miRTarBase - #MIRT176908


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pre-miRNA Information
pre-miRNA hsa-mir-548g   
Genomic Coordinates chr4: 147344629 - 147344717
Synonyms MIRN548G, hsa-mir-548g, MIR548G
Description Homo sapiens miR-548g stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-548g-3p
Sequence 54| AAAACUGUAAUUACUUUUGUAC |75
Evidence Experimental
Experiments Illumina
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 13 4 - 147344652 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs754839148 7 dbSNP
rs1265742987 13 dbSNP
rs1282926622 15 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TRUB1   
Synonyms PUS4
Description TruB pseudouridine synthase family member 1
Transcript NM_139169   
Expression
Putative miRNA Targets on TRUB1
3'UTR of TRUB1
(miRNA target sites are highlighted)		 
>TRUB1|NM_139169|3'UTR
   1 GATTGGCCTGGGAATATCATCATTTTCTAGTTGACATTTGAATCCTGTGTGCAGATGCAGAATGACAAGCTGCATTCAAA
  81 AGACAAACAATATGTCTTTTTTTTTTTTGCATGAAGAAAAATGTCTATCATTTACAGTTTCAATAGCACATAATTTATTT
 161 TCTATGCATTATAAATGGCCTTGCAGTTGGCTCAGTTGTTTGTTGTGTTGTGAAATGTTTTAGGATTTTTTGTATTGTGA
 241 AAATATGAATATGATTGGATTCAGAAAAATTAACTTTCTGAATTTGATCTGTCTTCAGTCTTGTGAAAAAGTTGAACAAA
 321 TTTCCTAATCAAAGAAAAAAGTATGAGCTCCATGTTTCTTTAGTTTCACAAAAATGACCATAATTTAGTGTTATTTTTAC
 401 TTTATTTAGGCTTCCTGGTGGCTTCATTTTATTGAAATTCTTTAAATTGTTTAAAGTGGCCATTATTGATCTCTTTCTTC
 481 TGTTTTGGAGAGTTTATTATTAAAAACATTTCTTTGATAAAATGGCCATCATCTAGTAATACCTGTGTTTGTTTAGATCT
 561 TGGAAATGAATAAGCTTTGATAATATTTGTAAATGAACCAAATTATTACTGCTACCACTAACAGGTTGTAAATAGAAGAC
 641 TAATACTTAATTAAAGTCACCTTCCTACCATTAGAGCAGAAGACAGCTCCTATAGTTTTGTATTTTGGCAGCTATGAGAT
 721 ATTTTCATGGTAATGTCAACATGGTCAAGCACTTTGTACCAAGTTATTAAGTAACATAATTTTTAAAATTTAAAGAATGT
 801 GTCTTCAACTAAAAACTTTATTCTTTAGCATTTATTTATATTTCTCTGTAGGGTGTTCCCTGTGACATTGTCTCTTTAGT
 881 TTGCTCTTTCAAGAGATACTTACAGATGTTGAGATGGCTGCCCTGCATTTCCAGCTAATCTCTTCTGCTCTAAATATTTA
 961 AAAACAGTTCTTCTCAAACATTTTCATTCAGATAGCTTTCTGAAAGTTCCCTATCCCTCTTTACCATAATTTTTTAAATG
1041 TAGCCACATTGTAATAGTAAACTTCATATATAATGAGTGCTTCATATTTTTGTTATGGGAAAGCAATATATTATGCAGCC
1121 AGTCTGTAGAAACATTCAGATCCCTCTTCCTTTACTCAAATACAGTTTCAAAAGGAAGACTCATGAGAAATTTCATAAAA
1201 TACAAGTTTTTAGATGTTTATGCTTTGCCTTTCTTTTTAAAGGTGTTTTCCTGCTTTGTAGTCTCTAACTCTGAAATTTA
1281 AAATATGTAAACTAAAGTGGTTTTATTTGTGCTTAACCCAATTTAAACTCAATGTAAAATGTTATATATGCATCAGTACA
1361 GCATTTTCAACATATTGGCAACATATTTTAAATGAAAACACTAAAACAATTCTTAGTATGAGACAAAACTGTAAGGAAAA
1441 AGAGTGTTAATACCATGATGCATTAACATAAAATATCAAACACACAAAGTCATAAAATGAAAATTTACAGTTTTACCTGT
