miRTarBase - #MIRT555975


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pre-miRNA Information
pre-miRNA hsa-mir-938   
Genomic Coordinates chr10: 29602264 - 29602346
Synonyms MIRN938, hsa-mir-938, MIR938
Description Homo sapiens miR-938 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-938
Sequence 15| UGCCCUUAAAGGUGAACCCAGU |36
Evidence Experimental
Experiments Cloned
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN28704008 2 COSMIC
COSN31533921 5 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs12416605 2 dbSNP
rs1348880424 3 dbSNP
rs1205636191 4 dbSNP
rs757919276 12 dbSNP
rs754296125 14 dbSNP
rs573596343 17 dbSNP
rs756660742 18 dbSNP
rs753092730 21 dbSNP
Putative Targets

Gene Information
Gene Symbol NPTN   
Synonyms GP55, GP65, SDFR1, SDR1, np55, np65
Description neuroplastin
Transcript NM_001161363   
Other Transcripts NM_001161364 , NM_012428 , NM_017455   
Expression
Putative miRNA Targets on NPTN
3'UTR of NPTN
(miRNA target sites are highlighted)		 
>NPTN|NM_001161363|3'UTR
   1 GTACTGCTTACAATATCTTTAGGTTCCTGAAACTGGTGGCAACATGACCTGCTAAAATTTTCTGCTTGGACCTCTTTGGT
  81 TCTCTCCCCTTTCAAGTGAGCAACACCACAATGACTGTCTAAAGCATGCCTTATTTAGCCTCTCCTGTAAGGGTGATCTA
 161 GCCAGGTACATTTTAAACAATGCTTCAGTGTAGAAGGTGTAAACTATTTTGGGCTTGATGTGCTGTGAATGTTGCTTTTT
 241 TTTTTCCTTTGTTAAAATATTTAAATAGAAGTGAAAAGGTCCTCTGAGGATCAGATCATGCATGCGCCATTTTTTACTTA
 321 ATGCAGCTGTTAAATTGGCAAAGCTCTAAAATGCACTGCTGCCATCTAGTGATACACTTTTGTAAAGTACAGCAAAACCT
 401 ACAGATATATACAGTATATAAATATATATATATATATATTTATATTTTTGGGGGTGGGAGAAATCCAAAATAAAGTAAAT
 481 GCTTGTTTCATTTTTAAGCTGCTGATATTCATTCCTTATTGTATGTTGTCAGATGAGGAAATTGTGCAGTTCTGGTACAT
 561 AAAGATGAGTAATATAAACTGAAATCTATAATTTTAAGGGCTTAACCTGTGACTTTAATAAGCTGGAACAGTCCACTGAA
 641 TGGGTATAATGAATTGCAGTATATACGTATGATTGCTTTTTAAGTGATTATCTTTTCTTCTGTTAAGTCATGTAAATTCA
 721 TAAATCCTTTTGCACTGATGTGTTGAACCTTATTCTTGTACATTCATTCAATCAAGGCAAACTTTTATAATTTTTCTTTT
 801 GTTTCCAATGACCTTGAAATGTTATAGCATGGTAATATTCTATGCAACTATAGTTATACTTTTTGGTTTGACACTGTATT
 881 TTTTCACATTGATTTACTGGTTGATGATAGATTTTATAACCTAACGGTTCTCATGCGGTGCGTAATTGTAGATGCATGTA
 961 CTTGTGTGTTTTGTGTAATTATTGAAGTGCAATGATGTATAAAAAAGTGGATTCACCTGTTTTTAAAAATAAAACATTGA
1041 TAAAAGGTGTTTGGATAATA
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' ugacccAAGUGGAAAUUCCCGu 5'
                | :| :||||||||| 
Target 5' gaaatcTATAATTTTAAGGGCt 3'
 581 - 602 156.00 -12.20
2 
miRNA  3' ugACCCAAGUGGAAAUUCCCGu 5'
            | |  || ||| ||||||: 
Target 5' ttTAGCCTCTCCTGTAAGGGTg 3'
 134 - 155 144.00 -12.70
3 
miRNA  3' ugACCCAAGUGGAAAUUCccgu 5'
            | | ||||::||||||    
Target 5' gcTTGTTTCATTTTTAAGctgc 3'
 481 - 502 116.00 -13.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN8176465 166 COSMIC
COSN26401123 201 COSMIC
COSN8176464 306 COSMIC
COSN5756480 315 COSMIC
COSN23741472 507 COSMIC
COSN1684086 572 COSMIC
COSN1684084 780 COSMIC
COSN26105036 790 COSMIC
COSN31490514 909 COSMIC
COSN28673588 962 COSMIC
COSN8477769 1025 COSMIC
