCCAGAGCTACTGGCACCTACCCCGAGCATCTCTCTCTGTAAGCAGCTTCAGGGGCAGTCCGTTTC
 961 TCTGTGCTTCTGAAACCCCCTTCTCACGTTTCAGGCCCCAGTTTTAACTCAAGGCCTGGGGCAGGGGCGTTTAATTGATG
1041 ATGACAGAGGACACAGGTTTTTGCCAGCAAAAAGGAAAACCAAGGCTTGGTGGAAGGGAAAGGTGGTGTGTCCCCTGTTC
1121 CCTATTCCATCTCCCTGGGACTTCCTGCTCATCATAGTACCCAGTGAGCCCAGAGATCCTACTAGACTGGGTCAGCAATT
1201 CTAGAGAACCTTCCGGAATAGTCTGGGAACATGGTCAAGGTGGAAGGGGCTCCCCTAGAGAGGGTGGGGGTGTAGTTACT
1281 TCCCAGTTGGCCAGAAAACTGGGCCTTGCAGACCCCCTTAGCATTTTTTCCCTTTTTTTCCTTCCCTGCTTTCTACTTCT
1361 TTGGGGAGCCCCTTGTGTTTTGGAGTCTGACTGGAGTCTCGCATCCTGGGGCCTGCTCCATCCATCCCTCCTGGGCGCCA
1441 GACCCTCCATCCAAGCCCTGTGTCTTTCCATAGTCAGGGTCAGGCCCTGCATCTATTCCAAGGGGCACTCAGTACACATT
1521 CCATAAATTAGCTGGGTGTCCCTGCACGCCCACCCCATGAAACTCGAGCAGGTCTCTGGAAGCCATTTGTTAAAAAAAAA
1601 AAAAAAAGTTTTAAAAATACCTTTTAATTTTCTGGTAATTCCAGTTCTTTGAAGCATCCTCTGCTGGGTCTTGGGGTGTG
1681 TGGATGGATTGGCTGTCTGATGGGATTGGTAACCCCTCGCTACTCAAGATGGGGGGATACAAACACCTTCAGGGAAGGGG
1761 AGCCTGGTTCTTCTCGTTTTCCTTTTTTTTTTTTTTTTTAAAAAAAAACTATTTAATTTTTTAATTTATTTTTGGTTGTT
1841 TTTTGCACAATGAAGTTTCAGCTTCTCAACCTTCTCCCCTACCCAGGGCTGTGGACCCAGACTGGCCTTGAGCCACAGTC
1921 CCTCTTTCCCTCCTCACCCTCTTCCCCCTGCGGGCTCCCGGGTCTGTCCATTTGTTACTGTGCTGTGCTGGGGATTGGCG
2001 CCGAGGTGGCGTGAGATTCCACTTGTGTAGAACTTTGTTGAGTAAAGATCAGTTTCTTGTGAACTCCTTA
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' ggGGUGGAAAAGAAGGGGg 5'
            :||||   |||||||| 
Target 5' ccTCACC--CTCTTCCCCc 3'
1932 - 1948 153.00 -27.30
2
miRNA  3' ggGGUGGAAAA-GAAGGGGg 5'
            || ::|||| ||||||: 
Target 5' tcCCTTTTTTTCCTTCCCTg 3'
1329 - 1348 145.00 -18.60
3
miRNA  3' gggguggaaaaGAAGGGGg 5'
                     ||||||| 
Target 5' aatccagatgcCTTCCCCg 3'
125 - 143 140.00 -15.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31504146 9 COSMIC
COSN28161975 21 COSMIC
COSN26565119 33 COSMIC
COSN31528480 123 COSMIC
COSN31531697 236 COSMIC
COSN28709569 409 COSMIC
COSN31563282 480 COSMIC
COSN31539927 505 COSMIC
COSN26042863 513 COSMIC
COSN31543563 527 COSMIC
COSN32058530 535 COSMIC
COSN31595684 615 COSMIC
COSN21731164 629 COSMIC
COSN31600954 647 COSMIC
COSN20115467 1057 COSMIC
COSN27035152 1110 COSMIC
COSN28461251 1111 COSMIC
COSN21642252 1297 COSMIC
COSN30080724 1439 COSMIC
COSN31595681 1491 COSMIC
COSN31591581 1601 COSMIC
COSN20115465 1674 COSMIC
COSN7354110 1862 COSMIC
COSN16255123 1880 COSMIC
COSN17076204 1881 COSMIC
COSN30653991 1899 COSMIC
COSN19356431 1910 COSMIC
COSN8604980 1992 COSMIC
COSN30715311 1997 COSMIC
COSN28868058 2049 COSMIC
COSN24395353 2093 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs956247007 1 dbSNP
rs773772249 2 dbSNP
rs1422962182 3 dbSNP
rs1301312223 6 dbSNP
rs770315588 7 dbSNP
rs748647034 8 dbSNP
rs781740087 11 dbSNP
rs372878686 12 dbSNP
rs1193988691 14 dbSNP
rs1316034265 15 dbSNP
rs745383330 16 dbSNP
rs1258539552 18 dbSNP
rs1246840772 20 dbSNP
rs766960714 23 dbSNP
rs778529837 27 dbSNP
rs1211050367 29 dbSNP
rs1207682440 31 dbSNP
rs756958656 34 dbSNP
rs1260887756 39 dbSNP
rs1483342282 40 dbSNP
rs1244522799 41 dbSNP
rs1192334465 45 dbSNP
rs973523174 50 dbSNP
rs965017454 54 dbSNP
rs1459371104 57 dbSNP
rs910784631 60 dbSNP
rs572328564 61 dbSNP
rs193063858 62 dbSNP
rs559572812 63 dbSNP
rs74668716 64 dbSNP
rs954832117 65 dbSNP
rs1023391891 68 dbSNP
rs1321995666 77 dbSNP
rs1291557171 79 dbSNP
rs1401843948 83 dbSNP
rs1031775692 87 dbSNP
rs1012038130 92 dbSNP
rs1217285289 93 dbSNP
rs1280420198 95 dbSNP
rs1312448421 96 dbSNP
rs963303396 97 dbSNP
rs1215412782 99 dbSNP
rs1226141909 100 dbSNP
rs532105127 103 dbSNP
rs1260486820 105 dbSNP
rs1488981246 113 dbSNP
rs1193671154 114 dbSNP
rs1016608790 115 dbSNP
rs998917997 117 dbSNP
rs1381356018 120 dbSNP
rs968773945 121 dbSNP
rs1051509632 123 dbSNP
rs1309893464 124 dbSNP
rs1158273735 125 dbSNP
rs1448827521 125 dbSNP
rs997302472 133 dbSNP
rs1319004001 134 dbSNP
rs1330477385 137 dbSNP
rs1434165450 138 dbSNP
rs1374555999 143 dbSNP
rs1371443657 144 dbSNP
rs900258800 145 dbSNP
rs1022168432 147 dbSNP
rs1010737585 154 dbSNP
rs761221004 155 dbSNP
rs1033976912 161 dbSNP
rs1039178392 164 dbSNP
rs565030258 166 dbSNP
rs1419523965 172 dbSNP
rs947558561 175 dbSNP
rs1350733888 177 dbSNP
rs914798905 182 dbSNP
rs1167118566 183 dbSNP
rs1378718982 188 dbSNP
rs1441732617 190 dbSNP
rs1003219030 195 dbSNP
rs1390075186 203 dbSNP
rs934659830 205 dbSNP
rs1325440639 214 dbSNP
rs906162756 222 dbSNP
rs1047486648 224 dbSNP
rs970077635 225 dbSNP
rs1179826064 228 dbSNP