1521 TCATATCTAGTGCCCCACAGTGTGTGTCAACCAAAGGTGGCAGTGGCTACATCTGCCTGTTGGACTGGTACAGGTTACAA
1601 TATGTCCTCTTCCATTGCAAATTAAAGTCCAAATAGAGAAATACTTAGGTTTTAGAACACATCAGAGGTATTTCTGCTGT
1681 ATTTTTCACCTTAAAAATTGACACAGAGTTTACTAATAGAGGAGTAGAGATTGTTGACCATTTTTAAAAAACGATAGCCA
1761 CTCTTTTTCTTTTATGTTTAAAACTGAAGTTTTGCCAAATGGGAAAATTACTGTTACCTCTACCATCTTAATGTAGTAAC
1841 TTTAGAATTTAAATTTTTATATTACTATTTTCCTTTTTGTTGTTCACATAGTCTTAAGGCACCTATACTTTTAAATTGAC
1921 TTTTTCATTTGATATTATCTATATGTATGTAGTTGTGATAATGATTATTTTAATTATATTACTTTATACTCTTAATTTAT
2001 TTAGAGTATTTCTCTATTGCTGAATACTTAAGTAGTTTTAAATTTTATTATGATAAATTCCTGGGAGGGGGATTATTTAG
2081 TGAAATAATATGAAGAACTTTATGACTTATGTTTGCCTTATTGCATTCCCAAAGAGTTGTAACATTTTACAGTGTTACCA
2161 TTTGAGTAGGGGTTTTATATGTTGTTGCTAATTTAGTAAACATAGGAGAGAAATCAAAGTTTTTCTGATTTGCTTTTATG
2241 TGATTTATCTGTATACTTTGTTCATTTATATAAATAAATGTCTTAATGGTTTCTATACATA
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' caUGUUUU-CAUU--AAUGUCAAAa 5'
            |:|||| | ||  ||||||||| 
Target 5' tcATAAAATGAAAATTTACAGTTTt 3'
 1490 - 1514 170.00 -8.50
2 
miRNA  3' caUGUUUUCA-----UUAAUGUCAAAa 5'
            | ||| ||     | ||||||||| 
Target 5' agAAAAATGTCTATCATTTACAGTTTc 3'
 115 - 141 160.00 -6.80
3 
miRNA  3' cauguuuucaUUAAUGUCAAAa 5'
                    || |||||||| 
Target 5' tcctttactcAAATACAGTTTc 3'
 1148 - 1169 152.00 -6.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31523643 10 COSMIC
COSN30491141 11 COSMIC
COSN31497253 17 COSMIC
COSN27855128 19 COSMIC
COSN30189817 40 COSMIC
COSN30154457 46 COSMIC
COSN30528151 88 COSMIC
COSN31600558 90 COSMIC
COSN20107600 109 COSMIC
COSN29023368 109 COSMIC
COSN30101785 126 COSMIC
COSN30462599 126 COSMIC
COSN30148074 142 COSMIC
COSN30532417 146 COSMIC
COSN1472242 153 COSMIC
COSN5278597 224 COSMIC
COSN29864966 249 COSMIC
COSN26584847 731 COSMIC
COSN31529602 804 COSMIC
COSN20107603 858 COSMIC
COSN27757538 2110 COSMIC
COSN27757549 2111 COSMIC
COSN20225932 2225 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs188877724 2 dbSNP
rs769683844 4 dbSNP
rs373579925 7 dbSNP
rs1448851372 9 dbSNP
rs1391358274 17 dbSNP
rs1387175407 18 dbSNP
rs367763476 18 dbSNP
rs932835537 20 dbSNP
rs762386127 28 dbSNP
rs570417032 30 dbSNP
rs756392899 37 dbSNP
rs777765996 45 dbSNP
rs761409331 49 dbSNP
rs1225933763 52 dbSNP
rs1299685467 53 dbSNP
rs891234485 55 dbSNP
rs913511307 56 dbSNP
rs1178786585 58 dbSNP
rs1236130845 60 dbSNP
rs1442039994 71 dbSNP
rs1251735887 73 dbSNP
rs1193367857 77 dbSNP
rs1452603370 78 dbSNP
rs1269925799 83 dbSNP
rs1202927519 85 dbSNP
rs1439051303 90 dbSNP
rs1349539383 97 dbSNP
rs35714321 97 dbSNP
