pre-miRNA Information
pre-miRNA hsa-mir-4524a   
Genomic Coordinates chr17: 69099564 - 69099632
Description Homo sapiens miR-4524a stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4524a-5p
Sequence 6| AUAGCAGCAUGAACCUGUCUCA |27
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1322445998 8 dbSNP
rs1350790266 13 dbSNP
rs1263495678 21 dbSNP
Putative Targets

Gene Information
Gene Symbol USP53   
Synonyms -
Description ubiquitin specific peptidase 53
Transcript NM_019050   
Expression
Putative miRNA Targets on USP53
3'UTR of USP53
(miRNA target sites are highlighted)
>USP53|NM_019050|3'UTR
   1 AGTGAAAAAGGACTAGACCTGTGTTACATAATAATCTTGGTTCAAGCTGCCCTTCTGAACAAAGATATAAACCTAGCATA
  81 CATTGTAATAGATAACTGGTAAAACTGACCAACTTTTACTTCTCAGAGGCCATTTAAATATAATAGGAACCTACTGACCA
 161 AACCTAGTGATACATAAAATTAAAGCCTGTGGCATTTTTAAAGTTGTTAATCACTATACATATGTATGTGTATATGTGTA
 241 TACACATATATAATTTTATGATCAATATCTTAGATATTTTAGAAATTCCCTTTGAATAGTCTTGGCGTGCCGTGAAAAAT
 321 AGAAAATCAGGGAGATATAATAATTCATTTGTCATATGCTACAGTTGAATAAAAATTAAATTTGTCCCCCTATTTTGTGG
 401 CCAGTAGACTGGGAAGTATTAAACTAACCAGTACTCATGTATGGAGATTATAAACTATGCTAATTGAAAAGTACCAGGTG
 481 ATACATAGCCTGGTACTTTTTTGTCAAAGAATTGCTTTATGAAGAAGCACTTTCTAATGGGTAACCAGAAAAGGGCTTCA
 561 CCCATTTGTTTTTGACTTCTATGATAGTCACTGCATATGATCCCTTTAAGTGTCTTTAAAAAAAATGACTTATGAATTTG
 641 ATAGCATTTGGGGAAAAAAAGCCTTATATGATTAACAATTTGTAAGTTTTCAAGATCGGATGGAATTTAATTTTGCTCCT
 721 AGAATTTTTGTCTTCAGAATATCTAGTTAAGATAAATTAGGCCTTTGACTATTATAGGTATTCATAAATGCTACTTTAGC
 801 CATGTAAGTTAAAAAGTTAAAATACTTAAACTTTAGTGTATTTATTTATCTCGTTACTTTTTTTCTAATTTTATATGAAA
 881 TGTGAAAGGTCTTTATTTTGGTTTGGTTTACTTTGGGCTGCTAACCACCAGTGTTAGGAATTAATGTAGGGCACCCTCTT
 961 ATTGGGAATGTCACTGTAATTGCCTACATTTTCTTTGCTGTAATATTACCTGCTTATAGGTTGTCAACCCATTTTATCTG
1041 AATTTGAAAATCTATCTAGGTTTCCAGATTAAATTTCTACCTTTCATATAGAGAGTTTAATTTTAATAAAATGTTTAATT
1121 AGAGCATCCTTCCCTTTTATTCTACTTTGAACAAATAGTAATTTTACCCCAACTACTTTTCATGAAGAGTGCTTTGAAAA
1201 TTAAAGGAATTTTTATTATTATGGTAACCTTATGAGTAAAAATAAGTTACTTTAATTGCTTTATTTCGTTAGTTGTCATT
1281 TTATTTTGTACTATGCTGGTAAACTAATTGTGGTTTAGAATAGTTTTATGTTCACTCCTGATAACTGAGAAACAGAACTA
1361 AAGTTTTCCTTACATTGCTAAATGGATAAACCTCATATTCAATAAACTAGTAAATGTAGCCACTTGACTGATTGCGTAAA
1441 TCGTGTTAAAACATTCTAAAATGTTGTAACTAATTTAATGTGAATACTGTTAAACAGAAAATAATTGCTTATAAAAGTCT
1521 AACTTCACCCAGTTACCAAGTCTTGGCCAAATTTTATCTTCTGCCTATAGTTTTTACTAGCCTTTTTAAACTATAATAGT
1601 GAGTGATCATTACTTTATATTCTCGTAAGTTAGAAATACTTGAATGCCAAATTAATTTTGTTTTAAGAAAGCTTATTTTT
1681 AACATAATTTTTTAGTGTGGAGGGTTTGTAAATAATGTAAAGTTTGTAAACCTGTATTTAAAATACCAAAGTTTTTCTTC
1761 TTTTATAACATTGTAAGATACTAGAAAAATGGGCTTCAAGTTTTTTAATAGCTTTCACAGTTTGTGTAGTTTTTTTTTTC
1841 TATTTGGTTAAGATGTGAGTTGGAAATGTATTATTTGAAACATTTAAACTAATTTTTGTATTTAACAGCAGTCTCAGACA
1921 TTTGTCTTTTCAACTCAGTTGAGTTGTAGATATCAAATAGAAATGTCCAGTTTTGCCTCTTTTAAGTACTGTCCAGTTGA
2001 AACCTCCTGACTCATGTACTACTACACAAACTAGAAAATGCCCATTTATTTTTGTTGATTCAACACTCCAGATACAGATT
2081 GATACATATATACTAATCATTTTATTTCATGTAAAAGTTTTACATCTAGGGTGCCTATTTATTTTTATAGATGCTTTCAT