rs1378710205 228 dbSNP
rs1283154729 229 dbSNP
rs1442146010 232 dbSNP
rs929080953 233 dbSNP
rs898906226 235 dbSNP
rs1177041761 236 dbSNP
rs1037865045 237 dbSNP
rs1248130873 240 dbSNP
rs543008536 241 dbSNP
rs1005249902 245 dbSNP
rs1016165160 245 dbSNP
rs1471853748 245 dbSNP
rs373243036 245 dbSNP
rs910806467 245 dbSNP
rs1329111194 248 dbSNP
rs575633783 249 dbSNP
rs950408425 249 dbSNP
rs1029971248 254 dbSNP
rs1333105140 254 dbSNP
rs1338281438 254 dbSNP
rs988102138 279 dbSNP
rs933356409 282 dbSNP
rs900226402 290 dbSNP
rs924632469 293 dbSNP
rs1218536567 295 dbSNP
rs773948686 301 dbSNP
rs1341904684 302 dbSNP
rs1196677819 304 dbSNP
rs554811653 307 dbSNP
rs1021715942 310 dbSNP
rs989331903 315 dbSNP
rs1038814615 316 dbSNP
rs1011731192 319 dbSNP
rs1425608002 334 dbSNP
rs189203088 335 dbSNP
rs373274869 335 dbSNP
rs893316983 335 dbSNP
rs1033613494 337 dbSNP
rs183389597 343 dbSNP
rs1397381662 358 dbSNP
rs906432204 362 dbSNP
rs553927979 374 dbSNP
rs539270365 377 dbSNP
rs1313004483 379 dbSNP
rs1025964958 384 dbSNP
rs1369412226 387 dbSNP
rs571643667 402 dbSNP
rs767847252 405 dbSNP
rs1399998344 411 dbSNP
rs879817581 412 dbSNP
rs556629597 413 dbSNP
rs1228641522 414 dbSNP
rs759896357 418 dbSNP
rs1343198519 419 dbSNP
rs1365172353 424 dbSNP
rs537804187 425 dbSNP
rs147800598 426 dbSNP
rs1051921106 434 dbSNP
rs1191528413 436 dbSNP
rs933599316 438 dbSNP
rs1362594996 442 dbSNP
rs1158971930 444 dbSNP
rs1434126156 447 dbSNP
rs549433229 448 dbSNP
rs924851339 453 dbSNP
rs1269842623 455 dbSNP
rs974152712 456 dbSNP
rs1436261815 458 dbSNP
rs941873336 459 dbSNP
rs375299699 460 dbSNP
rs909075999 460 dbSNP
rs983314238 460 dbSNP
rs1299445072 464 dbSNP
rs529994205 465 dbSNP
rs1490104120 471 dbSNP
rs1263416258 472 dbSNP
rs374909792 474 dbSNP
rs1304464699 485 dbSNP
rs1030269167 486 dbSNP
rs566025726 487 dbSNP
rs964401873 498 dbSNP
rs766573905 499 dbSNP
rs778409118 504 dbSNP
rs959252990 505 dbSNP
rs926471787 506 dbSNP
rs1437393208 508 dbSNP
rs1298994531 512 dbSNP
rs547264573 513 dbSNP
rs532343744 515 dbSNP
rs1293465440 516 dbSNP
rs564778777 525 dbSNP
rs1032223000 526 dbSNP
rs549867193 528 dbSNP
rs1376495477 529 dbSNP
rs940663849 537 dbSNP
rs1238215037 538 dbSNP
rs531171509 539 dbSNP
rs1382801385 540 dbSNP
rs962980572 543 dbSNP
rs1016035810 544 dbSNP
rs1244066768 545 dbSNP
rs1263624740 550 dbSNP
rs1379878296 552 dbSNP
rs535825581 558 dbSNP
rs948705781 559 dbSNP
rs1480300690 560 dbSNP
rs1237307354 562 dbSNP
rs542246454 565 dbSNP
rs1178572480 567 dbSNP
rs1038448157 574 dbSNP
rs1423921534 575 dbSNP
rs1195346356 576 dbSNP
rs1416380638 579 dbSNP
rs941410123 588 dbSNP
rs1327056879 589 dbSNP
rs1400003320 591 dbSNP
rs190690537 593 dbSNP
rs1260359640 594 dbSNP
rs1374249619 594 dbSNP
rs1200515974 596 dbSNP
rs1484232281 599 dbSNP
rs1261139986 602 dbSNP
rs908630248 603 dbSNP
rs573315154 604 dbSNP
rs888860242 610 dbSNP
rs186841797 615 dbSNP
rs1052400743 616 dbSNP
rs1206287663 621 dbSNP
rs560883772 622 dbSNP
rs997691924 623 dbSNP
rs1482703374 627 dbSNP
rs903438695 628 dbSNP
rs1258983432 629 dbSNP
rs1229818543 637 dbSNP
rs1476503793 638 dbSNP
rs1041958390 649 dbSNP
rs947384204 650 dbSNP
rs867647572 656 dbSNP
rs914552496 658 dbSNP
rs1055779874 659 dbSNP
rs1408583983 660 dbSNP
rs1172923959 664 dbSNP
rs937450991 668 dbSNP
rs964370729 669 dbSNP
rs1295030731 671 dbSNP
rs1396648293 673 dbSNP
rs1405042241 674 dbSNP
rs1335255031 675 dbSNP
rs1469638752 676 dbSNP
rs1311191091 677 dbSNP
rs1357443096 678 dbSNP
rs1401394956 680 dbSNP
rs1017315300 681 dbSNP
rs1415404191 683 dbSNP
rs1172384459 685 dbSNP
rs1460200040 686 dbSNP
rs928728835 688 dbSNP
rs1372138382 689 dbSNP
rs982391384 690 dbSNP
rs970493371 691 dbSNP
rs1216143180 693 dbSNP
rs909224467 693 dbSNP
rs957324750 695 dbSNP
rs1424994088 698 dbSNP
rs1241234374 704 dbSNP
rs1182844667 707 dbSNP
rs1031434072 708 dbSNP
rs558432743 710 dbSNP
rs1259819119 714 dbSNP
rs1048943222 715 dbSNP
rs999417247 716 dbSNP
rs931921847 720 dbSNP
rs545231526 721 dbSNP
rs578127235 722 dbSNP
rs1013157907 725 dbSNP
rs1297617280 726 dbSNP
rs1250948618 727 dbSNP
rs77129227 736 dbSNP
rs1343407464 737 dbSNP
rs1245639207 744 dbSNP
rs1385030224 750 dbSNP
rs1313559838 751 dbSNP
rs1366632641 752 dbSNP
rs894740709 754 dbSNP
rs919181797 756 dbSNP
rs1452473706 757 dbSNP
rs1348089428 759 dbSNP
rs971925203 763 dbSNP
rs1283222305 764 dbSNP
rs887160338 767 dbSNP
rs1218544066 770 dbSNP
rs963247578 778 dbSNP
