pre-miRNA Information
pre-miRNA hsa-mir-4747   
Genomic Coordinates chr19: 4932687 - 4932740
Description Homo sapiens miR-4747 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4747-5p
Sequence 1| AGGGAAGGAGGCUUGGUCUUAG |22
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs560927363 4 dbSNP
rs1471226927 10 dbSNP
rs763137545 12 dbSNP
rs767337154 15 dbSNP
rs775298039 16 dbSNP
rs760472311 19 dbSNP
rs1207950315 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol SPSB1   
Synonyms SSB-1, SSB1
Description splA/ryanodine receptor domain and SOCS box containing 1
Transcript NM_025106   
Expression
Putative miRNA Targets on SPSB1
3'UTR of SPSB1
(miRNA target sites are highlighted)
>SPSB1|NM_025106|3'UTR
   1 CGTTCGCCATCATACCGCCAGCGCGACAGCCACCTGGTGCCAACTCACTGAGCCGCCTGCCGCTGGGGCCGCCGCACCCT
  81 GCACCTTGGACCGGCATCCGTAGCCATGGACAGAGGTCCCTGGTCTTCCCTCATCCTCCGTGGCTGCCTCCATGGGACAA
 161 GGACCGATTCCAACACAGGCTCCTCTTTCCCCCTTCCCGACATCAGCAGAAGGCAGCATCCCTGCATGCCGTCCGTATAC
 241 AACCCCTCTTTGAAAAAAGACACAGAGAATAAACTCCTACGAAAGCCCTACATTGAGCTCCAATCTGCTCGGGGTGGGAC
 321 GGGTGCTTCCCACACCTCTGGGAGAAGGCTGCAGCCACCTGGGGGTCCCAGGGTGGTGGGGGTGGCAGGTGGTACCACAG
 401 CTCTGAGAGCAGATACCAGGGGTACTAAGAGGTGCTTAGACAAGGGCTGGTGCCCGGCCCAGGGTGCCCAGCGGGGCCAT
 481 GCCATGGCAGATAAAGCTCAGGACGTCAAAAACTCACCATGGACCCCAAGGCAGAAACCAAGAACTGTCTGCAGGCAAAT
 561 AAGCACCCAGCACCCATCCTGGCTGCCGGTGCCCCGTACCCTGTATTTATTCTTTTAACAATAACAAAAGCCATTTATTT
 641 ATTCCATCTAGAAAGGAAACCCTGTTTCAGTCCCCTCTCTCTGGCTGTTCTGTTACTTTCCTTCCACCTGTGCCCTCCCT
 721 GGGATATGTATGCCTCGCCCGCCCTCCCTGGGCACATGTGCACACGTGCCCAGGCACAAGTATGTCTCTGGGTCCCTTGC
 801 CCTGCAGTTTCCAGGGGGCTCTGCTCCAAGTTCCCTAGCGGGCCCCTCAGGGAGAAATAGCCTCACGTGCAATCTGGGTG
 881 TCTTCGGGGGCCCGTCTGGAAGGGCTGCAGCAATTCCCCTGTGTCTCCAGGTAACCAGCTAACTCTTGGGCTCAGGCACC
 961 CTTGCACAGGGTTGCATTTCTTTAGTCTTCTGTGGGTCTTTTGATGTGGGTTTGATTTTGCTTTTGCTTTTCTAGCTGAG
1041 ATTTCCCAAGTGCATCCTCAGAAGCTCTGGGTGTGCCAGAGGACCCCCAGAACTAAGAAGGGAGGGCGAGTGGGTCTCCA
1121 TTCCCCGAGAAGCCGGGGGCAGGGTGGGATGGGGAAGACCAGGAGCAGAGTCGAGCCTCACAGAAGCCAGCGCGGGTCTC
1201 TGCTCAGCACCCCAGCCGGGGCTCTGGACCCAGGGTAACAGCCCCAGTTCATCCCAACCCCTCTCAGAGCCTCAAGAGGG
1281 GTAGCTCGGCTGCCGGAAGAGAGGGGTGCCCTATCCCTGGCAACCCCTCCACGTAGCGTACCCCAGCACCTGCCACCGCC
1361 TTTGCCATTTCTTTGAGCTTGAAGTTAACTCTCTTAGAGTCTAACTTTGGTTCATTTCTGCACAGGTACAATAGATGACT
1441 TTATTTGTTTAAAATGTTTAATATATATACATACATATATATATATTTGTCTGTAAGAATTATGTTTTAAACAGCTGCTG
1521 TAGAGTACCTTTTTTTAAGTAAATCTTACAGTGGAGTATATTTTTTAAAGCACAAAATTGGTGCCAAGACTGGGTGAGAA
1601 ATGTACATTACCCCCTTATTATTTTGACGGTTTTTTTTTTCGGGGCAGGGGACCTTACCTGTAAGACTTTTAAAGATTTT
1681 CCTCCCTCCTGTTTCAGGTGGGTCACATTCTGATGAATGTTTCCCTTGTACAGATCCCAGCTTATGGCCTTGACCCAGCC
1761 GTCCTCACAGATGCCGGGTGACCCTCTAGCTCTCTCTGCATCTCCCACCCCCCGACACCCTGGGACCCTCGACCCCACCC
1841 TTCTTTCCTACCAGCCCAGAGCCTTGTGGCTTGTACAGTTTTGAAACTCCCGTTCTATTTTATGATGGTTGATAATAGTC
1921 AGTAACCTAATAAAGGAACGTTTGTTAAAATATCAAAAAAAAAAAAAAA
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' gaUUCUGGUUC--GGAGGAAGGGa 5'
            || | ||:|  ||||:||||| 
Target 5' ccAACA-CAGGCTCCTCTTTCCCc 3'
170 - 192 149.00 -19.50
2
miRNA  3' gauUCUGGUUC---GGA--GGAAGGGa 5'
             :||| :||   |||  :|||||| 
Target 5' catGGACAGAGGTCCCTGGTCTTCCCt 3'
105 - 131 141.00 -19.70
3
miRNA  3' gauuCUGGUUCGGAGG-AAGGGa 5'
              || :::|:|||| ||||| 
Target 5' gggcGAGTGGGTCTCCATTCCCc 3'
1104 - 1126 134.00 -20.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30493041 6 COSMIC
COSN26550688 7 COSMIC
COSN30495540 7 COSMIC
