miRTarBase - #MIRT039586


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pre-miRNA Information
pre-miRNA hsa-mir-628   
Genomic Coordinates chr15: 55372940 - 55373034
Synonyms MIRN628, hsa-mir-628, MIR628
Description Homo sapiens miR-628 stem-loop
Comment The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies .
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-628-3p
Sequence 61| UCUAGUAAGAGUGGCAGUCGA |81
Evidence Experimental
Experiments Microarray
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 7 15 - 55372968 29233923 MiREDiBase
A-to-I 8 15 - 55372967 29233923 MiREDiBase
C-to-U 19 15 - 55372956 20591823 MiREDiBase
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN26969715 1 COSMIC
COSN30123186 10 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1410255602 2 dbSNP
rs1401315366 3 dbSNP
rs1322836365 4 dbSNP
rs1158103480 8 dbSNP
rs1216611749 11 dbSNP
rs749619551 13 dbSNP
rs778157225 18 dbSNP
rs756600789 19 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TGFBRAP1   
Synonyms TRAP-1, TRAP1, VPS3
Description transforming growth factor beta receptor associated protein 1
Transcript NM_001142621   
Other Transcripts NM_004257   
Expression
Putative miRNA Targets on TGFBRAP1
3'UTR of TGFBRAP1
(miRNA target sites are highlighted)		 
>TGFBRAP1|NM_001142621|3'UTR
   1 AAAGCTTGGCCCAAGGGTGCGAGGGGAACTCCGAGTTCTTTCTGAGCCTGCTGGACATGAAGAGCAGATGACCACCATGC
  81 TCTGTGTCAGCCAGGACGAAGGGAGACATCTGGGTGCCAGGGAGCCTTCCGTCCATACGCAACAAGGACTCCTCGCTGCT
 161 GACCAGGCTCTATGAATGTACATGGAATGACCAGGCTCTATGAATGTACATGGAAAACCCCTAAAAATCCCCAAAACAGA
 241 AACATACAAGAGTTCACCTGTCCAGGTACATAGTAATCCAAGACAGAGGTCTACTTTGAAAAAAAAAAAAAGGGAGTCTT
 321 CCTCATGCAGTCCAGACCCAGGTGGGGGATCCCCCACCACCCCCACACTCCAACCTTTAGACTCATGTTTGCACTGGAAA
 401 CGTGGCTTCACCATGGCTGGCGACAAAGTCCTCTCTTGCCTGGGTGAGTGGCGAGGGCACAGAGCCTCATGGGGGTCAGC
 481 CTTGCCCTCCTGCAGAAACACGTTCTCCATCCACGCCGCTCACTCATGGGCCCATTTCCCAGGGTTACCTCGTGGGCTCT
 561 GCCTTTGCCCTCAGAAACGGCTGACCCTGGAGAAGTACCTTTGTTCCTTCTTTCTTCCTCTCCGGCTCTCAGCTCCCAAA
 641 AGATTCTGCCTTGTGTACCCAAGCACTCACTCTTGGGTGAACTAATGCTTCTGGCTGCCTAGCAAGTGAAGATCTGTTGA
 721 GAAACTGAGAACGCTCCAAGAGAGAAGCTGCTCTCCCCTCCTTGAAGAAGCCGCGGACACGGGAAACCCACGGCGGGCAA
 801 GGGCCCAGCTGTGTGCTCCTTTCCTGTCATGGCATCTGCTGATTTGAAACTCCATGACGAACACGTTGAACTAAACATTT
 881 TTATTTAAATTTGTATCATGTTCGTAGTTGCTCTCTTGTTGAGAGAGTCATCTGTCCTGTTTGTTAGGGGTATTTTTTCT
 961 TGTTAAAATGTATCTCCTGTTGAATACTCGGGAAATTCAAAGGGAAGTGTGGTCAGCACACACTGAGCGTTCTTTTCTGG
1041 AGAGGCCGGTTTTAGCCTCGTACCTTTAGCAGGACCGACAGCGGGTGGAAGGGCCCGTGTGCTGGATGGGGGTGTCGCCT
1121 CCTGGATGGCACACCCTCCCGAGGACATCCAGACAGGCTGTGTCACCCTCCAGCACTTTATGTGCCTGCTCTGAGGTGTC
1201 CTGAACACACAGCAACGGCCTCTCCTTCATCACAGGCCGGGGATTCCTTTTGTGTTTCTGTATAACATCGATGACGAGCT
1281 GAAGCTGTTGTCACTTCACTGCCCTCTTTGGAATTTCTTCATTGTGCTGACTGATTCTATTAGGGGCTAACAATAAAGGC
1361 AGTCTACCCACTACTATCATGCTTGGGAAACAAGCGTCAGCTTGTACATATGACAAGAGAGGACCCTGAATACACCCTCT
1441 CTTCATCAGCCCAAGCCTTACTGAGGTGGGATGAAGACCTCATTCTCTGTTCTTTAAAACATGTTTCGTGAACTAATATT
1521 GGTCCATGTATTTTTTGTCCTTTTGGGACTCTAAGTGGGTCAAGAAGCAAAAACATCCATGTGTTGTTTGGGGGGAATTG
1601 GCACCATTTTTTCCTGACTATGTTTCAATTAACTAAAGAATAAATGATGAAGAAATTCTCCTTGTAGCACAACTGTATGC
1681 TGTGTAAATTGGTGTGAGCTCAAAGCCCAGTCATGTGTTTTACCTGTGGGTGACTCTGTTGTAGAATGGTCATATTACTG
1761 CATATGTTATCATGACAACTTGTGAGTTTGAGTTTATATTTCTCAAAGAACAAGTTACCCGTATATGCAACATTGCGCCA
1841 TTAAAAGCTTATTTCTCTGTACACAAAATGGGTAAAATCTTGAAAAAACTTAGTAATTTCTCATTCCTAACACACAGACA
1921 GAGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCG
2001 ATTCTGCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGTGCATGCCACCACGCCCAGCTAATTTTTGTATTTTTAGTA
2081 GAGACGGGGTTTCACCATGTTGGCCAGGATGGTCTCGGTCTCCTGACCTCGTGATCTGCCTGCCTCGGCCTCCCAAAGTG