2161 CCAGTTATAAGCTTATTATAACTTTGTAAATATTTCAGCCAACAGTTGTAATGTTTAAAATACTTACCTTCAGAATGTTA
2241 TATTTTCATGTGAAATCAATTTCTTCTAATTCAAAAAAATTTTAAGATAAACTGATTTTTAAGTTTAAAAAAAAAAAAAA
2321 AAAA
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' acUCUGUCCAAGU---A--CGACGAUa 5'
            :| : ||||:|   |  ||||||| 
Target 5' ttGGTTTGGTTTACTTTGGGCTGCTAa 3'
898 - 924 150.00 -12.20
2
miRNA  3' acucuguCCAAGUACGACGaua 5'
                 |||||| |||||   
Target 5' taatcttGGTTCAAGCTGCcct 3'
32 - 53 127.00 -14.32
3
miRNA  3' acuCUGUCCAAG-UACGACGAUa 5'
             |:||  ||: | |:||:|| 
Target 5' tgtGGCATTTTTAAAGTTGTTAa 3'
188 - 210 123.00 -7.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN20075010 27 COSMIC
COSN26438987 49 COSMIC
COSN30480982 52 COSMIC
COSN9005532 312 COSMIC
COSN14471984 313 COSMIC
COSN7727960 315 COSMIC
COSN6793833 322 COSMIC
COSN20100495 626 COSMIC
COSN1983797 1437 COSMIC
COSN25029952 1453 COSMIC
COSN7772286 1839 COSMIC
COSN20100505 2054 COSMIC
COSN19248100 2226 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1396854154 2 dbSNP
rs1452472975 13 dbSNP
rs1174768020 14 dbSNP
rs1373108501 16 dbSNP
rs778653161 19 dbSNP
rs759424753 21 dbSNP
rs1399083651 24 dbSNP
rs376139957 25 dbSNP
rs779864035 28 dbSNP
rs1345838220 31 dbSNP
rs1244642519 32 dbSNP
rs1373893028 34 dbSNP
rs746865221 35 dbSNP
rs768983135 36 dbSNP
rs777005536 39 dbSNP
rs1200495719 52 dbSNP
rs557713002 53 dbSNP
rs1452002614 54 dbSNP
rs1207663284 57 dbSNP
rs1025754006 70 dbSNP
rs1245853028 73 dbSNP
rs907113049 76 dbSNP
rs1471800449 77 dbSNP
rs1258554019 83 dbSNP
rs1002776477 86 dbSNP
rs1365530460 92 dbSNP
rs1437429969 97 dbSNP
rs1376707770 108 dbSNP
rs1329729039 109 dbSNP
rs1449379613 122 dbSNP
rs1188676673 127 dbSNP
rs1175912609 134 dbSNP
rs1413440395 139 dbSNP
rs951653469 151 dbSNP
rs1174013908 155 dbSNP
rs1420835932 160 dbSNP
rs1423812819 165 dbSNP
rs878921744 168 dbSNP
rs762267175 170 dbSNP
rs1176548447 201 dbSNP
rs1458878132 217 dbSNP
rs767981463 223 dbSNP
rs1209299305 224 dbSNP
rs139713098 225 dbSNP
rs990500921 226 dbSNP
rs916353306 231 dbSNP
rs1353270978 232 dbSNP
rs1320060391 233 dbSNP
rs1449498237 239 dbSNP
rs1302814596 266 dbSNP
rs533802916 266 dbSNP
rs1343666124 269 dbSNP
rs553663422 278 dbSNP
rs1289297382 292 dbSNP
rs1378304879 295 dbSNP
rs1379315942 296 dbSNP
rs1434722158 296 dbSNP
rs1156418370 297 dbSNP
rs760735214 298 dbSNP
rs1441359857 304 dbSNP
rs181511594 307 dbSNP
rs902324520 308 dbSNP
rs1295073429 313 dbSNP
rs1334883009 316 dbSNP
rs186515577 321 dbSNP
rs1487977408 322 dbSNP
rs1284181055 330 dbSNP
rs1050964981 335 dbSNP
rs553174506 335 dbSNP
rs749530485 335 dbSNP
rs964853080 341 dbSNP
rs149770638 345 dbSNP
rs1227170575 347 dbSNP
rs1312435717 347 dbSNP
rs1381975356 348 dbSNP
rs1285239804 352 dbSNP
rs1030527676 361 dbSNP
rs765742405 366 dbSNP
rs190857484 385 dbSNP
rs182337189 386 dbSNP
rs907850786 387 dbSNP
rs1163817482 388 dbSNP
rs1415906086 389 dbSNP