COSN32062589 66 COSMIC
COSN32063780 85 COSMIC
COSN6473462 236 COSMIC
COSN22734346 260 COSMIC
COSN19383556 459 COSMIC
COSN28774851 501 COSMIC
COSN31563044 575 COSMIC
COSN20090131 633 COSMIC
COSN8146745 915 COSMIC
COSN10056472 924 COSMIC
COSN6473463 1052 COSMIC
COSN32056899 1062 COSMIC
COSN30543979 1124 COSMIC
COSN24981168 1192 COSMIC
COSN31486573 1372 COSMIC
COSN31608725 1414 COSMIC
COSN31602568 1487 COSMIC
COSN20094283 1641 COSMIC
COSN26659214 1874 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs778131096 2 dbSNP
rs751759865 3 dbSNP
rs200653520 6 dbSNP
rs781568490 7 dbSNP
rs1397978882 8 dbSNP
rs1030933695 10 dbSNP
rs1334606290 16 dbSNP
rs954870189 17 dbSNP
rs746342692 18 dbSNP
rs770055673 19 dbSNP
rs542296327 20 dbSNP
rs780406718 23 dbSNP
rs749638452 24 dbSNP
rs991600776 25 dbSNP
rs768363537 26 dbSNP
rs773961593 28 dbSNP
rs1421696830 29 dbSNP
rs1166581909 30 dbSNP
rs761362730 35 dbSNP
rs1461387152 40 dbSNP
rs1214919802 41 dbSNP
rs1306151570 42 dbSNP
rs771562509 45 dbSNP
rs139808151 47 dbSNP
rs773056435 49 dbSNP
rs1432610799 55 dbSNP
rs377243114 56 dbSNP
rs927300234 62 dbSNP
rs937444203 63 dbSNP
rs977299822 64 dbSNP
rs1230901702 67 dbSNP
rs992900547 71 dbSNP
rs563773990 72 dbSNP
rs1042201892 74 dbSNP
rs965559226 75 dbSNP
rs976629841 93 dbSNP
rs1452800138 94 dbSNP
rs921118836 100 dbSNP
rs112475092 101 dbSNP
rs900141702 107 dbSNP
rs141989891 108 dbSNP
rs566779186 115 dbSNP
rs909548996 125 dbSNP
rs778521609 133 dbSNP
rs1036986459 140 dbSNP
rs898089912 141 dbSNP
rs1003561281 152 dbSNP
rs1460883958 153 dbSNP
rs11121390 163 dbSNP
rs184177728 167 dbSNP
rs552494328 169 dbSNP
rs1456941776 174 dbSNP
rs568039685 175 dbSNP
rs529027354 183 dbSNP
rs1163385893 184 dbSNP
rs1021722613 189 dbSNP
rs1401424934 193 dbSNP
rs968675535 200 dbSNP
rs963650117 201 dbSNP
rs1319575814 203 dbSNP
rs2275458 209 dbSNP
rs1307313363 229 dbSNP
rs1031984893 231 dbSNP
rs568968666 232 dbSNP
rs1273520393 235 dbSNP
rs2275457 236 dbSNP
rs958700695 238 dbSNP
rs993325547 241 dbSNP
rs921086798 243 dbSNP
rs917379466 256 dbSNP
rs1251582561 260 dbSNP
rs534769003 260 dbSNP
rs967429295 263 dbSNP
rs557198475 264 dbSNP
rs557651211 265 dbSNP
rs977924619 266 dbSNP
rs1397460188 268 dbSNP
rs983795809 269 dbSNP
rs923756848 282 dbSNP
rs1340145066 289 dbSNP
rs1245590889 293 dbSNP
rs1398194200 295 dbSNP
rs1267374276 296 dbSNP
rs909643727 304 dbSNP
rs1322016150 311 dbSNP
rs1345331923 311 dbSNP
rs939659499 312 dbSNP
rs1036717669 314 dbSNP
rs927649625 321 dbSNP
rs1269114227 323 dbSNP
rs1466557896 335 dbSNP
rs1481758144 355 dbSNP
rs1207792781 356 dbSNP
rs936610719 362 dbSNP
rs1490463635 364 dbSNP
rs1053680546 372 dbSNP
rs762248858 374 dbSNP
rs1427339402 375 dbSNP
rs1170573841 377 dbSNP
rs1253618440 379 dbSNP
rs931624832 380 dbSNP
rs1292628777 383 dbSNP
rs772979732 388 dbSNP
rs566457609 390 dbSNP
rs1369710540 396 dbSNP
rs1471540123 415 dbSNP
rs1339091594 416 dbSNP
rs1381675832 417 dbSNP
rs1309385915 418 dbSNP
rs894611086 418 dbSNP
rs542938845 422 dbSNP
rs890243802 423 dbSNP
rs1004618191 424 dbSNP
rs553129905 430 dbSNP
rs1396828729 438 dbSNP
rs1314873947 440 dbSNP
rs574769910 446 dbSNP
rs1228279401 451 dbSNP
rs1043135971 456 dbSNP
rs1187089750 457 dbSNP
rs1034568584 467 dbSNP
rs1331903909 473 dbSNP
rs535578989 474 dbSNP
rs1385484634 483 dbSNP
rs1425613964 484 dbSNP
rs1255842902 495 dbSNP
rs773171397 500 dbSNP
rs76910624 501 dbSNP
rs766287186 505 dbSNP
rs1014292873 506 dbSNP
rs1290009047 514 dbSNP
rs1200695867 516 dbSNP
