pre-miRNA Information
pre-miRNA hsa-mir-4486   
Genomic Coordinates chr11: 19575310 - 19575372
Description Homo sapiens miR-4486 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4486
Sequence 5| GCUGGGCGAGGCUGGCA |21
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs774299284 8 dbSNP
rs902172817 14 dbSNP
rs1222795726 17 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol AAED1   
Synonyms C9orf21
Description AhpC/TSA antioxidant enzyme domain containing 1
Transcript NM_153698   
Expression
Putative miRNA Targets on AAED1
3'UTR of AAED1
(miRNA target sites are highlighted)
>AAED1|NM_153698|3'UTR
   1 CTTAAAATGCACTCAGTCACTTTCAACTGGACCTTCTGGAATGTGACCTTCAATGCCTGGGTGTAATATCCTCGTGCAGT
  81 GTCTAACCTGCTGTCCCTTCCCAGCCTTTGAGGAGTTAGGGAAGCATAAAGGGGGCTTGAACCTGTTGAATTGCATGCTG
 161 GGAAGCATCAGTTGTCAAAATATGTTATATACTTCCATTTTATAACTTTTAACATTTTATACAAAAAAAATGAATATACA
 241 AAATATAACTTTAAAAGCTATAAAATCATAAATACTCTAAATTATTTTACATTATGGTATATTCAGTCAATGAAAGAGTT
 321 TTTTGGCAATATAAATTCTGACAGTATATAAGGGGACAGGAGAACAACACAAGACCATTATATTCAGTGAAGAAGGCAAA
 401 ATATCAAATCTGTCAACAATGTAACTGCATTTTTATATGTATATATTTGTATTTTTGTATGCTTTGGAAAAAGACAGGAA
 481 ATAAACACCAAAATGTTGCCAGTAGGTAAAAAAAAAAAAAAAAAA
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' acgGUCGGAGCGGGUCg 5'
             :| |||||: ||| 
Target 5' taaTATCCTCGTGCAGt 3'
64 - 80 110.00 -15.50
2
miRNA  3' acGGUCGGAGCGGGUCg 5'
            |:: || : ||||| 
Target 5' tgCTGTCCCTTCCCAGc 3'
89 - 105 103.00 -16.30
3
miRNA  3' acGGUCGGAGCGGGUCg 5'
            ||  |  :|||::| 
Target 5' gaCCTTCAATGCCTGGg 3'
45 - 61 95.00 -12.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30165933 1 COSMIC
COSN30511513 13 COSMIC
COSN30143406 30 COSMIC
COSN20345427 32 COSMIC
COSN31534182 74 COSMIC
COSN31510564 131 COSMIC
COSN30497582 142 COSMIC
COSN30189142 162 COSMIC
COSN32062655 165 COSMIC
COSN28782240 191 COSMIC
COSN7578908 239 COSMIC
COSN28084675 699 COSMIC
COSN23910327 1255 COSMIC
COSN23921863 1256 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs138737168 1 dbSNP
rs372486104 12 dbSNP
rs1008166318 14 dbSNP
rs1438669314 19 dbSNP
rs776008132 26 dbSNP
rs763600709 27 dbSNP
rs1250645920 30 dbSNP
rs1418093970 33 dbSNP
rs1461660843 40 dbSNP
rs761143298 44 dbSNP
rs1471193738 54 dbSNP
rs181375725 63 dbSNP
rs1359134601 68 dbSNP
rs546934940 73 dbSNP
rs1045122076 74 dbSNP
rs1409364889 76 dbSNP
rs1286760480 78 dbSNP
rs1223937910 82 dbSNP
rs948107386 83 dbSNP
rs896496099 87 dbSNP
rs528772616 97 dbSNP
rs541443440 106 dbSNP
rs1251317481 119 dbSNP
rs1053291542 126 dbSNP
rs1369584969 132 dbSNP
rs1164790870 134 dbSNP
rs570683294 135 dbSNP
rs935623464 143 dbSNP
rs934402985 146 dbSNP
rs979663646 151 dbSNP
rs1247967950 152 dbSNP
