pre-miRNA Information
pre-miRNA hsa-mir-3689d-1   
Genomic Coordinates chr9: 134849609 - 134849682
Description Homo sapiens miR-3689d-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA hsa-mir-3689d-2   
Genomic Coordinates chr9: 134850277 - 134850356
Description Homo sapiens miR-3689d-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3689d
Sequence 2| GGGAGGUGUGAUCUCACACUCG |23
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs551722268 8 dbSNP
rs143142996 8 dbSNP
rs1236297052 12 dbSNP
rs573148947 14 dbSNP
rs1210004979 14 dbSNP
rs1217460444 14 dbSNP
rs762590109 18 dbSNP
rs574332265 18 dbSNP
rs1164353021 21 dbSNP
rs963741171 21 dbSNP
rs1177416877 22 dbSNP
rs765777344 22 dbSNP
Putative Targets

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' gcucacacUCUAGUGUGGAGGg 5'
                  ||| | ||||||| 
Target 5' agcaccccAGACCTCACCTCCa 3'
88 - 109 154.00 -15.20
2
miRNA  3' gcUCACACUCUAGUGUGGAGGg 5'
            | ||  |  || ||||||| 
Target 5' tcACTGCAACCTC-CACCTCCg 3'
582 - 602 147.00 -11.80
3
miRNA  3' gcucacacucuaGUGUGGAGGg 5'
                      |||||:||| 
Target 5' cctccacttcccCACACTTCCc 3'
270 - 291 134.00 -16.60
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 GSM545214. RNA binding protein: AGO3. Condition:Control PAR-CLIP data was present in GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection PAR-CLIP data was present in GSM545217. RNA binding protein: AGO2. Condition:miR-7 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 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 GSM545214
Method / RBP PAR-CLIP / AGO3
Cell line / Condition HEK293 / Control
Location of target site ENST00000372470.3 | 3UTR | CCUCCACCUCCGGGUUC
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 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 3 for dataset GSM545217
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-7 transfection
Location of target site ENST00000372470.3 | 3UTR | CAACCUCCACCUCCGGGUUCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 4 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
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
231 hsa-miR-3689d Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059166 TXNIP thioredoxin interacting protein 2 4
MIRT080699 KIAA1468 KIAA1468 2 2
MIRT218770 CDKN1A cyclin dependent kinase inhibitor 1A 2 2
MIRT278059 KHNYN KH and NYN domain containing 2 2
MIRT345933 EIF4A1 eukaryotic translation initiation factor 4A1 2 2
MIRT366238 VMA21 VMA21, vacuolar ATPase assembly factor 2 2
MIRT449689 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT451149 C19orf53 chromosome 19 open reading frame 53 2 2
MIRT451266 NDUFA11 NADH:ubiquinone oxidoreductase subunit A11 2 2
MIRT451375 C19orf43 telomerase RNA component interacting RNase 2 2
MIRT451570 CIAPIN1 cytokine induced apoptosis inhibitor 1 2 2
MIRT451585 HIRIP3 HIRA interacting protein 3 2 2
MIRT451614 MEIS3P1 Meis homeobox 3 pseudogene 1 2 2