rs1364166594 522 dbSNP
rs575934517 526 dbSNP
rs763121892 544 dbSNP
rs546450090 553 dbSNP
rs1028198936 564 dbSNP
rs967458815 576 dbSNP
rs1247836287 577 dbSNP
rs1283597975 582 dbSNP
rs371555692 588 dbSNP
rs573623462 589 dbSNP
rs957833673 590 dbSNP
rs921908617 594 dbSNP
rs1243327879 596 dbSNP
rs931882095 597 dbSNP
rs1446101507 600 dbSNP
rs1406198649 602 dbSNP
rs1400558227 610 dbSNP
rs1160451778 612 dbSNP
rs983931633 613 dbSNP
rs1016614823 622 dbSNP
rs1468262155 626 dbSNP
rs1051467690 627 dbSNP
rs754991670 630 dbSNP
rs1454756511 633 dbSNP
rs1307436577 640 dbSNP
rs1173610537 648 dbSNP
rs760088144 673 dbSNP
rs1224147011 674 dbSNP
rs972929015 676 dbSNP
rs927649015 678 dbSNP
rs1310396465 680 dbSNP
rs767615567 688 dbSNP
rs540924800 698 dbSNP
rs993062788 700 dbSNP
rs1196360370 713 dbSNP
rs76773239 715 dbSNP
rs1469894943 727 dbSNP
rs1178173293 731 dbSNP
rs188916696 738 dbSNP
rs145753296 739 dbSNP
rs1176389163 741 dbSNP
rs562574208 742 dbSNP
rs903163171 743 dbSNP
rs998902553 745 dbSNP
rs1033016119 746 dbSNP
rs934752570 747 dbSNP
rs957447220 748 dbSNP
rs1029228788 750 dbSNP
rs989361643 750 dbSNP
rs953342146 754 dbSNP
rs1053649242 757 dbSNP
rs751810595 766 dbSNP
rs576524369 767 dbSNP
rs778990450 776 dbSNP
rs532840771 781 dbSNP
rs1438070553 782 dbSNP
rs1281992559 783 dbSNP
rs1234931556 787 dbSNP
rs1489981895 803 dbSNP
rs1028167879 805 dbSNP
rs889718013 810 dbSNP
rs1005448289 811 dbSNP
rs1199316984 814 dbSNP
rs1339699960 819 dbSNP
rs1016716740 822 dbSNP
rs987766901 824 dbSNP
rs1166256896 830 dbSNP
rs1203801428 833 dbSNP
rs911570678 838 dbSNP
rs961545309 840 dbSNP
rs1363478432 841 dbSNP
rs1404167580 849 dbSNP
rs940301958 852 dbSNP
rs551195365 854 dbSNP
rs1269056523 859 dbSNP
rs1339531757 861 dbSNP
rs1266363454 867 dbSNP
rs1433528159 868 dbSNP
rs1178032006 869 dbSNP
rs972471125 875 dbSNP
rs1222227588 881 dbSNP
rs1270187085 885 dbSNP
rs80331445 886 dbSNP
rs41301983 887 dbSNP
rs1169230194 889 dbSNP
rs1188493287 892 dbSNP
rs60444586 894 dbSNP
rs1423688154 895 dbSNP
rs568370340 919 dbSNP
rs1367268959 921 dbSNP
rs573099250 930 dbSNP
rs1317633230 936 dbSNP
rs1326491102 946 dbSNP
rs1432301748 946 dbSNP
rs181317570 947 dbSNP
rs375019976 960 dbSNP
rs998850010 961 dbSNP
rs1358958338 968 dbSNP
rs1032964669 969 dbSNP
rs926139200 973 dbSNP
rs539933388 976 dbSNP
rs893247649 977 dbSNP
rs997319237 985 dbSNP
rs934825306 991 dbSNP
rs1028840841 995 dbSNP
rs1295943976 997 dbSNP
rs1053175164 1001 dbSNP
rs1362493286 1011 dbSNP
rs901265585 1011 dbSNP
rs1386854618 1016 dbSNP
rs558437021 1017 dbSNP
rs987412191 1018 dbSNP
rs573428021 1022 dbSNP
rs147807989 1027 dbSNP
rs141223867 1034 dbSNP
rs1334142700 1037 dbSNP
rs1005422435 1046 dbSNP
rs769128578 1047 dbSNP
rs9442601 1052 dbSNP
rs1264774377 1057 dbSNP
rs78841739 1058 dbSNP
rs562126839 1074 dbSNP
rs1352076711 1078 dbSNP
rs930429649 1080 dbSNP
rs1195262814 1088 dbSNP
rs1460981147 1101 dbSNP
rs994421507 1105 dbSNP
rs747602790 1108 dbSNP
rs960720707 1109 dbSNP
rs143472419 1128 dbSNP
rs1045870443 1133 dbSNP
rs1174243628 1135 dbSNP
rs9728893 1136 dbSNP
rs967743386 1145 dbSNP
rs762669083 1147 dbSNP
rs1164241576 1155 dbSNP
rs1338232421 1160 dbSNP
rs1393886812 1161 dbSNP
rs1389991389 1169 dbSNP
rs1328628735 1173 dbSNP
rs1336764562 1174 dbSNP
rs1350966866 1177 dbSNP
rs1459899042 1181 dbSNP
rs978968204 1183 dbSNP
rs926203891 1186 dbSNP
rs1281994301 1188 dbSNP
rs1322838257 1190 dbSNP
rs956203555 1193 dbSNP
rs989401493 1195 dbSNP
rs1337718224 1197 dbSNP
