pre-miRNA Information
pre-miRNA hsa-mir-548t   
Genomic Coordinates chr4: 173268160 - 173268233
Description Homo sapiens miR-548t stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-548t-3p
Sequence 46| AAAAACCACAAUUACUUUUGCACCA |70
Evidence Not_experimental
Experiments
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 2 4 + 173268206 29233923 MiREDiBase
A-to-I 3 4 + 173268207 29233923 MiREDiBase
A-to-I 4 4 + 173268208 29233923 MiREDiBase
A-to-I 10 4 + 173268214 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs73872515 5 dbSNP
rs1426966747 6 dbSNP
rs1158401109 21 dbSNP
rs943938928 24 dbSNP
Putative Targets

Gene Information
Gene Symbol PIWIL2   
Synonyms CT80, HILI, PIWIL1L, mili
Description piwi like RNA-mediated gene silencing 2
Transcript NM_001135721   
Other Transcripts NM_018068   
Expression
Putative miRNA Targets on PIWIL2
3'UTR of PIWIL2
(miRNA target sites are highlighted)
>PIWIL2|NM_001135721|3'UTR
   1 CTGCACAGCTTGGAGATGGGCTGGTGAGAAGAAAGGCGGCCTCAGAACTCAGCTGTGACTCTTGCAGAATCAACAGAGAC
  81 TGAAGTGGGCTTTTGTGTTATAATTTTCCCTTTCTCCAACCCTGTAGAATAAGATTTCTTTCTTGTCTTTTAAACCTAAT
 161 ATCACCAAGAAGCAAGTTTCTGAGTAACAGCTGAAAATGGCCTTGTTGCCTGTGTAGAGCAAGTTACGGTGGTACTGCCA
 241 CTCTGCAGGTGGAGCGGGTGACTCTGGGGGACCATTAAGACCTCCAGACCGGGTGCGGTGGTTCACACCTGTAATCCAAG
 321 CACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCAGGAGATCAAGACCATCCTGGCCAACATGGTGAAACCCCGTCTC
 401 TACTAAAATACAAAAAAATTAGCCGGGTGTGGCGGTGCACGCCTGTAGTCCCAGCTACTCAGGAGGCTAAGGCAGGAGAA
 481 TCGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACGCCACTGCACTCCAGCCTGTTGACAAAGCAAGACTC
 561 TGTCTC
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' accacGUUUUCAUUAA---CACC--AAAAa 5'
               ||| || :| |   ||||  |||| 
Target 5' agaatCAACAGAGACTGAAGTGGGCTTTTg 3'
66 - 95 120.00 -6.50
2
miRNA  3' acCACGUU---UUCAUUAACACCAaaaa 5'
            |||:|:   |||| |  |||||    
Target 5' ctGTGTAGAGCAAGTTACGGTGGTactg 3'
210 - 237 111.00 -12.36
3
miRNA  3' accACGUUU---UCAUUAACACCAAaaa 5'
             | ||:|   :|| :  ||||||   
Target 5' accTCCAGACCGGGT-GCGGTGGTTcac 3'
280 - 306 109.00 -13.32
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN8518716 16 COSMIC
COSN30151361 46 COSMIC
COSN31483802 62 COSMIC
COSN26122505 256 COSMIC
COSN6919326 341 COSMIC
COSN8077385 1886 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1034302162 6 dbSNP
rs1412021679 7 dbSNP
rs762242190 13 dbSNP
rs1324711622 15 dbSNP
rs770300263 20 dbSNP
rs773520260 29 dbSNP
rs1292082913 34 dbSNP
rs1162708743 36 dbSNP
rs763344374 38 dbSNP
rs369374921 39 dbSNP
rs373489346 43 dbSNP
rs1282669154 46 dbSNP
rs1259822543 56 dbSNP
rs543761404 64 dbSNP
rs1047040694 65 dbSNP
rs891027436 73 dbSNP
rs777006652 82 dbSNP
rs112922283 84 dbSNP
rs1429203287 86 dbSNP
rs1027085703 95 dbSNP
rs111874544 102 dbSNP
rs140159733 110 dbSNP
rs762214011 116 dbSNP
rs951052776 125 dbSNP
rs769406552 130 dbSNP
rs1324273310 133 dbSNP
rs1297295824 134 dbSNP
rs1019323405 135 dbSNP
rs1393544214 139 dbSNP
rs1156446519 146 dbSNP
rs1022372070 153 dbSNP
rs1395269452 155 dbSNP
rs569210516 157 dbSNP
rs965966166 160 dbSNP
rs975543020 171 dbSNP
rs1167364610 174 dbSNP
rs1474479923 175 dbSNP
