miRTarBase - #MIRT442773


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pre-miRNA Information
pre-miRNA hsa-mir-4480   
Genomic Coordinates chr10: 12578753 - 12578823
Description Homo sapiens miR-4480 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4480
Sequence 44| AGCCAAGUGGAAGUUACUUUA |64
Evidence Experimental
Experiments Illumina
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 1 10 + 12578796 23291724, 27587585 MiREDiBase
A-to-I 12 10 + 12578807 23291724, 27587585 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs929437808 7 dbSNP
rs1454494557 9 dbSNP
rs1345041659 17 dbSNP
rs561601367 21 dbSNP
Putative Targets

Gene Information
Gene Symbol JAG1   
Synonyms AGS, AGS1, AHD, AWS, CD339, HJ1, JAGL1
Description jagged 1
Transcript NM_000214   
Expression
Putative miRNA Targets on JAG1
3'UTR of JAG1
(miRNA target sites are highlighted)		 
>JAG1|NM_000214|3'UTR
   1 CAGACCGCGGGCACTGCCGCCGCTAGGTAGAGTCTGAGGGCTTGTAGTTCTTTAAACTGTCGTGTCATACTCGAGTCTGA
  81 GGCCGTTGCTGACTTAGAATCCCTGTGTTAATTTAAGTTTTGACAAGCTGGCTTACACTGGCAATGGTAGTTTCTGTGGT
 161 TGGCTGGGAAATCGAGTGCCGCATCTCACAGCTATGCAAAAAGCTAGTCAACAGTACCCTGGTTGTGTGTCCCCTTGCAG
 241 CCGACACGGTCTCGGATCAGGCTCCCAGGAGCCTGCCCAGCCCCCTGGTCTTTGAGCTCCCACTTCTGCCAGATGTCCTA
 321 ATGGTGATGCAGTCTTAGATCATAGTTTTATTTATATTTATTGACTCTTGAGTTGTTTTTGTATATTGGTTTTATGATGA
 401 CGTACAAGTAGTTCTGTATTTGAAAGTGCCTTTGCAGCTCAGAACCACAGCAACGATCACAAATGACTTTATTATTTATT
 481 TTTTTTAATTGTATTTTTGTTGTTGGGGGAGGGGAGACTTTGATGTCAGCAGTTGCTGGTAAAATGAAGAATTTAAAGAA
 561 AAAAATGTCAAAAGTAGAACTTTGTATAGTTATGTAAATAATTCTTTTTTATTAATCACTGTGTATATTTGATTTATTAA
 641 CTTAATAATCAAGAGCCTTAAAACATCATTCCTTTTTATTTATATGTATGTGTTTAGAATTGAAGGTTTTTGATAGCATT
 721 GTAAGCGTATGGCTTTATTTTTTTGAACTCTTCTCATTACTTGTTGCCTATAAGCCAAAATTAAGGTGTTTGAAAATAGT
 801 TTATTTTAAAACAATAGGATGGGCTTCTGTGCCCAGAATACTGATGGAATTTTTTTGTACGACGTCAGATGTTTAAAACA
 881 CCTTCTATAGCATCACTTAAAACACGTTTTAAGGACTGACTGAGGCAGTTTGAGGATTAGTTTAGAACAGGTTTTTTTGT
 961 TTGTTTGTTTTTTGTTTTTCTGCTTTAGACTTGAAAAGAGACAGGCAGGTGATCTGCTGCAGAGCAGTAAGGGAACAAGT
1041 TGAGCTATGACTTAACATAGCCAAAATGTGAGTGGTTGAATATGATTAAAAATATCAAATTAATTGTGTGAACTTGGAAG
1121 CACACCAATCTTACTTTGTAAATTCTGATTTCTTTTCACCATTCGTACATAATACTGAACCACTTGTAGATTTGATTTTT
1201 TTTTTTAATCTACTGCATTTAGGGAGTATTCTAATAAGCTAGTTGAATACTTGAACCATAAAATGTCCAGTAAGATCACT
1281 GTTTAGATTTGCCATAGAGTACACTGCCTGCCTTAAGTGAGGAAATCAAAGTGCTATTACGAAGTTCAAGATCAAAAAGG
1361 CTTATAAAACAGAGTAATCTTGTTGGTTCACCATTGAGACCGTGAAGATACTTTGTATTGTCCTATTAGTGTTATATGAA
1441 CATACAAATGCATCTTTGATGTGTTGTTCTTGGCAATAAATTTTGAAAAGTAATATTTATTAAATTTTTTTGTATGAAAA
1521 CATGGAACAGTGTGGCCTCTTCTGAGCTTACGTAGTTCTACCGGCTTTGCCATGTGCTTCTGCCACCCTGCTGAGTCTGT
1601 TCTGGTAATCGGGGTATAATAGGCTCTGCCTGACAGAGGGATGGAGGAAGAACTGAAAGGCTTTTCAACCACAAAACTCA