MIRT451763 ZNF611 zinc finger protein 611 2 6
MIRT452383 LY6E lymphocyte antigen 6 family member E 2 4
MIRT452573 ZFP69B ZFP69 zinc finger protein B 2 2
MIRT452735 PTGES3L prostaglandin E synthase 3 like 2 6
MIRT452867 LAX1 lymphocyte transmembrane adaptor 1 2 2
MIRT452975 CABP4 calcium binding protein 4 2 2
MIRT453215 CERS1 ceramide synthase 1 2 2
MIRT453259 PARP11 poly(ADP-ribose) polymerase family member 11 2 2
MIRT453449 GLG1 golgi glycoprotein 1 2 2
MIRT453479 PITPNM3 PITPNM family member 3 2 2
MIRT453663 CD207 CD207 molecule 2 6
MIRT453724 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 2 2
MIRT453760 RANGAP1 Ran GTPase activating protein 1 2 2
MIRT454181 AP1S3 adaptor related protein complex 1 sigma 3 subunit 2 6
MIRT454330 PPARA peroxisome proliferator activated receptor alpha 2 2
MIRT454338 CDKL1 cyclin dependent kinase like 1 2 2
MIRT454427 GTF2F1 general transcription factor IIF subunit 1 2 2
MIRT454665 FBXL18 F-box and leucine rich repeat protein 18 2 2
MIRT454825 POLR2J3 RNA polymerase II subunit J3 2 2
MIRT455130 TBC1D25 TBC1 domain family member 25 2 2
MIRT455166 SUV39H1 suppressor of variegation 3-9 homolog 1 2 2
MIRT455416 RXRB retinoid X receptor beta 2 2
MIRT455668 GLO1 glyoxalase I 2 2
MIRT455999 CYP2C19 cytochrome P450 family 2 subfamily C member 19 2 2
MIRT456446 TMEM81 transmembrane protein 81 2 2
MIRT456642 NOS1AP nitric oxide synthase 1 adaptor protein 2 2
MIRT456728 TMEM239 transmembrane protein 239 2 2
MIRT457131 ASPH aspartate beta-hydroxylase 2 2
MIRT457157 MXRA7 matrix remodeling associated 7 2 2
MIRT457358 POFUT2 protein O-fucosyltransferase 2 2 2
MIRT457458 UNC119B unc-119 lipid binding chaperone B 2 2
MIRT457619 UPK3BL uroplakin 3B like 1 2 2
MIRT457692 ZNF587 zinc finger protein 587 2 2
MIRT457727 SMOX spermine oxidase 2 2
MIRT457788 VWA1 von Willebrand factor A domain containing 1 2 2
MIRT457875 THEM6 thioesterase superfamily member 6 2 4
MIRT457909 ZNF212 zinc finger protein 212 2 2
MIRT458395 ABCF1 ATP binding cassette subfamily F member 1 2 2
MIRT458496 MARVELD2 MARVEL domain containing 2 2 2
MIRT458544 CYP2B6 cytochrome P450 family 2 subfamily B member 6 2 2
MIRT458577 TCOF1 treacle ribosome biogenesis factor 1 2 2
MIRT458732 CES2 carboxylesterase 2 2 2
MIRT458814 ZNF843 zinc finger protein 843 2 2
MIRT458931 SAMD4B sterile alpha motif domain containing 4B 2 2
MIRT459341 ZNF17 zinc finger protein 17 2 2
MIRT459365 MPLKIP M-phase specific PLK1 interacting protein 2 6
MIRT459572 NLGN2 neuroligin 2 2 2
MIRT460015 DTX3L deltex E3 ubiquitin ligase 3L 2 4
MIRT460144 ASB16 ankyrin repeat and SOCS box containing 16 2 2
MIRT460653 IGFBP4 insulin like growth factor binding protein 4 2 2
MIRT460798 VPS33A VPS33A, CORVET/HOPS core subunit 2 2
MIRT461058 KCNK6 potassium two pore domain channel subfamily K member 6 2 4
MIRT461458 SLC19A3 solute carrier family 19 member 3 2 2
MIRT461572 SCO1 SCO1, cytochrome c oxidase assembly protein 2 4
MIRT461927 TNFSF14 TNF superfamily member 14 2 2