2161 CTGGGATTACAGGCGTGAGCCACTGCGCCCAGCCAACACTAGTCATTTTTATTTTTTCACTGAACATTGATCAATACTCT
2241 AAAATGTTTGTCATCCTTTAGAATAATGGGAATTAAAGTTGAGCAGTTTTCCATCTCTACCAAATCCTTCACCACAAGCA
2321 GCATTCTATTACAGTATGAAGAATTGTCTCATATGTTAAAACTGTACTTTTCTCTAACCTTTCTCTCACTCCTACAAGGC
2401 CCTTTTCTCAAATCATATTTCTGAGAGAAATGTATGGTTCTTTCTCACAGGCCTGCTGATTTGTAACTGTGCCATCGAAT
2481 AGAGCAATTAGATCCATCAGACCTTTTTCCCCTCATTAGGTTCAGTGGAACCATTCTGGTTAAAACAGCATGAACTGAAC
2561 TCAGTTTACATTCATATTCTATGGGCAATACCATTTGGTTTTTGGAACTGTTTATCTGCTGTTCCCTATCAAGTATTAAT
2641 GTAGGGATGTCACTCAGGCTGCGTTGCACTGGGCTGAGTTCAACTGCGACGCTCTCACTGACGCGTGCTTACATGTGCTT
2721 CTCACTTCCGGAGCACAGGCAGGTGGCTGCGGGGTCCCAGCTCTGAATGGATGCCCATGATGCAACTGGGGCAGCCCTTG
2801 CTTTTTGCTTGCTCTCCCACAGAAACCTTTGTCCTTGCAACTTTATCCTTTGTCCCGATTGGGTCCCAGATACACAAAAT
2881 GTACAAATGTAAACTTGCTCATTTTATTAAAATTCTTTTAGTTCTTTGTTCTTTCTGTAATTTTTTAAAATAAAAATTGC
2961 CTTGATGGAGTGATGGTTTTCACTCGCACCATAAAAAAAAAAAAAAAAA
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' agcuGACGGUGAGAAUGAUCu 5'
              |||:| : :||::||| 
Target 5' tcatCTGTCCTGTTTGTTAGg 3'
 928 - 948 125.00 -12.80
2 
miRNA  3' agcuGACGGUGAGAAUGAUCu 5'
              :|| :|:|:||| ||| 
Target 5' atttTTG-TATTTTTAGTAGa 3'
 2063 - 2082 124.00 -9.30
3 
miRNA  3' agcUG-ACGGUGAGAAUGAUcu 5'
             || |||:  |:|||:||  
Target 5' taaACTTGCTCATTTTATTAaa 3'
 2890 - 2911 122.00 -5.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30473005 12 COSMIC
COSN30106800 15 COSMIC
COSN31546330 17 COSMIC
COSN30450034 21 COSMIC
COSN31509543 22 COSMIC
COSN31599066 42 COSMIC
COSN30179165 44 COSMIC
COSN8980472 72 COSMIC
COSN31510879 79 COSMIC
COSN13925900 102 COSMIC
COSN31264072 160 COSMIC
COSN29030300 280 COSMIC
COSM36950 298 COSMIC
COSN27307781 299 COSMIC
COSN22118330 422 COSMIC
COSN22044973 501 COSMIC
COSN2488310 566 COSMIC
COSN28241939 733 COSMIC
COSN6150636 1162 COSMIC
COSN6553421 1222 COSMIC
COSN8980471 1238 COSMIC
COSM7205963 1343 COSMIC
COSN1221008 1457 COSMIC
COSN6150635 1540 COSMIC
COSN24541053 1619 COSMIC
COSN32097928 1658 COSMIC
COSN30545320 1736 COSMIC
COSN31488605 1761 COSMIC
COSN19623762 1779 COSMIC
COSN15323652 1836 COSMIC
COSN31582724 1837 COSMIC
COSN24450926 1926 COSMIC
COSN26689199 1951 COSMIC
COSN29508942 1965 COSMIC
COSN31597413 1966 COSMIC
COSN28573940 2000 COSMIC
COSN8980470 2021 COSMIC
COSN32097927 2136 COSMIC
COSN15271767 2476 COSMIC
COSN8264050 2508 COSMIC
COSN8980469 2694 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs754468183 1 dbSNP
rs748985933 5 dbSNP
rs779646367 8 dbSNP
rs1031064642 9 dbSNP
rs369127087 10 dbSNP
rs750183351 12 dbSNP
rs1393105725 13 dbSNP
rs767369006 16 dbSNP
rs527980337 19 dbSNP
rs370797276 20 dbSNP
rs1287433617 21 dbSNP
rs764329667 23 dbSNP
rs1346235273 26 dbSNP
rs763103630 27 dbSNP
rs775896205 30 dbSNP
rs765515996 32 dbSNP
rs911402854 33 dbSNP
rs987005851 46 dbSNP
rs1165884206 47 dbSNP
rs1166967587 52 dbSNP
rs1018108953 58 dbSNP
rs1426927745 64 dbSNP
rs955663075 67 dbSNP
rs922925250 82 dbSNP
rs1006806166 87 dbSNP
rs1176527432 95 dbSNP
rs971733940 97 dbSNP
rs961752125 102 dbSNP
rs888396822 108 dbSNP
rs1297015511 114 dbSNP
rs1360647979 117 dbSNP
rs1401134754 126 dbSNP
rs1048212960 130 dbSNP
rs994424670 131 dbSNP
rs560455687 138 dbSNP
rs1016402565 139 dbSNP
rs1056909653 140 dbSNP
rs1213971963 148 dbSNP
rs1427534150 154 dbSNP
rs1285391704 155 dbSNP
rs1488692416 160 dbSNP
rs938288826 172 dbSNP
rs1266607088 173 dbSNP
rs545669470 175 dbSNP
rs1191502728 177 dbSNP
rs958747828 178 dbSNP
rs1157743358 182 dbSNP
rs1380359774 183 dbSNP
rs1034215574 185 dbSNP
rs1368463033 186 dbSNP
rs878996001 187 dbSNP
rs375132177 188 dbSNP
rs577597935 191 dbSNP
rs1002787589 195 dbSNP