COSN19294450 1106 COSMIC
COSN8477768 1153 COSMIC
COSN31482716 1336 COSMIC
COSN26649855 1377 COSMIC
COSN31579161 1575 COSMIC
COSN31570977 1643 COSMIC
COSN6279719 1705 COSMIC
COSN8590331 1779 COSMIC
COSN31564030 1789 COSMIC
COSN31609906 1890 COSMIC
COSN31565184 1893 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs375565473 1 dbSNP
rs764516729 3 dbSNP
rs373487999 10 dbSNP
rs1357895767 12 dbSNP
rs1313020236 13 dbSNP
rs1336387769 14 dbSNP
rs763262357 14 dbSNP
rs1368320534 19 dbSNP
rs775968558 26 dbSNP
rs1462326108 31 dbSNP
rs1293772434 33 dbSNP
rs773128397 42 dbSNP
rs1447212237 44 dbSNP
rs1338444250 47 dbSNP
rs992276758 48 dbSNP
rs770181597 49 dbSNP
rs759868547 50 dbSNP
rs1398153895 53 dbSNP
rs375541627 56 dbSNP
rs1327595389 62 dbSNP
rs1333536236 63 dbSNP
rs1417099096 65 dbSNP
rs976580162 69 dbSNP
rs959440685 71 dbSNP
rs966115032 71 dbSNP
rs912423081 72 dbSNP
rs1340319621 86 dbSNP
rs1033702854 87 dbSNP
rs1486699476 91 dbSNP
rs1391622222 99 dbSNP
rs985250904 103 dbSNP
rs953991214 104 dbSNP
rs1021477345 108 dbSNP
rs145276366 115 dbSNP
rs903821364 115 dbSNP
rs1374651848 116 dbSNP
rs1475531173 130 dbSNP
rs1296829232 133 dbSNP
rs1409554486 135 dbSNP
rs571447016 151 dbSNP
rs190565866 170 dbSNP
rs1394869680 172 dbSNP
rs1298168638 177 dbSNP
rs1327401454 195 dbSNP
rs1226883108 199 dbSNP
rs186145104 201 dbSNP
rs1040518650 202 dbSNP
rs955721464 205 dbSNP
rs1031303462 212 dbSNP
rs1235080458 212 dbSNP
rs1485303677 212 dbSNP
rs1263517310 215 dbSNP
rs200122152 221 dbSNP
rs1367960273 235 dbSNP
rs1387963058 235 dbSNP
rs567587447 236 dbSNP
rs1455337373 243 dbSNP
rs1173710566 248 dbSNP
rs1394012462 248 dbSNP
rs140941304 249 dbSNP
rs1421132524 257 dbSNP
rs777069389 264 dbSNP
rs768962277 269 dbSNP
rs1386077244 272 dbSNP
rs1382029490 274 dbSNP
rs1319017438 282 dbSNP
rs1373436019 283 dbSNP
rs1044994112 293 dbSNP
rs1235389138 294 dbSNP
rs930324399 297 dbSNP
rs1345838350 298 dbSNP
rs1230891955 304 dbSNP
rs762695808 305 dbSNP
rs1482594745 306 dbSNP
rs918890197 311 dbSNP
rs1246037404 316 dbSNP
rs972398727 317 dbSNP
rs949988606 318 dbSNP
rs917126331 320 dbSNP
rs991301738 322 dbSNP
rs959470428 323 dbSNP
rs888053308 326 dbSNP
rs1453721560 327 dbSNP
rs1157397257 334 dbSNP
rs1049354810 344 dbSNP
rs979485266 351 dbSNP
rs1285924689 355 dbSNP
rs761099645 361 dbSNP
rs968463023 366 dbSNP
rs919253333 367 dbSNP
rs1264360718 372 dbSNP
rs1307857548 380 dbSNP
rs1040372010 392 dbSNP
rs1227769382 399 dbSNP
rs772672764 402 dbSNP
rs944818866 403 dbSNP
rs910623283 408 dbSNP
rs1213882864 412 dbSNP
rs1010275322 418 dbSNP
rs1487327136 420 dbSNP
rs1239075013 424 dbSNP
rs1178395605 425 dbSNP
rs1318389943 427 dbSNP
rs902076583 428 dbSNP
rs1180669998 431 dbSNP
rs1420393937 433 dbSNP
rs7163212 442 dbSNP
rs953895814 453 dbSNP
rs10851862 455 dbSNP
rs144431827 456 dbSNP
rs1048800596 460 dbSNP
rs1372715815 469 dbSNP
rs1409066790 480 dbSNP
rs1286411310 481 dbSNP
rs955945844 496 dbSNP
rs181152849 501 dbSNP
rs1002535701 502 dbSNP