rs1405047225 180 dbSNP
rs199838016 183 dbSNP
rs1301920660 185 dbSNP
rs968482980 189 dbSNP
rs1196021274 195 dbSNP
rs921546412 205 dbSNP
rs1307504160 207 dbSNP
rs958262961 211 dbSNP
rs1194680891 212 dbSNP
rs1238675478 215 dbSNP
rs978045759 220 dbSNP
rs1228761042 221 dbSNP
rs1259197797 223 dbSNP
rs1301031296 224 dbSNP
rs772807964 228 dbSNP
rs537375399 229 dbSNP
rs1328110990 236 dbSNP
rs1268205723 239 dbSNP
rs765818300 243 dbSNP
rs146962844 244 dbSNP
rs1168694689 247 dbSNP
rs1179425883 248 dbSNP
rs1251781491 256 dbSNP
rs573905095 257 dbSNP
rs1180039234 259 dbSNP
rs1454995211 262 dbSNP
rs1232742791 265 dbSNP
rs7006367 266 dbSNP
rs1435556695 267 dbSNP
rs553116132 268 dbSNP
rs1205388330 278 dbSNP
rs1346652988 282 dbSNP
rs137881849 284 dbSNP
rs919670890 285 dbSNP
rs545084344 286 dbSNP
rs1345452998 287 dbSNP
rs113813799 291 dbSNP
rs575163069 292 dbSNP
rs1048275981 296 dbSNP
rs542934036 298 dbSNP
rs1373809947 302 dbSNP
rs1372455292 306 dbSNP
rs561198541 307 dbSNP
rs1435724148 312 dbSNP
rs1039641889 332 dbSNP
rs899698637 334 dbSNP
rs1471464299 335 dbSNP
rs528670224 336 dbSNP
rs1019814744 341 dbSNP
rs965083419 343 dbSNP
rs929319873 344 dbSNP
rs996992425 348 dbSNP
rs375229150 350 dbSNP
rs958169803 352 dbSNP
rs565470425 356 dbSNP
rs990146058 359 dbSNP
rs1357361122 368 dbSNP
rs1442772830 383 dbSNP
rs914118397 386 dbSNP
rs967152783 388 dbSNP
rs982122657 389 dbSNP
rs1207319472 393 dbSNP
rs1221894694 396 dbSNP
rs532524717 397 dbSNP
rs767372116 405 dbSNP
rs189621230 410 dbSNP
rs1030967712 412 dbSNP
rs960655078 414 dbSNP
rs992408214 415 dbSNP
rs1023880363 416 dbSNP
rs915756878 418 dbSNP
rs931096325 419 dbSNP
rs1048831666 424 dbSNP
rs368343605 425 dbSNP
rs1410009331 426 dbSNP
rs1409281070 428 dbSNP
rs1164840335 432 dbSNP
rs1004311949 433 dbSNP
rs1040694171 434 dbSNP
rs1182564579 435 dbSNP
rs1382915022 441 dbSNP
rs900821430 442 dbSNP
rs1213319133 466 dbSNP
rs1450808096 470 dbSNP
rs920062694 472 dbSNP
rs1170450474 481 dbSNP
rs1353888973 483 dbSNP
rs143452575 492 dbSNP
rs1304421341 493 dbSNP
rs1027994373 494 dbSNP
rs1453732898 498 dbSNP
rs1314619706 499 dbSNP
rs893979097 501 dbSNP
rs1433244757 502 dbSNP
rs1389919570 506 dbSNP
rs912273203 513 dbSNP
rs1325804712 516 dbSNP
rs1460380061 517 dbSNP
rs1011072046 525 dbSNP
rs1021654374 526 dbSNP
rs1405460197 527 dbSNP
rs1418272092 528 dbSNP
rs966968922 529 dbSNP
rs1248466225 531 dbSNP
rs1040056413 533 dbSNP
rs1274998912 534 dbSNP
rs536621661 537 dbSNP
rs1222322836 539 dbSNP
rs1307450226 540 dbSNP
rs982749295 546 dbSNP
rs1271140160 547 dbSNP
rs182105781 558 dbSNP
rs1203010807 561 dbSNP
rs1265432296 566 dbSNP
rs10710520 567 dbSNP
rs1303179010 567 dbSNP
rs1439197764 567 dbSNP
rs1457970064 567 dbSNP
rs71206516 567 dbSNP
rs947269668 569 dbSNP
rs1035032232 581 dbSNP
rs1431295817 582 dbSNP
rs902981126 584 dbSNP
rs1177376347 585 dbSNP
rs1203371374 586 dbSNP
rs1240888343 590 dbSNP
rs567529410 591 dbSNP
rs1486619648 592 dbSNP
rs959327335 593 dbSNP
rs1418133513 600 dbSNP
rs990907484 608 dbSNP
rs1426701308 609 dbSNP
rs1480339570 615 dbSNP
rs999567515 620 dbSNP
rs1206848980 623 dbSNP
rs1178490693 625 dbSNP
rs920676806 633 dbSNP
rs1279899559 640 dbSNP
