pre-miRNA Information
pre-miRNA hsa-mir-125b-2   
Genomic Coordinates chr21: 16590237 - 16590325
Synonyms MIRN125B2, MIR125B2
Description Homo sapiens miR-125b-2 stem-loop
Comment This miRNA sequence is predicted based on homology to a verified miRNA from mouse .
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-125b-2-3p
Sequence 54| UCACAAGUCAGGCUCUUGGGAC |75
Evidence Experimental
Experiments Cloned
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 3 21 + 16590292 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs575583557 6 dbSNP
rs1331783293 22 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol CD101   
Synonyms EWI-101, IGSF2, V7
Description CD101 molecule
Transcript NM_004258   
Expression
Putative miRNA Targets on CD101
3'UTR of CD101
(miRNA target sites are highlighted)
>CD101|NM_004258|3'UTR
   1 ATCCCAAGAGGCACCTGCAGCCAGGAAGGAAAGCTTGTTTTACAGCTTCCTGCCTTGCTGCCTGTTTCTTCCCAAGCCCC
  81 GTGTGGAATGTGGTGACCTAGTCACCTGGAACCAGCTCCTGACAGACCCCGGCAACTTCTAGATGAACCCAAGTGAACTT
 161 TCCTCATTACCATCCTGAAGTCACTACCCCAGGGGGAGCTATAGCTTCATGACCGTAACATGTGACCTGTGTGCTGGCAG
 241 GACGACTCACTGCGGCTGCGCCACTGGGACCCCTCCCCTACATGCACCAATGCACTCTCTCCCCTCTCCATCACCCCATA
 321 AAACCCTCCTGTCACTTTCCTTCAGAGACACCGCTTTGGAGAGTATTCCCAGCGCTCTCCTTGCTTGTGACAAGTAAAAA
 401 AAAAAAAAAACTCCTTTTCATCAAAACTC
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' caGGGUUCUC----GGACUGAACACu 5'
            :|| || |    ||| :|||||| 
Target 5' atTCCCAGCGCTCTCCTTGCTTGTGa 3'
365 - 390 142.00 -19.60
2
miRNA  3' caGGGUUCUCGGACUGAACACu 5'
            ::|| || | | || |||| 
Target 5' gcTTCATGACCGTAACATGTGa 3'
204 - 225 128.00 -9.80
3
miRNA  3' caGGGUUCUC---GGAC---------------UGAACAcu 5'
            ||||||||   ||||               :|||||  
Target 5' atCCCAAGAGGCACCTGCAGCCAGGAAGGAAAGCTTGTtt 3'
1 - 40 116.00 -25.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30463145 6 COSMIC
COSN9361494 431 COSMIC
COSN25403215 442 COSMIC
COSN21498326 1238 COSMIC
COSN19308644 1316 COSMIC
COSN19308597 1454 COSMIC
COSN29595126 1625 COSMIC
COSN8336355 1913 COSMIC
COSN26697771 2004 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs112438489 4 dbSNP
rs367845374 6 dbSNP
rs111277178 13 dbSNP
rs745821238 15 dbSNP
rs374720941 17 dbSNP
rs769559350 20 dbSNP
rs1026734094 23 dbSNP
rs537901434 25 dbSNP
rs1218872707 26 dbSNP
rs777917572 26 dbSNP
rs1356438649 28 dbSNP
rs34169609 28 dbSNP
rs748980231 36 dbSNP
rs1317610261 37 dbSNP
rs368881987 38 dbSNP
rs768541387 40 dbSNP
rs774199006 41 dbSNP
rs371924370 50 dbSNP
rs1340363169 52 dbSNP
rs1370844046 59 dbSNP
rs1294877841 64 dbSNP
rs1364877089 72 dbSNP
rs529233728 73 dbSNP
rs1374767702 74 dbSNP
rs1311050661 77 dbSNP
rs1045574877 80 dbSNP
rs1345270820 87 dbSNP
rs1157860073 96 dbSNP
rs138265623 97 dbSNP
rs928398202 102 dbSNP
rs1189092375 103 dbSNP
rs1024676829 105 dbSNP
rs1475119423 106 dbSNP
rs1255956946 108 dbSNP
rs1226042810 110 dbSNP
rs934390405 124 dbSNP
rs114640861 136 dbSNP
rs1323697498 144 dbSNP
rs41302812 149 dbSNP
rs1233659482 157 dbSNP
rs978147501 163 dbSNP
rs182336907 164 dbSNP
rs958493340 174 dbSNP
rs989672090 176 dbSNP
rs1362638687 182 dbSNP
rs922129139 185 dbSNP
rs769440570 193 dbSNP
rs1451087253 195 dbSNP
rs1265016869 196 dbSNP
rs1351248857 198 dbSNP
rs1165213024 199 dbSNP
rs41302810 206 dbSNP
rs149623012 207 dbSNP
rs1196411045 208 dbSNP
rs1429606081 210 dbSNP
rs1248701549 227 dbSNP
rs1449437958 234 dbSNP
rs1261688466 244 dbSNP
rs1187228463 247 dbSNP
