miRTarBase - #MIRT442647


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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 POP4   
Synonyms RPP29
Description POP4 homolog, ribonuclease P/MRP subunit
Transcript NM_006627   
Expression
Putative miRNA Targets on POP4
3'UTR of POP4
(miRNA target sites are highlighted)		 
>POP4|NM_006627|3'UTR
   1 ATTCTTTGCCGTCTAAGGCAGTTGTTTATGACAGCTGAAAACTGGACACTCCCTAAATGTCCACCTTTCAGTGAAGAGAT
  81 AGTTAAGCCAATTCCATTTATAGACCACCTCCAGCCAGTGACGCTCCGAGTTGAGGATGTTGAACAACATGGGAAGGTCG
 161 CAGCGTACTAAGTGAAGAAGTCAGAGGACAGAGGAATTTCTCTTTCTAGGAGATTTTCATTTTGTGTGACTCCCATGGGG
 241 AGGAACAGACTGGCAGGAAGCACACCGGGGTTAACACTGGTTGACTTGAATAGGATTATTCGATTTTTAAAAATACTTTT
 321 CCATGTTTTCTGAGTGCTCTATGATAAATCAGTTGCATCTGTGATAATACAGTACATATGTGGACATAAACAGGGATCAA
 401 ATAAAGGAGGTATTGCTGCAGTCCAGCCAGGTTGAAAGGGAAGGGGGGTCCCCAAAGGTCCATTGGATGGCAGGTGTCTA
 481 CAGAGGCTCGCCTTTGGGTGGAACTCTGACCCACCTAAGGTTTACTTTGCTATTTCAGGAAGGTTGAAGAGGATTGAAGG
 561 GTGAGTTGCTAAGTGACTTAGGGTTTATTCACTTCAGGAATCATAGCTGGGGTGGACCCCAGGAGCAGAGTACTGCATGC
 641 AGCTGTGCCCATGCATGGTTGCCCCAGCGTAGTGAGATGGGACCTGCCGCAGCATGCCCACTCCTGAGCTGCCAGGCTGA
 721 GCCATGGAGGACTGAAAGGAGGTCGCCCGGCATCACCTCCCGAGGTGAGACCTGCTGCAAAAGCCAAGCCAGCAGCATTG
 801 ACGCCCTTTGATATCTTCGCCATTTTTGCTGCTGAAAGACTTGGCTTTTCAGTCTGACCCTGGCCCTCTGTGACCATGTG
 881 TCTGTAAAGCCAGTGGGTCAGGCCCTTCCATGCAGGGCCAGAGGAAAAGCGGGCCCAGGGCTGCAGTGAGAGCGGGGCAG
 961 GGGACCAGCCTACCAGATGGGTTGGAAACATGGCTCAGAAGGACCAACTACCCCTTCCCTTTGAGGAGCAAGTCTCTGCC
1041 GATCAGCAAGGCAAGGCCAGGAGCCCTCCTGGCGAAAGGCAGGCCACAAATCTGTTCTCCCCCAGGAGAAGTAGCAGTGC
1121 CAGGGCTTTGCGTTTCTGGTAACTTCCACCCAAACCACACCAGAGAGAAACACCGTAGTGGAGAAGGGAAGTGGGAGCGC
1201 TGACTGCTGTGTGCCAGGAGAGTAGAAAGGCCCAGGTCTGTGCCACCACCCCTCCCCAAAGCTCAGTGCACCCAGAGTCT
1281 CACAGGGACCAACACGGTGCCTCGGTCCTGCTTCCATCCATGCAAGTGTCCTCCGCTCACCAGGGTGTTCTGAGGCAGCT
1361 CAAGTGCTCTCCCCCAAGCAGCACGCAGTCACCGCTGCCAGTGATGAACACACGCACGGGCTAGGCACATGGAGCCCAAG
1441 CACACTGCCACCTCGGACACGGGCCCCGGCCCAGCGACTGCCTTGTGGTGTGGCCGTCCTCATCTGCCACAGGAAGACAG
1521 ACTTCGAGGGACCTCTTGCCTAAGGCCTCGCTGACTCAAGGGTAGATTGAGATTTGGACCTAATAGGCTCCAGAACTGTG
1601 CTTTGAGCTACAGGGTGGCTGCAGGATGAGACGGATGCAGTTCAAAGTGCAGGATGTGCTGCCTTTATTACCTGCTTTCC
1681 CGCTGAGCAAATCCCTGTCTTGAGTGGGAAGTGGCATCTATTCCCCCAGCCATCTGAAAATGCTGTGTTCATAACCAAAT
1761 AGGTGCTGTAGCTTCCTAGCCATCCCGCTCTTACCCGCCCCTCTGCAATGTAAAAGGCGTCCACTGTTGTGTAAATACAC
1841 AGTTGCTTTCCAGAAAAGTTGTAGGTACCACTTGCAAAAAAAAAAAAAAAAAA
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' auuucauugaaggUGAACCGa 5'