rs1319543924 504 dbSNP
rs777349132 508 dbSNP
rs971584066 509 dbSNP
rs1022703428 510 dbSNP
rs1251329597 511 dbSNP
rs769865004 511 dbSNP
rs1036025545 523 dbSNP
rs1260258272 530 dbSNP
rs149254446 530 dbSNP
rs543632088 534 dbSNP
rs1187640713 535 dbSNP
rs887953331 546 dbSNP
rs917157552 547 dbSNP
rs1171401445 559 dbSNP
rs1343701870 566 dbSNP
rs1427926825 584 dbSNP
rs1049219245 586 dbSNP
rs1314892450 592 dbSNP
rs531840638 594 dbSNP
rs1415391391 596 dbSNP
rs1302036537 607 dbSNP
rs1376723792 607 dbSNP
rs1215895945 610 dbSNP
rs1472178860 616 dbSNP
rs1340785259 619 dbSNP
rs1429737775 627 dbSNP
rs1281891959 630 dbSNP
rs993788304 634 dbSNP
rs1201236780 648 dbSNP
rs781184080 651 dbSNP
rs898068597 653 dbSNP
rs1187281281 664 dbSNP
rs1419043214 666 dbSNP
rs1447929534 668 dbSNP
rs561258295 669 dbSNP
rs1040804535 670 dbSNP
rs1340855433 676 dbSNP
rs190255722 679 dbSNP
rs746323427 679 dbSNP
rs572401689 682 dbSNP
rs944704106 683 dbSNP
rs1289282071 689 dbSNP
rs1363971648 700 dbSNP
rs889089580 700 dbSNP
rs1050481432 710 dbSNP
rs34685693 714 dbSNP
rs1304916592 715 dbSNP
rs1265920024 717 dbSNP
rs1219112725 719 dbSNP
rs946771564 722 dbSNP
rs979961454 723 dbSNP
rs1207708263 725 dbSNP
rs1216913360 732 dbSNP
rs1323719614 733 dbSNP
rs914411205 738 dbSNP
rs1231473461 740 dbSNP
rs1253635993 748 dbSNP
rs1477759436 749 dbSNP
rs968159240 751 dbSNP
rs1331074264 756 dbSNP
rs1296892059 760 dbSNP
rs7168262 765 dbSNP
rs545469477 766 dbSNP
rs770207379 776 dbSNP
rs934608567 776 dbSNP
rs1319889494 783 dbSNP
rs924539745 787 dbSNP
rs981539440 793 dbSNP
rs1455256292 796 dbSNP
rs988147723 798 dbSNP
rs1371028743 799 dbSNP
rs971105955 799 dbSNP
rs1272609144 800 dbSNP
rs1019174547 802 dbSNP
rs1267830138 805 dbSNP
rs578156072 809 dbSNP
rs1007726936 811 dbSNP
rs1193794471 816 dbSNP
rs1022608617 818 dbSNP
rs1245671179 821 dbSNP
rs1196808848 824 dbSNP
rs1187323181 829 dbSNP
rs1471112933 832 dbSNP
rs1182815672 837 dbSNP
rs1410900366 852 dbSNP
rs1455463412 854 dbSNP
rs1461514972 861 dbSNP
rs1390961532 868 dbSNP
rs1027770848 869 dbSNP
rs1199146432 876 dbSNP
rs1320992693 884 dbSNP
rs1355782824 889 dbSNP
rs991239734 893 dbSNP
rs1288309136 894 dbSNP
rs1348966852 901 dbSNP
rs951772438 902 dbSNP
rs751347285 903 dbSNP
rs1235505283 904 dbSNP
rs1027858316 906 dbSNP
rs993666109 916 dbSNP
rs1335996680 918 dbSNP
rs1252474165 925 dbSNP
rs1355909323 925 dbSNP
rs1275137169 935 dbSNP
rs898094324 936 dbSNP
rs1036465276 939 dbSNP
rs1013932847 941 dbSNP
rs1250957758 943 dbSNP
rs1019209306 950 dbSNP
rs1363567175 951 dbSNP
rs1296988090 957 dbSNP
rs117439586 962 dbSNP
rs1472224947 965 dbSNP
rs1161095414 976 dbSNP
rs1385316730 989 dbSNP
rs1332412305 991 dbSNP
rs1429860422 996 dbSNP
rs1055721314 1000 dbSNP
rs1394133844 1011 dbSNP
rs1401231837 1013 dbSNP
rs185788844 1027 dbSNP
rs1313859016 1028 dbSNP
rs1050350349 1031 dbSNP
rs1340263169 1035 dbSNP
rs1242829325 1036 dbSNP
rs10766 1038 dbSNP
rs1272168034 1046 dbSNP
rs946843561 1054 dbSNP
