miRTarBase - #MIRT485628


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pre-miRNA Information
pre-miRNA hsa-mir-4640   
Genomic Coordinates chr6: 30890883 - 30890972
Description Homo sapiens miR-4640 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4640-5p
Sequence 9| UGGGCCAGGGAGCAGCUGGUGGG |31
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1392105945 7 dbSNP
rs939712790 9 dbSNP
rs762825841 15 dbSNP
rs71552023 20 dbSNP
rs1305909531 21 dbSNP
rs750017220 21 dbSNP
rs1375436057 23 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Biomarker Information
Biomarker ID Name Type Discovered From Mode Level Source Testing Methods
B32FZJ miR-4640 Safety Biomarker (SAF) Clinical/Experimental Data Expression lower Urine Quantitative polymerase chain reaction
Gene Information
Gene Symbol EEPD1   
Synonyms HSPC107
Description endonuclease/exonuclease/phosphatase family domain containing 1
Transcript NM_030636   
Expression
Putative miRNA Targets on EEPD1
3'UTR of EEPD1
(miRNA target sites are highlighted)		 
>EEPD1|NM_030636|3'UTR
   1 TGACACCAAATCCATGTGTCCACCCTGGGACCCAGGAGGGCACAGCCAAGGAATGAGCCCTGTGGGGTGACGCTTCAGGG
  81 CAGAGCTGCCTTTTAATTTTTATTCTCAGAGCATCAGCACTTGAGGCCTTGCCCCACGCCTTCTCTGTGGACCATTCAGG
 161 ACCTCCAGTGGGGGTGGCGTGCCAGGCGCGTACCCCACCAGGTGGGCAAAGCAGAAACCTGCGGGGAGCGGAGACGCCTT
 241 TTATCTCTGGATGCCACAGACCTGAGCAGCATTGGGCTGGCTGTCCGCTGCTGACTGGATGGCAGCACAAAGACAATATG
 321 AGCAGAGGGAGGAGAAGAAGGGGTGCTCAGGCTGCGGGCCACAGTCCAGCAGCGCCAGAAGCACTCATTTCTGACCACCA
 401 GGCTATGACGTTCCTGCTGCGCATTACAGAAAGCTTTTAACTGTGATCAGGCACTCTGCTCAGATACATTGAGTGGCGAT
 481 TTTTAGTTTTGTTTTGAAAAAATAAACAGATTAACCTGCCTCGCTGCAGTGAGAGCATGGGACAAGTCCGCCACAGCCCT
 561 CCCCCGCCCCCTTCCCCCGCCCCCCAACGCGCAGTGTGTATTTGCACCACGGCAGGTGCCTCTGTGTGGAGCTAGGGTCA
 641 AGCCCTGAGCAGCTTCACTTCCCCTGCGCCTTTTATGTCCCCACCTTGAGGCCTTGCAGAGGCGCCTCTCAAGGCCCCAT
 721 CAGCTCGCCGGGACCTCTGTGAAGCCTCTCTGTCATCTCCCCTTCCCAGCCCCTCCTTCATCCCCTGCCTCCTTCACCAG
 801 CCTGGCTTTTGCCTGGAGCACTATTTGTTTAGTTCTCTTTGCAGGACAAGAATTCTCTCAGGGTGGTATCACCTCCTCCC
 881 TCCTCCCCACTCACTCCAGTTTTTAGCCCGGAGCCTCCTGTGGTTGACTATCAGGAATGTGTGCTGTGTCAGGATACATA
 961 GGAAGTTGACCTCGGGGTATCATGGAGAGTGTCCCTCCTAGTGGCTGGAGGTAGGGACAGTTGGTTGTGGGGCTGGAGAG
1041 AGGTTGTGGGGAGGAAGCGAGGATGCGTGCCTGCCACTAGGCATCTGCATCCCCGAGCCCAAGCCAGGAGGGATTTCCCT
1121 TAGGCAACACCATCCCAGGGAGATCTGCCACAATTTGCGTTTCACAGCTGAAGACGCTGAGGCTTAGAGAGCTCGACCTC
1201 CTCAAGGTCACACCACTGGGTAAATAGAGGGATGCAGACTCAGGTTTTGCTATGTGCTCACATTTCAACTTTATGCTTAA
1281 CATGAATGGAAAAATATGAAAGTAAATAGTGAAAAGGTAAGTTATGAGCTTAGATTACCTAGATTATTCCAGTATCCCAT
1361 GGAAGCTGAGGACTTATTCCGCTTTCCACACCGAACACTAAATGTGGACCAGTATCAAGAACCCTCCTGTCCCCACGCAG
1441 TGTAAACCCAGTGGCTTCTCTGACCTGGAGCTGATGGGCCGTGAAGGGGGCCTATTTTTCTCCAAAGGCCATCCTTTTGG
1521 GGCCACCTGGCTCCAAGAAGCATCGCTGGTCTTGGGGACGGGAAGGGAACCCTCTTCCAGGAGCTCTAAGGGTACTTGGG
1601 AATCAATTGTGTCCATTCTGAGGTCTCTCCAGTGGGAGGGCGGCAGCTCCTGTCCCTGGGTTCAGGCTGTGCTTCTGGAA
1681 GCATCGAAATGGGATGTCTGAGCCTTGAGGAAAAGCAGCAGGGTTAGCATTAAAGTCAAGAGGGGCAGCTCAGGATGCTA
1761 CCAGGGAGCACATCGTTTCTGGTGCCTCATCTAAAGGTGAAACCTCCCCTACATTCACCAGCCGGATGTCCCAAATCCCT