rs1016374707 780 dbSNP
rs722571 781 dbSNP
rs1397152972 785 dbSNP
rs1454851057 790 dbSNP
rs1158179251 795 dbSNP
rs953291843 804 dbSNP
rs1333862838 812 dbSNP
rs1405872431 813 dbSNP
rs1402448563 820 dbSNP
rs929104569 821 dbSNP
rs1040306623 822 dbSNP
rs1395383681 825 dbSNP
rs943232894 833 dbSNP
rs1459001019 835 dbSNP
rs1030042381 838 dbSNP
rs1382794249 839 dbSNP
rs1162366541 840 dbSNP
rs910471868 845 dbSNP
rs1239902402 848 dbSNP
rs1179459808 853 dbSNP
rs1223799242 854 dbSNP
rs1285603240 861 dbSNP
rs1436965189 863 dbSNP
rs1468398944 867 dbSNP
rs1212255984 869 dbSNP
rs538352445 878 dbSNP
rs1210589678 884 dbSNP
rs957089837 893 dbSNP
rs975921525 895 dbSNP
rs1471205435 897 dbSNP
rs140106305 899 dbSNP
rs147951107 900 dbSNP
rs11542174 902 dbSNP
rs1011857867 912 dbSNP
rs1166888664 919 dbSNP
rs1394925596 935 dbSNP
rs1245328658 940 dbSNP
rs1445669606 944 dbSNP
rs1326461849 950 dbSNP
rs893374862 955 dbSNP
rs769392497 968 dbSNP
rs1283058356 986 dbSNP
rs1355091909 993 dbSNP
rs1231988579 994 dbSNP
rs75508418 995 dbSNP
rs937355584 1000 dbSNP
rs533642390 1001 dbSNP
rs1045779629 1013 dbSNP
rs949234060 1014 dbSNP
rs919116371 1015 dbSNP
rs1256873599 1030 dbSNP
rs887137724 1033 dbSNP
rs1418404743 1034 dbSNP
rs1464927681 1035 dbSNP
rs971859861 1037 dbSNP
rs776931616 1038 dbSNP
rs1410159787 1042 dbSNP
rs1332991769 1044 dbSNP
rs998302990 1047 dbSNP
rs901264773 1051 dbSNP
rs34801836 1057 dbSNP
rs5827160 1058 dbSNP
rs941988469 1058 dbSNP
rs1419750742 1059 dbSNP
rs1382125632 1060 dbSNP
rs1196591317 1067 dbSNP
rs943196973 1068 dbSNP
rs1484734788 1069 dbSNP
rs547670025 1070 dbSNP
rs1258173916 1076 dbSNP
rs910447619 1078 dbSNP
rs909131702 1082 dbSNP
rs779496737 1088 dbSNP
rs986203377 1096 dbSNP
rs1374567309 1097 dbSNP
rs935663720 1100 dbSNP
rs1469440625 1101 dbSNP
rs953040816 1102 dbSNP
rs538425754 1106 dbSNP
rs1030508434 1108 dbSNP
rs1377927758 1110 dbSNP
rs924337033 1111 dbSNP
rs722572 1115 dbSNP
rs748146424 1118 dbSNP
rs1293955198 1119 dbSNP
rs1328561288 1121 dbSNP
rs1221902049 1124 dbSNP
rs1488628764 1136 dbSNP
rs971084863 1143 dbSNP
rs1286964561 1145 dbSNP
rs1302968346 1145 dbSNP
rs1222510761 1147 dbSNP
rs1345943648 1156 dbSNP
rs917017659 1162 dbSNP
rs1281099214 1172 dbSNP
rs1485534859 1173 dbSNP
rs1020493015 1174 dbSNP
rs1203306321 1176 dbSNP
rs991585959 1178 dbSNP
rs1447374252 1185 dbSNP
rs1192727465 1190 dbSNP
rs1011743360 1194 dbSNP
rs1455284064 1198 dbSNP
rs893418242 1198 dbSNP
rs1275884926 1211 dbSNP
rs1225701646 1212 dbSNP
rs549741854 1213 dbSNP
rs1017583879 1231 dbSNP
rs1302089084 1234 dbSNP
rs1453760181 1236 dbSNP
rs539254679 1240 dbSNP
rs1001947229 1244 dbSNP
rs1287637025 1251 dbSNP
rs1387702415 1260 dbSNP
rs1383156138 1275 dbSNP
rs1400115336 1282 dbSNP
rs1346386540 1284 dbSNP
rs779101167 1292 dbSNP
rs1005838795 1296 dbSNP
rs907170984 1297 dbSNP
rs1045811616 1313 dbSNP
rs1316415576 1331 dbSNP
rs1025609215 1345 dbSNP
rs951450502 1345 dbSNP
rs755107938 1346 dbSNP
rs879164240 1347 dbSNP
rs1212885274 1351 dbSNP
rs1250887165 1352 dbSNP
rs754125029 1357 dbSNP
rs766666569 1360 dbSNP
rs1193875941 1366 dbSNP
rs1249300706 1372 dbSNP
rs570230616 1373 dbSNP
rs941831416 1375 dbSNP
rs1039840246 1383 dbSNP
rs1416807246 1383 dbSNP
rs1174143211 1387 dbSNP
rs77738821 1398 dbSNP
rs1164726913 1406 dbSNP
rs1392728676 1409 dbSNP
rs182555548 1411 dbSNP
rs1054774937 1412 dbSNP
rs189574189 1413 dbSNP
rs1389781202 1419 dbSNP
rs1309203950 1421 dbSNP
rs1317502023 1429 dbSNP
rs144257660 1441 dbSNP
rs1243980232 1443 dbSNP
rs903103522 1444 dbSNP
rs771106869 1452 dbSNP
rs967153580 1463 dbSNP
rs1446972540 1465 dbSNP
rs1020043444 1466 dbSNP
rs1041343499 1469 dbSNP
rs1473242389 1474 dbSNP
rs949736675 1483 dbSNP
rs990318893 1491 dbSNP
rs1463362350 1500 dbSNP
rs369401898 1508 dbSNP
rs1282246018 1515 dbSNP
rs957524817 1518 dbSNP
rs1035025347 1519 dbSNP
rs916981892 1522 dbSNP
rs376802655 1542 dbSNP
rs1351182515 1546 dbSNP
rs937501665 1549 dbSNP
rs530082557 1550 dbSNP
rs1357234150 1560 dbSNP
rs1233709046 1573 dbSNP
rs377321434 1574 dbSNP
rs1305465411 1581 dbSNP
rs560577421 1585 dbSNP
rs1251458520 1590 dbSNP
rs1485065284 1606 dbSNP
rs1208032946 1608 dbSNP
rs994128144 1620 dbSNP
rs374752524 1623 dbSNP
rs1025919700 1629 dbSNP
rs567673926 1630 dbSNP
rs957030319 1634 dbSNP
rs1038383941 1645 dbSNP
rs941871213 1647 dbSNP
rs887595075 1648 dbSNP
rs1171112802 1661 dbSNP
rs1410811807 1671 dbSNP
rs1377253246 1674 dbSNP
rs1448652064 1674 dbSNP
