miRTarBase - #MIRT525431


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pre-miRNA Information
pre-miRNA hsa-mir-4778   
Genomic Coordinates chr2: 66358249 - 66358328
Description Homo sapiens miR-4778 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4778-3p
Sequence 51| UCUUCUUCCUUUGCAGAGUUGA |72
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs936001904 2 dbSNP
rs925922703 3 dbSNP
rs184768286 8 dbSNP
rs1249073833 10 dbSNP
rs977504360 13 dbSNP
rs192300002 18 dbSNP
Putative Targets

Gene Information
Gene Symbol PROX2   
Synonyms PROX-2
Description prospero homeobox 2
Transcript NM_001080408   
Expression
Putative miRNA Targets on PROX2
3'UTR of PROX2
(miRNA target sites are highlighted)		 
>PROX2|NM_001080408|3'UTR
   1 CTGTTTCGGGGTTAAGATCCCACAACGTGAGGAGTGACTGGCTAGGGTTTCCTGGGTTTGTCTTAAAGGGCAATTTAGCT
  81 GTAGTCATATAAAAAGGGCACAAGGAAATCTCCTCTATCAAAACAGGTACTATTACCATTTTGATCATTTATTTCCCTTT
 161 CCAGAATCATCAGAAATTTAACTATAAAATGTACTAACTATATTGGTGTATTGGTAGTATATTGTAAAAGGAACACAAGT
 241 TTCCAATCAGAAGACTTGAAGCTCAACTCCATTGTTTCCAGGTGTTGTGACCCTGGGAACTTCCTGGTATCTCTGTATCT
 321 GTAAAATGAGGTTGTTAAGGATTAAAGGACAGTATGTCCTATGCAATGTCATTCACACACAAATGTCAGTTTTTTGAGCC
 401 CCTCTTTCAGATAAGGTTATCTTATTTGGGGTTTTTACAAATTGCTGTTTTTAGTCACCTAATTATAAAGCGCCATCTAT
 481 TTGCTAGATACTTTCACATACTTTAAGCTTTTCACCCTGAAAAGTAGTTATTATCATCATTTAAAAGATGACCAAACAGA
 561 AGCTTTAGAACTGCAAGGTAACTCGCCAAAGCCTATGAGGCTAGGACATCTGGGTTGATAGGGACAGTCAGGAGCCTGGA
 641 GGAACCAAGACTTTCTGATGCCCAACTGCATGCTGGACCCATCTCCTGCAGCTAACTCAGGATCTCAAGCAGGACCCCAC
 721 CCCTAGTAAGCATCCAGCGCTGACAGGGCACCGTCACCTGACAACTCCTGCCCAGCACTTAGGAGCACTTCACCGCCCAA
 801 GATTTCTGCTGATCATTTCAGCAAACTCAAGACAAACTTTATGCAGGACTTGAGTGTTGCTGTTTATTCACATTTGTCTG
 881 CTGGAAGAGTTTATCAGCTGGATAATGCAAATAGTCTCCAGCTGACCATTGCAATTGGTGCCCCAACCTCATATATGCAG
 961 AAGAAGCTGAACTTCAGACTGTGAAAGGTAGAAAGGGCCTTAGGAGATCATCTGGCCCATGCTGCTTAAATTGGGAAGGA
1041 AGAACCGCAGTCCAGACAGGAGGCTTGCACAGGCTGTGCACAGCCTTGCAGATGATAAATGGCATAACTGGGACAAATGC
1121 AGCATCACACAGAAATGGAAATTCTCCCACTCCATAACAAAATTACAGTCCATGGCTGACCTTCCACTGATGAAGGAATT
1201 CATGAAATCAACATTTCCCCCTGCTGCTGGCCCAGCACAATTGTGACCCACTCTTGAGTATATAGGCAAGGCATGTACAA
1281 AGCTGAGTAACTGCATCTGTCTTCTAAGCTAGTCAGGATCAAGTCTTTGTAAGCACTGCCAAAGGTACGCCGGGTGGGGT
1361 GGGGTGGGGGTAATACACAGCTCGGGCTTTGTAGTCCTGATAAGGGGTGTCTGTGAGTTCATTAGCTTCTTTCCTGTCTA
1441 TATAAAACAAGTTTCATATTCGGCTACTCAACTTCCATAATTTTTCTGGTGGGGTGTTGCTGGAGCAGATGAGATAAAAT
1521 CCCTAAACTATTACTAGAACTATCAGCATAAAAAGTATGAAAGATGAATTTTCCTTTGAATTTTCTCTTCAAACAGCTGA
1601 AAGGAAAAACAAAACAGACTTAGCCCAAACCCATCTTTACAGGCTAAAGGTTAAGTGCCCTCCAGTACATCCAATTGCAC
1681 TCAGAAGATCTTTGCCCTATTTTCACAAAAATGAAGGAATCTGCCAAACCTAAGTTTTAAACACAGGCAAGCATGGAGTG
1761 CTCTGAGCAAGGGCAATCAGTTTTCTGTGTCCGGACATAGTAGAAGAACCCTCTATCCAGAGTGACATTACATACCTAAG
1841 TTAGACATACAGGGGAAACAAGTTCACATGACTGTCCAATAGAGAGCAGCCCTTCTTCTGTCCCAAACCTGAAATTCATT
1921 AGTGTGTGTTTAAAGACTGAGCCAAGTCACCTCCAGGGCAGTGAACCTTGTCTCAGGGACCAATGAGATGAAATGTACAA
2001 GCTCAAATTGAAAACATTTGTGTACTGCAGTCTTTCCAGGAAGTGTTCTCTAACCACTGAGCTAAACACAGAAGAATGTA
2081 TAAATATGTATGCTCTGCC
