miRTarBase - #MIRT060732


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pre-miRNA Information
pre-miRNA hsa-mir-4282   
Genomic Coordinates chr6: 72967687 - 72967753
Description Homo sapiens miR-4282 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4282
Sequence 40| UAAAAUUUGCAUCCAGGA |57
Evidence Experimental
Experiments SOLiD
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN32074657 13 COSMIC
COSN6331413 18 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1195771339 5 dbSNP
rs755058572 6 dbSNP
rs1245753664 11 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol RPS3   
Synonyms S3
Description ribosomal protein S3
Transcript NM_001005   
Expression
Putative miRNA Targets on RPS3
3'UTR of RPS3
(miRNA target sites are highlighted)		 
>RPS3|NM_001005|3'UTR
   1 CAGGGTCTCCTTGGCAGCTGTATTCTGGAGTCTGGATGTTGCTCTCTAAAGACCTTTAATAAAATTTTGTACAAAGACAC
  81 AAGGTCTGACTAGACTGTTCAGTATTCAGACTGAGGGGCATGTTGGCCTCTGGAGCATTACATATCTTCTTGGTTTTAAC
 161 CATACTTGTGGTATTTGCAAGGGCCAGAACAGTAAGACCCAAGCAGAGCCAACCAGAGAAATAATATTTGTGTGATAGAG
 241 AAGGCTGATAGCAAGCAAGGCAGCACCTTGATTCGTTGTCCTGTAGTTCAGGATTGTAGGTTTAGAAGAGGGATATGTTT
 321 GAGTTTTTCCTATGCATAAGGCGATCCACGTTGCACATAGAAAGTGAATATAAATGGCCATTATATTTTGTGTCATGCTG
 401 TGCTCTAAGTGTTCTTTACATATGTACTCGTTAATCAACCTCTCTAAAGTGTAAAGGAAATTTGCTTGCACCACTGAAGG
 481 CACATAAGGCTCAGAAGTAAATTTGCCTAAGCAGTATAAAGCTATCATTAGAATCCACATTCCTAAGTTGTGTTCTCTTA
 561 GGGGATCATGGAACCAGTCATTGGTACTACAGGCTATTATGTTCTGGAGAACTGTGAAGAACATTTAAATTGTCTCTGAT
 641 TTTATCTATCAATGTTTTGAAGTATTTTCTACCAGTGTCTGTACTTCACAAGAAATTCGGCACTATTTTTTCAGGCAAAA
 721 CTAGTGAGGGACAGGTTGGCTTGAAAATCATGAGACTGTTGTTAAATCAGATGCTGGTTGATCACAGAGGGGACTTCCAG
 801 GGAAAGCTGTTATCAGGTGGCTGCTTCCTGGTGATGCAGCCTGGCTGATGAGATAACCCTGGCTCCACAGATGGCTTAGC
 881 AGGTGCTGTGATGATTTGGTTTTCTTCTCAATTAGACTGAGCTGCACATGGTGTTTATATTGCTTGGCACATGGTAAGGG
 961 CTTAATATTTGAGGTAATTATGTAGGGCGTACACTGACAAGTATCTGACCCCCCCTTCCTTTTTGACTCATAAATTGGTC
1041 ATCTTAACCATTTAAGTGTACACTTCTATAGTGACAGAGTTAGCCCTCTGTCCAAGGGATTTGCATCTGTGGATTCAACC
1121 AACTTTGGGTCAAAAATAATCAAAAAGGATGGTTGTGTGTGTATTGAACATGTAGACTTATTTTTCTTATTTTCAAAATA
1201 CTATATTTTCTTGTCACTTATTTTCTTGTACACTGCAGTTGTAACAGCTATGTAGCATGTACATTAGGTATTAAAAGTAA
1281 TCCAGTGAAGATTGAAAGTCTAAAAAAAAAAAAAAAAAA
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' aggaccuacgUUUAAAAu 5'
                    ||||||| 
Target 5' acctttaataAAATTTTg 3'
 52 - 69 140.00 -6.20
2 
miRNA  3' agGACCU-ACGUUUAAAau 5'
            | ||| ||:|::|||  
Target 5' ttCAGGATTGTAGGTTTag 3'
 287 - 305 108.00 -7.80
3 
miRNA  3' aggACCUA----CGUUUAAAau 5'
             |||||     ||| |||  
Target 5' ctgTGGATTCAACCAACTTTgg 3'
 1107 - 1128 101.00 -6.01
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30107981 26 COSMIC
COSN5264109 52 COSMIC
COSN30128495 53 COSMIC
COSN31524324 61 COSMIC
COSN30704707 93 COSMIC
COSN1542972 148 COSMIC
COSN23467574 314 COSMIC
COSN18714190 443 COSMIC
COSN136856 609 COSMIC
COSN20049836 997 COSMIC
COSN10091856 1016 COSMIC
COSN1542973 1102 COSMIC
COSN5918668 1143 COSMIC
COSN15671688 1180 COSMIC
COSN30080723 1289 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs374596699 2 dbSNP
rs879020583 6 dbSNP
rs892599702 8 dbSNP
rs945617487 10 dbSNP
rs1338184656 12 dbSNP
rs1212360333 14 dbSNP
rs375851508 18 dbSNP
rs773904943 20 dbSNP
rs775465477 21 dbSNP
rs1266551692 23 dbSNP
rs935808490 24 dbSNP
rs747079232 25 dbSNP
rs760739715 31 dbSNP
rs1359449878 35 dbSNP
rs915825942 36 dbSNP
rs569247955 39 dbSNP
rs1401352352 42 dbSNP
rs776897747 47 dbSNP
rs1248373246 48 dbSNP
rs140288831 52 dbSNP
rs1169770696 53 dbSNP
rs769539545 54 dbSNP
rs1407669072 57 dbSNP
rs771365890 69 dbSNP
rs1018467998 82 dbSNP
rs1382260755 87 dbSNP
rs1176919295 88 dbSNP
rs556868870 91 dbSNP
rs899592917 92 dbSNP
rs995638721 93 dbSNP
rs1190026710 111 dbSNP
rs1026828266 112 dbSNP
rs951212439 118 dbSNP
rs1231923316 144 dbSNP
rs1272519233 151 dbSNP