rs1269446765 1690 dbSNP
rs1359610010 1690 dbSNP
rs773262218 1690 dbSNP
rs879113120 1690 dbSNP
rs1050668363 1694 dbSNP
rs545707856 1698 dbSNP
rs1018369268 1700 dbSNP
rs1486975833 1701 dbSNP
rs796356190 1710 dbSNP
rs893891406 1723 dbSNP
rs923175193 1725 dbSNP
rs1188605752 1738 dbSNP
rs1040102486 1745 dbSNP
rs945655129 1746 dbSNP
rs1391053025 1753 dbSNP
rs868433785 1758 dbSNP
rs556437282 1760 dbSNP
rs1171914498 1764 dbSNP
rs1396962011 1768 dbSNP
rs912991868 1769 dbSNP
rs989867594 1777 dbSNP
rs1032808780 1781 dbSNP
rs1317573199 1791 dbSNP
rs1432670504 1792 dbSNP
rs149173356 1792 dbSNP
rs578085385 1795 dbSNP
rs186041378 1801 dbSNP
rs1238590389 1809 dbSNP
rs980671144 1813 dbSNP
rs1222650081 1815 dbSNP
rs1284210113 1818 dbSNP
rs1218432693 1819 dbSNP
rs1249020436 1819 dbSNP
rs1315612714 1819 dbSNP
rs1185895135 1828 dbSNP
rs11542173 1832 dbSNP
rs971714465 1834 dbSNP
rs1460268844 1839 dbSNP
rs949701029 1842 dbSNP
rs1255055928 1843 dbSNP
rs1478408195 1844 dbSNP
rs1158023052 1846 dbSNP
rs1024473723 1848 dbSNP
rs1033118566 1852 dbSNP
rs1308929183 1855 dbSNP
rs1393458668 1858 dbSNP
rs1402349610 1858 dbSNP
rs1270415433 1859 dbSNP
rs1213497963 1863 dbSNP
rs1379208832 1864 dbSNP
rs1317096563 1865 dbSNP
rs544866869 1868 dbSNP
rs937071418 1874 dbSNP
rs1331278202 1877 dbSNP
rs1450436347 1879 dbSNP
rs1063903 1880 dbSNP
rs9467 1881 dbSNP
rs1230769274 1882 dbSNP
rs1269246020 1882 dbSNP
rs1292326501 1882 dbSNP
rs141687742 1882 dbSNP
rs868115219 1882 dbSNP
rs1444083398 1883 dbSNP
rs1231240365 1884 dbSNP
rs1356517062 1884 dbSNP
rs1471159665 1884 dbSNP
rs1166779464 1885 dbSNP
rs1391052794 1885 dbSNP
rs1408989724 1885 dbSNP
rs1417007795 1885 dbSNP
rs1459699856 1885 dbSNP
rs1231882721 1886 dbSNP
rs1326358194 1886 dbSNP
rs1355334041 1886 dbSNP
rs1355776759 1886 dbSNP
rs1409840684 1886 dbSNP
rs57928803 1886 dbSNP
rs773938632 1886 dbSNP
rs779986693 1886 dbSNP
rs1168553188 1887 dbSNP
rs1326134456 1889 dbSNP
rs1409459939 1890 dbSNP
rs1189864222 1891 dbSNP
rs1195442529 1891 dbSNP
rs1205903032 1891 dbSNP
rs1271069526 1891 dbSNP
rs1457155812 1891 dbSNP
rs1484087321 1891 dbSNP
rs1023803862 1893 dbSNP
rs1385878198 1894 dbSNP
rs1474920753 1895 dbSNP
rs574170948 1904 dbSNP
rs796394990 1910 dbSNP
rs1429863919 1915 dbSNP
rs1311706990 1916 dbSNP
rs984282715 1921 dbSNP
rs1243037638 1923 dbSNP
rs930149443 1926 dbSNP
rs1481792990 1932 dbSNP
rs555906126 1937 dbSNP
rs1230849767 1938 dbSNP
rs1268663147 1943 dbSNP
rs918824294 1949 dbSNP
rs1272545114 1951 dbSNP
rs977039868 1952 dbSNP
rs749057740 1953 dbSNP
rs1315496258 1960 dbSNP
rs1247311345 1963 dbSNP
rs994136454 1969 dbSNP
rs1295528938 1971 dbSNP
rs777582718 1973 dbSNP
rs1278561097 1976 dbSNP
rs547866367 1978 dbSNP
rs755968082 1984 dbSNP
rs961333999 1985 dbSNP
rs534133480 1987 dbSNP
rs1347875928 1994 dbSNP
rs1165435460 2002 dbSNP
rs1172535992 2005 dbSNP
rs1445195651 2006 dbSNP
rs767503639 2011 dbSNP
rs1186136370 2016 dbSNP
rs754946490 2023 dbSNP
rs762359855 2024 dbSNP
rs751757599 2026 dbSNP
rs766696892 2028 dbSNP
rs889857160 2029 dbSNP
rs1435972337 2032 dbSNP
rs1223623216 2033 dbSNP
rs1050308332 2034 dbSNP
rs996407524 2037 dbSNP
rs901761909 2039 dbSNP
rs985866082 2041 dbSNP
rs865962070 2042 dbSNP
rs1327092788 2044 dbSNP
rs1324531820 2049 dbSNP
rs1467617741 2056 dbSNP
rs1300901781 2061 dbSNP
rs1385272553 2062 dbSNP
rs1167656490 2066 dbSNP
rs1369946672 2070 dbSNP
rs1304751689 2071 dbSNP
rs1424996206 2075 dbSNP
rs1235449326 2081 dbSNP
rs945707425 2082 dbSNP
rs1369877863 2083 dbSNP
rs912878097 2084 dbSNP
rs1463120917 2085 dbSNP
rs1000018073 2092 dbSNP
rs527784359 2093 dbSNP
rs1431118850 2095 dbSNP
rs565419609 2098 dbSNP
rs1054509950 2102 dbSNP
rs573209662 2104 dbSNP
rs1020157432 2106 dbSNP
rs1200610780 2108 dbSNP
rs1482932773 2110 dbSNP
rs1273183690 2112 dbSNP
rs1207898592 2117 dbSNP
rs1340194855 2118 dbSNP
rs1434426521 2119 dbSNP
rs895747120 2120 dbSNP
rs1055350351 2124 dbSNP
rs762427748 2130 dbSNP
rs935792468 2132 dbSNP
rs927033400 2144 dbSNP
rs1405401018 2146 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 GSM545212. RNA binding protein: AGO1. Condition:Control PAR-CLIP data was present in GSM545214. RNA binding protein: AGO3. Condition:Control PAR-CLIP data was present in GSM545215. RNA binding protein: AGO4. Condition:Control ...

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

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 30000.0
