pre-miRNA Information
pre-miRNA hsa-mir-4477a   
Genomic Coordinates chr9: 41233755 - 41233835
Description Homo sapiens miR-4477a stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4477a
Sequence 48| CUAUUAAGGACAUUUGUGAUUC |69
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1281813060 1 dbSNP
rs1352899679 1 dbSNP
rs1283566158 2 dbSNP
rs1236244724 4 dbSNP
rs75019967 4 dbSNP
rs1348124293 5 dbSNP
rs34026740 8 dbSNP
rs1288237115 9 dbSNP
rs71262206 10 dbSNP
rs1355759977 11 dbSNP
rs1300249508 16 dbSNP
rs1328879592 18 dbSNP
rs139133717 20 dbSNP
Putative Targets

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' cuuAGUGUUUA--CAG--GAAUUauc 5'
             |||:||||  |||  |||||   
Target 5' gacTCATAAATTGGTCATCTTAAcca 3'
1025 - 1050 131.00 -7.12
2
miRNA  3' cuUAGUGUUUACAGGAAUUAuc 5'
            ||:||| || |:|||::|  
Target 5' gcATTACATATCTTCTTGGTtt 3'
135 - 156 124.00 -9.30
3
miRNA  3' cuuAGUGUUUAC---AGGAAUUAuc 5'
             |:||| |||   || |||||  
Target 5' tctTTACATATGTACTCGTTAATca 3'
413 - 437 119.00 -5.40
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.

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
134 hsa-miR-4477a Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT055843 PLEKHA1 pleckstrin homology domain containing A1 2 10
MIRT061259 AMOTL1 angiomotin like 1 2 4
MIRT071895 BTF3L4 basic transcription factor 3 like 4 2 6
MIRT076933 MLLT6 MLLT6, PHD finger containing 2 2
MIRT078652 ICT1 mitochondrial ribosomal protein L58 2 2
MIRT083633 PRNP prion protein 2 2
MIRT091629 RPL15 ribosomal protein L15 2 4
MIRT107076 PPP6C protein phosphatase 6 catalytic subunit 2 2
MIRT111191 TRIM33 tripartite motif containing 33 2 2
MIRT114515 ARF6 ADP ribosylation factor 6 2 2
MIRT175250 PSAT1 phosphoserine aminotransferase 1 2 4
MIRT175430 ACSL4 acyl-CoA synthetase long chain family member 4 2 2
MIRT178687 FAM102B family with sequence similarity 102 member B 2 2
MIRT189771 CDADC1 cytidine and dCMP deaminase domain containing 1 2 2
MIRT229450 RPL10 ribosomal protein L10 2 2
MIRT244899 PHF6 PHD finger protein 6 2 2
MIRT249189 AKIRIN1 akirin 1 2 8
MIRT261134 TRIM8 tripartite motif containing 8 2 2
MIRT275561 ZIC5 Zic family member 5 2 4
MIRT275652 ABHD13 abhydrolase domain containing 13 2 2
MIRT288082 UTP18 UTP18, small subunit processome component 2 2
MIRT303605 MTHFD2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase 2 2
MIRT307924 ARL8B ADP ribosylation factor like GTPase 8B 2 2
MIRT316787 FOXC1 forkhead box C1 2 2
MIRT326910 SCML2 Scm polycomb group protein like 2 2 2
MIRT327713 SPIN4 spindlin family member 4 2 2
MIRT331632 AASDHPPT aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 2 2
MIRT342506 TMOD3 tropomodulin 3 2 4
MIRT354470 LRRC58 leucine rich repeat containing 58 2 2
MIRT378711 TRIM24 tripartite motif containing 24 2 2
MIRT407462 YDJC YdjC chitooligosaccharide deacetylase homolog 2 2