rs548208880 160 dbSNP
rs1283257534 165 dbSNP
rs75859266 167 dbSNP
rs534316538 170 dbSNP
rs1285616333 176 dbSNP
rs17887076 178 dbSNP
rs566662301 186 dbSNP
rs1027950118 189 dbSNP
rs970731696 190 dbSNP
rs1358624794 192 dbSNP
rs1156978448 197 dbSNP
rs1414743320 198 dbSNP
rs980809840 198 dbSNP
rs1008193156 201 dbSNP
rs1471979532 203 dbSNP
rs1194926345 204 dbSNP
rs1257237921 204 dbSNP
rs926594401 205 dbSNP
rs936773644 206 dbSNP
rs989936668 207 dbSNP
rs538415618 211 dbSNP
rs1198252975 213 dbSNP
rs1245050539 214 dbSNP
rs1214393826 218 dbSNP
rs182636819 222 dbSNP
rs966076096 230 dbSNP
rs945524596 231 dbSNP
rs1052040553 235 dbSNP
rs1278608119 236 dbSNP
rs1389371859 241 dbSNP
rs1338310504 242 dbSNP
rs1288241768 244 dbSNP
rs1350550333 245 dbSNP
rs187596101 245 dbSNP
rs1325674549 255 dbSNP
rs912132655 257 dbSNP
rs1460065341 260 dbSNP
rs1417461910 266 dbSNP
rs943587462 271 dbSNP
rs1039388335 272 dbSNP
rs957225951 272 dbSNP
rs193247523 273 dbSNP
rs915709845 275 dbSNP
rs1488489593 284 dbSNP
rs948666209 286 dbSNP
rs775737842 288 dbSNP
rs1218828104 294 dbSNP
rs1048131045 295 dbSNP
rs1396789092 298 dbSNP
rs1220190696 299 dbSNP
rs1385812503 301 dbSNP
rs868483610 303 dbSNP
rs1321093646 308 dbSNP
rs745383592 311 dbSNP
rs1332309164 316 dbSNP
rs1003991324 317 dbSNP
rs927998491 322 dbSNP
rs1304846727 325 dbSNP
rs1393958840 325 dbSNP
rs1342007739 329 dbSNP
rs1467451458 332 dbSNP
rs554620227 333 dbSNP
rs1253378459 334 dbSNP
rs1340400321 337 dbSNP
rs1191186186 341 dbSNP
rs1453295729 347 dbSNP
rs760828131 349 dbSNP
rs775176943 352 dbSNP
rs574320762 359 dbSNP
rs1250542677 363 dbSNP
rs1002492332 365 dbSNP
rs995039940 368 dbSNP
rs558872000 387 dbSNP
rs1232127554 400 dbSNP
rs559948277 401 dbSNP
rs1247368802 402 dbSNP
rs1371534898 411 dbSNP
rs1447525095 412 dbSNP
rs1466922712 430 dbSNP
rs1361361010 434 dbSNP
rs532223085 443 dbSNP
rs1433488613 457 dbSNP
rs546130158 464 dbSNP
rs1380359750 468 dbSNP
rs76334133 469 dbSNP
rs75185648 470 dbSNP
rs1019587785 478 dbSNP
rs1161060500 488 dbSNP
rs548442040 491 dbSNP
rs998908567 492 dbSNP
rs1354398957 495 dbSNP
rs1031416774 499 dbSNP
rs957126243 500 dbSNP
rs1348230724 501 dbSNP
rs1319229107 505 dbSNP
rs989818195 507 dbSNP
rs568138444 509 dbSNP
rs527640303 526 dbSNP
rs981409404 530 dbSNP
rs1311501043 532 dbSNP
rs928522722 534 dbSNP
rs1361777120 536 dbSNP
rs145075910 539 dbSNP
rs939404673 540 dbSNP
rs943634785 546 dbSNP
rs1327364348 555 dbSNP
rs1165042788 556 dbSNP
rs1425273172 556 dbSNP
rs1255119977 557 dbSNP
rs1187045929 561 dbSNP
rs1265309280 564 dbSNP
rs1206927118 565 dbSNP
rs972053901 570 dbSNP
rs1282677419 571 dbSNP
rs1260297731 572 dbSNP
rs747545 579 dbSNP
rs1214412632 585 dbSNP
rs1267516386 586 dbSNP
rs539899839 589 dbSNP
rs143641060 590 dbSNP
rs569038781 591 dbSNP
rs1300620480 594 dbSNP
rs1423057589 594 dbSNP
rs1322565452 596 dbSNP
rs1459119190 596 dbSNP
rs34828342 596 dbSNP
rs760437109 607 dbSNP
rs1163919264 608 dbSNP
rs1478040653 608 dbSNP
rs1202114835 609 dbSNP
rs889305016 610 dbSNP
rs1475292503 611 dbSNP
rs1157859765 613 dbSNP
rs886875469 615 dbSNP
rs943520646 622 dbSNP
rs538160013 627 dbSNP
rs778337697 630 dbSNP
rs1046220631 632 dbSNP
rs17883464 635 dbSNP
rs1031300469 642 dbSNP
rs574381231 662 dbSNP
rs1386264584 672 dbSNP
rs138295736 675 dbSNP
rs1301324511 677 dbSNP
rs768768736 701 dbSNP
rs892780300 704 dbSNP
rs1324844109 707 dbSNP
rs187463373 708 dbSNP
rs1023122432 710 dbSNP
rs1367861723 712 dbSNP
rs1034009471 716 dbSNP
rs1387637381 718 dbSNP
rs1475023751 722 dbSNP
rs775287596 724 dbSNP
rs768536181 725 dbSNP
rs1433478433 726 dbSNP
rs1199606867 727 dbSNP
rs958085801 730 dbSNP
rs969939002 734 dbSNP
rs1010896270 738 dbSNP
rs1342202127 743 dbSNP
rs1244823049 751 dbSNP
rs1289071199 753 dbSNP
rs11546202 755 dbSNP
rs11546228 756 dbSNP
rs1210269601 760 dbSNP
rs949551131 763 dbSNP
rs1260743812 768 dbSNP
rs1213314421 769 dbSNP
rs1445247545 779 dbSNP