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 GSM714645. RNA binding protein: AGO2. Condition:completeT1 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
Experimental Support 3 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions hESCs (WA-09)
Disease 30000.0
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 SRR359787. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Lipchina I; Elkabetz Y; Hafner M; Sheridan et al., 2011, Genes & development.

Article - Lipchina I; Elkabetz Y; Hafner M; Sheridan et al.
- Genes & development, 2011
MicroRNAs are important regulators in many cellular processes, including stem cell self-renewal. Recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. However, their role in human embryonic stem (ES) cells (hESCs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. Here, we performed comprehensive microRNA profiling in hESCs and in purified neural and mesenchymal derivatives. Using a combination of AGO cross-linking and microRNA perturbation experiments, together with computational prediction, we identified the targets of the miR-302/367 cluster, the most abundant microRNAs in hESCs. Functional studies identified novel roles of miR-302/367 in maintaining pluripotency and regulating hESC differentiation. We show that in addition to its role in TGF-beta signaling, miR-302/367 promotes bone morphogenetic protein (BMP) signaling by targeting BMP inhibitors TOB2, DAZAP2, and SLAIN1. This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area.
LinkOut: [PMID: 22012620]
Experimental Support 4 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 5 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions MCF7
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 SRR1045082. RNA binding protein: AGO2. Condition:Untreated ...

- Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology.

Article - Farazi TA; Ten Hoeve JJ; Brown M; et al.
- Genome biology, 2014
BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
LinkOut: [PMID: 24398324]
Experimental Support 6 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HCT116
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 ERX177605. RNA binding protein: AGO2. Condition:KO_D_AGO_CLIP_2_7 PAR-CLIP data was present in ERX177615. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_3_5 PAR-CLIP data was present in ERX177618. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_3_8 PAR-CLIP data was present in ERX177627. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_4_5 PAR-CLIP data was present in ERX177629. RNA binding protein: AGO2. Condition:KO_D_AGO_CLIP_4_7 PAR-CLIP data was present in ERX177603. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_2_5 PAR-CLIP data was present in ERX177623. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_4_1 PAR-CLIP data was present in ERX177609. RNA binding protein: AGO2. Condition:KO_D_AGO_CLIP_2_11 PAR-CLIP data was present in ERX177610. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_2_12 PAR-CLIP data was present in ERX177617. RNA binding protein: AGO2. Condition:KO_D_AGO_CLIP_3_7 PAR-CLIP data was present in ERX177622. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_3_12 PAR-CLIP data was present in ERX177633. RNA binding protein: AGO2. Condition:KO_D_AGO_CLIP_4_11 PAR-CLIP data was present in ERX177634. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_4_12 PAR-CLIP data was present in ERX177606. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_2_8 PAR-CLIP data was present in ERX177600. RNA binding protein: AGO2. Condition:p53_V_Ago_CLIP_2_2 PAR-CLIP data was present in ERX177612. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_3_2 PAR-CLIP data was present in ERX177624. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_4_2 PAR-CLIP data was present in ERX177621. RNA binding protein: AGO2. Condition:KO_D_AGO_CLIP_3_11 PAR-CLIP data was present in ERX177614. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_3_4 PAR-CLIP data was present in ERX177602. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_2_4 PAR-CLIP data was present in ERX177630. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_4_8 PAR-CLIP data was present in ERX177599. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_2_1 PAR-CLIP data was present in ERX177611. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_3_1 ...