rs1243095850 393 dbSNP
rs1483196525 402 dbSNP
rs1186376249 410 dbSNP
rs1260232851 413 dbSNP
rs1475542109 414 dbSNP
rs963411370 431 dbSNP
rs1219139015 445 dbSNP
rs973859792 456 dbSNP
rs1158592750 458 dbSNP
rs916660499 467 dbSNP
rs530065544 477 dbSNP
rs1323828917 486 dbSNP
rs1274396823 490 dbSNP
rs1025785073 493 dbSNP
rs1044197674 494 dbSNP
rs1003085527 498 dbSNP
rs1362247869 503 dbSNP
rs1292534369 504 dbSNP
rs1328105895 508 dbSNP
rs1159529970 509 dbSNP
rs1456229346 513 dbSNP
rs1036311501 515 dbSNP
rs778528469 526 dbSNP
rs1398385070 530 dbSNP
rs1421656108 534 dbSNP
rs938579724 536 dbSNP
rs185479004 544 dbSNP
rs565298073 546 dbSNP
rs990922966 548 dbSNP
rs1356030185 572 dbSNP
rs1274186840 575 dbSNP
rs891423291 576 dbSNP
rs1011234175 582 dbSNP
rs573082988 586 dbSNP
rs1229009086 594 dbSNP
rs190774391 596 dbSNP
rs923778811 613 dbSNP
rs935113162 616 dbSNP
rs11352825 618 dbSNP
rs397995151 618 dbSNP
rs398083445 618 dbSNP
rs200293487 619 dbSNP
rs995955800 620 dbSNP
rs1398041779 622 dbSNP
rs1172668502 626 dbSNP
rs200986599 626 dbSNP
rs912503346 631 dbSNP
rs1030475067 633 dbSNP
rs758458048 634 dbSNP
rs1005097419 645 dbSNP
rs1486322122 646 dbSNP
rs1181132576 647 dbSNP
rs1231298237 654 dbSNP
rs3204760 654 dbSNP
rs1015182919 655 dbSNP
rs183383701 661 dbSNP
rs963999061 662 dbSNP
rs973423747 664 dbSNP
rs1240611271 670 dbSNP
rs1196859723 672 dbSNP
rs995560902 680 dbSNP
rs1424735045 684 dbSNP
rs1047099356 691 dbSNP
rs887277613 698 dbSNP
rs1349601211 701 dbSNP
rs1303611476 704 dbSNP
rs1239182821 705 dbSNP
rs1003031764 708 dbSNP
rs1432573483 711 dbSNP
rs1175347802 712 dbSNP
rs1330858450 718 dbSNP
rs1035852215 719 dbSNP
rs561595617 720 dbSNP
rs969472363 722 dbSNP
rs982181894 733 dbSNP
rs928433409 736 dbSNP
rs1326256478 738 dbSNP
rs1436599022 740 dbSNP
rs959238724 741 dbSNP
rs530101470 747 dbSNP
rs1336966165 755 dbSNP
rs560644690 763 dbSNP
rs77183839 765 dbSNP
rs1198241925 766 dbSNP
rs777839708 768 dbSNP
rs550238525 770 dbSNP
rs1215400810 772 dbSNP
rs1351308682 776 dbSNP
rs750514363 777 dbSNP
rs1239419413 792 dbSNP
rs879875638 803 dbSNP
rs1042715882 804 dbSNP
rs900179527 805 dbSNP
rs1310432541 806 dbSNP
rs1416737522 811 dbSNP
rs1376117683 816 dbSNP
rs1297878216 818 dbSNP
rs563500073 839 dbSNP
rs1387672844 846 dbSNP
rs1159512117 849 dbSNP
rs923725092 853 dbSNP
rs76733321 854 dbSNP
rs529695236 857 dbSNP
rs1271539283 866 dbSNP
rs1439572722 868 dbSNP
rs1205332556 869 dbSNP
rs1252601629 876 dbSNP
rs543414544 882 dbSNP
rs1051511336 891 dbSNP
rs563090115 892 dbSNP
rs1452881721 897 dbSNP
rs780911979 898 dbSNP
rs145774384 901 dbSNP
rs1015544948 912 dbSNP
rs942629437 916 dbSNP
rs899394040 926 dbSNP
rs1166049417 927 dbSNP
rs995512755 934 dbSNP
rs1356246307 940 dbSNP
rs1052633 949 dbSNP
rs11558600 956 dbSNP
rs571318180 963 dbSNP
rs931272230 973 dbSNP
rs969365185 983 dbSNP
rs1319168144 986 dbSNP
rs1405170242 987 dbSNP
rs1047046415 995 dbSNP
rs769096486 998 dbSNP
