miRTarBase - #MIRT455841


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pre-miRNA Information
pre-miRNA hsa-mir-3160-1   
Genomic Coordinates chr11: 46451805 - 46451889
Description Homo sapiens miR-3160-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA hsa-mir-3160-2   
Genomic Coordinates chr11: 46451807 - 46451887
Description Homo sapiens miR-3160-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3160-3p
Sequence 54| AGAGCUGAGACUAGAAAGCCCA |75
Evidence Experimental
Experiments Illumina
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN30582333 1 COSMIC
COSN1535547 3 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1396368683 1 dbSNP
rs1162409303 2 dbSNP
rs1404378453 12 dbSNP
rs1171960732 14 dbSNP
rs1324633375 16 dbSNP
rs1187765019 16 dbSNP
rs1300058326 19 dbSNP
rs1432898407 21 dbSNP
rs1011279103 22 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol MPL   
Synonyms C-MPL, CD110, MPLV, THCYT2, TPOR
Description MPL proto-oncogene, thrombopoietin receptor
Transcript NM_005373   
Expression
Putative miRNA Targets on MPL
3'UTR of MPL
(miRNA target sites are highlighted)		 
>MPL|NM_005373|3'UTR
   1 GGACAGGCTCCTCACTCCCAGTTCCCTGGACAGAGCTAAACTCTCGAGACTTCTCTGTGAACTTCCCTACCCTACCCCCA
  81 CAACACAAGCACCCCAGACCTCACCTCCATCCCCCTCTGTCTGCCCTCACAATTAGGCTTCATTGCACTGATCTTACTCT
 161 ACTGCTGCTGACATAAAACCAGGACCCTTTCTCCACAGGCAGGCTCATTTCACTAAGCTCCTCCTTTACTTTCTCTCTCC
 241 TCTTTGATGTCAAACGCCTTGAAAACAAGCCTCCACTTCCCCACACTTCCCATTTACTCTTGAGACTACTTCAATTAGTT
 321 CCCCTACTACACTTTGCTAGTGAAACTGCCCAGGCAAAGTGCACCTCAAATCTTCTAATTCCAAGATCCAATAGGATCTC
 401 GTTAATCATCAGTTCCTTTGATCTCGCTGTAAGATTTGTCAAGGCTGACTACTCACTTCTCCTTTAAATTCTTTCCTACC
 481 TTGGTCCTGCCTCTTTGAGTATATTAGTAGGTTTTTTTTATTTGTTTGAGACAGGGTCTCACTCTGTCACCCAGGCTGCA
 561 GTGCAATGGCGCGATCTCAGCTCACTGCAACCTCCACCTCCGGGTTCAAGCGATTCTTGTGCCTCGGCCTCCCTAGTAGC
 641 TGGGATTACAGGCGCACACCACCACACACAGCTAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGACGGAGCCTTGCT
 721 CTGTTGCCAGACTGGAGTGCAGTGGCACGATCTCGGCTCACTGCAACCTCTGCCTCCCGGGTTCAAGCCATTCTGCCTCA
 801 GCCTCCCAAGTAGCTGGGAGTACAGGCGTCTGCCACCATGCCTAATTTTTTTCTATTTTTAGGAGAGACCGGTTTTCACC
 881 ACGTTGGCCAGGATGGTCTCGATATCCTGATCTCGTGATCCGCCTGCCTCTGCCTCCCAAAGTGCTGGGATTACAGGTGT
 961 GACCCACTGCGCACAGCCCCAGCTAATTTTCATATTTTTAGTAGAGACAGGGTTTTGCCATGTTGCCCAGGCTGGTCTTG
1041 AACTCCTAACCTCGGGTGATCCACCCACCTTGGCCTCCCAAAGTGTTAGGATTACAGGCATGAGCCACTGCGCCCGGCTG
1121 AGTGTACTAGTAGTTAAGAGAATAAACTAGATCTAGAATCAGAGCTGGATTCAATTCCTGTCCTTCACATTTACTAGCTG
1201 TGCAACCTTGGGCACATAACTTAATGTCTTTGAGCCTTAGTTTTTTCATCTGTAAAACAGGGATAATAACAGCACCCCAT
1281 AGAGTTGTGACGAGGATTGAGATAATCTAAGTAAAGCACAGTCCCTAGGACATAGTAAATGATTCATATATCCGAACTAC
1361 TGTTATAATTATTCCTTCTTACTCTCCTCTTCTAGCATTTCTTCCAATTATTACAGTCCTTCAAGATTCCATTTCTTAAC
1441 AGTCTCCAATCCCATCTATTCTCTGCCTTTACTATATGTTGACCATTCCAAAGTTCTTATCTCTAGCTCAGACATCTACT