rs397824028 97 dbSNP
rs1174162890 109 dbSNP
rs1302663516 109 dbSNP
rs1345603169 109 dbSNP
rs1396759001 110 dbSNP
rs1416273721 111 dbSNP
rs753679087 112 dbSNP
rs1358818973 114 dbSNP
rs1360161652 117 dbSNP
rs1443191628 117 dbSNP
rs1298866041 122 dbSNP
rs757008642 128 dbSNP
rs369521836 136 dbSNP
rs1393790942 151 dbSNP
rs1300343108 157 dbSNP
rs116249739 165 dbSNP
rs780380796 167 dbSNP
rs1304846945 186 dbSNP
rs1350596159 199 dbSNP
rs7071789 204 dbSNP
rs1050172726 208 dbSNP
rs1218155783 218 dbSNP
rs995873834 224 dbSNP
rs1484438657 226 dbSNP
rs755442598 248 dbSNP
rs538551300 258 dbSNP
rs1307781902 264 dbSNP
rs1219668630 275 dbSNP
rs1347077846 281 dbSNP
rs111283639 285 dbSNP
rs1006039165 288 dbSNP
rs1036586205 290 dbSNP
rs1206145667 315 dbSNP
rs1279158324 331 dbSNP
rs1340088999 331 dbSNP
rs1255973343 340 dbSNP
rs149219476 344 dbSNP
rs897636807 345 dbSNP
rs1333624319 346 dbSNP
rs79799745 358 dbSNP
rs1193986561 367 dbSNP
rs1405043845 370 dbSNP
rs1013442804 375 dbSNP
rs1166485132 380 dbSNP
rs1476968740 381 dbSNP
rs1423876718 397 dbSNP
rs1024793971 413 dbSNP
rs111561407 421 dbSNP
rs1195325224 424 dbSNP
rs1024860459 427 dbSNP
rs971392838 449 dbSNP
rs1001532137 463 dbSNP
rs1034465790 466 dbSNP
rs977857862 470 dbSNP
rs924978318 471 dbSNP
rs1424549562 472 dbSNP
rs957737594 479 dbSNP
rs1318256507 482 dbSNP
rs1259755739 484 dbSNP
rs1173116664 487 dbSNP
rs554875052 493 dbSNP
rs570036995 510 dbSNP
rs1353818978 515 dbSNP
rs913409318 516 dbSNP
rs143216263 524 dbSNP
rs921549379 536 dbSNP
rs967543017 544 dbSNP
rs1327501121 546 dbSNP
rs1326926856 552 dbSNP
rs1465576269 556 dbSNP
rs370893108 557 dbSNP
rs1401398649 567 dbSNP
rs1333387833 590 dbSNP
rs932887838 594 dbSNP
rs1434937179 599 dbSNP
rs571729290 602 dbSNP
rs912723033 611 dbSNP
rs1412688229 614 dbSNP
rs1181908235 615 dbSNP
rs923484853 623 dbSNP
rs1231093311 645 dbSNP
rs1177855619 653 dbSNP
rs1362012669 653 dbSNP
rs931684448 660 dbSNP
rs1050037388 665 dbSNP
rs1320108710 669 dbSNP
rs1289514455 670 dbSNP
rs1228948187 671 dbSNP
rs908990370 673 dbSNP
rs1277860023 674 dbSNP
rs1446651509 675 dbSNP
rs148296541 682 dbSNP
rs371358824 693 dbSNP
rs1439218474 712 dbSNP
rs1348942381 717 dbSNP
rs1316845085 720 dbSNP
rs1165116976 722 dbSNP
rs941794051 726 dbSNP
rs1214113004 728 dbSNP
rs957045228 730 dbSNP
rs1274801313 734 dbSNP
rs1440207972 740 dbSNP
rs1239986006 743 dbSNP
rs770282700 747 dbSNP
rs757885892 749 dbSNP
rs1247079097 750 dbSNP
rs1222502791 751 dbSNP
rs1453573533 752 dbSNP
rs898539635 759 dbSNP
rs776273584 767 dbSNP
rs1283913397 780 dbSNP