rs1442707595 1010 dbSNP
rs1167796666 1011 dbSNP
rs1035061513 1018 dbSNP
rs1423450636 1022 dbSNP
rs938751521 1028 dbSNP
rs1057488853 1030 dbSNP
rs1243521825 1048 dbSNP
rs1372125914 1050 dbSNP
rs1450874618 1054 dbSNP
rs894616748 1055 dbSNP
rs774739264 1057 dbSNP
rs1227153901 1058 dbSNP
rs1215553098 1061 dbSNP
rs1013594343 1063 dbSNP
rs1021839079 1073 dbSNP
rs1216895320 1079 dbSNP
rs1341511169 1080 dbSNP
rs1000568320 1090 dbSNP
rs766735812 1090 dbSNP
rs1329770072 1091 dbSNP
rs956826295 1092 dbSNP
rs1030658429 1106 dbSNP
rs1442025821 1114 dbSNP
rs956465134 1114 dbSNP
rs1169115210 1115 dbSNP
rs1407755919 1116 dbSNP
rs1421002229 1125 dbSNP
rs1168201814 1136 dbSNP
rs1477491391 1137 dbSNP
rs1392800919 1142 dbSNP
rs1342160109 1146 dbSNP
rs1215239143 1148 dbSNP
rs112606530 1152 dbSNP
rs1196641175 1166 dbSNP
rs1019878090 1169 dbSNP
rs553636946 1170 dbSNP
rs1273787161 1174 dbSNP
rs552305588 1175 dbSNP
rs1343153822 1176 dbSNP
rs1467294494 1178 dbSNP
rs975737355 1181 dbSNP
rs1215736492 1183 dbSNP
rs565721458 1184 dbSNP
rs1253902103 1185 dbSNP
rs919881489 1201 dbSNP
rs187919912 1202 dbSNP
rs1355848059 1229 dbSNP
rs947295626 1233 dbSNP
rs778394481 1244 dbSNP
rs1328949164 1253 dbSNP
rs1392900551 1264 dbSNP
rs201941333 1268 dbSNP
rs748493559 1268 dbSNP
rs865941076 1269 dbSNP
rs933581220 1270 dbSNP
rs921574088 1294 dbSNP
rs1175468601 1295 dbSNP
rs931642290 1297 dbSNP
rs565916811 1309 dbSNP
rs938780250 1323 dbSNP
rs1057184418 1332 dbSNP
rs894638469 1338 dbSNP
rs193170286 1344 dbSNP
rs1353516084 1351 dbSNP
rs1043610419 1360 dbSNP
rs904804598 1361 dbSNP
rs1374704732 1366 dbSNP
rs999089542 1369 dbSNP
rs1446688380 1374 dbSNP
rs1030691114 1375 dbSNP
rs892107279 1376 dbSNP
rs890204951 1381 dbSNP
rs575998655 1383 dbSNP
rs1462586779 1392 dbSNP
rs1008399284 1405 dbSNP
rs780408153 1418 dbSNP
rs533863321 1422 dbSNP
rs1259692702 1429 dbSNP
rs1387474807 1429 dbSNP
rs145986881 1436 dbSNP
rs995061955 1437 dbSNP
rs147816769 1443 dbSNP
rs1432175066 1444 dbSNP
rs905487639 1446 dbSNP
rs1293240233 1456 dbSNP
rs1317852673 1461 dbSNP
rs541678606 1462 dbSNP
rs72676016 1463 dbSNP
rs530464257 1467 dbSNP
rs1274026301 1469 dbSNP
rs2175383 1471 dbSNP
rs1203124508 1476 dbSNP
rs908559656 1482 dbSNP
rs1263643837 1490 dbSNP
rs1447384190 1495 dbSNP
rs956775127 1498 dbSNP
rs1286717117 1511 dbSNP
rs938657569 1512 dbSNP
rs1345544853 1513 dbSNP
rs1010079051 1514 dbSNP
rs1459808531 1517 dbSNP
rs1419863305 1541 dbSNP
rs1165772496 1549 dbSNP
rs1255318740 1560 dbSNP
rs1477506567 1566 dbSNP
rs1259948096 1568 dbSNP
rs187789672 1569 dbSNP
rs968958600 1583 dbSNP
rs1246474245 1587 dbSNP
rs1212438731 1590 dbSNP
rs978666283 1594 dbSNP
rs1337589372 1604 dbSNP
rs1274290589 1606 dbSNP
rs921836613 1607 dbSNP
rs1043270241 1625 dbSNP
rs532551442 1625 dbSNP
rs1306383447 1626 dbSNP
rs1383549560 1641 dbSNP
rs926086284 1656 dbSNP
rs934913102 1656 dbSNP
rs987113522 1661 dbSNP
rs1053330064 1673 dbSNP
rs1157173482 1686 dbSNP
rs1387536889 1697 dbSNP