- Krell J; Stebbing J; Carissimi C; Dabrowska et al., 2016, Genome research.

Article - Krell J; Stebbing J; Carissimi C; Dabrowska et al.
- Genome research, 2016
DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.
LinkOut: [PMID: 26701625]
Experimental Support 7 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 SRX1760639. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP-MDV_A PAR-CLIP data was present in SRX1760583. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP_A PAR-CLIP data was present in SRX1760591. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP_B PAR-CLIP data was present in SRX1760641. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP-MDV_B ...

- 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 GSM4903830
Method / RBP HITS-CLIP / AGO
Cell line / Condition Human neurons / CTLTD_shCTL_b
Location of target site NM_001136195 | 3UTR | CGUCCGUCCGUCCGUCCGUCCAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161238
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_013433 | 3UTR | CAGCUUCUCAACCUUCUCCCCUACCCAGGGCUGUGGACCCAGACUGGCCUUGAGCCACAGUCCCUCUUUCCCUCCUCACCCUCUUCCCCCUGCGGGCUCCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_001136195 | 3UTR | UUCUCAACCUUCUCCCCUACCCAGGGCUGUGGACCCAGACUGGCCUUGAGCCACAGUCCCUCUUUCCCUCCUCACCCUCUUCCCCCUGCGGGCUCCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_001136195 | 3UTR | UUCUCAACCUUCUCCCCUACCCAGGGCUGUGGACCCAGACUGGCCUUGAGCCACAGUCCCUCUUUCCCUCCUCACCCUCUUCCCCCUGCGGGCUCCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_001136195 | 3UTR | UCAACCUUCUCCCCUACCCAGGGCUGUGGACCCAGACUGGCCUUGAGCCACAGUCCCUCUUUCCCUCCUCACCCUCUUCCCCCUGCGGGCUCCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_013433 | 3UTR | CUCCCCUACCCAGGGCUGUGGACCCAGACUGGCCUUGAGCCACAGUCCCUCUUUCCCUCCUCACCCUCUUCCCCCUGCGGGCUCCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_001136195 | 3UTR | ACCUUCUCCCCUACCCAGGGCUGUGGACCCAGACUGGCCUUGAGCCACAGUCCCUCUUUCCCUCCUCACCCUCUUCCCCCUGCGGGCUCCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM545212
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / Control
Location of target site ENST00000425528.1 | 3UTR | UCCCCGUCCGUCCGUCCGUCCGUCCAUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 9 for dataset GSM545214
Method / RBP PAR-CLIP / AGO3
Cell line / Condition HEK293 / Control
Location of target site ENST00000425528.1 | 3UTR | CCCGUCCGUCCGUCCGUCCGUCCAUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 10 for dataset GSM545215
Method / RBP PAR-CLIP / AGO4
Cell line / Condition HEK293 / Control
Location of target site ENST00000425528.1 | 3UTR | UCCCCGUCCGUCCGUCCGUCCGUCCAUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 11 for dataset GSM714645
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repB
Location of target site ENST00000425528.1 | 3UTR | CCCGUCCGUCCGUCCGUCCGUCCAUCCG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 12 for dataset SRR359787
Method / RBP PAR-CLIP / AGO2
Cell line / Condition hESCs (WA-09) / 4-thiouridine, RNase T1
Location of target site ENST00000425528.1 | 3UTR | UCCCCGUCCGUCCGUCCGUCCGUCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22012620 / SRX103431
CLIP-seq Viewer Link
CLIP-seq Support 13 for dataset SRR1045082
Method / RBP PAR-CLIP / AGO2
Cell line / Condition MCF7 / Untreated
Location of target site ENST00000425528.1 | 3UTR | CCCCGUCCGUCCGUCCGUCCGUCCAUCCG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24398324 / SRX388831
CLIP-seq Viewer Link
CLIP-seq Support 14 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000425528.1 | 3UTR | UCCCUCUUUCCCUCCUCACCCUCUUCCCCCUG
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
181 hsa-miR-4271 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT066209 MARCH9 membrane associated ring-CH-type finger 9 2 2
MIRT079367 CCDC137 coiled-coil domain containing 137 2 2
MIRT081183 MIDN midnolin 2 4
MIRT083278 ZCCHC3 zinc finger CCHC-type containing 3 2 6
MIRT086207 HOXD13 homeobox D13 2 2
MIRT133713 SKI SKI proto-oncogene 2 4
MIRT150653 SLC27A1 solute carrier family 27 member 1 2 2
MIRT159166 NRBP1 nuclear receptor binding protein 1 2 2
MIRT160059 TET3 tet methylcytosine dioxygenase 3 2 4
MIRT180856 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT181931 MARK2 microtubule affinity regulating kinase 2 2 2
MIRT190628 BCL2L2-PABPN1 BCL2L2-PABPN1 readthrough 2 2
MIRT190654 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT196107 MPRIP myosin phosphatase Rho interacting protein 2 2
MIRT263248 SGPL1 sphingosine-1-phosphate lyase 1 2 2
MIRT321168 EIF4H eukaryotic translation initiation factor 4H 2 2
MIRT338624 SHMT2 serine hydroxymethyltransferase 2 2 2
MIRT366301 GDI1 GDP dissociation inhibitor 1 2 4
MIRT375172 ARIH1 ariadne RBR E3 ubiquitin protein ligase 1 2 2
MIRT441488 NCEH1 neutral cholesterol ester hydrolase 1 2 2
MIRT442333 WNT9B Wnt family member 9B 2 2
MIRT443889 CNKSR3 CNKSR family member 3 2 2
MIRT445880 WBP1L WW domain binding protein 1 like 2 2
MIRT449312 MRO maestro 2 2
MIRT449844 BCL2L13 BCL2 like 13 2 2
MIRT450304 DRAXIN dorsal inhibitory axon guidance protein 2 2
MIRT450515 EMX1 empty spiracles homeobox 1 2 2
MIRT451243 ZNF444 zinc finger protein 444 2 2
MIRT451713 OLR1 oxidized low density lipoprotein receptor 1 2 2