1681 TCTGGAGTTCTCAAAGACCTGGGGCTGCTGTGAAGCTGGAACTGCGGGAGCCCCATCTAGGGGAGCCTTGATTCCCTTGT
1761 TATTCAACAGCAAGTGTGAATACTGCTTGAATAAACACCACTGGATTAATGGCCA
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' auUUCAUUGA---AGGUGAACCga 5'
            || |||:|   |  ||||||  
Target 5' caAATTAATTGTGTGAACTTGGaa 3'
 1096 - 1119 135.00 -8.10
2 
miRNA  3' auuucauugaagguGAACCGa 5'
                        |||||| 
Target 5' tttgatgtgttgttCTTGGCa 3'
 1455 - 1475 120.00 -7.10
3 
miRNA  3' auUUC-AUUGAAGGUGAACCGa 5'
            ||| |::||| ||| |||| 
Target 5' acAAGCTGGCTTACAC-TGGCa 3'
 123 - 143 119.00 -12.80
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
246431 2 ClinVar
337742 6 ClinVar
598431 7 ClinVar
596594 9 ClinVar
897615 18 ClinVar
337741 21 ClinVar
337740 253 ClinVar
337739 297 ClinVar
337738 378 ClinVar
337737 398 ClinVar
337736 401 ClinVar
337735 487 ClinVar
896022 521 ClinVar
337734 566 ClinVar
896021 587 ClinVar
337733 619 ClinVar
337732 641 ClinVar
337731 650 ClinVar
337730 756 ClinVar
337729 857 ClinVar
895739 881 ClinVar
337728 914 ClinVar
337727 970 ClinVar
337726 971 ClinVar
337725 1084 ClinVar
337724 1098 ClinVar
337723 1132 ClinVar
337722 1137 ClinVar
337721 1207 ClinVar
337720 1215 ClinVar
337719 1224 ClinVar
895738 1440 ClinVar
337718 1493 ClinVar
337717 1512 ClinVar
337716 1535 ClinVar
898713 1551 ClinVar
337715 1572 ClinVar
898712 1612 ClinVar
337714 1637 ClinVar
898711 1668 ClinVar
COSN31500609 6 COSMIC
COSN5133059 8 COSMIC
COSN31611952 11 COSMIC
COSN30465707 47 COSMIC
COSN30149292 50 COSMIC
COSN31599303 61 COSMIC
COSN30172632 66 COSMIC
COSN30500591 69 COSMIC
COSN28867183 80 COSMIC
COSN30108876 98 COSMIC
COSN31572814 116 COSMIC
COSN31560573 173 COSMIC
COSN1245192 175 COSMIC
COSN13846915 181 COSMIC
COSN24307056 459 COSMIC
COSN20116264 479 COSMIC
COSN28249926 487 COSMIC
COSN28249925 518 COSMIC
COSN31575977 551 COSMIC
COSN28250506 570 COSMIC
COSN30544697 664 COSMIC
COSN28732512 803 COSMIC
COSN1863832 823 COSMIC
COSN20116262 849 COSMIC
COSN29002033 1195 COSMIC
COSN19664704 1196 COSMIC
COSN24306986 1226 COSMIC
COSN31547367 1261 COSMIC
COSN31482794 1469 COSMIC
COSN21826894 1493 COSMIC
COSN28742630 1530 COSMIC
COSN28766583 1572 COSMIC
COSN31480123 1692 COSMIC
COSN2509752 1727 COSMIC
rs7828 1132 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs879254256 2 dbSNP
rs376881523 6 dbSNP
rs879800923 7 dbSNP
rs752554040 8 dbSNP
rs372620326 9 dbSNP
rs1405586394 12 dbSNP
rs369078424 14 dbSNP
rs1160652210 18 dbSNP
rs371402694 19 dbSNP
rs778183555 19 dbSNP
rs554327524 21 dbSNP
rs375704631 22 dbSNP
rs760303270 24 dbSNP
rs772828707 25 dbSNP
rs771910747 28 dbSNP
rs1215764958 29 dbSNP
rs1445606117 32 dbSNP
rs771633785 33 dbSNP