rs911587078 1698 dbSNP
rs1401027586 1713 dbSNP
rs892127025 1719 dbSNP
rs1371381872 1720 dbSNP
rs1354130975 1741 dbSNP
rs1416694579 1746 dbSNP
rs192658163 1748 dbSNP
rs566201333 1749 dbSNP
rs1429332859 1750 dbSNP
rs1294024093 1752 dbSNP
rs552051497 1758 dbSNP
rs1470075230 1761 dbSNP
rs527487966 1766 dbSNP
rs1335374574 1770 dbSNP
rs1198547154 1772 dbSNP
rs1480059935 1773 dbSNP
rs184689891 1774 dbSNP
rs1041099476 1779 dbSNP
rs1307733535 1780 dbSNP
rs1302182006 1782 dbSNP
rs1231842800 1787 dbSNP
rs1262745490 1793 dbSNP
rs568533820 1816 dbSNP
rs1351037562 1820 dbSNP
rs1394504976 1821 dbSNP
rs1299972510 1824 dbSNP
rs1171975975 1830 dbSNP
rs1358826587 1830 dbSNP
rs899606227 1830 dbSNP
rs1455892361 1835 dbSNP
rs996978095 1840 dbSNP
rs1209901989 1841 dbSNP
rs1278088127 1843 dbSNP
rs1253210539 1844 dbSNP
rs1486652971 1847 dbSNP
rs1188010321 1848 dbSNP
rs567128892 1856 dbSNP
rs1440628094 1860 dbSNP
rs1197056422 1881 dbSNP
rs1480653287 1885 dbSNP
rs1026791612 1892 dbSNP
rs952515619 1893 dbSNP
rs1249269022 1894 dbSNP
rs1349862256 1901 dbSNP
rs1004089261 1905 dbSNP
rs1015504851 1915 dbSNP
rs1416816426 1916 dbSNP
rs1308998961 1936 dbSNP
rs1392077027 1939 dbSNP
rs1354877662 1944 dbSNP
rs1183487322 1951 dbSNP
rs960222428 1956 dbSNP
rs1436809285 1958 dbSNP
rs536102012 1959 dbSNP
rs1158429507 1968 dbSNP
rs1420631997 1982 dbSNP
rs915879005 1987 dbSNP
rs1183132143 1993 dbSNP
rs1419207358 2003 dbSNP
rs1256181871 2008 dbSNP
rs970184536 2015 dbSNP
rs1486452327 2016 dbSNP
rs930800628 2017 dbSNP
rs776940769 2018 dbSNP
rs1204355748 2020 dbSNP
rs1348226994 2024 dbSNP
rs537111624 2040 dbSNP
rs1239662340 2043 dbSNP
rs1374144131 2047 dbSNP
rs1323 2053 dbSNP
rs72524687 2053 dbSNP
rs5861420 2054 dbSNP
rs1437174989 2055 dbSNP
rs201914280 2055 dbSNP
rs1317848219 2073 dbSNP
rs777081379 2074 dbSNP
rs1303953370 2077 dbSNP
rs934774177 2080 dbSNP
rs1159715250 2087 dbSNP
rs141439951 2088 dbSNP
rs1416247019 2090 dbSNP
rs1056362658 2092 dbSNP
rs1475875181 2099 dbSNP
rs944939206 2107 dbSNP
rs1191998060 2111 dbSNP
rs1445124715 2115 dbSNP
rs1336633573 2119 dbSNP
rs1205432294 2120 dbSNP
rs892485307 2124 dbSNP
rs1009615269 2128 dbSNP
rs1022808447 2132 dbSNP
rs1233292361 2136 dbSNP
rs1235246108 2139 dbSNP
rs899469551 2140 dbSNP
rs1301035912 2149 dbSNP
rs968193255 2160 dbSNP
rs570731431 2164 dbSNP
rs1225503043 2166 dbSNP
rs1349940465 2179 dbSNP
rs1319398946 2191 dbSNP
rs1440556469 2202 dbSNP
rs759713008 2204 dbSNP
rs570596516 2209 dbSNP
rs752597119 2228 dbSNP
rs1328469437 2235 dbSNP
rs1462598911 2242 dbSNP
rs1479334801 2247 dbSNP
rs1028852481 2249 dbSNP
rs1197052622 2251 dbSNP
rs1167030393 2268 dbSNP
rs888194824 2273 dbSNP
rs1250780489 2284 dbSNP
rs953260490 2302 dbSNP
rs987406206 2303 dbSNP
rs1453460727 2306 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions MCF7
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 SRR1045082. RNA binding protein: AGO2. Condition:Untreated ...

- Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' acucuguccAAGUACGACGAUa 5'
                   ||:: ||||||| 
Target 5' ----uuuacUUUGGGCUGCUAa 3'
1 - 18
Article - Farazi TA; Ten Hoeve JJ; Brown M; et al.
- Genome biology, 2014
BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
LinkOut: [PMID: 24398324]
CLIP-seq Support 1 for dataset SRR1045082
Method / RBP PAR-CLIP / AGO2
Cell line / Condition MCF7 / Untreated
Location of target site ENST00000450251.1 | 3UTR | UUUACUUUGGGCUGCUAACCACCAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24398324 / SRX388831
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
180 hsa-miR-4524a-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT055251 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT055826 PLEKHA1 pleckstrin homology domain containing A1 2 2
MIRT060573 CCND1 cyclin D1 2 2
MIRT061013 C1ORF21 chromosome 1 open reading frame 21 2 6
MIRT064694 CCND2 cyclin D2 2 4
MIRT075268 SNTB2 syntrophin beta 2 2 4
MIRT079668 NAPG NSF attachment protein gamma 2 12
MIRT081651 CCNE1 cyclin E1 2 4
MIRT082996 PNPLA6 patatin like phospholipase domain containing 6 2 2
MIRT083463 RALGAPB Ral GTPase activating protein non-catalytic beta subunit 2 4
MIRT085755 RIF1 replication timing regulatory factor 1 2 2
MIRT086022 UBR3 ubiquitin protein ligase E3 component n-recognin 3 (putative) 2 2
MIRT087431 ZNRF3 zinc and ring finger 3 2 2
MIRT088786 SOCS5 suppressor of cytokine signaling 5 2 2
MIRT089221 ACTR2 ARP2 actin related protein 2 homolog 2 2
MIRT093696 PI4K2B phosphatidylinositol 4-kinase type 2 beta 2 6
MIRT095090 SEC24A SEC24 homolog A, COPII coat complex component 2 4
MIRT096249 CANX calnexin 2 2
MIRT100215 PPP1R11 protein phosphatase 1 regulatory inhibitor subunit 11 2 2
MIRT100746 VEGFA vascular endothelial growth factor A 2 12
MIRT100904 CD2AP CD2 associated protein 2 2
MIRT102647 UBN2 ubinuclein 2 2 10
MIRT103882 FOXK1 forkhead box K1 2 2
MIRT104246 DMTF1 cyclin D binding myb like transcription factor 1 2 2
MIRT106310 ZFHX4 zinc finger homeobox 4 2 6
MIRT107696 RECK reversion inducing cysteine rich protein with kazal motifs 2 2
MIRT114943 CHAC1 ChaC glutathione specific gamma-glutamylcyclotransferase 1 2 2
MIRT117671 SCAMP4 secretory carrier membrane protein 4 2 2
MIRT133799 SKI SKI proto-oncogene 2 2
MIRT140167 SPRED1 sprouty related EVH1 domain containing 1 2 2
MIRT142279 DCTN5 dynactin subunit 5 2 8
MIRT143288 N4BP1 NEDD4 binding protein 1 2 2
MIRT165939 CREBRF CREB3 regulatory factor 2 2
MIRT175251 PSAT1 phosphoserine aminotransferase 1 2 6
MIRT186381 PNRC2 proline rich nuclear receptor coactivator 2 2 2
MIRT191470 PPM1A protein phosphatase, Mg2+/Mn2+ dependent 1A 2 2
MIRT196480 TAOK1 TAO kinase 1 2 2
MIRT201470 SNRPB2 small nuclear ribonucleoprotein polypeptide B2 2 8
MIRT204615 HSPE1-MOB4 HSPE1-MOB4 readthrough 2 8
MIRT204646 MOB4 MOB family member 4, phocein 2 8
MIRT204749 BZW1 basic leucine zipper and W2 domains 1 2 12
MIRT206031 NUP50 nucleoporin 50 2 6
MIRT211196 FGF2 fibroblast growth factor 2 2 4
MIRT229353 ZNF449 zinc finger protein 449 2 2
MIRT247138 WEE1 WEE1 G2 checkpoint kinase 2 4
MIRT249461 ZNF691 zinc finger protein 691 2 4
MIRT256314 CDC42SE2 CDC42 small effector 2 2 2
MIRT258419 WIPI2 WD repeat domain, phosphoinositide interacting 2 2 2
MIRT265083 CHEK1 checkpoint kinase 1 2 2
MIRT270561 SETD1B SET domain containing 1B 2 2
MIRT274749 RAB3IP RAB3A interacting protein 2 2
MIRT277515 PPP2R5C protein phosphatase 2 regulatory subunit B'gamma 2 4
MIRT289642 CBX2 chromobox 2 2 2
MIRT301001 MTMR3 myotubularin related protein 3 2 2