rs1195489793 1199 dbSNP
rs922818260 1204 dbSNP
rs559918873 1206 dbSNP
rs1049840430 1207 dbSNP
rs911183176 1211 dbSNP
rs996950997 1218 dbSNP
rs1178008162 1219 dbSNP
rs1370936892 1224 dbSNP
rs1050234888 1225 dbSNP
rs1168207201 1226 dbSNP
rs1433854611 1230 dbSNP
rs540467112 1238 dbSNP
rs1297841790 1249 dbSNP
rs1412077814 1254 dbSNP
rs1301762575 1257 dbSNP
rs1345467205 1258 dbSNP
rs1363703607 1270 dbSNP
rs941374765 1272 dbSNP
rs1038263322 1279 dbSNP
rs560079566 1281 dbSNP
rs549021124 1282 dbSNP
rs891211694 1288 dbSNP
rs1008769922 1289 dbSNP
rs897083796 1295 dbSNP
rs994125133 1296 dbSNP
rs1056689374 1298 dbSNP
rs1219983727 1300 dbSNP
rs1290897763 1301 dbSNP
rs993391676 1307 dbSNP
rs1192901489 1312 dbSNP
rs1259051499 1316 dbSNP
rs896351758 1319 dbSNP
rs1303449092 1320 dbSNP
rs1215502974 1325 dbSNP
rs1265957633 1328 dbSNP
rs34229353 1329 dbSNP
rs567580887 1329 dbSNP
rs1391634341 1331 dbSNP
rs1027335286 1333 dbSNP
rs951766852 1334 dbSNP
rs1023391463 1338 dbSNP
rs537734625 1339 dbSNP
rs1425809433 1347 dbSNP
rs1471971291 1357 dbSNP
rs1000545536 1358 dbSNP
rs183916038 1359 dbSNP
rs1367661207 1383 dbSNP
rs1243438949 1396 dbSNP
rs924761916 1400 dbSNP
rs1314082038 1431 dbSNP
rs1236486604 1440 dbSNP
rs1414640599 1444 dbSNP
rs934930429 1449 dbSNP
rs956471058 1455 dbSNP
rs1485220351 1456 dbSNP
rs989105299 1459 dbSNP
rs1249447318 1461 dbSNP
rs922759672 1461 dbSNP
rs1442365806 1462 dbSNP
rs1388603930 1464 dbSNP
rs565658026 1467 dbSNP
rs1323038275 1468 dbSNP
rs1346592108 1472 dbSNP
rs1049744952 1475 dbSNP
rs914582971 1475 dbSNP
rs932685595 1475 dbSNP
rs1390986405 1479 dbSNP
rs1445367911 1480 dbSNP
rs576457460 1484 dbSNP
rs553031053 1488 dbSNP
rs1008298636 1497 dbSNP
rs1040251327 1507 dbSNP
rs375968461 1521 dbSNP
rs1234634361 1530 dbSNP
rs1316290628 1533 dbSNP
rs993420963 1537 dbSNP
rs1269440292 1548 dbSNP
rs766229917 1548 dbSNP
rs1459639794 1550 dbSNP
rs1202630051 1554 dbSNP
rs1243393566 1571 dbSNP
rs1483746446 1574 dbSNP
rs955541786 1576 dbSNP
rs951993120 1579 dbSNP
rs1418984842 1592 dbSNP
rs1160607130 1597 dbSNP
rs1414273980 1599 dbSNP
rs985476726 1603 dbSNP
rs569272649 1605 dbSNP
rs1336247187 1606 dbSNP
rs539945213 1608 dbSNP
rs796136938 1619 dbSNP
rs1296215292 1620 dbSNP
rs1372394872 1623 dbSNP
rs558245844 1626 dbSNP
rs567087057 1627 dbSNP
rs1440850523 1628 dbSNP
rs1209708955 1629 dbSNP
rs924791363 1629 dbSNP
rs956170218 1630 dbSNP
rs112184797 1631 dbSNP
rs1202067134 1631 dbSNP
rs141993039 1631 dbSNP
rs1480549546 1631 dbSNP
rs1491210269 1631 dbSNP
rs756411903 1631 dbSNP
rs1183460452 1632 dbSNP
rs1238083458 1633 dbSNP
rs1254600367 1641 dbSNP
rs1479473419 1642 dbSNP
rs534376800 1643 dbSNP
rs1416348278 1645 dbSNP
rs1168681206 1651 dbSNP
rs555658207 1652 dbSNP
rs1410227118 1659 dbSNP
rs574306930 1666 dbSNP
rs1038760873 1668 dbSNP
rs1343601562 1685 dbSNP
rs918627110 1686 dbSNP
rs1274904761 1690 dbSNP
rs929877710 1696 dbSNP
rs1056421046 1708 dbSNP
rs914845047 1709 dbSNP
rs1412355657 1711 dbSNP
rs1206353992 1717 dbSNP
rs1333134395 1719 dbSNP
rs896279326 1720 dbSNP
rs1359427685 1722 dbSNP
rs544566145 1728 dbSNP
rs1247358114 1729 dbSNP
rs569903640 1731 dbSNP
rs1012093155 1734 dbSNP
rs912541408 1745 dbSNP
rs1044807239 1751 dbSNP
rs1416073116 1759 dbSNP
rs903622919 1760 dbSNP
rs555784779 1761 dbSNP
rs1031071817 1762 dbSNP
rs1423895275 1765 dbSNP
rs944118189 1777 dbSNP
rs1351103284 1778 dbSNP
rs1349719717 1791 dbSNP
rs577171248 1795 dbSNP
rs1269185806 1800 dbSNP
rs1365497484 1804 dbSNP