1521 ACAGCACTGTGATGCTTTATGCAACTAACTGTTTACATATCTGTCCCCTGCTACTAGATTGTGAGCTCCTTGAGGGAAAG
1601 GAACATGATTTATTTGTCCTTTTCCCCCAGCACCTAGAGTAGTGCTTGGTGCATGATAGTAGGCCTTCAATAAATTTTTT
1681 CTAAATGAATGA
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' acCCGAAAGAUCAGAGUCGAGa 5'
            |||   | | ||||||||| 
Target 5' atGGC--GCGA-TCTCAGCTCa 3'
 566 - 584 151.00 -17.00
2 
miRNA  3' acCCGAAAG--AUCAG-AGUCGAGa 5'
            || | ||  || || ||||:|| 
Target 5' taGGATCTCGTTAATCATCAGTTCc 3'
 392 - 416 142.00 -11.20
3 
miRNA  3' acCCGAAAGAUCAGAGUCGAGa 5'
            |||   | | ||||:|||| 
Target 5' gtGGC--ACGA-TCTCGGCTCa 3'
 742 - 760 135.00 -14.80
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
297412 87 ClinVar
297413 95 ClinVar
874178 171 ClinVar
874179 184 ClinVar
875108 205 ClinVar
875109 256 ClinVar
875110 327 ClinVar
297414 365 ClinVar
297415 401 ClinVar
297416 574 ClinVar
875111 579 ClinVar
876059 602 ClinVar
876060 613 ClinVar
297417 658 ClinVar
297418 663 ClinVar
297419 676 ClinVar
297420 676 ClinVar
297421 710 ClinVar
876061 726 ClinVar
297422 749 ClinVar
297423 872 ClinVar
297424 883 ClinVar
877017 902 ClinVar
877018 915 ClinVar
297425 925 ClinVar
877019 971 ClinVar
297426 972 ClinVar
874231 1022 ClinVar
297427 1055 ClinVar
297428 1113 ClinVar
297429 1117 ClinVar
297430 1127 ClinVar
297431 1181 ClinVar
297432 1217 ClinVar
874232 1221 ClinVar
297433 1352 ClinVar
297434 1487 ClinVar
297435 1507 ClinVar
297436 1507 ClinVar
297437 1604 ClinVar
297438 1675 ClinVar
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs756235478 1 dbSNP
rs1411707603 5 dbSNP
rs556314326 8 dbSNP
rs1042072149 11 dbSNP
rs371858774 16 dbSNP
rs375202792 17 dbSNP
rs569647683 19 dbSNP
rs1337566394 20 dbSNP
rs1163980616 25 dbSNP
rs779134942 27 dbSNP
rs745669443 29 dbSNP
rs538671145 32 dbSNP
rs779909585 35 dbSNP
rs1003314631 36 dbSNP
rs1257728350 40 dbSNP
rs1345602476 41 dbSNP
rs1007224072 43 dbSNP
rs1366952649 45 dbSNP
rs1055697147 46 dbSNP
rs778468275 46 dbSNP
rs369565019 47 dbSNP
rs1006001227 60 dbSNP
rs1464893110 71 dbSNP
rs957509102 76 dbSNP
rs1016058121 78 dbSNP
rs777930147 87 dbSNP
rs993281223 89 dbSNP
rs77858532 95 dbSNP
rs1228737644 96 dbSNP
rs1030383952 100 dbSNP
rs954391992 106 dbSNP
rs1355322303 109 dbSNP
rs186807040 112 dbSNP
rs911475629 115 dbSNP
rs964324625 116 dbSNP
rs554711682 117 dbSNP
rs771532230 120 dbSNP
rs1392247812 129 dbSNP
rs1281924764 132 dbSNP
rs1449181904 136 dbSNP
rs990284202 150 dbSNP
rs1201593105 151 dbSNP
rs1273544269 158 dbSNP
rs914747185 161 dbSNP
rs946085267 162 dbSNP
rs1041791244 164 dbSNP
rs574563778 171 dbSNP
rs928734354 173 dbSNP
rs1228514763 184 dbSNP
rs1271961783 187 dbSNP
rs1204199442 189 dbSNP
rs1345397832 191 dbSNP
rs1276580488 197 dbSNP
rs938693392 205 dbSNP
rs781777434 209 dbSNP