rs552382021 155 dbSNP
rs1183985458 156 dbSNP
rs1173166717 169 dbSNP
rs1355178402 171 dbSNP
rs1483242873 183 dbSNP
rs1267979853 184 dbSNP
rs1367643713 189 dbSNP
rs1405808799 192 dbSNP
rs1220002250 196 dbSNP
rs1292675573 211 dbSNP
rs1361452236 221 dbSNP
rs1365233608 223 dbSNP
rs1265965045 225 dbSNP
rs145187742 231 dbSNP
rs946865836 231 dbSNP
rs975162764 231 dbSNP
rs902703168 232 dbSNP
rs963766825 232 dbSNP
rs1315257621 236 dbSNP
rs1019304184 237 dbSNP
rs754388756 239 dbSNP
rs565188116 241 dbSNP
rs1221293607 244 dbSNP
rs1309410962 245 dbSNP
rs1410708955 246 dbSNP
rs1345245613 249 dbSNP
rs1487745552 253 dbSNP
rs947003913 256 dbSNP
rs1188784890 265 dbSNP
rs986452175 266 dbSNP
rs951355249 267 dbSNP
rs916828287 272 dbSNP
rs1166744509 275 dbSNP
rs1387179617 280 dbSNP
rs1425465844 285 dbSNP
rs532846899 291 dbSNP
rs990993394 303 dbSNP
rs147155053 310 dbSNP
rs1452424249 315 dbSNP
rs1361603119 319 dbSNP
rs939363148 328 dbSNP
rs1364321766 329 dbSNP
rs1402066242 331 dbSNP
rs927959162 332 dbSNP
rs995388897 339 dbSNP
rs973247608 341 dbSNP
rs961467152 342 dbSNP
rs898333268 358 dbSNP
rs1320264174 359 dbSNP
rs1218342376 362 dbSNP
rs143630506 364 dbSNP
rs983949313 367 dbSNP
rs1187237664 370 dbSNP
rs1245041950 372 dbSNP
rs1445379560 372 dbSNP
rs188625567 382 dbSNP
rs1196933144 396 dbSNP
rs1028249302 403 dbSNP
rs185571017 404 dbSNP
rs540499016 417 dbSNP
rs1173636875 428 dbSNP
rs1056412068 435 dbSNP
rs1267956312 435 dbSNP
rs1204551799 438 dbSNP
rs1338691604 443 dbSNP
rs1382866305 457 dbSNP
rs900851899 467 dbSNP
rs1481486414 471 dbSNP
rs999930838 475 dbSNP
rs1031316258 478 dbSNP
rs1375010294 478 dbSNP
rs999039263 486 dbSNP
rs1129517 487 dbSNP
rs1207376402 493 dbSNP
rs1044377059 498 dbSNP
rs1265594351 506 dbSNP
rs1323020787 507 dbSNP
rs1281632119 509 dbSNP
rs904263502 532 dbSNP
rs1332111090 534 dbSNP
rs1295457885 537 dbSNP
rs1381070948 540 dbSNP
rs946950242 543 dbSNP
rs1387805979 546 dbSNP
rs1178000678 550 dbSNP
rs573085533 553 dbSNP
rs1321920629 556 dbSNP
rs781629242 558 dbSNP
rs1471519523 573 dbSNP
rs1404825096 593 dbSNP
rs1173884541 597 dbSNP
rs1478882007 600 dbSNP
rs1413865360 602 dbSNP
rs1378027092 608 dbSNP
rs942456498 610 dbSNP
rs1350230010 620 dbSNP
rs1426613360 621 dbSNP
rs1226989181 625 dbSNP
rs73656916 626 dbSNP
rs1346266175 633 dbSNP
rs1200397984 639 dbSNP
rs1276509783 640 dbSNP
rs116736147 645 dbSNP
rs1206117160 650 dbSNP
rs1251420142 650 dbSNP
rs1471468637 651 dbSNP
rs1460977153 652 dbSNP
rs371859847 652 dbSNP
rs951113455 659 dbSNP
rs918226475 661 dbSNP
rs974402275 692 dbSNP
rs1261497030 695 dbSNP
rs1421011718 698 dbSNP
rs962636821 703 dbSNP
rs1055317432 704 dbSNP
rs546056701 720 dbSNP
rs1368276996 725 dbSNP
