miRTarBase - #MIRT091681


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pre-miRNA Information
pre-miRNA hsa-mir-4307   
Genomic Coordinates chr14: 26908642 - 26908725
Description Homo sapiens miR-4307 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4307
Sequence 56| AAUGUUUUUUCCUGUUUCC |74
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1056441032 1 dbSNP
rs776987575 3 dbSNP
rs948027524 8 dbSNP
rs930210474 12 dbSNP
rs191460273 13 dbSNP
rs538831777 14 dbSNP
rs1158802910 15 dbSNP
rs1047679599 17 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol RARB   
Synonyms HAP, MCOPS12, NR1B2, RARbeta1, RRB2
Description retinoic acid receptor beta
Transcript NM_000965   
Other Transcripts NM_016152   
Expression
Putative miRNA Targets on RARB
3'UTR of RARB
(miRNA target sites are highlighted)		 
>RARB|NM_000965|3'UTR
   1 GACATTTTCTAGCTACTTCAAACATTCCCCAGTACCTTCAGTTCCAGGATTTAAAATGCAAGAAAAAACATTTTTACTGC
  81 TGCTTAGTTTTTGGACTGAAAAGATATTAAAACTCAAGAAGGACCAAGAAGTTTTCATATGTATCAATATATATACTCCT
 161 CACTGTGTAACTTACCTAGAAATACAAACTTTTCCAATTTTAAAAAATCAGCCATTTCATGCAACCAGAAACTAGTTAAA
 241 AGCTTCTATTTTCCTCTTTGAACACTCAAGATTGCATGGCAAAGACCCAGTCAAAATGATTTACCCCTGGTTAAGTTTCT
 321 GAAGACTTTGTACATACAGAAGTATGGCTCTGTTCTTTCTATACTGTATGTTTGGTGCTTTCCTTTTGTCTTGCATACTC
 401 AAAATAACCATGACACCAAGGTTATGAAATAGACTACTGTACACGTCTACCTAGGTTCAAAAAGATAACTGTCTTGCTTT
 481 CATGGAATAGTCAAGACATCAAGGTAAGGAAACAGGACTATTGACAGGACTATTGTACAGTATGACAAGATAAGGCTGAA
 561 GATATTCTACTTTAGTTAGTATGGAAGCTTGTCTTTGCTCTTTCTGATGCTCTCAAACTGCATCTTTTATTTCATGTTGC
 641 CCAGTAAAAGTATACAAATTCCCTGCACTAGCAGAAGAGAATTCTGTATCAGTGTAACTGCCAGTTCAGTTAATCAAATG
 721 TCATTTGTTCAATTGTTAATGTCACTTTAAATTAAAAGTGGTTTATTACTTGTTTAATGACATAACTACACAGTTAGTTA
 801 AAAAAAATTTTTTTACAGTAATGATAGCCTCCAAGGCAGAAACACTTTTCAGTGTTAAGTTTTTGTTTACTTGTTCACAA
 881 GCCATTAGGGAAATTTCATGGGATAATTAGCAGGCTGGTCTACCACCTGGACCATGTAACTCTAGTGTCCTTCCTGATTC
 961 ATGCCTGATATTGGGATTTTTTTTTCCAGCCTTCTTGATGCCAAGGGGCTAATTAATATTAACAACTCCCAAAGAAACAG
1041 GCATAGAATCTGCCTCCTTTGACCTTGTTCAATCACTATGAAGCAGAGTGAAAGCTGTGGTAGAGTGGTTAACAGATACA
1121 AGTGTCAGTTTCTTAGTTCTCATTTAAGCACTAGTGGAATTTTTTTTTTTTGATATATTAGCAAGTCTGTGATGTACTTT
1201 CACTGGCTCTGTTTGTACATTGAGATTGTTTGTTTAACAATGCTTTCTATGTTCATATACTGTTTACCTTTTTCCATGGA
1281 GTCTCCTGGCAAAGAATAAAATATATTTATTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1361 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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' ccUUU--GUCCUUUUUUGUAa 5'
            |||  || |||||||||| 
Target 5' taAAATGCAAGAAAAAACATt 3'
 52 - 72 167.00 -10.20
2 
miRNA  3' ccUUUGUCCUUUUUUGUAa 5'
            :||:| |  ||:|||| 
Target 5' tgGAATA-GTCAAGACATc 3'
 483 - 500 132.00 -8.80
3 
miRNA  3' ccUUUGUCCUUUUUUGUAa 5'
            ::||  |||||:|:|| 
Target 5' ttGGAC-TGAAAAGATATt 3'
 91 - 108 124.00 -7.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN1943336 14 COSMIC