rs114275537 35 dbSNP
rs868577256 44 dbSNP
rs774786943 46 dbSNP
rs1384322056 47 dbSNP
rs1424294839 50 dbSNP
rs186487018 60 dbSNP
rs1351698592 62 dbSNP
rs537795369 64 dbSNP
rs779194971 71 dbSNP
rs1189761362 72 dbSNP
rs755345769 73 dbSNP
rs568996129 80 dbSNP
rs1015890222 84 dbSNP
rs181408895 85 dbSNP
rs1382446543 86 dbSNP
rs1246267708 87 dbSNP
rs1291513893 88 dbSNP
rs1314679763 93 dbSNP
rs1214457578 99 dbSNP
rs1261287918 104 dbSNP
rs1012617532 111 dbSNP
rs1181633489 117 dbSNP
rs898824375 117 dbSNP
rs1186241950 131 dbSNP
rs983132474 136 dbSNP
rs1416223013 142 dbSNP
rs113529940 143 dbSNP
rs1158449425 144 dbSNP
rs535528560 145 dbSNP
rs1459287862 146 dbSNP
rs1196052120 148 dbSNP
rs1030239488 154 dbSNP
rs1335267865 156 dbSNP
rs1004572715 169 dbSNP
rs997456741 169 dbSNP
rs900331145 173 dbSNP
rs1047191531 174 dbSNP
rs778889928 180 dbSNP
rs1249091221 181 dbSNP
rs1017888352 185 dbSNP
rs1307096286 210 dbSNP
rs189368987 215 dbSNP
rs1335389722 217 dbSNP
rs1292610502 218 dbSNP
rs1039951351 225 dbSNP
rs7265435 228 dbSNP
rs1461636650 235 dbSNP
rs140136358 242 dbSNP
rs533118865 243 dbSNP
rs942977558 245 dbSNP
rs570683547 247 dbSNP
rs1329727849 248 dbSNP
rs780887274 253 dbSNP
rs6077859 260 dbSNP
rs1394654686 279 dbSNP
rs1167185367 281 dbSNP
rs1332508648 282 dbSNP
rs757122162 284 dbSNP
rs1417703622 285 dbSNP
rs756876336 295 dbSNP
rs575525743 297 dbSNP
rs551362808 299 dbSNP
rs981901680 323 dbSNP
rs1353057123 327 dbSNP
rs938302362 331 dbSNP
rs1441071026 334 dbSNP
rs531566424 342 dbSNP
rs916435598 353 dbSNP
rs1221121909 354 dbSNP
rs1282639671 354 dbSNP
rs1324169701 365 dbSNP
rs1233839409 366 dbSNP
rs1436972811 367 dbSNP
rs777219419 370 dbSNP
rs1252780949 377 dbSNP
rs886056512 378 dbSNP
rs1436835720 393 dbSNP
rs1197353030 394 dbSNP
rs562655817 398 dbSNP
rs1174793325 400 dbSNP
rs886056511 401 dbSNP
rs542746042 402 dbSNP
rs908966748 403 dbSNP
rs1468541114 404 dbSNP
rs983227719 414 dbSNP
rs963651360 422 dbSNP
rs950344521 436 dbSNP
rs1015861473 454 dbSNP
rs1302003157 455 dbSNP
rs1030041491 456 dbSNP
rs1352810485 470 dbSNP
rs1279888835 474 dbSNP
rs1438560885 477 dbSNP
rs1268296245 481 dbSNP
rs1338558656 485 dbSNP
rs950440263 486 dbSNP
rs1344563163 487 dbSNP
rs3842434 487 dbSNP
rs1220456695 489 dbSNP
rs1291176191 491 dbSNP
rs975988971 492 dbSNP
rs1452206481 503 dbSNP
rs997712445 505 dbSNP
rs1238145215 506 dbSNP
rs901332026 510 dbSNP
rs1475331575 511 dbSNP
rs1040303692 513 dbSNP
rs183692377 518 dbSNP
rs755826715 521 dbSNP
rs1162489611 522 dbSNP
rs1334189497 522 dbSNP
rs1390852304 527 dbSNP
rs964989968 530 dbSNP
rs1017414849 546 dbSNP
rs1328193261 552 dbSNP
rs1325779571 562 dbSNP
rs894067362 564 dbSNP
rs1380259930 566 dbSNP
rs139536676 566 dbSNP
rs1393875962 567 dbSNP