rs1269928994 732 dbSNP
rs1225739545 735 dbSNP
rs1367885689 737 dbSNP
rs1305277136 744 dbSNP
rs138106729 746 dbSNP
rs1233155206 747 dbSNP
rs557126998 758 dbSNP
rs1341528212 760 dbSNP
rs1012013848 762 dbSNP
rs1274048889 763 dbSNP
rs972747676 764 dbSNP
rs180960736 767 dbSNP
rs767142798 774 dbSNP
rs1267791343 779 dbSNP
rs1450882786 783 dbSNP
rs568326091 791 dbSNP
rs189275413 792 dbSNP
rs1167061756 797 dbSNP
rs984168312 798 dbSNP
rs534963884 804 dbSNP
rs1189217729 808 dbSNP
rs1426091933 808 dbSNP
rs1163900886 812 dbSNP
rs1391886630 814 dbSNP
rs1386609541 816 dbSNP
rs1028134882 817 dbSNP
rs1322109034 821 dbSNP
rs774093801 822 dbSNP
rs965309983 825 dbSNP
rs770737646 827 dbSNP
rs1011588960 837 dbSNP
rs1241413585 838 dbSNP
rs900743118 838 dbSNP
rs1266311481 844 dbSNP
rs1355339596 850 dbSNP
rs1207804902 854 dbSNP
rs7046055 859 dbSNP
rs552343190 860 dbSNP
rs1187857625 861 dbSNP
rs1245661406 866 dbSNP
rs531057854 870 dbSNP
rs1445991386 872 dbSNP
rs904146669 875 dbSNP
rs1187782158 880 dbSNP
rs912350832 890 dbSNP
rs1021338283 894 dbSNP
rs185712465 895 dbSNP
rs1194378950 896 dbSNP
rs1344828169 897 dbSNP
rs550365171 900 dbSNP
rs1363095314 901 dbSNP
rs1454686795 903 dbSNP
rs901778930 905 dbSNP
rs1012592337 907 dbSNP
rs1242902644 919 dbSNP
rs11299970 928 dbSNP
rs1208014925 928 dbSNP
rs1254896000 928 dbSNP
rs1262201962 928 dbSNP
rs1329691458 928 dbSNP
rs1476301917 928 dbSNP
rs1275971566 929 dbSNP
rs1245935182 935 dbSNP
rs750016047 943 dbSNP
rs1358074829 945 dbSNP
rs1038646624 946 dbSNP
rs1159036406 948 dbSNP
rs1468051667 949 dbSNP
rs1303445107 950 dbSNP
rs918268032 952 dbSNP
rs1449621223 956 dbSNP
rs1309496141 957 dbSNP
rs973749201 962 dbSNP
rs1340645324 966 dbSNP
rs962623921 967 dbSNP
rs895337436 972 dbSNP
rs1327841430 978 dbSNP
rs1286256499 980 dbSNP
rs1389460420 981 dbSNP
rs916493094 994 dbSNP
rs193249150 995 dbSNP
rs1169118276 996 dbSNP
rs1423874684 1002 dbSNP
rs369910101 1003 dbSNP
rs575431210 1004 dbSNP
rs1473173755 1010 dbSNP
rs1435358686 1011 dbSNP
rs1034775488 1019 dbSNP
rs1377124185 1022 dbSNP
rs1464651294 1023 dbSNP
rs1000035773 1034 dbSNP
rs1409465744 1035 dbSNP
rs577952185 1038 dbSNP
rs1305889003 1042 dbSNP
rs1369550061 1047 dbSNP
rs966790565 1050 dbSNP
rs376881309 1051 dbSNP
rs1309906406 1053 dbSNP
rs1010889462 1055 dbSNP
rs906778526 1057 dbSNP
rs1340949878 1061 dbSNP
rs900795449 1063 dbSNP
rs1037481083 1066 dbSNP
rs1192260036 1067 dbSNP
rs7029007 1070 dbSNP
rs909843049 1071 dbSNP
rs1170509262 1083 dbSNP
rs1390877258 1083 dbSNP
rs1048526066 1085 dbSNP
rs1429270500 1092 dbSNP
rs546121434 1099 dbSNP
rs1351386317 1100 dbSNP
rs1047870152 1104 dbSNP
rs921126451 1110 dbSNP
rs1365346771 1113 dbSNP
rs1278563299 1117 dbSNP