rs1035643356 784 dbSNP
rs1275546448 790 dbSNP
rs961601132 791 dbSNP
rs1339278344 797 dbSNP
rs1248746759 798 dbSNP
rs1444022160 799 dbSNP
rs545479112 800 dbSNP
rs972607903 813 dbSNP
rs1387385302 818 dbSNP
rs1458593835 820 dbSNP
rs113077609 825 dbSNP
rs1158403844 828 dbSNP
rs1235804473 828 dbSNP
rs1325016005 832 dbSNP
rs1383221632 836 dbSNP
rs1384451921 837 dbSNP
rs919279741 841 dbSNP
rs1350947425 843 dbSNP
rs966802477 846 dbSNP
rs1321756381 850 dbSNP
rs1365316027 852 dbSNP
rs930603582 856 dbSNP
rs987514009 861 dbSNP
rs776321527 866 dbSNP
rs1180974828 868 dbSNP
rs1402771078 887 dbSNP
rs1409177670 888 dbSNP
rs1266499736 890 dbSNP
rs1436594428 891 dbSNP
rs1393333114 892 dbSNP
rs1193160012 897 dbSNP
rs1440521145 899 dbSNP
rs1234862665 900 dbSNP
rs534790024 903 dbSNP
rs1420389612 913 dbSNP
rs943590256 913 dbSNP
rs553591383 914 dbSNP
rs1364893483 917 dbSNP
rs975047346 921 dbSNP
rs934931786 928 dbSNP
rs751686290 929 dbSNP
rs1053270016 939 dbSNP
rs1311518769 943 dbSNP
rs576203355 944 dbSNP
rs1377643862 948 dbSNP
rs1415682531 963 dbSNP
rs1340857768 965 dbSNP
rs1441120108 965 dbSNP
rs1307621660 970 dbSNP
rs1371393857 973 dbSNP
rs1393225028 979 dbSNP
rs35287469 986 dbSNP
rs17881991 993 dbSNP
rs983771608 1006 dbSNP
rs1420407647 1009 dbSNP
rs905599220 1010 dbSNP
rs1231972651 1012 dbSNP
rs1002595858 1020 dbSNP
rs766283708 1021 dbSNP
rs961178685 1023 dbSNP
rs1484962266 1026 dbSNP
rs1257455278 1042 dbSNP
rs1216648152 1043 dbSNP
rs939783065 1044 dbSNP
rs4556572 1045 dbSNP
rs1046125416 1046 dbSNP
rs1348284010 1050 dbSNP
rs4348932 1051 dbSNP
rs937822361 1054 dbSNP
rs1055076593 1055 dbSNP
rs1356691494 1066 dbSNP
rs1294867681 1067 dbSNP
rs1249195784 1082 dbSNP
rs373250720 1088 dbSNP
rs893725820 1089 dbSNP
rs1298767187 1090 dbSNP
rs113326571 1095 dbSNP
rs547500846 1096 dbSNP
rs984787842 1097 dbSNP
rs1172293420 1098 dbSNP
rs1400339892 1103 dbSNP
rs910672297 1104 dbSNP
rs1474446920 1116 dbSNP
rs756325192 1126 dbSNP
rs1195047595 1129 dbSNP
rs1009026590 1131 dbSNP
rs778154937 1138 dbSNP
rs1239856705 1140 dbSNP
rs146526678 1141 dbSNP
rs754170456 1143 dbSNP
rs965159894 1144 dbSNP
rs976168595 1145 dbSNP
rs112084193 1151 dbSNP
rs1274688405 1151 dbSNP
rs934815813 1165 dbSNP
rs7123178 1166 dbSNP
rs569074088 1169 dbSNP
rs1298876632 1173 dbSNP
rs914821461 1175 dbSNP
rs1359868912 1176 dbSNP
rs1268465107 1178 dbSNP
rs139188001 1180 dbSNP
rs1395436093 1181 dbSNP
rs1328175357 1182 dbSNP
rs1305574567 1184 dbSNP
rs1430779775 1185 dbSNP
rs554590475 1185 dbSNP
rs1418050636 1186 dbSNP
rs1185381991 1190 dbSNP
rs184601455 1197 dbSNP
rs1478087670 1199 dbSNP
rs1044459800 1202 dbSNP
rs568307777 1210 dbSNP
rs1467802000 1222 dbSNP
rs1270541205 1227 dbSNP
rs905490514 1236 dbSNP
rs1308961333 1238 dbSNP
rs1204764921 1239 dbSNP
rs1264406945 1241 dbSNP
rs534074991 1249 dbSNP
rs1213987257 1251 dbSNP
rs779352824 1262 dbSNP
rs1305790516 1267 dbSNP
rs745365005 1270 dbSNP
rs377137847 1275 dbSNP
rs1370580595 1279 dbSNP
rs1194921999 1286 dbSNP
rs1255454454 1293 dbSNP
rs1463872794 1297 dbSNP
rs1353227737 1311 dbSNP
rs1455032763 1314 dbSNP
rs1434737102 1320 dbSNP
rs1188400741 1327 dbSNP
rs1417791116 1335 dbSNP
rs553523072 1342 dbSNP
rs576742020 1346 dbSNP
rs981848652 1351 dbSNP
rs1411914746 1358 dbSNP
rs368212968 1363 dbSNP
rs1453395281 1368 dbSNP
rs1056856277 1371 dbSNP
rs1178681653 1380 dbSNP
rs1171356415 1388 dbSNP
rs141510920 1394 dbSNP
rs12288089 1395 dbSNP
rs75563460 1398 dbSNP
rs1327943598 1401 dbSNP
rs1210707440 1405 dbSNP
rs372129459 1408 dbSNP
rs1395132713 1412 dbSNP
rs1434276497 1420 dbSNP
rs1268262368 1428 dbSNP
rs1232242563 1436 dbSNP
rs1055386621 1444 dbSNP
rs17879451 1445 dbSNP
rs1311614261 1447 dbSNP
rs1393434372 1451 dbSNP
rs1371650973 1461 dbSNP
rs1006768637 1466 dbSNP
rs946623268 1470 dbSNP
rs964712008 1471 dbSNP
rs1377843950 1473 dbSNP
rs1171178481 1479 dbSNP
rs1042318746 1481 dbSNP