COSN30110775 29 COSMIC
COSN31500386 30 COSMIC
COSN30467530 49 COSMIC
COSN30507339 69 COSMIC
COSN28139711 98 COSMIC
COSN31608249 104 COSMIC
COSN28864713 140 COSMIC
COSN30722137 155 COSMIC
COSN7760117 162 COSMIC
COSN30169237 268 COSMIC
COSN23245070 375 COSMIC
COSN31549903 395 COSMIC
COSN28140135 473 COSMIC
COSN31532300 483 COSMIC
COSN26689919 568 COSMIC
COSN31520393 656 COSMIC
COSN20098222 798 COSMIC
COSN31584166 808 COSMIC
COSN24299634 809 COSMIC
COSN31606843 810 COSMIC
COSN20607735 932 COSMIC
COSN26639297 946 COSMIC
COSN20098228 1040 COSMIC
COSN7603390 1069 COSMIC
COSN25156343 1096 COSMIC
COSN30161564 1103 COSMIC
COSN29002201 1158 COSMIC
COSN1275283 1172 COSMIC
COSN27507922 1172 COSMIC
COSN31566102 1244 COSMIC
rs116199914 249 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs150640333 5 dbSNP
rs1231325075 11 dbSNP
rs927788295 14 dbSNP
rs760021600 16 dbSNP
rs1414131688 17 dbSNP
rs768047630 18 dbSNP
rs752865177 20 dbSNP
rs1248578346 22 dbSNP
rs1402279601 24 dbSNP
rs111671607 25 dbSNP
rs1397485001 26 dbSNP
rs756213540 28 dbSNP
rs369611883 30 dbSNP
rs990674425 33 dbSNP
rs1409725863 34 dbSNP
rs754044677 36 dbSNP
rs1352669238 37 dbSNP
rs1231554572 51 dbSNP
rs1207049231 59 dbSNP
rs558545649 63 dbSNP
rs185533944 67 dbSNP
rs916251369 69 dbSNP
rs534469545 70 dbSNP
rs1407637287 73 dbSNP
rs28509419 84 dbSNP
rs1373071836 89 dbSNP
rs554355759 92 dbSNP
rs1246083970 94 dbSNP
rs1440835262 95 dbSNP
rs952686359 97 dbSNP
rs1330406778 100 dbSNP
rs1335591626 102 dbSNP
rs574334526 105 dbSNP
rs1432049752 108 dbSNP
rs1371601587 114 dbSNP
rs1173376967 122 dbSNP
rs1453178078 126 dbSNP
rs1427859313 128 dbSNP
rs79679061 129 dbSNP
rs190921496 134 dbSNP
rs577416577 137 dbSNP
rs1296250909 138 dbSNP
rs976499292 140 dbSNP
rs935060170 142 dbSNP
rs1225129391 143 dbSNP
rs1279161607 152 dbSNP
rs746455367 164 dbSNP
rs1370477959 168 dbSNP
rs550782092 171 dbSNP
rs1410105671 173 dbSNP
rs546194290 174 dbSNP
rs1325673166 176 dbSNP
rs1312721322 178 dbSNP
rs1433173054 180 dbSNP
rs182678391 183 dbSNP
rs1177359896 186 dbSNP
rs1400228191 186 dbSNP
rs866195693 192 dbSNP
rs1405939780 193 dbSNP
rs1161437067 202 dbSNP
rs1224365883 202 dbSNP
rs932317887 209 dbSNP
rs1257075108 210 dbSNP
rs1053312014 219 dbSNP
rs1049980704 220 dbSNP
rs754625858 229 dbSNP
rs926174096 234 dbSNP
rs1215031606 247 dbSNP
rs901315445 247 dbSNP
rs116199914 249 dbSNP
rs1269534689 249 dbSNP
rs77458929 259 dbSNP
rs1381742414 267 dbSNP
rs891966943 276 dbSNP
rs1303764151 281 dbSNP
rs1430710944 287 dbSNP
rs748532131 288 dbSNP
rs1343938087 293 dbSNP
rs753225214 308 dbSNP
rs1161551063 309 dbSNP
rs764751279 310 dbSNP
rs1417432860 313 dbSNP
rs770242021 317 dbSNP
rs1162996726 322 dbSNP
rs1005589807 324 dbSNP
rs562262449 325 dbSNP
rs961512913 328 dbSNP
rs972763611 338 dbSNP
rs1034834829 340 dbSNP
rs1484890676 347 dbSNP
rs1045808670 351 dbSNP
rs960489861 353 dbSNP