rs181753810 575 dbSNP
rs189337768 584 dbSNP
rs1211712420 586 dbSNP
rs1409408656 586 dbSNP
rs1446946040 592 dbSNP
rs1209834030 600 dbSNP
rs1158352213 603 dbSNP
rs923978341 604 dbSNP
rs1361637641 606 dbSNP
rs1046509667 607 dbSNP
rs774699632 608 dbSNP
rs1473530845 611 dbSNP
rs749342125 615 dbSNP
rs903714977 617 dbSNP
rs146144464 619 dbSNP
rs916400373 620 dbSNP
rs1322410496 621 dbSNP
rs991080044 625 dbSNP
rs1009648723 626 dbSNP
rs1451610655 636 dbSNP
rs1204266823 639 dbSNP
rs1341282309 640 dbSNP
rs866626696 641 dbSNP
rs1277859948 646 dbSNP
rs1349995292 646 dbSNP
rs909143688 649 dbSNP
rs572952606 650 dbSNP
rs1203425910 653 dbSNP
rs950382997 653 dbSNP
rs1256488347 654 dbSNP
rs1443797505 670 dbSNP
rs1029985280 671 dbSNP
rs755353118 678 dbSNP
rs184875157 693 dbSNP
rs1472623048 694 dbSNP
rs964839750 700 dbSNP
rs1370594737 719 dbSNP
rs1301303900 723 dbSNP
rs1433068901 725 dbSNP
rs938234712 726 dbSNP
rs905458683 727 dbSNP
rs1327042375 729 dbSNP
rs1007482496 734 dbSNP
rs1038505571 736 dbSNP
rs941511358 739 dbSNP
rs1248714352 745 dbSNP
rs1410479121 745 dbSNP
rs746781162 753 dbSNP
rs45534738 756 dbSNP
rs1223368286 768 dbSNP
rs1256954855 775 dbSNP
rs575347969 776 dbSNP
rs555381992 782 dbSNP
rs1347522654 787 dbSNP
rs1193770936 791 dbSNP
rs1249349638 795 dbSNP
rs1483137115 796 dbSNP
rs866366575 797 dbSNP
rs577740265 807 dbSNP
rs999813333 808 dbSNP
rs1379177455 815 dbSNP
rs1394171070 815 dbSNP
rs929074835 821 dbSNP
rs1166410736 823 dbSNP
rs1370179211 839 dbSNP
rs1188935564 847 dbSNP
rs1476115300 848 dbSNP
rs1242566920 849 dbSNP
rs1343640979 850 dbSNP
rs1386734273 852 dbSNP
rs3840074 857 dbSNP
rs1192424552 860 dbSNP
rs1445019120 861 dbSNP
rs1273547440 863 dbSNP
rs922898587 864 dbSNP
rs1218802441 869 dbSNP
rs1206779256 875 dbSNP
rs1288996590 877 dbSNP
rs1490029874 879 dbSNP
rs1191747708 881 dbSNP
rs975764855 882 dbSNP
rs1426585117 885 dbSNP
rs1192182992 887 dbSNP
rs964630878 897 dbSNP
rs1211387787 905 dbSNP
rs535594347 906 dbSNP
rs1170669733 911 dbSNP
rs111277443 914 dbSNP
rs1457447595 918 dbSNP
rs1054934856 920 dbSNP
rs1393502157 924 dbSNP
rs1380971551 934 dbSNP
rs1297330128 946 dbSNP
rs979397368 951 dbSNP
rs1366332108 953 dbSNP
rs1216347032 959 dbSNP
rs909086888 959 dbSNP
rs941864270 959 dbSNP
rs1320635045 962 dbSNP
rs1362784342 963 dbSNP
rs1267207217 968 dbSNP
rs1484858788 970 dbSNP
rs886056510 970 dbSNP
rs748163677 971 dbSNP
rs1429207165 974 dbSNP
rs754512600 974 dbSNP
rs1190798211 993 dbSNP
rs1383617063 1002 dbSNP
rs968285179 1002 dbSNP
rs1423381334 1003 dbSNP
rs566556315 1013 dbSNP
rs1351624537 1014 dbSNP
rs1452300189 1020 dbSNP
rs1320412640 1023 dbSNP
rs1389903820 1032 dbSNP
rs567253428 1036 dbSNP
rs1020780508 1040 dbSNP
rs1334363069 1045 dbSNP
