miRTarBase - #MIRT301229


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pre-miRNA Information
pre-miRNA hsa-mir-4656   
Genomic Coordinates chr7: 4788565 - 4788639
Description Homo sapiens miR-4656 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4656
Sequence 10| UGGGCUGAGGGCAGGAGGCCUGU |32
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1257485407 2 dbSNP
rs71535143 5 dbSNP
rs933178228 7 dbSNP
rs895666746 9 dbSNP
rs1053330554 11 dbSNP
rs1327822621 13 dbSNP
rs934599733 16 dbSNP
rs1260841927 19 dbSNP
rs1371177672 22 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol SH3BP4   
Synonyms BOG25, TTP
Description SH3 domain binding protein 4
Transcript NM_014521   
Expression
Putative miRNA Targets on SH3BP4
3'UTR of SH3BP4
(miRNA target sites are highlighted)		 
>SH3BP4|NM_014521|3'UTR
   1 ATGGGTCCCCTCCCCTCCTGCTGCTCTGGAGTGCAAGCCCTCTTCTGCCCTGCGTGCCCTGCTGTCACCGCGGAGCTGAA
  81 GAGGGAGGAAGGGGCGGCTGCTCAGACAGATTTAGGGCCCGCCAGCTAGGCTACACCCATCATGCGCCGCCCTCCTCCAT
 161 CGAGGGAGAGGCCTGAAGGGACTGCCTACTGCAGCTCGTTGCCAATCACATAGCTTTCTATTTGTTAAGTATAAATTTAA
 241 ATTTAAAATCACTTTTTTAACGAATGGGGGGAAGGGATCTATGAGAAAGGTGGTATCTAATTTTTTTATGGACCATAAAG
 321 GTTTAAAAGAAAATAGGGGCACAGGCTGTTGAGGTTTTTATGTTGTTATAGACCTTTTTAAATTATGTTAGAGATGTATA
 401 TAGGTATTTAAAGGTCACTGGGAGCGTTTCTGATTCCCGGCCACACTTTGCATTTCAACACTCAGCCCGGAAAGATGCTC
 481 GTTCGGTTGTTGGACCTCTTTCACTCCCTGCGTGTAAGAAGGTGAATCACGTGGGAAAAAGTGGCTTTTCAGTAAACGGG
 561 TACAGCTCATTCTTTCTGAGAAGGCCCCAGGTCCTGCTCCCTCCTCGGATTTGATTGTCTTCCGTGCTTTGCCTCACTCG
 641 TAGTAAATGACCATCCATAGAATATGTGAATCTTTGGTGAGCTTCAGTGGGCAGAGTGAAGTCCCGCATTAGCATTTAGG
 721 TGCCCTGAGCTGTTTCTGCCAATAGATTAGAAAGCAGCCATGAGTTGACAGTCTTTAGGGCCCCTGCCAGTGTGCAATTA
 801 GTCATTGACAAGAACAATGCCATTTGAGAGTGAGGTGGTCCCTGCTGCTACGAGGCCATTGTACTGTTTTTTCCTTGAGG
 881 TCAAAGCAGTGCTTCCCATAGAGTTTGCTGCCTCTTCTGTGGACAGGAAGAAAACTTCATGACCGAATCAGAGCCTTGGT
 961 GGCCACTGACTCTCGTGCTTATTGCAGATGCTGTGGTTGGCCTCACAAGCAACGCCTTATGCTGATGTGCAGAGGTGCCA
1041 GCTGCCATTTGCCAAACTCTGCATTTCATTTCATCTAAGGCTTAACCCCTCTTCCTTCCTGGTGTACCTGTGTCTCCTCG
1121 GAAGGAAGTCATAGTTTAGATGAAACCATTTTTTGTACAATGTAAAGATCATCTGAGCAAGATGAGCATTTTGTAAAAAT
1201 GAAAATGTGACTCACATAAAATCAGGAACTTGACACAGTGTTGCATTAATAACTTTAGGGTGCAGACATGCTGTGTGAAT
1281 CTCACAATGCGTCGTAGATGTCGCGTGTTGGAAGGGAGCAGGAGGAAGGACTGATACTGGCAAATCAGTAGAGTGAGGTG
1361 ATCCTTAGCAACGTGCCAGGACACTTCCTGTGTGCCTGCAGTTGTCAGGGACCATTTGGGATCCCGAATCTCATTCTCTA
1441 AAACTGCTTTCTTGAAACATGTTACTTCCTTAGTATAATCAATGTATACTCCCTTACTGGCCTGAAACGTTGTATAGCTA