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' aguugAGACGUUUCCUUCUUCu 5'
               | ||||   ||||||| 
Target 5' tcataTATGCA---GAAGAAGc 3'
 949 - 967 150.00 -10.80
2 
miRNA  3' agUUGAGACGUUUCCUUCUUcu 5'
            || | || :|||||||||  
Target 5' ttAAAT-TGGGAAGGAAGAAcc 3'
 1026 - 1046 147.00 -14.10
3 
miRNA  3' aguUGAGACG-UUU---CCUUCUUcu 5'
             |||  || |||    ||||||  
Target 5' accACTGAGCTAAACACAGAAGAAtg 3'
 2053 - 2078 131.00 -7.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26774339 299 COSMIC
COSN30606130 715 COSMIC
COSN28480504 760 COSMIC
COSM7843909 795 COSMIC
COSM8520240 814 COSMIC
COSM8984692 831 COSMIC
COSM8873808 852 COSMIC
COSM6001185 932 COSMIC
COSM6276012 941 COSMIC
COSN31569998 1132 COSMIC
COSN31538893 1157 COSMIC
COSN21452839 1224 COSMIC
COSN24604834 1278 COSMIC
COSN4758868 1563 COSMIC
COSN19372149 1990 COSMIC
COSN25347321 2010 COSMIC
COSN8849915 2063 COSMIC
rs61978928 121 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1325511544 3 dbSNP
rs1176216428 4 dbSNP
rs751506425 7 dbSNP
rs763965108 8 dbSNP
rs1336037944 11 dbSNP
rs1440242141 12 dbSNP
rs757873542 22 dbSNP
rs200145421 23 dbSNP
rs764627344 24 dbSNP
rs529831386 26 dbSNP
rs1471245976 27 dbSNP
rs895040141 29 dbSNP
rs1403167512 30 dbSNP
rs141359648 33 dbSNP
rs762210488 34 dbSNP
rs1234880885 35 dbSNP
rs1454733352 36 dbSNP
rs775020807 37 dbSNP
rs775658360 38 dbSNP
rs1256954632 47 dbSNP
rs1054740621 51 dbSNP
rs1317989225 70 dbSNP
rs1310848593 73 dbSNP
rs938981901 87 dbSNP
rs922413553 88 dbSNP
rs1312759748 96 dbSNP
rs1036981841 101 dbSNP
rs927743794 105 dbSNP
rs1359396850 107 dbSNP
rs747096539 111 dbSNP
rs1319704361 112 dbSNP
rs907887477 114 dbSNP
rs984767316 115 dbSNP
rs1323824979 116 dbSNP
rs61978928 121 dbSNP
rs146599159 127 dbSNP
rs1432442448 145 dbSNP
rs1165534915 148 dbSNP
rs1176542656 160 dbSNP
rs1379089429 185 dbSNP
rs1425831414 193 dbSNP
rs990859389 198 dbSNP
rs1329504044 200 dbSNP
rs549334217 205 dbSNP
rs1465641200 210 dbSNP
rs1035138014 213 dbSNP
rs962973443 215 dbSNP
rs1018498600 217 dbSNP
rs1488421951 220 dbSNP
rs999744213 221 dbSNP
rs188512911 222 dbSNP
rs955546354 224 dbSNP
rs1257001769 228 dbSNP
rs34893831 234 dbSNP
rs1318083285 235 dbSNP
rs1022387174 239 dbSNP
rs1244415330 244 dbSNP
rs1488120065 246 dbSNP
rs1191668097 254 dbSNP
rs1010606417 259 dbSNP
rs1246330538 259 dbSNP
rs889447762 262 dbSNP
rs114899270 272 dbSNP
rs866277368 276 dbSNP
rs1296419711 278 dbSNP
rs999998021 299 dbSNP
rs1172637454 307 dbSNP
rs1348130593 308 dbSNP
rs902375762 328 dbSNP
rs1436433633 333 dbSNP
rs997924156 336 dbSNP
rs1347835693 337 dbSNP
rs554176159 340 dbSNP
rs1228614956 374 dbSNP
rs1340759778 376 dbSNP
rs1215893884 378 dbSNP
rs1367128012 380 dbSNP
rs1010674131 382 dbSNP
rs753398951 396 dbSNP
rs533923041 401 dbSNP
rs1287174322 412 dbSNP
rs895071254 425 dbSNP
rs17102763 427 dbSNP
rs1293819388 429 dbSNP
rs867235530 431 dbSNP
rs1192647121 439 dbSNP
rs1263555092 442 dbSNP
rs1476369821 453 dbSNP
rs1478271322 469 dbSNP
rs1294254049 471 dbSNP
rs1459508050 472 dbSNP