rs547018736 642 dbSNP
rs896524063 649 dbSNP
rs1302576119 650 dbSNP
rs534906995 667 dbSNP
rs1334378063 675 dbSNP
rs1404227921 676 dbSNP
rs1295907815 680 dbSNP
rs1411151458 684 dbSNP
rs1370726953 685 dbSNP
rs1433098893 686 dbSNP
rs1387257215 687 dbSNP
rs187065258 689 dbSNP
rs1432623797 692 dbSNP
rs577746240 694 dbSNP
rs1176669341 695 dbSNP
rs538390643 703 dbSNP
rs1184374188 704 dbSNP
rs1361323201 705 dbSNP
rs752513612 714 dbSNP
rs1013525313 718 dbSNP
rs191503261 726 dbSNP
rs1486847693 732 dbSNP
rs1256995765 734 dbSNP
rs575133938 742 dbSNP
rs1315604333 762 dbSNP
rs149388112 767 dbSNP
rs974698285 768 dbSNP
rs1027159144 771 dbSNP
rs542175408 776 dbSNP
rs1416982811 785 dbSNP
rs1311882261 795 dbSNP
rs562668176 801 dbSNP
rs900854082 818 dbSNP
rs932279843 824 dbSNP
rs554133202 825 dbSNP
rs573245346 826 dbSNP
rs1049506669 829 dbSNP
rs183702426 844 dbSNP
rs1343296821 850 dbSNP
rs147322760 853 dbSNP
rs532703328 859 dbSNP
rs1186038990 860 dbSNP
rs779188177 865 dbSNP
rs920900769 867 dbSNP
rs371514808 868 dbSNP
rs544402183 872 dbSNP
rs1263012828 876 dbSNP
rs188374348 882 dbSNP
rs1035234110 885 dbSNP
rs1480047937 889 dbSNP
rs115677806 890 dbSNP
rs758440496 899 dbSNP
rs896554746 906 dbSNP
rs1014060912 907 dbSNP
rs1359680587 908 dbSNP
rs1322443777 909 dbSNP
rs990814350 911 dbSNP
rs1393683343 913 dbSNP
rs1162821524 921 dbSNP
rs1459523307 922 dbSNP
rs138977571 926 dbSNP
rs1369206525 927 dbSNP
rs566869122 932 dbSNP
rs780032415 939 dbSNP
rs952141920 940 dbSNP
rs983917286 943 dbSNP
rs1271849085 949 dbSNP
rs1160099792 950 dbSNP
rs1207491539 958 dbSNP
rs193295730 972 dbSNP
rs1027642834 973 dbSNP
rs1305523042 974 dbSNP
rs1304991277 976 dbSNP
rs1299496332 983 dbSNP
rs1346719188 983 dbSNP
rs939815282 990 dbSNP
rs1004366607 991 dbSNP
rs546858805 995 dbSNP
rs185503685 997 dbSNP
rs538777575 998 dbSNP
rs373051784 1000 dbSNP
rs1167533567 1001 dbSNP
rs1460695047 1002 dbSNP
rs1224046730 1008 dbSNP
rs1169563311 1019 dbSNP
rs1454115331 1032 dbSNP
rs568651137 1049 dbSNP
rs1251604051 1051 dbSNP
rs975534598 1060 dbSNP
rs769130520 1066 dbSNP
rs868015467 1069 dbSNP
rs1194768830 1071 dbSNP
rs149430963 1077 dbSNP
rs893449275 1079 dbSNP
rs781694328 1082 dbSNP
rs1042497995 1085 dbSNP
rs978734915 1086 dbSNP
rs902684338 1097 dbSNP
rs1228784410 1105 dbSNP
rs924517471 1112 dbSNP
rs1272986547 1119 dbSNP
rs1291809389 1129 dbSNP
rs554169546 1130 dbSNP
rs144766071 1135 dbSNP
rs1056770505 1138 dbSNP
rs1234462445 1139 dbSNP
rs1389767151 1163 dbSNP
rs200692508 1165 dbSNP
rs1056910931 1171 dbSNP
rs1308867427 1176 dbSNP
rs917048913 1182 dbSNP
rs1470383148 1185 dbSNP
rs1176343395 1186 dbSNP
rs71513883 1194 dbSNP
rs1045556336 1199 dbSNP
rs905228561 1201 dbSNP
rs1180395854 1203 dbSNP
rs1012274660 1210 dbSNP
rs1481791507 1220 dbSNP
rs1253521709 1232 dbSNP
rs1205499858 1233 dbSNP
rs995901707 1246 dbSNP
rs770204196 1263 dbSNP
rs772861929 1264 dbSNP
rs559174499 1275 dbSNP
rs1424657401 1277 dbSNP
rs952110817 1287 dbSNP
rs1004974564 1288 dbSNP
rs1015382926 1293 dbSNP
rs1414439129 1294 dbSNP
rs1373906033 1300 dbSNP
rs1337988486 1308 dbSNP
rs961273557 1309 dbSNP
rs1286897267 1312 dbSNP
rs976546090 1315 dbSNP
rs1370758788 1316 dbSNP