rs562305410 1495 dbSNP
rs1363949284 1496 dbSNP
rs1160852999 1501 dbSNP
rs1188438465 1502 dbSNP
rs1416994645 1502 dbSNP
rs1491450940 1502 dbSNP
rs1491548235 1503 dbSNP
rs902541009 1504 dbSNP
rs1008889531 1516 dbSNP
rs1018918756 1532 dbSNP
rs1485388640 1536 dbSNP
rs1261474390 1548 dbSNP
rs1241438669 1552 dbSNP
rs1315427585 1552 dbSNP
rs1215675959 1553 dbSNP
rs900603154 1559 dbSNP
rs996238653 1563 dbSNP
rs988928258 1585 dbSNP
rs1028247496 1586 dbSNP
rs1413562973 1589 dbSNP
rs1476610212 1591 dbSNP
rs1385030530 1597 dbSNP
rs754445370 1598 dbSNP
rs572683678 1614 dbSNP
rs1187421214 1620 dbSNP
rs980359778 1625 dbSNP
rs746623357 1628 dbSNP
rs1015110505 1631 dbSNP
rs541674780 1635 dbSNP
rs961055901 1644 dbSNP
rs896906318 1653 dbSNP
rs929829545 1659 dbSNP
rs564345276 1661 dbSNP
rs982195751 1663 dbSNP
rs1395294494 1664 dbSNP
rs758031132 1676 dbSNP
rs1291883534 1685 dbSNP
rs1048265564 1686 dbSNP
rs1327567795 1689 dbSNP
rs888257516 1694 dbSNP
rs1456689843 1696 dbSNP
rs1380049379 1698 dbSNP
rs1383743762 1699 dbSNP
rs886506012 1708 dbSNP
rs768213817 1712 dbSNP
rs927625895 1714 dbSNP
rs1462767340 1715 dbSNP
rs959386706 1728 dbSNP
rs1391998987 1732 dbSNP
rs1316101612 1733 dbSNP
rs1007232097 1734 dbSNP
rs780590362 1735 dbSNP
rs1195360907 1737 dbSNP
rs1426851856 1739 dbSNP
rs1346856436 1741 dbSNP
rs1018176555 1744 dbSNP
rs1271624090 1750 dbSNP
rs1209668268 1753 dbSNP
rs1301971512 1754 dbSNP
rs900523756 1756 dbSNP
rs1224526675 1757 dbSNP
rs997522428 1758 dbSNP
rs1303581924 1759 dbSNP
rs1442643575 1760 dbSNP
rs533317830 1761 dbSNP
rs1353247818 1764 dbSNP
rs1324950304 1774 dbSNP
rs915092250 1775 dbSNP
rs1391785051 1782 dbSNP
rs1398498212 1789 dbSNP
rs138310514 1793 dbSNP
rs1234729975 1797 dbSNP
rs1293423793 1808 dbSNP
rs946515233 1809 dbSNP
rs1327832054 1812 dbSNP
rs1042357711 1818 dbSNP
rs1021769399 1821 dbSNP
rs576254954 1821 dbSNP
rs1455737230 1822 dbSNP
rs1251388852 1823 dbSNP
rs1198519619 1833 dbSNP
rs796373676 1853 dbSNP
rs923867406 1853 dbSNP
rs1194562067 1858 dbSNP
rs563809869 1868 dbSNP
rs1280413519 1870 dbSNP
rs1235928776 1876 dbSNP
rs1216966501 1879 dbSNP
rs1040781703 1880 dbSNP
rs1273883411 1882 dbSNP
rs1442609362 1883 dbSNP
rs1257254659 1887 dbSNP
rs1326656835 1889 dbSNP
rs900468743 1893 dbSNP
rs1390749009 1899 dbSNP
rs1484847628 1901 dbSNP
rs1313500841 1907 dbSNP
rs1436667691 1909 dbSNP
rs1190307053 1910 dbSNP
rs1393460794 1920 dbSNP
rs1172235587 1926 dbSNP
rs996700527 1927 dbSNP
rs1365879065 1932 dbSNP
rs1180188949 1935 dbSNP
rs1483006909 1942 dbSNP
rs1258841417 1944 dbSNP
rs1049144594 1949 dbSNP
rs1484420515 1949 dbSNP
rs1472007702 1951 dbSNP
rs887968474 1951 dbSNP
rs1004991722 1956 dbSNP
rs1223967541 1958 dbSNP
rs992499644 1963 dbSNP
rs918223320 1987 dbSNP
rs1156845662 1989 dbSNP
rs1410070449 1994 dbSNP
rs1355934813 1995 dbSNP
rs1295088596 1996 dbSNP
rs17879240 2003 dbSNP
rs1416647680 2004 dbSNP
rs1357479171 2007 dbSNP
rs929729764 2009 dbSNP
rs888308828 2012 dbSNP
rs942529293 2014 dbSNP
rs971637227 2017 dbSNP
rs1003087979 2019 dbSNP
rs1419158535 2021 dbSNP
rs1035105497 2027 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 6188.0
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' aggaccuacgUUUAAAAu 5'
                    ||||||| 
Target 5' accuuuaauaAAAUUUUg 3'
 		7 - 24
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 GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000278572.6 | 3UTR | CUAAAGACCUUUAAUAAAAUUUUGUACAAAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
280 hsa-miR-4282 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT057628 LCOR ligand dependent nuclear receptor corepressor 2 2
MIRT060732 RPS3 ribosomal protein S3 2 2
MIRT063371 ETNK1 ethanolamine kinase 1 2 2
MIRT066257 LRIG3 leucine rich repeats and immunoglobulin like domains 3 2 4
MIRT070774 HIF1A hypoxia inducible factor 1 alpha subunit 2 2