rs748517287 198 dbSNP
rs907142147 206 dbSNP
rs1294461286 207 dbSNP
rs556099612 215 dbSNP
rs1230962964 216 dbSNP
rs531353194 216 dbSNP
rs70953504 216 dbSNP
rs1238231613 218 dbSNP
rs1354692891 223 dbSNP
rs1044485575 229 dbSNP
rs543988534 233 dbSNP
rs1222267601 244 dbSNP
rs1248232760 245 dbSNP
rs1479567117 246 dbSNP
rs529751973 248 dbSNP
rs1238336061 251 dbSNP
rs1441189087 252 dbSNP
rs1267100552 253 dbSNP
rs1161111806 257 dbSNP
rs1242542688 266 dbSNP
rs1320525513 270 dbSNP
rs1405290786 271 dbSNP
rs1054914311 294 dbSNP
rs1352136429 298 dbSNP
rs75199411 299 dbSNP
rs1331138030 300 dbSNP
rs1377861263 307 dbSNP
rs200573901 311 dbSNP
rs1228801385 312 dbSNP
rs1355814929 312 dbSNP
rs752886250 312 dbSNP
rs1315992093 313 dbSNP
rs889949799 313 dbSNP
rs62154712 314 dbSNP
rs1197728547 326 dbSNP
rs1258524770 332 dbSNP
rs1051230951 333 dbSNP
rs934234469 344 dbSNP
rs918812070 347 dbSNP
rs1236371541 348 dbSNP
rs564295759 351 dbSNP
rs140377677 354 dbSNP
rs989642555 355 dbSNP
rs972979292 363 dbSNP
rs1395717452 365 dbSNP
rs1464538450 366 dbSNP
rs1170381008 367 dbSNP
rs1295756398 381 dbSNP
rs935516914 383 dbSNP
rs1332504583 386 dbSNP
rs1340105634 393 dbSNP
rs1448759457 398 dbSNP
rs1286057853 401 dbSNP
rs146729524 402 dbSNP
rs1160011234 404 dbSNP
rs144730650 410 dbSNP
rs1278606804 412 dbSNP
rs1319807735 413 dbSNP
rs958518743 419 dbSNP
rs1277396093 421 dbSNP
rs1442676904 430 dbSNP
rs1211560765 431 dbSNP
rs1239909240 434 dbSNP
rs965473851 440 dbSNP
rs1018268632 448 dbSNP
rs755452176 452 dbSNP
rs1478971778 471 dbSNP
rs952635445 475 dbSNP
rs1027328081 478 dbSNP
rs376980877 480 dbSNP
rs1358776243 489 dbSNP
rs952812383 495 dbSNP
rs539696414 501 dbSNP
rs1230744263 502 dbSNP
rs1274053674 514 dbSNP
rs545714516 517 dbSNP
rs1033054928 518 dbSNP
rs1283252657 519 dbSNP
rs1002613575 521 dbSNP
rs1007369598 526 dbSNP
rs1197466594 528 dbSNP
rs1488154430 530 dbSNP
rs889899015 534 dbSNP
rs1197139001 539 dbSNP
rs905638779 557 dbSNP
rs117012196 559 dbSNP
rs1051139555 573 dbSNP
rs770901746 577 dbSNP
rs1351013859 582 dbSNP
rs372037155 585 dbSNP
rs1419107122 586 dbSNP
rs947061892 587 dbSNP
rs894030960 589 dbSNP
rs1362330344 590 dbSNP
rs1234599527 595 dbSNP
rs571571263 598 dbSNP
rs1054456746 604 dbSNP
rs779494827 610 dbSNP
rs1322611170 611 dbSNP
rs550111442 623 dbSNP
rs924110461 624 dbSNP
rs1037653667 638 dbSNP
rs369643878 639 dbSNP
rs976922100 650 dbSNP
rs1240189878 651 dbSNP
rs531698762 666 dbSNP
rs908865283 667 dbSNP
rs1208650674 669 dbSNP
rs911320686 677 dbSNP
rs547843699 689 dbSNP
rs952829447 695 dbSNP
rs1439345635 696 dbSNP
rs756853937 697 dbSNP
rs752019686 698 dbSNP
rs567373819 704 dbSNP
rs1026864362 709 dbSNP
rs981206828 711 dbSNP
rs971186551 732 dbSNP
rs755640138 733 dbSNP
rs1379149712 737 dbSNP
rs989133330 744 dbSNP
rs1196550342 747 dbSNP
rs957335145 748 dbSNP
rs1033415760 753 dbSNP
rs961316865 758 dbSNP
rs1338251800 760 dbSNP
rs1035506801 762 dbSNP
rs1243451039 764 dbSNP
rs182622252 772 dbSNP
rs527916907 773 dbSNP
rs905587029 774 dbSNP
rs560718495 775 dbSNP
rs889805203 780 dbSNP
rs1252735558 781 dbSNP
rs1422069429 788 dbSNP
rs1023150482 791 dbSNP
rs1011209512 794 dbSNP
rs892798811 795 dbSNP
rs1052829052 797 dbSNP
rs545401972 805 dbSNP
rs902803279 810 dbSNP
rs1394909908 817 dbSNP
rs1312842156 818 dbSNP
rs1041178778 823 dbSNP
rs1341575429 848 dbSNP
rs1235722115 850 dbSNP
rs944222031 854 dbSNP
rs1279331867 855 dbSNP
rs527560664 858 dbSNP
rs141005920 859 dbSNP
rs931454461 860 dbSNP
rs756968815 864 dbSNP
rs1199893583 865 dbSNP
rs1257010489 866 dbSNP
rs926954682 870 dbSNP
rs758719173 895 dbSNP
rs949822329 898 dbSNP
rs72834059 899 dbSNP
rs961264929 903 dbSNP
rs72834058 904 dbSNP
rs1465280911 915 dbSNP
rs1302889830 918 dbSNP
