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 ZNF200   
Synonyms -
Description zinc finger protein 200
Transcript NM_001145446   
Other Transcripts NM_001145447 , NM_001145448 , NM_003454 , NM_198087 , NM_198088   
Expression
Putative miRNA Targets on ZNF200
3'UTR of ZNF200
(miRNA target sites are highlighted)
>ZNF200|NM_001145446|3'UTR
   1 TACTGGGAACCCTTTCTGGGTCTGATGGTGCTGCCTCAACCTGAGAGCTTTCATAAGTAGTTCTGAATTCCCAAGCTGCC
  81 TAAAAAGGTATAAATGTGTAAAAATCTCATTATTGCCAAAATTGGATAAATGCCCATCTTAGCTAAAACCTCAAATTGCT
 161 AGAAAATTCACAGGGAAGAAAACATTTCAAGGGCTATACCTCAGCATCTAGGCTTTTTGGACTAAGGAGCTTTCCTTTTT
 241 GAAGTTATATGATAATGTACAGGTCACAGATCCCCTTTCCCAACACTTTGAAGATGAATCTGGAGTCTGCTTACTTGGAA
 321 GGCAAAGAGTGACTTGTGTCTATTGAAAGTATATCCGTTTTCCCCCCACATGGGGATTCATACTTGAGAAATAGTGCAAA
 401 GATGCTTATCTGGAACTGTGTTCTGGTGAAAGAACCAAATTACTGGCTTGTTAGCCAACAGCTTCTGATAGCAATTCATA
 481 TAACCCTCTAAGAATACCTGTTTAAGTCTTGAGTGTTGAAAGGAATTGTTTACTTTGGAATATAGGAAAACAGTTGAATG
 561 TCAGACTCTCATTTGTATGTGATCTAAATTTGCAATCAATTTCAATAATATTTACAATTTGTGATAAAACTGACTTTTAC
 641 AGATTCCTTTTCACAACATAATTTAGGTGTCTACTGTTCTTATTGTATTTTGTTCTGCTGTTGATCTCTCCAGCAGCCGT
 721 CTCATGCTTCTCCCTTGCTAAAAGAAGTTTGGATTACTCAGGCAGGGCCATCCAGCCCCACCACTAGAAAAGCTCTTCAG
 801 AATCTTGTCCCTCTGTTGAGCCCAGATCTCATGTGCTACGAAGGAAACCCCAAGACCCAGAGAGGAAGGGTCAACCTGGA
 881 GGCAGGAAAAAGTTGGCTTGGATCCATGTCTCATCAATAACCTTACCATATGCTTAGGTCCCCTCTATGCTGTCATCAGA
 961 CCTTTGGCAATGGGGTGGTCACTACCTCACAAGGCAAAGTGTTGTATGATTAGAAATTACGTCTCCAGTGGTTAGCTCAC
1041 ATTGCCTCTCAAGAGACAGGTTTCCAGGTGTCTTCATTGTAGTGGGTATTAATTGTCTTCAGCCTCTTGATATCCATACC
1121 TTCCTGTCCTCTGCCTAGAAGCAAGGCCAGCGGTGCCTTTACGGACTGATCGTGTGGTGCGATTTAGGGATTCTTCAGTT
1201 TTGCTTGCTTTAGGTTTCCAAAAGTTATACATTGGTGTTTTGATTGGAATAAAGAAATCCTATAAGCTATTTGGGAAAAA
1281 TTATAGTGTATGTTTCCCATCCAGAAACATGCCTTTCTATTTATTAGAGTATTATATTCCTGTGAAAATTTTTCTAATTT
1361 TCTTCACTTGTTTTACACAATTTTGTTATTGTAGTTTTTTCCATTATATTTTTATAGTTGATTATTGCTTTTACATGGGA
1441 AAGTTATTTTTAATTATATATTTGTATAGTCATCTCACTGTTGTTAATTTTCAATAGTTTGTTGGTTTAGTTCTGTTAAC
1521 TTTTGGTAAAATGACACCATCTACAAAGAATAGTTTTTGTTTCTTGC
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' ccuuUGUCC--UUUUUUGUAa 5'
              |||||  |:||||||| 
Target 5' attcACAGGGAAGAAAACATt 3'
166 - 186 161.00 -13.00
2
miRNA  3' ccUUUGUCCUUUUUUGUaa 5'
            :||:|  ::||||||  
Target 5' tgGAATATAGGAAAACAgt 3'
536 - 554 133.00 -10.50
3
miRNA  3' ccuuuGUCCUUUUUUGUAa 5'
               ::||||||| :|| 
Target 5' ctattTGGGAAAAATTATa 3'
1267 - 1285 114.00 -5.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30467848 12 COSMIC
COSN27005903 16 COSMIC
COSN31553179 89 COSMIC
COSN31613008 124 COSMIC
COSN30462332 138 COSMIC
COSN31600145 153 COSMIC
COSN31604252 183 COSMIC
COSN5406581 196 COSMIC
COSN8231870 248 COSMIC
COSN29993651 326 COSMIC
COSN6546142 367 COSMIC
COSN5759902 783 COSMIC
COSN20960376 807 COSMIC