rs79215662 354 dbSNP
rs1208819195 360 dbSNP
rs767626769 362 dbSNP
rs1246590381 365 dbSNP
rs1321928695 366 dbSNP
rs1313964669 367 dbSNP
rs1446989409 382 dbSNP
rs916533702 383 dbSNP
rs1363650729 390 dbSNP
rs539214127 395 dbSNP
rs946625112 406 dbSNP
rs1323071183 409 dbSNP
rs1435938424 411 dbSNP
rs1001474226 412 dbSNP
rs1459691567 417 dbSNP
rs531156615 418 dbSNP
rs549884153 419 dbSNP
rs865926884 421 dbSNP
rs116830066 424 dbSNP
rs1391968134 431 dbSNP
rs1189088098 437 dbSNP
rs1453688903 442 dbSNP
rs1480446293 443 dbSNP
rs538225518 445 dbSNP
rs935111817 446 dbSNP
rs1015802044 448 dbSNP
rs1040105836 450 dbSNP
rs1204283797 451 dbSNP
rs961243188 452 dbSNP
rs1340419365 455 dbSNP
rs1229839661 465 dbSNP
rs1300488684 465 dbSNP
rs201783636 466 dbSNP
rs1375531569 467 dbSNP
rs756444113 472 dbSNP
rs1299367315 478 dbSNP
rs901348082 491 dbSNP
rs934179842 493 dbSNP
rs1297770334 509 dbSNP
rs1427612074 510 dbSNP
rs552675376 512 dbSNP
rs1168971037 513 dbSNP
rs566186144 515 dbSNP
rs754210363 516 dbSNP
rs953799736 522 dbSNP
rs1433204611 524 dbSNP
rs988332177 525 dbSNP
rs1175078590 530 dbSNP
rs1383958948 531 dbSNP
rs925681866 533 dbSNP
rs1380528117 541 dbSNP
rs1206306816 547 dbSNP
rs138745362 547 dbSNP
rs890067360 550 dbSNP
rs1254712339 556 dbSNP
rs1235535986 559 dbSNP
rs1331709086 566 dbSNP
rs1304816232 579 dbSNP
rs1347488953 583 dbSNP
rs1408283732 584 dbSNP
rs1352552348 585 dbSNP
rs1006203851 589 dbSNP
rs1413873531 592 dbSNP
rs1038386237 598 dbSNP
rs1400002331 598 dbSNP
rs1053382285 604 dbSNP
rs897124674 607 dbSNP
rs1362754597 610 dbSNP
rs1156290644 616 dbSNP
rs1473406541 620 dbSNP
rs1252000423 621 dbSNP
rs773416762 621 dbSNP
rs1183370532 624 dbSNP
rs1485521147 625 dbSNP
rs1254719550 646 dbSNP
rs1282687840 647 dbSNP
rs1310715724 649 dbSNP
rs1241436062 657 dbSNP
rs1346297035 658 dbSNP
rs994215861 660 dbSNP
rs913363613 665 dbSNP
rs1350324492 667 dbSNP
rs1226647321 669 dbSNP
rs1331494459 670 dbSNP
rs1335906160 673 dbSNP
rs373252864 673 dbSNP
rs757706750 673 dbSNP
rs1271622974 675 dbSNP
rs1035034297 679 dbSNP
rs565798103 682 dbSNP
rs1264629307 684 dbSNP
rs757128494 684 dbSNP
rs937458028 687 dbSNP
rs1049046280 688 dbSNP
rs377355554 688 dbSNP
rs1005845717 695 dbSNP
rs1159376193 696 dbSNP
rs1471585435 698 dbSNP
rs1367135610 701 dbSNP
rs1012075896 704 dbSNP
rs1190030448 708 dbSNP
rs1443569705 710 dbSNP
rs1206924012 712 dbSNP
rs779025563 712 dbSNP
rs1466274271 713 dbSNP
rs1023873420 717 dbSNP
rs1015523313 718 dbSNP
rs1354482649 731 dbSNP
rs968023673 731 dbSNP
rs534911648 734 dbSNP
rs1245160131 739 dbSNP
rs546188032 741 dbSNP
rs1325798586 744 dbSNP
rs1366151676 747 dbSNP
rs201492992 749 dbSNP
rs745367643 749 dbSNP
rs1293073911 752 dbSNP
rs567400066 754 dbSNP
rs745894688 754 dbSNP
rs1165371805 756 dbSNP
rs1473299762 765 dbSNP
rs1390130833 766 dbSNP
rs1365572635 770 dbSNP
rs757967908 770 dbSNP
rs1393363832 776 dbSNP
rs1307907879 783 dbSNP