rs906190466 474 dbSNP
rs1404816071 482 dbSNP
rs1368713971 484 dbSNP
rs554733085 488 dbSNP
rs763744364 498 dbSNP
rs537660483 502 dbSNP
rs1367989514 515 dbSNP
rs1418349172 521 dbSNP
rs1047498210 522 dbSNP
rs568667289 527 dbSNP
rs551953316 528 dbSNP
rs532313772 530 dbSNP
rs930698082 532 dbSNP
rs1192118646 535 dbSNP
rs550982598 536 dbSNP
rs566639023 538 dbSNP
rs368532127 541 dbSNP
rs1268659220 550 dbSNP
rs1317143605 552 dbSNP
rs916561866 558 dbSNP
rs1215718517 572 dbSNP
rs12882109 573 dbSNP
rs1286514108 574 dbSNP
rs920317857 584 dbSNP
rs760122399 585 dbSNP
rs1205469477 597 dbSNP
rs370329203 606 dbSNP
rs1472543597 609 dbSNP
rs775007028 611 dbSNP
rs911508436 613 dbSNP
rs1438419185 614 dbSNP
rs985705912 619 dbSNP
rs529630174 620 dbSNP
rs1402775147 622 dbSNP
rs1331871537 624 dbSNP
rs145897808 624 dbSNP
rs922582755 628 dbSNP
rs978091201 632 dbSNP
rs1389552215 635 dbSNP
rs1373956826 640 dbSNP
rs1348740998 642 dbSNP
rs1307465616 645 dbSNP
rs967217835 646 dbSNP
rs544282484 649 dbSNP
rs1217259254 651 dbSNP
rs1010703464 652 dbSNP
rs1277585370 657 dbSNP
rs1442068817 662 dbSNP
rs959191074 665 dbSNP
rs1372625616 667 dbSNP
rs140695864 670 dbSNP
rs377010267 671 dbSNP
rs1364877505 680 dbSNP
rs1027966303 697 dbSNP
rs1378510863 712 dbSNP
rs879086035 715 dbSNP
rs1171198390 719 dbSNP
rs763488034 730 dbSNP
rs1201677612 733 dbSNP
rs1424812837 735 dbSNP
rs997955149 736 dbSNP
rs1471875445 738 dbSNP
rs1003852546 739 dbSNP
rs906420798 746 dbSNP
rs1047867558 751 dbSNP
rs769246547 752 dbSNP
rs763337705 753 dbSNP
rs772001399 753 dbSNP
rs1462613205 754 dbSNP
rs1337478682 756 dbSNP
rs1261155923 759 dbSNP
rs1434127729 760 dbSNP
rs1274062260 762 dbSNP
rs563122029 763 dbSNP
rs1351131024 764 dbSNP
rs546407255 766 dbSNP
rs577643863 767 dbSNP
rs1198078487 772 dbSNP
rs781328818 776 dbSNP
rs773641606 784 dbSNP
rs770182656 785 dbSNP
rs746089547 786 dbSNP
rs145861708 788 dbSNP
rs777509235 793 dbSNP
rs758407699 794 dbSNP
rs748527087 795 dbSNP
rs1480954490 796 dbSNP
rs1050036943 805 dbSNP
rs778551242 808 dbSNP
rs1185554290 814 dbSNP
rs754378888 816 dbSNP
rs1241277308 820 dbSNP
rs1202949099 822 dbSNP
rs753557520 828 dbSNP
rs1178190252 831 dbSNP
rs766079680 837 dbSNP
rs762300540 838 dbSNP
rs1349534793 839 dbSNP
rs1315271199 842 dbSNP
rs1260670079 843 dbSNP
rs1167997671 845 dbSNP
rs1182221127 846 dbSNP
rs934252187 847 dbSNP
rs888272692 852 dbSNP
rs752011856 854 dbSNP
rs764345215 858 dbSNP
rs1432109893 859 dbSNP
rs1331513706 867 dbSNP
rs978502347 870 dbSNP
rs1347419933 875 dbSNP
rs1316707148 877 dbSNP
rs763575908 881 dbSNP
rs1400465859 884 dbSNP
rs1366474679 889 dbSNP
rs1338725862 894 dbSNP
rs1165701836 909 dbSNP
rs966650962 912 dbSNP
rs56216877 915 dbSNP
rs779218344 915 dbSNP
rs574704227 916 dbSNP
rs1384706484 918 dbSNP
rs555050362 921 dbSNP
rs1189222696 922 dbSNP
rs370161030 929 dbSNP
rs1243729100 931 dbSNP
rs1318545015 933 dbSNP
rs139680482 935 dbSNP
rs769925258 936 dbSNP
rs1208629197 937 dbSNP
rs1292124286 941 dbSNP
rs1224267741 947 dbSNP
rs769019857 948 dbSNP
rs939440003 951 dbSNP
rs1290435478 957 dbSNP
