pre-miRNA Information
pre-miRNA hsa-mir-2115   
Genomic Coordinates chr3: 48316360 - 48316459
Description Homo sapiens miR-2115 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-2115-3p
Sequence 58| CAUCAGAAUUCAUGGAGGCUAG |79
Evidence Experimental
Experiments 454
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN31490809 22 COSMIC
COSN31579735 22 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs543123304 18 dbSNP
rs1450988157 21 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol MTPAP   
Synonyms PAPD1, SPAX4
Description mitochondrial poly(A) polymerase
Transcript NM_018109   
Expression
Putative miRNA Targets on MTPAP
3'UTR of MTPAP
(miRNA target sites are highlighted)
>MTPAP|NM_018109|3'UTR
   1 TGGCTGCTACATTGTGTAAAGAACTGGGCTTAGCCTATCAAATGGTCTGTGGACTTACTTGGAAAAACTGATTTGAAACT
  81 TTCACAGATCTCAGCTTTCATCTGATGTCACTTTTCATGATCTTCTCATTGGCCCCCTTAACCTGGTCTGAAGTTCTGGG
 161 ATGTTTTCAGTTTGATCAGTCTGATACTCAGTGGCACTTTATTAAAACATCAGCTGTGGAGTGTGGCGGTGCACACCTGT
 241 AGTCCCAGCTGCTCAGGAGGCTGAGGCAGGAGGATCTCTTGAGCCCAGGATTTTGAATCCATCGTGGACAACATAGCAAG
 321 ATTCCATCTCTAAAAAAAATGAAAATAAACATAAGCCACAAGGAATGGGTGAAAGATTATTGTAATGTGCTTTAACTAAA
 401 TAGGTAAATATACTAAACAAATGCTAAAACTCAGTTTTAGGATGAAACCATTGTTGATATCCACATCAGTCCCTGTTTAG
 481 AAAACATTTAAAATGACTTTTAGTTATGTACAGTACGTTGGCAATGAATACATTAAGCTTCAAAATTTGGTAGTGCTCTC
 561 GAATATGTATATTTGTATTTTTCAAGCGAAGTTCTCTTATTCACATATAAATTAAAGTGGGTTGGTACTGATATCAAAAA
 641 ATGTTTATGTTTTTAGAACAGACATTTCAGTCACTGCATTCTTAGGTATTCCAAACCAAATATGATGACATCAATAGATT
 721 GCATTTTAAAAATATTGTTTGATTTTTCTATTTTCAAAAATAAAATTCTGTTTCTAACTAAAATGTGATATTCCCAGTAT
 801 TCCTTCACATCTCTTTTGAGAACTCCCCTCTTCCTGCAGGAAAGAGACATATTTGTCTCTCAGTATATGCAGAAAATTGG
 881 TTCCAGGACCATCCACGTACACCCAGATCTGCACACACTGAACTCCTTCAGTCCTGTGGAGCCCGTGCATGGGAGAATTC
 961 CACCTTGCACATAAGCAGATTTTGCATCCTGTGAAAGTACTGTATTTTCTTTCTTTCTTTTTTTTTTTTTTTTTTTTTTG
1041 AGACAGAGTCTCGCTCTGTCGCCCAGGCTAGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCTGCCTCCCAGGTTC
1121 ACGCCATTCTCCTGCCTCAGCCTCTCTGAGTAGCTGGGACTATAGGTGCCCGCCACCACGCCCGGACAATTTTTTTGTAT
1201 TTTTAGTAGAGACAGGGTTTCACCATGGTCTCGATCTCCCGACCTCGTGATCAGCCCACCTCAACCTCCCAAAGTGCTGG
1281 GATTACAAGCGTGAGCCACCATGCCTGGCCGAGAATACTGTATTTTCAATCCAAGTTTGGTTGGAAAAAATCTGTGTGTA
1361 AATGGACTTCGCAGTTGAAACCCATGTTGTTCAATGGGCAACTGTATATTGAAATTTAATTTCCATTACATTCTCTGTGG
1441 AGCAACTTTTTTGCTTTGTTTCGTTTTGTTTCTGAGACGGAGTTTTGCTCTTGTTGCCCAGGCTGGGGTGCAATGGCACA
1521 ATCTCAGCTCACTGCAACCTCCGCCTCCCGGATTCAAGTGATTCTCCTGCCTCAGCTGGGATTACAGGCGCCCACCACCA
1601 AGCCCAGCTAATTTTTGTAGTTTTAGTAGGGACAGGGTTTCACCATGTTGGCCAGGCTGATCTCGAACTCCTGACCTCAG
1681 GTGATCGCCCACCTTGGCCTTCCAAAGTGTTGGAATTACAGGCGTGAGCCACTGCACCTGGCTTCTGTGGAGTAACTTTC
1761 TATTTAAGAAGCAAGTAAGGCCTGGGCATAGCGGCACATGCCTGTAGTCCCAGGTACTTGGGAGGCCGAGGCACAAGGAC
1841 TGCTTGAACCTGGGAGGCAGAGGCTGCAGTGAGCTGAGATCACAGCACTGTACTCCATCCTGGGCGACAGTGAGACTCTC
1921 TCAAAGGAAAAGAAGCAAGTAGTATAGTGTTTAAAAACAGACTTGAGCGAGACTGGCTCAATGACAAGTTACTCAGTCTC
2001 TTGGGGCCCCTGTTTGATCTGTAAAATGGGGATCATGATCAGATCAATGTGAGGATTAAGCGAGGGATGTAGGAAAATGC
2081 TAGGTCAGTGCATTTTCCTGGCGCGAAGTAAATGTTACTTCTCTTTAACTGTTGCCTTTCGGTGTTTGTGGTATGTAATT
2161 ACCTTTTTTGCTACTCAAAATTCAGATTTAGAGTTTGTAGTACTTTAAAAATTTTTCCCATTTAAATTTTATGTCAGAAA
2241 TTATAATGGGTTCTGCATGGGATATTTTAAGAAACTCAGCATTGTTATGAAGCAAATGAATTCTGTGTCCTTGTGTCTGT
2321 GCTATTGGATTGCACATTTGACACCAACAAATATCAGTGTTCTGTACAGGCGATGTCTTTAAAAGCCATTTTTCATTTGT
2401 TCTTTATTTTGTTGGGCTAGAAATCCATATTGATTTAAAAAGCTTAAAAAGCATAAACCACTTAAGGGTTTCTAAATGAA
2481 ATTTTTTTTTCTGTTCACAGATATTTAGTCAGATATTTTCTTTTTTAGGTTGGTGCTAGGTGTAATATGGTTATTTAAGC
2561 ACATAAAGTATGTGTATGGGTTAGCATTTTCTTTTCTTTTTGGTAATTTGTAGGACAGCCTTGACACTAGGCTGTTTTAC
2641 TTTTCAGAATCAGATTTAATTATGTGATTAATTTTAAATCTACAAAGACTTGTTTTTTGTTTTTTTTTTTGAGAGCAAAT
2721 CTTGCTCTGTCACCCAGGCTAGACTGCAGTGGTGCGATCTCGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGCGATAC
2801 TCCTGCCCCAGCCTCCCAAGTAACTGGGATTACAGGCGCCTGCCACCATGCCTAGCTAATTTTTGTATGTTAGTAGAGAC
2881 GGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAATTCCTGACCTCAAGTGATCTACCTGTCTCAGCCTCTCAAAGTGCTG
2961 GGATTACAGGTTACAGGTGTGAGCCACCGCACCTGGCCTACAAAGACCCTTTTTTTTTTTTTTTTTTGAGATGGGTCTCC
3041 CTCTGTCACCCAGGCTGGAGAGTGCAGTGATCTTGGCTCACTGAAACCTCCACTTCCCGGGTTCAGGTGATTCTTCTGCC