1841 TTAGCCAGATTGCTTTTTGCAACCAAAGCTGTGGACAGAAAAGCCTCCTTAAGTGAGCTGAGGGGACAGGAAATCCAATC
1921 AGATGACCTTTGTGTTCGTAATCGGGCTTGAGCCAGAGGCTGGGGAGCTGAGTCCCAGCCAAACCTCACTGGCCCTTTTG
2001 CTTTTCACGCCCAGGGCTCAGTGGCCCAGGAAGTGTGCTGGGCAGCCTGTTCTTACTCCAGCTCAACCCATTGGGTGTTG
2081 GCTGTTTTTGGTTTTAGTTGTTGTTTTGTATTTTGTTGTTTTAATTAATAGGCTTTATTTGTAAGAGCAGTTTTATGTTT
2161 ACAGAAAAATTAGGCACAAAGGGATTCCCATATCCCTCCTCTTCTTTGCATATTTCCCCCTCTAATTAGCATGTTGCATT
2241 AGCATGGCACTTTGTTACAACTGATGAACTTGTATTCATTATTAGCTACAGTGTTCATAGTTTATATTAAAGTTCACTCT
2321 TTGTGTTGTGCATCCTA
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' ggguGGUCG---ACGAGGGACCGGGu 5'
              |||||     ||| ||||||| 
Target 5' agtcCCAGCCAAACCTCACTGGCCCt 3'
 1971 - 1996 159.00 -26.50
2 
miRNA  3' ggGUGGUCGA----CGAGGGACCGGGu 5'
            ||:|  :|    ||  ||||||:| 
Target 5' gcCATCCTTTTGGGGCCACCTGGCTCc 3'
 1508 - 1534 135.00 -24.30
3 
miRNA  3' ggguGGUCGACGAGGGACCGGGu 5'
              ||||  ||||  |||||| 
Target 5' acgcCCAG-GGCTCAGTGGCCCa 3'
 2007 - 2028 134.00 -28.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN28613298 27 COSMIC
COSN31498022 33 COSMIC
COSN31962769 38 COSMIC
COSN20091559 68 COSMIC
COSN30190409 80 COSMIC
COSN31571660 97 COSMIC
COSN19690511 153 COSMIC
COSN17718294 188 COSMIC
COSN26441200 191 COSMIC
COSN19484399 237 COSMIC
COSN28720803 237 COSMIC
COSN1348990 277 COSMIC
COSN28650625 312 COSMIC
COSN28764609 353 COSMIC
COSN17182190 421 COSMIC
COSN28792474 455 COSMIC
COSN8300833 1128 COSMIC
COSN19608579 1305 COSMIC
COSN18993997 1336 COSMIC
COSN9987013 1484 COSMIC
COSN21726424 1592 COSMIC
COSN1348991 1625 COSMIC
COSN15690739 1945 COSMIC
COSN21972932 2200 COSMIC
COSN7979218 2250 COSMIC
rs10848 312 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs751140558 1 dbSNP
rs200527094 2 dbSNP
rs1460144339 6 dbSNP
rs1473029636 7 dbSNP
rs1169216911 10 dbSNP
rs1054309484 14 dbSNP
rs756635003 15 dbSNP
rs780471655 16 dbSNP
rs556537571 17 dbSNP
rs374760101 19 dbSNP
rs574402588 19 dbSNP
rs1347300641 20 dbSNP
rs1405394396 24 dbSNP
rs779441923 25 dbSNP
rs1324403147 26 dbSNP
rs196614 27 dbSNP
rs1253242073 28 dbSNP
rs747135350 30 dbSNP
rs770871529 33 dbSNP
rs561138594 34 dbSNP
rs755649474 34 dbSNP
rs776394170 39 dbSNP
rs371443591 43 dbSNP
rs1234981642 48 dbSNP
rs1210878960 51 dbSNP
rs1331116002 54 dbSNP
rs1296323890 58 dbSNP
rs960609602 66 dbSNP
rs1041478911 67 dbSNP
rs542902259 68 dbSNP
rs1320946248 70 dbSNP
rs77013955 72 dbSNP
rs751889591 73 dbSNP
rs894730410 81 dbSNP
rs1467778666 82 dbSNP
rs1378271134 87 dbSNP
rs1188069453 91 dbSNP
rs1448176642 91 dbSNP
rs1250482526 93 dbSNP
rs1189805173 118 dbSNP
rs984923787 132 dbSNP
rs566593787 136 dbSNP
rs1016408869 138 dbSNP
rs943153058 139 dbSNP
rs73686815 140 dbSNP
rs1225600841 146 dbSNP
rs2241142 153 dbSNP
rs934198046 162 dbSNP
rs369525400 169 dbSNP
rs1485684009 170 dbSNP
rs954782891 173 dbSNP
rs1338413879 178 dbSNP
rs1052712480 180 dbSNP
rs1376341773 182 dbSNP
rs1409575884 184 dbSNP
rs1168001483 186 dbSNP
rs1427852953 188 dbSNP
rs557172557 190 dbSNP