MIRT461953 C3 complement C3 2 2
MIRT462278 KRR1 KRR1, small subunit processome component homolog 2 2
MIRT462744 EFNB1 ephrin B1 2 2
MIRT463136 ZNF451 zinc finger protein 451 2 4
MIRT463566 ZBTB39 zinc finger and BTB domain containing 39 2 6
MIRT463866 WNT7B Wnt family member 7B 2 2
MIRT464326 UST uronyl 2-sulfotransferase 2 2
MIRT464796 UBE2F ubiquitin conjugating enzyme E2 F (putative) 2 2
MIRT465034 TTC39C tetratricopeptide repeat domain 39C 2 2
MIRT466207 TMED10 transmembrane p24 trafficking protein 10 2 2
MIRT467007 SSBP2 single stranded DNA binding protein 2 2 2
MIRT467029 SRSF1 serine and arginine rich splicing factor 1 2 4
MIRT468001 SKI SKI proto-oncogene 2 2
MIRT468031 SIKE1 suppressor of IKBKE 1 2 6
MIRT468575 SERBP1 SERPINE1 mRNA binding protein 1 2 6
MIRT468834 RRM2 ribonucleotide reductase regulatory subunit M2 2 2
MIRT468970 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT469450 REL REL proto-oncogene, NF-kB subunit 2 6
MIRT470888 PLXND1 plexin D1 2 2
MIRT470953 PKM pyruvate kinase, muscle 2 2
MIRT471828 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT472590 NACC1 nucleus accumbens associated 1 2 2
MIRT472805 MTMR12 myotubularin related protein 12 2 2
MIRT472818 MTMR10 myotubularin related protein 10 2 6
MIRT472914 MSN moesin 2 2
MIRT474558 KLHDC3 kelch domain containing 3 2 2
MIRT474716 KIF13A kinesin family member 13A 2 6
MIRT475279 TOR1AIP2 torsin 1A interacting protein 2 2 2
MIRT475300 IFNLR1 interferon lambda receptor 1 2 2
MIRT475759 HDLBP high density lipoprotein binding protein 2 2
MIRT475786 HDGF heparin binding growth factor 2 2
MIRT475933 GXYLT2 glucoside xylosyltransferase 2 2 8
MIRT476212 GNS glucosamine (N-acetyl)-6-sulfatase 2 2
MIRT476238 GNPNAT1 glucosamine-phosphate N-acetyltransferase 1 2 4
MIRT476799 FNDC3B fibronectin type III domain containing 3B 2 2
MIRT477988 DNAL1 dynein axonemal light chain 1 2 2
MIRT478317 DDN dendrin 2 2
MIRT479257 CHSY1 chondroitin sulfate synthase 1 2 2
MIRT479344 CEP97 centrosomal protein 97 2 2
MIRT479522 CDCA4 cell division cycle associated 4 2 2
MIRT479906 CCDC117 coiled-coil domain containing 117 2 6
MIRT481147 AVL9 AVL9 cell migration associated 2 6
MIRT481735 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT482089 ALG8 ALG8, alpha-1,3-glucosyltransferase 2 2
MIRT482389 AEN apoptosis enhancing nuclease 2 2
MIRT483093 TFPI tissue factor pathway inhibitor 2 2
MIRT484246 ANK1 ankyrin 1 2 2
MIRT484342 EPN1 epsin 1 2 4
MIRT489141 C5orf38 chromosome 5 open reading frame 38 2 2
MIRT489163 MRPL12 mitochondrial ribosomal protein L12 2 4
MIRT489547 SOX11 SRY-box 11 2 4
MIRT489780 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT489799 KRT80 keratin 80 2 6
MIRT490535 KIAA1715 lunapark, ER junction formation factor 2 2
MIRT492198 SOCS1 suppressor of cytokine signaling 1 2 2
MIRT492283 SHISA6 shisa family member 6 2 4
MIRT501059 SMARCAD1 SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 2 4