                       ||||||| 
Target 5' ttgctgctgaaagACTTGGCt 3'
 826 - 846 140.00 -10.50
2 
miRNA  3' auuuCAUUGAAGGUGAACcga 5'
              |||: | |||||||   
Target 5' agttGTAGGTACCACTTGcaa 3'
 1857 - 1877 125.00 -11.72
3 
miRNA  3' auuucAUUGAAGGUGAACCGa 5'
               |||  |::|||| || 
Target 5' ccaccTAAGGTTTACTTTGCt 3'
 511 - 531 124.00 -7.00
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26989923 5 COSMIC
COSN6552270 11 COSMIC
COSN30566702 20 COSMIC
COSN30512409 45 COSMIC
COSN30185987 49 COSMIC
COSN31555619 55 COSMIC
COSN30182724 63 COSMIC
COSN23015362 64 COSMIC
COSN20131422 129 COSMIC
COSN30513962 148 COSMIC
COSN22870401 231 COSMIC
COSN208807 259 COSMIC
COSN30137267 270 COSMIC
COSN20115681 429 COSMIC
COSN26514095 553 COSMIC
COSN21565919 621 COSMIC
COSN23632404 701 COSMIC
COSN15662901 706 COSMIC
COSN59881 910 COSMIC
COSN6141624 955 COSMIC
COSN505797 1199 COSMIC
COSN29209351 1387 COSMIC
COSN31652982 1566 COSMIC
COSN20115682 1567 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs779795933 2 dbSNP
rs201552591 4 dbSNP
rs116235956 11 dbSNP
rs189372850 12 dbSNP
rs1462892083 18 dbSNP
rs755803699 19 dbSNP
rs779656928 20 dbSNP
rs1456098930 21 dbSNP
rs1178410464 24 dbSNP
rs899777366 27 dbSNP
rs749101521 28 dbSNP
rs938880779 29 dbSNP
rs1405220214 30 dbSNP
rs768398213 33 dbSNP
rs1470109988 35 dbSNP
rs778911203 40 dbSNP
rs1321360002 42 dbSNP
rs747974592 43 dbSNP
rs772028611 44 dbSNP
rs776618371 49 dbSNP
rs992979010 52 dbSNP
rs561509755 60 dbSNP
rs1300949685 68 dbSNP
rs1317900983 76 dbSNP
rs1048088205 79 dbSNP
rs915647396 88 dbSNP
rs1455557692 90 dbSNP
rs530370053 108 dbSNP
rs546985925 111 dbSNP
rs1411381414 117 dbSNP
rs948505292 123 dbSNP
rs530336840 124 dbSNP
rs559266504 128 dbSNP
rs1376075747 129 dbSNP
rs1198602104 132 dbSNP
rs145599797 138 dbSNP
rs1024699153 148 dbSNP
rs1464814488 150 dbSNP
rs1267009608 154 dbSNP
rs1223534416 157 dbSNP
rs898832170 158 dbSNP
rs550990301 160 dbSNP
rs1270455108 161 dbSNP
rs1047655192 163 dbSNP
rs570994277 165 dbSNP
rs541511531 166 dbSNP
rs1250894145 172 dbSNP
rs1003071862 179 dbSNP
rs1432896055 183 dbSNP
rs1034999072 187 dbSNP
rs1008719151 190 dbSNP
rs1179468750 198 dbSNP
rs1470958423 201 dbSNP
rs959028472 203 dbSNP
rs990144046 205 dbSNP
rs1475849611 208 dbSNP
rs1375180015 209 dbSNP
rs1187058376 210 dbSNP
rs1449450292 212 dbSNP
rs1244218563 223 dbSNP
rs567092722 223 dbSNP
rs1367543298 224 dbSNP
rs780053868 225 dbSNP
rs899911920 227 dbSNP
rs1293153360 231 dbSNP
rs1339655166 236 dbSNP
rs1374401210 239 dbSNP