1521 CTTATTCAGATACTGAAGACCAACGGACTGAAAAAAAGAACAAACATTAGCTATTTTATGCTGCAAGAACCAGGACACAC
1601 AATTCGCCAATCATCCCACCATATAACCTTCGATTGTGCTTCTCAACTCCACCCCATAATTTCTCCCAGAGACCATCTAT
1681 CACCTTTTCCCCAAAGAAGAAACAAAACCAGTTGCACCTTAAACCATGGATATTTTTTCCTCAGGGGCTTTAAATAGTTT
1761 CCTATGCAACGTGTCTTGTAGCACAAATAAAATTCTACAAAAGTTGCAGTAAATTTTATTTGGATATTTTAACCTGTTAA
1841 GTGTGTGTGTGTTTTCTGTACCCAACCAGACTTTAAATAAAACAAACATGAAACCTAAAAAAAAAAAA
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' ugucCG-GAGGACGGGAGUCGGGu 5'
              || :|:|  | |||||||| 
Target 5' ctttGCATTTCAACACTCAGCCCg 3'
 446 - 469 155.00 -20.60
2 
miRNA  3' ugUCCGGAGGACGGGAGUCGGGu 5'
            | ||  |||  |:|| |||| 
Target 5' gcAAGC--CCT--CTTCTGCCCt 3'
 33 - 51 121.00 -18.10
3 
miRNA  3' ugUCCGGA------GGACGG--GA-GUCGGGu 5'
            ||||||       |||||  || ||||:| 
Target 5' agAGGCCTGAAGGGACTGCCTACTGCAGCTCg 3'
 167 - 198 121.00 -25.80
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN18727006 54 COSMIC
COSN28592727 68 COSMIC
COSN30535039 72 COSMIC
COSN23612045 97 COSMIC
COSN30120000 97 COSMIC
COSN31572759 103 COSMIC
COSN28778111 106 COSMIC
COSN31551719 150 COSMIC
COSN6175046 236 COSMIC
COSN30166662 339 COSMIC
COSN30538206 349 COSMIC
COSN21074807 673 COSMIC
COSN7240445 875 COSMIC
COSN32063259 945 COSMIC
COSN6681610 1187 COSMIC
COSN7240446 1348 COSMIC
COSN5500297 1431 COSMIC
COSN15812341 1535 COSMIC
COSN22890995 1601 COSMIC
COSN31544971 1606 COSMIC
COSN30538866 1740 COSMIC
COSN30172872 1798 COSMIC
COSN28813747 1843 COSMIC
COSN8990311 1848 COSMIC
COSN22872467 1886 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs554560358 3 dbSNP
rs749153165 5 dbSNP
rs1421939551 8 dbSNP
rs1465508906 13 dbSNP
rs1172039801 14 dbSNP
rs377494526 16 dbSNP
rs200133390 17 dbSNP
rs1321147143 20 dbSNP
rs774296563 24 dbSNP
rs747618777 29 dbSNP
rs375870121 30 dbSNP
rs771576042 33 dbSNP
rs772683228 34 dbSNP
rs1278804770 35 dbSNP
rs1388124219 36 dbSNP
rs1283494811 38 dbSNP
rs377640440 40 dbSNP
rs769239614 46 dbSNP
rs907454514 46 dbSNP
rs1003163759 48 dbSNP
rs765488534 50 dbSNP
rs775971150 51 dbSNP
rs1401346834 53 dbSNP
rs10929083 54 dbSNP
rs559766068 55 dbSNP
rs1158691136 70 dbSNP
rs752281042 71 dbSNP
rs576422631 72 dbSNP
rs962829030 73 dbSNP
rs1423346472 74 dbSNP
rs1254644478 75 dbSNP
rs973762906 76 dbSNP
rs546124835 83 dbSNP
rs996638937 89 dbSNP
rs1267963041 92 dbSNP
rs950988744 96 dbSNP
rs777996771 97 dbSNP
rs912304548 98 dbSNP
rs563175533 100 dbSNP
rs955284462 112 dbSNP