rs1214592153 958 dbSNP
rs1003354569 963 dbSNP
rs1326060292 964 dbSNP
rs1364755759 967 dbSNP
rs992001405 968 dbSNP
rs771262752 974 dbSNP
rs1346530947 976 dbSNP
rs1305284143 979 dbSNP
rs1426412321 982 dbSNP
rs1026196647 983 dbSNP
rs759558106 988 dbSNP
rs1399650917 993 dbSNP
rs1296531036 994 dbSNP
rs1365148007 997 dbSNP
rs978580714 998 dbSNP
rs1171251664 1004 dbSNP
rs1411712266 1011 dbSNP
rs1206918073 1012 dbSNP
rs1284186800 1013 dbSNP
rs1421643904 1017 dbSNP
rs1225320343 1031 dbSNP
rs945588616 1039 dbSNP
rs375456732 1046 dbSNP
rs540339696 1047 dbSNP
rs1263407490 1050 dbSNP
rs915383228 1052 dbSNP
rs989763716 1055 dbSNP
rs538424942 1057 dbSNP
rs1446400052 1061 dbSNP
rs1186436421 1062 dbSNP
rs201880589 1064 dbSNP
rs868711870 1064 dbSNP
rs1016042928 1065 dbSNP
rs1379505601 1078 dbSNP
rs1007301115 1080 dbSNP
rs1289736995 1084 dbSNP
rs184546582 1088 dbSNP
rs888841220 1089 dbSNP
rs867294411 1093 dbSNP
rs1203145569 1102 dbSNP
rs546544732 1104 dbSNP
rs1050367612 1108 dbSNP
rs528699475 1118 dbSNP
rs1268692117 1124 dbSNP
rs1383551665 1169 dbSNP
rs901432235 1174 dbSNP
rs1230088808 1180 dbSNP
rs561129210 1196 dbSNP
rs976378864 1210 dbSNP
rs1042637843 1216 dbSNP
rs1282463199 1217 dbSNP
rs1244392269 1229 dbSNP
rs945418880 1230 dbSNP
rs529700561 1235 dbSNP
rs965033406 1240 dbSNP
rs1336626686 1244 dbSNP
rs1015388528 1246 dbSNP
rs1433345205 1261 dbSNP
rs1004349412 1263 dbSNP
rs1321824887 1274 dbSNP
rs1419511763 1285 dbSNP
rs1161039118 1293 dbSNP
rs888314532 1294 dbSNP
rs915225032 1308 dbSNP
rs1411044610 1315 dbSNP
rs780147498 1320 dbSNP
rs1406977563 1336 dbSNP
rs1162103314 1339 dbSNP
rs1329990683 1340 dbSNP
rs1373268584 1342 dbSNP
rs1392416456 1345 dbSNP
rs989554900 1348 dbSNP
rs1464601835 1350 dbSNP
rs1369833290 1351 dbSNP
rs567103624 1352 dbSNP
rs1464280992 1355 dbSNP
rs1236970125 1356 dbSNP
rs1248355945 1360 dbSNP
rs938115390 1362 dbSNP
rs1012853617 1363 dbSNP
rs1210545778 1365 dbSNP
rs1199058039 1369 dbSNP
rs1430231899 1370 dbSNP
rs1449765934 1370 dbSNP
rs66591704 1376 dbSNP
rs1353974119 1380 dbSNP
rs530664109 1381 dbSNP
rs1056969856 1383 dbSNP
rs1365977078 1384 dbSNP
rs564954584 1390 dbSNP
rs1283590228 1393 dbSNP
rs10220695 1394 dbSNP
rs1364955373 1407 dbSNP
rs1216336540 1414 dbSNP
rs1271717345 1416 dbSNP
rs1307542840 1416 dbSNP
rs745800897 1423 dbSNP
rs945426068 1424 dbSNP
rs745397695 1425 dbSNP
rs971985981 1425 dbSNP
rs1298754781 1426 dbSNP
rs1481561771 1433 dbSNP
rs1054326762 1434 dbSNP
rs932898928 1439 dbSNP
rs1429164633 1440 dbSNP
rs1437960223 1441 dbSNP
rs1348632815 1444 dbSNP
rs1322380614 1451 dbSNP
rs963067704 1456 dbSNP
rs576445998 1458 dbSNP
rs557193152 1462 dbSNP
rs1304134650 1463 dbSNP
rs560851122 1466 dbSNP
rs1007209757 1467 dbSNP
rs1397804210 1468 dbSNP
rs1269196969 1477 dbSNP
rs1362129210 1478 dbSNP
rs374943417 1481 dbSNP
rs544608458 1488 dbSNP
rs1030050432 1489 dbSNP
rs1390604394 1495 dbSNP
rs753649390 1514 dbSNP
rs908189041 1521 dbSNP
rs998797257 1525 dbSNP
rs982564207 1527 dbSNP
rs193144203 1529 dbSNP
rs1188371762 1531 dbSNP
rs1411632463 1537 dbSNP
