miRTarBase - #MIRT093523


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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 GALNT7   
Synonyms GALNAC-T7, GalNAcT7
Description polypeptide N-acetylgalactosaminyltransferase 7
Transcript NM_017423   
Expression
Putative miRNA Targets on GALNT7
3'UTR of GALNT7
(miRNA target sites are highlighted)		 
>GALNT7|NM_017423|3'UTR
   1 AGAGAAAAAAATAAACCAATAACCTACCTACTGACAAGTAAATTTATACAGGACTGAAAACCGCCTGAAACCTGCTGCAA
  81 CTATTGTTATTAACTCTGTATAGCTCCAAACCTGGAACCTCCTGATCAGTTTGAAGGACATTGATAAACTGTGATTTTAC
 161 AATAACATTATCATCTGCAGTTACTGTTTACAAGACTGCTTTTACCTTAAACTTTGTAGATGTTTACATCTTTTTGTTGT
 241 GTTTTAAGATGATGTTGGTAATTTGTGCCTTTAGCTCTGTTTTATTAGACAGAGTTAAAGCATGTTGTCTTCTTTGGGAT
 321 TACACTCAGGGGTCTGAAAGGCAGTTTGATTTTTATTTTTAACACACTTGAAAAAAGGTTGGAGTAGCCAGACTTTCATA
 401 TATAACTTGGTGATTATCAACCTGTTGTGTCTTTATTTAATTTTACATCTTTTTGAAGCACTGCCACAGGTTATTAGCCA
 481 AGGTGGCCTTCCTTCACAGTCATGCTGCTTTTTTGAAAGGTGAATTTCAACACATTTAGTGCCTCTTTCATTTCTCAGTA
 561 TATATTTCAAGAGCTTGTGATGAAATCTATAGGATGGTAATGATGGACTTGTCACCTGTATGGGGAATACTTTTACTACT
 641 CAGAAATGAATTTATGTGCTGCCATTTGCTATAAAGTTGAACTTTGTATGGCTTGAAAAAGAAATGACAATATGGAACAT
 721 CCCAAGGCTGTCCCATAGGGTTGGAAGTTGTGTAGCATTCACTCCCTTACCTACTGGCATTCCCAGTGCCCTCTGTCCAT
 801 ACCTACTTCTAGGATTGCAAAGGAGTCTTCCAACTAGAGAAAAATTGTCCACTGACATTTGGGATTTACTTTTCTCCAAT
 881 ACCTGCCAATACAGAAAACTATTATCAGTTGTTATTGTTATCCCTTGAAAGCGAGGGTGACAAAAACAACAAAACACCGT
 961 TATAAACACATCAAAGGTTCATTCTGACTGAGGTAAGACTTTCCAAGCCCTTGTTAGATTAGGCCTTATAAAACTTGTGT
1041 GCATTATAACCTAAGCTGTGCAACCTGTGAAGCCAAGAGTGAACTGATGTTTCATTTATATTTTCATCCAAATGACATTA
1121 TCTGCACGTTTTTAAAATTTAAAAACAAAGGACTATTTAAAAATACAGTTTATTAACAAACGTGAACTACTTTCTGTTAC
1201 ATTAGGTGTTCCCTAGTGTTTCTTAATTTCTTTTTAGAAAGTGTATTTTTATTAGTATTTTTCCGGTGAACAGAAGATTT
1281 GTTTGGATTTAAACATTTACTAAGACAGTACCTATTAGGAAAACCAAATATTGCAAATGGTCAATTCGATTTTAATTTCT
1361 CAAAAGATACTCTGTTATCCAGAAGATTAAAATGCCTACATTGAGTGCTTAAAAAAAAAAAAACAACTGTGATGATGTGA
1441 GCAGAATGGCAAGTAAGTTAAGCATTTTTGATCCTGTAATCATGGTATCATTACAATGAAAGGAATTCACAAACTACTGC
1521 CAGAGGAAGTTTGTTTTTTAATTTAAGAGGGAAATATAACCTATAAATTTGTTTCTTCCAAGCTTAGCTCTTAAATTTGG
1601 AGACTCAAAGTTAAACATCCTCAACAGAGTTTTATTTATAATTTTGAATTGTCAATTTGTATTTTGCTACTGATCTGTGA
1681 TCAACCATTTTAACTTTCATCTCTAGGGATGTTTAACATTTATAATTGCAAAATAAACCAACTATAAAAAAAGAAACTAA
1761 GAGAGAATTGGTACTTTAATTACTTGTGTGTTTGCAAATAGGCTCCATTTTCCATGTTGAGTAGATTATAACCTTATTAA
1841 CTATGCATAGGCCTAAGAAAGGTGGCAATGAACTGTGCATGTAAATTTTAAATGGGTACTTTGTGCAATTCGTTAAAAGA