rs1182406788 1324 dbSNP
rs1413591060 1324 dbSNP
rs1474651232 1327 dbSNP
rs1235405550 1333 dbSNP
rs1326605263 1333 dbSNP
rs1442792129 1333 dbSNP
rs532404568 1336 dbSNP
rs1019802271 1337 dbSNP
rs551011607 1337 dbSNP
rs953982956 1337 dbSNP
rs560720575 1345 dbSNP
rs188399228 1347 dbSNP
rs1449212008 1348 dbSNP
rs544752714 1348 dbSNP
rs968441391 1348 dbSNP
rs562933945 1349 dbSNP
rs923679653 1353 dbSNP
rs939531117 1354 dbSNP
rs869131758 1355 dbSNP
rs1056630626 1356 dbSNP
rs955967452 1356 dbSNP
rs2290274 1357 dbSNP
rs917122326 1359 dbSNP
rs1248583716 1362 dbSNP
rs1213081226 1363 dbSNP
rs1185646640 1365 dbSNP
rs1012515388 1366 dbSNP
rs542321701 1374 dbSNP
rs1049306739 1393 dbSNP
rs1292279898 1394 dbSNP
rs887786461 1395 dbSNP
rs948555945 1398 dbSNP
rs1045182547 1402 dbSNP
rs560506248 1407 dbSNP
rs1005289304 1417 dbSNP
rs1015043815 1427 dbSNP
rs966513272 1438 dbSNP
rs1048440544 1444 dbSNP
rs887073601 1446 dbSNP
rs940258477 1448 dbSNP
rs1435121091 1452 dbSNP
rs997532750 1453 dbSNP
rs1347667899 1455 dbSNP
rs191515983 1462 dbSNP
rs1405553019 1463 dbSNP
rs1418379845 1466 dbSNP
rs1328665843 1470 dbSNP
rs901374890 1479 dbSNP
rs1490508228 1482 dbSNP
rs9314350 1491 dbSNP
rs1192997356 1496 dbSNP
rs767527690 1498 dbSNP
rs1248567306 1499 dbSNP
rs571476369 1507 dbSNP
rs904287373 1511 dbSNP
rs111739642 1518 dbSNP
rs967775474 1525 dbSNP
rs978150824 1539 dbSNP
rs923740690 1540 dbSNP
rs1271379947 1542 dbSNP
rs939099245 1543 dbSNP
rs1056195804 1546 dbSNP
rs916755302 1550 dbSNP
rs1031303760 1556 dbSNP
rs955664609 1557 dbSNP
rs948161729 1559 dbSNP
rs868421696 1571 dbSNP
rs532293054 1572 dbSNP
rs142833631 1573 dbSNP
rs1436590617 1583 dbSNP
rs940729612 1585 dbSNP
rs1036752966 1586 dbSNP
rs1390614932 1590 dbSNP
rs183667500 1591 dbSNP
rs997565316 1594 dbSNP
rs1431327984 1595 dbSNP
rs1374847924 1597 dbSNP
rs1427205530 1602 dbSNP
rs920412530 1603 dbSNP
rs1476052450 1619 dbSNP
rs760530238 1621 dbSNP
rs889657464 1623 dbSNP
rs1249884015 1627 dbSNP
rs763804298 1635 dbSNP
rs1471169710 1640 dbSNP
rs1483573440 1642 dbSNP
rs868180657 1643 dbSNP
rs1006671881 1648 dbSNP
rs115748785 1652 dbSNP
rs372922296 1655 dbSNP
rs554208702 1656 dbSNP
rs78562015 1674 dbSNP
rs1314396511 1678 dbSNP
rs978014221 1680 dbSNP
rs1302592593 1682 dbSNP
rs758574396 1684 dbSNP
rs901402965 1685 dbSNP
rs1286049364 1692 dbSNP
rs766676082 1693 dbSNP
rs1370816148 1697 dbSNP
rs1319761573 1699 dbSNP
rs991909339 1705 dbSNP
rs1326502178 1710 dbSNP
rs1472297554 1711 dbSNP
rs1409909900 1717 dbSNP
rs1184573621 1727 dbSNP
rs1473014092 1728 dbSNP
rs1255756559 1731 dbSNP
rs916329453 1733 dbSNP
rs146100353 1744 dbSNP
rs1257087270 1749 dbSNP
rs1215771144 1759 dbSNP
rs1325511616 1761 dbSNP
rs985350206 1763 dbSNP
rs1223921777 1766 dbSNP
rs1229715757 1768 dbSNP
rs904653267 1784 dbSNP
rs1323160395 1786 dbSNP
rs377382935 1790 dbSNP
rs940953903 1791 dbSNP
rs1036583354 1798 dbSNP
rs1031377439 1805 dbSNP
rs1456675643 1807 dbSNP
rs553041972 1813 dbSNP
rs1457840828 1814 dbSNP
rs1005407798 1815 dbSNP
rs1163023055 1818 dbSNP
rs1425905753 1820 dbSNP
rs1257352533 1822 dbSNP
rs1264035099 1824 dbSNP
rs1463893624 1825 dbSNP
rs1013858954 1829 dbSNP
rs1447643187 1831 dbSNP