rs879097676 114 dbSNP
rs186859482 121 dbSNP
rs986708226 122 dbSNP
rs1383253396 123 dbSNP
rs1319569170 129 dbSNP
rs975587666 132 dbSNP
rs1259091447 138 dbSNP
rs1469379102 142 dbSNP
rs924589029 144 dbSNP
rs542424733 146 dbSNP
rs755864623 147 dbSNP
rs562101787 149 dbSNP
rs527788792 150 dbSNP
rs1187012221 152 dbSNP
rs1172227894 153 dbSNP
rs936935883 162 dbSNP
rs564348476 163 dbSNP
rs1289043527 165 dbSNP
rs1158174293 182 dbSNP
rs1382914800 189 dbSNP
rs547907552 191 dbSNP
rs914669506 196 dbSNP
rs1359994596 198 dbSNP
rs948859687 199 dbSNP
rs1428340010 206 dbSNP
rs1328024954 207 dbSNP
rs1319208404 209 dbSNP
rs868805925 211 dbSNP
rs1363944215 215 dbSNP
rs1046952897 222 dbSNP
rs928819848 225 dbSNP
rs1438546366 233 dbSNP
rs570897623 238 dbSNP
rs1048029283 242 dbSNP
rs1317249410 248 dbSNP
rs1263926401 250 dbSNP
rs886747712 252 dbSNP
rs746348092 253 dbSNP
rs1003892513 262 dbSNP
rs1266349587 266 dbSNP
rs533347833 267 dbSNP
rs1213847626 268 dbSNP
rs1359576023 272 dbSNP
rs995442530 275 dbSNP
rs1468439110 277 dbSNP
rs1189920845 290 dbSNP
rs552214001 291 dbSNP
rs996586880 293 dbSNP
rs1028100706 296 dbSNP
rs1343816439 301 dbSNP
rs1025532154 303 dbSNP
rs1405596321 316 dbSNP
rs951061513 317 dbSNP
rs1420002292 320 dbSNP
rs138751391 321 dbSNP
rs373065963 322 dbSNP
rs771073282 327 dbSNP
rs963814992 328 dbSNP
rs956199506 338 dbSNP
rs1479675277 340 dbSNP
rs1426725446 342 dbSNP
rs4589703 347 dbSNP
rs958158309 349 dbSNP
rs75378194 350 dbSNP
rs1202356001 355 dbSNP
rs145499586 355 dbSNP
rs1022081391 360 dbSNP
rs1273651778 380 dbSNP
rs1165759798 391 dbSNP
rs1187065732 396 dbSNP
rs970120940 401 dbSNP
rs1321201675 402 dbSNP
rs1393743428 420 dbSNP
rs1224413530 421 dbSNP
rs1349944086 423 dbSNP
rs1459838415 426 dbSNP
rs79452962 427 dbSNP
rs928767432 431 dbSNP
rs938846792 436 dbSNP
rs1444478961 439 dbSNP
rs983671302 440 dbSNP
rs1373936124 442 dbSNP
rs914150384 443 dbSNP
rs1468538938 466 dbSNP
rs908123134 467 dbSNP
rs949456262 468 dbSNP
rs1304596424 469 dbSNP
rs567913641 470 dbSNP
rs942317882 476 dbSNP
rs533682112 478 dbSNP
rs553436139 479 dbSNP
rs1038033094 481 dbSNP
rs1470894700 481 dbSNP
rs898184622 482 dbSNP
rs1459802761 485 dbSNP
rs1264845367 486 dbSNP
rs1204064060 492 dbSNP
rs1220035321 507 dbSNP
rs1282450191 511 dbSNP
rs576458867 512 dbSNP
rs545806183 513 dbSNP
rs551571305 514 dbSNP
rs576682949 531 dbSNP
rs898339368 532 dbSNP
rs1457028023 536 dbSNP
rs995331364 539 dbSNP
rs1156447341 554 dbSNP
rs1476310460 558 dbSNP
rs141248637 559 dbSNP