1921 AGATACTCTATGAATATGATTCTATATATTGAAATCAGAAAACCTACCAAACAAAAACATCAGAAGCTGCTGCCATAATG
2001 ACTATTTTCTACTGTAGGCTGCTTTGGAAATAATTCCCATATCCTTGCTTTGTAAGTTGGTAATATCACTATGCATTTCT
2081 ACACATTTTATAAATTTGATTTATGCAGATTTTGATACACTGTATGTTTCTGTAGAAATTGTATAAATATTCAAAATTTT
2161 ATTAGGATAAATTTGAGAAACTTACGTATATCTTAATTCTGGGTTGCTTGTTTTTTAGGTGACAAAAATAAAATATTGTA
2241 TTTTAATTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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' caggguUCUCGGA-----CUGAACACu 5'
                || ||||      ||||||| 
Target 5' tagattAG-GCCTTATAAAACTTGTGt 3'
 1015 - 1040 143.00 -11.70
2 
miRNA  3' caggguucucggACUGAACACu 5'
                      | ||||||| 
Target 5' ttggtactttaaTTACTTGTGt 3'
 1768 - 1789 142.00 -8.70
3 
miRNA  3' caGGGUUCUCGGACUGAACACu 5'
            ::|||||     :|||||| 
Target 5' atTTCAAGA-----GCTTGTGa 3'
 564 - 580 135.00 -16.40
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30170336 3 COSMIC
COSN28866847 12 COSMIC
COSN30457432 18 COSMIC
COSN19657175 29 COSMIC
COSN30506851 30 COSMIC
COSN20075011 45 COSMIC
COSN14102551 64 COSMIC
COSN28185957 106 COSMIC
COSN30715037 108 COSMIC
COSN20075118 113 COSMIC
COSN30162780 120 COSMIC
COSN31480759 128 COSMIC
COSN24720747 150 COSMIC
COSN31585632 194 COSMIC
COSN30165650 516 COSMIC
COSN31526884 631 COSMIC
COSN16740958 852 COSMIC
COSN8374136 1042 COSMIC
COSN31609991 1386 COSMIC
COSN27420538 1424 COSMIC
COSN31515627 1504 COSMIC
COSN24424798 1567 COSMIC
COSN22505752 1691 COSMIC
COSN24300480 1712 COSMIC
COSN26671234 1903 COSMIC
COSN26573215 1912 COSMIC
COSN31538702 1912 COSMIC
COSN28692036 1943 COSMIC
COSN31480466 1959 COSMIC
COSN6814777 2068 COSMIC
COSN31528102 2094 COSMIC
COSN31562904 2186 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1005505657 4 dbSNP
rs1228930216 5 dbSNP
rs1409972965 5 dbSNP
rs1164725583 9 dbSNP
rs779436570 13 dbSNP
rs1427082471 14 dbSNP
rs35007233 16 dbSNP
rs746399267 17 dbSNP
rs771685808 18 dbSNP
rs183336314 20 dbSNP
rs959030914 28 dbSNP
rs757213717 29 dbSNP
rs1227763851 30 dbSNP
rs371601909 33 dbSNP
rs1350142596 34 dbSNP
rs373630379 36 dbSNP
rs1224607824 37 dbSNP
rs377469489 41 dbSNP
rs1292300905 47 dbSNP
rs761600369 48 dbSNP
rs1213218702 50 dbSNP
rs1039098647 63 dbSNP
rs901821956 64 dbSNP
rs1184929968 67 dbSNP
rs1240782974 71 dbSNP
rs997499841 79 dbSNP
rs1489642603 84 dbSNP
rs1247558644 91 dbSNP
rs977711146 95 dbSNP
rs1472173524 98 dbSNP