rs558997601 1833 dbSNP
rs1261663347 1839 dbSNP
rs1329320876 1859 dbSNP
rs1264479000 1861 dbSNP
rs755117673 1866 dbSNP
rs781656414 1868 dbSNP
rs1323253053 1870 dbSNP
rs1313110550 1873 dbSNP
rs577506856 1874 dbSNP
rs970393211 1890 dbSNP
rs1322547242 1895 dbSNP
rs370806417 1898 dbSNP
rs980010724 1908 dbSNP
rs1027903911 1911 dbSNP
rs889187610 1912 dbSNP
rs1459605959 1913 dbSNP
rs984237466 1915 dbSNP
rs1385148910 1918 dbSNP
rs1006750617 1927 dbSNP
rs1168284730 1930 dbSNP
rs1448048180 1931 dbSNP
rs1392559040 1941 dbSNP
rs1189839297 1942 dbSNP
rs1381163779 1950 dbSNP
rs1266103474 1957 dbSNP
rs908614215 1960 dbSNP
rs940026191 1964 dbSNP
rs1022568917 1979 dbSNP
rs538154005 1983 dbSNP
rs748296285 1995 dbSNP
rs1339874540 1999 dbSNP
rs999855610 2000 dbSNP
rs1329135212 2006 dbSNP
rs1330485397 2007 dbSNP
rs1231411849 2018 dbSNP
rs1049968797 2019 dbSNP
rs1391635079 2023 dbSNP
rs1030876868 2028 dbSNP
rs556826577 2030 dbSNP
rs1428201983 2035 dbSNP
rs1372845689 2037 dbSNP
rs1169748741 2039 dbSNP
rs1477964757 2048 dbSNP
rs575072845 2058 dbSNP
rs143633649 2063 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions BT474
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 GSM1395166. RNA binding protein: AGO. Condition:BT474 AGO HITS-CLIP Replicate 1 ...

- Pillai MM; Gillen AE; Yamamoto TM; Kline E; et al., 2014, Breast cancer research and treatment.

Article - Pillai MM; Gillen AE; Yamamoto TM; Kline E; et al.
- Breast cancer research and treatment, 2014
miRNAs regulate the expression of genes in both normal physiology and disease. While miRNAs have been demonstrated to play a pivotal role in aspects of cancer biology, these reports have generally focused on the regulation of single genes. Such single-gene approaches have significant limitations, relying on miRNA expression levels and heuristic predictions of mRNA-binding sites. This results in only circumstantial evidence of miRNA-target interaction and typically leads to large numbers of false positive predictions. Here, we used a genome-wide approach (high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation, HITS-CLIP) to define direct miRNA-mRNA interactions in three breast cancer subtypes (estrogen receptor positive, Her2 amplified, and triple negative). Focusing on steroid receptor signaling, we identified two novel regulators of the ER pathway (miR-9-5p and miR-193a/b-3p), which together target multiple genes involved in ER signaling. Moreover, this approach enabled the definition of miR-9-5p as a global regulator of steroid receptor signaling in breast cancer. We show that miRNA targets and networks defined by HITS-CLIP under physiologic conditions are predictive of patient outcomes and provide global insight into miRNA regulation in breast cancer.
LinkOut: [PMID: 24906430]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Cardiac Tissues
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 GSM2202481. RNA binding protein: AGO2. Condition:S6_LV_61yo_Male_AGO2_bound_RNA ...

- Spengler RM; Zhang X; Cheng C; McLendon JM; et al., 2016, Nucleic acids research.

Article - Spengler RM; Zhang X; Cheng C; McLendon JM; et al.