3121 TCAGCCTCCTGAGTAGCTGGGATTACAGGTGCATGCCACCACACCTGGCTAAGTTTTCTATTTTTAGTAGAGATGGGGTT
3201 TTACTCTGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGACCTGCCCACCTCGCCCTCCCAAAATGCTGGGATTA
3281 CAGGCATGAGCCACCACGCCTGGCTGCAAAGACCTTTTAATACACAGTTTTAAAGTCTGTTCAACTGAATATAGACTACA
3361 GACAAATATATTTTCTCATAACTTTAGTGTATCACAACCCAGATTTTTAAAATATTTTTATTACGTGATAGTGATAACTA
3441 GCAATTATTTGTCATTGCTGTTTCTTAATTAAAAATAATTGCAATGTTAAGTAAAACTTTTTTCAAGTTTTTTTCTTCTA
3521 TAACTATTACTAGGCTTTCATTCAGTAGCTTTCACCTGTAATGAGTTTTACTAAGTATGTGAAAGTAATTTTGATAGGAG
3601 ACTACCCAGATCAAAACGATTTCAGCTATAGCCCACTAGTATAATTCCTGGAGCTATTATCCATCTTTAGAAAATTTGAG
3681 AATTAGCCAGAGACTTTCTAGGAAATAACGATTAGCCTGAAACGTTATAGGAAAACTGTGTGTAATTATCTCATTCACCT
3761 TCAGTTACCATAAAGGAGAAGGGAAAATAAAGTTGAGTTGAAATAAGA
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' gaUCGGAGGUACU-UAAGACUAc 5'
            | ::|:|||||  |||| || 
Target 5' tcACTTTTCATGATCTTCTCATt 3'
108 - 130 132.00 -8.20
2
miRNA  3' gaUCGGAGGUACUUAAGACUAc 5'
            |||:|:||     |||||| 
Target 5' tcAGCTTTCA-----TCTGATg 3'
91 - 107 130.00 -15.80
3
miRNA  3' gauCGGAGGU---ACU--UAAGACUAc 5'
             |::|:||   |||  | |||||| 
Target 5' gatGTTTTCAGTTTGATCAGTCTGATa 3'
160 - 186 129.00 -10.10
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
1196895 146 ClinVar
COSN30129433 21 COSMIC
COSN31559045 65 COSMIC
COSN28689415 102 COSMIC
COSN31510933 104 COSMIC
COSN16131000 127 COSMIC
COSN30115769 148 COSMIC
COSN26435656 161 COSMIC
COSN28893126 283 COSMIC
COSN31600556 289 COSMIC
COSN29459300 331 COSMIC
COSN20107019 397 COSMIC
COSN1485540 648 COSMIC
COSN15369872 695 COSMIC
COSN6966516 1021 COSMIC
COSN1485539 1246 COSMIC
COSN9204309 1264 COSMIC
COSN4693225 1478 COSMIC
COSN2465733 1713 COSMIC
COSN17724474 1797 COSMIC
COSN6966515 1857 COSMIC
COSN17787337 1903 COSMIC
COSN6068420 2035 COSMIC
COSN21185725 2298 COSMIC
COSN16940178 2372 COSMIC
COSN17741097 2481 COSMIC
COSN20107018 2699 COSMIC
COSN24332931 3027 COSMIC
COSN10065872 3070 COSMIC
COSN15000168 3098 COSMIC
COSN15921063 3723 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs751550052 9 dbSNP
rs1469430148 10 dbSNP
rs766465158 11 dbSNP
rs118148487 12 dbSNP
rs765272329 14 dbSNP
rs1251168965 16 dbSNP
rs1270978719 22 dbSNP
rs761644627 24 dbSNP
rs182202969 27 dbSNP
rs1339058754 34 dbSNP
rs763800159 39 dbSNP
rs760343765 40 dbSNP
rs1417106226 41 dbSNP
rs771597303 44 dbSNP
rs942207515 45 dbSNP
rs372062811 46 dbSNP
rs554862786 47 dbSNP
rs1273925082 49 dbSNP
rs1459087321 53 dbSNP
rs915994428 56 dbSNP
rs1334534116 58 dbSNP
rs145835981 59 dbSNP
rs1401579418 60 dbSNP
rs565370348 62 dbSNP
rs1332047752 63 dbSNP
rs34240191 63 dbSNP
rs943182913 69 dbSNP
rs36080907 73 dbSNP
rs551659305 82 dbSNP
rs538401522 84 dbSNP
rs571328710 90 dbSNP
rs967258488 104 dbSNP
rs984628588 105 dbSNP
rs1021558954 114 dbSNP
rs1421777301 120 dbSNP
rs989942735 122 dbSNP
rs1185764775 124 dbSNP
rs549663716 126 dbSNP
rs1365721095 132 dbSNP
rs951945985 134 dbSNP
rs35494590 136 dbSNP
rs1358655605 140 dbSNP
rs1437127852 142 dbSNP
rs34660258 146 dbSNP
rs1189523465 156 dbSNP
rs1355285711 159 dbSNP
rs1440259844 160 dbSNP
rs955046719 161 dbSNP
rs1308747994 164 dbSNP
rs1335961579 168 dbSNP
rs1237820011 170 dbSNP
rs1025706015 175 dbSNP
rs1349335954 180 dbSNP
rs1211527105 184 dbSNP
rs757206839 186 dbSNP
rs1202890258 187 dbSNP
rs1482193770 194 dbSNP
rs1197306958 203 dbSNP
rs1241988687 205 dbSNP
rs753718869 211 dbSNP
rs898044538 212 dbSNP
rs1037958259 214 dbSNP
rs971678276 219 dbSNP
rs35331130 220 dbSNP
rs1378561698 223 dbSNP
rs1006338344 226 dbSNP
rs561134023 227 dbSNP
rs549334116 228 dbSNP
rs1458829314 229 dbSNP
rs1259140611 234 dbSNP
rs1170212963 247 dbSNP
rs1464901241 253 dbSNP
rs1013071313 254 dbSNP
rs1397612241 259 dbSNP
rs763601028 265 dbSNP
rs894676964 271 dbSNP
rs1055866214 276 dbSNP
rs1234384398 278 dbSNP
rs1357468828 279 dbSNP
rs958520077 284 dbSNP
rs530097439 287 dbSNP
rs938740948 303 dbSNP
rs1286524824 304 dbSNP
rs928748756 306 dbSNP
rs1243259009 310 dbSNP
rs1382616614 336 dbSNP
rs1033157480 349 dbSNP
rs770905280 351 dbSNP
rs1194315375 357 dbSNP
rs568272068 359 dbSNP
rs1431980918 372 dbSNP