rs1476803066 925 dbSNP
rs1376819820 928 dbSNP
rs1417144339 929 dbSNP
rs1296822735 934 dbSNP
rs1340451711 935 dbSNP
rs981244778 943 dbSNP
rs1194189773 947 dbSNP
rs543585358 950 dbSNP
rs1232858620 959 dbSNP
rs1443769781 962 dbSNP
rs540313577 970 dbSNP
rs1011741368 971 dbSNP
rs573102673 972 dbSNP
rs1262340436 978 dbSNP
rs557905739 979 dbSNP
rs76038924 989 dbSNP
rs765681921 990 dbSNP
rs954010579 999 dbSNP
rs1176406758 1022 dbSNP
rs998220346 1028 dbSNP
rs1157557416 1029 dbSNP
rs1360392803 1036 dbSNP
rs1432171247 1047 dbSNP
rs961463356 1048 dbSNP
rs998501614 1050 dbSNP
rs763809862 1057 dbSNP
rs762884060 1059 dbSNP
rs11685266 1060 dbSNP
rs889948760 1064 dbSNP
rs1285465387 1069 dbSNP
rs1049959128 1076 dbSNP
rs191195892 1077 dbSNP
rs1866040 1079 dbSNP
rs1037009213 1082 dbSNP
rs868220072 1083 dbSNP
rs928504051 1085 dbSNP
rs1437456054 1088 dbSNP
rs567308064 1095 dbSNP
rs912953504 1096 dbSNP
rs981361112 1097 dbSNP
rs970042001 1102 dbSNP
rs1172643468 1103 dbSNP
rs773469728 1105 dbSNP
rs1457686931 1112 dbSNP
rs990028697 1114 dbSNP
rs957331556 1116 dbSNP
rs1031403381 1117 dbSNP
rs1308624648 1125 dbSNP
rs549095616 1141 dbSNP
rs534004126 1142 dbSNP
rs1366213248 1144 dbSNP
rs925789052 1151 dbSNP
rs998442582 1153 dbSNP
rs1866039 1157 dbSNP
rs1018604624 1160 dbSNP
rs1438109250 1161 dbSNP
rs1239157187 1164 dbSNP
rs551910312 1166 dbSNP
rs922585435 1171 dbSNP
rs1470842586 1175 dbSNP
rs1179640787 1180 dbSNP
rs1412199161 1181 dbSNP
rs1423795101 1182 dbSNP
rs1257930695 1191 dbSNP
rs1229418805 1193 dbSNP
rs1166070892 1198 dbSNP
rs80075317 1200 dbSNP
rs1464253602 1201 dbSNP
rs976748749 1207 dbSNP
rs563243886 1209 dbSNP
rs551287747 1216 dbSNP
rs1378315501 1218 dbSNP
rs995706357 1226 dbSNP
rs1233866104 1233 dbSNP
rs1185674462 1235 dbSNP
rs1315896379 1238 dbSNP
rs2241796 1239 dbSNP
rs1037127493 1243 dbSNP
rs763618081 1260 dbSNP
rs939965653 1262 dbSNP
rs116705526 1267 dbSNP
rs1212306161 1269 dbSNP
rs1350661660 1270 dbSNP
rs540351103 1275 dbSNP
rs1234021131 1276 dbSNP
rs1479971456 1294 dbSNP
rs1420672574 1300 dbSNP
rs1336679491 1303 dbSNP
rs1309490711 1344 dbSNP
rs774707242 1346 dbSNP
rs1372783667 1351 dbSNP
rs1170446304 1352 dbSNP
rs1411910456 1357 dbSNP
rs1420427494 1357 dbSNP
rs1332237811 1359 dbSNP
rs1313546480 1361 dbSNP
rs948632019 1362 dbSNP
rs1002440129 1365 dbSNP
rs1415307903 1367 dbSNP
rs1243722253 1370 dbSNP
rs915854220 1373 dbSNP
rs1314584325 1382 dbSNP
rs1416636881 1383 dbSNP
rs990366692 1387 dbSNP
rs1338379185 1388 dbSNP
rs1217740352 1394 dbSNP
rs572857739 1395 dbSNP
rs924323443 1396 dbSNP
rs1453902874 1403 dbSNP
rs1287801790 1404 dbSNP
rs1013906203 1407 dbSNP
rs977138114 1408 dbSNP
rs1485681369 1414 dbSNP
rs891460896 1414 dbSNP
rs1260177367 1416 dbSNP
rs796774730 1420 dbSNP
rs1193361974 1431 dbSNP
rs1243092158 1434 dbSNP
rs1476509927 1436 dbSNP
rs1018552371 1439 dbSNP
rs985835516 1440 dbSNP
rs1435345785 1441 dbSNP
rs904350319 1444 dbSNP
rs1358523060 1445 dbSNP
rs564132890 1459 dbSNP
rs1028585575 1478 dbSNP
rs1238262322 1479 dbSNP
rs545934849 1494 dbSNP
rs1049570291 1501 dbSNP
rs186252525 1509 dbSNP
rs1434051367 1510 dbSNP
rs556872629 1520 dbSNP
rs932554919 1525 dbSNP
rs1273815257 1526 dbSNP
rs1348187374 1542 dbSNP
rs922494127 1545 dbSNP
rs1352105427 1552 dbSNP
rs976654194 1552 dbSNP
rs898669472 1560 dbSNP
rs768931295 1564 dbSNP
rs535344154 1569 dbSNP
rs1015811951 1575 dbSNP
rs1285376678 1580 dbSNP
rs939997747 1586 dbSNP
rs577471391 1590 dbSNP
rs1252557708 1591 dbSNP
rs1004294581 1592 dbSNP
rs907317227 1601 dbSNP
rs952931891 1603 dbSNP
rs1033835673 1613 dbSNP
rs1159020614 1614 dbSNP
rs1387060285 1617 dbSNP
rs772699409 1620 dbSNP
rs980907776 1620 dbSNP
rs1442697386 1621 dbSNP