rs1019060349 256 dbSNP
rs911968074 270 dbSNP
rs1213299369 276 dbSNP
rs1333828105 279 dbSNP
rs940716446 281 dbSNP
rs1271058641 285 dbSNP
rs1229394902 291 dbSNP
rs1308003849 297 dbSNP
rs1294847178 314 dbSNP
rs1387483594 328 dbSNP
rs144483553 330 dbSNP
rs1372543546 332 dbSNP
rs966136980 335 dbSNP
rs1439738307 336 dbSNP
rs897071860 344 dbSNP
rs1425613991 345 dbSNP
rs993543982 346 dbSNP
rs1026366386 352 dbSNP
rs995793610 357 dbSNP
rs1462877156 359 dbSNP
rs1372993882 374 dbSNP
rs1048289255 376 dbSNP
rs1434909879 377 dbSNP
rs573784221 381 dbSNP
rs1193185423 384 dbSNP
rs35911016 386 dbSNP
rs1467288417 393 dbSNP
rs1347702455 394 dbSNP
rs1240335021 395 dbSNP
rs1455000774 397 dbSNP
rs952156770 399 dbSNP
rs984787121 412 dbSNP
rs762861469 419 dbSNP
rs544288486 428 dbSNP
rs1250625427 432 dbSNP
rs34610469 439 dbSNP
rs895021978 451 dbSNP
rs1012016850 456 dbSNP
rs915839869 458 dbSNP
rs969950806 460 dbSNP
rs1288983006 464 dbSNP
rs1232978584 475 dbSNP
rs764169839 485 dbSNP
rs1368328217 486 dbSNP
rs1024707409 491 dbSNP
rs1330541957 510 dbSNP
rs970853768 511 dbSNP
rs999203514 512 dbSNP
rs1432882270 516 dbSNP
rs1317004265 521 dbSNP
rs563094935 526 dbSNP
rs981307167 539 dbSNP
rs1383264853 540 dbSNP
rs928450284 544 dbSNP
rs79223638 545 dbSNP
rs1053291670 550 dbSNP
rs545408360 562 dbSNP
rs1312309822 566 dbSNP
rs17229389 569 dbSNP
rs947063859 570 dbSNP
rs989770942 575 dbSNP
rs1049392532 579 dbSNP
rs1193909230 586 dbSNP
rs17235780 588 dbSNP
rs953557456 595 dbSNP
rs987610665 599 dbSNP
rs912000199 601 dbSNP
rs1245462486 603 dbSNP
rs1473341469 609 dbSNP
rs781602682 622 dbSNP
rs1335492693 636 dbSNP
rs1412033029 642 dbSNP
rs1007761187 650 dbSNP
rs1159363085 655 dbSNP
rs1040562981 661 dbSNP
rs1387294127 665 dbSNP
rs1455126073 666 dbSNP
rs972095771 668 dbSNP
rs753064671 679 dbSNP
rs1159314813 681 dbSNP
rs756550569 685 dbSNP
rs1026835554 691 dbSNP
rs370941000 699 dbSNP
rs17235787 701 dbSNP
rs139167491 702 dbSNP
rs1022957799 712 dbSNP
rs947902969 718 dbSNP
rs1187141632 730 dbSNP
rs1205253765 731 dbSNP
rs1484379619 731 dbSNP
rs970003124 731 dbSNP
rs1225749246 733 dbSNP
rs1258653186 734 dbSNP
rs1289144792 735 dbSNP
rs749284845 736 dbSNP
rs1413498074 740 dbSNP
rs906290251 746 dbSNP
rs999716642 751 dbSNP
rs955875013 755 dbSNP
rs1265054761 760 dbSNP
rs988643265 762 dbSNP
rs1210023118 764 dbSNP
rs1462758050 768 dbSNP
rs914335113 771 dbSNP
rs1236143917 776 dbSNP
rs1471755352 782 dbSNP
rs1243813055 786 dbSNP
rs1193261588 787 dbSNP
rs17235793 794 dbSNP
rs985567615 797 dbSNP
rs1215214516 809 dbSNP
rs893488656 815 dbSNP
rs910888846 816 dbSNP
rs1010564355 820 dbSNP
rs1471337848 827 dbSNP
rs531708785 831 dbSNP
rs187715603 836 dbSNP
rs1324766572 838 dbSNP
rs1430036365 838 dbSNP
rs953588583 843 dbSNP
rs1328123276 846 dbSNP
rs1040619891 847 dbSNP
rs771992243 853 dbSNP
rs987638568 857 dbSNP
rs142471730 858 dbSNP
rs1356079903 864 dbSNP
rs1403460347 868 dbSNP
rs1047880171 870 dbSNP
rs962227021 874 dbSNP
rs1474773712 875 dbSNP
rs539604664 877 dbSNP
rs920671106 878 dbSNP
rs193103441 887 dbSNP
rs1023017427 893 dbSNP
rs1219805512 894 dbSNP
rs1439931429 904 dbSNP
rs566757861 905 dbSNP
rs1408195235 906 dbSNP
rs1214533368 907 dbSNP
rs1002849739 909 dbSNP
rs916515775 914 dbSNP
rs1345791122 920 dbSNP
rs369189667 920 dbSNP
rs1219172813 924 dbSNP
rs1370519248 929 dbSNP
rs1324155096 942 dbSNP
rs113855697 962 dbSNP
rs67722240 962 dbSNP
rs71582589 962 dbSNP
rs1309666020 980 dbSNP