MIRT501094 SLC5A6 solute carrier family 5 member 6 2 4
MIRT503870 CBS cystathionine-beta-synthase 2 2
MIRT507981 BCL2L13 BCL2 like 13 2 4
MIRT508125 AMD1 adenosylmethionine decarboxylase 1 2 2
MIRT508205 SLC35E1 solute carrier family 35 member E1 2 2
MIRT508385 SPTBN2 spectrin beta, non-erythrocytic 2 2 4
MIRT510308 PDRG1 p53 and DNA damage regulated 1 2 2
MIRT510462 ZDHHC18 zinc finger DHHC-type containing 18 2 2
MIRT512227 ATXN3 ataxin 3 2 8
MIRT512665 STEAP3 STEAP3 metalloreductase 2 2
MIRT514184 PGPEP1 pyroglutamyl-peptidase I 2 2
MIRT515053 EBNA1BP2 EBNA1 binding protein 2 2 2
MIRT515138 ZNF799 zinc finger protein 799 2 4
MIRT515452 ZNF747 zinc finger protein 747 2 2
MIRT515791 COL4A3BP collagen type IV alpha 3 binding protein 2 2
MIRT515905 AGTPBP1 ATP/GTP binding protein 1 2 2
MIRT516129 MRPS16 mitochondrial ribosomal protein S16 2 6
MIRT516679 ZNF860 zinc finger protein 860 2 4
MIRT516750 ZNF100 zinc finger protein 100 2 2
MIRT516971 OR7D2 olfactory receptor family 7 subfamily D member 2 2 2
MIRT517491 NPAP1 nuclear pore associated protein 1 2 2
MIRT517774 PROM2 prominin 2 2 2
MIRT517938 ZNF431 zinc finger protein 431 2 4
MIRT518386 ZNF250 zinc finger protein 250 2 2
MIRT520621 TMEM41B transmembrane protein 41B 2 2
MIRT521028 SLC30A5 solute carrier family 30 member 5 2 2
MIRT521454 RAD51 RAD51 recombinase 2 2
MIRT521564 PTPLB 3-hydroxyacyl-CoA dehydratase 2 1 1
MIRT521581 PTBP2 polypyrimidine tract binding protein 2 2 2
MIRT522263 NKRF NFKB repressing factor 2 2
MIRT522410 MXI1 MAX interactor 1, dimerization protein 2 2
MIRT522543 MED28 mediator complex subunit 28 2 6
MIRT522915 KCNE3 potassium voltage-gated channel subfamily E regulatory subunit 3 2 2
MIRT523029 IGF1 insulin like growth factor 1 2 2
MIRT523854 ESPL1 extra spindle pole bodies like 1, separase 2 4
MIRT524184 DFFA DNA fragmentation factor subunit alpha 2 2
MIRT524520 CDK19 cyclin dependent kinase 19 2 2
MIRT524674 C12orf5 TP53 induced glycolysis regulatory phosphatase 2 2
MIRT530257 ZNF620 zinc finger protein 620 2 2
MIRT540691 BMP3 bone morphogenetic protein 3 2 2
MIRT540976 C17orf85 nuclear cap binding subunit 3 2 2
MIRT545505 NAP1L1 nucleosome assembly protein 1 like 1 2 2
MIRT545631 GGCX gamma-glutamyl carboxylase 2 2
MIRT547358 NAA30 N(alpha)-acetyltransferase 30, NatC catalytic subunit 2 2
MIRT550701 MPL MPL proto-oncogene, thrombopoietin receptor 2 4
MIRT550717 PMPCA peptidase, mitochondrial processing alpha subunit 2 4
MIRT551203 NCR3LG1 natural killer cell cytotoxicity receptor 3 ligand 1 2 2
MIRT553999 SRGAP1 SLIT-ROBO Rho GTPase activating protein 1 2 4
MIRT561081 LLPH LLP homolog, long-term synaptic facilitation 2 2
MIRT563523 TAF8 TATA-box binding protein associated factor 8 2 2
MIRT564463 SLC35E2 solute carrier family 35 member E2 2 2
MIRT565233 TRAF6 TNF receptor associated factor 6 2 2
MIRT566618 NKAP NFKB activating protein 2 2
MIRT569527 AP5Z1 adaptor related protein complex 5 zeta 1 subunit 2 2