rs970906128 1622 dbSNP
rs868239361 1635 dbSNP
rs1046126531 1647 dbSNP
rs948768360 1650 dbSNP
rs1322272638 1655 dbSNP
rs894355578 1658 dbSNP
rs1353507998 1659 dbSNP
rs1419729941 1662 dbSNP
rs1208410317 1664 dbSNP
rs1272992670 1666 dbSNP
rs1054380279 1667 dbSNP
rs935958508 1677 dbSNP
rs924439022 1682 dbSNP
rs977253918 1683 dbSNP
rs1418721795 1684 dbSNP
rs1236600313 1686 dbSNP
rs1407709951 1696 dbSNP
rs1192196058 1698 dbSNP
rs1182666029 1706 dbSNP
rs944438428 1712 dbSNP
rs553606772 1713 dbSNP
rs1365413896 1719 dbSNP
rs1471795537 1724 dbSNP
rs749750455 1726 dbSNP
rs1395027631 1736 dbSNP
rs1009833449 1741 dbSNP
rs1479279369 1743 dbSNP
rs891455459 1747 dbSNP
rs780513555 1762 dbSNP
rs953080132 1763 dbSNP
rs1028954673 1769 dbSNP
rs1308577910 1770 dbSNP
rs1338018932 1779 dbSNP
rs2460255 1779 dbSNP
rs1335842067 1782 dbSNP
rs1235538582 1784 dbSNP
rs1256355957 1791 dbSNP
rs1199371692 1813 dbSNP
rs1480444499 1820 dbSNP
rs181975696 1821 dbSNP
rs534037021 1823 dbSNP
rs1288254143 1826 dbSNP
rs1015759772 1830 dbSNP
rs149794731 1835 dbSNP
rs78776566 1836 dbSNP
rs559088250 1837 dbSNP
rs932463067 1847 dbSNP
rs1476025955 1852 dbSNP
rs1168311093 1856 dbSNP
rs1372093068 1861 dbSNP
rs1462214988 1869 dbSNP
rs1299381249 1870 dbSNP
rs1399510905 1872 dbSNP
rs756875302 1878 dbSNP
rs901015456 1889 dbSNP
rs1312737207 1901 dbSNP
rs1279042086 1909 dbSNP
rs1356697912 1914 dbSNP
rs1040906547 1919 dbSNP
rs939966028 1921 dbSNP
rs1220779024 1923 dbSNP
rs1253134394 1924 dbSNP
rs540066388 1926 dbSNP
rs139707945 1930 dbSNP
rs188878920 1933 dbSNP
rs1258089406 1941 dbSNP
rs894472834 1942 dbSNP
rs931344836 1946 dbSNP
rs529583043 1949 dbSNP
rs1000056095 1950 dbSNP
rs1400554185 1951 dbSNP
rs768340908 1953 dbSNP
rs374085269 1957 dbSNP
rs1172012847 1958 dbSNP
rs1375578707 1961 dbSNP
rs1433520328 1963 dbSNP
rs1041508257 1965 dbSNP
rs944555910 1968 dbSNP
rs546576645 1970 dbSNP
rs1417201313 1972 dbSNP
rs1359435309 1982 dbSNP
rs1177209473 1983 dbSNP
rs528174172 1990 dbSNP
rs185929673 1993 dbSNP
rs35886351 2000 dbSNP
rs920266843 2006 dbSNP
rs530762956 2021 dbSNP
rs962937684 2022 dbSNP
rs908815251 2024 dbSNP
rs982921586 2033 dbSNP
rs1191654834 2046 dbSNP
rs1485646910 2050 dbSNP
rs1238227330 2051 dbSNP
rs145677383 2053 dbSNP
rs1260089553 2054 dbSNP
rs377509792 2057 dbSNP
rs1486035164 2066 dbSNP
rs541740486 2070 dbSNP
rs1453475380 2071 dbSNP
rs968372925 2076 dbSNP
rs1396426675 2082 dbSNP
rs1012993034 2085 dbSNP
rs1345118660 2086 dbSNP
rs1454593748 2093 dbSNP
rs1291021521 2097 dbSNP
rs1262285272 2106 dbSNP
rs181092353 2109 dbSNP
rs1304237681 2112 dbSNP
rs189583511 2116 dbSNP
rs1000170890 2117 dbSNP
rs1306154128 2118 dbSNP
rs1317474331 2123 dbSNP
rs540670529 2130 dbSNP
rs1041623691 2131 dbSNP
rs1008644828 2132 dbSNP
rs1398895733 2134 dbSNP
rs1437203174 2139 dbSNP
rs890294339 2140 dbSNP
rs573147203 2146 dbSNP
rs538030840 2147 dbSNP
rs920362227 2149 dbSNP
rs1445378842 2166 dbSNP
rs1161692780 2170 dbSNP
rs558267802 2174 dbSNP
rs940353964 2175 dbSNP
rs539525440 2186 dbSNP
rs569455211 2187 dbSNP
rs1297734665 2189 dbSNP
rs372091879 2190 dbSNP
rs1426454782 2200 dbSNP
rs983036095 2204 dbSNP
rs1427943234 2211 dbSNP
rs1333804117 2218 dbSNP
rs1233677165 2224 dbSNP
rs879351484 2233 dbSNP
rs554852471 2234 dbSNP
rs1274618784 2242 dbSNP
rs557554557 2242 dbSNP
rs1004121448 2252 dbSNP
rs972089412 2253 dbSNP
rs917408849 2264 dbSNP
rs1481238329 2268 dbSNP
rs1179404827 2272 dbSNP
rs992088470 2278 dbSNP
rs958791743 2284 dbSNP
rs535038638 2285 dbSNP
rs1475063307 2290 dbSNP
rs4851752 2293 dbSNP
rs1199092315 2295 dbSNP
rs1459012871 2298 dbSNP
rs1256039677 2300 dbSNP
rs1411305105 2301 dbSNP
rs1355243263 2304 dbSNP
rs184278484 2312 dbSNP