rs955927509 984 dbSNP
rs947940143 987 dbSNP
rs1368675061 988 dbSNP
rs534035663 989 dbSNP
rs1174972166 990 dbSNP
rs1454382001 991 dbSNP
rs906400017 999 dbSNP
rs935160698 1000 dbSNP
rs1206252972 1004 dbSNP
rs555412744 1006 dbSNP
rs1233838539 1016 dbSNP
rs34147105 1016 dbSNP
rs1021454045 1023 dbSNP
rs1482340830 1033 dbSNP
rs968914669 1034 dbSNP
rs985233522 1035 dbSNP
rs893528520 1045 dbSNP
rs537965792 1047 dbSNP
rs1481893402 1064 dbSNP
rs533027853 1072 dbSNP
rs1374400919 1077 dbSNP
rs370187170 1086 dbSNP
rs1441298670 1099 dbSNP
rs976371085 1100 dbSNP
rs3835637 1118 dbSNP
rs923555313 1118 dbSNP
rs34049179 1120 dbSNP
rs3767779 1120 dbSNP
rs1374353043 1125 dbSNP
rs578137490 1129 dbSNP
rs1477377655 1136 dbSNP
rs183949138 1137 dbSNP
rs1009185358 1138 dbSNP
rs115596010 1139 dbSNP
rs145927178 1146 dbSNP
rs1260148680 1147 dbSNP
rs1189313778 1153 dbSNP
rs371245778 1162 dbSNP
rs776663714 1163 dbSNP
rs1218087920 1164 dbSNP
rs1317740432 1165 dbSNP
rs1283899510 1168 dbSNP
rs761200324 1174 dbSNP
rs952107353 1177 dbSNP
rs1002902195 1178 dbSNP
rs374952196 1179 dbSNP
rs188446533 1180 dbSNP
rs560970120 1181 dbSNP
rs1300531754 1182 dbSNP
rs971368865 1188 dbSNP
rs982461948 1195 dbSNP
rs1157929179 1198 dbSNP
rs1455942378 1201 dbSNP
rs1035684214 1203 dbSNP
rs764858286 1204 dbSNP
rs935176332 1210 dbSNP
rs1364761479 1220 dbSNP
rs531577727 1221 dbSNP
rs750039026 1226 dbSNP
rs549896981 1232 dbSNP
rs762524702 1238 dbSNP
rs1241678256 1239 dbSNP
rs1207091846 1241 dbSNP
rs1326751661 1242 dbSNP
rs192300788 1263 dbSNP
rs565370810 1267 dbSNP
rs766033937 1288 dbSNP
rs533028176 1290 dbSNP
rs1310556469 1294 dbSNP
rs753007482 1298 dbSNP
rs914980314 1300 dbSNP
rs1362084385 1301 dbSNP
rs946413614 1303 dbSNP
rs1006656890 1304 dbSNP
rs1432417355 1305 dbSNP
rs756499126 1311 dbSNP
rs1050162031 1312 dbSNP
rs1326995587 1324 dbSNP
rs1461306832 1328 dbSNP
rs1018003969 1337 dbSNP
rs1173172668 1344 dbSNP
rs551558076 1345 dbSNP
rs1340471230 1356 dbSNP
rs375131380 1360 dbSNP
rs1469963632 1375 dbSNP
rs1290070612 1378 dbSNP
rs1450575303 1385 dbSNP
rs1214077985 1386 dbSNP
rs566509735 1388 dbSNP
rs1196185800 1399 dbSNP
rs1263533975 1401 dbSNP
rs1243326993 1413 dbSNP
rs1450073535 1416 dbSNP
rs1296187181 1418 dbSNP
rs976424840 1447 dbSNP
rs1372715184 1448 dbSNP
rs11337228 1449 dbSNP
rs1370523333 1449 dbSNP
rs1386500246 1449 dbSNP
rs1411705747 1449 dbSNP
rs1462922369 1449 dbSNP
rs367652545 1449 dbSNP
rs1008547533 1451 dbSNP
rs1187850301 1461 dbSNP
rs78156924 1466 dbSNP
rs1395857476 1467 dbSNP
rs1388097054 1468 dbSNP
rs1426255573 1469 dbSNP
rs1165244482 1471 dbSNP
rs1391672695 1476 dbSNP
rs1041053715 1480 dbSNP
rs1480916243 1481 dbSNP
rs868606549 1488 dbSNP
rs918250353 1489 dbSNP
rs898047432 1492 dbSNP
rs3767778 1493 dbSNP
rs1390907423 1494 dbSNP
rs1027782768 1497 dbSNP
rs909427349 1501 dbSNP
rs1309559043 1505 dbSNP
rs1436546136 1506 dbSNP
rs1392398875 1513 dbSNP
rs1350395792 1515 dbSNP
rs1306732567 1518 dbSNP
rs1297422647 1525 dbSNP
rs549274869 1533 dbSNP
rs1012993774 1535 dbSNP
rs1022987716 1536 dbSNP
rs971400141 1542 dbSNP
rs184514980 1543 dbSNP
rs927890340 1550 dbSNP
rs537828746 1551 dbSNP
rs577720098 1555 dbSNP
rs556031484 1556 dbSNP
rs1257574666 1559 dbSNP
rs374625873 1560 dbSNP
rs1355270730 1564 dbSNP
rs1199425228 1568 dbSNP
rs915110407 1575 dbSNP
rs1207688539 1583 dbSNP
rs946526862 1587 dbSNP
rs1285826054 1595 dbSNP
rs1050194013 1599 dbSNP
rs927395552 1606 dbSNP
rs1305991664 1609 dbSNP