rs550315113 240 dbSNP
rs1364376720 243 dbSNP
rs996973673 252 dbSNP
rs1338822500 267 dbSNP
rs967372578 267 dbSNP
rs977478170 268 dbSNP
rs148905508 271 dbSNP
rs1376756214 275 dbSNP
rs1167106869 286 dbSNP
rs1429471768 291 dbSNP
rs968761472 302 dbSNP
rs536514122 303 dbSNP
rs553017209 306 dbSNP
rs1293254861 317 dbSNP
rs1186022854 324 dbSNP
rs943853474 326 dbSNP
rs1039563403 340 dbSNP
rs543747283 345 dbSNP
rs773517857 349 dbSNP
rs1202796875 350 dbSNP
rs1031903806 353 dbSNP
rs1048306541 361 dbSNP
rs762896788 371 dbSNP
rs7283 373 dbSNP
rs1337788941 375 dbSNP
rs992947666 377 dbSNP
rs1046118985 378 dbSNP
rs906306467 402 dbSNP
rs1003453244 406 dbSNP
rs1165861040 408 dbSNP
rs774656628 411 dbSNP
rs530386856 417 dbSNP
rs376142522 433 dbSNP
rs760153330 440 dbSNP
rs1021902060 443 dbSNP
rs1470161029 443 dbSNP
rs538644357 445 dbSNP
rs181663107 447 dbSNP
rs1179628484 448 dbSNP
rs1482506097 449 dbSNP
rs575803329 459 dbSNP
rs1319867314 474 dbSNP
rs1289013381 475 dbSNP
rs1224429970 480 dbSNP
rs544718228 482 dbSNP
rs386808534 488 dbSNP
rs2042968 489 dbSNP
rs45529438 490 dbSNP
rs1020098784 491 dbSNP
rs540892355 497 dbSNP
rs560599368 501 dbSNP
rs965529281 506 dbSNP
rs1349838846 507 dbSNP
rs1319499550 511 dbSNP
rs1400048530 550 dbSNP
rs1402925245 552 dbSNP
rs1453931483 554 dbSNP
rs369866406 561 dbSNP
rs1156310457 567 dbSNP
rs1472092947 573 dbSNP
rs1377704306 577 dbSNP
rs1227224147 582 dbSNP
rs45590931 587 dbSNP
rs1308854345 588 dbSNP
rs544594230 596 dbSNP
rs983974473 599 dbSNP
rs2115370 605 dbSNP
rs939671380 607 dbSNP
rs1208127271 611 dbSNP
rs763695308 621 dbSNP
rs1303621685 622 dbSNP
rs1217853455 623 dbSNP
rs753550781 628 dbSNP
rs530482038 636 dbSNP
rs756661921 646 dbSNP
rs150983678 648 dbSNP
rs567428062 649 dbSNP
rs1235640722 650 dbSNP
rs1433583192 652 dbSNP
rs865896255 668 dbSNP
rs548292731 670 dbSNP
rs1317972011 672 dbSNP
rs1234909057 678 dbSNP
rs1011012803 683 dbSNP
rs529830311 688 dbSNP
rs546809768 689 dbSNP
rs1456185836 693 dbSNP
rs998852257 699 dbSNP
rs1177855190 706 dbSNP
rs937743383 719 dbSNP
rs1424285052 733 dbSNP
rs1186879065 737 dbSNP
rs1451272832 738 dbSNP
rs1420340557 742 dbSNP
rs1430467142 745 dbSNP
rs1168803631 746 dbSNP
rs73927204 749 dbSNP
rs750316509 750 dbSNP
rs1014459290 752 dbSNP
rs1021107996 756 dbSNP
rs1311820568 757 dbSNP
rs1023052959 758 dbSNP
rs577546078 762 dbSNP
rs894622562 763 dbSNP
rs1011763066 765 dbSNP
rs1021869508 766 dbSNP
rs1288895446 772 dbSNP
rs1379316809 773 dbSNP
rs755691795 777 dbSNP
rs1363457616 779 dbSNP
rs1464283712 786 dbSNP