rs887005278 560 dbSNP
rs1008335620 561 dbSNP
rs1244879553 562 dbSNP
rs1008023051 569 dbSNP
rs1422185215 570 dbSNP
rs1172580099 577 dbSNP
rs191319148 580 dbSNP
rs1291042351 582 dbSNP
rs1461410037 584 dbSNP
rs1243863178 585 dbSNP
rs891708211 588 dbSNP
rs1296255254 589 dbSNP
rs1011940710 593 dbSNP
rs1415055608 601 dbSNP
rs774481569 606 dbSNP
rs1353159719 607 dbSNP
rs571644647 607 dbSNP
rs1215880817 608 dbSNP
rs1295655041 611 dbSNP
rs10675591 612 dbSNP
rs142622480 612 dbSNP
rs980155232 614 dbSNP
rs1162440294 616 dbSNP
rs1422190852 622 dbSNP
rs1387053937 623 dbSNP
rs761808254 623 dbSNP
rs988267966 624 dbSNP
rs1035786406 625 dbSNP
rs1272974259 635 dbSNP
rs970991678 640 dbSNP
rs562352534 641 dbSNP
rs983636468 653 dbSNP
rs1220408929 657 dbSNP
rs1490850574 658 dbSNP
rs1293172015 663 dbSNP
rs926664350 663 dbSNP
rs183288605 669 dbSNP
rs942284232 671 dbSNP
rs973517775 687 dbSNP
rs974087128 691 dbSNP
rs919569154 695 dbSNP
rs546186785 706 dbSNP
rs1049434227 707 dbSNP
rs890876677 712 dbSNP
rs1480988370 716 dbSNP
rs886910305 734 dbSNP
rs1428867267 738 dbSNP
rs1396690754 765 dbSNP
rs1428901318 775 dbSNP
rs1388549340 776 dbSNP
rs1435159064 777 dbSNP
rs1197480498 789 dbSNP
rs1481468621 791 dbSNP
rs943985218 796 dbSNP
rs150313699 804 dbSNP
rs1479977904 806 dbSNP
rs1253573191 807 dbSNP
rs1357124069 810 dbSNP
rs1205708721 815 dbSNP
rs1432381324 817 dbSNP
rs1323223001 835 dbSNP
rs1052947767 839 dbSNP
rs899503200 840 dbSNP
rs1346852012 841 dbSNP
rs1214522257 849 dbSNP
rs564547573 850 dbSNP
rs996910881 851 dbSNP
rs187833011 852 dbSNP
rs893541784 853 dbSNP
rs1011471099 857 dbSNP
rs1021976940 860 dbSNP
rs1440924188 863 dbSNP
rs750167575 865 dbSNP
rs1001540319 867 dbSNP
rs1481581346 873 dbSNP
rs1430230319 874 dbSNP
rs760460064 891 dbSNP
rs1417366627 892 dbSNP
rs1485558591 896 dbSNP
rs1186735048 899 dbSNP
rs137918424 904 dbSNP
rs960104942 905 dbSNP
rs1261581982 908 dbSNP
rs1205959901 909 dbSNP
rs115108610 912 dbSNP
rs1015075054 914 dbSNP
rs1034338631 917 dbSNP
rs1402112816 919 dbSNP
rs959438863 926 dbSNP
rs1309079310 931 dbSNP
rs1159315894 933 dbSNP
rs1344215850 939 dbSNP
rs1432309673 945 dbSNP
rs1327324689 948 dbSNP
rs531681029 955 dbSNP
rs373491031 965 dbSNP
rs973651288 975 dbSNP
rs922194938 976 dbSNP
rs567949782 988 dbSNP
rs765952633 993 dbSNP
rs983509953 1002 dbSNP
rs1158170837 1010 dbSNP
rs1451749372 1012 dbSNP
rs1285284045 1013 dbSNP
rs533717643 1014 dbSNP
rs1241819545 1015 dbSNP
rs1185858633 1016 dbSNP
rs1256452905 1017 dbSNP