MIRT408226 SMAD5 SMAD family member 5 2 4
MIRT441824 ALG14 ALG14, UDP-N-acetylglucosaminyltransferase subunit 2 2
MIRT442783 CHD8 chromodomain helicase DNA binding protein 8 2 2
MIRT443184 NHS NHS actin remodeling regulator 2 4
MIRT447615 CUL3 cullin 3 2 2
MIRT450156 DSEL dermatan sulfate epimerase-like 2 2
MIRT454801 NEDD9 neural precursor cell expressed, developmentally down-regulated 9 2 2
MIRT463050 ZNF644 zinc finger protein 644 2 2
MIRT467400 SOCS3 suppressor of cytokine signaling 3 2 2
MIRT468174 SGMS1 sphingomyelin synthase 1 2 2
MIRT468949 RPS14 ribosomal protein S14 2 6
MIRT469835 R3HDM4 R3H domain containing 4 2 2
MIRT470724 POFUT1 protein O-fucosyltransferase 1 2 2
MIRT470902 PLIN3 perilipin 3 2 2
MIRT472467 NAPG NSF attachment protein gamma 2 12
MIRT472602 NAA50 N(alpha)-acetyltransferase 50, NatE catalytic subunit 2 2
MIRT492350 SEMA7A semaphorin 7A (John Milton Hagen blood group) 2 2
MIRT493840 FOXN3 forkhead box N3 2 4
MIRT496318 DOCK9 dedicator of cytokinesis 9 2 2
MIRT500159 CLEC2D C-type lectin domain family 2 member D 2 8
MIRT500535 XPO4 exportin 4 2 4
MIRT503916 FBXL13 F-box and leucine rich repeat protein 13 2 4
MIRT504003 SAT1 spermidine/spermine N1-acetyltransferase 1 2 4
MIRT505647 SHMT1 serine hydroxymethyltransferase 1 2 4
MIRT506574 MIER3 MIER family member 3 2 4
MIRT506945 HS3ST3B1 heparan sulfate-glucosamine 3-sulfotransferase 3B1 2 4
MIRT508196 RPS19 ribosomal protein S19 2 6
MIRT511417 HSPA13 heat shock protein family A (Hsp70) member 13 2 4
MIRT512326 ACTB actin beta 2 4
MIRT515376 RPL7 ribosomal protein L7 2 2
MIRT520422 TUBG1 tubulin gamma 1 2 4
MIRT524844 ARPP19 cAMP regulated phosphoprotein 19 2 2
MIRT526320 UGT2A1 UDP glucuronosyltransferase family 2 member A1 complex locus 2 2
MIRT526561 UGT2A2 UDP glucuronosyltransferase family 2 member A2 2 2
MIRT528027 FEZ2 fasciculation and elongation protein zeta 2 2 2
MIRT529874 RBM43 RNA binding motif protein 43 2 2
MIRT530826 CLEC4D C-type lectin domain family 4 member D 2 2
MIRT531334 GDPD1 glycerophosphodiester phosphodiesterase domain containing 1 2 2
MIRT532068 CCNB1 cyclin B1 2 4
MIRT532870 ZNF566 zinc finger protein 566 2 2
MIRT535580 NUP35 nucleoporin 35 2 2
MIRT537644 ERGIC2 ERGIC and golgi 2 2 4
MIRT537725 ELAVL2 ELAV like RNA binding protein 2 2 2
MIRT538894 BRI3BP BRI3 binding protein 2 2
MIRT538945 BMP2K BMP2 inducible kinase 2 2
MIRT540703 PDPK1 3-phosphoinositide dependent protein kinase 1 2 4
MIRT543210 TMEM117 transmembrane protein 117 2 3
MIRT543357 LYRM2 LYR motif containing 2 2 2
MIRT544905 CLSPN claspin 2 2
MIRT545532 ARF3 ADP ribosylation factor 3 2 2
MIRT546446 SMOC1 SPARC related modular calcium binding 1 2 2
MIRT546882 PURB purine rich element binding protein B 2 4
MIRT547440 MED13 mediator complex subunit 13 2 2
MIRT548027 GOLIM4 golgi integral membrane protein 4 2 2
MIRT548673 CRNKL1 crooked neck pre-mRNA splicing factor 1 2 2