rs577224455 788 dbSNP
rs780439178 791 dbSNP
rs1220704797 795 dbSNP
rs1355016840 796 dbSNP
rs541561655 802 dbSNP
rs1475798883 817 dbSNP
rs552882783 820 dbSNP
rs1046787096 821 dbSNP
rs1367275550 833 dbSNP
rs542284583 835 dbSNP
rs1294516919 840 dbSNP
rs895085220 842 dbSNP
rs1013494997 850 dbSNP
rs905101711 851 dbSNP
rs1001563182 854 dbSNP
rs1419849764 856 dbSNP
rs10687517 857 dbSNP
rs10674304 858 dbSNP
rs373685025 859 dbSNP
rs1171615721 872 dbSNP
rs141439536 877 dbSNP
rs1425561060 888 dbSNP
rs544968508 893 dbSNP
rs542124190 899 dbSNP
rs1323506604 903 dbSNP
rs1346266898 904 dbSNP
rs1488694239 908 dbSNP
rs1012088381 910 dbSNP
rs563544592 911 dbSNP
rs769621091 914 dbSNP
rs999734766 922 dbSNP
rs530839902 924 dbSNP
rs1339508169 925 dbSNP
rs1406708298 928 dbSNP
rs775395402 936 dbSNP
rs1337954497 938 dbSNP
rs958004930 941 dbSNP
rs1277243356 963 dbSNP
rs1400240316 964 dbSNP
rs974460826 966 dbSNP
rs1361821284 968 dbSNP
rs1028603309 985 dbSNP
rs1465442981 1008 dbSNP
rs1359722555 1011 dbSNP
rs1177932386 1025 dbSNP
rs560922674 1036 dbSNP
rs1426591871 1044 dbSNP
rs1421743385 1055 dbSNP
rs777018847 1063 dbSNP
rs41317246 1069 dbSNP
rs1478275420 1070 dbSNP
rs987010727 1082 dbSNP
rs1265362219 1087 dbSNP
rs1353970549 1095 dbSNP
rs1227485934 1097 dbSNP
rs1212668205 1106 dbSNP
rs1284872459 1107 dbSNP
rs1257825743 1108 dbSNP
rs1218817766 1109 dbSNP
rs1342016059 1114 dbSNP
rs564111883 1116 dbSNP
rs1309932193 1118 dbSNP
rs1394986930 1125 dbSNP
rs1448601707 1135 dbSNP
rs1304578135 1143 dbSNP
rs1218960154 1146 dbSNP
rs1464014952 1153 dbSNP
rs1399194219 1155 dbSNP
rs1171169556 1159 dbSNP
rs986322114 1160 dbSNP
rs1413161548 1161 dbSNP
rs1426092399 1170 dbSNP
rs908897577 1171 dbSNP
rs1423378276 1177 dbSNP
rs1256966638 1178 dbSNP
rs941673013 1183 dbSNP
rs972228628 1190 dbSNP
rs1488108852 1206 dbSNP
rs1188895360 1209 dbSNP
rs138352069 1215 dbSNP
rs1263381500 1222 dbSNP
rs1243421159 1224 dbSNP
rs1472032856 1230 dbSNP
rs1314260521 1234 dbSNP
rs73372680 1236 dbSNP
rs1409373780 1241 dbSNP
rs566125081 1246 dbSNP
rs530205033 1259 dbSNP
rs1398887379 1265 dbSNP
rs1448802874 1265 dbSNP
rs931369865 1268 dbSNP
rs1161621038 1272 dbSNP
rs937927728 1287 dbSNP
rs1053674730 1290 dbSNP
rs1438361066 1312 dbSNP
rs1380267836 1318 dbSNP
rs1179650737 1321 dbSNP
rs548390883 1323 dbSNP
rs141707421 1351 dbSNP
rs1055159354 1353 dbSNP
rs774097513 1357 dbSNP
rs1011536527 1364 dbSNP
rs949318503 1369 dbSNP
rs1046346883 1370 dbSNP
rs145705275 1371 dbSNP
rs902404522 1373 dbSNP
rs999386480 1379 dbSNP
rs1352888166 1381 dbSNP
rs143426603 1387 dbSNP