rs140431015 375 dbSNP
rs1042010480 378 dbSNP
rs41288991 382 dbSNP
rs1465424078 386 dbSNP
rs767138697 387 dbSNP
rs914488439 391 dbSNP
rs1245317486 398 dbSNP
rs3074958 403 dbSNP
rs33935115 403 dbSNP
rs1039741610 404 dbSNP
rs869142433 404 dbSNP
rs1292460471 411 dbSNP
rs1164708136 412 dbSNP
rs1471775308 418 dbSNP
rs1384479494 421 dbSNP
rs1216266938 426 dbSNP
rs1296190149 433 dbSNP
rs1306769713 433 dbSNP
rs1216535830 441 dbSNP
rs1256454649 450 dbSNP
rs1337255083 459 dbSNP
rs190168952 460 dbSNP
rs1246207741 463 dbSNP
rs1487514409 468 dbSNP
rs1178747191 499 dbSNP
rs942778126 501 dbSNP
rs1440965646 502 dbSNP
rs909993316 503 dbSNP
rs1477724532 504 dbSNP
rs990099752 508 dbSNP
rs1420418016 514 dbSNP
rs369923625 517 dbSNP
rs1163558183 524 dbSNP
rs1347668084 525 dbSNP
rs751934748 532 dbSNP
rs1432281267 538 dbSNP
rs1339730109 541 dbSNP
rs911067690 543 dbSNP
rs1203359028 547 dbSNP
rs565380881 553 dbSNP
rs1451753665 556 dbSNP
rs930494175 558 dbSNP
rs986666095 560 dbSNP
rs919154063 561 dbSNP
rs955268558 563 dbSNP
rs766591470 565 dbSNP
rs1229116378 567 dbSNP
rs993794226 569 dbSNP
rs962387881 570 dbSNP
rs1320068898 586 dbSNP
rs1016459372 587 dbSNP
rs1218006540 588 dbSNP
rs1261879171 589 dbSNP
rs1488265892 590 dbSNP
rs1192041772 591 dbSNP
rs1260065277 596 dbSNP
rs763517044 598 dbSNP
rs972395516 599 dbSNP
rs1180991782 604 dbSNP
rs1006452754 605 dbSNP
rs916896788 607 dbSNP
rs1159224753 611 dbSNP
rs894748993 614 dbSNP
rs1359306849 616 dbSNP
rs991193417 620 dbSNP
rs1314586995 621 dbSNP
rs1056338604 625 dbSNP
rs543624016 627 dbSNP
rs1283867224 633 dbSNP
rs1377228260 634 dbSNP
rs907240968 635 dbSNP
rs1279264229 647 dbSNP
rs1437457024 648 dbSNP
rs1332989359 651 dbSNP
rs1325300771 654 dbSNP
rs1422469546 657 dbSNP
rs1364925934 658 dbSNP
rs1310080637 659 dbSNP
rs1159155461 660 dbSNP
rs1421051893 663 dbSNP
rs1353002996 664 dbSNP
rs1215153655 676 dbSNP
rs1032773289 681 dbSNP
rs576243812 703 dbSNP
rs1000341005 714 dbSNP
rs554825841 715 dbSNP
rs1236038170 717 dbSNP
rs1470977142 727 dbSNP
rs1177357247 730 dbSNP
rs536575171 734 dbSNP
rs571704253 735 dbSNP
rs1175515977 738 dbSNP
rs1248055185 741 dbSNP
rs998836342 743 dbSNP
rs901466278 750 dbSNP
rs1331980340 756 dbSNP
rs770014653 760 dbSNP
rs531778676 783 dbSNP
rs1287439776 785 dbSNP
rs1332276679 793 dbSNP
rs1219433248 803 dbSNP
rs1238013320 807 dbSNP
rs761961279 823 dbSNP
rs914603416 824 dbSNP
rs1006922260 825 dbSNP
rs1346353741 826 dbSNP
rs1219113983 827 dbSNP
rs1439863367 836 dbSNP
rs888504020 843 dbSNP
rs1237183785 847 dbSNP
rs1456099833 861 dbSNP
rs1054353250 867 dbSNP
rs1395115464 870 dbSNP
rs930440426 871 dbSNP
rs897672205 875 dbSNP
rs1421459157 879 dbSNP
rs1410316634 887 dbSNP
rs777032497 893 dbSNP
rs942567641 896 dbSNP
rs553527117 897 dbSNP
rs1444773518 898 dbSNP
rs1331685520 901 dbSNP
rs184491511 904 dbSNP
rs1273569387 911 dbSNP
rs559414913 912 dbSNP
rs1341995138 918 dbSNP
rs949988709 919 dbSNP
rs1257091552 920 dbSNP
rs768918609 922 dbSNP
rs1315709749 928 dbSNP
rs1402923265 932 dbSNP
rs1215138950 934 dbSNP
rs745708498 944 dbSNP
rs917200467 945 dbSNP
rs987001823 946 dbSNP
rs1196749088 948 dbSNP
rs545765327 950 dbSNP
rs770566668 951 dbSNP
rs1343314417 957 dbSNP
rs1157773053 962 dbSNP
rs1414510814 968 dbSNP
rs1421154767 971 dbSNP
rs1464266863 973 dbSNP
rs991531002 984 dbSNP
rs1426886891 995 dbSNP
rs538631392 997 dbSNP
rs181379992 998 dbSNP
rs1264349026 1004 dbSNP
rs1196232045 1009 dbSNP
rs918325336 1012 dbSNP
rs1487609390 1013 dbSNP
rs1322193272 1015 dbSNP
rs370609320 1017 dbSNP
rs1401096041 1018 dbSNP
rs1278002654 1019 dbSNP
rs1210965958 1020 dbSNP
rs11007978 1021 dbSNP
rs1234807311 1021 dbSNP
rs1265655637 1022 dbSNP
rs1444182240 1022 dbSNP
rs1207528432 1023 dbSNP
rs1276846141 1024 dbSNP
rs538024660 1025 dbSNP
rs1488593812 1026 dbSNP
rs1318791077 1028 dbSNP
rs1278633059 1034 dbSNP
rs1161560434 1040 dbSNP
rs1189959939 1040 dbSNP
rs1260783982 1040 dbSNP
rs1280789657 1040 dbSNP
rs1359098811 1040 dbSNP
rs1362498858 1040 dbSNP
rs1369240811 1040 dbSNP
rs1376925527 1040 dbSNP
rs1420847322 1040 dbSNP
rs1472538840 1040 dbSNP
rs1476057910 1040 dbSNP
rs1491202482 1040 dbSNP
rs61386643 1040 dbSNP