rs1410371486 1808 dbSNP
rs1010866114 1809 dbSNP
rs1357825549 1810 dbSNP
rs1222378055 1812 dbSNP
rs897664171 1813 dbSNP
rs544712634 1814 dbSNP
rs955511275 1815 dbSNP
rs985612399 1819 dbSNP
rs1048878799 1821 dbSNP
rs887717548 1831 dbSNP
rs1383150116 1832 dbSNP
rs1163713533 1844 dbSNP
rs1018423071 1846 dbSNP
rs1398400781 1849 dbSNP
rs1316992053 1852 dbSNP
rs756734034 1857 dbSNP
rs1436819063 1859 dbSNP
rs906847969 1864 dbSNP
rs1380960639 1866 dbSNP
rs974221917 1869 dbSNP
rs1203107208 1873 dbSNP
rs200659889 1874 dbSNP
rs1244528363 1875 dbSNP
rs1468431068 1876 dbSNP
rs918578401 1877 dbSNP
rs956869301 1884 dbSNP
rs929992961 1888 dbSNP
rs559780616 1892 dbSNP
rs917851584 1893 dbSNP
rs947844237 1909 dbSNP
rs1267552632 1911 dbSNP
rs537338666 1917 dbSNP
rs990755837 1920 dbSNP
rs1044901050 1930 dbSNP
rs1241548046 1940 dbSNP
rs1021776957 1941 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions C8166 , 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 GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3 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' gauucugguucGGAGGAAGGGa 5'
                     || ||||||| 
Target 5' ------ucuuuCCCCCUUCCCg 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 GSM1462572
Method / RBP PAR-CLIP / AGO2
Cell line / Condition C8166 / C8166 NL4-3
Location of target site ENST00000328089.6 | 3UTR | UUUCCCCCUUCCCGAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1462573
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl BaL
Location of target site ENST00000328089.6 | 3UTR | UCUUUCCCCCUUCCCG
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
215 hsa-miR-4747-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT061689 BTG2 BTG anti-proliferation factor 2 2 2
MIRT062834 BCL7A BCL tumor suppressor 7A 2 2
MIRT079371 CCDC137 coiled-coil domain containing 137 2 2
MIRT081190 MIDN midnolin 2 4
MIRT081724 ZNF507 zinc finger protein 507 2 2
MIRT110565 ZMYND11 zinc finger MYND-type containing 11 2 2
MIRT133724 SKI SKI proto-oncogene 2 4
MIRT146689 MINK1 misshapen like kinase 1 2 2
MIRT150676 SLC27A1 solute carrier family 27 member 1 2 2
MIRT159196 NRBP1 nuclear receptor binding protein 1 2 2
MIRT180865 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT190659 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT196111 MPRIP myosin phosphatase Rho interacting protein 2 2
MIRT232390 SP1 Sp1 transcription factor 2 2
MIRT331070 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 4
MIRT338632 SHMT2 serine hydroxymethyltransferase 2 2 2
MIRT407441 CTDSP1 CTD small phosphatase 1 2 2
MIRT444276 NKX6-1 NK6 homeobox 1 2 2
MIRT444834 PDE6D phosphodiesterase 6D 2 2
MIRT445452 EXT1 exostosin glycosyltransferase 1 2 2
MIRT445644 NPY4R neuropeptide Y receptor Y4 2 2
MIRT446157 RPL12 ribosomal protein L12 2 2
MIRT446608 HIP1 huntingtin interacting protein 1 2 2
MIRT447108 CLPX caseinolytic mitochondrial matrix peptidase chaperone subunit 2 2
MIRT449314 MRO maestro 2 2
MIRT450305 DRAXIN dorsal inhibitory axon guidance protein 2 2
MIRT451245 ZNF444 zinc finger protein 444 2 2
MIRT451714 OLR1 oxidized low density lipoprotein receptor 1 2 2
MIRT451908 ILK integrin linked kinase 2 2
MIRT452183 KIAA1456 KIAA1456 2 2
MIRT452610 REPIN1 replication initiator 1 2 2
MIRT453422 GLG1 golgi glycoprotein 1 2 2
MIRT454006 ALKBH5 alkB homolog 5, RNA demethylase 2 2
MIRT455072 ARHGAP39 Rho GTPase activating protein 39 2 2
MIRT455319 TTLL9 tubulin tyrosine ligase like 9 2 2