rs973104891 788 dbSNP
rs1170887099 796 dbSNP
rs538978430 799 dbSNP
rs1388270436 803 dbSNP
rs558942161 804 dbSNP
rs1445131202 807 dbSNP
rs879910265 813 dbSNP
rs758460222 814 dbSNP
rs569282427 815 dbSNP
rs1323876306 816 dbSNP
rs140852746 819 dbSNP
rs147058657 820 dbSNP
rs1276278761 821 dbSNP
rs911587538 822 dbSNP
rs944567793 827 dbSNP
rs1233598974 830 dbSNP
rs1207776855 835 dbSNP
rs1340547932 836 dbSNP
rs1311482323 841 dbSNP
rs369713872 845 dbSNP
rs1274328724 847 dbSNP
rs1216431726 848 dbSNP
rs1038977743 860 dbSNP
rs1242710557 863 dbSNP
rs921739279 864 dbSNP
rs1028840013 866 dbSNP
rs952535663 884 dbSNP
rs540453713 890 dbSNP
rs45589732 897 dbSNP
rs1167718830 898 dbSNP
rs45496800 898 dbSNP
rs1174639094 903 dbSNP
rs768598517 904 dbSNP
rs138416321 905 dbSNP
rs1053085437 906 dbSNP
rs982447269 911 dbSNP
rs1423275803 912 dbSNP
rs1160461703 914 dbSNP
rs895827338 915 dbSNP
rs1482195657 918 dbSNP
rs927614306 928 dbSNP
rs375627279 931 dbSNP
rs1489758887 934 dbSNP
rs1264167049 935 dbSNP
rs1242015050 944 dbSNP
rs1207667730 949 dbSNP
rs1023193750 954 dbSNP
rs970309959 955 dbSNP
rs995004775 957 dbSNP
rs1297083926 962 dbSNP
rs1348222981 963 dbSNP
rs1345701107 974 dbSNP
rs564507142 979 dbSNP
rs915020320 991 dbSNP
rs1387070624 995 dbSNP
rs1406413448 998 dbSNP
rs950495282 1012 dbSNP
rs1291664133 1015 dbSNP
rs1274564443 1019 dbSNP
rs1457317668 1036 dbSNP
rs983609857 1037 dbSNP
rs190269964 1041 dbSNP
rs965715013 1042 dbSNP
rs534358058 1044 dbSNP
rs10413641 1045 dbSNP
rs903428518 1057 dbSNP
rs780573541 1061 dbSNP
rs1435231190 1062 dbSNP
rs1286251302 1065 dbSNP
rs1209808278 1067 dbSNP
rs999081231 1070 dbSNP
rs560805826 1074 dbSNP
rs529841308 1075 dbSNP
rs1351488006 1077 dbSNP
rs546477192 1077 dbSNP
rs901145739 1081 dbSNP
rs1214504345 1083 dbSNP
rs560296047 1085 dbSNP
rs532403953 1089 dbSNP
rs1201300481 1093 dbSNP
rs923771480 1095 dbSNP
rs1322650419 1101 dbSNP
rs774543950 1103 dbSNP
rs747342859 1104 dbSNP
rs1455676467 1105 dbSNP
rs1053622921 1107 dbSNP
rs570647742 1112 dbSNP
rs950038751 1114 dbSNP
rs1376350225 1126 dbSNP
rs760011774 1132 dbSNP
rs1005335620 1133 dbSNP
rs8105791 1133 dbSNP
rs2042969 1136 dbSNP
rs1463123089 1140 dbSNP
rs760979004 1141 dbSNP
rs982029489 1142 dbSNP
rs1346671555 1147 dbSNP
rs927882077 1149 dbSNP
rs1027784418 1150 dbSNP
rs1365885965 1162 dbSNP
rs1299674019 1163 dbSNP
rs1432783350 1168 dbSNP
rs886615021 1170 dbSNP
rs1426095199 1172 dbSNP
rs1004607968 1175 dbSNP
rs1018686669 1176 dbSNP
rs1400261170 1182 dbSNP
rs990913072 1187 dbSNP