rs141994588 1047 dbSNP
rs1377969676 1057 dbSNP
rs560803845 1059 dbSNP
rs539570580 1062 dbSNP
rs1357955456 1074 dbSNP
rs1228478173 1078 dbSNP
rs1314252721 1082 dbSNP
rs148175963 1084 dbSNP
rs550425435 1098 dbSNP
rs886056509 1098 dbSNP
rs752660387 1106 dbSNP
rs1268660340 1125 dbSNP
rs1466143181 1130 dbSNP
rs7828 1132 dbSNP
rs1236626529 1133 dbSNP
rs886056508 1137 dbSNP
rs1182628158 1144 dbSNP
rs1173522256 1148 dbSNP
rs568937350 1152 dbSNP
rs1017780179 1155 dbSNP
rs1159127781 1158 dbSNP
rs1413336020 1158 dbSNP
rs985606766 1164 dbSNP
rs750552812 1165 dbSNP
rs1358875866 1167 dbSNP
rs1002627761 1169 dbSNP
rs958185097 1179 dbSNP
rs759372939 1186 dbSNP
rs1032539532 1191 dbSNP
rs1166862067 1197 dbSNP
rs1476782671 1198 dbSNP
rs1288979429 1199 dbSNP
rs1331160925 1206 dbSNP
rs1211150628 1207 dbSNP
rs1221544691 1207 dbSNP
rs1277693865 1207 dbSNP
rs34134142 1207 dbSNP
rs1259618835 1211 dbSNP
rs886056507 1215 dbSNP
rs1181532453 1223 dbSNP
rs886056506 1224 dbSNP
rs1485231872 1235 dbSNP
rs1235882233 1243 dbSNP
rs1252557068 1253 dbSNP
rs1206915068 1254 dbSNP
rs902784537 1255 dbSNP
rs1424927935 1256 dbSNP
rs1039007526 1258 dbSNP
rs1415378651 1261 dbSNP
rs1005840210 1265 dbSNP
rs1352390446 1270 dbSNP
rs1428644863 1286 dbSNP
rs1308117446 1297 dbSNP
rs1351759963 1301 dbSNP
rs1403052953 1304 dbSNP
rs1274157211 1326 dbSNP
rs887265634 1327 dbSNP
rs1220736426 1336 dbSNP
rs776346798 1340 dbSNP
rs895190824 1341 dbSNP
rs1204618290 1351 dbSNP
rs370588890 1353 dbSNP
rs1275475875 1354 dbSNP
rs1484047092 1355 dbSNP
rs997231746 1359 dbSNP
rs1055618379 1361 dbSNP
rs1478596346 1370 dbSNP
rs1337566215 1375 dbSNP
rs1347614650 1382 dbSNP
rs923029523 1392 dbSNP
rs1040153505 1400 dbSNP
rs1414473402 1401 dbSNP
rs144673060 1402 dbSNP
rs1422184723 1411 dbSNP
rs1300664286 1415 dbSNP
rs1443898569 1417 dbSNP
rs1354793283 1423 dbSNP
rs943011907 1425 dbSNP
rs1463661553 1427 dbSNP
rs192062515 1437 dbSNP
rs763639733 1438 dbSNP
rs1227967490 1456 dbSNP
rs1298575531 1461 dbSNP
rs1344456506 1462 dbSNP
rs1208128896 1464 dbSNP
rs1289171514 1466 dbSNP
rs1452701535 1469 dbSNP
rs1224382183 1470 dbSNP
rs910259099 1478 dbSNP
rs1165571481 1480 dbSNP
rs78471165 1493 dbSNP
rs755862800 1502 dbSNP
rs979752507 1502 dbSNP
rs1471558170 1505 dbSNP
rs571057258 1512 dbSNP
rs1047579514 1513 dbSNP
rs1481077562 1515 dbSNP
rs968002374 1520 dbSNP
rs546900345 1521 dbSNP
rs771125031 1522 dbSNP
rs1196762028 1526 dbSNP
rs1387690342 1530 dbSNP
rs1469880948 1532 dbSNP
rs1274309167 1534 dbSNP
rs765273169 1535 dbSNP
rs960747883 1536 dbSNP
rs533534251 1541 dbSNP
rs1333401721 1545 dbSNP
rs1242799288 1547 dbSNP
rs760811504 1551 dbSNP
rs139100145 1552 dbSNP
rs943032890 1561 dbSNP
rs1002314789 1562 dbSNP
rs776777731 1563 dbSNP