rs1215878111 1041 dbSNP
rs1353728392 1041 dbSNP
rs1486553821 1041 dbSNP
rs1491270316 1041 dbSNP
rs1200801666 1046 dbSNP
rs1255160801 1047 dbSNP
rs1423496233 1048 dbSNP
rs1250624338 1052 dbSNP
rs747551806 1053 dbSNP
rs1440389110 1054 dbSNP
rs1359829394 1058 dbSNP
rs567498745 1061 dbSNP
rs1378976932 1066 dbSNP
rs11007977 1070 dbSNP
rs1303822596 1072 dbSNP
rs978514458 1073 dbSNP
rs147162471 1082 dbSNP
rs560402083 1083 dbSNP
rs962337222 1085 dbSNP
rs547425437 1086 dbSNP
rs532024069 1090 dbSNP
rs1307065053 1091 dbSNP
rs1349977131 1093 dbSNP
rs1233796444 1101 dbSNP
rs1255222333 1102 dbSNP
rs565198590 1103 dbSNP
rs1198993199 1104 dbSNP
rs1458321373 1105 dbSNP
rs959178933 1106 dbSNP
rs1034608845 1115 dbSNP
rs966001333 1117 dbSNP
rs184042029 1122 dbSNP
rs1177364408 1124 dbSNP
rs1377470283 1129 dbSNP
rs1172456296 1131 dbSNP
rs1235811458 1132 dbSNP
rs1445503832 1134 dbSNP
rs1203061457 1136 dbSNP
rs907401148 1140 dbSNP
rs1007281085 1141 dbSNP
rs192369724 1150 dbSNP
rs1026995033 1157 dbSNP
rs1310291218 1159 dbSNP
rs1469969111 1163 dbSNP
rs1361414501 1167 dbSNP
rs994206264 1168 dbSNP
rs1010346212 1171 dbSNP
rs1318884103 1172 dbSNP
rs759650878 1175 dbSNP
rs562864066 1176 dbSNP
rs1312627133 1179 dbSNP
rs143434359 1180 dbSNP
rs942682168 1183 dbSNP
rs187696084 1184 dbSNP
rs895697583 1185 dbSNP
rs1055717123 1189 dbSNP
rs936955903 1199 dbSNP
rs572357252 1206 dbSNP
rs1351161912 1208 dbSNP
rs1457970030 1214 dbSNP
rs1292931548 1215 dbSNP
rs1365426536 1215 dbSNP
rs1051057463 1216 dbSNP
rs933806081 1217 dbSNP
rs1400632038 1220 dbSNP
rs1401697928 1224 dbSNP
rs1278644969 1225 dbSNP
rs918451989 1227 dbSNP
rs1339545612 1228 dbSNP
rs1218304613 1232 dbSNP
rs755673105 1233 dbSNP
rs1332930318 1236 dbSNP
rs554470702 1240 dbSNP
rs978462232 1241 dbSNP
rs1487793511 1243 dbSNP
rs1165848520 1244 dbSNP
rs780761903 1246 dbSNP
rs1264373279 1247 dbSNP
rs1477684979 1248 dbSNP
rs1426089873 1249 dbSNP
rs1191110356 1252 dbSNP
rs1415498163 1260 dbSNP
rs544645644 1264 dbSNP
rs990406817 1269 dbSNP
rs1394390277 1270 dbSNP
rs959108538 1274 dbSNP
rs1240322592 1278 dbSNP
rs1175694851 1285 dbSNP
rs1480390325 1288 dbSNP
rs1035005785 1290 dbSNP
rs879924134 1291 dbSNP
rs981744753 1292 dbSNP
rs1268698510 1301 dbSNP
rs1381630664 1308 dbSNP
rs1323467720 1309 dbSNP
rs977297260 1310 dbSNP
rs971953623 1311 dbSNP
rs1244673092 1313 dbSNP
rs1357308017 1317 dbSNP
rs1376978729 1319 dbSNP
rs577602663 1322 dbSNP
rs555965851 1328 dbSNP
rs953002211 1333 dbSNP
rs1389328127 1343 dbSNP
rs1239513218 1349 dbSNP
rs1372088244 1351 dbSNP
rs1294521127 1354 dbSNP
rs1180874052 1360 dbSNP
rs1026922838 1370 dbSNP
rs796291535 1371 dbSNP
rs1459740250 1377 dbSNP
rs1159251447 1381 dbSNP
rs1010420280 1386 dbSNP
rs766794606 1397 dbSNP
rs12775702 1401 dbSNP
rs994155840 1403 dbSNP
rs1163488607 1409 dbSNP
rs1420453968 1415 dbSNP
rs1382248460 1416 dbSNP
rs763177290 1430 dbSNP
rs139425224 1438 dbSNP
rs1242396291 1446 dbSNP
rs1310005311 1448 dbSNP
rs76157214 1452 dbSNP
rs1353630340 1453 dbSNP
rs1222529042 1454 dbSNP
rs1281199056 1458 dbSNP
rs1051435633 1460 dbSNP
rs1025074323 1462 dbSNP
rs1240881769 1463 dbSNP
rs567461491 1463 dbSNP
rs555563278 1478 dbSNP
rs765817559 1479 dbSNP
rs1437782281 1480 dbSNP
rs1490773838 1486 dbSNP
rs1001449389 1491 dbSNP
rs185747359 1501 dbSNP
rs1042731760 1502 dbSNP
rs941199949 1504 dbSNP
rs1354246928 1505 dbSNP
rs1261989005 1511 dbSNP
rs193245525 1512 dbSNP
rs11007976 1513 dbSNP
rs944170525 1528 dbSNP
rs1388946228 1530 dbSNP
rs1368826938 1531 dbSNP
rs1218994915 1534 dbSNP
rs1261594029 1538 dbSNP
rs1319560910 1538 dbSNP
rs1198839854 1539 dbSNP
rs1161987804 1542 dbSNP
rs937658853 1543 dbSNP
rs1302852547 1547 dbSNP
rs113270668 1549 dbSNP
rs571644447 1550 dbSNP
rs1362948950 1551 dbSNP
rs1444600126 1552 dbSNP
rs971642441 1555 dbSNP
rs543132772 1564 dbSNP
rs1467404103 1567 dbSNP
rs1171627188 1568 dbSNP
rs1156925104 1571 dbSNP
rs1453114580 1576 dbSNP
rs1408275187 1589 dbSNP
rs952949994 1590 dbSNP
rs1332192806 1594 dbSNP
rs790759 1601 dbSNP
rs1281805056 1608 dbSNP
rs1342716070 1611 dbSNP
rs1380940788 1613 dbSNP
rs1218912269 1620 dbSNP
rs1178494812 1621 dbSNP
rs1336954888 1630 dbSNP
rs1211091243 1631 dbSNP