MIRT070871 EIF2S1 eukaryotic translation initiation factor 2 subunit alpha 2 4
MIRT078056 PCTP phosphatidylcholine transfer protein 2 2
MIRT078408 DCAF7 DDB1 and CUL4 associated factor 7 2 4
MIRT084059 PPP1R3D protein phosphatase 1 regulatory subunit 3D 2 2
MIRT093537 GALNT7 polypeptide N-acetylgalactosaminyltransferase 7 2 6
MIRT096072 SFXN1 sideroflexin 1 2 2
MIRT098316 REV3L REV3 like, DNA directed polymerase zeta catalytic subunit 2 2
MIRT100493 UHRF1BP1 UHRF1 binding protein 1 2 2
MIRT102254 HBP1 HMG-box transcription factor 1 2 4
MIRT105318 VPS37A VPS37A, ESCRT-I subunit 2 2
MIRT114143 MZT1 mitotic spindle organizing protein 1 2 4
MIRT114873 DICER1 dicer 1, ribonuclease III 2 2
MIRT134683 PNRC2 proline rich nuclear receptor coactivator 2 2 2
MIRT137640 RCOR1 REST corepressor 1 2 2
MIRT155449 CCNT2 cyclin T2 2 4
MIRT165656 DCTN4 dynactin subunit 4 2 2
MIRT177570 CSTF2T cleavage stimulation factor subunit 2 tau variant 2 4
MIRT188514 E2F7 E2F transcription factor 7 2 10
MIRT193019 TMOD3 tropomodulin 3 2 4
MIRT195823 GADD45A growth arrest and DNA damage inducible alpha 2 2
MIRT195885 DEPDC1 DEP domain containing 1 2 6
MIRT206029 NUP50 nucleoporin 50 2 6
MIRT212148 CLCN3 chloride voltage-gated channel 3 2 2
MIRT213999 DCP2 decapping mRNA 2 2 2
MIRT214650 HNRNPA0 heterogeneous nuclear ribonucleoprotein A0 2 2
MIRT221568 CBX3 chromobox 3 2 2
MIRT224544 ZNF623 zinc finger protein 623 2 2
MIRT227654 SET SET nuclear proto-oncogene 2 2
MIRT229992 CHIC1 cysteine rich hydrophobic domain 1 2 2
MIRT238968 QKI QKI, KH domain containing RNA binding 2 2
MIRT239825 ACTB actin beta 2 2
MIRT241084 ZXDA zinc finger, X-linked, duplicated A 2 4
MIRT244852 ZBTB5 zinc finger and BTB domain containing 5 2 2
MIRT264534 TARDBP TAR DNA binding protein 2 2
MIRT271438 SKI SKI proto-oncogene 2 2
MIRT271597 ENAH ENAH, actin regulator 2 2
MIRT294332 ZNF264 zinc finger protein 264 2 2
MIRT296341 PARD6B par-6 family cell polarity regulator beta 2 2
MIRT301715 TEF TEF, PAR bZIP transcription factor 2 2
MIRT308549 ZNF654 zinc finger protein 654 2 2
MIRT313866 DEPDC1B DEP domain containing 1B 2 2
MIRT315529 MARCKS myristoylated alanine rich protein kinase C substrate 2 2
MIRT321066 RABGEF1 RAB guanine nucleotide exchange factor 1 2 2
MIRT343777 NUTF2 nuclear transport factor 2 2 2
MIRT359109 MAP1B microtubule associated protein 1B 2 2
MIRT397393 GOLGA3 golgin A3 2 4
MIRT400822 CPEB2 cytoplasmic polyadenylation element binding protein 2 2 2
MIRT442171 DSEL dermatan sulfate epimerase-like 2 2
MIRT442777 JAG1 jagged 1 2 2
MIRT442862 SCARF1 scavenger receptor class F member 1 2 4
MIRT442919 PCBD2 pterin-4 alpha-carbinolamine dehydratase 2 2 2
MIRT444567 TRA2B transformer 2 beta homolog 2 2
MIRT444718 CMSS1 cms1 ribosomal small subunit homolog (yeast) 2 2
MIRT445018 RBMS3 RNA binding motif single stranded interacting protein 3 2 2
MIRT445853 LRRC1 leucine rich repeat containing 1 2 2
MIRT446242 HELZ helicase with zinc finger 2 2
MIRT446542 GOLGA8B golgin A8 family member B 2 2
MIRT446643 SPTY2D1 SPT2 chromatin protein domain containing 1 2 2
MIRT446948 ZMAT3 zinc finger matrin-type 3 2 4
MIRT447061 KCNAB1 potassium voltage-gated channel subfamily A member regulatory beta subunit 1 2 2
MIRT447327 ZSCAN21 zinc finger and SCAN domain containing 21 2 2
MIRT447995 CDX1 caudal type homeobox 1 2 2
MIRT448543 RHEBP1 RHEB pseudogene 1 2 6
MIRT448752 HINT1 histidine triad nucleotide binding protein 1 2 2
MIRT448772 GOLGA8A golgin A8 family member A 2 2
MIRT449342 WDR26 WD repeat domain 26 2 2
MIRT450011 SLC16A6 solute carrier family 16 member 6 2 4
MIRT450229 PCNX pecanex homolog 1 2 2
MIRT450340 MRPL17 mitochondrial ribosomal protein L17 2 4
MIRT450381 MSI2 musashi RNA binding protein 2 2 2
MIRT450759 PGGT1B protein geranylgeranyltransferase type I subunit beta 2 2
MIRT450809 NRCAM neuronal cell adhesion molecule 2 2