rs1226246257 1119 dbSNP
rs929731140 1120 dbSNP
rs1225710114 1122 dbSNP
rs896881921 1123 dbSNP
rs1323846410 1124 dbSNP
rs976573044 1126 dbSNP
rs189046298 1131 dbSNP
rs1351974289 1144 dbSNP
rs965713670 1151 dbSNP
rs924554242 1152 dbSNP
rs941021794 1155 dbSNP
rs369150943 1156 dbSNP
rs1186879677 1157 dbSNP
rs990699063 1157 dbSNP
rs563510551 1158 dbSNP
rs968426276 1160 dbSNP
rs1163738372 1161 dbSNP
rs1021223788 1165 dbSNP
rs374908491 1166 dbSNP
rs184279480 1175 dbSNP
rs1363797719 1177 dbSNP
rs1033844899 1184 dbSNP
rs1003714248 1194 dbSNP
rs1379377676 1196 dbSNP
rs943046822 1201 dbSNP
rs1227395664 1208 dbSNP
rs1473665432 1210 dbSNP
rs1413012516 1211 dbSNP
rs989516622 1212 dbSNP
rs1211106052 1213 dbSNP
rs1489979357 1213 dbSNP
rs1206852229 1215 dbSNP
rs1239299478 1216 dbSNP
rs1248963608 1219 dbSNP
rs1181564452 1220 dbSNP
rs1223002824 1220 dbSNP
rs1473477810 1231 dbSNP
rs1451654407 1240 dbSNP
rs1282888347 1241 dbSNP
rs1209650490 1243 dbSNP
rs1222569275 1243 dbSNP
rs1230582714 1243 dbSNP
rs1280823797 1243 dbSNP
rs1289400654 1243 dbSNP
rs1300770707 1243 dbSNP
rs1329012315 1243 dbSNP
rs1353922891 1243 dbSNP
rs1359238128 1243 dbSNP
rs1441602268 1243 dbSNP
rs1443136872 1243 dbSNP
rs1446827865 1243 dbSNP
rs1455597226 1243 dbSNP
rs34951542 1243 dbSNP
rs57395499 1243 dbSNP
rs576309753 1243 dbSNP
rs1206320838 1244 dbSNP
rs1425238957 1245 dbSNP
rs1413452868 1246 dbSNP
rs1330696139 1251 dbSNP
rs1288606631 1253 dbSNP
rs1222657520 1255 dbSNP
rs552933134 1256 dbSNP
rs1276507792 1257 dbSNP
rs778372814 1259 dbSNP
rs1277171033 1260 dbSNP
rs1344557622 1261 dbSNP
rs1345767625 1261 dbSNP
rs1318576842 1263 dbSNP
rs1458889667 1264 dbSNP
rs1389578625 1268 dbSNP
rs1341932421 1277 dbSNP
rs1176067736 1281 dbSNP
rs1247175728 1288 dbSNP
rs1431774715 1288 dbSNP
rs1427756071 1289 dbSNP
rs1477670538 1293 dbSNP
rs1192162844 1294 dbSNP
rs906658405 1300 dbSNP
rs1475353386 1306 dbSNP
rs148266166 1310 dbSNP
rs1017580071 1311 dbSNP
rs1186061760 1317 dbSNP
rs1465910922 1318 dbSNP
rs1004846606 1321 dbSNP
rs1167641679 1324 dbSNP
rs1268361837 1325 dbSNP
rs1009173990 1326 dbSNP
rs1202681400 1328 dbSNP
rs888470687 1329 dbSNP
rs1310190910 1334 dbSNP
rs1325979744 1342 dbSNP
rs1335515607 1346 dbSNP
rs1436403098 1347 dbSNP
rs1301257806 1348 dbSNP
rs1471239236 1349 dbSNP
rs890684993 1350 dbSNP
rs1026920381 1354 dbSNP
rs1337734422 1359 dbSNP
rs375408574 1365 dbSNP
rs903574997 1367 dbSNP
rs1290346156 1368 dbSNP
rs1048411183 1370 dbSNP
rs1361104008 1371 dbSNP
rs932755012 1376 dbSNP
rs1249335176 1384 dbSNP
rs1449597830 1386 dbSNP
rs1295329177 1391 dbSNP
rs1038128263 1392 dbSNP
rs1459138717 1395 dbSNP
rs372094979 1401 dbSNP
rs577116746 1402 dbSNP
rs1405286599 1405 dbSNP