rs1297269285 1565 dbSNP
rs1016968867 1570 dbSNP
rs1443854506 1571 dbSNP
rs529989723 1571 dbSNP
rs8708 1572 dbSNP
rs1473478946 1585 dbSNP
rs1156902057 1586 dbSNP
rs1411139406 1586 dbSNP
rs1457622175 1587 dbSNP
rs1161112180 1590 dbSNP
rs887359214 1608 dbSNP
rs576007775 1611 dbSNP
rs998342074 1612 dbSNP
rs1460827287 1614 dbSNP
rs1333733174 1620 dbSNP
rs1341187282 1623 dbSNP
rs1450291870 1624 dbSNP
rs759256948 1627 dbSNP
rs978267466 1631 dbSNP
rs1329092893 1632 dbSNP
rs886056505 1637 dbSNP
rs1161001350 1639 dbSNP
rs1343253865 1648 dbSNP
rs1025648822 1650 dbSNP
rs1278847953 1655 dbSNP
rs772158210 1656 dbSNP
rs1179369319 1666 dbSNP
rs943169809 1668 dbSNP
rs1472897082 1671 dbSNP
rs1051495 1673 dbSNP
rs374266140 1674 dbSNP
rs1033716439 1679 dbSNP
rs1177037475 1685 dbSNP
rs1006245301 1693 dbSNP
rs1465333704 1710 dbSNP
rs910177971 1715 dbSNP
rs188522416 1725 dbSNP
rs1041494534 1726 dbSNP
rs371323625 1727 dbSNP
rs1306263252 1736 dbSNP
rs1349905008 1737 dbSNP
rs1043399179 1741 dbSNP
rs1309760449 1744 dbSNP
rs901721494 1747 dbSNP
rs1803055 1756 dbSNP
rs1040691871 1757 dbSNP
rs1256282203 1771 dbSNP
rs571947914 1784 dbSNP
rs753174376 1785 dbSNP
rs1346697439 1786 dbSNP
rs1202542657 1798 dbSNP
rs1216885987 1811 dbSNP
rs1273317933 1813 dbSNP
rs1483086439 1814 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions BC-3
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 GSM796039. RNA binding protein: AGO2. Condition:4-Thiouridine PAR-CLIP data was present in GSM796040. RNA binding protein: AGO2. Condition:4-Thiouridine ...

- Gottwein E; Corcoran DL; Mukherjee N; et al., 2011, Cell host & microbe.

Article - Gottwein E; Corcoran DL; Mukherjee N; et al.
- Cell host & microbe, 2011
Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus (KSHV) and frequently also harbors Epstein-Barr virus (EBV). The expression of KSHV- and EBV-encoded microRNAs (miRNAs) in PELs suggests a role for these miRNAs in latency and lymphomagenesis. Using PAR-CLIP, a technology which allows the direct and transcriptome-wide identification of miRNA targets, we delineate the target sites for all viral and cellular miRNAs expressed in PEL cell lines. The resulting data set revealed that KSHV miRNAs directly target more than 2000 cellular mRNAs, including many involved in pathways relevant to KSHV pathogenesis. Moreover, 58% of these mRNAs are also targeted by EBV miRNAs, via distinct binding sites. In addition to a known viral analog of cellular miR-155, we show that KSHV encodes a viral miRNA that mimics cellular miR-142-3p function. In summary, this study identifies an extensive list of KSHV miRNA targets, which are likely to influence viral replication and pathogenesis.