MIRT307149 CTDSPL CTD small phosphatase like 2 4
MIRT309021 USP53 ubiquitin specific peptidase 53 2 2
MIRT314100 PIK3R1 phosphoinositide-3-kinase regulatory subunit 1 2 8
MIRT319338 CAPZA2 capping actin protein of muscle Z-line alpha subunit 2 2 2
MIRT320619 ZNRF2 zinc and ring finger 2 2 2
MIRT324285 LURAP1L leucine rich adaptor protein 1 like 2 2
MIRT446498 ASCC1 activating signal cointegrator 1 complex subunit 1 2 2
MIRT448437 TLL1 tolloid like 1 2 2
MIRT461537 ACTR3B ARP3 actin related protein 3 homolog B 2 2
MIRT463162 ZNF367 zinc finger protein 367 2 10
MIRT463493 ZC3H10 zinc finger CCCH-type containing 10 2 2
MIRT465154 TSC22D2 TSC22 domain family member 2 2 2
MIRT466418 TFAP2A transcription factor AP-2 alpha 2 8
MIRT468278 SFT2D2 SFT2 domain containing 2 2 2
MIRT469399 REL REL proto-oncogene, NF-kB subunit 2 6
MIRT471941 NR6A1 nuclear receptor subfamily 6 group A member 1 2 2
MIRT473688 MAPK8 mitogen-activated protein kinase 8 2 4
MIRT479618 CDC25A cell division cycle 25A 2 2
MIRT482098 AKT3 AKT serine/threonine kinase 3 2 4
MIRT483995 ATAD5 ATPase family, AAA domain containing 5 2 12
MIRT485205 PRKAR2A protein kinase cAMP-dependent type II regulatory subunit alpha 2 8
MIRT498763 C3orf38 chromosome 3 open reading frame 38 2 8
MIRT498961 ORC4 origin recognition complex subunit 4 2 8
MIRT499440 ODF2L outer dense fiber of sperm tails 2 like 2 8
MIRT500080 L2HGDH L-2-hydroxyglutarate dehydrogenase 2 8
MIRT500305 ZNF622 zinc finger protein 622 2 8
MIRT500410 ZMAT3 zinc finger matrin-type 3 2 8
MIRT500789 TLK1 tousled like kinase 1 2 6
MIRT500930 SRPR SRP receptor alpha subunit 2 6
MIRT500943 SREK1 splicing regulatory glutamic acid and lysine rich protein 1 2 8
MIRT501068 SMAD7 SMAD family member 7 2 8
MIRT501711 PARD6B par-6 family cell polarity regulator beta 2 2
MIRT502627 DDX3X DEAD-box helicase 3, X-linked 2 8
MIRT502910 CDCA4 cell division cycle associated 4 2 8
MIRT502935 CDC37L1 cell division cycle 37 like 1 2 8
MIRT504531 ZNF620 zinc finger protein 620 2 6
MIRT505106 YTHDC1 YTH domain containing 1 2 6
MIRT505337 TMEM245 transmembrane protein 245 2 6
MIRT505383 TMEM100 transmembrane protein 100 2 2
MIRT505678 SESTD1 SEC14 and spectrin domain containing 1 2 6
MIRT506157 PLAG1 PLAG1 zinc finger 2 8
MIRT506183 PHKA1 phosphorylase kinase regulatory subunit alpha 1 2 6
MIRT506475 MYO5A myosin VA 2 6
MIRT506826 KIF23 kinesin family member 23 2 6
MIRT507160 GAS2L3 growth arrest specific 2 like 3 2 2
MIRT507511 DYNLL2 dynein light chain LC8-type 2 2 4
MIRT507845 CCNE2 cyclin E2 2 6
MIRT510403 ZNF507 zinc finger protein 507 2 2
MIRT518078 TRIM35 tripartite motif containing 35 2 2
MIRT518982 NNT nicotinamide nucleotide transhydrogenase 2 4
MIRT521045 SLC2A3 solute carrier family 2 member 3 2 4
MIRT521190 SBNO1 strawberry notch homolog 1 2 6
MIRT522088 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 4
MIRT524846 ARPP19 cAMP regulated phosphoprotein 19 2 2
MIRT527787 TMEM44 transmembrane protein 44 2 4
MIRT537803 EFNB2 ephrin B2 2 4
MIRT540830 GNAT1 G protein subunit alpha transducin 1 2 4
MIRT541140 PISD phosphatidylserine decarboxylase 2 2
MIRT541419 CBX4 chromobox 4 2 2
MIRT543517 PRSS21 protease, serine 21 2 2
MIRT543824 GSG1 germ cell associated 1 2 2
MIRT544959 UGT2B4 UDP glucuronosyltransferase family 2 member B4 2 2
MIRT545179 MAP4K2 mitogen-activated protein kinase kinase kinase kinase 2 2 4
MIRT545335 CCDC83 coiled-coil domain containing 83 2 2
MIRT545518 RSL24D1 ribosomal L24 domain containing 1 2 2
MIRT545670 DECR1 2,4-dienoyl-CoA reductase 1 2 2
MIRT545931 ZBTB44 zinc finger and BTB domain containing 44 2 4