rs1481334976 1633 dbSNP
rs1289892829 1636 dbSNP
rs531732686 1637 dbSNP
rs764453368 1646 dbSNP
rs561056504 1647 dbSNP
rs961402734 1659 dbSNP
rs542784548 1661 dbSNP
rs148270062 1664 dbSNP
rs1198351749 1665 dbSNP
rs1165078909 1667 dbSNP
rs560607129 1668 dbSNP
rs1405312458 1670 dbSNP
rs1033083631 1672 dbSNP
rs1006999408 1675 dbSNP
rs954290239 1678 dbSNP
rs545710285 1686 dbSNP
rs577560434 1687 dbSNP
rs556162959 1688 dbSNP
rs386742557 1689 dbSNP
rs1284304986 1691 dbSNP
rs1355014669 1692 dbSNP
rs897038367 1693 dbSNP
rs1009868919 1698 dbSNP
rs768551174 1709 dbSNP
rs1005333794 1713 dbSNP
rs1215646371 1719 dbSNP
rs1256292287 1723 dbSNP
rs1445526275 1724 dbSNP
rs1224968490 1729 dbSNP
rs891470261 1737 dbSNP
rs888309050 1738 dbSNP
rs1444050803 1739 dbSNP
rs1054782330 1752 dbSNP
rs771051315 1756 dbSNP
rs760963882 1760 dbSNP
rs927715066 1762 dbSNP
rs1397470060 1764 dbSNP
rs1334371056 1769 dbSNP
rs1046029165 1770 dbSNP
rs1342983498 1775 dbSNP
rs1316825169 1778 dbSNP
rs943801943 1780 dbSNP
rs544233072 1781 dbSNP
rs763102450 1790 dbSNP
rs1049853472 1791 dbSNP
rs945077864 1792 dbSNP
rs542047338 1793 dbSNP
rs920137078 1798 dbSNP
rs1257114955 1800 dbSNP
rs972966097 1800 dbSNP
rs1460971601 1806 dbSNP
rs913479253 1819 dbSNP
rs1240028108 1827 dbSNP
rs143156077 1828 dbSNP
rs1362466339 1833 dbSNP
rs989094366 1835 dbSNP
rs114362931 1840 dbSNP
rs1478012869 1842 dbSNP
rs926087499 1844 dbSNP
rs986046111 1849 dbSNP
rs1190928914 1853 dbSNP
rs1427779796 1857 dbSNP
rs1256256428 1859 dbSNP
rs959471620 1871 dbSNP
rs1446009600 1873 dbSNP
rs1304743970 1888 dbSNP
rs1204960699 1890 dbSNP
rs533942846 1891 dbSNP
rs566694558 1895 dbSNP
rs954122556 1897 dbSNP
rs1030164554 1898 dbSNP
rs111446694 1899 dbSNP
rs961393667 1904 dbSNP
rs1015452414 1905 dbSNP
rs187490112 1906 dbSNP
rs968543456 1916 dbSNP
rs1177205347 1917 dbSNP
rs1269003980 1920 dbSNP
rs1249018001 1922 dbSNP
rs1435365771 1923 dbSNP
rs1021519420 1933 dbSNP
rs1227352456 1935 dbSNP
rs796790518 1938 dbSNP
rs1341535792 1939 dbSNP
rs1317282049 1940 dbSNP
rs1400442007 1942 dbSNP
rs867064868 1955 dbSNP
rs888379633 1969 dbSNP
rs11598508 1972 dbSNP
rs529387573 1979 dbSNP
rs608872 1980 dbSNP
rs906281436 1984 dbSNP
rs1282429029 1990 dbSNP
rs1221959917 1996 dbSNP
rs1398370418 1996 dbSNP
rs1046606964 1998 dbSNP
rs1318771501 2021 dbSNP
rs1165876428 2022 dbSNP
rs1461438213 2026 dbSNP
rs1249622540 2029 dbSNP
rs749049144 2038 dbSNP
rs1368939319 2039 dbSNP
rs777733763 2040 dbSNP
rs149503842 2042 dbSNP
rs608973 2048 dbSNP
rs936209260 2049 dbSNP
rs1242215193 2055 dbSNP
rs926201869 2061 dbSNP
rs985608189 2062 dbSNP
rs1427491636 2066 dbSNP
rs748016971 2068 dbSNP
rs922701899 2071 dbSNP
rs1452778553 2078 dbSNP
rs898659436 2081 dbSNP
rs977269737 2092 dbSNP
rs961340777 2097 dbSNP
rs780770819 2102 dbSNP
rs77162406 2103 dbSNP
rs560610244 2104 dbSNP
rs199684615 2105 dbSNP
rs1293553842 2106 dbSNP
rs539793687 2108 dbSNP
rs1034015252 2115 dbSNP
rs1323557588 2125 dbSNP
rs1246216942 2126 dbSNP
rs761049243 2127 dbSNP
rs1294548059 2133 dbSNP
rs1219260624 2135 dbSNP
rs551775332 2139 dbSNP
rs1243943986 2140 dbSNP
rs1264260122 2140 dbSNP
rs533632117 2141 dbSNP
rs1384467768 2158 dbSNP
rs1002038057 2164 dbSNP
rs938028616 2176 dbSNP
rs1162921792 2189 dbSNP
rs1383325747 2192 dbSNP
rs926655842 2199 dbSNP
rs1159059297 2207 dbSNP
rs1344338617 2210 dbSNP
rs1309984238 2217 dbSNP
rs746708525 2218 dbSNP
rs906388807 2219 dbSNP
rs1381514890 2248 dbSNP
rs1444654460 2252 dbSNP
rs1334152847 2255 dbSNP
rs1024710375 2257 dbSNP
rs1009298518 2260 dbSNP
rs1314399216 2268 dbSNP
rs1242896627 2269 dbSNP
rs1357925678 2269 dbSNP
rs1326637702 2287 dbSNP
rs892234616 2288 dbSNP
rs1316668745 2292 dbSNP
rs1409118332 2307 dbSNP
rs1238835862 2309 dbSNP
rs540994 2312 dbSNP
rs1182449236 2316 dbSNP
rs1165384375 2322 dbSNP
rs936325515 2325 dbSNP
rs758884180 2328 dbSNP
rs1441493038 2330 dbSNP
rs1422287979 2334 dbSNP
rs1179155951 2337 dbSNP
rs182811963 2341 dbSNP
rs1384081890 2342 dbSNP
rs1407028217 2343 dbSNP
rs1398732498 2347 dbSNP
rs750804398 2350 dbSNP
rs765911103 2351 dbSNP
rs544202683 2354 dbSNP
rs1336192387 2357 dbSNP
rs1380609903 2367 dbSNP
rs1351333807 2369 dbSNP
rs922784277 2371 dbSNP