rs1464690718 1406 dbSNP
rs1361152391 1410 dbSNP
rs1054695715 1411 dbSNP
rs1390895909 1413 dbSNP
rs939295829 1428 dbSNP
rs927889441 1430 dbSNP
rs978363615 1431 dbSNP
rs368673706 1432 dbSNP
rs1284570529 1433 dbSNP
rs1355456986 1440 dbSNP
rs943893577 1444 dbSNP
rs915018181 1450 dbSNP
rs1191124499 1455 dbSNP
rs1425112897 1456 dbSNP
rs924411914 1456 dbSNP
rs1187900632 1459 dbSNP
rs1369397183 1460 dbSNP
rs1475112842 1462 dbSNP
rs1248156004 1464 dbSNP
rs773208674 1465 dbSNP
rs964760175 1472 dbSNP
rs147955449 1482 dbSNP
rs969022201 1492 dbSNP
rs143664673 1493 dbSNP
rs1397996410 1505 dbSNP
rs914268893 1508 dbSNP
rs1339624529 1509 dbSNP
rs570116991 1510 dbSNP
rs548787216 1511 dbSNP
rs1272351573 1512 dbSNP
rs535182396 1527 dbSNP
rs1342814621 1528 dbSNP
rs1483980540 1529 dbSNP
rs140468832 1538 dbSNP
rs1003004781 1541 dbSNP
rs994118030 1545 dbSNP
rs769690155 1547 dbSNP
rs970936205 1550 dbSNP
rs1016280113 1554 dbSNP
rs1254424849 1559 dbSNP
rs754525913 1577 dbSNP
rs1314421517 1579 dbSNP
rs1004357272 1583 dbSNP
rs888626793 1584 dbSNP
rs1381546945 1588 dbSNP
rs1467686298 1593 dbSNP
rs1303705998 1609 dbSNP
rs1027033725 1611 dbSNP
rs1375020017 1616 dbSNP
rs1441929949 1620 dbSNP
rs1369136811 1622 dbSNP
rs1413179596 1628 dbSNP
rs57883397 1630 dbSNP
rs1350947682 1633 dbSNP
rs146817614 1636 dbSNP
rs1304846591 1638 dbSNP
rs1313406119 1642 dbSNP
rs1233287634 1644 dbSNP
rs1041038569 1645 dbSNP
rs894879960 1647 dbSNP
rs1163380674 1649 dbSNP
rs1206936307 1656 dbSNP
rs1421555162 1659 dbSNP
rs1242479713 1666 dbSNP
rs1466365838 1666 dbSNP
rs1483616575 1666 dbSNP
rs59028960 1666 dbSNP
rs750499955 1666 dbSNP
rs373639589 1670 dbSNP
rs1054748365 1671 dbSNP
rs1461330533 1674 dbSNP
rs1482594016 1677 dbSNP
rs1369578485 1679 dbSNP
rs1387284966 1680 dbSNP
rs1302058959 1683 dbSNP
rs1249288964 1685 dbSNP
rs1207073416 1692 dbSNP
rs1483305877 1695 dbSNP
rs944059756 1701 dbSNP
rs1274963433 1704 dbSNP
rs557056948 1711 dbSNP
rs538439634 1712 dbSNP
rs1489714072 1717 dbSNP
rs145053522 1718 dbSNP
rs552463650 1720 dbSNP
rs1042309416 1723 dbSNP
rs1421968009 1726 dbSNP
rs1190719195 1731 dbSNP
rs945250940 1739 dbSNP
rs530853736 1741 dbSNP
rs747103440 1742 dbSNP
rs753488522 1743 dbSNP
rs58884236 1751 dbSNP
rs758659202 1763 dbSNP
rs1436600457 1767 dbSNP
rs991319153 1778 dbSNP
rs145332921 1793 dbSNP
rs928413707 1797 dbSNP
rs574827059 1798 dbSNP
rs962029517 1803 dbSNP
rs1455928952 1804 dbSNP
rs1484636499 1805 dbSNP
rs1222917016 1807 dbSNP
rs1369747986 1810 dbSNP
rs1015814597 1815 dbSNP
rs1273152296 1816 dbSNP
rs1467549127 1816 dbSNP
rs1210613381 1817 dbSNP
rs1248736288 1823 dbSNP
rs1164893168 1835 dbSNP
rs559465942 1836 dbSNP
rs1185060103 1840 dbSNP