rs892435152 191 dbSNP
rs1472799235 194 dbSNP
rs1236076506 195 dbSNP
rs1158913422 199 dbSNP
rs1442612129 201 dbSNP
rs1017583105 214 dbSNP
rs567292047 219 dbSNP
rs1022330261 223 dbSNP
rs536218033 224 dbSNP
rs1002327162 227 dbSNP
rs1409216232 231 dbSNP
rs1306794809 232 dbSNP
rs1352855262 233 dbSNP
rs990055563 236 dbSNP
rs553140352 237 dbSNP
rs914443542 250 dbSNP
rs945858121 251 dbSNP
rs1274597963 254 dbSNP
rs1343261845 255 dbSNP
rs1217137046 263 dbSNP
rs572954125 273 dbSNP
rs539268379 281 dbSNP
rs972362708 283 dbSNP
rs1026248514 287 dbSNP
rs781752981 288 dbSNP
rs558875201 293 dbSNP
rs1165542250 303 dbSNP
rs1475712263 308 dbSNP
rs10848 312 dbSNP
rs1484759216 321 dbSNP
rs938416093 324 dbSNP
rs1249596932 332 dbSNP
rs578089413 333 dbSNP
rs1449762077 343 dbSNP
rs1291882774 347 dbSNP
rs910253267 349 dbSNP
rs1245937282 351 dbSNP
rs1286303675 352 dbSNP
rs1226786284 356 dbSNP
rs942314123 357 dbSNP
rs1435801475 369 dbSNP
rs544584340 371 dbSNP
rs898044416 372 dbSNP
rs943120628 375 dbSNP
rs1388358504 389 dbSNP
rs1046660 392 dbSNP
rs1030471027 406 dbSNP
rs144098642 410 dbSNP
rs1408313974 411 dbSNP
rs1166773276 421 dbSNP
rs14827 422 dbSNP
rs1476725537 424 dbSNP
rs777988896 427 dbSNP
rs1411044886 428 dbSNP
rs1265986409 429 dbSNP
rs934190970 437 dbSNP
rs1053094746 441 dbSNP
rs1323418626 444 dbSNP
rs2516 455 dbSNP
rs771118958 459 dbSNP
rs1018052650 465 dbSNP
rs191011286 468 dbSNP
rs533025684 470 dbSNP
rs183077671 473 dbSNP
rs1276754032 476 dbSNP
rs187410632 478 dbSNP
rs905195545 479 dbSNP
rs1459115752 480 dbSNP
rs1346178954 486 dbSNP
rs1174842137 490 dbSNP
rs1002252245 492 dbSNP
rs1412402006 497 dbSNP
rs1426653077 507 dbSNP
rs1035114657 519 dbSNP
rs896285124 523 dbSNP
rs868724196 524 dbSNP
rs1486040140 529 dbSNP
rs1255198641 532 dbSNP
rs1288977428 550 dbSNP
rs1310723319 551 dbSNP
rs762688469 552 dbSNP
rs1235167912 560 dbSNP
rs977668812 561 dbSNP
rs1449723238 564 dbSNP
rs1195255314 565 dbSNP
rs928464051 566 dbSNP
rs966507944 567 dbSNP
rs1360581357 568 dbSNP
rs1253922459 572 dbSNP
rs979702070 573 dbSNP
rs1170338885 574 dbSNP
rs1413171239 574 dbSNP
rs1429119130 575 dbSNP
rs1186867849 578 dbSNP
rs1392124077 579 dbSNP
rs1211889821 580 dbSNP
rs926041085 580 dbSNP
rs545012288 581 dbSNP
rs1272572298 582 dbSNP
rs552596547 585 dbSNP
rs1389193875 586 dbSNP
rs1407492119 587 dbSNP
rs1386327442 588 dbSNP
rs866217803 589 dbSNP
rs1388316770 590 dbSNP
rs1433937141 592 dbSNP
rs1313048621 602 dbSNP
rs771481187 609 dbSNP
rs1294878739 610 dbSNP
rs991239536 611 dbSNP
rs2241143 612 dbSNP
rs984713592 615 dbSNP
rs1037296075 616 dbSNP
rs1425281482 617 dbSNP
rs898096797 626 dbSNP
rs929550877 627 dbSNP
rs1482888351 646 dbSNP
rs1249689124 648 dbSNP
rs1197674877 655 dbSNP
rs1481020013 659 dbSNP
rs1052389123 664 dbSNP
rs1017185366 667 dbSNP
rs28465447 668 dbSNP
rs1294361871 669 dbSNP
rs1227385290 675 dbSNP
rs775455073 677 dbSNP
rs1308481216 678 dbSNP
rs1215377743 681 dbSNP
rs1391422697 691 dbSNP
rs1389414884 692 dbSNP
rs1291652488 693 dbSNP
rs975778561 696 dbSNP
rs1273614124 704 dbSNP