rs1329069784 1395 dbSNP
rs1322685521 1399 dbSNP
rs1386378087 1401 dbSNP
rs1355848584 1404 dbSNP
rs1305000465 1420 dbSNP
rs1418016604 1421 dbSNP
rs1360435313 1458 dbSNP
rs1032574796 1462 dbSNP
rs537352130 1464 dbSNP
rs558680805 1469 dbSNP
rs1376247270 1476 dbSNP
rs1284031756 1477 dbSNP
rs193223551 1484 dbSNP
rs1028655437 1488 dbSNP
rs954381590 1499 dbSNP
rs953517874 1501 dbSNP
rs987062971 1517 dbSNP
rs375220059 1518 dbSNP
rs986356299 1519 dbSNP
rs1286113430 1520 dbSNP
rs1218650744 1523 dbSNP
rs1019836533 1524 dbSNP
rs1274005407 1544 dbSNP
rs961906595 1561 dbSNP
rs1331897237 1568 dbSNP
rs963416670 1572 dbSNP
rs972948953 1578 dbSNP
rs1359910954 1584 dbSNP
rs534795507 1592 dbSNP
rs1298917364 1595 dbSNP
rs1402907740 1598 dbSNP
rs1400759179 1601 dbSNP
rs1456629821 1605 dbSNP
rs920072734 1625 dbSNP
rs1466923953 1630 dbSNP
rs1190966619 1631 dbSNP
rs1477307777 1639 dbSNP
rs1258539117 1646 dbSNP
rs971750484 1655 dbSNP
rs931446566 1666 dbSNP
rs1233816006 1680 dbSNP
rs990899300 1681 dbSNP
rs1442132295 1682 dbSNP
rs1346791950 1693 dbSNP
rs916627342 1702 dbSNP
rs542727702 1705 dbSNP
rs981831257 1707 dbSNP
rs1278901855 1708 dbSNP
rs1157364368 1709 dbSNP
rs1433059083 1714 dbSNP
rs949380612 1718 dbSNP
rs1339210575 1726 dbSNP
rs1380178367 1737 dbSNP
rs926455576 1744 dbSNP
rs1397122780 1746 dbSNP
rs1046409366 1747 dbSNP
rs1169010927 1752 dbSNP
rs376356913 1753 dbSNP
rs1434799313 1754 dbSNP
rs1173758196 1756 dbSNP
rs902457082 1759 dbSNP
rs184402076 1760 dbSNP
rs78889955 1763 dbSNP
rs1236401828 1770 dbSNP
rs1188089702 1788 dbSNP
rs1378807798 1793 dbSNP
rs1236085325 1795 dbSNP
rs1197837183 1797 dbSNP
rs41299149 1799 dbSNP
rs1308485910 1812 dbSNP
rs1259007423 1820 dbSNP
rs995986154 1844 dbSNP
rs1045657 1848 dbSNP
rs1257809951 1856 dbSNP
rs1343184996 1867 dbSNP
rs575559413 1868 dbSNP
rs1329689275 1873 dbSNP
rs1259171050 1875 dbSNP
rs57841310 1881 dbSNP
rs903159657 1889 dbSNP
rs997570229 1891 dbSNP
rs1459377329 1903 dbSNP
rs1008535026 1906 dbSNP
rs774285526 1909 dbSNP
rs367776095 1917 dbSNP
rs961680034 1918 dbSNP
rs1378453645 1921 dbSNP
rs1455069991 1921 dbSNP
rs994817524 1923 dbSNP
rs1027191615 1926 dbSNP
rs1016506840 1932 dbSNP
rs1206838393 1938 dbSNP
rs546124789 1942 dbSNP
rs1450105699 1949 dbSNP
rs1289211393 1958 dbSNP
rs963648206 1964 dbSNP
rs990951694 1978 dbSNP
rs1375427464 1989 dbSNP
rs1244775054 1992 dbSNP
rs1465287005 1992 dbSNP
rs1168151599 1993 dbSNP
rs1348997522 1995 dbSNP
rs756303199 2002 dbSNP
rs970785202 2006 dbSNP
rs982140295 2007 dbSNP
rs1025995549 2013 dbSNP