rs541128669 1840 dbSNP
rs866803827 1842 dbSNP
rs983442309 1849 dbSNP
rs1409317813 1853 dbSNP
rs1163994076 1854 dbSNP
rs1415520102 1861 dbSNP
rs954737534 1866 dbSNP
rs1184015299 1868 dbSNP
rs372636078 1869 dbSNP
rs1428196264 1871 dbSNP
rs972357485 1874 dbSNP
rs1381755870 1876 dbSNP
rs1027148783 1877 dbSNP
rs997046964 1879 dbSNP
rs1333253613 1882 dbSNP
rs899900456 1896 dbSNP
rs1208034932 1898 dbSNP
rs1316464880 1900 dbSNP
rs1016411907 1906 dbSNP
rs1489492104 1915 dbSNP
rs150068867 1922 dbSNP
rs1008199416 1933 dbSNP
rs903189143 1938 dbSNP
rs75000149 1939 dbSNP
rs779369484 1940 dbSNP
rs537318415 1941 dbSNP
rs766007901 1944 dbSNP
rs576705188 1945 dbSNP
rs554851473 1946 dbSNP
rs575916382 1960 dbSNP
rs928377306 1961 dbSNP
rs1412198451 1966 dbSNP
rs1280687316 1979 dbSNP
rs1293537024 1990 dbSNP
rs1456265967 2011 dbSNP
rs760392355 2019 dbSNP
rs1348790850 2047 dbSNP
rs1210515165 2049 dbSNP
rs570907237 2051 dbSNP
rs943183731 2053 dbSNP
rs910349552 2059 dbSNP
rs940331759 2062 dbSNP
rs1161015772 2063 dbSNP
rs1457548287 2064 dbSNP
rs367984175 2064 dbSNP
rs1376904379 2074 dbSNP
rs1196505599 2075 dbSNP
rs1468554649 2076 dbSNP
rs1192370962 2084 dbSNP
rs1425264867 2085 dbSNP
rs1433703135 2091 dbSNP
rs1171418353 2093 dbSNP
rs148935100 2102 dbSNP
rs1329999706 2103 dbSNP
rs1431974068 2103 dbSNP
rs200451808 2103 dbSNP
rs1440659803 2114 dbSNP
rs952928207 2121 dbSNP
rs1027263441 2124 dbSNP
rs1371887305 2126 dbSNP
rs919284017 2129 dbSNP
rs1301572791 2133 dbSNP
rs187081938 2133 dbSNP
rs1187939689 2136 dbSNP
rs1196107532 2144 dbSNP
rs1463644263 2148 dbSNP
rs1435939271 2156 dbSNP
rs1223761485 2157 dbSNP
rs1253056902 2166 dbSNP
rs972456869 2173 dbSNP
rs1209638737 2181 dbSNP
rs568160010 2183 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293/HeLa
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in GSM1067870. RNA binding protein: AGO2. Condition:Ago2 IP-seq (mitotic cells) ...

- Kishore S; Gruber AR; Jedlinski DJ; Syed et al., 2013, Genome biology.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' acggucggagCGGGucg 5'
                    ||:|   
Target 5' gagugcaaugGCUC--- 3'
7 - 20
Article - Kishore S; Gruber AR; Jedlinski DJ; Syed et al.
- Genome biology, 2013
BACKGROUND: In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequence long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins. RESULTS: Analysis of these data sets reveals that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently cataloged. We further find that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs reveals that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein. CONCLUSIONS: We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon.