rs531727534 2383 dbSNP
rs1373133160 2386 dbSNP
rs940077170 2387 dbSNP
rs573697205 2388 dbSNP
rs1007852618 2395 dbSNP
rs1323851821 2399 dbSNP
rs1202588400 2400 dbSNP
rs1220908381 2411 dbSNP
rs1458693546 2413 dbSNP
rs1281258063 2419 dbSNP
rs1232218708 2421 dbSNP
rs1359275052 2424 dbSNP
rs1192709850 2442 dbSNP
rs190388606 2443 dbSNP
rs1480897841 2457 dbSNP
rs776452704 2458 dbSNP
rs1404088345 2460 dbSNP
rs187071676 2466 dbSNP
rs995212924 2470 dbSNP
rs952751093 2471 dbSNP
rs1276996829 2482 dbSNP
rs1033590341 2490 dbSNP
rs1346518431 2501 dbSNP
rs1222569614 2505 dbSNP
rs1280967150 2516 dbSNP
rs981122449 2521 dbSNP
rs898273745 2528 dbSNP
rs1460373292 2535 dbSNP
rs970691011 2536 dbSNP
rs1025199997 2540 dbSNP
rs1436036853 2547 dbSNP
rs1345912887 2558 dbSNP
rs1009411281 2563 dbSNP
rs1490115485 2564 dbSNP
rs557453068 2565 dbSNP
rs1403045690 2566 dbSNP
rs892182255 2570 dbSNP
rs1427481784 2578 dbSNP
rs1364834614 2580 dbSNP
rs7091551 2581 dbSNP
rs1168604397 2594 dbSNP
rs1401907234 2596 dbSNP
rs1418832772 2603 dbSNP
rs896712811 2606 dbSNP
rs1326075449 2607 dbSNP
rs1057121466 2616 dbSNP
rs1404705322 2617 dbSNP
rs1287744860 2628 dbSNP
rs375795447 2638 dbSNP
rs541816218 2645 dbSNP
rs372239832 2650 dbSNP
rs1336851655 2654 dbSNP
rs1229995781 2668 dbSNP
rs1292396765 2675 dbSNP
rs979468806 2677 dbSNP
rs1219985459 2678 dbSNP
rs888806725 2680 dbSNP
rs1448978291 2684 dbSNP
rs764254808 2690 dbSNP
rs1218283718 2692 dbSNP
rs1241637312 2693 dbSNP
rs1431917858 2697 dbSNP
rs1197650013 2699 dbSNP
rs1166078199 2700 dbSNP
rs946767794 2704 dbSNP
rs1424510388 2706 dbSNP
rs1405787701 2710 dbSNP
rs11415607 2711 dbSNP
rs1162096484 2711 dbSNP
rs1317153710 2711 dbSNP
rs746039362 2711 dbSNP
rs1449606986 2712 dbSNP
rs537378170 2712 dbSNP
rs1315061574 2714 dbSNP
rs914020399 2715 dbSNP
rs1243621925 2716 dbSNP
rs988635433 2718 dbSNP
rs1445336711 2719 dbSNP
rs1351091498 2722 dbSNP
rs760628834 2724 dbSNP
rs956067426 2725 dbSNP
rs1283913871 2728 dbSNP
rs1283812071 2732 dbSNP
rs1445435907 2746 dbSNP
rs932871907 2749 dbSNP
rs557973284 2752 dbSNP
rs1185502907 2754 dbSNP
rs539266110 2755 dbSNP
rs1041159222 2761 dbSNP
rs138894624 2762 dbSNP
rs908628504 2767 dbSNP
rs1048492457 2774 dbSNP
rs1158297378 2775 dbSNP
rs1344852247 2779 dbSNP
rs987112708 2781 dbSNP
rs1336849157 2788 dbSNP
rs556852122 2795 dbSNP
rs1432362397 2796 dbSNP
rs1311367980 2800 dbSNP
rs1336191723 2802 dbSNP
rs926596078 2807 dbSNP
rs7091615 2808 dbSNP
rs995162032 2810 dbSNP
rs1205753971 2817 dbSNP
rs1263881867 2819 dbSNP
rs962407057 2820 dbSNP
rs567349497 2826 dbSNP
rs549060882 2828 dbSNP
rs1470014870 2833 dbSNP
rs112634765 2837 dbSNP
rs1174772016 2838 dbSNP
rs1181584185 2846 dbSNP
rs1362374842 2849 dbSNP
rs896655023 2855 dbSNP
rs1404811023 2858 dbSNP
rs1056669187 2865 dbSNP
rs1002456413 2867 dbSNP
rs1442256627 2869 dbSNP
rs1397127714 2873 dbSNP
rs1390706721 2874 dbSNP
rs1420918931 2876 dbSNP
rs987971825 2880 dbSNP
rs1332579470 2881 dbSNP
rs956560722 2881 dbSNP
rs1322994494 2882 dbSNP
rs190790470 2883 dbSNP
rs946715289 2886 dbSNP
rs1032080539 2888 dbSNP
rs1195710169 2890 dbSNP
rs1000640161 2892 dbSNP
rs1490942845 2899 dbSNP
rs1199774842 2908 dbSNP
rs1210852015 2912 dbSNP
rs1171939286 2915 dbSNP
rs1462849930 2918 dbSNP
rs1461461678 2923 dbSNP
rs1296347983 2927 dbSNP
rs1367289156 2934 dbSNP
rs953174242 2946 dbSNP
rs773000412 2953 dbSNP
rs551901893 2955 dbSNP
rs1345152340 2972 dbSNP
rs1201590398 2983 dbSNP
rs1385259063 2985 dbSNP
rs1322546855 2987 dbSNP
rs1295942531 2988 dbSNP
rs1216268113 2989 dbSNP
rs1227432236 2991 dbSNP
rs1359717572 2994 dbSNP
rs1250117893 3000 dbSNP
rs1269110237 3006 dbSNP
rs112082886 3008 dbSNP
rs1384602586 3009 dbSNP
rs1334267146 3010 dbSNP
rs997196589 3013 dbSNP
rs1449217684 3018 dbSNP
rs1187878326 3021 dbSNP
rs1261862582 3023 dbSNP
rs1427404917 3025 dbSNP
rs1387028109 3027 dbSNP
rs11310410 3028 dbSNP
rs1290855143 3028 dbSNP
rs1362823931 3028 dbSNP
rs1425147580 3028 dbSNP
rs397709519 3028 dbSNP
rs748586324 3028 dbSNP
rs776841621 3028 dbSNP
rs1469668237 3029 dbSNP
rs1295414328 3030 dbSNP
rs1355488108 3030 dbSNP
rs1247285730 3034 dbSNP
rs1291564681 3037 dbSNP
rs944842121 3041 dbSNP