rs1284807599 226 dbSNP
rs1351095997 230 dbSNP
rs1056231147 237 dbSNP
rs1218431899 256 dbSNP
rs958693945 257 dbSNP
rs1306355966 259 dbSNP
rs894361148 267 dbSNP
rs1403404810 271 dbSNP
rs144331455 272 dbSNP
rs1477361121 275 dbSNP
rs1377554841 279 dbSNP
rs555958797 281 dbSNP
rs1037472248 282 dbSNP
rs897678555 283 dbSNP
rs1203953045 291 dbSNP
rs568253162 293 dbSNP
rs1280538809 296 dbSNP
rs1198506285 300 dbSNP
rs753950232 302 dbSNP
rs1344219395 307 dbSNP
rs1268620974 309 dbSNP
rs993769452 315 dbSNP
rs1208018621 322 dbSNP
rs1352369079 323 dbSNP
rs1286496461 325 dbSNP
rs1239250048 331 dbSNP
rs940924473 337 dbSNP
rs1473192900 343 dbSNP
rs1441818300 363 dbSNP
rs138892634 365 dbSNP
rs1336633777 380 dbSNP
rs1413057800 392 dbSNP
rs923416118 395 dbSNP
rs1160497612 397 dbSNP
rs558390922 401 dbSNP
rs1007220010 402 dbSNP
rs1176105738 422 dbSNP
rs933752019 426 dbSNP
rs1050763351 427 dbSNP
rs1185156242 428 dbSNP
rs990420060 448 dbSNP
rs1413238817 450 dbSNP
rs1336772709 457 dbSNP
rs889533041 460 dbSNP
rs1326966749 464 dbSNP
rs1448075379 468 dbSNP
rs1266378549 473 dbSNP
rs942416756 480 dbSNP
rs773809357 481 dbSNP
rs1446314093 485 dbSNP
rs978031411 488 dbSNP
rs1321611726 494 dbSNP
rs575782596 503 dbSNP
rs893077431 508 dbSNP
rs928727399 512 dbSNP
rs1387080906 517 dbSNP
rs1010135107 520 dbSNP
rs1405380169 524 dbSNP
rs1415535405 536 dbSNP
rs535370572 538 dbSNP
rs1161051463 541 dbSNP
rs1443598775 542 dbSNP
rs1020141798 545 dbSNP
rs1248463901 546 dbSNP
rs765780152 549 dbSNP
rs761545265 556 dbSNP
rs1463540642 564 dbSNP
rs1241383258 567 dbSNP
rs771437539 571 dbSNP
rs772813059 572 dbSNP
rs959033022 573 dbSNP
rs192016153 574 dbSNP
rs565438629 579 dbSNP
rs962336268 593 dbSNP
rs915928762 599 dbSNP
rs527941032 602 dbSNP
rs1280583851 603 dbSNP
rs1436609780 605 dbSNP
rs923445618 612 dbSNP
rs1037571354 613 dbSNP
rs1236497160 617 dbSNP
rs1423669913 622 dbSNP
rs182807417 626 dbSNP
rs1170257917 627 dbSNP
rs897771796 629 dbSNP
rs1418741517 638 dbSNP
rs986256603 640 dbSNP
rs911003155 643 dbSNP
rs1248583067 650 dbSNP
rs567818153 654 dbSNP
rs1054147033 655 dbSNP
rs1207765015 657 dbSNP
rs886046352 658 dbSNP
rs1763698 663 dbSNP
rs1330073639 666 dbSNP
rs1397582562 668 dbSNP
rs75425122 673 dbSNP
rs77858547 675 dbSNP
rs1010600218 676 dbSNP
rs1176499914 676 dbSNP
rs1184660062 676 dbSNP
rs1197373602 676 dbSNP
rs1211256818 676 dbSNP
rs1222398265 676 dbSNP
rs1251162034 676 dbSNP
rs1252848115 676 dbSNP
rs1261753492 676 dbSNP
rs1314467037 676 dbSNP
rs1350380894 676 dbSNP
rs1350525573 676 dbSNP
rs1353751059 676 dbSNP
rs1370344097 676 dbSNP
rs1422890772 676 dbSNP
rs1434900413 676 dbSNP
rs1480121575 676 dbSNP
rs1486196539 676 dbSNP
rs752218261 676 dbSNP
rs886046353 676 dbSNP
rs1021880945 677 dbSNP
rs79736278 678 dbSNP
rs1329180987 679 dbSNP
rs1372146453 679 dbSNP
rs1041615955 680 dbSNP