rs1157901827 2028 dbSNP
rs1440269978 2033 dbSNP
rs1463897629 2037 dbSNP
rs766625520 2039 dbSNP
rs1330368068 2050 dbSNP
rs549393535 2061 dbSNP
rs1189300650 2064 dbSNP
rs1477144397 2066 dbSNP
rs1388412174 2067 dbSNP
rs970768514 2068 dbSNP
rs945837977 2072 dbSNP
rs981865446 2073 dbSNP
rs926321481 2083 dbSNP
rs1282767870 2098 dbSNP
rs1318073960 2111 dbSNP
rs1309581546 2114 dbSNP
rs935302737 2119 dbSNP
rs1329402605 2124 dbSNP
rs187694487 2130 dbSNP
rs570906644 2138 dbSNP
rs989305015 2139 dbSNP
rs915167412 2142 dbSNP
rs1337715366 2149 dbSNP
rs1297063817 2157 dbSNP
rs1420205925 2159 dbSNP
rs1279079696 2164 dbSNP
rs1346934056 2168 dbSNP
rs915129395 2173 dbSNP
rs1173688714 2180 dbSNP
rs1320217087 2190 dbSNP
rs945332500 2199 dbSNP
rs1200325179 2204 dbSNP
rs931828544 2206 dbSNP
rs1257791940 2207 dbSNP
rs1042669761 2216 dbSNP
rs1261062950 2218 dbSNP
rs1193107564 2224 dbSNP
rs1050192948 2225 dbSNP
rs924644175 2226 dbSNP
rs890227002 2240 dbSNP
rs1489133226 2242 dbSNP
rs572829038 2246 dbSNP
rs1008587676 2248 dbSNP
rs1212141330 2250 dbSNP
rs1208450124 2251 dbSNP
rs1311903701 2253 dbSNP
rs1265817239 2256 dbSNP
rs552748624 2260 dbSNP
rs561412799 2261 dbSNP
rs1315730308 2269 dbSNP
rs1276984005 2271 dbSNP
rs994473227 2273 dbSNP
rs1476622630 2278 dbSNP
rs1027656307 2289 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 142940.0
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 142940.0
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 ENST00000298746.3 | 3UTR | UUCAAUAGCACAUAAUUUAUUUUCUAUGCAUUAUAAAUG
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 ENST00000298746.3 | 3UTR | UUUCAAUAGCACAUAAUUUAUUUUCUAUGCAUUAUAAAUG
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
GSE38974 Chronic obstructive pulmonary disease 0.283 8.5e-2 0.335 5.1e-2 25 Click to see details
GSE42095 Differentiated embryonic stem cells -0.288 9.1e-2 -0.075 3.7e-1 23 Click to see details
GSE32688 Pancreatic cancer 0.088 3.2e-1 0.025 4.5e-1 32 Click to see details
GSE28544 Breast cancer 0.05 4.1e-1 0.177 2.0e-1 24 Click to see details
GSE28260 Renal cortex and medulla 0.054 4.3e-1 0.176 2.8e-1 13 Click to see details
GSE26953 Aortic valvular endothelial cells 0.006 4.9e-1 -0.112 3.0e-1 24 Click to see details
GSE38226 Liver fibrosis -0.002 5.0e-1 0.010 4.8e-1 21 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
83 hsa-miR-548g-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT080708 ZCCHC2 zinc finger CCHC-type containing 2 2 2
MIRT109233 VMA21 VMA21, vacuolar ATPase assembly factor 2 8