rs575076500 1538 dbSNP
rs190537693 1540 dbSNP
rs894033932 1541 dbSNP
rs1317273708 1544 dbSNP
rs1293982699 1547 dbSNP
rs185614009 1552 dbSNP
rs1341694984 1558 dbSNP
rs1381345732 1565 dbSNP
rs1246690997 1570 dbSNP
rs1317030777 1573 dbSNP
rs937978247 1575 dbSNP
rs1002733736 1578 dbSNP
rs558599990 1612 dbSNP
rs982215822 1623 dbSNP
rs949263735 1631 dbSNP
rs1317747231 1633 dbSNP
rs906557900 1643 dbSNP
rs1042759182 1644 dbSNP
rs192425701 1649 dbSNP
rs1241382788 1651 dbSNP
rs1460902893 1655 dbSNP
rs1184822821 1656 dbSNP
rs1245497703 1658 dbSNP
rs1275868901 1666 dbSNP
rs1009659434 1669 dbSNP
rs919082623 1672 dbSNP
rs553051150 1675 dbSNP
rs1053866134 1689 dbSNP
rs1404767068 1696 dbSNP
rs1452717350 1699 dbSNP
rs932843037 1707 dbSNP
rs1274785985 1708 dbSNP
rs151072003 1718 dbSNP
rs1332347076 1720 dbSNP
rs1041347846 1723 dbSNP
rs1016152161 1729 dbSNP
rs1279954291 1730 dbSNP
rs1305606035 1734 dbSNP
rs536199105 1737 dbSNP
rs1428763679 1742 dbSNP
rs985804070 1747 dbSNP
rs1352513025 1751 dbSNP
rs567542528 1752 dbSNP
rs944242245 1759 dbSNP
rs1261492580 1763 dbSNP
rs1322996422 1771 dbSNP
rs1204402867 1777 dbSNP
rs1370776076 1778 dbSNP
rs714788 1792 dbSNP
rs1030534515 1793 dbSNP
rs1181662686 1798 dbSNP
rs997257757 1803 dbSNP
rs1233870995 1805 dbSNP
rs1424135880 1809 dbSNP
rs965959343 1810 dbSNP
rs952502258 1822 dbSNP
rs1478947621 1826 dbSNP
rs536767201 1836 dbSNP
rs919710946 1840 dbSNP
rs537020406 1848 dbSNP
rs1021137018 1856 dbSNP
rs111575499 1868 dbSNP
rs894068416 1874 dbSNP
rs1053955861 1878 dbSNP
rs1252813526 1884 dbSNP
rs1329430797 1885 dbSNP
rs1337380458 1886 dbSNP
rs958561651 1889 dbSNP
rs1282332461 1892 dbSNP
rs1206819122 1917 dbSNP
rs1310831148 1918 dbSNP
rs1285295514 1919 dbSNP
rs1337502245 1923 dbSNP
rs773701440 1924 dbSNP
rs116935234 1925 dbSNP
rs1439982401 1928 dbSNP
rs1220742466 1931 dbSNP
rs1268547157 1939 dbSNP
rs1220352155 1942 dbSNP
rs905171599 1946 dbSNP
rs1046944694 1948 dbSNP
rs1201076291 1959 dbSNP
rs949508097 1960 dbSNP
rs1474776963 1963 dbSNP
rs1168482074 1986 dbSNP
rs1398562974 1998 dbSNP
rs967662912 2008 dbSNP
rs186721912 2012 dbSNP
rs182077825 2013 dbSNP
rs893801841 2018 dbSNP
rs76861947 2021 dbSNP
rs1324824631 2023 dbSNP
rs1226772559 2027 dbSNP
rs1270791130 2038 dbSNP
rs1342096339 2041 dbSNP
rs996919546 2042 dbSNP
rs547164541 2051 dbSNP
rs1490609511 2058 dbSNP
rs1041209121 2064 dbSNP
rs1358398741 2079 dbSNP
rs1259217585 2085 dbSNP
rs1446004162 2089 dbSNP
rs191699750 2089 dbSNP
rs145414176 2092 dbSNP
rs909165307 2093 dbSNP
rs986046560 2096 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions hESCs (WA-09)
Disease 283571.0
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 SRR359787. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Lipchina I; Elkabetz Y; Hafner M; Sheridan et al., 2011, Genes & development.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' agUUGA---GACGUUU-CCUUCUUCu 5'
            |:||   || ||:|  | : ||| 
Target 5' --AGCUGAACUUCAGACUGUGAAAG- 3'
 		1 - 23
Article - Lipchina I; Elkabetz Y; Hafner M; Sheridan et al.