COSN22469710 862 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1441940937 1 dbSNP
rs372250551 3 dbSNP
rs1239056421 6 dbSNP
rs1404884909 11 dbSNP
rs750254728 13 dbSNP
rs1213372273 22 dbSNP
rs1473277792 25 dbSNP
rs1057070657 28 dbSNP
rs1472854674 29 dbSNP
rs764561810 33 dbSNP
rs761055013 34 dbSNP
rs369689299 40 dbSNP
rs767714437 41 dbSNP
rs916821191 47 dbSNP
rs759738060 50 dbSNP
rs992436908 62 dbSNP
rs35985482 66 dbSNP
rs1453814879 70 dbSNP
rs1160568691 78 dbSNP
rs1400812523 79 dbSNP
rs574939505 82 dbSNP
rs1335665170 84 dbSNP
rs75276653 88 dbSNP
rs182690348 91 dbSNP
rs967491291 92 dbSNP
rs1352116952 94 dbSNP
rs879081757 95 dbSNP
rs565646249 103 dbSNP
rs931494432 104 dbSNP
rs1342836961 106 dbSNP
rs1021390507 108 dbSNP
rs777799548 110 dbSNP
rs1486119053 115 dbSNP
rs1204709995 125 dbSNP
rs972510032 133 dbSNP
rs1484253202 134 dbSNP
rs772322941 136 dbSNP
rs192270233 137 dbSNP
rs1269247191 138 dbSNP
rs1192892492 142 dbSNP
rs538653050 144 dbSNP
rs1425338589 148 dbSNP
rs1018128787 150 dbSNP
rs1305827093 152 dbSNP
rs1372137850 154 dbSNP
rs575688095 161 dbSNP
rs1322708471 169 dbSNP
rs1329263255 170 dbSNP
rs569725344 171 dbSNP
rs890949812 174 dbSNP
rs1047297321 179 dbSNP
rs796338443 181 dbSNP
rs1227884436 196 dbSNP
rs1272790308 200 dbSNP
rs1344627867 201 dbSNP
rs1196721551 202 dbSNP
rs994035518 205 dbSNP
rs1486235002 208 dbSNP
rs898545992 213 dbSNP
rs748411505 214 dbSNP
rs953959311 223 dbSNP
rs1166221467 224 dbSNP
rs1391610167 229 dbSNP
rs549904563 230 dbSNP
rs1430075780 231 dbSNP
rs1162429623 234 dbSNP
rs1032702312 238 dbSNP
rs1221855719 244 dbSNP
rs1388386884 245 dbSNP
rs1324151090 247 dbSNP
rs564285809 248 dbSNP
rs966558068 249 dbSNP
rs779227622 254 dbSNP
rs1325251516 255 dbSNP
rs754306814 257 dbSNP
rs142446752 264 dbSNP
rs1382354802 265 dbSNP
rs188001665 275 dbSNP
rs924217737 276 dbSNP
rs978639871 278 dbSNP
rs895920784 279 dbSNP
rs780619321 283 dbSNP
rs1186109875 285 dbSNP
rs1334285551 287 dbSNP
rs373161780 289 dbSNP
rs1428676064 294 dbSNP
rs1470727369 297 dbSNP
rs1001967166 303 dbSNP
rs1459276755 303 dbSNP
rs183784756 306 dbSNP
rs1455626922 307 dbSNP
rs989881751 307 dbSNP
rs1367441746 311 dbSNP
rs1312322333 313 dbSNP
rs1474288315 315 dbSNP
rs1247414464 317 dbSNP
rs1049160387 318 dbSNP
rs931490684 321 dbSNP
rs1207395129 322 dbSNP
rs1269416940 323 dbSNP
rs963678545 327 dbSNP
rs1037205470 329 dbSNP
rs1253604161 330 dbSNP
rs1017929282 332 dbSNP
rs1188370847 336 dbSNP
rs943746700 340 dbSNP
rs752563064 344 dbSNP
rs1471529141 352 dbSNP
rs986436523 355 dbSNP
rs369388362 356 dbSNP
rs759777007 359 dbSNP
rs192381194 361 dbSNP
rs532382558 364 dbSNP
rs1416929300 367 dbSNP
rs1263965989 368 dbSNP
rs759474395 369 dbSNP
rs1227044254 370 dbSNP
rs925223208 371 dbSNP
rs979795045 375 dbSNP
rs966608503 383 dbSNP
rs1337839973 386 dbSNP
rs17136280 395 dbSNP
rs543602600 397 dbSNP
rs867006093 400 dbSNP