MIRT135069 HNRNPU heterogeneous nuclear ribonucleoprotein U 2 4
MIRT176908 TRUB1 TruB pseudouridine synthase family member 1 2 4
MIRT187756 ESYT1 extended synaptotagmin 1 2 2
MIRT219528 PNRC1 proline rich nuclear receptor coactivator 1 2 2
MIRT384836 FAM76A family with sequence similarity 76 member A 2 2
MIRT442370 ZC3HAV1L zinc finger CCCH-type containing, antiviral 1 like 2 2
MIRT446664 MXI1 MAX interactor 1, dimerization protein 2 4
MIRT447674 PACSIN2 protein kinase C and casein kinase substrate in neurons 2 2 2
MIRT450710 RNF152 ring finger protein 152 2 2
MIRT452118 IFITM1 interferon induced transmembrane protein 1 2 2
MIRT467979 SKIL SKI like proto-oncogene 2 4
MIRT468891 RREB1 ras responsive element binding protein 1 2 4
MIRT470413 PPP1R15B protein phosphatase 1 regulatory subunit 15B 2 2
MIRT470554 COASY Coenzyme A synthase 2 2
MIRT475010 KANSL1 KAT8 regulatory NSL complex subunit 1 2 10
MIRT476035 GSE1 Gse1 coiled-coil protein 2 4
MIRT490477 FEM1C fem-1 homolog C 2 2
MIRT493500 IPMK inositol polyphosphate multikinase 2 2
MIRT501311 RPS21 ribosomal protein S21 2 2
MIRT502582 E2F6 E2F transcription factor 6 2 2
MIRT503132 BAG4 BCL2 associated athanogene 4 2 2
MIRT506779 KLHL15 kelch like family member 15 2 4
MIRT508052 ATXN1 ataxin 1 2 4
MIRT511964 ELOVL5 ELOVL fatty acid elongase 5 2 6
MIRT512117 CREBZF CREB/ATF bZIP transcription factor 2 2
MIRT512167 CD164 CD164 molecule 2 6
MIRT526614 ZNF780A zinc finger protein 780A 2 2
MIRT526703 SGOL1 shugoshin 1 2 2
MIRT527494 OCIAD1 OCIA domain containing 1 2 2
MIRT530854 RAG1 recombination activating 1 2 2
MIRT533638 TMSB4X thymosin beta 4, X-linked 2 2
MIRT537704 ELL2 elongation factor for RNA polymerase II 2 2 4
MIRT539145 ARF6 ADP ribosylation factor 6 2 4
MIRT543127 ZFP36L1 ZFP36 ring finger protein like 1 2 2
MIRT543627 ASXL2 additional sex combs like 2, transcriptional regulator 2 2
MIRT544519 GTF2E2 general transcription factor IIE subunit 2 2 2
MIRT544835 ZNF639 zinc finger protein 639 2 2
MIRT545699 NUTF2 nuclear transport factor 2 2 2
MIRT546077 VEZF1 vascular endothelial zinc finger 1 2 2
MIRT546285 TMEM30A transmembrane protein 30A 2 4
MIRT547003 PPP2CA protein phosphatase 2 catalytic subunit alpha 2 2
MIRT548582 DNAJB14 DnaJ heat shock protein family (Hsp40) member B14 2 2
MIRT549692 ZNF598 zinc finger protein 598 2 2
MIRT553594 TMED4 transmembrane p24 trafficking protein 4 2 2
MIRT553939 STARD3NL STARD3 N-terminal like 2 2
MIRT556620 LCOR ligand dependent nuclear receptor corepressor 2 2
MIRT558247 E2F3 E2F transcription factor 3 2 2