rs1158840431 99 dbSNP
rs1409627753 101 dbSNP
rs768741426 112 dbSNP
rs73872559 120 dbSNP
rs1281262953 122 dbSNP
rs1220764597 124 dbSNP
rs376076318 126 dbSNP
rs1269297352 134 dbSNP
rs935694202 140 dbSNP
rs1016810783 146 dbSNP
rs959569123 149 dbSNP
rs1390309057 150 dbSNP
rs1320639761 154 dbSNP
rs113077097 155 dbSNP
rs538919191 155 dbSNP
rs141053550 181 dbSNP
rs572267728 182 dbSNP
rs1174547387 200 dbSNP
rs910326344 206 dbSNP
rs1435318161 212 dbSNP
rs971040279 216 dbSNP
rs192584005 217 dbSNP
rs762164660 221 dbSNP
rs372990613 222 dbSNP
rs981128489 223 dbSNP
rs1447374801 228 dbSNP
rs1209478879 245 dbSNP
rs1460891431 267 dbSNP
rs150260684 271 dbSNP
rs901301412 282 dbSNP
rs1312614350 287 dbSNP
rs1221894541 293 dbSNP
rs1267210124 301 dbSNP
rs990094059 305 dbSNP
rs1366955248 319 dbSNP
rs1297810566 323 dbSNP
rs1451339829 324 dbSNP
rs1323967966 326 dbSNP
rs1301676498 333 dbSNP
rs1205553894 342 dbSNP
rs1360195035 346 dbSNP
rs1170194820 350 dbSNP
rs930246410 354 dbSNP
rs1428178591 361 dbSNP
rs765792472 370 dbSNP
rs1047339919 376 dbSNP
rs1189434304 380 dbSNP
rs1444131710 381 dbSNP
rs773653201 383 dbSNP
rs759051441 386 dbSNP
rs1483537308 387 dbSNP
rs1234283942 388 dbSNP
rs574828987 399 dbSNP
rs1468238439 401 dbSNP
rs1034296251 405 dbSNP
rs1202790338 407 dbSNP
rs894577680 410 dbSNP
rs1344010754 412 dbSNP
rs1274956919 413 dbSNP
rs943225336 432 dbSNP
rs1319464112 434 dbSNP
rs1314268502 440 dbSNP
rs138946471 444 dbSNP
rs149244596 445 dbSNP
rs1298062698 447 dbSNP
rs967579504 448 dbSNP
rs1372769802 459 dbSNP
rs1169540899 467 dbSNP
rs933319155 472 dbSNP
rs755839164 475 dbSNP
rs1032964387 478 dbSNP
rs1167037130 480 dbSNP
rs1413984395 495 dbSNP
rs1329580902 529 dbSNP
rs1048224356 549 dbSNP
rs1408290668 551 dbSNP
rs1287934627 563 dbSNP
rs1345972865 570 dbSNP
rs779972925 571 dbSNP
rs747148049 584 dbSNP
rs763620753 590 dbSNP
rs1266804832 592 dbSNP
rs957255024 596 dbSNP
rs532572089 597 dbSNP
rs910188916 601 dbSNP
rs545288303 607 dbSNP
rs1288317147 612 dbSNP
rs944478264 616 dbSNP
rs1227090736 626 dbSNP
rs753054112 635 dbSNP
rs1309020403 639 dbSNP
rs1016534043 647 dbSNP
rs1388869774 649 dbSNP
rs1295483170 655 dbSNP
rs1458510600 656 dbSNP
rs1363296171 657 dbSNP
rs976198210 672 dbSNP
rs1426627203 679 dbSNP
rs919011180 683 dbSNP
rs1012449853 685 dbSNP
rs1344163356 686 dbSNP
rs1022703411 707 dbSNP
rs930169182 711 dbSNP
rs565185377 727 dbSNP
rs1047204838 730 dbSNP
rs1204085786 736 dbSNP
rs753752399 738 dbSNP
rs888722429 740 dbSNP