rs554492457 783 dbSNP
rs1029530400 784 dbSNP
rs1450085032 784 dbSNP
rs953774072 787 dbSNP
rs979731507 788 dbSNP
rs10548794 792 dbSNP
rs1338461228 792 dbSNP
rs35219452 792 dbSNP
rs533975133 792 dbSNP
rs774577588 792 dbSNP
rs1230577328 796 dbSNP
rs1365817811 797 dbSNP
rs56768779 797 dbSNP
rs749492135 797 dbSNP
rs1491368759 798 dbSNP
rs923631240 798 dbSNP
rs985210350 799 dbSNP
rs1167076440 800 dbSNP
rs58499503 800 dbSNP
rs1432234514 803 dbSNP
rs188986088 808 dbSNP
rs545264042 808 dbSNP
rs923054163 809 dbSNP
rs1199901396 812 dbSNP
rs931701113 819 dbSNP
rs1272279912 820 dbSNP
rs1207027410 821 dbSNP
rs146684489 822 dbSNP
rs772418347 840 dbSNP
rs1222387352 851 dbSNP
rs878933939 851 dbSNP
rs1216995970 853 dbSNP
rs1346461291 853 dbSNP
rs200244003 854 dbSNP
rs1441089758 856 dbSNP
rs950335483 856 dbSNP
rs201349875 857 dbSNP
rs755954727 857 dbSNP
rs759019717 857 dbSNP
rs927503488 862 dbSNP
rs1413233908 871 dbSNP
rs1177445608 877 dbSNP
rs1427408926 882 dbSNP
rs1049949764 886 dbSNP
rs1249331611 889 dbSNP
rs1173217295 892 dbSNP
rs557003083 896 dbSNP
rs544555643 898 dbSNP
rs1472423455 901 dbSNP
rs1249804279 902 dbSNP
rs1184097590 903 dbSNP
rs1483234424 904 dbSNP
rs1236871444 907 dbSNP
rs937385838 915 dbSNP
rs1437398513 916 dbSNP
rs1227242518 918 dbSNP
rs193139742 918 dbSNP
rs941640257 927 dbSNP
rs887745179 933 dbSNP
rs970692581 934 dbSNP
rs1385618025 937 dbSNP
rs1424011940 940 dbSNP
rs1162517359 941 dbSNP
rs1038988060 942 dbSNP
rs897057264 943 dbSNP
rs1456717541 947 dbSNP
rs1240706661 948 dbSNP
rs998141634 949 dbSNP
rs113191461 950 dbSNP
rs375568160 952 dbSNP
rs889632362 955 dbSNP
rs1006616968 956 dbSNP
rs199576341 956 dbSNP
rs1237919701 960 dbSNP
rs1032782614 963 dbSNP
rs1463129864 965 dbSNP
rs113216805 972 dbSNP
rs779551528 975 dbSNP
rs1020406829 977 dbSNP
rs140956529 977 dbSNP
rs1056390486 979 dbSNP
rs971616127 981 dbSNP
rs573202997 985 dbSNP
rs542517908 986 dbSNP
rs1434506830 988 dbSNP
rs1386600764 991 dbSNP
rs562401762 993 dbSNP
rs1012275393 995 dbSNP
rs531089631 1004 dbSNP
rs927430391 1006 dbSNP
rs868764581 1007 dbSNP
rs1162442096 1009 dbSNP
rs981189487 1009 dbSNP
rs1414482644 1010 dbSNP
rs1187892317 1011 dbSNP
rs1311141301 1012 dbSNP
rs1249406706 1014 dbSNP
rs1487956401 1015 dbSNP
rs985255417 1015 dbSNP
rs1308779091 1017 dbSNP
rs183022432 1018 dbSNP
rs940800179 1021 dbSNP
rs371314595 1024 dbSNP
rs55887864 1024 dbSNP
rs1000794989 1029 dbSNP
rs1367189594 1030 dbSNP
rs1051022799 1031 dbSNP
rs3832215 1035 dbSNP
rs397934113 1035 dbSNP
rs866092236 1035 dbSNP
rs56197612 1036 dbSNP
rs1427815961 1038 dbSNP
rs1247118010 1039 dbSNP
rs1250242330 1040 dbSNP
rs1391865913 1040 dbSNP
rs1456213245 1041 dbSNP
rs1205170522 1042 dbSNP
rs1432040980 1043 dbSNP
rs1264868493 1045 dbSNP
rs1031368132 1049 dbSNP
rs1443720106 1052 dbSNP
rs1054726519 1056 dbSNP
rs892876120 1058 dbSNP
rs563186488 1060 dbSNP
rs368368463 1069 dbSNP