rs1444473313 2316 dbSNP
rs765237567 2322 dbSNP
rs568721789 2341 dbSNP
rs1354774202 2344 dbSNP
rs1415116013 2346 dbSNP
rs1321740136 2347 dbSNP
rs75725426 2354 dbSNP
rs1213696355 2355 dbSNP
rs1166835145 2362 dbSNP
rs1226242207 2364 dbSNP
rs1460072426 2364 dbSNP
rs1430755240 2366 dbSNP
rs1255968622 2383 dbSNP
rs926619831 2389 dbSNP
rs1189059942 2391 dbSNP
rs1260140818 2392 dbSNP
rs1378048161 2393 dbSNP
rs1008762468 2394 dbSNP
rs35057708 2394 dbSNP
rs1045167666 2397 dbSNP
rs1411688789 2398 dbSNP
rs949489900 2409 dbSNP
rs1374748475 2413 dbSNP
rs890398166 2415 dbSNP
rs918069889 2431 dbSNP
rs528128074 2432 dbSNP
rs988740951 2434 dbSNP
rs1429777011 2436 dbSNP
rs956906472 2437 dbSNP
rs1028808117 2444 dbSNP
rs1363667688 2452 dbSNP
rs570332638 2453 dbSNP
rs1447929038 2454 dbSNP
rs780551708 2457 dbSNP
rs79742962 2468 dbSNP
rs114038778 2469 dbSNP
rs1212304906 2476 dbSNP
rs940300580 2477 dbSNP
rs886097597 2480 dbSNP
rs1445577910 2483 dbSNP
rs1192961709 2484 dbSNP
rs1242870354 2484 dbSNP
rs1476542336 2485 dbSNP
rs563154331 2491 dbSNP
rs996549479 2493 dbSNP
rs965128536 2494 dbSNP
rs1350538085 2499 dbSNP
rs1175364253 2500 dbSNP
rs1019374158 2502 dbSNP
rs950309965 2503 dbSNP
rs1399846772 2509 dbSNP
rs1004430930 2510 dbSNP
rs1167079065 2515 dbSNP
rs886950275 2526 dbSNP
rs917504974 2532 dbSNP
rs1302042503 2533 dbSNP
rs570481749 2539 dbSNP
rs866401994 2542 dbSNP
rs1235864396 2548 dbSNP
rs1277081933 2549 dbSNP
rs937513160 2556 dbSNP
rs541578083 2563 dbSNP
rs905194038 2570 dbSNP
rs140147022 2581 dbSNP
rs1466420778 2583 dbSNP
rs1212119908 2585 dbSNP
rs746644333 2586 dbSNP
rs1252616604 2589 dbSNP
rs1454733239 2593 dbSNP
rs1201120577 2597 dbSNP
rs1361971495 2608 dbSNP
rs1441268208 2610 dbSNP
rs1469598676 2618 dbSNP
rs967470436 2621 dbSNP
rs1158923487 2626 dbSNP
rs949433098 2640 dbSNP
rs1459687173 2647 dbSNP
rs1324728133 2658 dbSNP
rs559263586 2662 dbSNP
rs762052074 2663 dbSNP
rs1326341380 2667 dbSNP
rs540954042 2678 dbSNP
rs77690588 2687 dbSNP
rs192275647 2688 dbSNP
rs1231877944 2689 dbSNP
rs546293687 2690 dbSNP
rs527495548 2691 dbSNP
rs575768482 2697 dbSNP
rs1218788374 2700 dbSNP
rs1004619902 2702 dbSNP
rs201222218 2703 dbSNP
rs1437147679 2704 dbSNP
rs557589243 2705 dbSNP
rs768969503 2713 dbSNP
rs1474082828 2716 dbSNP
rs560445609 2729 dbSNP
rs1046071885 2730 dbSNP
rs1019744106 2741 dbSNP
rs775898670 2742 dbSNP
rs1391476882 2743 dbSNP
rs1305398566 2746 dbSNP
rs1391308814 2749 dbSNP
rs896036252 2750 dbSNP
rs1056453014 2767 dbSNP
rs147510950 2769 dbSNP
rs1249845120 2785 dbSNP
rs926115036 2787 dbSNP
rs978930003 2791 dbSNP
rs946118336 2796 dbSNP
rs995406773 2818 dbSNP
rs1484680116 2819 dbSNP
rs905136380 2821 dbSNP
rs913338313 2826 dbSNP
rs1425174663 2828 dbSNP
rs1365065108 2839 dbSNP
rs1372150291 2840 dbSNP
rs1013567118 2844 dbSNP
rs1169991551 2854 dbSNP
rs143259329 2856 dbSNP
rs542146431 2857 dbSNP
rs1378234025 2859 dbSNP
rs1180880940 2871 dbSNP
rs921834599 2876 dbSNP
rs904016146 2879 dbSNP
rs1433668001 2891 dbSNP
rs867373527 2900 dbSNP
rs1293644590 2947 dbSNP
rs866910068 2947 dbSNP
rs1189422861 2962 dbSNP
rs1326100699 2965 dbSNP
rs1228222980 2966 dbSNP
rs1276915338 2969 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Flp-In T-REx 293-hAGO1 cells
Location of target site 3'UTR
Original Description (Extracted from the article) ... Validation of interactions identified by CLASH suppports their reliability. ...

- Helwak A; Kudla G; Dudnakova T; Tollervey D, 2013, Cell.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' agCUGACGGUGAGAAUGAUCu 5'
            ||||| : |   ||:||| 
Target 5' ctGACTGATTC---TATTAGg 3'
 		30 - 47
2 
miRNA  3' agcUGACGGUGAG-------AAUGAucu 5'