rs981098902 753 dbSNP
rs73872561 763 dbSNP
rs3775590 764 dbSNP
rs990451474 771 dbSNP
rs184568522 772 dbSNP
rs1376468526 775 dbSNP
rs529735023 794 dbSNP
rs1329680084 796 dbSNP
rs894433866 800 dbSNP
rs1387551316 803 dbSNP
rs1014345534 813 dbSNP
rs1024852458 816 dbSNP
rs1389319538 822 dbSNP
rs903260355 824 dbSNP
rs577402778 826 dbSNP
rs745729823 838 dbSNP
rs923347510 845 dbSNP
rs1379153047 849 dbSNP
rs998718400 852 dbSNP
rs1427556993 861 dbSNP
rs146941910 863 dbSNP
rs1039327296 882 dbSNP
rs1245773524 890 dbSNP
rs1032820629 898 dbSNP
rs1406573863 902 dbSNP
rs1269364494 907 dbSNP
rs907843257 915 dbSNP
rs957285878 915 dbSNP
rs1330274203 916 dbSNP
rs1258145736 917 dbSNP
rs569279016 924 dbSNP
rs1364775006 934 dbSNP
rs142395216 942 dbSNP
rs1228115904 945 dbSNP
rs942054908 959 dbSNP
rs986008854 960 dbSNP
rs758577746 964 dbSNP
rs1333508760 976 dbSNP
rs1412676251 977 dbSNP
rs1404195770 978 dbSNP
rs1292060868 991 dbSNP
rs1038346716 996 dbSNP
rs895425355 1001 dbSNP
rs1387987039 1035 dbSNP
rs1017271698 1038 dbSNP
rs1170059157 1064 dbSNP
rs1449616194 1065 dbSNP
rs1241971455 1070 dbSNP
rs1184704098 1079 dbSNP
rs538259266 1080 dbSNP
rs1225219955 1085 dbSNP
rs1258826171 1085 dbSNP
rs1012418629 1090 dbSNP
rs1046635129 1094 dbSNP
rs1451367810 1105 dbSNP
rs137995292 1108 dbSNP
rs1002999828 1112 dbSNP
rs566030851 1123 dbSNP
rs919029544 1128 dbSNP
rs950453169 1129 dbSNP
rs982932255 1132 dbSNP
rs1342216784 1135 dbSNP
rs1334711771 1149 dbSNP
rs955871382 1153 dbSNP
rs1011263488 1155 dbSNP
rs1167992653 1157 dbSNP
rs1430015886 1165 dbSNP
rs143552054 1165 dbSNP
rs1412535989 1178 dbSNP
rs113852863 1181 dbSNP
rs575005075 1182 dbSNP
rs1370751688 1183 dbSNP
rs1188818109 1191 dbSNP
rs1291970352 1193 dbSNP
rs1389830427 1197 dbSNP
rs186474233 1198 dbSNP
rs1207671134 1213 dbSNP
rs974637849 1222 dbSNP
rs950129573 1265 dbSNP
rs192538227 1266 dbSNP
rs114139762 1268 dbSNP
rs1284774742 1272 dbSNP
rs1428294188 1283 dbSNP
rs1433755627 1286 dbSNP
rs1315082151 1288 dbSNP
rs1227695373 1295 dbSNP
rs1348491935 1302 dbSNP
rs546219303 1303 dbSNP
rs998909785 1307 dbSNP
rs1360952313 1308 dbSNP
rs112436840 1310 dbSNP
rs1054296335 1327 dbSNP
rs768992199 1342 dbSNP
rs1348966532 1348 dbSNP
rs184851635 1349 dbSNP
rs1406642866 1350 dbSNP
rs527573091 1362 dbSNP
rs770005917 1364 dbSNP
rs3839159 1368 dbSNP
rs397841437 1368 dbSNP
rs1250473925 1370 dbSNP
rs1410316165 1376 dbSNP
rs1184813038 1378 dbSNP
rs1463893832 1396 dbSNP