rs907117261 682 dbSNP
rs1002741170 684 dbSNP
rs1276399138 685 dbSNP
rs1357378449 692 dbSNP
rs1175564209 696 dbSNP
rs1034581952 702 dbSNP
rs1345615175 702 dbSNP
rs869264061 706 dbSNP
rs894580777 706 dbSNP
rs1203071331 707 dbSNP
rs1274097007 708 dbSNP
rs185654501 710 dbSNP
rs977581293 711 dbSNP
rs1036269192 714 dbSNP
rs1203635253 715 dbSNP
rs1330404478 716 dbSNP
rs758861942 737 dbSNP
rs1006692383 740 dbSNP
rs1315977428 741 dbSNP
rs1312922295 744 dbSNP
rs1266895334 746 dbSNP
rs190071085 749 dbSNP
rs961981237 750 dbSNP
rs972038067 754 dbSNP
rs1161468505 755 dbSNP
rs555453881 756 dbSNP
rs1363464255 767 dbSNP
rs1165703708 779 dbSNP
rs1169212922 780 dbSNP
rs182233357 781 dbSNP
rs1183356731 788 dbSNP
rs753837289 790 dbSNP
rs1466684445 798 dbSNP
rs1168020154 799 dbSNP
rs759257463 813 dbSNP
rs1384727453 820 dbSNP
rs916027184 821 dbSNP
rs1485235048 824 dbSNP
rs1265481242 825 dbSNP
rs1246593959 828 dbSNP
rs1345960681 829 dbSNP
rs765093709 830 dbSNP
rs1399303537 832 dbSNP
rs1228782654 836 dbSNP
rs572052263 839 dbSNP
rs1316076749 846 dbSNP
rs1380637142 846 dbSNP
rs1342325699 847 dbSNP
rs1384402855 849 dbSNP
rs1228161704 852 dbSNP
rs973416663 854 dbSNP
rs558480493 863 dbSNP
rs1264953828 869 dbSNP
rs942478899 871 dbSNP
rs540648773 872 dbSNP
rs777894453 883 dbSNP
rs945733700 884 dbSNP
rs1041396467 885 dbSNP
rs1191713317 891 dbSNP
rs1259984257 900 dbSNP
rs1428416392 901 dbSNP
rs1267506501 902 dbSNP
rs186474263 915 dbSNP
rs757471629 916 dbSNP
rs1290509929 923 dbSNP
rs886046354 925 dbSNP
rs565546786 930 dbSNP
rs755757589 955 dbSNP
rs146322472 958 dbSNP
rs894268797 962 dbSNP
rs1006309856 968 dbSNP
rs1166155294 969 dbSNP
rs777372120 971 dbSNP
rs886046355 972 dbSNP
rs1456036898 975 dbSNP
rs1020638850 980 dbSNP
rs903394624 987 dbSNP
rs1406780137 989 dbSNP
rs999530153 992 dbSNP
rs1363966493 996 dbSNP
rs1035832457 997 dbSNP
rs1399139588 1002 dbSNP
rs960469084 1003 dbSNP
rs577681127 1012 dbSNP
rs1378651632 1019 dbSNP
rs1200390256 1020 dbSNP
rs761485378 1021 dbSNP
rs1038231812 1022 dbSNP
rs1267774664 1024 dbSNP
rs991643154 1035 dbSNP
rs897908745 1039 dbSNP
rs1182502345 1041 dbSNP
rs1483820701 1048 dbSNP
rs139528456 1055 dbSNP
rs1030271792 1057 dbSNP
rs1345638087 1059 dbSNP
rs1257634167 1064 dbSNP
rs1225458929 1070 dbSNP
rs1296123341 1072 dbSNP
rs35225340 1077 dbSNP
rs558674779 1080 dbSNP
rs1410728054 1081 dbSNP
rs954976356 1089 dbSNP
rs781763610 1096 dbSNP
rs919255020 1104 dbSNP
rs1017780558 1112 dbSNP
rs543515941 1113 dbSNP
rs756380169 1114 dbSNP
rs989660533 1116 dbSNP
rs144177827 1117 dbSNP
rs1353299511 1124 dbSNP
rs1230755725 1126 dbSNP
rs543250497 1127 dbSNP
rs1180842772 1129 dbSNP
rs1442743256 1132 dbSNP
rs1257968629 1145 dbSNP
rs556230116 1163 dbSNP
rs1201742766 1165 dbSNP
rs117166528 1181 dbSNP
rs1288618260 1183 dbSNP
rs1262658696 1197 dbSNP