LinkOut: [PMID: 23706177]
CLIP-seq Support 1 for dataset GSM1067870
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293/HeLa / Ago2 IP-seq (mitotic cells)
Location of target site ENST00000375234.3 | 3UTR | AGGCUGGAGUGCAAUGGCUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23706177 / GSE43666
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
108 hsa-miR-4486 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT254654 NF2 neurofibromin 2 2 2
MIRT458684 MRI1 methylthioribose-1-phosphate isomerase 1 2 2
MIRT470845 PLXND1 plexin D1 2 2
MIRT493011 NANOS1 nanos C2HC-type zinc finger 1 2 2
MIRT497264 GRK6 G protein-coupled receptor kinase 6 2 2
MIRT497675 SYNGR1 synaptogyrin 1 2 2
MIRT498219 TLN2 talin 2 2 2
MIRT498310 BCL11B B-cell CLL/lymphoma 11B 2 2
MIRT504048 TOMM5 translocase of outer mitochondrial membrane 5 2 2
MIRT519959 ZCCHC8 zinc finger CCHC-type containing 8 2 2
MIRT531521 NOM1 nucleolar protein with MIF4G domain 1 2 2
MIRT533144 WNT10A Wnt family member 10A 2 2
MIRT533541 TPR translocated promoter region, nuclear basket protein 2 2
MIRT533681 TMEM86A transmembrane protein 86A 2 2
MIRT540321 PIGR polymeric immunoglobulin receptor 2 2
MIRT540719 GUF1 GUF1 homolog, GTPase 2 2
MIRT541566 ZNF43 zinc finger protein 43 2 4
MIRT541787 TBCCD1 TBCC domain containing 1 2 2
MIRT541925 ORC1 origin recognition complex subunit 1 2 4
MIRT542232 FUT9 fucosyltransferase 9 2 2
MIRT542285 POLR3K RNA polymerase III subunit K 2 2
MIRT542299 QTRTD1 queuine tRNA-ribosyltransferase accessory subunit 2 2 4
MIRT542368 PAICS phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthase 2 2
MIRT542441 C3 complement C3 2 4
MIRT542475 APOC3 apolipoprotein C3 2 2
MIRT542535 MRPS10 mitochondrial ribosomal protein S10 2 2
MIRT542640 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT542788 PLEKHA3 pleckstrin homology domain containing A3 2 2
MIRT552104 PPP1R1A protein phosphatase 1 regulatory inhibitor subunit 1A 2 2
MIRT564913 YTHDF1 YTH N6-methyladenosine RNA binding protein 1 2 2
MIRT568606 ACVR2A activin A receptor type 2A 2 2
MIRT607389 LANCL3 LanC like 3 2 2
MIRT607451 ZNF543 zinc finger protein 543 2 2
MIRT610058 MYBPC1 myosin binding protein C, slow type 2 2
MIRT610793 KLK2 kallikrein related peptidase 2 2 2
MIRT617176 GOSR2 golgi SNAP receptor complex member 2 2 2
MIRT620579 WBSCR27 methyltransferase like 27 2 4
MIRT622085 SRPX2 sushi repeat containing protein, X-linked 2 2 2
MIRT622542 PXMP4 peroxisomal membrane protein 4 2 2
MIRT630009 PDE6B phosphodiesterase 6B 2 2
MIRT631813 PTDSS2 phosphatidylserine synthase 2 2 2
MIRT632721 MSANTD4 Myb/SANT DNA binding domain containing 4 with coiled-coils 2 2
MIRT632757 MED28 mediator complex subunit 28 2 2
MIRT634821 ASB6 ankyrin repeat and SOCS box containing 6 2 2
MIRT635255 FBXL20 F-box and leucine rich repeat protein 20 2 2
MIRT637082 SELPLG selectin P ligand 2 2
MIRT637357 ZNF460 zinc finger protein 460 2 2
MIRT637472 DEFB105B defensin beta 105B 2 4
MIRT637504 DEFB105A defensin beta 105A 2 4
MIRT639022 AAK1 AP2 associated kinase 1 2 2
MIRT641012 ANKFY1 ankyrin repeat and FYVE domain containing 1 2 2
MIRT642170 HEBP2 heme binding protein 2 2 2
MIRT648977 ACAD8 acyl-CoA dehydrogenase family member 8 2 2
MIRT650515 UFM1 ubiquitin fold modifier 1 2 2
MIRT650949 INMT indolethylamine N-methyltransferase 2 2
MIRT658354 FAM65B RHO family interacting cell polarization regulator 2 2 2
MIRT660736 ALG14 ALG14, UDP-N-acetylglucosaminyltransferase subunit 2 2
MIRT662191 MEI1 meiotic double-stranded break formation protein 1 2 2
MIRT663045 SLC16A4 solute carrier family 16 member 4 2 2
MIRT664811 IRAK3 interleukin 1 receptor associated kinase 3 2 2
MIRT665161 SF3A1 splicing factor 3a subunit 1 2 4
MIRT665346 YES1 YES proto-oncogene 1, Src family tyrosine kinase 2 2
MIRT666493 SBNO1 strawberry notch homolog 1 2 2
MIRT666545 RNF115 ring finger protein 115 2 2
MIRT669351 BMP3 bone morphogenetic protein 3 2 2
MIRT669904 KIAA0754 KIAA0754 2 4