rs910288864 1610 dbSNP
rs1356705794 1613 dbSNP
rs944366116 1615 dbSNP
rs1343292004 1616 dbSNP
rs1387345225 1616 dbSNP
rs538313136 1626 dbSNP
rs1188044409 1633 dbSNP
rs1457540809 1634 dbSNP
rs1367651007 1635 dbSNP
rs1472624237 1642 dbSNP
rs1476127311 1645 dbSNP
rs1161672705 1653 dbSNP
rs1414279021 1654 dbSNP
rs1263317185 1663 dbSNP
rs1457781002 1666 dbSNP
rs1464689468 1668 dbSNP
rs142219529 1673 dbSNP
rs898074780 1674 dbSNP
rs993729898 1677 dbSNP
rs544925672 1679 dbSNP
rs1335346141 1681 dbSNP
rs1328314391 1682 dbSNP
rs1340246280 1685 dbSNP
rs887970154 1688 dbSNP
rs1042995231 1693 dbSNP
rs979533874 1695 dbSNP
rs904421454 1696 dbSNP
rs1414363759 1697 dbSNP
rs542943970 1698 dbSNP
rs187313855 1699 dbSNP
rs1227204177 1703 dbSNP
rs971432615 1704 dbSNP
rs1215883295 1705 dbSNP
rs1265659782 1705 dbSNP
rs1003290267 1706 dbSNP
rs1031640255 1713 dbSNP
rs1289746998 1718 dbSNP
rs576069222 1721 dbSNP
rs965141955 1730 dbSNP
rs151232840 1731 dbSNP
rs1022201165 1732 dbSNP
rs1363267089 1734 dbSNP
rs1305913785 1735 dbSNP
rs1350285033 1736 dbSNP
rs557266619 1736 dbSNP
rs867832099 1738 dbSNP
rs1403512057 1739 dbSNP
rs746468784 1741 dbSNP
rs191635555 1742 dbSNP
rs184351377 1743 dbSNP
rs541134156 1744 dbSNP
rs11803368 1747 dbSNP
rs139140235 1748 dbSNP
rs772362350 1749 dbSNP
rs913281998 1755 dbSNP
rs1401961581 1756 dbSNP
rs367613724 1763 dbSNP
rs946093299 1768 dbSNP
rs1394602346 1775 dbSNP
rs1340139183 1778 dbSNP
rs1309505970 1779 dbSNP
rs1043438980 1782 dbSNP
rs888002679 1785 dbSNP
rs948909525 1794 dbSNP
rs1044505538 1800 dbSNP
rs1274025529 1806 dbSNP
rs907307513 1810 dbSNP
rs1039557264 1815 dbSNP
rs1308567183 1824 dbSNP
rs780446730 1828 dbSNP
rs1032167685 1829 dbSNP
rs1368193398 1831 dbSNP
rs1175030718 1836 dbSNP
rs1414654764 1839 dbSNP
rs891816078 1843 dbSNP
rs1171169425 1845 dbSNP
rs1471366803 1846 dbSNP
rs746763379 1849 dbSNP
rs149938927 1852 dbSNP
rs768538516 1855 dbSNP
rs967933145 1858 dbSNP
rs147621538 1862 dbSNP
rs531589136 1865 dbSNP
rs761874402 1866 dbSNP
rs549758871 1888 dbSNP
rs1311816350 1897 dbSNP
rs866988056 1898 dbSNP
rs918989132 1900 dbSNP
rs1217197765 1911 dbSNP
rs1005250856 1919 dbSNP
rs571120178 1923 dbSNP
rs929001140 1925 dbSNP
rs1197287447 1926 dbSNP
rs984399447 1937 dbSNP
rs17036747 1938 dbSNP
rs769620498 1950 dbSNP
rs948942023 1960 dbSNP
rs1448192044 1974 dbSNP
rs969000518 1975 dbSNP
rs1044622860 1977 dbSNP
rs1402759040 1992 dbSNP
rs1249723572 1996 dbSNP
rs1158951057 1999 dbSNP
rs907404750 2002 dbSNP
rs980357622 2004 dbSNP
rs1434924177 2007 dbSNP
rs938829091 2010 dbSNP
rs1182464384 2012 dbSNP
rs1482969830 2014 dbSNP
rs2296449 2028 dbSNP
rs1377523240 2038 dbSNP
rs891844462 2038 dbSNP
rs1218245521 2039 dbSNP
rs2296448 2041 dbSNP
rs1268495497 2042 dbSNP
rs1227634782 2044 dbSNP
rs765974906 2047 dbSNP
rs1326973570 2048 dbSNP
rs1021596071 2051 dbSNP
rs1170927735 2059 dbSNP
rs903779979 2061 dbSNP
rs1300662099 2063 dbSNP
rs115248167 2070 dbSNP
rs146555417 2082 dbSNP
rs1320299961 2084 dbSNP
rs965935076 2096 dbSNP
rs925948804 2098 dbSNP
rs576333524 2102 dbSNP
rs1369114048 2103 dbSNP
rs1423270134 2105 dbSNP
rs1411695403 2121 dbSNP
rs942672620 2128 dbSNP
rs1039612482 2135 dbSNP
rs901076002 2139 dbSNP
rs751251024 2147 dbSNP
rs1300540770 2148 dbSNP
rs533159540 2149 dbSNP
rs1463377908 2152 dbSNP
rs1267098012 2163 dbSNP
rs933851712 2181 dbSNP
rs950481629 2187 dbSNP
rs555211268 2190 dbSNP
rs1047326540 2195 dbSNP
rs886900802 2197 dbSNP