MIRT455357 KDM5C lysine demethylase 5C 2 2
MIRT455589 TAF12 TATA-box binding protein associated factor 12 2 2
MIRT455711 EIF4EBP2 eukaryotic translation initiation factor 4E binding protein 2 2 2
MIRT455860 TMEM254 transmembrane protein 254 2 2
MIRT455919 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 2
MIRT455946 CYP4A22 cytochrome P450 family 4 subfamily A member 22 2 2
MIRT456935 LRP10 LDL receptor related protein 10 2 2
MIRT457223 AP3D1 adaptor related protein complex 3 delta 1 subunit 2 2
MIRT457431 NOL10 nucleolar protein 10 2 2
MIRT457470 SLC35F6 solute carrier family 35 member F6 2 2
MIRT457907 ZNF212 zinc finger protein 212 2 2
MIRT458046 TSEN54 tRNA splicing endonuclease subunit 54 2 2
MIRT458073 RNLS renalase, FAD dependent amine oxidase 2 2
MIRT458234 NXPH3 neurexophilin 3 2 2
MIRT458307 TNFAIP8L3 TNF alpha induced protein 8 like 3 2 2
MIRT458378 ITM2C integral membrane protein 2C 2 2
MIRT458967 ZNF436 zinc finger protein 436 2 2
MIRT459099 CYP4A11 cytochrome P450 family 4 subfamily A member 11 2 2
MIRT459446 TMEM37 transmembrane protein 37 2 2
MIRT459671 VPS37C VPS37C, ESCRT-I subunit 2 2
MIRT460727 ASXL3 additional sex combs like 3, transcriptional regulator 2 2
MIRT460744 SRP14 signal recognition particle 14 2 2
MIRT461531 C14orf1 ergosterol biosynthesis 28 homolog 2 2
MIRT461752 DDX11 DEAD/H-box helicase 11 2 2
MIRT461837 F2RL3 F2R like thrombin or trypsin receptor 3 2 2
MIRT462019 RIF1 replication timing regulatory factor 1 2 2
MIRT462631 PHF5A PHD finger protein 5A 2 2
MIRT462772 ZNF8 zinc finger protein 8 2 2
MIRT463032 ZNF689 zinc finger protein 689 2 2
MIRT463886 WNT7B Wnt family member 7B 2 2
MIRT463995 WDTC1 WD and tetratricopeptide repeats 1 2 2
MIRT464371 URM1 ubiquitin related modifier 1 2 2
MIRT465342 TPM3 tropomyosin 3 2 4
MIRT465515 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT465602 TNRC6A trinucleotide repeat containing 6A 2 2
MIRT465697 TNPO2 transportin 2 2 10
MIRT466988 SSRP1 structure specific recognition protein 1 2 4
MIRT467630 SLC7A5 solute carrier family 7 member 5 2 2
MIRT468132 SH3PXD2A SH3 and PX domains 2A 2 2
MIRT468322 SF3B3 splicing factor 3b subunit 3 2 2
MIRT468502 SESN2 sestrin 2 2 2
MIRT468881 RREB1 ras responsive element binding protein 1 2 2
MIRT469322 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 2 2
MIRT469562 RARA retinoic acid receptor alpha 2 2
MIRT469898 PTRF caveolae associated protein 1 2 2
MIRT470045 PTGFRN prostaglandin F2 receptor inhibitor 2 2
MIRT470068 PTGES2 prostaglandin E synthase 2 2 2
MIRT470238 PRRC2A proline rich coiled-coil 2A 2 2
MIRT470390 PPP1R16B protein phosphatase 1 regulatory subunit 16B 2 2
MIRT470500 PPP1R11 protein phosphatase 1 regulatory inhibitor subunit 11 2 2
MIRT470689 POLR2D RNA polymerase II subunit D 2 2
MIRT470704 POGK pogo transposable element derived with KRAB domain 2 2
MIRT471083 PIK3C2B phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta 2 2
MIRT472482 NACC2 NACC family member 2 2 2
MIRT473583 MAT2A methionine adenosyltransferase 2A 2 2
MIRT474554 KLHDC3 kelch domain containing 3 2 2
MIRT474651 KLF13 Kruppel like factor 13 2 2
MIRT474843 KHSRP KH-type splicing regulatory protein 2 2
MIRT474934 KCTD15 potassium channel tetramerization domain containing 15 2 2
MIRT475573 HNRNPC heterogeneous nuclear ribonucleoprotein C (C1/C2) 2 2
MIRT476045 GRSF1 G-rich RNA sequence binding factor 1 2 2