rs914989101 1193 dbSNP
rs1167315412 1199 dbSNP
rs1392591088 1199 dbSNP
rs1281111626 1200 dbSNP
rs1241075144 1210 dbSNP
rs965814540 1213 dbSNP
rs974396857 1214 dbSNP
rs946482426 1215 dbSNP
rs553077296 1217 dbSNP
rs1042168368 1221 dbSNP
rs1253596534 1221 dbSNP
rs1199688666 1223 dbSNP
rs1342675299 1241 dbSNP
rs1028702368 1244 dbSNP
rs924733387 1245 dbSNP
rs764455920 1247 dbSNP
rs1239365771 1253 dbSNP
rs538219918 1257 dbSNP
rs45462597 1260 dbSNP
rs1284863855 1264 dbSNP
rs935177986 1265 dbSNP
rs568453042 1267 dbSNP
rs992030514 1268 dbSNP
rs996855078 1272 dbSNP
rs1333696794 1273 dbSNP
rs1410640376 1283 dbSNP
rs1372837189 1292 dbSNP
rs1306548230 1294 dbSNP
rs572855942 1296 dbSNP
rs1211771391 1297 dbSNP
rs534349099 1299 dbSNP
rs45518039 1304 dbSNP
rs577039858 1305 dbSNP
rs1005556278 1309 dbSNP
rs143804286 1332 dbSNP
rs2042970 1335 dbSNP
rs886586474 1346 dbSNP
rs1003813358 1350 dbSNP
rs1473487833 1359 dbSNP
rs1034923619 1367 dbSNP
rs1161004986 1370 dbSNP
rs146387340 1375 dbSNP
rs1019158368 1380 dbSNP
rs901590052 1381 dbSNP
rs990492786 1382 dbSNP
rs138921553 1385 dbSNP
rs1028627471 1386 dbSNP
rs968129253 1388 dbSNP
rs758013969 1394 dbSNP
rs1031319040 1395 dbSNP
rs1388038332 1407 dbSNP
rs1337295580 1410 dbSNP
rs956681122 1412 dbSNP
rs1163570250 1413 dbSNP
rs923715205 1414 dbSNP
rs773233524 1415 dbSNP
rs1282531389 1418 dbSNP
rs934829082 1419 dbSNP
rs1247043241 1420 dbSNP
rs1215391556 1429 dbSNP
rs977364491 1430 dbSNP
rs1449788659 1431 dbSNP
rs1272643845 1441 dbSNP
rs922872148 1449 dbSNP
rs1331531092 1452 dbSNP
rs1286633670 1457 dbSNP
rs1456716120 1457 dbSNP
rs1368800434 1460 dbSNP
rs1276973762 1462 dbSNP
rs991946630 1469 dbSNP
rs560988194 1476 dbSNP
rs1244272239 1477 dbSNP
rs537013687 1484 dbSNP
rs1444679462 1485 dbSNP
rs1457271294 1495 dbSNP
rs1184728545 1496 dbSNP
rs1367407352 1497 dbSNP
rs1475505497 1499 dbSNP
rs932865132 1502 dbSNP
rs1421095537 1508 dbSNP
rs1477003073 1510 dbSNP
rs574400624 1523 dbSNP
rs575242704 1526 dbSNP
rs1266285308 1527 dbSNP
rs1215424374 1531 dbSNP
rs888425400 1536 dbSNP
rs1281190230 1537 dbSNP
rs1217762328 1540 dbSNP
rs941379936 1545 dbSNP
rs751560795 1546 dbSNP
rs754755798 1550 dbSNP
rs1337193728 1551 dbSNP
rs781111937 1552 dbSNP
rs370610750 1558 dbSNP
rs927268605 1561 dbSNP
rs374809540 1565 dbSNP
rs3214564 1566 dbSNP
rs397726866 1566 dbSNP
rs1359311761 1568 dbSNP
rs1178004321 1575 dbSNP
rs1412495778 1580 dbSNP
rs1003372825 1585 dbSNP
rs1169189072 1601 dbSNP
rs1451250941 1609 dbSNP
rs930658163 1613 dbSNP
rs1035296575 1623 dbSNP