- Nucleic acids research, 2016
MicroRNAs (miRs) have emerged as key biological effectors in human health and disease. These small noncoding RNAs are incorporated into Argonaute (Ago) proteins, where they direct post-transcriptional gene silencing via base-pairing with target transcripts. Although miRs have become intriguing biological entities and attractive therapeutic targets, the translational impacts of miR research remain limited by a paucity of empirical miR targeting data, particularly in human primary tissues. Here, to improve our understanding of the diverse roles miRs play in cardiovascular function and disease, we applied high-throughput methods to globally profile miR:target interactions in human heart tissues. We deciphered Ago2:RNA interactions using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across >2200 target transcripts. Our initial exploration of this interactome revealed an abundance of miR target sites in gene coding regions, including several sites pointing to new miR-29 functions in regulating cardiomyocyte calcium, growth and metabolism. Also, we uncovered several clinically-relevant interactions involving common genetic variants that alter miR targeting events in cardiomyopathy-associated genes. Overall, these data provide a critical resource for bolstering translational miR research in heart, and likely beyond.
LinkOut: [PMID: 27418678]
CLIP-seq Support 1 for dataset GSM1395166
Method / RBP HITS-CLIP / AGO
Cell line / Condition BT474 / BT474 AGO HITS-CLIP Replicate 1
Location of target site ENST00000356766.6 | 3UTR | CUUUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUCUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24906430 / GSE57855
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
168 hsa-miR-548t-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059365 ANP32E acidic nuclear phosphoprotein 32 family member E 2 2
MIRT072839 ARIH1 ariadne RBR E3 ubiquitin protein ligase 1 2 6
MIRT076945 PCGF2 polycomb group ring finger 2 2 6
MIRT083941 TFAP2C transcription factor AP-2 gamma 2 2
MIRT085401 ETS2 ETS proto-oncogene 2, transcription factor 2 2
MIRT109790 KLHL15 kelch like family member 15 2 2
MIRT114046 AKAP11 A-kinase anchoring protein 11 2 10
MIRT130165 TXNIP thioredoxin interacting protein 2 6
MIRT150013 MIDN midnolin 2 2
MIRT181258 ASH1L ASH1 like histone lysine methyltransferase 2 2
MIRT205594 NCL nucleolin 2 2
MIRT222253 ACTB actin beta 2 4
MIRT245653 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 4
MIRT250947 CDK5R1 cyclin dependent kinase 5 regulatory subunit 1 2 4
MIRT252497 NWD1 NACHT and WD repeat domain containing 1 2 2
MIRT271990 ARF1 ADP ribosylation factor 1 2 4
MIRT280804 RNF11 ring finger protein 11 2 2
MIRT293803 FEM1A fem-1 homolog A 2 2
MIRT318231 RREB1 ras responsive element binding protein 1 2 2
MIRT341455 ATP6V0B ATPase H+ transporting V0 subunit b 2 2
MIRT347413 CEBPG CCAAT/enhancer binding protein gamma 2 4
MIRT351860 PLEKHA3 pleckstrin homology domain containing A3 2 2
MIRT357983 GRPEL2 GrpE like 2, mitochondrial 2 2
MIRT377094 PPP1CB protein phosphatase 1 catalytic subunit beta 2 2
MIRT407303 IGFBP5 insulin like growth factor binding protein 5 2 2
MIRT441564 LMOD3 leiomodin 3 2 2
MIRT442364 ZC3H12C zinc finger CCCH-type containing 12C 2 2
MIRT443228 ARL5B ADP ribosylation factor like GTPase 5B 2 2
MIRT443404 HMX3 H6 family homeobox 3 2 2
MIRT446055 NR5A2 nuclear receptor subfamily 5 group A member 2 2 2
MIRT448277 ZNF652 zinc finger protein 652 2 2
MIRT450822 KCNB1 potassium voltage-gated channel subfamily B member 1 2 2
MIRT453016 CCDC115 coiled-coil domain containing 115 2 17
MIRT454463 PPP2R2B protein phosphatase 2 regulatory subunit Bbeta 2 2
MIRT456360 CITED2 Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 2 2 2
MIRT460007 DNALI1 dynein axonemal light intermediate chain 1 2 2