rs71096895 2208 dbSNP
rs1005714549 2217 dbSNP
rs1433299647 2218 dbSNP
rs558928499 2224 dbSNP
rs1341116669 2232 dbSNP
rs1393359110 2234 dbSNP
rs368717360 2235 dbSNP
rs760923960 2236 dbSNP
rs969695940 2237 dbSNP
rs1049182 2241 dbSNP
rs1489524795 2250 dbSNP
rs764579699 2251 dbSNP
rs577145641 2252 dbSNP
rs1266733694 2259 dbSNP
rs551785405 2265 dbSNP
rs938874266 2266 dbSNP
rs1034623905 2267 dbSNP
rs960266600 2275 dbSNP
rs1449178179 2277 dbSNP
rs559581540 2281 dbSNP
rs913316860 2282 dbSNP
rs1225701449 2285 dbSNP
rs967533256 2295 dbSNP
rs1302410804 2299 dbSNP
rs1351215186 2306 dbSNP
rs1310389601 2313 dbSNP
rs1366040560 2313 dbSNP
rs1410465987 2314 dbSNP
rs1370050006 2315 dbSNP
rs1166843161 2319 dbSNP
rs1467744950 2323 dbSNP
rs979264853 2329 dbSNP
rs1176504819 2334 dbSNP
rs1432391734 2344 dbSNP
rs527526898 2350 dbSNP
rs947418589 2357 dbSNP
rs1184291637 2365 dbSNP
rs112199464 2368 dbSNP
rs1250389685 2373 dbSNP
rs542845660 2374 dbSNP
rs561024343 2375 dbSNP
rs35163967 2386 dbSNP
rs150174445 2388 dbSNP
rs901735019 2395 dbSNP
rs1225852034 2401 dbSNP
rs1306252828 2408 dbSNP
rs1314571458 2411 dbSNP
rs1323783863 2413 dbSNP
rs1038546220 2416 dbSNP
rs1302520082 2417 dbSNP
rs1465318478 2417 dbSNP
rs1472877227 2417 dbSNP
rs72440795 2417 dbSNP
rs997363552 2428 dbSNP
rs1179321580 2429 dbSNP
rs1001897206 2430 dbSNP
rs1056135467 2432 dbSNP
rs1467139999 2432 dbSNP
rs896110685 2452 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HeLa
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in Chi_124B_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + B ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
CLIP-seq Support 1 for dataset Chi_124B_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell miR-124 + B
Location of target site ENST00000256652.4 | 3UTR | ACAAGUAAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
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
GSE34608 Pulmonary tuberculosis and sarcoidosis 0.559 5.2e-3 0.310 9.2e-2 20 Click to see details
GSE19536 Breast cancer -0.203 2.1e-2 -0.215 1.6e-2 100 Click to see details
GSE35602 Colorectal cancer stromal tissue -0.403 2.3e-2 -0.288 8.1e-2 25 Click to see details
GSE17498 Multiple myeloma -0.214 9.2e-2 -0.188 1.2e-1 40 Click to see details
GSE19350 CNS germ cell tumors -0.363 1.2e-1 -0.428 8.3e-2 12 Click to see details
GSE28544 Breast cancer 0.231 1.4e-1 0.285 8.9e-2 24 Click to see details
GSE38226 Liver fibrosis -0.236 1.5e-1 -0.196 2.0e-1 21 Click to see details
GSE15076 Monocyte-derived dendritic cells -0.857 1.7e-1 -0.500 3.3e-1 3 Click to see details
GSE21687 Ependynoma primary tumors 0.095 2.3e-1 0.128 1.6e-1 64 Click to see details
GSE38974 Chronic obstructive pulmonary disease 0.14 2.5e-1 0.099 3.2e-1 25 Click to see details
GSE28260 Renal cortex and medulla -0.163 3.0e-1 -0.319 1.4e-1 13 Click to see details
GSE26953 Aortic valvular endothelial cells 0.102 3.2e-1 0.038 4.3e-1 24 Click to see details
GSE19783 ER+ ER+ breast cancer -0.105 3.3e-1 -0.068 3.9e-1 20 Click to see details
GSE32688 Pancreatic cancer 0.053 3.9e-1 -0.135 2.3e-1 32 Click to see details
GSE21032 Prostate cancer -0.027 4.0e-1 -0.010 4.6e-1 83 Click to see details
GSE19783 ER- ER- breast cancer 0.001 5.0e-1 -0.048 3.4e-1 79 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
THCA -0.425 0 -0.472 0 59 Click to see details
BRCA 0.324 0 0.327 0 84 Click to see details
HNSC 0.387 0.01 0.230 0.07 42 Click to see details