MIRT550435 LLGL2 LLGL2, scribble cell polarity complex component 2 2
MIRT551850 RPS3 ribosomal protein S3 2 2
MIRT556072 MRFAP1 Morf4 family associated protein 1 2 2
MIRT556554 LIMS1 LIM zinc finger domain containing 1 2 2
MIRT557132 HOXA13 homeobox A13 2 2
MIRT557875 FEM1B fem-1 homolog B 2 4
MIRT558146 ELK4 ELK4, ETS transcription factor 2 2
MIRT558862 CD2AP CD2 associated protein 2 2
MIRT558884 CCNE1 cyclin E1 2 4
MIRT558907 CBX5 chromobox 5 2 2
MIRT559175 BRAP BRCA1 associated protein 2 2
MIRT560860 GAL3ST3 galactose-3-O-sulfotransferase 3 2 2
MIRT561729 PPIF peptidylprolyl isomerase F 2 2
MIRT564024 CEBPB CCAAT/enhancer binding protein beta 2 2
MIRT564366 TRMT5 tRNA methyltransferase 5 2 2
MIRT564609 ZNF703 zinc finger protein 703 2 2
MIRT565494 AZF1 azoospermia factor 1 2 2
MIRT565577 SLC6A8 solute carrier family 6 member 8 2 2
MIRT566947 LEPROT leptin receptor overlapping transcript 2 2
MIRT567293 HNRNPA2B1 heterogeneous nuclear ribonucleoprotein A2/B1 2 2
MIRT567308 HMGN2 high mobility group nucleosomal binding domain 2 2 2
MIRT568048 CHSY1 chondroitin sulfate synthase 1 2 2
MIRT571807 PHF19 PHD finger protein 19 2 2
MIRT609234 RBM23 RNA binding motif protein 23 2 2
MIRT610328 SSX5 SSX family member 5 2 2
MIRT611428 UGT8 UDP glycosyltransferase 8 2 4
MIRT611709 SLFN13 schlafen family member 13 2 2
MIRT612069 CEP135 centrosomal protein 135 2 4
MIRT617676 JRKL JRK like 2 2
MIRT623684 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 2 2
MIRT635634 PRR15L proline rich 15 like 2 2
MIRT636422 MBOAT2 membrane bound O-acyltransferase domain containing 2 2 2
MIRT637011 GPATCH11 G-patch domain containing 11 2 2
MIRT644150 C4orf3 chromosome 4 open reading frame 3 2 2
MIRT648562 MEMO1 mediator of cell motility 1 2 2
MIRT650752 WNT16 Wnt family member 16 2 2
MIRT651914 UEVLD UEV and lactate/malate dehyrogenase domains 2 2
MIRT653556 SLC38A7 solute carrier family 38 member 7 2 2
MIRT692277 XRN2 5'-3' exoribonuclease 2 2 2
MIRT697650 WNK1 WNK lysine deficient protein kinase 1 2 2
MIRT703876 ERCC6 ERCC excision repair 6, chromatin remodeling factor 2 2
MIRT704615 CLIP1 CAP-Gly domain containing linker protein 1 2 2
MIRT708562 BBOX1 gamma-butyrobetaine hydroxylase 1 2 2
MIRT709614 KBTBD6 kelch repeat and BTB domain containing 6 2 2
MIRT712955 SGCD sarcoglycan delta 2 2
MIRT713502 DCAF17 DDB1 and CUL4 associated factor 17 2 2
MIRT720239 GPBP1 GC-rich promoter binding protein 1 2 2
MIRT724255 GLUD1 glutamate dehydrogenase 1 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4477a Imatinib 5291 NSC743414 approved sensitive High Gastrointestinal Stromal Tumor cell line (882R-NC, 882R-OE, 882R-KD)
hsa-miR-4477a Osimertinib 71496458 NSC779217 approved resistant cell line (HCC827)
hsa-miR-4477a Vemurafenib 42611257 NSC761431 approved resistant cell line (451Lu)

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