- Genes & development, 2011
MicroRNAs are important regulators in many cellular processes, including stem cell self-renewal. Recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. However, their role in human embryonic stem (ES) cells (hESCs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. Here, we performed comprehensive microRNA profiling in hESCs and in purified neural and mesenchymal derivatives. Using a combination of AGO cross-linking and microRNA perturbation experiments, together with computational prediction, we identified the targets of the miR-302/367 cluster, the most abundant microRNAs in hESCs. Functional studies identified novel roles of miR-302/367 in maintaining pluripotency and regulating hESC differentiation. We show that in addition to its role in TGF-beta signaling, miR-302/367 promotes bone morphogenetic protein (BMP) signaling by targeting BMP inhibitors TOB2, DAZAP2, and SLAIN1. This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area.
LinkOut: [PMID: 22012620]
CLIP-seq Support 1 for dataset SRR359787
Method / RBP PAR-CLIP / AGO2
Cell line / Condition hESCs (WA-09) / 4-thiouridine, RNase T1
Location of target site ENST00000556084.2 | 3UTR | AGCUGAACUUCAGACUGUGAAAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22012620 / SRX103431
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
169 hsa-miR-4778-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT199338 YES1 YES proto-oncogene 1, Src family tyrosine kinase 2 4
MIRT203028 MAP3K2 mitogen-activated protein kinase kinase kinase 2 2 2
MIRT260646 CDKN1A cyclin dependent kinase inhibitor 1A 2 2
MIRT336468 SRP9 signal recognition particle 9 2 2
MIRT389212 SERTAD2 SERTA domain containing 2 2 2
MIRT441814 TENM1 teneurin transmembrane protein 1 2 2
MIRT444029 GREM1 gremlin 1, DAN family BMP antagonist 2 4
MIRT454171 HIST1H2BK histone cluster 1 H2B family member k 2 2
MIRT469663 RABEPK Rab9 effector protein with kelch motifs 2 2
MIRT495579 PLEKHA8 pleckstrin homology domain containing A8 2 2
MIRT498340 PRELID2 PRELI domain containing 2 2 2
MIRT498696 LYRM2 LYR motif containing 2 2 6
MIRT504156 OPN5 opsin 5 2 4
MIRT506321 OTUD4 OTU deubiquitinase 4 2 4
MIRT507608 DCAF7 DDB1 and CUL4 associated factor 7 2 2
MIRT525431 PROX2 prospero homeobox 2 2 2
MIRT526973 PAX7 paired box 7 2 2
MIRT527814 TMEM74B transmembrane protein 74B 2 2
MIRT527960 MTAP methylthioadenosine phosphorylase 2 2
MIRT528083 NOL9 nucleolar protein 9 2 2
MIRT528480 STAMBPL1 STAM binding protein like 1 2 2
MIRT528947 PNMA5 paraneoplastic Ma antigen family member 5 2 2
MIRT530687 C8orf46 chromosome 8 open reading frame 46 2 2
MIRT531733 SLC2A9 solute carrier family 2 member 9 2 2
MIRT532445 PLGRKT plasminogen receptor with a C-terminal lysine 2 2
MIRT533331 UNK unkempt family zinc finger 2 2
MIRT534205 SLC38A9 solute carrier family 38 member 9 2 2
MIRT534322 SHISA6 shisa family member 6 2 2
MIRT535197 PLCL1 phospholipase C like 1 (inactive) 2 2
MIRT538076 DIAPH2 diaphanous related formin 2 2 2
MIRT539250 ANKRD50 ankyrin repeat domain 50 2 2
MIRT548733 CREBRF CREB3 regulatory factor 2 2
MIRT556406 LRRC8B leucine rich repeat containing 8 VRAC subunit B 2 2
MIRT559576 AP1AR adaptor related protein complex 1 associated regulatory protein 2 2
MIRT567661 ERGIC2 ERGIC and golgi 2 2 2
MIRT572750 FAM204A family with sequence similarity 204 member A 2 2
MIRT609355 ZNF664 zinc finger protein 664 2 2
MIRT611194 TMEM105 transmembrane protein 105 2 2
MIRT611545 BIRC5 baculoviral IAP repeat containing 5 2 4
MIRT611690 NODAL nodal growth differentiation factor 2 2
MIRT611810 FCRL4 Fc receptor like 4 2 2