MIRT569639 QPCT glutaminyl-peptide cyclotransferase 2 2
MIRT570253 SSPN sarcospan 2 2
MIRT570570 OTUD7B OTU deubiquitinase 7B 2 2
MIRT570621 MTF2 metal response element binding transcription factor 2 2 2
MIRT571098 ISLR2 immunoglobulin superfamily containing leucine rich repeat 2 2 2
MIRT575196 Entpd4 ectonucleoside triphosphate diphosphohydrolase 4 2 2
MIRT575554 Cd99 CD99 antigen 2 2
MIRT575634 Gnl3l guanine nucleotide binding protein-like 3 (nucleolar)-like 2 2
MIRT608267 NOP14 NOP14 nucleolar protein 2 2
MIRT609314 FXYD6 FXYD domain containing ion transport regulator 6 2 2
MIRT627670 RPL28 ribosomal protein L28 2 2
MIRT631185 TSPAN14 tetraspanin 14 2 2
MIRT631964 YIPF5 Yip1 domain family member 5 2 2
MIRT632885 GINM1 glycoprotein integral membrane 1 2 2
MIRT642618 CDKN3 cyclin dependent kinase inhibitor 3 2 2
MIRT645609 TSPAN6 tetraspanin 6 2 2
MIRT662227 PGBD4 piggyBac transposable element derived 4 2 2
MIRT662329 MYLK3 myosin light chain kinase 3 2 2
MIRT662725 LRRC3C leucine rich repeat containing 3C 2 2
MIRT665520 USP14 ubiquitin specific peptidase 14 2 2
MIRT666634 RBMS2 RNA binding motif single stranded interacting protein 2 2 2
MIRT668969 CNBP CCHC-type zinc finger nucleic acid binding protein 2 2
MIRT670925 DESI1 desumoylating isopeptidase 1 2 2
MIRT673939 ZNF500 zinc finger protein 500 2 2
MIRT674675 PLCE1 phospholipase C epsilon 1 2 2
MIRT675230 MAK male germ cell associated kinase 2 2
MIRT680864 MACC1 MACC1, MET transcriptional regulator 2 2
MIRT681047 ZDBF2 zinc finger DBF-type containing 2 2 2
MIRT681105 CEP57L1 centrosomal protein 57 like 1 2 2
MIRT683553 HAVCR1 hepatitis A virus cellular receptor 1 2 2
MIRT684508 C1orf174 chromosome 1 open reading frame 174 2 2
MIRT684812 BRIX1 BRX1, biogenesis of ribosomes 2 2
MIRT685981 CCDC77 coiled-coil domain containing 77 2 2
MIRT686709 TBC1D19 TBC1 domain family member 19 2 2
MIRT686867 SLC25A32 solute carrier family 25 member 32 2 2
MIRT688908 C11orf84 chromosome 11 open reading frame 84 2 2
MIRT691208 KLHL30 kelch like family member 30 2 2
MIRT692298 CNNM3 cyclin and CBS domain divalent metal cation transport mediator 3 2 2
MIRT694380 MTA1 metastasis associated 1 2 2
MIRT696497 COX6B1 cytochrome c oxidase subunit 6B1 2 2
MIRT700686 POLR3D RNA polymerase III subunit D 2 2
MIRT701088 PAPOLG poly(A) polymerase gamma 2 2
MIRT703373 GAPVD1 GTPase activating protein and VPS9 domains 1 2 2
MIRT706189 SAR1B secretion associated Ras related GTPase 1B 2 2
MIRT706648 SMIM19 small integral membrane protein 19 2 2
MIRT709466 KRTAP19-1 keratin associated protein 19-1 2 2
MIRT709699 DMWD DM1 locus, WD repeat containing 2 2
MIRT710693 LYRM4 LYR motif containing 4 2 2
MIRT713457 DNAJC11 DnaJ heat shock protein family (Hsp40) member C11 2 2
MIRT722409 RARS2 arginyl-tRNA synthetase 2, mitochondrial 2 2
MIRT725391 MAP3K9 mitogen-activated protein kinase kinase kinase 9 2 2
MIRT725548 DNMT3A DNA methyltransferase 3 alpha 2 2

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