             |||||| |||       || ||   
Target 5' ---ACTGCC-CTCTTTGGAATTTCTtca 3'
 		1 - 24
Article - Helwak A; Kudla G; Dudnakova T; Tollervey D
- Cell, 2013
MicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets, we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human AGO1. Here, we report data sets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, nonseed base pairing. 18% of miRNA-mRNA interactions involve the miRNA 3' end, with little evidence for 5' contacts, and some of these were functionally validated. Analyses of miRNA:mRNA base pairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding.
LinkOut: [PMID: 23622248]
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
GSE28260 Renal cortex and medulla 0.705 3.6e-3 0.797 5.5e-4 13 Click to see details
GSE26953 Aortic valvular endothelial cells 0.455 1.3e-2 0.485 8.1e-3 24 Click to see details
GSE28544 Breast cancer 0.445 1.5e-2 0.422 2.0e-2 24 Click to see details
GSE19350 CNS germ cell tumors -0.624 1.5e-2 -0.664 9.3e-3 12 Click to see details
GSE19783 ER- ER- breast cancer 0.228 2.2e-2 0.160 7.9e-2 79 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis -0.376 5.1e-2 -0.517 9.8e-3 20 Click to see details
GSE19536 Breast cancer 0.133 9.4e-2 0.084 2.0e-1 100 Click to see details
GSE14794 Lymphoblastoid cells -0.121 1.3e-1 -0.079 2.3e-1 90 Click to see details
GSE38226 Liver fibrosis 0.229 1.6e-1 0.241 1.5e-1 21 Click to see details
GSE38974 Chronic obstructive pulmonary disease -0.175 2.0e-1 -0.268 9.8e-2 25 Click to see details
GSE17498 Multiple myeloma -0.104 2.6e-1 0.011 4.7e-1 40 Click to see details
GSE17306 Multiple myeloma 0.073 3.1e-1 0.104 2.4e-1 49 Click to see details
GSE19783 ER+ ER+ breast cancer -0.107 3.3e-1 -0.232 1.6e-1 20 Click to see details
GSE21687 Ependynoma primary tumors -0.029 4.1e-1 -0.097 2.2e-1 64 Click to see details
GSE21849 B cell lymphoma 0.03 4.4e-1 -0.013 4.7e-1 29 Click to see details
GSE42095 Differentiated embryonic stem cells -0.027 4.5e-1 0.034 4.4e-1 23 Click to see details
GSE27834 Pluripotent stem cells 0.027 4.6e-1 0.021 4.7e-1 16 Click to see details
GSE32688 Pancreatic cancer -0.009 4.8e-1 0.200 1.4e-1 32 Click to see details
GSE32688 Pancreatic cancer -0.009 4.8e-1 0.200 1.4e-1 32 Click to see details
GSE32688 Pancreatic cancer -0.009 4.8e-1 0.200 1.4e-1 32 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
LUSC -0.384 0.01 -0.399 0.01 35 Click to see details
BRCA -0.304 0.04 -0.256 0.07 34 Click to see details
HNSC 0.25 0.07 -0.028 0.44 35 Click to see details
KIRC -0.217 0.09 -0.210 0.1 40 Click to see details
LUAD -0.447 0.1 -0.479 0.08 10 Click to see details
STAD -0.234 0.12 -0.213 0.14 28 Click to see details
PRAD 0.167 0.17 -0.039 0.41 36 Click to see details
BLCA -0.228 0.19 -0.331 0.1 17 Click to see details
THCA 0.102 0.22 0.043 0.37 58 Click to see details
KICH 0.153 0.25 0.106 0.32 22 Click to see details
UCEC -0.157 0.27 -0.232 0.18 18 Click to see details
KIRP -0.086 0.33 -0.217 0.13 29 Click to see details
ESCA 0.136 0.35 0.491 0.06 11 Click to see details
CESC -0.358 0.38 -0.500 0.33 3 Click to see details
PCPG 0.331 0.39 0.500 0.33 3 Click to see details
LIHC 0.039 0.4 -0.113 0.22 49 Click to see details
CHOL 0.094 0.42 -0.143 0.38 7 Click to see details
PAAD -0.133 0.43 0.200 0.4 4 Click to see details
PAAD -0.133 0.43 0.200 0.4 4 Click to see details
27 hsa-miR-628-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT039584 CDC14A cell division cycle 14A 1 1
MIRT039585 AGO1 argonaute 1, RISC catalytic component 2 3
MIRT039586 TGFBRAP1 transforming growth factor beta receptor associated protein 1 1 1
MIRT039587 LRP6 LDL receptor related protein 6 1 1