rs1488894737 1204 dbSNP
rs886046356 1217 dbSNP
rs6689207 1221 dbSNP
rs563079154 1223 dbSNP
rs946449856 1230 dbSNP
rs1341488246 1234 dbSNP
rs1339081703 1236 dbSNP
rs527426135 1240 dbSNP
rs1451173236 1242 dbSNP
rs1405991698 1245 dbSNP
rs1320648787 1246 dbSNP
rs1042030965 1248 dbSNP
rs902188204 1255 dbSNP
rs193122067 1262 dbSNP
rs928259189 1271 dbSNP
rs559905562 1273 dbSNP
rs938591783 1281 dbSNP
rs771727846 1283 dbSNP
rs1460869855 1284 dbSNP
rs1254844174 1288 dbSNP
rs372021668 1291 dbSNP
rs527705582 1292 dbSNP
rs941893851 1293 dbSNP
rs375523167 1300 dbSNP
rs772905876 1304 dbSNP
rs1223451406 1315 dbSNP
rs531904727 1330 dbSNP
rs1357247691 1332 dbSNP
rs1317615332 1342 dbSNP
rs1037530062 1346 dbSNP
rs1244228548 1348 dbSNP
rs897940018 1349 dbSNP
rs1385403891 1352 dbSNP
rs886046357 1352 dbSNP
rs1438713802 1354 dbSNP
rs746514982 1355 dbSNP
rs1342952110 1359 dbSNP
rs1013032736 1361 dbSNP
rs1051728459 1364 dbSNP
rs759735488 1365 dbSNP
rs1161507435 1367 dbSNP
rs541688073 1372 dbSNP
rs1443760033 1388 dbSNP
rs1460361238 1393 dbSNP
rs1023098944 1409 dbSNP
rs1474357261 1414 dbSNP
rs890423633 1429 dbSNP
rs1302239309 1433 dbSNP
rs994901460 1433 dbSNP
rs1400002569 1443 dbSNP
rs1026286080 1448 dbSNP
rs1397819220 1452 dbSNP
rs139194573 1453 dbSNP
rs1359127033 1458 dbSNP
rs1164767442 1465 dbSNP
rs183926045 1473 dbSNP
rs1216846940 1475 dbSNP
rs1018312117 1478 dbSNP
rs1269150053 1480 dbSNP
rs1436559036 1482 dbSNP
rs149940158 1487 dbSNP
rs570264040 1498 dbSNP
rs115780311 1507 dbSNP
rs911790375 1510 dbSNP
rs1423563035 1511 dbSNP
rs1370963272 1516 dbSNP
rs1172191555 1519 dbSNP
rs551999587 1520 dbSNP
rs144988440 1526 dbSNP
rs1408143638 1529 dbSNP
rs1418700542 1540 dbSNP
rs1021113208 1542 dbSNP
rs1480790561 1543 dbSNP
rs964630565 1549 dbSNP
rs1197569750 1556 dbSNP
rs1311879442 1558 dbSNP
rs1252261924 1569 dbSNP
rs974534100 1571 dbSNP
rs967135823 1580 dbSNP
rs977139322 1583 dbSNP
rs915094317 1584 dbSNP
rs188722111 1589 dbSNP
rs946418799 1593 dbSNP
rs142139493 1604 dbSNP
rs1403966580 1606 dbSNP
rs1484530373 1608 dbSNP
rs1204957423 1610 dbSNP
rs1243284631 1612 dbSNP
rs562243899 1622 dbSNP
rs1176435594 1624 dbSNP
rs923735852 1625 dbSNP
rs1439732736 1626 dbSNP
rs759490775 1627 dbSNP
rs1176657074 1630 dbSNP
rs1470890065 1631 dbSNP
rs960015531 1633 dbSNP
rs1174287386 1638 dbSNP
rs1480272755 1650 dbSNP
rs991164261 1658 dbSNP
rs568055116 1661 dbSNP
rs1419397586 1663 dbSNP
rs1175125548 1664 dbSNP
rs915844867 1665 dbSNP
rs1232626173 1675 dbSNP
rs536844021 1675 dbSNP
rs973228760 1682 dbSNP
rs35728788 1692 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
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 GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection ...

- Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell.

Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 4352.0
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 GSM714644. RNA binding protein: AGO2. Condition:completeT1 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
Experimental Support 3 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 GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

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

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]
Experimental Support 4 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions Prostate Tissue
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 SRX1760638. RNA binding protein: AGO2. Condition:AGO-CLIP-PC3-miR148 ...

- Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al., 2016, Neoplasia (New York, N.Y.).

Article - Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al.
- Neoplasia (New York, N.Y.), 2016
MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.
LinkOut: [PMID: 27292025]
CLIP-seq Support 1 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000372470.3 | 3UTR | CUCACUGCAACCUCCACCUCCGGGUUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000372470.3 | 3UTR | CUCACUGCAACCUCCACCUCCGGGUUCAAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000372470.3 | 3UTR | CUCACUGCAACCUCCACCUCCGGGUUCAAG
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
Click to see details
118 hsa-miR-3160-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT066658 DYRK2 dual specificity tyrosine phosphorylation regulated kinase 2 2 2
MIRT075318 SF3B3 splicing factor 3b subunit 3 2 4
MIRT077083 EIF1 eukaryotic translation initiation factor 1 2 2
MIRT100381 HSPA1B heat shock protein family A (Hsp70) member 1B 2 6
MIRT135259 TMBIM6 transmembrane BAX inhibitor motif containing 6 2 4
MIRT184913 ZNF268 zinc finger protein 268 2 2
MIRT218862 CDKN1A cyclin dependent kinase inhibitor 1A 2 2
MIRT446580 FPR2 formyl peptide receptor 2 2 2
MIRT448834 FGD4 FYVE, RhoGEF and PH domain containing 4 2 2
MIRT449455 RNF13 ring finger protein 13 2 2
MIRT452284 CARD8 caspase recruitment domain family member 8 2 2
MIRT452628 FAM162A family with sequence similarity 162 member A 2 2
MIRT453454 GLG1 golgi glycoprotein 1 2 2
MIRT454188 AP1S3 adaptor related protein complex 1 sigma 3 subunit 2 6
MIRT454434 GTF2F1 general transcription factor IIF subunit 1 2 2
MIRT454575 NT5DC3 5'-nucleotidase domain containing 3 2 2
MIRT455555 TRAF1 TNF receptor associated factor 1 2 6
MIRT455841 MPL MPL proto-oncogene, thrombopoietin receptor 2 6
MIRT455969 BCAS4 breast carcinoma amplified sequence 4 2 4
MIRT456805 SIGLEC14 sialic acid binding Ig like lectin 14 2 2
MIRT457320 DUSP19 dual specificity phosphatase 19 2 2
MIRT457366 POFUT2 protein O-fucosyltransferase 2 2 2
MIRT457684 ZNF587 zinc finger protein 587 2 2