MIRT670323 CEP57L1 centrosomal protein 57 like 1 2 2
MIRT670430 ELP2 elongator acetyltransferase complex subunit 2 2 2
MIRT670672 KIAA1551 KIAA1551 2 2
MIRT670746 HOOK3 hook microtubule tethering protein 3 2 2
MIRT670998 PTGIS prostaglandin I2 synthase 2 2
MIRT671290 RPL37A ribosomal protein L37a 2 2
MIRT671469 AGPAT6 glycerol-3-phosphate acyltransferase 4 2 2
MIRT671833 STIL STIL, centriolar assembly protein 2 2
MIRT673006 TAF1 TATA-box binding protein associated factor 1 2 2
MIRT675881 CSTF1 cleavage stimulation factor subunit 1 2 2
MIRT678625 OLFML2A olfactomedin like 2A 2 2
MIRT678790 NUPL2 nucleoporin like 2 2 2
MIRT679560 LIN9 lin-9 DREAM MuvB core complex component 2 2
MIRT681032 AAED1 AhpC/TSA antioxidant enzyme domain containing 1 2 2
MIRT682480 LIX1L limb and CNS expressed 1 like 2 2
MIRT682758 MDM2 MDM2 proto-oncogene 2 2
MIRT682810 TMCO1 transmembrane and coiled-coil domains 1 2 2
MIRT682867 C9orf156 tRNA methyltransferase O 2 2
MIRT689233 RPS19 ribosomal protein S19 2 2
MIRT689305 C5AR2 complement component 5a receptor 2 2 2
MIRT689363 ZNF101 zinc finger protein 101 2 2
MIRT689629 NAA30 N(alpha)-acetyltransferase 30, NatC catalytic subunit 2 2
MIRT689654 RBM23 RNA binding motif protein 23 2 2
MIRT690148 PPIL6 peptidylprolyl isomerase like 6 2 2
MIRT691407 DNA2 DNA replication helicase/nuclease 2 2 2
MIRT691847 OSCAR osteoclast associated, immunoglobulin-like receptor 2 2
MIRT692234 ALDH1B1 aldehyde dehydrogenase 1 family member B1 2 2
MIRT694320 NLRP9 NLR family pyrin domain containing 9 2 2
MIRT694365 CHST6 carbohydrate sulfotransferase 6 2 2
MIRT696215 LYZ lysozyme 2 2
MIRT697230 ZYG11A zyg-11 family member A, cell cycle regulator 2 2
MIRT700487 PTPRF protein tyrosine phosphatase, receptor type F 2 2
MIRT700612 PRKCA protein kinase C alpha 2 2
MIRT702456 KIAA1467 family with sequence similarity 234 member B 2 2
MIRT702990 HERPUD2 HERPUD family member 2 2 2
MIRT703998 EIF5A2 eukaryotic translation initiation factor 5A2 2 2
MIRT704701 CHRFAM7A CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion 2 2
MIRT712481 FSTL3 follistatin like 3 2 2
MIRT712781 ZNF154 zinc finger protein 154 2 2
MIRT714369 HP1BP3 heterochromatin protein 1 binding protein 3 2 2
MIRT722570 C1orf95 stum, mechanosensory transduction mediator homolog 2 2
MIRT722839 C17orf102 chromosome 17 open reading frame 102 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-4486 Dabrafenib 44462760 NSC764134 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-4486 Vemurafenib 42611257 NSC761431 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-4486 Doxorubicin 31703 NSC123127 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-miR-4486 Curcumin 969516 NSC32982 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-miR-4486 Paclitaxel 36314 NSC125973 approved resistant High Non-Small Cell Lung Cancer cell line (A549)
hsa-miR-4486 Fulvestrant 17756771 NSC719276 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-miR-4486 Tamoxifen 2733525 NSC180973 approved resistant High Breast Cancer cell line (MCF-7)
hsa-miR-4486 Cisplatin 5460033 NSC119875 approved sensitive High Gastric Cancer cell line (SGC7901)
hsa-miR-4486 Cisplatin 5460033 NSC119875 approved sensitive Low Gastric Cancer cell line (SGC-7901)
hsa-mir-4486 Dabrafenib 44462760 NSC764134 approved resistant cell line (A375)
hsa-mir-4486 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-miR-4486 Temozolomide 5394 NSC362856 approved resistant cell line (U251)
hsa-miR-4486 Doxorubicin 31703 NSC123127 approved resistant cell line (BAS)
hsa-miR-4486 Doxorubicin 31703 NSC123127 approved resistant cell line (HS578T)
hsa-miR-4486 Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-4486 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-4486 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)
hsa-miR-4486 Gemcitabine 60750 NSC613327 approved resistant cell line (Panc1-GR4)

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