rs1172918192 3049 dbSNP
rs548381001 3050 dbSNP
rs1217584400 3052 dbSNP
rs1260932520 3053 dbSNP
rs1485307154 3054 dbSNP
rs912380608 3060 dbSNP
rs1408740823 3063 dbSNP
rs1244394433 3064 dbSNP
rs1445218200 3066 dbSNP
rs1386092519 3074 dbSNP
rs1182880691 3087 dbSNP
rs1419381670 3091 dbSNP
rs901381503 3092 dbSNP
rs1160873362 3094 dbSNP
rs953950878 3097 dbSNP
rs769525031 3098 dbSNP
rs1004326919 3099 dbSNP
rs867941858 3103 dbSNP
rs1273301160 3106 dbSNP
rs1318643721 3109 dbSNP
rs1408358486 3113 dbSNP
rs1454017759 3126 dbSNP
rs1245985286 3130 dbSNP
rs1314956787 3132 dbSNP
rs887302138 3133 dbSNP
rs1377511725 3140 dbSNP
rs1225846334 3141 dbSNP
rs921193255 3142 dbSNP
rs1048564939 3148 dbSNP
rs931361925 3164 dbSNP
rs926736338 3165 dbSNP
rs962356708 3173 dbSNP
rs748109230 3180 dbSNP
rs1272171248 3186 dbSNP
rs949453618 3187 dbSNP
rs1241217756 3190 dbSNP
rs1004363976 3193 dbSNP
rs960527603 3196 dbSNP
rs1246145929 3207 dbSNP
rs1035581913 3208 dbSNP
rs563144387 3212 dbSNP
rs186065885 3214 dbSNP
rs956507056 3217 dbSNP
rs370491305 3222 dbSNP
rs528307297 3225 dbSNP
rs925083633 3226 dbSNP
rs1336096656 3230 dbSNP
rs979302515 3236 dbSNP
rs1357931536 3237 dbSNP
rs1444939801 3238 dbSNP
rs1299149862 3239 dbSNP
rs953210311 3241 dbSNP
rs1373553822 3255 dbSNP
rs528874419 3257 dbSNP
rs1028742663 3258 dbSNP
rs1044001867 3265 dbSNP
rs776395846 3267 dbSNP
rs1222383076 3269 dbSNP
rs561714982 3271 dbSNP
rs1164761751 3281 dbSNP
rs768254501 3286 dbSNP
rs1052484180 3296 dbSNP
rs1426699882 3297 dbSNP
rs539943549 3298 dbSNP
rs1180361047 3313 dbSNP
rs1431734634 3323 dbSNP
rs1480847842 3335 dbSNP
rs1004400379 3339 dbSNP
rs572855461 3344 dbSNP
rs564029933 3345 dbSNP
rs545948200 3347 dbSNP
rs746480562 3348 dbSNP
rs1252890354 3355 dbSNP
rs1178775725 3360 dbSNP
rs1479526136 3368 dbSNP
rs779815243 3369 dbSNP
rs1354378204 3372 dbSNP
rs995692307 3377 dbSNP
rs1050856336 3380 dbSNP
rs1305273915 3382 dbSNP
rs1345790190 3386 dbSNP
rs905273600 3389 dbSNP
rs932504295 3391 dbSNP
rs1272617873 3392 dbSNP
rs1361438434 3397 dbSNP
rs575130749 3398 dbSNP
rs1272181733 3400 dbSNP
rs556815049 3408 dbSNP
rs184053230 3425 dbSNP
rs758120075 3428 dbSNP
rs1222481979 3430 dbSNP
rs1490580956 3433 dbSNP
rs908202574 3442 dbSNP
rs1245126791 3451 dbSNP
rs982493825 3454 dbSNP
rs1052453793 3458 dbSNP
rs1187124871 3460 dbSNP
rs1419434644 3471 dbSNP
rs1373050599 3476 dbSNP
rs1304063328 3477 dbSNP
rs935205735 3478 dbSNP
rs1165889937 3481 dbSNP
rs565930333 3482 dbSNP
rs979633712 3485 dbSNP
rs931871784 3487 dbSNP
rs1364209867 3489 dbSNP
rs573686100 3495 dbSNP
rs555690133 3497 dbSNP
rs1430836854 3500 dbSNP
rs965787723 3505 dbSNP
rs1269009687 3510 dbSNP
rs1362981924 3514 dbSNP
rs1248015640 3516 dbSNP
rs1014516791 3520 dbSNP
rs983089233 3526 dbSNP
rs377058770 3545 dbSNP
rs1358459616 3562 dbSNP
rs12269422 3566 dbSNP
rs552207993 3571 dbSNP
rs996071483 3577 dbSNP
rs905390576 3589 dbSNP
rs11007975 3596 dbSNP
rs1011159512 3599 dbSNP
rs1013647532 3603 dbSNP
rs896584936 3604 dbSNP
rs1185929394 3609 dbSNP
rs1031405787 3612 dbSNP
rs768468336 3617 dbSNP
rs1008912587 3618 dbSNP
rs1052401575 3626 dbSNP
rs1386689744 3628 dbSNP
rs935319679 3631 dbSNP
rs540009676 3635 dbSNP
rs1043680462 3636 dbSNP
rs1050472841 3638 dbSNP
rs141224668 3639 dbSNP
rs1385777750 3644 dbSNP
rs190959333 3646 dbSNP
rs931793562 3658 dbSNP
rs551294093 3663 dbSNP
rs534612690 3694 dbSNP
rs976335769 3697 dbSNP
rs1038207252 3698 dbSNP
rs944428331 3702 dbSNP
rs1353142409 3709 dbSNP
rs757645927 3710 dbSNP
rs941258037 3712 dbSNP
rs983076281 3715 dbSNP
rs186191258 3719 dbSNP
rs908485765 3721 dbSNP
rs951749217 3723 dbSNP
rs754398934 3724 dbSNP
rs181660163 3725 dbSNP
rs563145479 3736 dbSNP
rs1365859644 3740 dbSNP
rs1470335496 3744 dbSNP
rs1382910561 3749 dbSNP
rs970061024 3752 dbSNP
rs1387236949 3761 dbSNP
rs1287129012 3787 dbSNP
rs1470678980 3794 dbSNP
rs980506502 3794 dbSNP
rs1336741797 3805 dbSNP
rs969164123 3806 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 55149.0
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]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions hESCs (WA-09)
Disease 55149.0
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.