MIRT463154 ZNF385A zinc finger protein 385A 2 6
MIRT463766 YPEL2 yippee like 2 2 2
MIRT468310 SFT2D2 SFT2 domain containing 2 2 2
MIRT470668 POLR2D RNA polymerase II subunit D 2 4
MIRT478517 CTTN cortactin 2 2
MIRT480507 C11orf57 chromosome 11 open reading frame 57 2 2
MIRT484718 INHBA inhibin beta A subunit 2 12
MIRT485494 HMGN2 high mobility group nucleosomal binding domain 2 2 2
MIRT487302 SLC38A9 solute carrier family 38 member 9 2 2
MIRT487771 ANKEF1 ankyrin repeat and EF-hand domain containing 1 2 16
MIRT491876 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta 2 2
MIRT494304 CEP120 centrosomal protein 120 2 2
MIRT495396 TRIM24 tripartite motif containing 24 2 2
MIRT495646 CDK1 cyclin dependent kinase 1 2 2
MIRT496665 TMEM237 transmembrane protein 237 2 2
MIRT496837 ZNF460 zinc finger protein 460 2 2
MIRT498638 CHD4 chromodomain helicase DNA binding protein 4 2 10
MIRT503928 FBXL13 F-box and leucine rich repeat protein 13 2 4
MIRT506063 PPP2R2A protein phosphatase 2 regulatory subunit Balpha 2 2
MIRT506582 MIER3 MIER family member 3 2 4
MIRT506606 MAT2A methionine adenosyltransferase 2A 2 4
MIRT506844 KIF23 kinesin family member 23 2 6
MIRT508536 RPP14 ribonuclease P/MRP subunit p14 2 4
MIRT509669 ZNF354B zinc finger protein 354B 2 10
MIRT511170 MBNL3 muscleblind like splicing regulator 3 2 6
MIRT512147 COX6B1 cytochrome c oxidase subunit 6B1 2 2
MIRT512831 ID4 inhibitor of DNA binding 4, HLH protein 2 6
MIRT514558 XRCC3 X-ray repair cross complementing 3 2 4
MIRT515856 AJAP1 adherens junctions associated protein 1 2 4
MIRT521848 PNISR PNN interacting serine and arginine rich protein 2 4
MIRT525364 SYNM synemin 2 2
MIRT527120 ARHGAP15 Rho GTPase activating protein 15 2 2
MIRT527271 FBLN2 fibulin 2 2 2
MIRT527439 COL4A3 collagen type IV alpha 3 chain 2 2
MIRT527658 CD300E CD300e molecule 2 2
MIRT528334 TBC1D22B TBC1 domain family member 22B 2 2
MIRT529033 EXOC8 exocyst complex component 8 2 2
MIRT529321 PDE5A phosphodiesterase 5A 2 2
MIRT529677 TRPV2 transient receptor potential cation channel subfamily V member 2 2 2
MIRT529846 SMTN smoothelin 2 2
MIRT530385 ZNF431 zinc finger protein 431 2 2
MIRT530913 GPR85 G protein-coupled receptor 85 2 2
MIRT531794 KDR kinase insert domain receptor 2 2
MIRT532246 KLF2 Kruppel like factor 2 2 4
MIRT532658 CBX7 chromobox 7 2 2
MIRT533630 TMX3 thioredoxin related transmembrane protein 3 2 2
MIRT534811 RAB33B RAB33B, member RAS oncogene family 2 2
MIRT534975 PSD3 pleckstrin and Sec7 domain containing 3 2 2
MIRT536588 ITPKB inositol-trisphosphate 3-kinase B 2 2
MIRT536779 HNRNPD heterogeneous nuclear ribonucleoprotein D 2 2
MIRT538764 CABLES1 Cdk5 and Abl enzyme substrate 1 2 2
MIRT539294 ANGEL2 angel homolog 2 2 2
MIRT539621 SHISA9 shisa family member 9 2 2
MIRT539651 BUB1 BUB1 mitotic checkpoint serine/threonine kinase 2 2
MIRT540347 OPHN1 oligophrenin 1 2 2
MIRT540413 PITPNC1 phosphatidylinositol transfer protein, cytoplasmic 1 2 2
MIRT541396 CDC27 cell division cycle 27 2 2
MIRT542916 HSBP1 heat shock factor binding protein 1 2 2
MIRT544710 EIF5A eukaryotic translation initiation factor 5A 2 4
MIRT544998 MFF mitochondrial fission factor 2 4
MIRT553289 TSPAN3 tetraspanin 3 2 2
MIRT553455 TNRC6C trinucleotide repeat containing 6C 2 2
MIRT553782 TAF13 TATA-box binding protein associated factor 13 2 2
MIRT554656 ROBO1 roundabout guidance receptor 1 2 2
MIRT555104 PURB purine rich element binding protein B 2 2
MIRT557235 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 2 2
MIRT560861 GAL3ST3 galactose-3-O-sulfotransferase 3 2 2
MIRT561545 SON SON DNA binding protein 2 2
MIRT561554 SLMO2 PRELI domain containing 3B 2 2
MIRT563764 ZNF678 zinc finger protein 678 2 2
MIRT565653 SIX4 SIX homeobox 4 2 2
MIRT568080 CELF2 CUGBP Elav-like family member 2 2 2
MIRT568759 MYBL1 MYB proto-oncogene like 1 2 2
MIRT569078 CADM2 cell adhesion molecule 2 2 2