rs1227718902 1060 dbSNP
rs925818172 1064 dbSNP
rs1042879297 1066 dbSNP
rs750508657 1072 dbSNP
rs946821478 1073 dbSNP
rs914003750 1074 dbSNP
rs180851622 1092 dbSNP
rs1387845033 1093 dbSNP
rs911859812 1093 dbSNP
rs966020361 1093 dbSNP
rs3088002 1094 dbSNP
rs757230211 1095 dbSNP
rs1444692158 1098 dbSNP
rs953627055 1116 dbSNP
rs546972419 1117 dbSNP
rs1401881427 1118 dbSNP
rs1394629333 1119 dbSNP
rs1244654583 1120 dbSNP
rs1320737706 1121 dbSNP
rs1054246616 1127 dbSNP
rs1366194921 1132 dbSNP
rs1028260350 1137 dbSNP
rs1295416601 1144 dbSNP
rs567525436 1148 dbSNP
rs139498570 1152 dbSNP
rs1441412141 1153 dbSNP
rs962491189 1165 dbSNP
rs1251700829 1168 dbSNP
rs1198487528 1171 dbSNP
rs1263672435 1172 dbSNP
rs1197870123 1183 dbSNP
rs1465058511 1184 dbSNP
rs60899283 1190 dbSNP
rs1340708081 1191 dbSNP
rs1274517392 1197 dbSNP
rs924416904 1199 dbSNP
rs1245597182 1207 dbSNP
rs1455209526 1212 dbSNP
rs1199012799 1214 dbSNP
rs1246869477 1216 dbSNP
rs867530654 1222 dbSNP
rs1013971363 1224 dbSNP
rs1282711170 1237 dbSNP
rs1389854563 1237 dbSNP
rs1318817629 1240 dbSNP
rs1373229758 1251 dbSNP
rs949967339 1252 dbSNP
rs1300732581 1254 dbSNP
rs1330449025 1255 dbSNP
rs1336518762 1255 dbSNP
rs1262212866 1259 dbSNP
rs1329612504 1261 dbSNP
rs1207670010 1278 dbSNP
rs915619269 1285 dbSNP
rs1001478228 1287 dbSNP
rs1043339257 1287 dbSNP
rs1055467977 1287 dbSNP
rs1209907407 1287 dbSNP
rs1265824003 1287 dbSNP
rs1413107616 1287 dbSNP
rs141791426 1287 dbSNP
rs1469566812 1287 dbSNP
rs1421009224 1291 dbSNP
rs1410937229 1293 dbSNP
rs1458668029 1295 dbSNP
rs1329320637 1300 dbSNP
rs1411393940 1302 dbSNP
rs1293007114 1322 dbSNP
rs1388686859 1323 dbSNP
rs1384940797 1326 dbSNP
rs533887040 1326 dbSNP
rs1227520169 1327 dbSNP
rs1350832382 1327 dbSNP
rs945919897 1327 dbSNP
rs891585274 1329 dbSNP
rs1368684058 1336 dbSNP
rs1323130044 1337 dbSNP
rs1221862391 1343 dbSNP
rs991144715 1349 dbSNP
rs1487235532 1350 dbSNP
rs951803646 1352 dbSNP
rs368097011 1355 dbSNP
rs972199122 1356 dbSNP
rs962246744 1361 dbSNP
rs1180470394 1362 dbSNP
rs1424818631 1362 dbSNP
rs944784986 1365 dbSNP
rs1420552668 1373 dbSNP
rs552018064 1378 dbSNP
rs1019494664 1379 dbSNP
rs1366755291 1382 dbSNP
rs1009156751 1386 dbSNP
rs1308755946 1387 dbSNP
rs986074999 1391 dbSNP
rs932263760 1397 dbSNP
rs920867351 1398 dbSNP
rs889365639 1405 dbSNP
rs1311596629 1406 dbSNP
rs1319601106 1412 dbSNP
rs962236715 1416 dbSNP
rs1015471247 1422 dbSNP
rs992619232 1429 dbSNP
rs115349578 1435 dbSNP
rs1363974454 1442 dbSNP
rs1239510162 1448 dbSNP
rs1483802053 1452 dbSNP
rs1181450899 1459 dbSNP
rs1254312200 1460 dbSNP
rs1430587707 1464 dbSNP
rs1034046886 1465 dbSNP
rs868246662 1479 dbSNP
rs551122684 1482 dbSNP
rs1360630396 1490 dbSNP
rs1010850906 1501 dbSNP
rs893916959 1506 dbSNP
rs1482268033 1508 dbSNP
rs532836758 1513 dbSNP
rs1251806839 1514 dbSNP
rs1297625595 1515 dbSNP
rs79810075 1516 dbSNP
rs1021546940 1523 dbSNP
rs1281376173 1528 dbSNP
rs1287832709 1529 dbSNP
rs1313349283 1532 dbSNP