MIRT450947 ATAD2 ATPase family, AAA domain containing 2 2 2
MIRT459095 CCPG1 cell cycle progression 1 2 2
MIRT462428 TWISTNB TWIST neighbor 2 2
MIRT465200 TROVE2 TROVE domain family member 2 2 4
MIRT467382 SON SON DNA binding protein 2 4
MIRT468546 SERP1 stress associated endoplasmic reticulum protein 1 2 2
MIRT471506 PDE4D phosphodiesterase 4D 2 2
MIRT471981 NR3C1 nuclear receptor subfamily 3 group C member 1 2 2
MIRT474478 KLHL11 kelch like family member 11 2 8
MIRT475011 KANSL1 KAT8 regulatory NSL complex subunit 1 2 8
MIRT480341 C5orf51 chromosome 5 open reading frame 51 2 2
MIRT482696 TEX9 testis expressed 9 2 6
MIRT483462 YTHDF1 YTH N6-methyladenosine RNA binding protein 1 2 6
MIRT485623 FAM217B family with sequence similarity 217 member B 2 2
MIRT485714 CASP16 caspase 16, pseudogene 2 8
MIRT486279 SEC23A Sec23 homolog A, coat complex II component 2 2
MIRT491000 PEBP1 phosphatidylethanolamine binding protein 1 2 4
MIRT492594 PPIL4 peptidylprolyl isomerase like 4 2 2
MIRT493365 KIF5B kinesin family member 5B 2 2
MIRT494316 CDKN1B cyclin dependent kinase inhibitor 1B 2 2
MIRT495208 EDN3 endothelin 3 2 2
MIRT497011 TCF15 transcription factor 15 2 2
MIRT498512 FRK fyn related Src family tyrosine kinase 2 2
MIRT498778 PARP15 poly(ADP-ribose) polymerase family member 15 2 2
MIRT501045 SMG1 SMG1, nonsense mediated mRNA decay associated PI3K related kinase 2 6
MIRT502939 CDC37L1 cell division cycle 37 like 1 2 8
MIRT504806 VHL von Hippel-Lindau tumor suppressor 2 6
MIRT505656 SHMT1 serine hydroxymethyltransferase 1 2 6
MIRT505964 RAB5C RAB5C, member RAS oncogene family 2 6
MIRT506322 OTUD4 OTU deubiquitinase 4 2 4
MIRT506803 KLHL15 kelch like family member 15 2 6
MIRT506917 KBTBD8 kelch repeat and BTB domain containing 8 2 4
MIRT507400 EMC7 ER membrane protein complex subunit 7 2 8
MIRT507471 EDEM3 ER degradation enhancing alpha-mannosidase like protein 3 2 6
MIRT508058 ATP13A3 ATPase 13A3 2 4
MIRT508135 AMD1 adenosylmethionine decarboxylase 1 2 2
MIRT509895 RPS23 ribosomal protein S23 2 4
MIRT510881 RAN RAN, member RAS oncogene family 2 8
MIRT513766 PEX5L peroxisomal biogenesis factor 5 like 2 4
MIRT516898 COPS8 COP9 signalosome subunit 8 2 2
MIRT518703 TIMD4 T-cell immunoglobulin and mucin domain containing 4 2 4
MIRT520429 TTPAL alpha tocopherol transfer protein like 2 6
MIRT521843 PNISR PNN interacting serine and arginine rich protein 2 4
MIRT522116 NUDT3 nudix hydrolase 3 2 4
MIRT525467 TMPRSS12 transmembrane protease, serine 12 2 2
MIRT525583 MTRNR2L7 MT-RNR2-like 7 2 2
MIRT525906 BUB1 BUB1 mitotic checkpoint serine/threonine kinase 2 2
MIRT526072 C11orf54 chromosome 11 open reading frame 54 2 2
MIRT526232 MTRNR2L5 MT-RNR2-like 5 2 4
MIRT526455 FAM71F2 family with sequence similarity 71 member F2 2 4
MIRT526515 POU5F1B POU class 5 homeobox 1B 2 2
MIRT528032 FEZ2 fasciculation and elongation protein zeta 2 2 2
MIRT528422 MRPS16 mitochondrial ribosomal protein S16 2 2
MIRT528995 ISLR2 immunoglobulin superfamily containing leucine rich repeat 2 2 4
MIRT529311 ATRNL1 attractin like 1 2 2
MIRT529376 SKP1 S-phase kinase associated protein 1 2 4
MIRT530015 SRRM1 serine and arginine repetitive matrix 1 2 2
MIRT530089 FMN2 formin 2 2 2
MIRT530942 ENPP6 ectonucleotide pyrophosphatase/phosphodiesterase 6 2 2
MIRT531229 HIST1H2BD histone cluster 1 H2B family member d 2 2
MIRT533088 YTHDF3 YTH N6-methyladenosine RNA binding protein 3 2 2
MIRT533299 USP46 ubiquitin specific peptidase 46 2 2
MIRT533318 UNKL unkempt family like zinc finger 2 2
MIRT533721 TMEM30A transmembrane protein 30A 2 2
MIRT534096 AZF1 azoospermia factor 1 2 2
MIRT534188 SLC7A11 solute carrier family 7 member 11 2 2
MIRT534493 SAR1B secretion associated Ras related GTPase 1B 2 2
MIRT536077 MBOAT2 membrane bound O-acyltransferase domain containing 2 2 2
MIRT536242 LRIG2 leucine rich repeats and immunoglobulin like domains 2 2 2