MIRT612746 MYOCD myocardin 2 2
MIRT614177 FAM53B family with sequence similarity 53 member B 2 2
MIRT614431 TAZ tafazzin 2 2
MIRT614586 SDC1 syndecan 1 2 2
MIRT615547 TNFSF15 TNF superfamily member 15 2 2
MIRT615872 BRD3 bromodomain containing 3 2 2
MIRT615970 ASCL1 achaete-scute family bHLH transcription factor 1 2 2
MIRT616024 PRRG4 proline rich and Gla domain 4 2 4
MIRT616242 NFIC nuclear factor I C 2 2
MIRT616282 HMGB1 high mobility group box 1 2 2
MIRT616674 PRR15 proline rich 15 2 2
MIRT618302 COL4A4 collagen type IV alpha 4 chain 2 2
MIRT618657 ATP6AP1L ATPase H+ transporting accessory protein 1 like 2 2
MIRT618754 SLC38A5 solute carrier family 38 member 5 2 2
MIRT619505 TXLNB taxilin beta 2 2
MIRT619545 GABRG2 gamma-aminobutyric acid type A receptor gamma2 subunit 2 2
MIRT619605 MKKS McKusick-Kaufman syndrome 2 2
MIRT619804 CDC42EP4 CDC42 effector protein 4 2 2
MIRT619923 NLRP9 NLR family pyrin domain containing 9 2 2
MIRT620442 SEMA3E semaphorin 3E 2 4
MIRT620730 CCL16 C-C motif chemokine ligand 16 2 2
MIRT625345 TAPBP TAP binding protein 2 2
MIRT627510 ST8SIA3 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3 2 2
MIRT632584 PLCXD3 phosphatidylinositol specific phospholipase C X domain containing 3 2 2
MIRT636901 RABGAP1L RAB GTPase activating protein 1 like 2 2
MIRT637873 UTP6 UTP6, small subunit processome component 2 2
MIRT639011 ABI2 abl interactor 2 2 2
MIRT639054 FPR1 formyl peptide receptor 1 2 2
MIRT639085 ADCYAP1 adenylate cyclase activating polypeptide 1 2 2
MIRT639589 RGS5 regulator of G protein signaling 5 2 2
MIRT639718 NPRL3 NPR3 like, GATOR1 complex subunit 2 2
MIRT639904 SRGAP2 SLIT-ROBO Rho GTPase activating protein 2 2 2
MIRT640392 ZNF785 zinc finger protein 785 2 2
MIRT640786 GRIK3 glutamate ionotropic receptor kainate type subunit 3 2 2
MIRT641290 SLAMF1 signaling lymphocytic activation molecule family member 1 2 2
MIRT641442 PELO pelota mRNA surveillance and ribosome rescue factor 2 2
MIRT642426 STAT3 signal transducer and activator of transcription 3 2 2
MIRT642682 KRT74 keratin 74 2 2
MIRT643362 TRIM10 tripartite motif containing 10 2 2
MIRT643982 DUSP28 dual specificity phosphatase 28 2 2
MIRT644466 ZNF747 zinc finger protein 747 2 2
MIRT644561 SPOP speckle type BTB/POZ protein 2 2
MIRT645748 FAM213A family with sequence similarity 213 member A 2 2
MIRT646737 FADS1 fatty acid desaturase 1 2 2
MIRT647446 SIX6 SIX homeobox 6 2 2
MIRT648317 SCNN1G sodium channel epithelial 1 gamma subunit 2 2
MIRT649327 POLG DNA polymerase gamma, catalytic subunit 2 2
MIRT649453 WDR70 WD repeat domain 70 2 2
MIRT650066 CCDC134 coiled-coil domain containing 134 2 2
MIRT650156 JUND JunD proto-oncogene, AP-1 transcription factor subunit 2 2
MIRT650317 TMX4 thioredoxin related transmembrane protein 4 2 2
MIRT650429 BBS9 Bardet-Biedl syndrome 9 2 2
MIRT651325 ZCCHC2 zinc finger CCHC-type containing 2 2 2
MIRT651843 USP13 ubiquitin specific peptidase 13 2 2
MIRT652532 TM9SF3 transmembrane 9 superfamily member 3 2 2
MIRT652816 TARDBP TAR DNA binding protein 2 2
MIRT652971 SUN2 Sad1 and UNC84 domain containing 2 2 2
MIRT653466 SLC5A12 solute carrier family 5 member 12 2 4
MIRT653568 SLC35B3 solute carrier family 35 member B3 2 2
MIRT655678 NUMBL NUMB like, endocytic adaptor protein 2 2
MIRT656785 KPNA4 karyopherin subunit alpha 4 2 2
MIRT656798 KNTC1 kinetochore associated 1 2 2
MIRT656988 KDM5A lysine demethylase 5A 2 2
MIRT657292 HOXB5 homeobox B5 2 2
MIRT657497 HBEGF heparin binding EGF like growth factor 2 4
MIRT658012 GABRB1 gamma-aminobutyric acid type A receptor beta1 subunit 2 2
MIRT658146 STXBP2 syntaxin binding protein 2 2 2