rs923066262 705 dbSNP
rs1017687670 707 dbSNP
rs550614929 712 dbSNP
rs1409985509 718 dbSNP
rs760590220 720 dbSNP
rs988316133 722 dbSNP
rs1010917609 725 dbSNP
rs1020936333 727 dbSNP
rs373526735 728 dbSNP
rs536282709 730 dbSNP
rs763658356 731 dbSNP
rs946910502 732 dbSNP
rs1035960896 751 dbSNP
rs1262071183 753 dbSNP
rs1429261128 759 dbSNP
rs1239331831 760 dbSNP
rs1044007275 761 dbSNP
rs1298640355 769 dbSNP
rs549047694 772 dbSNP
rs1476453673 776 dbSNP
rs1166226669 784 dbSNP
rs1319847428 793 dbSNP
rs1455404240 806 dbSNP
rs915670400 813 dbSNP
rs13224904 816 dbSNP
rs1454562581 824 dbSNP
rs1056502964 828 dbSNP
rs566612978 832 dbSNP
rs1386666682 833 dbSNP
rs1196912280 836 dbSNP
rs147314936 838 dbSNP
rs1254128922 845 dbSNP
rs1332897455 848 dbSNP
rs1338153207 856 dbSNP
rs929578868 861 dbSNP
rs1463779998 867 dbSNP
rs1264299556 870 dbSNP
rs558579027 878 dbSNP
rs867964217 879 dbSNP
rs1205345371 881 dbSNP
rs575774152 887 dbSNP
rs1293768311 888 dbSNP
rs1253715055 889 dbSNP
rs887611019 894 dbSNP
rs1348006280 900 dbSNP
rs1296714249 902 dbSNP
rs1006060291 903 dbSNP
rs1226338683 904 dbSNP
rs13224824 910 dbSNP
rs964325154 911 dbSNP
rs1486302807 913 dbSNP
rs997123453 918 dbSNP
rs1030441226 919 dbSNP
rs755413382 931 dbSNP
rs866150495 936 dbSNP
rs867877066 943 dbSNP
rs1436605079 947 dbSNP
rs554879050 949 dbSNP
rs1168432241 957 dbSNP
rs756687593 959 dbSNP
rs1375124834 963 dbSNP
rs968218406 966 dbSNP
rs1203261491 974 dbSNP
rs574787126 975 dbSNP
rs1254795385 977 dbSNP
rs926843876 981 dbSNP
rs1253587069 990 dbSNP
rs78522778 991 dbSNP
rs1056460767 1001 dbSNP
rs1314531336 1010 dbSNP
rs1471849077 1011 dbSNP
rs1010969919 1014 dbSNP
rs1161705869 1016 dbSNP
rs560121393 1018 dbSNP
rs377158209 1019 dbSNP
rs929369081 1019 dbSNP
rs1338507937 1047 dbSNP
rs902498699 1059 dbSNP
rs1416860552 1060 dbSNP
rs1399449138 1061 dbSNP
rs1048284829 1067 dbSNP
rs576777829 1068 dbSNP
rs944692403 1070 dbSNP
rs1416157336 1072 dbSNP
rs546002811 1084 dbSNP
rs562965107 1093 dbSNP
rs530650155 1095 dbSNP
rs1202463443 1096 dbSNP
rs1439078222 1097 dbSNP
rs1006030840 1100 dbSNP
rs1209178281 1101 dbSNP
rs1353913700 1105 dbSNP
rs550731100 1113 dbSNP
rs35223460 1117 dbSNP
rs1349780675 1131 dbSNP
rs900416627 1133 dbSNP
rs1356387014 1138 dbSNP
rs1287768003 1142 dbSNP
rs963122106 1154 dbSNP
rs973116252 1159 dbSNP
rs192103619 1160 dbSNP
rs530006837 1170 dbSNP
rs7803174 1171 dbSNP
rs138690216 1176 dbSNP
rs1009957488 1177 dbSNP
rs1232957457 1177 dbSNP
rs1198072672 1178 dbSNP
rs1350235787 1178 dbSNP
rs196617 1179 dbSNP
rs943587583 1180 dbSNP
rs1251792595 1183 dbSNP
rs1267683789 1186 dbSNP
rs968478697 1189 dbSNP
rs576569745 1190 dbSNP
rs1375620018 1195 dbSNP
rs1039234786 1196 dbSNP
rs552003690 1198 dbSNP
rs1328558997 1199 dbSNP
rs1179423037 1203 dbSNP
rs142695359 1214 dbSNP
rs946812055 1222 dbSNP
rs1432906658 1227 dbSNP
rs1197730961 1231 dbSNP
rs1392873417 1237 dbSNP
rs538100796 1240 dbSNP
rs1408054432 1247 dbSNP
rs1042487389 1253 dbSNP
rs779235250 1269 dbSNP
rs1254768779 1283 dbSNP
rs902551195 1288 dbSNP
rs1436101996 1289 dbSNP