MIRT476080 GRB2 growth factor receptor bound protein 2 2 2
MIRT476440 GBA2 glucosylceramidase beta 2 2 2
MIRT476764 FOSL2 FOS like 2, AP-1 transcription factor subunit 2 2
MIRT478785 CRTC2 CREB regulated transcription coactivator 2 2 2
MIRT479287 CHAC1 ChaC glutathione specific gamma-glutamylcyclotransferase 1 2 2
MIRT479505 CDH6 cadherin 6 2 2
MIRT479732 CCND1 cyclin D1 2 6
MIRT480352 C5orf24 chromosome 5 open reading frame 24 2 2
MIRT480407 C19orf47 chromosome 19 open reading frame 47 2 2
MIRT480859 BHLHB9 basic helix-loop-helix family member b9 2 2
MIRT481445 ARRB2 arrestin beta 2 2 2
MIRT481732 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT481824 AP2M1 adaptor related protein complex 2 mu 1 subunit 2 2
MIRT482566 ABHD2 abhydrolase domain containing 2 2 2
MIRT482607 ABHD14B abhydrolase domain containing 14B 2 2
MIRT483144 SYCE1L synaptonemal complex central element protein 1 like 2 2
MIRT483214 APOA1 apolipoprotein A1 2 6
MIRT483878 TGIF1 TGFB induced factor homeobox 1 2 2
MIRT483917 SPSB1 splA/ryanodine receptor domain and SOCS box containing 1 2 2
MIRT483939 LENG8 leukocyte receptor cluster member 8 2 4
MIRT484420 SNX19 sorting nexin 19 2 2
MIRT484489 SLC9A1 solute carrier family 9 member A1 2 2
MIRT484612 SIX3 SIX homeobox 3 2 6
MIRT484705 RNF11 ring finger protein 11 2 2
MIRT485107 SHISA6 shisa family member 6 2 2
MIRT485354 MYO1C myosin IC 2 4
MIRT485609 FOSL1 FOS like 1, AP-1 transcription factor subunit 2 4
MIRT487311 GLTSCR1 BRD4 interacting chromatin remodeling complex associated protein 2 2
MIRT487417 CACNB1 calcium voltage-gated channel auxiliary subunit beta 1 2 2
MIRT487695 CDK14 cyclin dependent kinase 14 2 2
MIRT487791 GPR20 G protein-coupled receptor 20 2 4
MIRT488042 PABPC1L2B poly(A) binding protein cytoplasmic 1 like 2B 2 2
MIRT488058 PABPC1L2A poly(A) binding protein cytoplasmic 1 like 2A 2 2
MIRT488237 DNLZ DNL-type zinc finger 2 4
MIRT488764 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT489401 TUBB2A tubulin beta 2A class IIa 2 2
MIRT489777 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT490099 FN3K fructosamine 3 kinase 2 2
MIRT490290 ISL2 ISL LIM homeobox 2 2 2
MIRT490378 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT491329 GFER growth factor, augmenter of liver regeneration 2 2
MIRT491435 MSX2 msh homeobox 2 2 2
MIRT491769 ZNF385A zinc finger protein 385A 2 2
MIRT491922 WNK2 WNK lysine deficient protein kinase 2 2 2
MIRT491983 UNK unkempt family zinc finger 2 2
MIRT492228 SLC48A1 solute carrier family 48 member 1 2 2
MIRT492404 SDK1 sidekick cell adhesion molecule 1 2 2
MIRT492767 PDGFB platelet derived growth factor subunit B 2 2
MIRT492966 NCS1 neuronal calcium sensor 1 2 2
MIRT493295 LLGL2 LLGL2, scribble cell polarity complex component 2 2
MIRT493650 HDLBP high density lipoprotein binding protein 2 2
MIRT493913 FAM127B retrotransposon Gag like 8A 2 4
MIRT495601 NKX2-5 NK2 homeobox 5 2 2
MIRT496875 AHCYL2 adenosylhomocysteinase like 2 2 2
MIRT498514 MYH14 myosin heavy chain 14 2 2
MIRT499178 RBPJL recombination signal binding protein for immunoglobulin kappa J region like 2 2
MIRT502143 KIF5B kinesin family member 5B 2 8
MIRT502692 CSNK1G1 casein kinase 1 gamma 1 2 4
MIRT508460 HOXB6 homeobox B6 2 4
MIRT510430 ZNF207 zinc finger protein 207 2 6
MIRT511837 GPATCH8 G-patch domain containing 8 2 4
MIRT512368 CPM carboxypeptidase M 2 2
MIRT512506 BTBD19 BTB domain containing 19 2 2
MIRT513065 ANKRD45 ankyrin repeat domain 45 2 2