rs750175723 1069 dbSNP
rs1421524250 1071 dbSNP
rs1429017840 1072 dbSNP
rs532241522 1072 dbSNP
rs1003052820 1078 dbSNP
rs1399630955 1079 dbSNP
rs1307185082 1080 dbSNP
rs1407702800 1082 dbSNP
rs1372353924 1087 dbSNP
rs552029959 1087 dbSNP
rs1034584425 1089 dbSNP
rs1465459614 1090 dbSNP
rs1375478099 1094 dbSNP
rs1177588118 1095 dbSNP
rs1480599913 1100 dbSNP
rs878956440 1102 dbSNP
rs958971494 1103 dbSNP
rs1464327212 1104 dbSNP
rs1254376530 1106 dbSNP
rs1196931622 1108 dbSNP
rs1254403650 1109 dbSNP
rs975768183 1109 dbSNP
rs1235426221 1114 dbSNP
rs922918341 1116 dbSNP
rs1447704423 1120 dbSNP
rs531631961 1122 dbSNP
rs1352143463 1123 dbSNP
rs1364754080 1124 dbSNP
rs746611789 1125 dbSNP
rs1304089799 1129 dbSNP
rs1215650696 1132 dbSNP
rs1387486639 1134 dbSNP
rs1156457676 1142 dbSNP
rs1473354400 1143 dbSNP
rs565670632 1144 dbSNP
rs911398327 1153 dbSNP
rs1365969180 1157 dbSNP
rs10638799 1160 dbSNP
rs1243713627 1160 dbSNP
rs1338645759 1160 dbSNP
rs1439789308 1160 dbSNP
rs941491895 1161 dbSNP
rs1277092560 1166 dbSNP
rs972566276 1170 dbSNP
rs200240335 1172 dbSNP
rs923238834 1172 dbSNP
rs1224978648 1173 dbSNP
rs1159522608 1174 dbSNP
rs1263323836 1176 dbSNP
rs575026903 1176 dbSNP
rs1038530217 1178 dbSNP
rs918880610 1180 dbSNP
rs1247555979 1182 dbSNP
rs1445743401 1182 dbSNP
rs1186752546 1183 dbSNP
rs1207806093 1183 dbSNP
rs1448962040 1185 dbSNP
rs578226135 1188 dbSNP
rs911127294 1190 dbSNP
rs1266960167 1194 dbSNP
rs1486189129 1195 dbSNP
rs1185859063 1196 dbSNP
rs1294766272 1197 dbSNP
rs1436569382 1207 dbSNP
rs930211402 1207 dbSNP
rs766234734 1210 dbSNP
rs1322420818 1211 dbSNP
rs751097260 1212 dbSNP
rs896464899 1216 dbSNP
rs1178886792 1223 dbSNP
rs547880212 1226 dbSNP
rs757216357 1226 dbSNP
rs1166810790 1229 dbSNP
rs753382197 1230 dbSNP
rs1430290787 1231 dbSNP
rs1242948596 1233 dbSNP
rs375252094 1236 dbSNP
rs1450066180 1241 dbSNP
rs1270860690 1242 dbSNP
rs1174465852 1243 dbSNP
rs528105037 1244 dbSNP
rs1432116312 1257 dbSNP
rs1325488267 1261 dbSNP
rs547979161 1261 dbSNP
rs1298061116 1263 dbSNP
rs1337804497 1274 dbSNP
rs781066188 1274 dbSNP
rs747969045 1280 dbSNP
rs1406205675 1282 dbSNP
rs948160887 1284 dbSNP
rs879824030 1287 dbSNP
rs1058378 1288 dbSNP
rs1305344832 1288 dbSNP
rs752432871 1291 dbSNP
rs903927925 1294 dbSNP
rs1001145201 1298 dbSNP
rs1006924323 1299 dbSNP
rs1420382007 1300 dbSNP
rs1030814538 1302 dbSNP
rs1016398371 1304 dbSNP
rs1477163436 1304 dbSNP
rs868153550 1313 dbSNP
rs1199904792 1314 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 5915.0
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 "PAR-CLIP data was present in GSM714645. 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 HEK293
Disease 5915.0
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 GSM1065667. RNA binding protein: AGO1. Condition:4-thiouridine "PAR-CLIP data was present in GSM1065668. RNA binding protein: AGO1. Condition:4-thiouridine "PAR-CLIP data was present in GSM1065669. RNA binding protein: AGO1. Condition:4-thiouridine ...

- Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature.

Article - Memczak S; Jens M; Elefsinioti A; Torti F; et al.
- Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
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_000965 | 3UTR | UGCAAGAAAAAACAUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_016152 | 3UTR | UGCAAGAAAAAACAUUUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_016152 | 3UTR | GCAAGAAAAAACAUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM545214
Method / RBP PAR-CLIP / AGO3
Cell line / Condition HEK293 / Control
Location of target site ENST00000437042.2 | 3UTR | AUUUUUACUGCUGCUUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000437042.2 | 3UTR | AAAAACAUUUUUACUGCUGCUUA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM545217
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-7 transfection
Location of target site ENST00000437042.2 | 3UTR | AUUUUUACUGCUGCUUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000437042.2 | 3UTR | AAAAAACAUUUUUACUGCUGCUUAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM714645
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repB
Location of target site ENST00000437042.2 | 3UTR | AAAAAACAUUUUUACUGCUGCUUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 9 for dataset GSM1065667
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_6
Location of target site ENST00000437042.2 | 3UTR | CAUUUUUACUGCUGCUUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 10 for dataset GSM1065668
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_7
Location of target site ENST00000437042.2 | 3UTR | AUUUUUACUGCUGCUUA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 11 for dataset GSM1065669
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_8
Location of target site ENST00000437042.2 | 3UTR | CAUUUUUACUGCUGCUUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
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
107 hsa-miR-4307 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT091681 RARB retinoic acid receptor beta 2 6
MIRT097311 AGGF1 angiogenic factor with G-patch and FHA domains 1 2 2
MIRT099878 SOX4 SRY-box 4 2 2
MIRT114514 ARF6 ADP ribosylation factor 6 2 2
MIRT163479 WNT5A Wnt family member 5A 2 2
MIRT186633 COX20 COX20, cytochrome c oxidase assembly factor 2 8
MIRT194921 TNRC6A trinucleotide repeat containing 6A 2 2
MIRT230189 AKAP17A A-kinase anchoring protein 17A 2 2
MIRT281397 MAPK6 mitogen-activated protein kinase 6 2 2
MIRT328018 RLIM ring finger protein, LIM domain interacting 2 2
MIRT354896 SEC62 SEC62 homolog, preprotein translocation factor 2 2
MIRT361422 PNRC1 proline rich nuclear receptor coactivator 1 2 2
MIRT442526 MOB3B MOB kinase activator 3B 2 2