rs1464221595 1294 dbSNP
rs1240212114 1296 dbSNP
rs1213896893 1298 dbSNP
rs1319005749 1299 dbSNP
rs959608133 1303 dbSNP
rs196618 1320 dbSNP
rs895752827 1326 dbSNP
rs771911080 1327 dbSNP
rs929311198 1330 dbSNP
rs1287545456 1338 dbSNP
rs1432426005 1339 dbSNP
rs1345457602 1346 dbSNP
rs183548460 1347 dbSNP
rs994587660 1352 dbSNP
rs1373795413 1354 dbSNP
rs1026024380 1369 dbSNP
rs983533596 1377 dbSNP
rs1174184909 1378 dbSNP
rs909285370 1381 dbSNP
rs775258479 1382 dbSNP
rs1188091350 1383 dbSNP
rs1486090223 1384 dbSNP
rs987165400 1392 dbSNP
rs534222719 1393 dbSNP
rs746950381 1394 dbSNP
rs965011101 1401 dbSNP
rs554016275 1406 dbSNP
rs577184027 1407 dbSNP
rs1307474143 1414 dbSNP
rs1293838343 1415 dbSNP
rs974979013 1417 dbSNP
rs546161462 1423 dbSNP
rs1283177278 1425 dbSNP
rs1412617728 1428 dbSNP
rs1376733896 1429 dbSNP
rs1207259494 1430 dbSNP
rs1428993767 1435 dbSNP
rs1352653254 1437 dbSNP
rs1252332214 1446 dbSNP
rs1412804516 1447 dbSNP
rs1187489402 1448 dbSNP
rs900385563 1451 dbSNP
rs62447801 1464 dbSNP
rs933215933 1465 dbSNP
rs946864421 1467 dbSNP
rs1480364837 1469 dbSNP
rs768519289 1470 dbSNP
rs1207257909 1477 dbSNP
rs556409502 1481 dbSNP
rs576479100 1482 dbSNP
rs1231055661 1490 dbSNP
rs1357024315 1492 dbSNP
rs924063913 1492 dbSNP
rs196619 1494 dbSNP
rs1299749544 1495 dbSNP
rs565893004 1506 dbSNP
rs1010296851 1523 dbSNP
rs1021319891 1527 dbSNP
rs368451692 1529 dbSNP
rs1460043659 1532 dbSNP
rs1001323311 1533 dbSNP
rs1355029292 1534 dbSNP
rs196620 1539 dbSNP
rs1188945333 1541 dbSNP
rs1418516682 1545 dbSNP
rs1248512045 1546 dbSNP
rs543869671 1560 dbSNP
rs540558142 1561 dbSNP
rs1025666905 1562 dbSNP
rs1273363964 1563 dbSNP
rs951022063 1568 dbSNP
rs1314606241 1572 dbSNP
rs899049231 1578 dbSNP
rs375642772 1580 dbSNP
rs1391873259 1582 dbSNP
rs1370208588 1585 dbSNP
rs868050284 1591 dbSNP
rs560456289 1592 dbSNP
rs994638747 1597 dbSNP
rs1165839003 1605 dbSNP
rs532046684 1607 dbSNP
rs196621 1610 dbSNP
rs531443100 1624 dbSNP
rs1018640506 1631 dbSNP
rs964366413 1632 dbSNP
rs547832600 1636 dbSNP
rs1275472797 1640 dbSNP
rs768063452 1642 dbSNP
rs1469146795 1643 dbSNP
rs73328603 1644 dbSNP
rs1247032136 1645 dbSNP
rs1204171434 1647 dbSNP
rs534091241 1650 dbSNP
rs554077636 1660 dbSNP
rs933166100 1661 dbSNP
rs1051625448 1670 dbSNP
rs924087113 1677 dbSNP
rs939480160 1681 dbSNP
rs1301086357 1684 dbSNP
rs761278615 1686 dbSNP
rs188768594 1687 dbSNP
rs148424558 1693 dbSNP
rs1381833158 1701 dbSNP
rs948060821 1703 dbSNP
rs1038301751 1711 dbSNP
rs1454327117 1719 dbSNP
rs1394564788 1722 dbSNP
rs1423207399 1722 dbSNP
rs1162642910 1723 dbSNP
rs1419779912 1725 dbSNP
rs1461707545 1728 dbSNP
rs1172313331 1730 dbSNP
rs920524284 1737 dbSNP
rs1396045179 1755 dbSNP
rs930536920 1756 dbSNP
rs556513272 1757 dbSNP
rs1205367846 1759 dbSNP
rs1184329273 1762 dbSNP
rs1042741331 1775 dbSNP
rs904191768 1776 dbSNP
rs1348552829 1780 dbSNP
rs142544402 1793 dbSNP
rs196622 1800 dbSNP
rs1224905724 1803 dbSNP
rs1327998304 1804 dbSNP
rs1400915567 1806 dbSNP
rs1374914769 1809 dbSNP
rs375119165 1812 dbSNP
rs1437087485 1815 dbSNP