rs1017434813 406 dbSNP
rs1012374360 413 dbSNP
rs960100402 416 dbSNP
rs1036205238 417 dbSNP
rs1184132763 422 dbSNP
rs1001539162 423 dbSNP
rs1408601007 432 dbSNP
rs905893225 434 dbSNP
rs1175448182 436 dbSNP
rs1055996555 450 dbSNP
rs1376004370 456 dbSNP
rs1048397038 458 dbSNP
rs1313740321 465 dbSNP
rs749938111 466 dbSNP
rs1056437320 478 dbSNP
rs897430669 479 dbSNP
rs939349699 480 dbSNP
rs574970457 481 dbSNP
rs1298470823 486 dbSNP
rs1313450164 487 dbSNP
rs1406407989 489 dbSNP
rs1330266899 490 dbSNP
rs1042671740 496 dbSNP
rs766999534 499 dbSNP
rs890861998 508 dbSNP
rs1488079760 515 dbSNP
rs1049984366 517 dbSNP
rs1265296755 523 dbSNP
rs143868755 528 dbSNP
rs187400675 532 dbSNP
rs1389758155 534 dbSNP
rs572614356 536 dbSNP
rs1384712868 537 dbSNP
rs1172980102 542 dbSNP
rs989849302 543 dbSNP
rs183052089 547 dbSNP
rs1436309438 552 dbSNP
rs538589953 554 dbSNP
rs1446490110 557 dbSNP
rs117320716 560 dbSNP
rs1181286367 566 dbSNP
rs556283783 567 dbSNP
rs1362580737 568 dbSNP
rs1275504398 571 dbSNP
rs1196905250 573 dbSNP
rs991931971 581 dbSNP
rs1320914401 592 dbSNP
rs955096726 593 dbSNP
rs1356315876 595 dbSNP
rs1025964731 599 dbSNP
rs1247625387 602 dbSNP
rs980559815 603 dbSNP
rs1247561739 604 dbSNP
rs1447813020 605 dbSNP
rs115981169 607 dbSNP
rs1027376638 608 dbSNP
rs995521105 610 dbSNP
rs1405168793 611 dbSNP
rs962857460 611 dbSNP
rs1308099218 616 dbSNP
rs897398143 633 dbSNP
rs1439490816 635 dbSNP
rs1015879431 636 dbSNP
rs1337343949 636 dbSNP
rs567432453 645 dbSNP
rs1008398464 647 dbSNP
rs1385822809 652 dbSNP
rs375050722 653 dbSNP
rs547248164 655 dbSNP
rs368904183 657 dbSNP
rs1226377271 664 dbSNP
rs747638449 665 dbSNP
rs527497249 673 dbSNP
rs1363684300 675 dbSNP
rs1267519431 683 dbSNP
rs371574392 683 dbSNP
rs1426637394 685 dbSNP
rs932356080 687 dbSNP
rs903621932 692 dbSNP
rs1180478411 697 dbSNP
rs1420483124 701 dbSNP
rs1035114867 708 dbSNP
rs766185683 710 dbSNP
rs1159105258 715 dbSNP
rs143368425 718 dbSNP
rs763929051 719 dbSNP
rs902534206 723 dbSNP
rs1445443532 726 dbSNP
rs1043030472 727 dbSNP
rs57324828 728 dbSNP
rs1227656749 733 dbSNP
rs532370870 741 dbSNP
rs1286408128 747 dbSNP
rs138019409 750 dbSNP
rs766084427 753 dbSNP
rs992069228 765 dbSNP
rs1183032654 772 dbSNP
rs147368795 780 dbSNP
rs1259990102 781 dbSNP
rs1486221424 782 dbSNP
rs530107713 786 dbSNP
rs561446982 790 dbSNP
rs1471474070 791 dbSNP
rs541224040 792 dbSNP
rs980647944 794 dbSNP
rs1412342993 798 dbSNP
rs553104223 799 dbSNP
rs1375793983 806 dbSNP
rs910959215 809 dbSNP
rs1337461373 814 dbSNP
rs1442848541 820 dbSNP
rs1280156592 821 dbSNP
rs986537719 822 dbSNP
rs772960982 828 dbSNP
rs190829015 831 dbSNP
rs1282702867 832 dbSNP
rs759447298 833 dbSNP
rs972820194 839 dbSNP
rs962620403 840 dbSNP
rs1405438783 848 dbSNP
rs1194996311 850 dbSNP
rs1395283533 852 dbSNP
rs1428785558 853 dbSNP
rs1166413045 855 dbSNP
rs1398388046 859 dbSNP