MIRT513267 SCUBE1 signal peptide, CUB domain and EGF like domain containing 1 2 4
MIRT513575 EVX1 even-skipped homeobox 1 2 2
MIRT515051 EBNA1BP2 EBNA1 binding protein 2 2 2
MIRT515790 COL4A3BP collagen type IV alpha 3 binding protein 2 2
MIRT521657 PRKD3 protein kinase D3 2 2
MIRT522679 LUZP1 leucine zipper protein 1 2 6
MIRT528845 RAB32 RAB32, member RAS oncogene family 2 2
MIRT533569 TOR1AIP1 torsin 1A interacting protein 1 2 2
MIRT543738 DHCR7 7-dehydrocholesterol reductase 2 2
MIRT544295 TSPYL1 TSPY like 1 2 2
MIRT544857 MYH2 myosin heavy chain 2 2 4
MIRT557323 HIATL1 major facilitator superfamily domain containing 14B 2 4
MIRT560522 TMEM98 transmembrane protein 98 2 2
MIRT561565 SLC6A9 solute carrier family 6 member 9 2 2
MIRT562374 ERI2 ERI1 exoribonuclease family member 2 2 2
MIRT565780 SEMA6D semaphorin 6D 2 2
MIRT569548 UNC119B unc-119 lipid binding chaperone B 2 2
MIRT569944 PRRT2 proline rich transmembrane protein 2 2 2
MIRT570016 COL1A2 collagen type I alpha 2 chain 2 2
MIRT572163 CRK CRK proto-oncogene, adaptor protein 2 2
MIRT572322 HSPB6 heat shock protein family B (small) member 6 2 2
MIRT573495 IQSEC3 IQ motif and Sec7 domain 3 2 2
MIRT574139 MARVELD1 MARVEL domain containing 1 2 2
MIRT609449 CCDC149 coiled-coil domain containing 149 2 2
MIRT610619 ARHGAP18 Rho GTPase activating protein 18 2 2
MIRT623355 LZIC leucine zipper and CTNNBIP1 domain containing 2 2
MIRT629854 ACOX1 acyl-CoA oxidase 1 2 2
MIRT630516 CDC73 cell division cycle 73 2 2
MIRT632535 PSMB2 proteasome subunit beta 2 2 2
MIRT633975 SLC35E2 solute carrier family 35 member E2 2 2
MIRT636408 MTHFD2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase 2 2
MIRT641722 LTBR lymphotoxin beta receptor 2 2
MIRT642661 RGS6 regulator of G protein signaling 6 2 2
MIRT649649 MAST3 microtubule associated serine/threonine kinase 3 2 2
MIRT650367 MOCS3 molybdenum cofactor synthesis 3 2 2
MIRT651355 ZBTB40 zinc finger and BTB domain containing 40 2 2
MIRT664840 HUS1 HUS1 checkpoint clamp component 2 2
MIRT667322 MYH9 myosin heavy chain 9 2 2
MIRT670680 SUGT1 SGT1 homolog, MIS12 kinetochore complex assembly cochaperone 2 2
MIRT674922 TRPM6 transient receptor potential cation channel subfamily M member 6 2 2
MIRT675919 CYP51A1 cytochrome P450 family 51 subfamily A member 1 2 2
MIRT676493 GJD3 gap junction protein delta 3 2 2
MIRT680162 ZDHHC20 zinc finger DHHC-type containing 20 2 2
MIRT688008 GSN gelsolin 2 2
MIRT688997 ATP6AP1 ATPase H+ transporting accessory protein 1 2 2
MIRT700337 RAB4A RAB4A, member RAS oncogene family 2 2
MIRT701344 NR4A3 nuclear receptor subfamily 4 group A member 3 2 2
MIRT703519 FKBP15 FK506 binding protein 15 2 2
MIRT703901 EPT1 selenoprotein I 2 2
MIRT705565 ARHGEF18 Rho/Rac guanine nucleotide exchange factor 18 2 2
MIRT709709 DNAJC11 DnaJ heat shock protein family (Hsp40) member C11 2 2
MIRT713108 TMBIM4 transmembrane BAX inhibitor motif containing 4 2 2
MIRT718426 ZNF85 zinc finger protein 85 2 2
MIRT719236 CYSLTR2 cysteinyl leukotriene receptor 2 2 2
MIRT719326 STAC SH3 and cysteine rich domain 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4747 Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-4747-5p Temozolomide 5394 NSC362856 approved sensitive cell line (U251)
hsa-miR-4747-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4747-5p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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