rs1403480142 1824 dbSNP
rs779876827 1824 dbSNP
rs757405271 1825 dbSNP
rs900212966 1830 dbSNP
rs368061196 1839 dbSNP
rs1474708545 1840 dbSNP
rs1254738083 1843 dbSNP
rs1295585910 1847 dbSNP
rs1336007759 1851 dbSNP
rs995849556 1854 dbSNP
rs1046455 1861 dbSNP
rs1194013257 1862 dbSNP
rs1025172351 1865 dbSNP
rs558972037 1870 dbSNP
rs879433965 1877 dbSNP
rs1005175563 1882 dbSNP
rs1355105644 1884 dbSNP
rs1416640092 1885 dbSNP
rs1341156925 1888 dbSNP
rs376040791 1891 dbSNP
rs963359333 1895 dbSNP
rs974772265 1900 dbSNP
rs992302962 1914 dbSNP
rs916661164 1916 dbSNP
rs150567484 1919 dbSNP
rs1185719892 1924 dbSNP
rs1259522269 1926 dbSNP
rs954844538 1928 dbSNP
rs969417687 1930 dbSNP
rs1189643543 1933 dbSNP
rs118038635 1939 dbSNP
rs913102458 1945 dbSNP
rs1439543726 1947 dbSNP
rs1250930421 1954 dbSNP
rs945914111 1976 dbSNP
rs762411212 1990 dbSNP
rs545737273 1993 dbSNP
rs3735402 1997 dbSNP
rs531178161 2005 dbSNP
rs547895867 2009 dbSNP
rs567799347 2010 dbSNP
rs944539354 2011 dbSNP
rs1055493884 2013 dbSNP
rs895544646 2017 dbSNP
rs1166644598 2031 dbSNP
rs1405656084 2037 dbSNP
rs73328607 2042 dbSNP
rs1156342090 2049 dbSNP
rs1043440873 2050 dbSNP
rs192721779 2054 dbSNP
rs781235126 2057 dbSNP
rs1005060719 2062 dbSNP
rs1466919394 2070 dbSNP
rs1016487193 2071 dbSNP
rs1215773201 2072 dbSNP
rs1452456238 2075 dbSNP
rs781507800 2076 dbSNP
rs1283865189 2079 dbSNP
rs200380809 2091 dbSNP
rs1222098273 2096 dbSNP
rs879745449 2097 dbSNP
rs1352952844 2100 dbSNP
rs1310549711 2129 dbSNP
rs1409647750 2131 dbSNP
rs748015789 2133 dbSNP
rs373396990 2137 dbSNP
rs1436716547 2139 dbSNP
rs1353228371 2147 dbSNP
rs376842753 2150 dbSNP
rs577660530 2159 dbSNP
rs746260344 2166 dbSNP
rs1028984233 2171 dbSNP
rs540136603 2177 dbSNP
rs184144145 2182 dbSNP
rs368854492 2184 dbSNP
rs1452567019 2189 dbSNP
rs987575581 2193 dbSNP
rs1346606801 2196 dbSNP
rs913022174 2197 dbSNP
rs967251390 2203 dbSNP
rs978651948 2211 dbSNP
rs1213915969 2215 dbSNP
rs925843198 2218 dbSNP
rs772595109 2220 dbSNP
rs762700844 2243 dbSNP
rs937270331 2245 dbSNP
rs1286909102 2248 dbSNP
rs189914113 2254 dbSNP
rs1346396287 2261 dbSNP
rs1306306873 2267 dbSNP
rs117958961 2275 dbSNP
rs974112246 2277 dbSNP
rs555934737 2279 dbSNP
rs951456055 2281 dbSNP
rs1360589383 2283 dbSNP
rs982764718 2291 dbSNP
rs1377146009 2298 dbSNP
rs1230980346 2301 dbSNP
rs1427634813 2302 dbSNP
rs949801206 2317 dbSNP
rs944610701 2319 dbSNP
rs572550627 2320 dbSNP
rs1424713369 2325 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM1462573. RNA binding protein: AGO2. Condition:TZM-bl BaL ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ggguggucgaCGAGGGACCGGgu 5'
                    |: : |||| |  
Target 5' -----aggaaGUGUGCUGGGC-- 3'
 		1 - 16
Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
CLIP-seq Support 1 for dataset GSM1462573
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl BaL
Location of target site ENST00000242108.4 | 3UTR | AGGAAGUGUGCUGGGC
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