rs747467348 1533 dbSNP
rs1209848070 1537 dbSNP
rs867954879 1538 dbSNP
rs891661648 1539 dbSNP
rs1041272856 1543 dbSNP
rs903025068 1545 dbSNP
rs1447753373 1549 dbSNP
rs1195626697 1552 dbSNP
rs1427138424 1558 dbSNP
rs1227762797 1561 dbSNP
rs1175079995 1565 dbSNP
rs1357231269 1573 dbSNP
rs530241282 1577 dbSNP
rs944816109 1579 dbSNP
rs1045971875 1581 dbSNP
rs950030087 1582 dbSNP
rs1281467400 1587 dbSNP
rs1050440223 1588 dbSNP
rs1432237093 1588 dbSNP
rs1348389104 1590 dbSNP
rs1368897878 1605 dbSNP
rs568615921 1608 dbSNP
rs549923581 1609 dbSNP
rs566113922 1610 dbSNP
rs1299562024 1617 dbSNP
rs1331690559 1620 dbSNP
rs930312459 1623 dbSNP
rs547453374 1624 dbSNP
rs1463743007 1632 dbSNP
rs1223861797 1633 dbSNP
rs1247427657 1634 dbSNP
rs756317119 1634 dbSNP
rs1321041648 1636 dbSNP
rs1190559202 1639 dbSNP
rs1426895260 1639 dbSNP
rs1190133712 1640 dbSNP
rs1043555 1643 dbSNP
rs1159695822 1644 dbSNP
rs1404214295 1646 dbSNP
rs771981201 1648 dbSNP
rs1160910975 1652 dbSNP
rs971845385 1657 dbSNP
rs1471855041 1659 dbSNP
rs1411697571 1661 dbSNP
rs1324881393 1666 dbSNP
rs1200527248 1668 dbSNP
rs1436339877 1670 dbSNP
rs992986039 1678 dbSNP
rs1352912957 1681 dbSNP
rs960168685 1685 dbSNP
rs1288188714 1687 dbSNP
rs1034120595 1688 dbSNP
rs962061565 1689 dbSNP
rs1021702080 1692 dbSNP
rs1220678075 1693 dbSNP
rs1266659354 1698 dbSNP
rs1182626838 1703 dbSNP
rs1263168017 1703 dbSNP
rs1410971398 1704 dbSNP
rs1220989927 1717 dbSNP
rs1164668140 1719 dbSNP
rs1043574 1720 dbSNP
rs1413817732 1725 dbSNP
rs201878917 1725 dbSNP
rs1321053975 1729 dbSNP
rs891688103 1733 dbSNP
rs912105577 1735 dbSNP
rs1286689864 1749 dbSNP
rs189356212 1755 dbSNP
rs1285027849 1756 dbSNP
rs750267862 1756 dbSNP
rs764635002 1759 dbSNP
rs1276945486 1760 dbSNP
rs761296417 1760 dbSNP
rs1344152202 1762 dbSNP
rs1491157320 1762 dbSNP
rs1491267074 1763 dbSNP
rs1435889306 1766 dbSNP
rs1328677919 1768 dbSNP
rs866925319 1772 dbSNP
rs1472298038 1773 dbSNP
rs1223850183 1774 dbSNP
rs1043589 1777 dbSNP
rs543285309 1783 dbSNP
rs760998251 1784 dbSNP
rs528011131 1787 dbSNP
rs377536307 1788 dbSNP
rs768246402 1789 dbSNP
rs1031386070 1793 dbSNP
rs899195732 1795 dbSNP
rs1321897996 1797 dbSNP
rs1043586 1798 dbSNP
rs1340093443 1817 dbSNP
rs1455330735 1817 dbSNP
rs1387393731 1820 dbSNP
rs1446169301 1820 dbSNP
rs1299828367 1824 dbSNP
rs1366055872 1829 dbSNP
rs1177643005 1831 dbSNP
rs1273793123 1831 dbSNP
rs1337412860 1836 dbSNP
rs1279135388 1840 dbSNP
rs999654894 1840 dbSNP
rs1441425721 1844 dbSNP
rs185604985 1848 dbSNP
rs1423753357 1854 dbSNP
rs1191116307 1855 dbSNP
rs1187445106 1857 dbSNP
rs1475988537 1857 dbSNP
rs1371817925 1861 dbSNP
rs1468092455 1878 dbSNP
rs779057991 1881 dbSNP
rs1249993109 1888 dbSNP
rs1186696055 1894 dbSNP
rs1401948286 1895 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 27020.0
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.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ugacccAAGUGGAAAUUCCCGu 5'