STAD -0.397 0.01 -0.467 0 32 Click to see details
ESCA 0.645 0.02 0.682 0.01 11 Click to see details
KICH 0.414 0.02 0.515 0 25 Click to see details
PCPG 0.997 0.02 1.000 0.5 3 Click to see details
CESC 0.937 0.11 1.000 0.5 3 Click to see details
LIHC -0.143 0.16 -0.125 0.2 49 Click to see details
PAAD 0.647 0.18 0.600 0.2 4 Click to see details
LUAD 0.248 0.22 0.406 0.1 12 Click to see details
PRAD -0.088 0.27 0.002 0.49 50 Click to see details
UCEC 0.142 0.28 0.226 0.18 19 Click to see details
KIRP 0.102 0.29 0.058 0.38 32 Click to see details
LUSC 0.062 0.36 0.103 0.27 38 Click to see details
BLCA 0.089 0.36 0.133 0.3 18 Click to see details
CHOL 0.083 0.42 0.033 0.47 9 Click to see details
KIRC 0.018 0.44 0.025 0.42 68 Click to see details
COAD 0.04 0.46 -0.071 0.43 8 Click to see details
COAD 0.04 0.46 -0.071 0.43 8 Click to see details
COAD 0.04 0.46 -0.071 0.43 8 Click to see details
91 hsa-miR-125b-2-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT038624 HN1L Jupiter microtubule associated homolog 2 1 1
MIRT038625 KDELC2 KDEL motif containing 2 1 1
MIRT038626 ABHD15 abhydrolase domain containing 15 1 1
MIRT038627 PPP1R12C protein phosphatase 1 regulatory subunit 12C 1 1
MIRT038628 MSANTD4 Myb/SANT DNA binding domain containing 4 with coiled-coils 1 1
MIRT038629 ASH2L ASH2 like histone lysine methyltransferase complex subunit 1 1
MIRT038630 USP22 ubiquitin specific peptidase 22 1 1
MIRT038631 CSTB cystatin B 1 1
MIRT038632 SYT2 synaptotagmin 2 1 1
MIRT038633 NDUFS7 NADH:ubiquinone oxidoreductase core subunit S7 1 1
MIRT038634 MTA2 metastasis associated 1 family member 2 1 1
MIRT053086 IGF1R insulin like growth factor 1 receptor 3 1
MIRT055788 PLEKHA1 pleckstrin homology domain containing A1 2 12
MIRT061248 AMOTL1 angiomotin like 1 2 10
MIRT061649 BTG2 BTG anti-proliferation factor 2 2 6
MIRT079046 TNRC6C trinucleotide repeat containing 6C 2 4
MIRT084583 BCL2L11 BCL2 like 11 2 8
MIRT093523 GALNT7 polypeptide N-acetylgalactosaminyltransferase 7 2 2
MIRT097383 LHFPL2 LHFPL tetraspan subfamily member 2 2 4
MIRT098030 SOBP sine oculis binding protein homolog 2 2
MIRT186262 TCEB3 elongin A 2 2
MIRT187284 DAZAP2 DAZ associated protein 2 2 10
MIRT361113 LRRC1 leucine rich repeat containing 1 2 2
MIRT443585 FAM84B family with sequence similarity 84 member B 2 2
MIRT452249 TRAM1 translocation associated membrane protein 1 2 2
MIRT476289 GMFB glia maturation factor beta 2 8
MIRT483871 MRPL12 mitochondrial ribosomal protein L12 2 2
MIRT484250 ANK1 ankyrin 1 2 2
MIRT499251 VAV3 vav guanine nucleotide exchange factor 3 2 4
MIRT502270 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 2 4
MIRT504652 RPL9 ribosomal protein L9 2 6
MIRT505210 UBN2 ubinuclein 2 2 6
MIRT512690 POP1 POP1 homolog, ribonuclease P/MRP subunit 2 2
MIRT517341 ZNF529 zinc finger protein 529 2 4
MIRT518946 LSG1 large 60S subunit nuclear export GTPase 1 2 2
MIRT520866 SUGT1 SGT1 homolog, MIS12 kinetochore complex assembly cochaperone 2 2
MIRT521236 SAR1A secretion associated Ras related GTPase 1A 2 2
MIRT528324 GIGYF2 GRB10 interacting GYF protein 2 2 2
MIRT533297 USP46 ubiquitin specific peptidase 46 2 2
MIRT541024 WEE1 WEE1 G2 checkpoint kinase 2 4
MIRT544034 ERRFI1 ERBB receptor feedback inhibitor 1 2 2
MIRT547037 POGZ pogo transposable element derived with ZNF domain 2 2
MIRT556102 MOAP1 modulator of apoptosis 1 2 2