MIRT071876 BTF3L4 basic transcription factor 3 like 4 2 2
MIRT097443 JMY junction mediating and regulatory protein, p53 cofactor 2 4
MIRT100100 ABT1 activator of basal transcription 1 2 8
MIRT147692 CBX4 chromobox 4 2 2
MIRT408248 PURA purine rich element binding protein A 2 2
MIRT442047 LRAT lecithin retinol acyltransferase 2 2
MIRT444412 RAB3IP RAB3A interacting protein 2 2
MIRT452599 REPIN1 replication initiator 1 2 2
MIRT469515 RBFOX2 RNA binding protein, fox-1 homolog 2 2 8
MIRT498192 AKR1B10 aldo-keto reductase family 1 member B10 2 2
MIRT500151 CREBBP CREB binding protein 2 2
MIRT507319 FAM60A SIN3-HDAC complex associated factor 2 6
MIRT508343 ZNF273 zinc finger protein 273 2 6
MIRT520480 TRIM13 tripartite motif containing 13 2 2
MIRT522461 MMP16 matrix metallopeptidase 16 2 4
MIRT547116 PHLPP2 PH domain and leucine rich repeat protein phosphatase 2 2 2
MIRT548675 CRNKL1 crooked neck pre-mRNA splicing factor 1 2 2
MIRT553756 TARBP2 TARBP2, RISC loading complex RNA binding subunit 2 4
MIRT559437 ARSJ arylsulfatase family member J 2 2
MIRT610490 GPC4 glypican 4 2 2
MIRT644682 TMCO1 transmembrane and coiled-coil domains 1 2 2
MIRT658214 FBXO21 F-box protein 21 2 2
MIRT756083 TP53 tumor protein p53 4 1
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-628 Cisplatin 5460033 NSC119875 approved sensitive cell line (BxPC3)
hsa-miR-628-3p Cisplatin 5460033 NSC119875 approved resistant High Tongue Squamous Cell Carcinoma cell line (Tca8113)
hsa-miR-628-3p Tamoxifen 2733525 NSC180973 approved resistant High Breast Cancer cell line (MCF-7, LY2)
hsa-miR-628-3p Erlotinib 176870 NSC718781 approved sensitive High Epithelial Cancer cell line (A549, UKY-29, H460, H1975, H1650, H3255, PC-9, H358)
hsa-miR-628-3p Siop Treatment Protocol sensitive High Nephroblastoma tissue
hsa-miR-628-3p Sunitinib 5329102 NSC750690 approved resistant High Metastatic Renal Cell Carcinoma tissue and cell line (Caki-2)
hsa-miR-628-3p Chemotherapy sensitive High Epithelial Ovarian Cancer tissue
hsa-miR-628-3p Platinum-based doublet chemotherapy resistant Low Lung Adenocarcinoma tissue
hsa-miR-628-3p Doxorubicin 31703 NSC123127 approved sensitive High Gastric Cancer cell line (SGC7901)
hsa-miR-628-3p Tamoxifen 2733525 NSC180973 approved resistant High Breast Cancer cell line (TAMR8)
hsa-miR-628-3p Aromatase Inhibitor sensitive Low Breast Cancer cell line (MCF-7)
hsa-miR-628-3p Dabrafenib 44462760 NSC764134 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-628-3p Vemurafenib 42611257 NSC761431 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-628-3p Ceritinib 57379345 NSC776422 approved sensitive High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-miR-628-3p Platinum 23939 sensitive High High-Grade Serous Ovarian Cancer tissue
hsa-miR-628-3p Cisplatin 5460033 NSC119875 approved sensitive High Bladder Cancer cell line (CDDP-R-BOY, CDDP-R-T24)
hsa-miR-628-3p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-628-3p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-628-3p Fluorouracil 3385 NSC19893 approved resistant cell line (KM12C) (72 h)
hsa-miR-628-3p Sunitinib 5329102 NSC750690 approved resistant tissue (CardB)
hsa-miR-628-3p Tamoxifen 2733525 NSC180973 approved resistant cell line (TamR8)
hsa-miR-628-3p Oxaliplatin 6857599 NSC266046 approved sensitive cell line (IGROV-1)
hsa-miR-628-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-628-3p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-628-3p Docetaxel+Cisplatin+5-Fluorouracil sensitive tissue (hypopharyngeal squamous cell carcinoma)

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