LinkOut: [PMID: 22100165]
CLIP-seq Support 1 for dataset GSM796039
Method / RBP PAR-CLIP / AGO2
Cell line / Condition BC-3 / 4-Thiouridine
Location of target site ENST00000254958.5 | 3UTR | UUGGCAAUAAAUUUUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22100165 / GSE32109
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM796040
Method / RBP PAR-CLIP / AGO2
Cell line / Condition BC-3 / 4-Thiouridine
Location of target site ENST00000254958.5 | 3UTR | UUGGCAAUAAAUUUUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22100165 / GSE32109
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
117 hsa-miR-4480 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT056040 MLLT10 MLLT10, histone lysine methyltransferase DOT1L cofactor 2 2
MIRT091259 FXR1 FMR1 autosomal homolog 1 2 4
MIRT117347 MAPRE2 microtubule associated protein RP/EB family member 2 2 2
MIRT234960 ZNF439 zinc finger protein 439 2 4
MIRT441356 ZNF75A zinc finger protein 75a 2 2
MIRT441426 STXBP2 syntaxin binding protein 2 2 2
MIRT441455 ZNF488 zinc finger protein 488 2 4
MIRT441524 ZBTB10 zinc finger and BTB domain containing 10 2 2
MIRT441576 EXOC5 exocyst complex component 5 2 2
MIRT441597 ABCB5 ATP binding cassette subfamily B member 5 2 6
MIRT441610 ATP13A4 ATPase 13A4 2 2
MIRT441698 CIT citron rho-interacting serine/threonine kinase 2 2
MIRT441714 FGF9 fibroblast growth factor 9 2 2
MIRT441784 MAPK8 mitogen-activated protein kinase 8 2 4
MIRT441795 EXOSC2 exosome component 2 2 2
MIRT441868 RNASEL ribonuclease L 2 2
MIRT441900 SLC9A8 solute carrier family 9 member A8 2 6
MIRT441919 FAM217B family with sequence similarity 217 member B 2 2
MIRT441928 C1orf109 chromosome 1 open reading frame 109 2 2
MIRT441938 RIMKLB ribosomal modification protein rimK like family member B 2 2
MIRT442157 DPY19L1 dpy-19 like C-mannosyltransferase 1 2 2
MIRT442172 AZF1 azoospermia factor 1 2 2
MIRT442208 IRS1 insulin receptor substrate 1 2 2
MIRT442237 DDX19A DEAD-box helicase 19A 2 2
MIRT442366 ZC3HAV1L zinc finger CCCH-type containing, antiviral 1 like 2 2
MIRT442572 SDC1 syndecan 1 2 2
MIRT442604 ZNF391 zinc finger protein 391 2 2
MIRT442609 MRC1 mannose receptor C-type 1 2 2
MIRT442647 POP4 POP4 homolog, ribonuclease P/MRP subunit 2 2
MIRT442658 OIP5 Opa interacting protein 5 2 6
MIRT442686 COX15 COX15, cytochrome c oxidase assembly homolog 2 2
MIRT442773 JAG1 jagged 1 2 2
MIRT442785 CHD8 chromodomain helicase DNA binding protein 8 2 2
MIRT442895 PLCB3 phospholipase C beta 3 2 2
MIRT442941 C17orf105 chromosome 17 open reading frame 105 2 2
MIRT442959 SGCD sarcoglycan delta 2 2
MIRT442998 EDAR ectodysplasin A receptor 2 2
MIRT443017 C21orf91 chromosome 21 open reading frame 91 2 2
MIRT443064 CASP5 caspase 5 2 2
MIRT443069 ABLIM1 actin binding LIM protein 1 2 2
MIRT443208 VPS36 vacuolar protein sorting 36 homolog 2 2
MIRT443237 ANKRD26 ankyrin repeat domain 26 2 2
MIRT443253 A1CF APOBEC1 complementation factor 2 2
MIRT443329 JUN Jun proto-oncogene, AP-1 transcription factor subunit 2 2
MIRT443333 NRAS NRAS proto-oncogene, GTPase 2 2
MIRT443349 STX7 syntaxin 7 2 2
MIRT443452 CLIC5 chloride intracellular channel 5 2 2
MIRT443547 GPR35 G protein-coupled receptor 35 2 2
MIRT443616 AVPR1A arginine vasopressin receptor 1A 2 2
MIRT443626 CPSF2 cleavage and polyadenylation specific factor 2 2 2
MIRT443730 ALPK3 alpha kinase 3 2 2
MIRT443786 ST13 ST13, Hsp70 interacting protein 2 2
MIRT443852 RGS6 regulator of G protein signaling 6 2 2
MIRT445483 KLF5 Kruppel like factor 5 2 2
MIRT471105 PHLDA2 pleckstrin homology like domain family A member 2 2 2
MIRT472329 NETO2 neuropilin and tolloid like 2 2 4