                | :| :||||||||| 
Target 5' -aaaucUAUAAUUUUAAGGGCu 3'
 		1 - 21
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 GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_017455 | 3UTR | UAAUUUUAAGGGCUUAACCUGUGACUUUAAUAAGCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
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 ENST00000345330.4 | 3UTR | AAAUCUAUAAUUUUAAGGGCUUAACCUG
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
GSE28544 Breast cancer 0.519 4.7e-3 0.615 6.9e-4 24 Click to see details
GSE28260 Renal cortex and medulla 0.659 7.1e-3 0.665 6.6e-3 13 Click to see details
GSE38226 Liver fibrosis 0.522 7.6e-3 0.017 4.7e-1 21 Click to see details
GSE32688 Pancreatic cancer -0.344 2.7e-2 -0.397 1.2e-2 32 Click to see details
GSE21687 Ependynoma primary tumors 0.198 5.8e-2 0.235 3.1e-2 64 Click to see details
GSE42095 Differentiated embryonic stem cells 0.256 1.2e-1 0.360 4.6e-2 23 Click to see details
GSE38974 Chronic obstructive pulmonary disease 0.093 3.3e-1 0.041 4.2e-1 25 Click to see details
GSE19350 CNS germ cell tumors -0.128 3.5e-1 0.316 1.6e-1 12 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis -0.081 3.7e-1 -0.380 4.9e-2 20 Click to see details
GSE26953 Aortic valvular endothelial cells -0.036 4.3e-1 -0.043 4.2e-1 24 Click to see details
GSE17498 Multiple myeloma -0.02 4.5e-1 -0.047 3.9e-1 40 Click to see details
GSE17498 Multiple myeloma -0.02 4.5e-1 -0.047 3.9e-1 40 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
-0.02 4.5e-1 -0.047 3.9e-1 40 Click to see details
-0.02 4.5e-1 -0.047 3.9e-1 40 Click to see details
-0.02 4.5e-1 -0.047 3.9e-1 40 Click to see details
-0.02 4.5e-1 -0.047 3.9e-1 40 Click to see details
-0.02 4.5e-1 -0.047 3.9e-1 40 Click to see details
54 hsa-miR-938 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT073757 NUBP1 nucleotide binding protein 1 2 2
MIRT092006 SNRK SNF related kinase 2 12
MIRT218174 MRPL18 mitochondrial ribosomal protein L18 2 2
MIRT485452 IVNS1ABP influenza virus NS1A binding protein 2 2
MIRT489857 ATP2A3 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3 2 2
MIRT495407 SPPL3 signal peptide peptidase like 3 2 4
MIRT495762 ZNF607 zinc finger protein 607 2 2
MIRT497391 RALY RALY heterogeneous nuclear ribonucleoprotein 2 2
MIRT499227 VAV3 vav guanine nucleotide exchange factor 3 2 4
MIRT507059 H3F3B H3 histone family member 3B 2 2
MIRT513671 SOCS5 suppressor of cytokine signaling 5 2 8
MIRT526922 IRGQ immunity related GTPase Q 2 4
MIRT527488 OCIAD1 OCIA domain containing 1 2 2
MIRT527566 ADCY7 adenylate cyclase 7 2 2
MIRT528081 NOL9 nucleolar protein 9 2 2
MIRT528535 CYP2C19 cytochrome P450 family 2 subfamily C member 19 2 4
MIRT533896 TBL1XR1 transducin beta like 1 X-linked receptor 1 2 2
MIRT536523 KCTD10 potassium channel tetramerization domain containing 10 2 2
MIRT541382 CDKN1A cyclin dependent kinase inhibitor 1A 2 2
MIRT550254 FAM120AOS family with sequence similarity 120A opposite strand 2 2