MIRT442629 NUDT12 nudix hydrolase 12 2 2
MIRT442685 SLC39A9 solute carrier family 39 member 9 2 2
MIRT444131 BRCA2 BRCA2, DNA repair associated 2 2
MIRT444174 RBM7 RNA binding motif protein 7 2 2
MIRT446045 TPR translocated promoter region, nuclear basket protein 2 2
MIRT447984 LINC00598 long intergenic non-protein coding RNA 598 2 2
MIRT460527 S100A11 S100 calcium binding protein A11 2 4
MIRT466861 STX6 syntaxin 6 2 2
MIRT468806 SAP18 Sin3A associated protein 18 2 6
MIRT480269 C8orf4 chromosome 8 open reading frame 4 2 2
MIRT493119 MKNK2 MAP kinase interacting serine/threonine kinase 2 2 6
MIRT499168 YRDC yrdC N6-threonylcarbamoyltransferase domain containing 2 8
MIRT500507 ZBTB34 zinc finger and BTB domain containing 34 2 2
MIRT503021 CAND1 cullin associated and neddylation dissociated 1 2 2
MIRT505314 TOR1AIP2 torsin 1A interacting protein 2 2 2
MIRT506123 PMAIP1 phorbol-12-myristate-13-acetate-induced protein 1 2 8
MIRT509346 CYP20A1 cytochrome P450 family 20 subfamily A member 1 2 4
MIRT509446 POU2F2 POU class 2 homeobox 2 2 6
MIRT509598 PEX26 peroxisomal biogenesis factor 26 2 2
MIRT516008 GPN2 GPN-loop GTPase 2 2 2
MIRT516120 SRPX2 sushi repeat containing protein, X-linked 2 2 4
MIRT522126 NELL2 neural EGFL like 2 2 2
MIRT523018 IL1RAPL1 interleukin 1 receptor accessory protein like 1 2 4
MIRT524015 DONSON downstream neighbor of SON 2 2
MIRT526307 JAKMIP2 janus kinase and microtubule interacting protein 2 2 2
MIRT526789 SGCD sarcoglycan delta 2 2
MIRT529141 CLCC1 chloride channel CLIC like 1 2 2
MIRT531336 GDPD1 glycerophosphodiester phosphodiesterase domain containing 1 2 2
MIRT531573 ILDR1 immunoglobulin like domain containing receptor 1 2 2
MIRT531831 MTPAP mitochondrial poly(A) polymerase 2 2
MIRT534994 PRR11 proline rich 11 2 6
MIRT535419 PDZD8 PDZ domain containing 8 2 2
MIRT535534 PAK2 p21 (RAC1) activated kinase 2 2 2
MIRT536649 INIP INTS3 and NABP interacting protein 2 2
MIRT543498 MDM2 MDM2 proto-oncogene 2 4
MIRT545392 PM20D2 peptidase M20 domain containing 2 2 2
MIRT545881 ZNF200 zinc finger protein 200 2 4
MIRT547931 HNRNPR heterogeneous nuclear ribonucleoprotein R 2 2
MIRT548109 GDAP2 ganglioside induced differentiation associated protein 2 2 2
MIRT549370 ANKS1A ankyrin repeat and sterile alpha motif domain containing 1A 2 2
MIRT549934 RPL7L1 ribosomal protein L7 like 1 2 4
MIRT550455 MYADM myeloid associated differentiation marker 2 4
MIRT550640 AR androgen receptor 2 2
MIRT550815 FAM229B family with sequence similarity 229 member B 2 2
MIRT551258 OPCML opioid binding protein/cell adhesion molecule like 2 2
MIRT551768 MED21 mediator complex subunit 21 2 2
MIRT552214 ATP5S ATP synthase, H+ transporting, mitochondrial Fo complex subunit s (factor B) 2 2
MIRT555472 POGZ pogo transposable element derived with ZNF domain 2 2
MIRT556008 MZT1 mitotic spindle organizing protein 1 2 2