rs909821252 859 dbSNP
rs1322848489 871 dbSNP
rs1366296393 874 dbSNP
rs1158533376 878 dbSNP
rs1438779136 879 dbSNP
rs35901599 884 dbSNP
rs990622901 889 dbSNP
rs1305796531 895 dbSNP
rs1371994157 896 dbSNP
rs1227946098 902 dbSNP
rs114316315 903 dbSNP
rs1341937481 905 dbSNP
rs1196842332 907 dbSNP
rs773313055 912 dbSNP
rs772095242 913 dbSNP
rs1467561622 917 dbSNP
rs1194955483 921 dbSNP
rs1283740736 921 dbSNP
rs577299375 922 dbSNP
rs545756459 926 dbSNP
rs576091276 928 dbSNP
rs1427562672 931 dbSNP
rs1190611880 937 dbSNP
rs142816870 940 dbSNP
rs867762743 941 dbSNP
rs997051024 947 dbSNP
rs1388473800 949 dbSNP
rs1463008939 949 dbSNP
rs1327929209 950 dbSNP
rs1395327892 952 dbSNP
rs1434582044 957 dbSNP
rs748321751 962 dbSNP
rs59243815 966 dbSNP
rs796467978 966 dbSNP
rs779137637 970 dbSNP
rs768946804 973 dbSNP
rs1284032830 975 dbSNP
rs1009177884 978 dbSNP
rs764653703 982 dbSNP
rs1273221600 983 dbSNP
rs1464077723 986 dbSNP
rs1242023682 997 dbSNP
rs1202897300 999 dbSNP
rs1011326236 1004 dbSNP
rs1447281008 1006 dbSNP
rs1448220580 1020 dbSNP
rs546183813 1021 dbSNP
rs138576394 1023 dbSNP
rs1296687223 1028 dbSNP
rs1453103009 1029 dbSNP
rs1007663279 1034 dbSNP
rs890664450 1037 dbSNP
rs1321193237 1038 dbSNP
rs1284906857 1040 dbSNP
rs926572559 1041 dbSNP
rs1223870792 1044 dbSNP
rs1333859948 1044 dbSNP
rs115320420 1046 dbSNP
rs1294413257 1053 dbSNP
rs1329130876 1057 dbSNP
rs1262045926 1067 dbSNP
rs1287042104 1070 dbSNP
rs930517839 1076 dbSNP
rs533703332 1077 dbSNP
rs1486547365 1080 dbSNP
rs920003777 1082 dbSNP
rs1346982441 1084 dbSNP
rs536071673 1091 dbSNP
rs1250953020 1095 dbSNP
rs933724481 1097 dbSNP
rs908505530 1107 dbSNP
rs1319235269 1113 dbSNP
rs1469451441 1115 dbSNP
rs1373919018 1116 dbSNP
rs1416986507 1119 dbSNP
rs571157483 1124 dbSNP
rs918335282 1128 dbSNP
rs986819808 1135 dbSNP
rs1390175150 1142 dbSNP
rs1036678495 1147 dbSNP
rs761447506 1151 dbSNP
rs567485080 1152 dbSNP
rs997418524 1155 dbSNP
rs1349656978 1156 dbSNP
rs61396108 1157 dbSNP
rs990757042 1159 dbSNP
rs1479585971 1160 dbSNP
rs150175768 1162 dbSNP
rs185668637 1163 dbSNP
rs117066731 1171 dbSNP
rs371688646 1172 dbSNP
rs1354326772 1177 dbSNP
rs1045030236 1178 dbSNP
rs1300451083 1179 dbSNP
rs1374748023 1180 dbSNP
rs561177467 1181 dbSNP
rs181555065 1192 dbSNP
rs1021474760 1196 dbSNP
rs1010895709 1199 dbSNP
rs1372716942 1203 dbSNP
rs958056713 1209 dbSNP
rs930465346 1215 dbSNP
rs1305584876 1219 dbSNP
rs1264580325 1220 dbSNP
rs140877275 1221 dbSNP
rs1007800449 1223 dbSNP
rs148311567 1228 dbSNP
rs746397368 1231 dbSNP
rs908643649 1232 dbSNP
rs994093266 1237 dbSNP
rs1419202459 1239 dbSNP
rs955438294 1240 dbSNP
rs565512133 1246 dbSNP
rs1173051570 1254 dbSNP
rs781590438 1258 dbSNP
rs1461436086 1262 dbSNP
rs530563917 1266 dbSNP
rs896876343 1267 dbSNP
rs144991775 1269 dbSNP
rs968707173 1271 dbSNP
rs1404236836 1272 dbSNP
rs1022394614 1277 dbSNP