rs1462019985 1017 dbSNP
rs912261478 1021 dbSNP
rs943788660 1022 dbSNP
rs899746211 1025 dbSNP
rs149445904 1036 dbSNP
rs1358706769 1043 dbSNP
rs117213817 1054 dbSNP
rs1192881874 1056 dbSNP
rs1454405524 1062 dbSNP
rs1340793513 1070 dbSNP
rs1244783638 1076 dbSNP
rs1317923699 1081 dbSNP
rs1380675822 1082 dbSNP
rs1387406510 1082 dbSNP
rs1053373847 1088 dbSNP
rs893445659 1094 dbSNP
rs1177538131 1095 dbSNP
rs913038329 1109 dbSNP
rs1383962701 1110 dbSNP
rs753487572 1120 dbSNP
rs144195663 1121 dbSNP
rs192900192 1126 dbSNP
rs1042941169 1130 dbSNP
rs1191485658 1138 dbSNP
rs1444984551 1141 dbSNP
rs1263384561 1151 dbSNP
rs1216756709 1152 dbSNP
rs1394495410 1158 dbSNP
rs185363002 1162 dbSNP
rs778364610 1169 dbSNP
rs1356790787 1171 dbSNP
rs1269447361 1176 dbSNP
rs1323421943 1179 dbSNP
rs1328469907 1184 dbSNP
rs542549677 1194 dbSNP
rs1004116018 1196 dbSNP
rs1444870449 1210 dbSNP
rs1363732764 1212 dbSNP
rs1280503559 1215 dbSNP
rs556077741 1216 dbSNP
rs1350112539 1217 dbSNP
rs1406530368 1225 dbSNP
rs1226727824 1227 dbSNP
rs1295229574 1230 dbSNP
rs75556478 1234 dbSNP
rs1476577533 1238 dbSNP
rs1004946473 1239 dbSNP
rs1193873163 1240 dbSNP
rs541664908 1244 dbSNP
rs1266067469 1257 dbSNP
rs1027673169 1262 dbSNP
rs1452166063 1266 dbSNP
rs1439484557 1268 dbSNP
rs1193894158 1275 dbSNP
rs1272174140 1275 dbSNP
rs950654247 1280 dbSNP
rs370868022 1285 dbSNP
rs983541309 1288 dbSNP
rs778285832 1291 dbSNP
rs550617180 1292 dbSNP
rs1437256435 1294 dbSNP
rs1335728917 1295 dbSNP
rs1327392026 1301 dbSNP
rs1412020771 1303 dbSNP
rs1189579184 1304 dbSNP
rs771759210 1305 dbSNP
rs976975301 1305 dbSNP
rs578053596 1306 dbSNP
rs1029156049 1310 dbSNP
rs1474624350 1310 dbSNP
rs1179505660 1318 dbSNP
rs921222311 1334 dbSNP
rs771290883 1337 dbSNP
rs748285305 1339 dbSNP
rs534156573 1348 dbSNP
rs906255959 1354 dbSNP
rs1003743609 1355 dbSNP
rs770100874 1356 dbSNP
rs1444909744 1359 dbSNP
rs1378289376 1364 dbSNP
rs868414588 1373 dbSNP
rs138754987 1374 dbSNP
rs1403489290 1384 dbSNP
rs1370293681 1385 dbSNP
rs895290795 1388 dbSNP
rs1295397980 1406 dbSNP
rs1414561933 1411 dbSNP
rs1406527087 1421 dbSNP
rs781294599 1426 dbSNP
rs201746521 1427 dbSNP
rs1238694236 1434 dbSNP
rs1292320312 1439 dbSNP
rs1244237117 1459 dbSNP
rs1282486236 1460 dbSNP
rs1182802524 1465 dbSNP
rs1459783772 1466 dbSNP
rs1239454270 1468 dbSNP
rs1211018008 1469 dbSNP
rs1027873099 1474 dbSNP
rs1215021132 1477 dbSNP
rs1042905338 1483 dbSNP
rs1282328798 1490 dbSNP
rs141783945 1493 dbSNP
rs772830185 1495 dbSNP