MIRT562283 GNA13 G protein subunit alpha 13 2 2
MIRT564370 TRMT5 tRNA methyltransferase 5 2 2
MIRT565846 SCML2 Scm polycomb group protein like 2 2 2
MIRT567312 HMGN2 high mobility group nucleosomal binding domain 2 2 2
MIRT567349 H3F3B H3 histone family member 3B 2 2
MIRT567567 FEN1 flap structure-specific endonuclease 1 2 2
MIRT571131 TMEM135 transmembrane protein 135 2 2
MIRT571964 KIF5B kinesin family member 5B 2 2
MIRT574477 RPS16 ribosomal protein S16 2 2
MIRT607516 LYRM7 LYR motif containing 7 2 4
MIRT607783 CYLC2 cylicin 2 2 2
MIRT608342 ZRANB1 zinc finger RANBP2-type containing 1 2 2
MIRT609703 GFRA1 GDNF family receptor alpha 1 2 2
MIRT609781 NHSL1 NHS like 1 2 2
MIRT610325 CBY3 chibby family member 3 2 4
MIRT612364 TMPPE transmembrane protein with metallophosphoesterase domain 2 4
MIRT623620 IGF2BP1 insulin like growth factor 2 mRNA binding protein 1 2 2
MIRT641038 PITPNB phosphatidylinositol transfer protein beta 2 2
MIRT644945 ATXN3L ataxin 3 like 2 2
MIRT653214 SP9 Sp9 transcription factor 2 2
MIRT666390 SHMT1 serine hydroxymethyltransferase 1 2 2
MIRT675538 KIAA1715 lunapark, ER junction formation factor 2 2
MIRT687817 ITPRIPL2 inositol 1,4,5-trisphosphate receptor interacting protein like 2 2 2
MIRT693448 PIK3CG phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma 2 2
MIRT695995 SNX19 sorting nexin 19 2 2
MIRT696117 SETD1A SET domain containing 1A 2 2
MIRT698322 TMEM136 transmembrane protein 136 2 2
MIRT699174 SMAD2 SMAD family member 2 2 2
MIRT708831 KLHL24 kelch like family member 24 2 2
MIRT711501 PGD phosphogluconate dehydrogenase 2 2
MIRT712829 TIGIT T-cell immunoreceptor with Ig and ITIM domains 2 2
MIRT713734 SUCO SUN domain containing ossification factor 2 2
MIRT720709 H2AFY H2A histone family member Y 2 2
MIRT722926 TLR4 toll like receptor 4 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-548g Cisplatin 5460033 NSC119875 approved resistant cell line (OE19)
hsa-mir-548g Docetaxel+Cisplatin+5-Fluorouracil sensitive tissue (hypopharyngeal squamous cell carcinoma)
hsa-miR-548g-3p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-548g-3p Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-548g-3p Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM16)
hsa-miR-548g-3p 4-Hydroxytamoxifen+Tamoxifen resistant cell line (LY2)
hsa-miR-548g-3p Oxaliplatin 6857599 NSC266046 approved resistant cell line (IGROV-1)
hsa-miR-548g-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)

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