MIRT658259 FAXC failed axon connections homolog 2 2
MIRT659051 DGKH diacylglycerol kinase eta 2 2
MIRT659171 DCTN3 dynactin subunit 3 2 2
MIRT659936 CACHD1 cache domain containing 1 2 2
MIRT660079 BZW1 basic leucine zipper and W2 domains 1 2 2
MIRT660167 BNIP3L BCL2 interacting protein 3 like 2 2
MIRT660292 BICC1 BicC family RNA binding protein 1 2 2
MIRT660317 BDP1 B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB 2 2
MIRT660340 BCAT1 branched chain amino acid transaminase 1 2 2
MIRT660447 ATP1A2 ATPase Na+/K+ transporting subunit alpha 2 2 2
MIRT661634 UGT2B28 UDP glucuronosyltransferase family 2 member B28 2 2
MIRT662438 RALGAPA1 Ral GTPase activating protein catalytic alpha subunit 1 2 2
MIRT664202 TBCA tubulin folding cofactor A 2 2
MIRT666436 SH2B3 SH2B adaptor protein 3 2 2
MIRT666666 RBM47 RNA binding motif protein 47 2 4
MIRT669253 C4orf36 chromosome 4 open reading frame 36 2 2
MIRT669502 ARL3 ADP ribosylation factor like GTPase 3 2 2
MIRT693912 HNRNPA1L2 heterogeneous nuclear ribonucleoprotein A1-like 2 2 2
MIRT700435 PURB purine rich element binding protein B 2 2
MIRT702857 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 2 2
MIRT708857 TMSB4X thymosin beta 4, X-linked 2 2
MIRT709030 KBTBD13 kelch repeat and BTB domain containing 13 2 2
MIRT709609 CXorf23 BCLAF1 and THRAP3 family member 3 2 2
MIRT709810 AR androgen receptor 2 2
MIRT709872 A1CF APOBEC1 complementation factor 2 2
MIRT710208 ENAH ENAH, actin regulator 2 2
MIRT710964 CMKLR1 chemerin chemokine-like receptor 1 2 2
MIRT711173 EMCN endomucin 2 2
MIRT711219 RETSAT retinol saturase 2 2
MIRT711345 FMNL2 formin like 2 2 2
MIRT711441 DLC1 DLC1 Rho GTPase activating protein 2 2
MIRT711631 PEBP1 phosphatidylethanolamine binding protein 1 2 2
MIRT711823 MAPK8IP3 mitogen-activated protein kinase 8 interacting protein 3 2 2
MIRT712164 SURF4 surfeit 4 2 2
MIRT712632 RNF103-CHMP3 RNF103-CHMP3 readthrough 2 2
MIRT713692 CYB5R4 cytochrome b5 reductase 4 2 2
MIRT714906 CHMP3 charged multivesicular body protein 3 2 2
MIRT715161 FIG4 FIG4 phosphoinositide 5-phosphatase 2 2
MIRT715430 SOCS5 suppressor of cytokine signaling 5 2 2
MIRT715660 ZBTB25 zinc finger and BTB domain containing 25 2 2
MIRT715968 FADS3 fatty acid desaturase 3 2 2
MIRT716203 TYW3 tRNA-yW synthesizing protein 3 homolog 2 2
MIRT716234 SRSF12 serine and arginine rich splicing factor 12 2 2
MIRT716251 PALM2 paralemmin 2 2 2
MIRT716375 CCBE1 collagen and calcium binding EGF domains 1 2 2
MIRT716490 PHACTR2 phosphatase and actin regulator 2 2 2
MIRT716744 APOL6 apolipoprotein L6 2 2
MIRT717624 AGPAT4 1-acylglycerol-3-phosphate O-acyltransferase 4 2 2
MIRT718480 TMEM151A transmembrane protein 151A 2 2
MIRT718805 PRKCB protein kinase C beta 2 2
MIRT719276 SETD7 SET domain containing lysine methyltransferase 7 2 2
MIRT719432 NPTX2 neuronal pentraxin 2 2 2
MIRT721011 ZNF619 zinc finger protein 619 2 2
MIRT721819 HEATR5A HEAT repeat containing 5A 2 2
MIRT721997 CLLU1OS chronic lymphocytic leukemia up-regulated 1 opposite strand 2 2
MIRT723143 METTL24 methyltransferase like 24 2 2
MIRT723213 PIP5K1C phosphatidylinositol-4-phosphate 5-kinase type 1 gamma 2 2
MIRT723427 MC2R melanocortin 2 receptor 2 2
MIRT723436 ADI1 acireductone dioxygenase 1 2 2
MIRT723542 PAGR1 PAXIP1 associated glutamate rich protein 1 2 2
MIRT724474 MMD monocyte to macrophage differentiation associated 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4778-3p Platinum 23939 sensitive tissue (non-small cell lung cancer)
hsa-miR-4778-3p Ceritinib 57379345 NSC776422 approved sensitive cell line (H3122)

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