MIRT458158 LYRM4 LYR motif containing 4 2 6
MIRT458641 SGPP2 sphingosine-1-phosphate phosphatase 2 2 2
MIRT459134 FADS6 fatty acid desaturase 6 2 2
MIRT459153 NARF nuclear prelamin A recognition factor 2 4
MIRT460460 NOM1 nucleolar protein with MIF4G domain 1 2 4
MIRT460974 STK17B serine/threonine kinase 17b 2 2
MIRT461439 ACSBG1 acyl-CoA synthetase bubblegum family member 1 2 2
MIRT461507 NEDD4L neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase 2 2
MIRT462490 GSR glutathione-disulfide reductase 2 2
MIRT462638 PHF5A PHD finger protein 5A 2 2
MIRT463279 ZFX zinc finger protein, X-linked 2 2
MIRT463360 ZFAND4 zinc finger AN1-type containing 4 2 2
MIRT465777 TMOD3 tropomodulin 3 2 2
MIRT466143 TMEM120B transmembrane protein 120B 2 2
MIRT468401 SETD3 SET domain containing 3 2 2
MIRT468998 RNPS1 RNA binding protein with serine rich domain 1 2 2
MIRT471574 PARD6B par-6 family cell polarity regulator beta 2 2
MIRT472108 NME2 NME/NM23 nucleoside diphosphate kinase 2 2 2
MIRT472125 NME1-NME2 NME1-NME2 readthrough 2 2
MIRT473020 MRPS14 mitochondrial ribosomal protein S14 2 2
MIRT473083 MORN4 MORN repeat containing 4 2 2
MIRT475598 HMGB2 high mobility group box 2 2 4
MIRT475937 GXYLT2 glucoside xylosyltransferase 2 2 8
MIRT476117 GPR157 G protein-coupled receptor 157 2 2
MIRT476406 GDE1 glycerophosphodiester phosphodiesterase 1 2 2
MIRT478003 DNAL1 dynein axonemal light chain 1 2 2
MIRT487969 IQSEC2 IQ motif and Sec7 domain 2 2 2
MIRT489418 TUBB2A tubulin beta 2A class IIa 2 2
MIRT491522 IL10RA interleukin 10 receptor subunit alpha 2 2
MIRT492673 PLEC plectin 2 2
MIRT493545 ICOSLG inducible T-cell costimulator ligand 2 2
MIRT513085 USP9X ubiquitin specific peptidase 9, X-linked 2 2
MIRT514009 CECR2 CECR2, histone acetyl-lysine reader 2 4
MIRT516683 ZNF860 zinc finger protein 860 2 2
MIRT518392 ZNF250 zinc finger protein 250 2 2
MIRT522683 LUZP1 leucine zipper protein 1 2 6
MIRT524488 CEP97 centrosomal protein 97 2 2
MIRT527457 CLEC12B C-type lectin domain family 12 member B 2 2
MIRT527705 IL17REL interleukin 17 receptor E like 2 2
MIRT531647 C19orf52 translocase of inner mitochondrial membrane 29 2 2
MIRT532381 UMPS uridine monophosphate synthetase 2 2
MIRT532588 MTHFD1 methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1 2 2
MIRT533555 TPM4 tropomyosin 4 2 2
MIRT548371 ENTPD5 ectonucleoside triphosphate diphosphohydrolase 5 2 4
MIRT550250 PVR poliovirus receptor 2 2
MIRT552555 ZFP36L2 ZFP36 ring finger protein like 2 2 4
MIRT554113 SMARCE1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 2 2
MIRT554131 SMARCA5 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 2 2
MIRT561344 ZBTB18 zinc finger and BTB domain containing 18 2 2
MIRT561638 RUNX3 runt related transcription factor 3 2 2
MIRT566497 PBX2P1 PBX homeobox 2 pseudogene 1 2 2