MIRT546102 USP48 ubiquitin specific peptidase 48 2 4
MIRT546598 SALL1 spalt like transcription factor 1 2 4
MIRT546626 RTN4 reticulon 4 2 2
MIRT547651 KPNA3 karyopherin subunit alpha 3 2 2
MIRT547987 HCFC2 host cell factor C2 2 4
MIRT548717 CRK CRK proto-oncogene, adaptor protein 2 2
MIRT548931 CDK17 cyclin dependent kinase 17 2 2
MIRT549067 CACUL1 CDK2 associated cullin domain 1 2 2
MIRT549266 ASH1L ASH1 like histone lysine methyltransferase 2 2
MIRT550460 OSCAR osteoclast associated, immunoglobulin-like receptor 2 4
MIRT550806 FAM229B family with sequence similarity 229 member B 2 2
MIRT552024 DNAJC10 DnaJ heat shock protein family (Hsp40) member C10 2 2
MIRT552334 ZNF704 zinc finger protein 704 2 2
MIRT552732 YRDC yrdC N6-threonylcarbamoyltransferase domain containing 2 2
MIRT553795 SZRD1 SUZ RNA binding domain containing 1 2 4
MIRT554694 RNF149 ring finger protein 149 2 2
MIRT555133 PTPRD protein tyrosine phosphatase, receptor type D 2 2
MIRT555264 PRDM4 PR/SET domain 4 2 2
MIRT556848 KANK1 KN motif and ankyrin repeat domains 1 2 4
MIRT557474 GPR27 G protein-coupled receptor 27 2 4
MIRT558018 EXT1 exostosin glycosyltransferase 1 2 2
MIRT558498 CYP26B1 cytochrome P450 family 26 subfamily B member 1 2 4
MIRT558579 CREBL2 cAMP responsive element binding protein like 2 2 4
MIRT558610 COX6B1 cytochrome c oxidase subunit 6B1 2 4
MIRT558650 CNKSR3 CNKSR family member 3 2 2
MIRT558986 CA8 carbonic anhydrase 8 2 2
MIRT559141 BTN3A3 butyrophilin subfamily 3 member A3 2 2
MIRT559327 ATP5G3 ATP synthase, H+ transporting, mitochondrial Fo complex subunit C3 (subunit 9) 2 2
MIRT562021 LANCL1 LanC like 1 2 2
MIRT562869 KIAA1456 KIAA1456 2 2
MIRT563074 SLC25A12 solute carrier family 25 member 12 2 2
MIRT563496 DLGAP3 DLG associated protein 3 2 2
MIRT563890 RAPH1 Ras association (RalGDS/AF-6) and pleckstrin homology domains 1 2 2
MIRT564311 CCNT1 cyclin T1 2 2
MIRT564942 XKR7 XK related 7 2 2
MIRT564979 WNK3 WNK lysine deficient protein kinase 3 2 2
MIRT565423 TEF TEF, PAR bZIP transcription factor 2 2
MIRT566824 MAP3K7 mitogen-activated protein kinase kinase kinase 7 2 2
MIRT571961 KIF5B kinesin family member 5B 2 2
MIRT575877 Cask calcium/calmodulin-dependent serine protein kinase (MAGUK family) 2 3
MIRT576523 Txlna taxilin alpha 2 2
MIRT614693 TRAK1 trafficking kinesin protein 1 2 2
MIRT616065 ZC3H14 zinc finger CCCH-type containing 14 2 2
MIRT618838 ASAH2B N-acylsphingosine amidohydrolase 2B 2 2
MIRT624626 ATXN2 ataxin 2 2 2
MIRT624652 ASAH2 N-acylsphingosine amidohydrolase 2 2 2
MIRT640314 MMAB methylmalonic aciduria (cobalamin deficiency) cblB type 2 2
MIRT659248 CUL3 cullin 3 2 2
MIRT680972 DCAF17 DDB1 and CUL4 associated factor 17 2 2
MIRT682261 RS1 retinoschisin 1 2 2
MIRT682505 GLP2R glucagon like peptide 2 receptor 2 2
MIRT693904 HNRNPA1L2 heterogeneous nuclear ribonucleoprotein A1-like 2 2 2
MIRT699214 SLCO3A1 solute carrier organic anion transporter family member 3A1 2 2
MIRT699373 SLC30A6 solute carrier family 30 member 6 2 2
MIRT699451 SLC16A9 solute carrier family 16 member 9 2 2
MIRT701230 OCRL OCRL, inositol polyphosphate-5-phosphatase 2 2
MIRT702849 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 2 2
MIRT706163 CASK calcium/calmodulin dependent serine protein kinase 2 3
MIRT718990 UTP15 UTP15, small subunit processome component 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4524a-5p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)
hsa-miR-4524a-5p Cetuximab resistant tissue (colorectal carcinoma)

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