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 GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000263063.4 | 3UTR | AUACUCAGUGGCACUUUAUUAAAACAUCAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset SRR359787
Method / RBP PAR-CLIP / AGO2
Cell line / Condition hESCs (WA-09) / 4-thiouridine, RNase T1
Location of target site ENST00000263063.4 | 3UTR | AUACUCAGUGGCACUUUAUUAAAACAUCA
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
LIHC 0.722 0.14 0.400 0.3 4 Click to see details
STAD 0.85 0.18 0.500 0.33 3 Click to see details
HNSC 0.237 0.21 0.248 0.2 14 Click to see details
BLCA 0.36 0.24 0.257 0.31 6 Click to see details
LUSC -0.185 0.25 -0.307 0.13 15 Click to see details
UCEC -0.203 0.43 -0.500 0.33 3 Click to see details
BRCA -0.013 0.47 0.010 0.48 31 Click to see details
BRCA -0.013 0.47 0.010 0.48 31 Click to see details
BRCA -0.013 0.47 0.010 0.48 31 Click to see details
BRCA -0.013 0.47 0.010 0.48 31 Click to see details
BRCA -0.013 0.47 0.010 0.48 31 Click to see details
BRCA -0.013 0.47 0.010 0.48 31 Click to see details
BRCA -0.013 0.47 0.010 0.48 31 Click to see details
80 hsa-miR-2115-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT057089 DDIT4 DNA damage inducible transcript 4 2 2
MIRT071216 FCF1 FCF1, rRNA-processing protein 2 2
MIRT226901 RAD23B RAD23 homolog B, nucleotide excision repair protein 2 2
MIRT235961 BACH1 BTB domain and CNC homolog 1 2 2
MIRT294569 ZNF460 zinc finger protein 460 2 4
MIRT321046 RAC1 Rac family small GTPase 1 2 4
MIRT359666 NUS1 NUS1 dehydrodolichyl diphosphate synthase subunit 2 8
MIRT366451 KLHL15 kelch like family member 15 2 2
MIRT405375 ZBTB18 zinc finger and BTB domain containing 18 2 2
MIRT441794 TCEAL5 transcription elongation factor A like 5 2 2
MIRT443295 TCEAL3 transcription elongation factor A like 3 2 2
MIRT455275 DDX39B DExD-box helicase 39B 2 2
MIRT458523 C5orf22 chromosome 5 open reading frame 22 2 2
MIRT464960 TWIST1 twist family bHLH transcription factor 1 2 2
MIRT466848 STX6 syntaxin 6 2 2
MIRT469252 RHOB ras homolog family member B 2 2
MIRT469825 RAB14 RAB14, member RAS oncogene family 2 4
MIRT470047 PTGFRN prostaglandin F2 receptor inhibitor 2 2
MIRT471420 PDP2 pyruvate dehyrogenase phosphatase catalytic subunit 2 2 2
MIRT472024 NPM1 nucleophosmin 1 2 2
MIRT484156 CENPN centromere protein N 2 2
MIRT485490 HMGN2 high mobility group nucleosomal binding domain 2 2 2
MIRT490462 PROSER2 proline and serine rich 2 2 2
MIRT493069 MTCH1 mitochondrial carrier 1 2 2
MIRT493573 HSP90AA1 heat shock protein 90 alpha family class A member 1 2 8
MIRT494919 NDUFC2-KCTD14 NDUFC2-KCTD14 readthrough 2 2
MIRT500439 ZMAT3 zinc finger matrin-type 3 2 2
MIRT500931 SRPR SRP receptor alpha subunit 2 4
MIRT501551 POC1B-GALNT4 POC1B-GALNT4 readthrough 2 2
MIRT501809 NEURL1B neuralized E3 ubiquitin protein ligase 1B 2 2
MIRT502415 GALNT4 polypeptide N-acetylgalactosaminyltransferase 4 2 2
MIRT506504 MSANTD4 Myb/SANT DNA binding domain containing 4 with coiled-coils 2 2
MIRT507861 CCNE2 cyclin E2 2 2
MIRT510511 YOD1 YOD1 deubiquitinase 2 6
MIRT516073 RAB42 RAB42, member RAS oncogene family 2 2
MIRT519030 KYNU kynureninase 2 6
MIRT521762 PPIL1 peptidylprolyl isomerase like 1 2 4
MIRT522898 KCNJ3 potassium voltage-gated channel subfamily J member 3 2 4
MIRT527370 MGARP mitochondria localized glutamic acid rich protein 2 2
MIRT530691 C8orf46 chromosome 8 open reading frame 46 2 2
MIRT530867 TRUB1 TruB pseudouridine synthase family member 1 2 2
MIRT531832 MTPAP mitochondrial poly(A) polymerase 2 4
MIRT533035 ZBTB5 zinc finger and BTB domain containing 5 2 2
MIRT533165 WIPF2 WAS/WASL interacting protein family member 2 2 2
MIRT533464 TRIM71 tripartite motif containing 71 2 2
MIRT534331 SHCBP1 SHC binding and spindle associated 1 2 2
MIRT539372 ADSS adenylosuccinate synthase 2 6
MIRT545951 ZBTB10 zinc finger and BTB domain containing 10 2 2
MIRT553283 TSR1 TSR1, ribosome maturation factor 2 2
MIRT553532 TMEM185B transmembrane protein 185B 2 4
MIRT556480 LIPA lipase A, lysosomal acid type 2 2
MIRT556975 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT557697 GATA6 GATA binding protein 6 2 2
MIRT558901 CCDC58 coiled-coil domain containing 58 2 2
MIRT559224 BLMH bleomycin hydrolase 2 2
MIRT559827 SLPI secretory leukocyte peptidase inhibitor 2 2
MIRT563435 SLC3A2 solute carrier family 3 member 2 2 2
MIRT569270 PCDH11X protocadherin 11 X-linked 2 2
MIRT571386 JKAMP JNK1/MAPK8-associated membrane protein 2 2
MIRT572567 AFF1 AF4/FMR2 family member 1 2 2
MIRT610400 AR androgen receptor 2 2
MIRT611058 ZNF621 zinc finger protein 621 2 2
MIRT635118 TMEM233 transmembrane protein 233 2 2
MIRT641617 DEFB118 defensin beta 118 2 2
MIRT642146 CHORDC1 cysteine and histidine rich domain containing 1 2 2
MIRT647295 C8orf33 chromosome 8 open reading frame 33 2 2
MIRT648155 MPLKIP M-phase specific PLK1 interacting protein 2 2
MIRT652780 TENM3 teneurin transmembrane protein 3 2 2
MIRT657356 HNRNPA2B1 heterogeneous nuclear ribonucleoprotein A2/B1 2 2
MIRT658718 ELN elastin 2 2
MIRT662441 RALGAPA1 Ral GTPase activating protein catalytic alpha subunit 1 2 2
MIRT665302 ZBTB38 zinc finger and BTB domain containing 38 2 2
MIRT699898 RUNX1 runt related transcription factor 1 2 2
MIRT700921 PDS5A PDS5 cohesin associated factor A 2 2
MIRT700992 PDE3A phosphodiesterase 3A 2 2
MIRT707397 DCAF4L1 DDB1 and CUL4 associated factor 4 like 1 2 2
MIRT711895 INSIG2 insulin induced gene 2 2 2
MIRT712072 XRCC5 X-ray repair cross complementing 5 2 2
MIRT716121 PTPLAD2 3-hydroxyacyl-CoA dehydratase 4 1 1
MIRT724470 SMAD2 SMAD family member 2 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-2115 Docetaxel+Cisplatin+5-Fluorouracil sensitive tissue (hypopharyngeal squamous cell carcinoma)
hsa-mir-2115 Decitabine 451668 approved sensitive tissue (esopheageal cancer)
hsa-miR-2115-3p Imatinib 5291 NSC743414 approved resistant High Chronic Myelogenous Leukemia cell line (K562)
hsa-miR-2115-3p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-2115-3p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-2115-3p Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-2115-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-2115-3p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-2115-3p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)

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