rs1355105085 1498 dbSNP
rs1314921824 1509 dbSNP
rs927140499 1510 dbSNP
rs746069174 1512 dbSNP
rs770031061 1513 dbSNP
rs1304238184 1521 dbSNP
rs1448392247 1522 dbSNP
rs561671529 1541 dbSNP
rs1257840784 1542 dbSNP
rs1420957554 1543 dbSNP
rs1380876541 1544 dbSNP
rs1162798800 1545 dbSNP
rs1004886411 1546 dbSNP
rs1415611305 1548 dbSNP
rs1019054475 1551 dbSNP
rs1057089281 1557 dbSNP
rs974828260 1559 dbSNP
rs895788461 1560 dbSNP
rs1005299294 1562 dbSNP
rs1291715061 1579 dbSNP
rs559554934 1580 dbSNP
rs921115461 1583 dbSNP
rs527549211 1590 dbSNP
rs953841641 1591 dbSNP
rs115336434 1600 dbSNP
rs915151579 1601 dbSNP
rs1355654216 1606 dbSNP
rs570263786 1607 dbSNP
rs188580289 1611 dbSNP
rs1029102222 1614 dbSNP
rs889305337 1624 dbSNP
rs1009078164 1632 dbSNP
rs1019166335 1633 dbSNP
rs965037263 1635 dbSNP
rs988883061 1636 dbSNP
rs939116302 1645 dbSNP
rs1422738857 1647 dbSNP
rs192558506 1648 dbSNP
rs1165278935 1653 dbSNP
rs1427669503 1655 dbSNP
rs968860897 1657 dbSNP
rs1478195935 1669 dbSNP
rs56161233 1674 dbSNP
rs146236903 1680 dbSNP
rs555371777 1684 dbSNP
rs1332280025 1691 dbSNP
rs572790913 1699 dbSNP
rs1049378931 1701 dbSNP
rs1255774993 1712 dbSNP
rs1220022378 1717 dbSNP
rs1340741406 1718 dbSNP
rs937171897 1719 dbSNP
rs992709330 1734 dbSNP
rs1402526437 1740 dbSNP
rs917157033 1746 dbSNP
rs940656044 1753 dbSNP
rs535290508 1765 dbSNP
rs1461310940 1769 dbSNP
rs1352482583 1771 dbSNP
rs866256422 1772 dbSNP
rs1173096652 1774 dbSNP
rs1004915195 1777 dbSNP
rs558439019 1778 dbSNP
rs578105369 1779 dbSNP
rs1197418207 1785 dbSNP
rs1019378729 1787 dbSNP
rs773134716 1794 dbSNP
rs1177075868 1808 dbSNP
rs1236307877 1809 dbSNP
rs1036762754 1811 dbSNP
rs1479866493 1814 dbSNP
rs8691 1818 dbSNP
rs1318212473 1822 dbSNP
rs1262089108 1823 dbSNP
rs1230477274 1837 dbSNP
rs1343875878 1839 dbSNP
rs966050354 1841 dbSNP
rs1301905830 1842 dbSNP
rs1390680035 1849 dbSNP
rs1374562750 1852 dbSNP
rs1198327824 1854 dbSNP
rs1333180547 1856 dbSNP
rs1419740270 1859 dbSNP
rs1447209204 1864 dbSNP
rs571489487 1866 dbSNP
rs1174490456 1875 dbSNP
rs1467661228 1882 dbSNP
rs116776840 1889 dbSNP
rs1158474242 1899 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 23677.0
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 GSM1065670. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' uguccgGAGGACG-GGAGUCGGGu 5'
                || :||| ::||| | | 
Target 5' ---acaCU-UUGCAUUUCAACACu 3'
 		1 - 20
Article - Memczak S; Jens M; Elefsinioti A; Torti F; et al.
- Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
CLIP-seq Support 1 for dataset GSM1065670
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / 4-thiouridine, 3_ML_LG
Location of target site ENST00000392011.2 | 3UTR | ACACUUUGCAUUUCAACACU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
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
48 hsa-miR-4656 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT135536 RAB5B RAB5B, member RAS oncogene family 2 2
MIRT168127 SOX4 SRY-box 4 2 2
MIRT301229 SH3BP4 SH3 domain binding protein 4 2 2
MIRT444362 TIMM8B translocase of inner mitochondrial membrane 8 homolog B 2 2
MIRT445909 SLC10A3 solute carrier family 10 member 3 2 2
MIRT447283 LAPTM5 lysosomal protein transmembrane 5 2 2
MIRT453797 KBTBD12 kelch repeat and BTB domain containing 12 2 2
MIRT456777 MTHFSD methenyltetrahydrofolate synthetase domain containing 2 2
MIRT459647 PCSK9 proprotein convertase subtilisin/kexin type 9 2 2
MIRT462333 BCL7B BCL tumor suppressor 7B 2 2
MIRT463535 ZBTB7A zinc finger and BTB domain containing 7A 2 2
MIRT465799 TMEM91 transmembrane protein 91 2 2
MIRT470647 POM121C POM121 transmembrane nucleoporin C 2 2
MIRT470837 PLXND1 plexin D1 2 2
MIRT471129 PHF19 PHD finger protein 19 2 2
MIRT483310 SLC35C2 solute carrier family 35 member C2 2 2
MIRT487264 CCNF cyclin F 2 2
MIRT491731 SEMA3F semaphorin 3F 2 2
MIRT497195 DRP2 dystrophin related protein 2 2 2
MIRT508384 SPTBN2 spectrin beta, non-erythrocytic 2 2 4
MIRT530496 FADS6 fatty acid desaturase 6 2 2
MIRT546995 PPP2CA protein phosphatase 2 catalytic subunit alpha 2 2
MIRT549790 KIAA0391 KIAA0391 2 2
MIRT560368 TAF8 TATA-box binding protein associated factor 8 2 2
MIRT566000 RNF4 ring finger protein 4 2 2
MIRT574035 PEX26 peroxisomal biogenesis factor 26 2 2
MIRT574231 DMRT2 doublesex and mab-3 related transcription factor 2 2 2
MIRT576139 Hmox1 heme oxygenase 1 2 2
MIRT576640 Mill2 MHC I like leukocyte 2 1 1
MIRT609875 RAD54L2 RAD54 like 2 2 4
MIRT622651 POU2F3 POU class 2 homeobox 3 2 4
MIRT628848 FAM151B family with sequence similarity 151 member B 2 2
MIRT634252 TIAL1 TIA1 cytotoxic granule associated RNA binding protein like 1 2 2
MIRT634672 GDE1 glycerophosphodiester phosphodiesterase 1 2 2
MIRT649087 FBXO25 F-box protein 25 2 2
MIRT665019 ELK1 ELK1, ETS transcription factor 2 2
MIRT666939 PMEPA1 prostate transmembrane protein, androgen induced 1 2 2
MIRT668960 CNBP CCHC-type zinc finger nucleic acid binding protein 2 2
MIRT675802 MED28 mediator complex subunit 28 2 2
MIRT684022 FOLR1 folate receptor 1 2 2
MIRT696480 COX6B1 cytochrome c oxidase subunit 6B1 2 2
MIRT705894 ADCY9 adenylate cyclase 9 2 2
MIRT709434 ZSCAN25 zinc finger and SCAN domain containing 25 2 2
MIRT713572 SLC2A8 solute carrier family 2 member 8 2 2
MIRT716697 HLA-B major histocompatibility complex, class I, B 2 2
MIRT719735 SLC39A11 solute carrier family 39 member 11 2 2
MIRT724907 DAO D-amino acid oxidase 2 2
MIRT725321 NFASC neurofascin 2 2
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-4656 Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-4656 Cisplatin 5460033 NSC119875 approved resistant High Hypopharyngeal Cancer cell line (FaDu)
hsa-mir-4656 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-miR-4656 Doxorubicin 31703 NSC123127 approved sensitive cell line (BAS)
hsa-miR-4656 Osimertinib 71496458 NSC779217 approved resistant cell line (H1975)
hsa-miR-4656 Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-4656 Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-4656 Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-miR-4656 Gemcitabine 60750 NSC613327 approved resistant cell line (MDA-231)
hsa-miR-4656 Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM16)

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