MIRT557878 FEM1B fem-1 homolog B 2 4
MIRT558486 DBN1 drebrin 1 2 2
MIRT560859 GAL3ST3 galactose-3-O-sulfotransferase 3 2 2
MIRT561521 AZF1 azoospermia factor 1 2 2
MIRT562090 KIAA0895 KIAA0895 2 2
MIRT563065 ZNF28 zinc finger protein 28 2 2
MIRT563487 ZWINT ZW10 interacting kinetochore protein 2 2
MIRT564286 CTCF CCCTC-binding factor 2 2
MIRT565627 SLC16A1 solute carrier family 16 member 1 2 2
MIRT566508 PAWR pro-apoptotic WT1 regulator 2 2
MIRT566978 LBR lamin B receptor 2 2
MIRT567180 IGFBP5 insulin like growth factor binding protein 5 2 2
MIRT568432 GDNF glial cell derived neurotrophic factor 2 2
MIRT570092 KANSL1L KAT8 regulatory NSL complex subunit 1 like 2 2
MIRT570565 PABPC1 poly(A) binding protein cytoplasmic 1 2 2
MIRT571385 JKAMP JNK1/MAPK8-associated membrane protein 2 2
MIRT572053 GPATCH8 G-patch domain containing 8 2 2
MIRT572333 CACNA1A calcium voltage-gated channel subunit alpha1 A 2 2
MIRT574528 PEG10 paternally expressed 10 2 2
MIRT575818 Igfbp4 insulin-like growth factor binding protein 4 2 2
MIRT608587 PPP2R1B protein phosphatase 2 scaffold subunit Abeta 2 4
MIRT610442 TSPAN15 tetraspanin 15 2 2
MIRT614994 GABRB1 gamma-aminobutyric acid type A receptor beta1 subunit 2 2
MIRT615014 ERGIC2 ERGIC and golgi 2 2 2
MIRT615078 CISD3 CDGSH iron sulfur domain 3 2 2
MIRT616180 SYT7 synaptotagmin 7 2 2
MIRT617191 CDH13 cadherin 13 2 2
MIRT617287 GTF2H3 general transcription factor IIH subunit 3 2 2
MIRT618714 ESD esterase D 2 2
MIRT621825 TIMM8B translocase of inner mitochondrial membrane 8 homolog B 2 2
MIRT624139 DLX3 distal-less homeobox 3 2 2
MIRT625991 IBA57 IBA57 homolog, iron-sulfur cluster assembly 2 2
MIRT626344 BLOC1S4 biogenesis of lysosomal organelles complex 1 subunit 4 2 2
MIRT634899 ZNF701 zinc finger protein 701 2 2
MIRT637848 SLC2A9 solute carrier family 2 member 9 2 2
MIRT639514 FYB FYN binding protein 1 2 2
MIRT642468 RSL1D1 ribosomal L1 domain containing 1 2 2
MIRT653670 SLC26A7 solute carrier family 26 member 7 2 2
MIRT655192 PHAX phosphorylated adaptor for RNA export 2 2
MIRT657011 KCNMB4 potassium calcium-activated channel subfamily M regulatory beta subunit 4 2 2
MIRT661008 ABCB11 ATP binding cassette subfamily B member 11 2 2
MIRT665816 TMEM161B transmembrane protein 161B 2 2
MIRT683852 ZNF208 zinc finger protein 208 2 2
MIRT700436 PURB purine rich element binding protein B 2 2
MIRT700517 PTPN14 protein tyrosine phosphatase, non-receptor type 14 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-4307 Tripterygium wilfordii Hook F resistant tissue
hsa-miR-4307 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4307 Neoadjuvant chemotherapy sensitive tissue (breast cancer)
hsa-miR-4307 Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide/Methotrexate/Gemcitabine sensitive cell line (Bats-72)

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