rs965975448 1402 dbSNP
rs11427838 1411 dbSNP
rs397828101 1411 dbSNP
rs565676151 1411 dbSNP
rs878880543 1411 dbSNP
rs997614837 1411 dbSNP
rs1208110625 1418 dbSNP
rs1025957548 1422 dbSNP
rs948252831 1422 dbSNP
rs1046687224 1424 dbSNP
rs1231459651 1425 dbSNP
rs906677163 1434 dbSNP
rs950485687 1435 dbSNP
rs758717740 1453 dbSNP
rs1438156245 1473 dbSNP
rs541348368 1480 dbSNP
rs962891350 1495 dbSNP
rs1331270218 1496 dbSNP
rs1319313577 1497 dbSNP
rs1455153209 1498 dbSNP
rs999713892 1501 dbSNP
rs1368057448 1507 dbSNP
rs189317657 1508 dbSNP
rs891581411 1522 dbSNP
rs1424881103 1543 dbSNP
rs1386390240 1545 dbSNP
rs1479130303 1549 dbSNP
rs1253820972 1556 dbSNP
rs916179980 1557 dbSNP
rs748527927 1561 dbSNP
rs1463582873 1563 dbSNP
rs1337279719 1589 dbSNP
rs1269985775 1595 dbSNP
rs1046159341 1598 dbSNP
rs1011649480 1603 dbSNP
rs924600069 1605 dbSNP
rs1276265371 1606 dbSNP
rs1220676774 1609 dbSNP
rs1367908908 1617 dbSNP
rs1384451567 1618 dbSNP
rs1021209424 1619 dbSNP
rs879733747 1623 dbSNP
rs1366733445 1627 dbSNP
rs1323204410 1628 dbSNP
rs996025251 1630 dbSNP
rs1311571775 1636 dbSNP
rs1335936625 1639 dbSNP
rs557095730 1641 dbSNP
rs575307172 1642 dbSNP
rs73872562 1646 dbSNP
rs1270470661 1649 dbSNP
rs1007427333 1651 dbSNP
rs558185658 1656 dbSNP
rs907950143 1660 dbSNP
rs374375729 1661 dbSNP
rs997415880 1669 dbSNP
rs1482889848 1685 dbSNP
rs1235630817 1702 dbSNP
rs1212006019 1703 dbSNP
rs1026407972 1709 dbSNP
rs1484285769 1712 dbSNP
rs1225708687 1718 dbSNP
rs563049504 1718 dbSNP
rs950348722 1723 dbSNP
rs763339589 1730 dbSNP
rs1297699691 1732 dbSNP
rs1227205080 1738 dbSNP
rs766960024 1739 dbSNP
rs773739109 1742 dbSNP
rs916547697 1743 dbSNP
rs573975837 1745 dbSNP
rs948056399 1745 dbSNP
rs1450685007 1759 dbSNP
rs1255777527 1760 dbSNP
rs1005841644 1766 dbSNP
rs148655217 1769 dbSNP
rs1392188240 1773 dbSNP
rs1171266908 1774 dbSNP
rs1423271992 1776 dbSNP
rs928232706 1779 dbSNP
rs1183517492 1781 dbSNP
rs1485908181 1791 dbSNP
rs1250814799 1798 dbSNP
rs1202677618 1799 dbSNP
rs1184227166 1800 dbSNP
rs1251477475 1814 dbSNP
rs1220251339 1815 dbSNP
rs1409539915 1818 dbSNP
rs935493522 1820 dbSNP
rs578087117 1825 dbSNP
rs1456507770 1830 dbSNP
rs543661528 1833 dbSNP
rs1311292327 1839 dbSNP
rs1356598528 1848 dbSNP
rs1052649179 1852 dbSNP
rs1177143721 1855 dbSNP
rs893971479 1858 dbSNP
rs947115654 1860 dbSNP
rs1298942152 1863 dbSNP
rs551745807 1866 dbSNP
rs763401499 1869 dbSNP
rs959103154 1870 dbSNP
rs1042806333 1875 dbSNP