MIRT569509 THYN1 thymocyte nuclear protein 1 2 2
MIRT571268 CDKN2AIP CDKN2A interacting protein 2 2
MIRT571809 PHF19 PHD finger protein 19 2 2
MIRT572554 DKK3 dickkopf WNT signaling pathway inhibitor 3 2 2
MIRT573782 SLC24A4 solute carrier family 24 member 4 2 4
MIRT576441 Ccdc115 coiled-coil domain containing 115 2 10
MIRT576712 Slc30a3 solute carrier family 30 (zinc transporter), member 3 2 3
MIRT608377 PIWIL2 piwi like RNA-mediated gene silencing 2 2 2
MIRT608484 NKTR natural killer cell triggering receptor 2 6
MIRT610186 FAM49A family with sequence similarity 49 member A 2 2
MIRT611631 EDIL3 EGF like repeats and discoidin domains 3 2 2
MIRT613534 TRA2B transformer 2 beta homolog 2 2
MIRT616221 PTPN11 protein tyrosine phosphatase, non-receptor type 11 2 2
MIRT622370 SALL1 spalt like transcription factor 1 2 2
MIRT624371 CDK12 cyclin dependent kinase 12 2 2
MIRT624995 ZNF665 zinc finger protein 665 2 4
MIRT626875 AP3B1 adaptor related protein complex 3 beta 1 subunit 2 2
MIRT627737 RAP2B RAP2B, member of RAS oncogene family 2 4
MIRT628490 ADAT2 adenosine deaminase, tRNA specific 2 2 2
MIRT633647 PLEKHG7 pleckstrin homology and RhoGEF domain containing G7 2 4
MIRT634028 SLC30A3 solute carrier family 30 member 3 2 3
MIRT635923 GLTSCR2 NOP53 ribosome biogenesis factor 2 2
MIRT638287 SERBP1 SERPINE1 mRNA binding protein 1 2 2
MIRT641959 RNF115 ring finger protein 115 2 2
MIRT643573 CTNNA3 catenin alpha 3 2 2
MIRT645180 NOL9 nucleolar protein 9 2 4
MIRT647497 ZNF639 zinc finger protein 639 2 2
MIRT647682 PCK1 phosphoenolpyruvate carboxykinase 1 2 2
MIRT648422 MYOZ3 myozenin 3 2 2
MIRT650113 ZCCHC9 zinc finger CCHC-type containing 9 2 2
MIRT651076 ZNF518B zinc finger protein 518B 2 4
MIRT651415 ZADH2 zinc binding alcohol dehydrogenase domain containing 2 2 2
MIRT651456 XKR4 XK related 4 2 2
MIRT653619 SLC30A4 solute carrier family 30 member 4 2 2
MIRT653637 SLC30A1 solute carrier family 30 member 1 2 2
MIRT654896 POU2F1 POU class 2 homeobox 1 2 2
MIRT656483 MAP3K9 mitogen-activated protein kinase kinase kinase 9 2 2
MIRT658016 GABRA4 gamma-aminobutyric acid type A receptor alpha4 subunit 2 2
MIRT658041 FZD10 frizzled class receptor 10 2 2
MIRT660093 BTBD3 BTB domain containing 3 2 2
MIRT663923 MAGEF1 MAGE family member F1 2 2
MIRT665882 TGIF2 TGFB induced factor homeobox 2 2 2
MIRT669051 CEP128 centrosomal protein 128 2 2
MIRT669711 AAGAB alpha and gamma adaptin binding protein 2 2
MIRT686812 SNX2 sorting nexin 2 2 4
MIRT689883 SOD2 superoxide dismutase 2 2 2
MIRT693274 GLRX2 glutaredoxin 2 2 4
MIRT697056 BCAR1 BCAR1, Cas family scaffolding protein 2 2
MIRT703297 GID4 GID complex subunit 4 homolog 2 2
MIRT704087 DYRK2 dual specificity tyrosine phosphorylation regulated kinase 2 2 2
MIRT707719 CDC6 cell division cycle 6 2 2
MIRT708136 GK5 glycerol kinase 5 (putative) 2 2
MIRT709212 KLHL30 kelch like family member 30 2 2
MIRT710062 RWDD2A RWD domain containing 2A 2 2
MIRT712770 POU6F2 POU class 6 homeobox 2 2 2
MIRT715073 TMTC1 transmembrane and tetratricopeptide repeat containing 1 2 2
MIRT715387 TADA3 transcriptional adaptor 3 2 2
MIRT717712 NCKAP1 NCK associated protein 1 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-548t Paclitaxel 36314 NSC125973 approved sensitive cell line (W1)
hsa-mir-548t Cisplatin 5460033 NSC119875 approved sensitive cell line (W1)
hsa-mir-548t Doxorubicin 31703 NSC123127 approved sensitive cell line (W1)
hsa-mir-548t Topotecan 60699 NSC609699 approved sensitive cell line (W1)
hsa-mir-548t Vincristine 5978 approved sensitive cell line (W1)
hsa-miR-548t-3p Oxaliplatin 6857599 NSC266046 approved sensitive High Colorectal Cancer cell line (SW480, HCT-116)
hsa-miR-548t-3p Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-548t-3p Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)

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