MIRT537524 FAM104A family with sequence similarity 104 member A 2 2
MIRT538088 DGKH diacylglycerol kinase eta 2 2
MIRT538475 CNBP CCHC-type zinc finger nucleic acid binding protein 2 2
MIRT538853 BTG1 BTG anti-proliferation factor 1 2 4
MIRT539075 GDNF glial cell derived neurotrophic factor 2 2
MIRT539480 ACVR2B activin A receptor type 2B 2 4
MIRT540210 ARHGAP18 Rho GTPase activating protein 18 2 2
MIRT541940 TSPAN2 tetraspanin 2 2 2
MIRT543812 COCH cochlin 2 2
MIRT545120 PDZRN4 PDZ domain containing ring finger 4 2 2
MIRT545571 GIMAP4 GTPase, IMAP family member 4 2 2
MIRT545989 XKR4 XK related 4 2 2
MIRT547213 PANK3 pantothenate kinase 3 2 4
MIRT547740 KIAA1468 KIAA1468 2 2
MIRT548022 GRB2 growth factor receptor bound protein 2 2 4
MIRT548032 GOLIM4 golgi integral membrane protein 4 2 2
MIRT548102 GFPT1 glutamine--fructose-6-phosphate transaminase 1 2 4
MIRT548217 FKBP1A FK506 binding protein 1A 2 2
MIRT548588 DDX3X DEAD-box helicase 3, X-linked 2 4
MIRT548953 CDC27 cell division cycle 27 2 2
MIRT549072 CACUL1 CDK2 associated cullin domain 1 2 2
MIRT550368 INCENP inner centromere protein 2 6
MIRT550546 MYZAP myocardial zonula adherens protein 2 2
MIRT551491 TMEM192 transmembrane protein 192 2 4
MIRT553078 UEVLD UEV and lactate/malate dehyrogenase domains 2 2
MIRT554104 SMU1 DNA replication regulator and spliceosomal factor 2 2
MIRT555127 PTPRG protein tyrosine phosphatase, receptor type G 2 2
MIRT555477 POC1B-GALNT4 POC1B-GALNT4 readthrough 2 2
MIRT555978 NPTN neuroplastin 2 2
MIRT557011 HPRT1 hypoxanthine phosphoribosyltransferase 1 2 2
MIRT557706 GALNT4 polypeptide N-acetylgalactosaminyltransferase 4 2 2
MIRT558333 DNAJC28 DnaJ heat shock protein family (Hsp40) member C28 2 4
MIRT558488 DBN1 drebrin 1 2 2
MIRT559942 ZNF567 zinc finger protein 567 2 2
MIRT561127 ATP2B1 ATPase plasma membrane Ca2+ transporting 1 2 2
MIRT561791 PAWR pro-apoptotic WT1 regulator 2 2
MIRT562438 EEF2 eukaryotic translation elongation factor 2 2 2
MIRT563102 PABPC4L poly(A) binding protein cytoplasmic 4 like 2 2
MIRT563212 ZNF813 zinc finger protein 813 2 2
MIRT563426 KIF3A kinesin family member 3A 2 2
MIRT563473 SPIN4 spindlin family member 4 2 2
MIRT564015 HSPA4 heat shock protein family A (Hsp70) member 4 2 4
MIRT564117 ZYG11B zyg-11 family member B, cell cycle regulator 2 2
MIRT564223 SDE2 SDE2 telomere maintenance homolog 2 2
MIRT564503 CACNG1 calcium voltage-gated channel auxiliary subunit gamma 1 2 2
MIRT564515 DUSP3 dual specificity phosphatase 3 2 2
MIRT564811 ZBTB21 zinc finger and BTB domain containing 21 2 2
MIRT565265 TPD52 tumor protein D52 2 2
MIRT566012 RHOB ras homolog family member B 2 2
MIRT566216 PTMA prothymosin, alpha 2 2
MIRT566638 NFYA nuclear transcription factor Y subunit alpha 2 2
MIRT566821 MAPK8 mitogen-activated protein kinase 8 2 2
MIRT566948 LEPROT leptin receptor overlapping transcript 2 2
MIRT567290 HNRNPAB heterogeneous nuclear ribonucleoprotein A/B 2 2
MIRT567895 CSTF2 cleavage stimulation factor subunit 2 2 2
MIRT568731 MTRNR2L3 MT-RNR2-like 3 2 2
MIRT571263 ZNF239 zinc finger protein 239 2 2
MIRT572593 EIF2AK4 eukaryotic translation initiation factor 2 alpha kinase 4 2 2
MIRT573827 TGOLN2 trans-golgi network protein 2 2 2
MIRT576391 Fhl2 four and a half LIM domains 2 2 2
MIRT609901 SMS spermine synthase 2 2
MIRT613710 ELMSAN1 ELM2 and Myb/SANT domain containing 1 2 2
MIRT614406 ADAT1 adenosine deaminase, tRNA specific 1 2 2
MIRT615042 DCX doublecortin 2 2
MIRT617514 C5orf45 MRN complex interacting protein 2 2
MIRT619476 PRDM10 PR/SET domain 10 2 2
MIRT620349 TLN1 talin 1 2 2
MIRT620910 PLA2G7 phospholipase A2 group VII 2 2
MIRT622131 SP4 Sp4 transcription factor 2 2
MIRT622955 OTUD7B OTU deubiquitinase 7B 2 2
MIRT623351 MAGI3 membrane associated guanylate kinase, WW and PDZ domain containing 3 2 2