rs141262441 1879 dbSNP
rs1475495607 1881 dbSNP
rs1408118051 1882 dbSNP
rs534987065 1897 dbSNP
rs1023103275 1905 dbSNP
rs1396559933 1909 dbSNP
rs972063320 1911 dbSNP
rs879119587 1912 dbSNP
rs1030186666 1913 dbSNP
rs981676031 1928 dbSNP
rs924852798 1930 dbSNP
rs1213705509 1931 dbSNP
rs1336153721 1937 dbSNP
rs1392811786 1939 dbSNP
rs1268005502 1941 dbSNP
rs1005117419 1955 dbSNP
rs200296689 1969 dbSNP
rs934682383 1973 dbSNP
rs990136065 1976 dbSNP
rs1286063701 1996 dbSNP
rs766773308 2003 dbSNP
rs775105699 2005 dbSNP
rs1386434845 2007 dbSNP
rs914682044 2008 dbSNP
rs1314416415 2009 dbSNP
rs1461984532 2010 dbSNP
rs150784852 2015 dbSNP
rs1023740133 2022 dbSNP
rs1255538604 2029 dbSNP
rs531052499 2039 dbSNP
rs1039292533 2040 dbSNP
rs1207651186 2050 dbSNP
rs1197831586 2051 dbSNP
rs982146757 2060 dbSNP
rs1268976632 2064 dbSNP
rs928196647 2066 dbSNP
rs901644472 2069 dbSNP
rs1207368866 2072 dbSNP
rs1427205284 2074 dbSNP
rs935561230 2077 dbSNP
rs1232934668 2080 dbSNP
rs866200355 2083 dbSNP
rs1431413881 2085 dbSNP
rs1175232245 2089 dbSNP
rs1354676876 2094 dbSNP
rs1463057961 2095 dbSNP
rs568526061 2100 dbSNP
rs1047680595 2101 dbSNP
rs781293940 2117 dbSNP
rs915387963 2121 dbSNP
rs1304081435 2122 dbSNP
rs946887154 2138 dbSNP
rs1385499308 2146 dbSNP
rs1171817663 2147 dbSNP
rs1042773687 2148 dbSNP
rs373139334 2151 dbSNP
rs886352231 2158 dbSNP
rs900283200 2163 dbSNP
rs1370154971 2173 dbSNP
rs1218025891 2178 dbSNP
rs1301185506 2182 dbSNP
rs1448408040 2182 dbSNP
rs1245675773 2184 dbSNP
rs1005874191 2186 dbSNP
rs1051412043 2187 dbSNP
rs930860005 2202 dbSNP
rs1015866373 2208 dbSNP
rs1004764554 2212 dbSNP
rs1235282285 2220 dbSNP
rs1295502430 2234 dbSNP
rs894918961 2235 dbSNP
rs537661263 2237 dbSNP
rs1326980731 2238 dbSNP
rs1482821513 2239 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.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' caggguucucggacUGAACACu 5'
                        ||||||| 
Target 5' -----ccuuauaaaACUUGUGu 3'
 		1 - 17
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]
CLIP-seq Support 1 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000265000.4 | 3UTR | CCUUAUAAAACUUGUGUGCAUUAUA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
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 0.642 3.6e-4 0.701 6.8e-5 24 Click to see details
GSE21687 Ependynoma primary tumors -0.356 1.9e-3 -0.273 1.5e-2 64 Click to see details