rs1470541481 1281 dbSNP
rs550974017 1282 dbSNP
rs1009704395 1284 dbSNP
rs1296113155 1286 dbSNP
rs576782474 1290 dbSNP
rs1231394316 1292 dbSNP
rs1034755895 1296 dbSNP
rs1168989536 1301 dbSNP
rs1214440739 1302 dbSNP
rs1241721121 1308 dbSNP
rs1485046628 1311 dbSNP
rs563212533 1312 dbSNP
rs904893128 1313 dbSNP
rs1163445741 1316 dbSNP
rs1420706839 1319 dbSNP
rs1461491133 1324 dbSNP
rs1317098840 1326 dbSNP
rs542219009 1327 dbSNP
rs927869153 1331 dbSNP
rs141175891 1333 dbSNP
rs1182484364 1335 dbSNP
rs945231901 1336 dbSNP
rs113439786 1339 dbSNP
rs370109019 1339 dbSNP
rs1183756819 1340 dbSNP
rs899101182 1348 dbSNP
rs913969920 1349 dbSNP
rs1295017176 1352 dbSNP
rs573586665 1360 dbSNP
rs1036172318 1377 dbSNP
rs1283729184 1378 dbSNP
rs1249365543 1380 dbSNP
rs1206570719 1382 dbSNP
rs1243006746 1383 dbSNP
rs940536729 1387 dbSNP
rs771460742 1389 dbSNP
rs553584338 1395 dbSNP
rs1245423774 1401 dbSNP
rs1260218061 1401 dbSNP
rs1475858859 1403 dbSNP
rs575822208 1404 dbSNP
rs190705795 1420 dbSNP
rs934075568 1423 dbSNP
rs986099276 1424 dbSNP
rs1159419017 1425 dbSNP
rs1374514484 1428 dbSNP
rs557703825 1430 dbSNP
rs1314555273 1432 dbSNP
rs537662522 1435 dbSNP
rs1444775445 1439 dbSNP
rs1441395952 1444 dbSNP
rs1278973870 1446 dbSNP
rs1371303109 1453 dbSNP
rs1225578733 1460 dbSNP
rs569013890 1462 dbSNP
rs368683192 1466 dbSNP
rs1209171715 1467 dbSNP
rs1163486061 1468 dbSNP
rs993665995 1474 dbSNP
rs975837169 1478 dbSNP
rs1422226969 1482 dbSNP
rs1386493736 1483 dbSNP
rs532623371 1484 dbSNP
rs1230639231 1486 dbSNP
rs1418103935 1486 dbSNP
rs1470860209 1492 dbSNP
rs1247957047 1493 dbSNP
rs915523084 1494 dbSNP
rs898009479 1495 dbSNP
rs1015339926 1496 dbSNP
rs1005337960 1500 dbSNP
rs11228 1501 dbSNP
rs1054755427 1502 dbSNP
rs1356260485 1503 dbSNP
rs1034724829 1513 dbSNP
rs1310164541 1513 dbSNP
rs1370446733 1513 dbSNP
rs1268167045 1515 dbSNP
rs1232392319 1516 dbSNP
rs1306024543 1519 dbSNP
rs151301181 1521 dbSNP
rs1195625127 1524 dbSNP
rs1271473538 1525 dbSNP
rs1440110735 1536 dbSNP
rs114194667 1544 dbSNP
rs1023278272 1548 dbSNP
rs1452120950 1551 dbSNP
rs1195134430 1554 dbSNP
rs567692085 1567 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 7752.0
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]
CLIP-seq Support 1 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000396868.3 | 3UTR | AAAACAUUUCAAGGGCUAUACCUCAGCAUCUA
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 ENST00000396868.3 | 3UTR | AAAACAUUUCAAGGGCUAUACCUCAGCAUCUAG
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 GSM714645
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repB
Location of target site ENST00000396868.3 | 3UTR | AAAACAUUUCAAGGGCUAUACCUCAGCAUCUAG
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
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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