MIRT451792 TLR5 toll like receptor 5 2 2
MIRT451823 ALDH3B1 aldehyde dehydrogenase 3 family member B1 2 2
MIRT451906 ILK integrin linked kinase 2 2
MIRT452181 KIAA1456 KIAA1456 2 4
MIRT452242 TRAM1 translocation associated membrane protein 1 2 2
MIRT452544 ZNF467 zinc finger protein 467 2 2
MIRT452605 REPIN1 replication initiator 1 2 2
MIRT454505 ZFYVE27 zinc finger FYVE-type containing 27 2 2
MIRT454657 FBXL18 F-box and leucine rich repeat protein 18 2 2
MIRT455354 KDM5C lysine demethylase 5C 2 2
MIRT455452 EPB41L4B erythrocyte membrane protein band 4.1 like 4B 2 2
MIRT455587 TAF12 TATA-box binding protein associated factor 12 2 2
MIRT456501 PFKFB2 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 2 2
MIRT456815 PIGP phosphatidylinositol glycan anchor biosynthesis class P 2 2
MIRT457425 NOL10 nucleolar protein 10 2 2
MIRT457468 SLC35F6 solute carrier family 35 member F6 2 2
MIRT457660 SERINC1 serine incorporator 1 2 2
MIRT458231 NXPH3 neurexophilin 3 2 2
MIRT458374 ITM2C integral membrane protein 2C 2 2
MIRT458667 GPR35 G protein-coupled receptor 35 2 2
MIRT459665 VPS37C VPS37C, ESCRT-I subunit 2 2
MIRT459825 TPP1 tripeptidyl peptidase 1 2 2
MIRT460564 FEM1A fem-1 homolog A 2 2
MIRT460725 ASXL3 additional sex combs like 3, transcriptional regulator 2 2
MIRT461121 RAB36 RAB36, member RAS oncogene family 2 2
MIRT461529 C14orf1 ergosterol biosynthesis 28 homolog 2 2
MIRT461750 DDX11 DEAD/H-box helicase 11 2 2
MIRT462570 STS steroid sulfatase 2 2
MIRT462798 NTN1 netrin 1 2 2
MIRT463030 ZNF689 zinc finger protein 689 2 2
MIRT463991 WDTC1 WD and tetratricopeptide repeats 1 2 2
MIRT464684 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 2
MIRT465439 TP53 tumor protein p53 2 2
MIRT465512 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT465649 TNPO2 transportin 2 2 10
MIRT465947 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 2
MIRT466028 TMEM189 transmembrane protein 189 2 2
MIRT468076 SHOC2 SHOC2, leucine rich repeat scaffold protein 2 6
MIRT468131 SH3PXD2A SH3 and PX domains 2A 2 2
MIRT468498 SESN2 sestrin 2 2 2
MIRT468879 RREB1 ras responsive element binding protein 1 2 2
MIRT469318 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 2 2
MIRT469558 RARA retinoic acid receptor alpha 2 2
MIRT469793 RAB15 RAB15, member RAS oncogene family 2 2
MIRT469896 PTRF caveolae associated protein 1 2 2
MIRT470235 PRRC2A proline rich coiled-coil 2A 2 2
MIRT470808 PLXND1 plexin D1 2 2
MIRT471597 PAQR5 progestin and adipoQ receptor family member 5 2 10
MIRT471710 OTUB1 OTU deubiquitinase, ubiquitin aldehyde binding 1 2 2
MIRT471752 OGT O-linked N-acetylglucosamine (GlcNAc) transferase 2 2
MIRT472978 MRRF mitochondrial ribosome recycling factor 2 2
MIRT473538 MAX MYC associated factor X 2 2
MIRT473581 MAT2A methionine adenosyltransferase 2A 2 2
MIRT473970 LRRC58 leucine rich repeat containing 58 2 2
MIRT474223 LCOR ligand dependent nuclear receptor corepressor 2 4
MIRT474553 KLHDC3 kelch domain containing 3 2 2
MIRT474777 KIAA0895L KIAA0895 like 2 2
MIRT476042 GRSF1 G-rich RNA sequence binding factor 1 2 2
MIRT476438 GBA2 glucosylceramidase beta 2 2 2
MIRT477773 E2F3 E2F transcription factor 3 2 4
MIRT477946 DPM2 dolichyl-phosphate mannosyltransferase subunit 2, regulatory 2 2
MIRT478782 CRTC2 CREB regulated transcription coactivator 2 2 2
MIRT479320 VPS72 vacuolar protein sorting 72 homolog 2 2
MIRT480405 C19orf47 chromosome 19 open reading frame 47 2 2
MIRT480593 BTRC beta-transducin repeat containing E3 ubiquitin protein ligase 2 2
MIRT480963 BBC3 BCL2 binding component 3 2 2
MIRT481127 AZIN1 antizyme inhibitor 1 2 4
MIRT481444 ARRB2 arrestin beta 2 2 2
MIRT481687 AR androgen receptor 2 2
MIRT481730 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT482386 AEN apoptosis enhancing nuclease 2 2
MIRT482564 ABHD2 abhydrolase domain containing 2 2 2
MIRT482605 ABHD14B abhydrolase domain containing 14B 2 2
MIRT483256 CITED4 Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4 2 4
MIRT483531 TAGLN2 transgelin 2 2 2
MIRT483840 UNC5B unc-5 netrin receptor B 2 4
MIRT483935 LENG8 leukocyte receptor cluster member 8 2 4
MIRT484414 SNX19 sorting nexin 19 2 2
MIRT484487 SLC9A1 solute carrier family 9 member A1 2 2
MIRT484609 SIX3 SIX homeobox 3 2 6
MIRT484703 RNF11 ring finger protein 11 2 2
MIRT485244 POGZ pogo transposable element derived with ZNF domain 2 2
MIRT485607 FOSL1 FOS like 1, AP-1 transcription factor subunit 2 4
MIRT485965 RTBDN retbindin 2 2
MIRT487308 GLTSCR1 BRD4 interacting chromatin remodeling complex associated protein 2 2
MIRT487329 SREBF1 sterol regulatory element binding transcription factor 1 2 4
MIRT487410 CACNB1 calcium voltage-gated channel auxiliary subunit beta 1 2 2
MIRT487607 C20orf96 chromosome 20 open reading frame 96 2 2
MIRT487689 CDK14 cyclin dependent kinase 14 2 2
MIRT487787 GPR20 G protein-coupled receptor 20 2 4
MIRT488026 ADO 2-aminoethanethiol dioxygenase 2 2
MIRT488476 B3GALNT2 beta-1,3-N-acetylgalactosaminyltransferase 2 2 2
MIRT488761 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT489161 MRPL12 mitochondrial ribosomal protein L12 2 4
MIRT489529 MRE11A MRE11 homolog, double strand break repair nuclease 2 8
MIRT489774 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT489878 MPLKIP M-phase specific PLK1 interacting protein 2 2