MIRT558320 DR1 down-regulator of transcription 1 2 2
MIRT558520 CSRNP3 cysteine and serine rich nuclear protein 3 2 2
MIRT566230 PTMA prothymosin, alpha 2 4
MIRT568437 ARPP19 cAMP regulated phosphoprotein 19 2 2
MIRT570584 OTUD7B OTU deubiquitinase 7B 2 2
MIRT571384 JKAMP JNK1/MAPK8-associated membrane protein 2 2
MIRT572798 SIGLEC14 sialic acid binding Ig like lectin 14 2 2
MIRT573864 C9orf78 chromosome 9 open reading frame 78 2 2
MIRT609930 SLC38A1 solute carrier family 38 member 1 2 4
MIRT610437 CSMD2 CUB and Sushi multiple domains 2 2 2
MIRT614407 MURC caveolae associated protein 4 2 2
MIRT618625 GREB1 growth regulation by estrogen in breast cancer 1 2 2
MIRT620605 SAP30 Sin3A associated protein 30 2 2
MIRT635313 FAM179A TOG array regulator of axonemal microtubules 2 2 2
MIRT635918 GLTSCR2 NOP53 ribosome biogenesis factor 2 2
MIRT638507 MAP3K9 mitogen-activated protein kinase kinase kinase 9 2 2
MIRT640597 TM9SF4 transmembrane 9 superfamily member 4 2 2
MIRT644066 IQCE IQ motif containing E 2 2
MIRT648287 TRAPPC2L trafficking protein particle complex 2 like 2 2
MIRT653089 SSR3 signal sequence receptor subunit 3 2 2
MIRT654651 PTAFR platelet activating factor receptor 2 2
MIRT658084 FOXR2 forkhead box R2 2 2
MIRT665306 ZBTB37 zinc finger and BTB domain containing 37 2 2
MIRT665974 SYTL4 synaptotagmin like 4 2 2
MIRT674905 RASSF9 Ras association domain family member 9 2 2
MIRT680085 THAP1 THAP domain containing 1 2 2
MIRT681487 DIP2A disco interacting protein 2 homolog A 2 2
MIRT691243 DFNB59 pejvakin 2 2
MIRT692361 AGTRAP angiotensin II receptor associated protein 2 2
MIRT693034 MB21D1 Mab-21 domain containing 1 2 2
MIRT694478 LRTOMT leucine rich transmembrane and O-methyltransferase domain containing 2 2
MIRT696069 ZNF264 zinc finger protein 264 2 2
MIRT696579 TTC21B tetratricopeptide repeat domain 21B 2 2
MIRT696759 MTFMT mitochondrial methionyl-tRNA formyltransferase 2 2
MIRT697306 ZNF652 zinc finger protein 652 2 2
MIRT698736 STX12 syntaxin 12 2 2
MIRT701055 PARP2 poly(ADP-ribose) polymerase 2 2 2
MIRT701197 OTUD3 OTU deubiquitinase 3 2 2
MIRT701334 NSD1 nuclear receptor binding SET domain protein 1 2 2
MIRT703617 FBXO45 F-box protein 45 2 2
MIRT708893 ZNF780A zinc finger protein 780A 2 2
MIRT711621 DGKH diacylglycerol kinase eta 2 2
MIRT713744 TMEM81 transmembrane protein 81 2 2
MIRT715060 TMTC1 transmembrane and tetratricopeptide repeat containing 1 2 2
MIRT719711 CD101 CD101 molecule 2 2
MIRT720293 DLGAP3 DLG associated protein 3 2 2
MIRT722605 CCDC152 coiled-coil domain containing 152 2 2
MIRT724565 ACSBG1 acyl-CoA synthetase bubblegum family member 1 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-125b-2 Ascorbate approved 54670067 Microarray Metastatic melanoma cell lines 25202679 2014 up-regualted
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-125b-2 Ceritinib 57379345 NSC776422 approved resistant High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-mir-125b-2 Methotrexate 126941 NSC740 approved resistant High Colorectal Adenocarcinoma cell line (HT-29)
hsa-mir-125b-2 Imatinib 5291 NSC743414 approved resistant High Chronic Myelogenous Leukemia tissue
hsa-mir-125b-2 Doxorubicin 31703 NSC123127 approved sensitive Low Hepatocellular Carcinoma cell line (Huh-7, HLE, HuH1)
hsa-mir-125b-2 Dabrafenib 44462760 NSC764134 approved resistant High Melanoma cell line (A375)
hsa-mir-125b-2 Dabrafenib 44462760 NSC764134 approved resistant cell line (A375)