MIRT472391 NDRG3 NDRG family member 3 2 2
MIRT473522 MAX MYC associated factor X 2 2
MIRT473874 MAFK MAF bZIP transcription factor K 2 6
MIRT476021 GTF2A1 general transcription factor IIA subunit 1 2 2
MIRT478320 DDN dendrin 2 2
MIRT492049 TNFSF9 TNF superfamily member 9 2 2
MIRT494851 ANKRD24 ankyrin repeat domain 24 2 2
MIRT494991 TSSC1 EARP complex and GARP complex interacting protein 1 2 2
MIRT495034 RASSF2 Ras association domain family member 2 2 2
MIRT495111 NOL10 nucleolar protein 10 2 2
MIRT495113 TRADD TNFRSF1A associated via death domain 2 2
MIRT495131 METTL24 methyltransferase like 24 2 2
MIRT495147 STAC2 SH3 and cysteine rich domain 2 2 2
MIRT495297 NUP54 nucleoporin 54 2 2
MIRT495341 RTN2 reticulon 2 2 2
MIRT495347 ATP5S ATP synthase, H+ transporting, mitochondrial Fo complex subunit s (factor B) 2 2
MIRT496682 DUSP18 dual specificity phosphatase 18 2 2
MIRT496743 TGFBR1 transforming growth factor beta receptor 1 2 2
MIRT496841 KCNIP2 potassium voltage-gated channel interacting protein 2 2 2
MIRT496852 GPAM glycerol-3-phosphate acyltransferase, mitochondrial 2 2
MIRT496889 FOXP1 forkhead box P1 2 2
MIRT496922 CLMN calmin 2 2
MIRT496990 TMEM231 transmembrane protein 231 2 2
MIRT497002 SNAP25 synaptosome associated protein 25 2 2
MIRT497058 C6orf223 chromosome 6 open reading frame 223 2 2
MIRT500529 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta 2 6
MIRT506048 PPP6C protein phosphatase 6 catalytic subunit 2 4
MIRT512163 CD164 CD164 molecule 2 6
MIRT527051 RDH13 retinol dehydrogenase 13 2 2
MIRT532282 TNFSF14 TNF superfamily member 14 2 2
MIRT534083 SPRY4 sprouty RTK signaling antagonist 4 2 2
MIRT534605 RNASEH1 ribonuclease H1 2 4
MIRT539509 ACSS3 acyl-CoA synthetase short chain family member 3 2 2
MIRT543069 ARID4B AT-rich interaction domain 4B 2 2
MIRT544233 CCBL2 kynurenine aminotransferase 3 2 2
MIRT544686 ZNF224 zinc finger protein 224 2 4
MIRT546269 TMEM30A transmembrane protein 30A 2 4
MIRT559069 C19orf47 chromosome 19 open reading frame 47 2 2
MIRT562768 RMI2 RecQ mediated genome instability 2 2 2
MIRT563974 HCFC1 host cell factor C1 2 2
MIRT564086 NSA2 NSA2, ribosome biogenesis homolog 2 2
MIRT564525 PDXP pyridoxal phosphatase 2 2
MIRT564613 ZNF703 zinc finger protein 703 2 2
MIRT566252 PTBP1 polypyrimidine tract binding protein 1 2 2
MIRT614420 ZNF440 zinc finger protein 440 2 2
MIRT618789 MTHFR methylenetetrahydrofolate reductase 2 2
MIRT619160 PPDPF pancreatic progenitor cell differentiation and proliferation factor 2 2
MIRT641778 ZDHHC7 zinc finger DHHC-type containing 7 2 4
MIRT653680 SLC25A36 solute carrier family 25 member 36 2 2
MIRT657861 GJD2 gap junction protein delta 2 2 2
MIRT660879 ADCYAP1R1 ADCYAP receptor type I 2 2
MIRT668781 DAAM1 dishevelled associated activator of morphogenesis 1 2 4
MIRT688559 DCAF16 DDB1 and CUL4 associated factor 16 2 2
MIRT695393 WDR41 WD repeat domain 41 2 2
MIRT698680 TCEA1 transcription elongation factor A1 2 2
MIRT700974 PDIA6 protein disulfide isomerase family A member 6 2 2
MIRT705055 C5orf15 chromosome 5 open reading frame 15 2 2
MIRT705864 AFF1 AF4/FMR2 family member 1 2 2
MIRT710586 CDCA4 cell division cycle associated 4 2 2
MIRT713904 IGF2R insulin like growth factor 2 receptor 2 2
MIRT717133 SKI SKI proto-oncogene 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
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4480 Cisplatin 5460033 NSC119875 approved sensitive cell line (CIS)
hsa-miR-4480 Cisplatin 5460033 NSC119875 approved resistant cell line (A549)

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