87 hsa-miR-4640-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT100106 ABT1 activator of basal transcription 1 2 8
MIRT248144 LMBR1L limb development membrane protein 1 like 2 2
MIRT327062 KLHL15 kelch like family member 15 2 2
MIRT347231 GATAD2A GATA zinc finger domain containing 2A 2 2
MIRT450221 CENPN centromere protein N 2 2
MIRT451264 NDUFA11 NADH:ubiquinone oxidoreductase subunit A11 2 2
MIRT452701 C1orf226 chromosome 1 open reading frame 226 2 2
MIRT453212 CERS1 ceramide synthase 1 2 2
MIRT454822 POLR2J3 RNA polymerase II subunit J3 2 2
MIRT454883 RAD50 RAD50 double strand break repair protein 2 2
MIRT455783 TAF8 TATA-box binding protein associated factor 8 2 2
MIRT455858 TMEM254 transmembrane protein 254 2 2
MIRT457615 UPK3BL uroplakin 3B like 1 2 2
MIRT457822 ITPRIP inositol 1,4,5-trisphosphate receptor interacting protein 2 4
MIRT458344 NOC2L NOC2 like nucleolar associated transcriptional repressor 2 2
MIRT458376 ITM2C integral membrane protein 2C 2 2
MIRT458928 SAMD4B sterile alpha motif domain containing 4B 2 2
MIRT459066 WFIKKN2 WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2 2 2
MIRT460138 ASB16 ankyrin repeat and SOCS box containing 16 2 2
MIRT460818 FSTL4 follistatin like 4 2 2
MIRT461285 COX10 COX10, heme A:farnesyltransferase cytochrome c oxidase assembly factor 2 2
MIRT462738 EFNB1 ephrin B1 2 2
MIRT464556 UBTF upstream binding transcription factor, RNA polymerase I 2 2
MIRT477910 DUSP2 dual specificity phosphatase 2 2 2
MIRT479073 CNNM4 cyclin and CBS domain divalent metal cation transport mediator 4 2 4
MIRT479534 CDC5L cell division cycle 5 like 2 4
MIRT485628 EEPD1 endonuclease/exonuclease/phosphatase family domain containing 1 2 2
MIRT489896 PPIC peptidylprolyl isomerase C 2 4
MIRT490737 SRCIN1 SRC kinase signaling inhibitor 1 2 2
MIRT491201 MLLT1 MLLT1, super elongation complex subunit 2 4
MIRT492681 PHYHIP phytanoyl-CoA 2-hydroxylase interacting protein 2 2
MIRT494593 ATG7 autophagy related 7 2 2
MIRT495061 PADI3 peptidyl arginine deiminase 3 2 4
MIRT496623 TMEM67 transmembrane protein 67 2 2
MIRT497177 ZBTB40 zinc finger and BTB domain containing 40 2 2
MIRT498217 TLN2 talin 2 2 2
MIRT498306 BCL11B B-cell CLL/lymphoma 11B 2 2
MIRT499668 NPHP3 nephrocystin 3 2 2
MIRT508080 ANKRD52 ankyrin repeat domain 52 2 2
MIRT509707 ANKRD23 ankyrin repeat domain 23 2 2
MIRT509841 FOS Fos proto-oncogene, AP-1 transcription factor subunit 2 2
MIRT512814 ARRDC2 arrestin domain containing 2 2 2
MIRT513353 SLIT1 slit guidance ligand 1 2 2
MIRT514293 FXYD5 FXYD domain containing ion transport regulator 5 2 2
MIRT516598 FAM89A family with sequence similarity 89 member A 2 4
MIRT516616 DARS2 aspartyl-tRNA synthetase 2, mitochondrial 2 2
MIRT518348 CCL5 C-C motif chemokine ligand 5 2 2
MIRT520130 WSB1 WD repeat and SOCS box containing 1 2 2
MIRT522072 ORAI2 ORAI calcium release-activated calcium modulator 2 2 2
MIRT526461 OSBPL5 oxysterol binding protein like 5 2 2
MIRT528278 MBL2 mannose binding lectin 2 2 2
MIRT534844 RAB15 RAB15, member RAS oncogene family 2 4