GSE21032 Prostate cancer -0.262 8.4e-3 -0.269 7.0e-3 83 Click to see details
GSE32688 Pancreatic cancer 0.375 1.7e-2 0.354 2.3e-2 32 Click to see details
GSE28260 Renal cortex and medulla 0.531 3.1e-2 0.582 1.8e-2 13 Click to see details
GSE38974 Chronic obstructive pulmonary disease 0.342 4.7e-2 0.150 2.4e-1 25 Click to see details
GSE42095 Differentiated embryonic stem cells -0.226 1.5e-1 -0.319 6.9e-2 23 Click to see details
GSE26953 Aortic valvular endothelial cells 0.213 1.6e-1 0.244 1.3e-1 24 Click to see details
GSE15076 Monocyte-derived dendritic cells -0.874 1.6e-1 -0.500 3.3e-1 3 Click to see details
GSE19783 ER+ ER+ breast cancer 0.226 1.7e-1 0.110 3.2e-1 20 Click to see details
GSE35602 Colorectal cancer stromal tissue -0.155 2.3e-1 0.078 3.6e-1 25 Click to see details
GSE17498 Multiple myeloma 0.118 2.3e-1 0.005 4.9e-1 40 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis 0.158 2.5e-1 0.487 1.5e-2 20 Click to see details
GSE19536 Breast cancer -0.058 2.8e-1 -0.008 4.7e-1 100 Click to see details
GSE19350 CNS germ cell tumors 0.11 3.7e-1 0.075 4.1e-1 12 Click to see details
GSE19783 ER- ER- breast cancer 0.038 3.7e-1 0.034 3.8e-1 79 Click to see details
GSE38226 Liver fibrosis 0.036 4.4e-1 0.331 7.1e-2 21 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
STAD -0.532 0 -0.526 0 32 Click to see details
LIHC -0.269 0.03 -0.247 0.04 49 Click to see details
PAAD -0.91 0.05 -1.000 0.5 4 Click to see details
UCEC -0.387 0.05 -0.546 0.01 19 Click to see details
PCPG 0.978 0.07 1.000 0.5 3 Click to see details
THCA 0.168 0.1 0.061 0.32 59 Click to see details
PRAD 0.169 0.12 0.044 0.38 50 Click to see details
ESCA -0.348 0.15 -0.282 0.2 11 Click to see details
CHOL -0.392 0.15 -0.383 0.15 9 Click to see details
LUSC 0.149 0.19 0.139 0.2 38 Click to see details
LUAD 0.279 0.19 0.273 0.2 12 Click to see details
KIRC -0.107 0.19 -0.089 0.24 68 Click to see details
BRCA 0.093 0.2 0.045 0.34 84 Click to see details
KICH 0.174 0.2 0.124 0.28 25 Click to see details
HNSC 0.087 0.29 0.125 0.22 42 Click to see details
BLCA 0.1 0.35 0.077 0.38 18 Click to see details
KIRP -0.061 0.37 -0.120 0.26 32 Click to see details
COAD -0.118 0.39 -0.214 0.31 8 Click to see details
CESC -0.018 0.49 -0.500 0.33 3 Click to see details
CESC -0.018 0.49 -0.500 0.33 3 Click to see details
CESC -0.018 0.49 -0.500 0.33 3 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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