hsa-mir-125b-2 Paclitaxel 36314 NSC125973 approved resistant cell line (W1)
hsa-mir-125b-2 Topotecan 60699 NSC609699 approved resistant cell line (W1)
hsa-mir-125b-2 Vincristine 5978 approved resistant cell line (W1)
hsa-mir-125b-2 Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-mir-125b-2 Tamoxifen 2733525 NSC180973 approved resistant tissue (ER-positive breast cancer)
hsa-mir-125b-2 Tamoxifen 2733525 NSC180973 approved sensitive cell line (MCF7)
hsa-mir-125b-2 Ceritinib 57379345 NSC776422 approved resistant cell line (H3122)
hsa-miR-125b-2-3p Platinum 23939 resistant High Ovarian Cancer tissue
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved sensitive Low Cervical Cancer tissue
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant High Gastric Cancer cell line (BGC823)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant High Gastric Cancer cell line (SGC-7901)
hsa-miR-125b-2-3p Vemurafenib 42611257 NSC761431 approved sensitive High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-125b-2-3p Dabrafenib 44462760 NSC764134 approved sensitive High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-125b-2-3p Ceritinib 57379345 NSC776422 approved resistant High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant High Gastric Cancer tissue
hsa-miR-125b-2-3p Fluorouracil 3385 NSC19893 approved resistant High Gastric Cancer tissue
hsa-miR-125b-2-3p Cyclophosphamide + Doxorubicin + Vincristine + Prednisone + Rituximab resistant High Diffuse Large B-Cell Lymphoma cell line (SU-DHL-2)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant High Gastric Cancer cell line (SGC-7901, BGC-823)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant High Lung Adenocarcinoma cell line (A549)
hsa-miR-125b-2-3p Oxaliplatin 6857599 NSC266046 approved sensitive Low Colorectal Cancer cell line (HCT8, HCT-116)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant High Ovarian Cancer cell line (A2780)
hsa-miR-125b-2-3p Antiepileptic Drug sensitive High Pediatric Epilepsy tissue
hsa-miR-125b-2-3p Vemurafenib 42611257 NSC761431 approved sensitive cell line (451Lu)
hsa-miR-125b-2-3p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant cell line (A549)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-miR-125b-2-3p 4-Hydroxytamoxifen+Tamoxifen resistant cell line (LY2)
hsa-miR-125b-2-3p Ethanol+Tamoxifen resistant cell line (LY2)
hsa-miR-125b-2-3p Methotrexate 126941 NSC740 approved resistant cell line (HT29)
hsa-miR-125b-2-3p Sunitinib 5329102 NSC750690 approved resistant tissue (CardB)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant cell line (A549)
hsa-miR-125b-2-3p Oxaliplatin 6857599 NSC266046 approved resistant cell line (IGROV-1)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant cell line (IGROV-1)
hsa-miR-125b-2-3p Paclitaxel 36314 NSC125973 approved resistant cell line (PC3PR70)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-125b-2-3p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)
hsa-miR-125b-2-3p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (100 ng/ml)
hsa-miR-125b-2-3p Ceritinib 57379345 NSC776422 approved resistant cell line (H3122)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant cell line (SGC-7901)
hsa-miR-125b-2-3p Cisplatin 5460033 NSC119875 approved resistant cell line (BGC-823)

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