MIRT542245 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT543299 ZNF585B zinc finger protein 585B 2 2
MIRT552456 ZNF410 zinc finger protein 410 2 2
MIRT553641 TJAP1 tight junction associated protein 1 2 2
MIRT557103 HOXA3 homeobox A3 2 2
MIRT570782 FANCA Fanconi anemia complementation group A 2 2
MIRT630912 ZMAT2 zinc finger matrin-type 2 2 2
MIRT631034 ZNF878 zinc finger protein 878 2 2
MIRT639017 AAK1 AP2 associated kinase 1 2 2
MIRT648596 ZYG11B zyg-11 family member B, cell cycle regulator 2 2
MIRT648939 ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle 2 2
MIRT652834 TACO1 translational activator of cytochrome c oxidase I 2 2
MIRT659347 CSRP1 cysteine and glycine rich protein 1 2 2
MIRT664163 APOBEC3F apolipoprotein B mRNA editing enzyme catalytic subunit 3F 2 2
MIRT670511 ZSCAN22 zinc finger and SCAN domain containing 22 2 2
MIRT671246 TMEM41B transmembrane protein 41B 2 2
MIRT672120 ATP6V0A2 ATPase H+ transporting V0 subunit a2 2 2
MIRT672313 CD3D CD3d molecule 2 2
MIRT672543 BRMS1L breast cancer metastasis-suppressor 1 like 2 2
MIRT673036 SGPL1 sphingosine-1-phosphate lyase 1 2 2
MIRT673814 DARS aspartyl-tRNA synthetase 2 2
MIRT674858 GINM1 glycoprotein integral membrane 1 2 2
MIRT674970 SH3BP2 SH3 domain binding protein 2 2 2
MIRT675185 KIF1C kinesin family member 1C 2 2
MIRT675219 UGDH UDP-glucose 6-dehydrogenase 2 2
MIRT675558 MED16 mediator complex subunit 16 2 2
MIRT682566 EIF4EBP1 eukaryotic translation initiation factor 4E binding protein 1 2 2
MIRT684640 PDE4C phosphodiesterase 4C 2 2
MIRT689722 ATXN2 ataxin 2 2 2
MIRT693594 SLC39A1 solute carrier family 39 member 1 2 2
MIRT704745 CDKN2B cyclin dependent kinase inhibitor 2B 2 2
MIRT712779 ZNF154 zinc finger protein 154 2 2
MIRT718118 OTOF otoferlin 2 2
MIRT720115 SAMD4A sterile alpha motif domain containing 4A 2 2
MIRT720275 EIF1AD eukaryotic translation initiation factor 1A domain containing 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4640 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4640 Fluorouracil 3385 NSC19893 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4640 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-miR-4640-5p Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-4640-5p Paclitaxel 36314 NSC125973 approved resistant High Non-Small Cell Lung Cancer cell line (A549)
hsa-miR-4640-5p Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (AsPC-1)
hsa-miR-4640-5p Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-4640-5p Osimertinib 71496458 NSC779217 approved resistant cell line (HCC827)
hsa-miR-4640-5p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-4640-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4640-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-4640-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-4640-5p Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-4640-5p Docetaxel+Cisplatin+5-Fluorouracil resistant tissue (hypopharyngeal squamous cell carcinoma)

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