rs1394239096 1633 dbSNP
rs1049089132 1634 dbSNP
rs1012132265 1643 dbSNP
rs1239387935 1644 dbSNP
rs1208486982 1649 dbSNP
rs1347671868 1654 dbSNP
rs908111857 1659 dbSNP
rs1231339593 1667 dbSNP
rs1340642063 1669 dbSNP
rs967676594 1670 dbSNP
rs1213436932 1671 dbSNP
rs977777124 1672 dbSNP
rs1304280227 1675 dbSNP
rs940991202 1676 dbSNP
rs1040525437 1678 dbSNP
rs902018733 1682 dbSNP
rs377736586 1683 dbSNP
rs1316351496 1698 dbSNP
rs966221700 1700 dbSNP
rs975865494 1707 dbSNP
rs182796540 1715 dbSNP
rs1424418738 1718 dbSNP
rs61731815 1721 dbSNP
rs1347696169 1723 dbSNP
rs1050188300 1726 dbSNP
rs1199259305 1728 dbSNP
rs903623381 1735 dbSNP
rs1253059392 1746 dbSNP
rs1207667255 1752 dbSNP
rs1000928579 1761 dbSNP
rs1030703229 1766 dbSNP
rs1251196705 1769 dbSNP
rs552428310 1770 dbSNP
rs1254784544 1771 dbSNP
rs1321839869 1775 dbSNP
rs1314249369 1776 dbSNP
rs562754552 1787 dbSNP
rs956833466 1788 dbSNP
rs1288759171 1789 dbSNP
rs2241609 1791 dbSNP
rs757372462 1794 dbSNP
rs941345457 1795 dbSNP
rs186545962 1797 dbSNP
rs1351754276 1798 dbSNP
rs1458317261 1798 dbSNP
rs568451704 1810 dbSNP
rs1024730445 1811 dbSNP
rs1037031425 1814 dbSNP
rs534003490 1819 dbSNP
rs939396152 1820 dbSNP
rs1471843566 1825 dbSNP
rs1056554632 1827 dbSNP
rs980132661 1829 dbSNP
rs927352332 1830 dbSNP
rs1379163965 1833 dbSNP
rs1012099466 1839 dbSNP
rs952196864 1851 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.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' auuucauugaaggugAACCGa 5'
                         ||||| 
Target 5' ---------------UUGGCu 3'
 		1 - 6
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 GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_006627 | 3UTR | UGACGCCCUUUGAUAUCUUCGCCAUUUUUGCUGCUGAAAGACUUGGCUUUUCAGUCUGACCCUGGCCCUCUGUGACCAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_006627 | 3UTR | CUUCGCCAUUUUUGCUGCUGAAAGACUUGGCUUUUCAGUCUGACCCUGGCCCUCUGUGACCAUGUGUCUGUAAAGCCAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM796039
Method / RBP PAR-CLIP / AGO2
Cell line / Condition BC-3 / 4-Thiouridine
Location of target site ENST00000221770.3 | 3UTR | UUGGCUUUUCAGUCUGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22100165 / GSE32109
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM796040
Method / RBP PAR-CLIP / AGO2
Cell line / Condition BC-3 / 4-Thiouridine
Location of target site ENST00000221770.3 | 3UTR | UUGGCUUUUCAGUCUGA
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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