MIRT490094 FN3K fructosamine 3 kinase 2 2
MIRT490202 PKNOX2 PBX/knotted 1 homeobox 2 2 2
MIRT490283 ISL2 ISL LIM homeobox 2 2 2
MIRT490377 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT491035 ALPK3 alpha kinase 3 2 2
MIRT491186 JUND JunD proto-oncogene, AP-1 transcription factor subunit 2 4
MIRT491766 ZNF385A zinc finger protein 385A 2 2
MIRT491888 YWHAE tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon 2 2
MIRT491981 UNK unkempt family zinc finger 2 2
MIRT492400 SDK1 sidekick cell adhesion molecule 1 2 2
MIRT493647 HDLBP high density lipoprotein binding protein 2 2
MIRT494010 DUSP9 dual specificity phosphatase 9 2 2
MIRT494167 CNOT6L CCR4-NOT transcription complex subunit 6 like 2 2
MIRT495712 PADI1 peptidyl arginine deiminase 1 2 2
MIRT496873 AHCYL2 adenosylhomocysteinase like 2 2 2
MIRT499175 RBPJL recombination signal binding protein for immunoglobulin kappa J region like 2 2
MIRT501652 PHLDA3 pleckstrin homology like domain family A member 3 2 2
MIRT506645 MAPK1 mitogen-activated protein kinase 1 2 4
MIRT510590 TUBB2A tubulin beta 2A class IIa 2 6
MIRT511907 FKBP1A FK506 binding protein 1A 2 2
MIRT513063 ANKRD45 ankyrin repeat domain 45 2 2
MIRT513104 DYNAP dynactin associated protein 2 2
MIRT521804 POM121C POM121 transmembrane nucleoporin C 2 2
MIRT523520 GLUL glutamate-ammonia ligase 2 2
MIRT525085 FRK fyn related Src family tyrosine kinase 2 2
MIRT530930 SCIN scinderin 2 2
MIRT533501 TRIM71 tripartite motif containing 71 2 2
MIRT538560 CECR2 CECR2, histone acetyl-lysine reader 2 2
MIRT544556 CSNK2A1 casein kinase 2 alpha 1 2 2
MIRT555912 ORMDL3 ORMDL sphingolipid biosynthesis regulator 3 2 2
MIRT560405 TMEM69 transmembrane protein 69 2 2
MIRT560664 RTN3 reticulon 3 2 2
MIRT564061 CDT1 chromatin licensing and DNA replication factor 1 2 2
MIRT565504 SP1 Sp1 transcription factor 2 2
MIRT570014 COL1A2 collagen type I alpha 2 chain 2 2
MIRT572321 HSPB6 heat shock protein family B (small) member 6 2 2
MIRT573229 TRIM21 tripartite motif containing 21 2 2
MIRT573487 IQSEC3 IQ motif and Sec7 domain 3 2 2
MIRT574137 MARVELD1 MARVEL domain containing 1 2 2
MIRT574323 ZNF703 zinc finger protein 703 2 2
MIRT620939 OSMR oncostatin M receptor 2 2
MIRT650080 MTL5 testis expressed metallothionein like protein 2 2
MIRT684553 ZNF708 zinc finger protein 708 2 2
MIRT685841 ANGEL1 angel homolog 1 2 2
MIRT688551 DCAF16 DDB1 and CUL4 associated factor 16 2 2
MIRT701985 MIER3 MIER family member 3 2 2
MIRT703899 EPT1 selenoprotein I 2 2
MIRT706388 MC2R melanocortin 2 receptor 2 2
MIRT707487 UGT2B4 UDP glucuronosyltransferase family 2 member B4 2 2
MIRT711885 INSIG2 insulin induced gene 2 2 2
MIRT719164 KIF6 kinesin family member 6 2 2
MIRT721294 C3orf36 chromosome 3 open reading frame 36 2 2
MIRT721775 ARL6IP4 ADP ribosylation factor like GTPase 6 interacting protein 4 2 2
MIRT723763 NKIRAS2 NFKB inhibitor interacting Ras like 2 2 2
MIRT725485 GPR26 G protein-coupled receptor 26 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-4 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 up-regulated
miR-4271 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved sensitive High Gastric Cancer cell line (BGC823)
hsa-miR-4271 Platinum-based doublet chemotherapy sensitive High Lung Adenocarcinoma tissue
hsa-miR-4271 Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-4271 Fluorouracil 3385 NSC19893 approved sensitive High Pancreatic Cancer cell line (PATU8988)
hsa-miR-4271 Cisplatin 5460033 NSC119875 approved resistant Low Tongue Squamous Cell Carcinoma cell line (CAL-27, SCC-9)
hsa-miR-4271 Paclitaxel 36314 NSC125973 approved resistant High Non-Small Cell Lung Cancer cell line (H460)
hsa-miR-4271 Anlotinib 25017411 NSC832523 sensitive Low Non-Small Cell Lung Cancer cell line (A549, PDC, H460)
hsa-miR-4271 Gefitinib 123631 NSC715055 approved sensitive Low Non-Small Cell Lung Cancer cell line (A549, PDC, H460)
hsa-miR-4271 Icotinib 22024915 NSC800770 sensitive Low Non-Small Cell Lung Cancer cell line (A549, PDC, H460)
hsa-miR-4271 Erlotinib 176870 NSC718781 approved sensitive Low Non-Small Cell Lung Cancer cell line (A549, PDC, H460)
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved resistant cell line (W1)
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-mir-4271 Androstenedione+Anastrozole resistant cell line (MCF-7)
hsa-mir-4271 Androstenedione+Letrozole resistant cell line (MCF-7)
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved sensitive cell line (BGC-823)
hsa-miR-4271 Cisplatin 5460033 NSC119875 approved resistant cell line (CAL-27) (cytosolic RNA)
hsa-miR-4271 Cisplatin 5460033 NSC119875 approved resistant cell line (CAL-27) (total RNA)
hsa-miR-4271 Osimertinib 71496458 NSC779217 approved resistant cell line (H1975)
hsa-miR-4271 Platinum-based doublet chemotherapy sensitive tissue (lung adenocarcinoma)
hsa-miR-4271 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4271 Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM16)
hsa-miR-4271 Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)
hsa-miR-4271 Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (100 ng/ml)
hsa-miR-4271 Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)

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