MIRT555975 NPTN neuroplastin 2 2
MIRT557394 H3F3C H3 histone family member 3C 2 2
MIRT568594 ADM adrenomedullin 2 2
MIRT571876 NCL nucleolin 2 2
MIRT572443 TRIM10 tripartite motif containing 10 2 2
MIRT610589 PRDM1 PR/SET domain 1 2 2
MIRT614044 THBS2 thrombospondin 2 2 2
MIRT618412 ATP2A2 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 2 2
MIRT623398 LHFPL2 LHFPL tetraspan subfamily member 2 2 2
MIRT623948 FBXO47 F-box protein 47 2 2
MIRT625349 MGLL monoglyceride lipase 2 2
MIRT635447 FAM180B family with sequence similarity 180 member B 2 2
MIRT638249 SLC16A9 solute carrier family 16 member 9 2 2
MIRT642662 RGS6 regulator of G protein signaling 6 2 2
MIRT646431 ARAP1 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 2 2
MIRT647172 ARGFX arginine-fifty homeobox 2 2
MIRT654891 POU2F1 POU class 2 homeobox 1 2 2
MIRT659337 CSE1L chromosome segregation 1 like 2 2
MIRT667407 MGAT5 mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase 2 2
MIRT698892 SPTBN2 spectrin beta, non-erythrocytic 2 2 2
MIRT703841 ETV3 ETS variant 3 2 2
MIRT708322 NT5C 5', 3'-nucleotidase, cytosolic 2 2
MIRT708934 CRY2 cryptochrome circadian clock 2 2 2
MIRT709745 UBD ubiquitin D 2 2
MIRT710265 FAM107A family with sequence similarity 107 member A 2 2
MIRT712576 ATP2B4 ATPase plasma membrane Ca2+ transporting 4 2 2
MIRT712645 TXNL4A thioredoxin like 4A 2 2
MIRT714833 SCAMP2 secretory carrier membrane protein 2 2 2
MIRT720673 SLC39A13 solute carrier family 39 member 13 2 2
MIRT723041 MAPT microtubule associated protein tau 2 2
MIRT723669 CTC1 CST telomere replication complex component 1 2 2
MIRT723772 ROBO4 roundabout guidance receptor 4 2 2
MIRT723812 OR1L8 olfactory receptor family 1 subfamily L member 8 2 2
MIRT736795 RBM5 RNA binding motif protein 5 2 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-938 Emodin NULL 3220 Microarray K562 cells 23744534 2013 down-regualted
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-938 Paclitaxel 36314 NSC125973 approved sensitive High Non-Small Cell Lung Cancer cell line (H358, H1155)
hsa-miR-938 Vemurafenib 42611257 NSC761431 approved resistant cell line (LM16)
hsa-miR-938 Vemurafenib 42611257 NSC761431 approved resistant cell line (LM43)
hsa-miR-938 4-Hydroxytamoxifen+Tamoxifen sensitive cell line (LY2)
hsa-miR-938 Ethanol+Tamoxifen sensitive cell line (LY2)
hsa-miR-938 Sunitinib 5329102 NSC750690 approved resistant tissue (CardB)
hsa-miR-938 Oxaliplatin 6857599 NSC266046 approved sensitive cell line (IGROV-1)
hsa-miR-938 Cisplatin 5460033 NSC119875 approved sensitive cell line (IGROV-1)
hsa-miR-938 Paclitaxel 36314 NSC125973 approved sensitive cell line (PC3PR70)
hsa-miR-938 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-938 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-938 Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)

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