MIRT623619 INTU inturned planar cell polarity protein 2 2
MIRT624409 CCDC171 coiled-coil domain containing 171 2 2
MIRT625171 CCS copper chaperone for superoxide dismutase 2 2
MIRT625685 RPP40 ribonuclease P/MRP subunit p40 2 2
MIRT625875 ALDH18A1 aldehyde dehydrogenase 18 family member A1 2 2
MIRT626002 FAM107A family with sequence similarity 107 member A 2 2
MIRT626872 HRH4 histamine receptor H4 2 4
MIRT628220 FKBP9 FK506 binding protein 9 2 2
MIRT628265 DIO2 iodothyronine deiodinase 2 2 2
MIRT628402 C8orf37 chromosome 8 open reading frame 37 2 2
MIRT630564 C3orf36 chromosome 3 open reading frame 36 2 4
MIRT631577 RASSF9 Ras association domain family member 9 2 2
MIRT635730 CCDC58 coiled-coil domain containing 58 2 2
MIRT636224 SLC8A1 solute carrier family 8 member A1 2 2
MIRT636613 CLIC5 chloride intracellular channel 5 2 2
MIRT638899 CDK9 cyclin dependent kinase 9 2 2
MIRT640167 ATXN7L1 ataxin 7 like 1 2 2
MIRT642070 GTDC1 glycosyltransferase like domain containing 1 2 2
MIRT643034 CHCHD7 coiled-coil-helix-coiled-coil-helix domain containing 7 2 2
MIRT644572 SPOP speckle type BTB/POZ protein 2 2
MIRT644954 IFNB1 interferon beta 1 2 2
MIRT645948 TTF2 transcription termination factor 2 2 2
MIRT646440 XRCC2 X-ray repair cross complementing 2 2 2
MIRT647896 EPN2 epsin 2 2 2
MIRT648276 ZNF582 zinc finger protein 582 2 2
MIRT649381 NEDD1 neural precursor cell expressed, developmentally down-regulated 1 2 2
MIRT650254 CD68 CD68 molecule 2 2
MIRT650333 ATP5S ATP synthase, H+ transporting, mitochondrial Fo complex subunit s (factor B) 2 2
MIRT651707 VMP1 vacuole membrane protein 1 2 2
MIRT651774 VASP vasodilator stimulated phosphoprotein 2 2
MIRT653144 SRPK2 SRSF protein kinase 2 2 2
MIRT654112 RPS6KA5 ribosomal protein S6 kinase A5 2 2
MIRT654161 RORB RAR related orphan receptor B 2 2
MIRT655716 MLF2 myeloid leukemia factor 2 2 2
MIRT657476 HDAC4 histone deacetylase 4 2 2
MIRT658095 FOXO1 forkhead box O1 2 2
MIRT658860 DTX3L deltex E3 ubiquitin ligase 3L 2 2
MIRT658988 DNAJA1 DnaJ heat shock protein family (Hsp40) member A1 2 2
MIRT660767 ALDH6A1 aldehyde dehydrogenase 6 family member A1 2 2
MIRT661622 C2orf15 chromosome 2 open reading frame 15 2 2
MIRT661694 TFDP2 transcription factor Dp-2 2 2
MIRT662208 PLA2G4E phospholipase A2 group IVE 2 2
MIRT662443 RALGAPA1 Ral GTPase activating protein catalytic alpha subunit 1 2 2
MIRT664422 ADH5 alcohol dehydrogenase 5 (class III), chi polypeptide 2 2
MIRT687505 NECAB1 N-terminal EF-hand calcium binding protein 1 2 2
MIRT689910 SOD2 superoxide dismutase 2 2 2
MIRT690781 PLA2G2C phospholipase A2 group IIC 2 2
MIRT698488 TIAL1 TIA1 cytotoxic granule associated RNA binding protein like 1 2 2
MIRT699685 SFMBT2 Scm like with four mbt domains 2 2 2
MIRT700926 PDS5A PDS5 cohesin associated factor A 2 2
MIRT702258 LMNB1 lamin B1 2 2
MIRT703166 GPR137C G protein-coupled receptor 137C 2 2
MIRT703242 GNS glucosamine (N-acetyl)-6-sulfatase 2 2
MIRT704737 CENPQ centromere protein Q 2 2
MIRT707310 GLRX2 glutaredoxin 2 2 2
MIRT710021 KCNQ5 potassium voltage-gated channel subfamily Q member 5 2 2
MIRT712212 SCOC short coiled-coil protein 2 2
MIRT714742 SETBP1 SET binding protein 1 2 2
MIRT718268 ZNF749 zinc finger protein 749 2 2
MIRT720553 DYRK4 dual specificity tyrosine phosphorylation regulated kinase 4 2 2
MIRT722248 RBM41 RNA binding motif protein 41 2 2
MIRT723767 MPLKIP M-phase specific PLK1 interacting protein 2 2
MIRT723977 KIAA0146 scaffolding protein involved in DNA repair 1 1
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-4 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4282 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4282 Neoadjuvant chemotherapy sensitive tissue (breast cancer)
hsa-miR-4282 Neoadjuvant chemotherapy sensitive tissue (breast cancer)

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