MIRT570583 OTUD7B OTU deubiquitinase 7B 2 2
MIRT572731 MCTS1 MCTS1, re-initiation and release factor 2 2
MIRT574041 PEX26 peroxisomal biogenesis factor 26 2 2
MIRT575231 Fut1 fucosyltransferase 1 2 2
MIRT606811 BICD2 BICD cargo adaptor 2 2 2
MIRT621016 CLSTN3 calsyntenin 3 2 2
MIRT637852 PDCL3 phosducin like 3 2 2
MIRT640477 ZNF557 zinc finger protein 557 2 2
MIRT642827 LINC00346 long intergenic non-protein coding RNA 346 2 2
MIRT643887 IMP4 IMP4, U3 small nucleolar ribonucleoprotein 2 2
MIRT664874 PCNXL2 pecanex homolog 2 2 2
MIRT680528 PRIM2 DNA primase subunit 2 2 2
MIRT680648 KIAA1456 KIAA1456 2 2
MIRT680807 ZNF578 zinc finger protein 578 2 2
MIRT680921 STX2 syntaxin 2 2 2
MIRT681112 CEP57L1 centrosomal protein 57 like 1 2 2
MIRT681147 INTS7 integrator complex subunit 7 2 2
MIRT681966 TFCP2 transcription factor CP2 2 2
MIRT684316 GTF3C4 general transcription factor IIIC subunit 4 2 2
MIRT684906 GSG2 histone H3 associated protein kinase 2 2
MIRT685499 MED16 mediator complex subunit 16 2 2
MIRT685929 MOCS3 molybdenum cofactor synthesis 3 2 2
MIRT686875 SLC25A32 solute carrier family 25 member 32 2 2
MIRT688204 FNIP1 folliculin interacting protein 1 2 2
MIRT688791 CCNB1 cyclin B1 2 2
MIRT689227 RPS19 ribosomal protein S19 2 2
MIRT690470 ZNF33A zinc finger protein 33A 2 2
MIRT691982 PLCXD1 phosphatidylinositol specific phospholipase C X domain containing 1 2 2
MIRT694006 PPIL4 peptidylprolyl isomerase like 4 2 2
MIRT694529 TRIM72 tripartite motif containing 72 2 2
MIRT695420 ADH5 alcohol dehydrogenase 5 (class III), chi polypeptide 2 2
MIRT695784 HSD17B12 hydroxysteroid 17-beta dehydrogenase 12 2 2
MIRT697799 UBXN2A UBX domain protein 2A 2 2
MIRT698275 TMEM2 transmembrane protein 2 2 2
MIRT698317 TMEM136 transmembrane protein 136 2 2
MIRT699971 RREB1 ras responsive element binding protein 1 2 2
MIRT700717 PNO1 partner of NOB1 homolog 2 2
MIRT701721 MTMR12 myotubularin related protein 12 2 2
MIRT701879 MPLKIP M-phase specific PLK1 interacting protein 2 2
MIRT702959 HIF1A hypoxia inducible factor 1 alpha subunit 2 2
MIRT706178 ZNF716 zinc finger protein 716 2 2
MIRT706463 SPRED1 sprouty related EVH1 domain containing 1 2 2
MIRT718154 TTC33 tetratricopeptide repeat domain 33 2 2
MIRT718711 ANKRD18A ankyrin repeat domain 18A 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3160-3p Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-3160-3p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-3160-3p Osimertinib 71496458 NSC779217 approved resistant cell line (HCC827)
hsa-miR-3160-3p Tripterygium wilfordii Hook F resistant tissue
hsa-miR-3160-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3160-3p Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)

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