miRTarBase - #MIRT083284


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pre-miRNA Information
pre-miRNA hsa-mir-4739   
Genomic Coordinates chr17: 79707176 - 79707249
Description Homo sapiens miR-4739 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4739
Sequence 10| AAGGGAGGAGGAGCGGAGGGGCCCU |34
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1416844919 3 dbSNP
rs1313792237 5 dbSNP
rs1350222948 10 dbSNP
rs1440530436 13 dbSNP
rs73410309 14 dbSNP
rs1223789593 15 dbSNP
rs1279007964 18 dbSNP
rs1345189697 22 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol ZCCHC3   
Synonyms C20orf99
Description zinc finger CCHC-type containing 3
Transcript NM_033089   
Expression
Putative miRNA Targets on ZCCHC3
3'UTR of ZCCHC3
(miRNA target sites are highlighted)		 
>ZCCHC3|NM_033089|3'UTR
   1 ACACCCGCCTGCCTGCCAGGGTGAACACACAGCCAGCTTATCCCTCTTAAGTGCCAAAACTTTTTTTTAAACCATTTTTT
  81 ATCGTTTTTGAAGGAGATCTTTTTAAAACCTACAAGAGACATCTCTCTATGCCTTCTTAAACCGAGTTTACTCCATTTCA
 161 GCCTGTTCTGAATTGGTGACTCTGTCACCAATAACGACTGCGGAGAACTGTAGCGTGCAGATGTGTTGCCCCTCCCTTTT
 241 AAAATTTTATTTTCGTTTTTCTATTGGGTATTTGTTTTGTTTCTTGTACTTTTTCTCTCTCTCCTTGCCCCCCTCCCGCC
 321 CTCCCCGCCCCATACCTTTTCTTCCCCTGGATTTTCACCCTTTGGGCTGCCTTGCTCATCTTTATGCCCCAGCACTAGGT
 401 ACGGGGCCCAACACGTGGTAGGCACTCCATCAGTGTTTGCTGAATTGAAAACATTGTTGACTGTGGCTTCTATCAGAGTG
 481 TCTACCTTTTGCAGCTCTTCCCCTCCCTCATTTAATTTGCTGCTTTTAATCTACGTGGTCTGAGAATTTGTGAAACCAGT
 561 GTTGTTAGAAGTGTATATAATCTGAATCAATAAGCTCTGAATGGTGGCCAAGGGCCTCTCTTATGGCACAAAGATGCATG
 641 GACTTCATGACAGCTCTTTTGGTGGCTCAGAAGCCATTTTTTATAGAATCATGGAATCTAGAATATTCCTGCTGGAAAGA
 721 ACCTGAGAGTTGGTTTGGACCAATTCCCTGGTTTTCCAGCAGATGAAACAGGCCCAAAGAGGTTAAATGACTGGGTGAAA
 801 ATCACATAGCTGTCTGGTGCCAGAGCCAGCCTATAGTAGAGTCCCCTGACCCCAAGCCCGGTGCTCATTCCACTACCTCT
 881 CACACTTCACAACAATTTCCTCAACACTTGAGGGCCCAGAAAGTCTGATCTCTCCAGAATGATCAGCCCAGAGGAATGCT
 961 GAGAAATCACCTGGAGGAGGGAGCAGAAAGAGAAGGTTTTTAAGGAGGGGCTTCTGAATACTTGGGAGATACGGAACGGA
1041 CCAAGGACCACACTCCAGGGTGCATTCGTTGCTCCCTGGGGCACCACTTCTGGATTACAGTGTGCCAGGTCCTTTGGAGG
1121 CCCTACCCCTTCCCCATTCATTGCCACCAGTGAGAAATGGGGGTGCCCCTGTGTAAAGAAACCTACCAAAGGTTTACATT
1201 TGCACCTTAGCCTCAATAGCTACGAACCCTAGAGAAGCAGCTAGCTGGAGCTCATGTGCAACTCCTGATTCTCAGGAGAA
1281 AGATGGATTTTAACCCAAAATTATGAGTGAGCTGTTAACTCTAAAATGTACTTGGGAGATAGGCCAAGCGAGAGGTCATG
1361 GGCCAACTAAGTGTTATCCAGTAGAAAAGACAGTACACTGCTTTTCTTTTAGTGTTTGCTTTTCCTTTGCTATATGTTTT
1441 GCTATTTCCTTGTGGCTTAGAATGTAAAATTGATTGTTAAAAGTTTTGTTCTGAATAAATATTTATCTTTTGTATTGCTA
1521 AAAAAAAAAAAAAAAAA
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' ucccGGGGA--GGCGAGGA--GGAGGGAa 5'
              ||::|  | ||||:|  ||||||| 
Target 5' tctaCCTTTTGCAGCTCTTCCCCTCCCTc 3'
 481 - 509 165.00 -24.70
2 
miRNA  3' uccCGGGGAGGCGAGGAGGAGGGAa 5'
             ||   | :|:| | ||||||| 
Target 5' cgtGCAGATGTGTTGCCCCTCCCTt 3'
 214 - 238 154.00 -21.50
3 
miRNA  3' ucccGGGGAGG--CGAGGAGGAGGGaa 5'
              :|:||||  || || ||||||  
Target 5' tctcTCTCTCCTTGC-CCCCCTCCCgc 3'
 294 - 319 146.00 -24.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30511536 7 COSMIC
COSN1082990 59 COSMIC
COSN13244990 69 COSMIC
COSN30525342 75 COSMIC
COSN30123952 100 COSMIC
COSN30116279 319 COSMIC
COSN15627012 332 COSMIC
COSN15627013 428 COSMIC
COSN30133479 433 COSMIC
COSN31548555 471 COSMIC
COSN30534195 612 COSMIC
COSN15627014 615 COSMIC
COSN15627015 632 COSMIC
COSN30544215 763 COSMIC
COSN31572242 806 COSMIC
COSN26637881 813 COSMIC
COSN26190232 909 COSMIC
COSN31482781 964 COSMIC
COSN31489569 964 COSMIC
COSN31540856 1033 COSMIC
COSN21903558 1035 COSMIC
COSN30112209 1068 COSMIC
COSN8610684 1086 COSMIC
COSN23396393 1194 COSMIC
COSN26708746 1221 COSMIC
COSN30143387 1225 COSMIC
COSN31489557 1306 COSMIC
COSN26585103 1351 COSMIC
COSN31529735 1371 COSMIC
COSN5968419 1403 COSMIC
COSN15627017 1425 COSMIC
COSN15627016 1429 COSMIC
COSN15627018 1493 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs763872038 4 dbSNP
rs751191179 6 dbSNP
rs371820165 7 dbSNP
rs1027913841 8 dbSNP
rs1206959284 11 dbSNP
rs1247628078 15 dbSNP
rs767113214 17 dbSNP
rs749900419 24 dbSNP
rs541476404 27 dbSNP
rs1232376398 30 dbSNP
rs780406252 31 dbSNP
rs1178246922 38 dbSNP
rs932517594 40 dbSNP
rs1046560 42 dbSNP
rs1455171892 44 dbSNP
rs1157855549 46 dbSNP
rs779108519 50 dbSNP
rs1201000522 61 dbSNP
rs1364271979 61 dbSNP
rs983687778 69 dbSNP
rs1461338953 70 dbSNP
rs1009423738 72 dbSNP
rs1464652242 72 dbSNP
rs1379848970 75 dbSNP
rs907555469 79 dbSNP
rs1021107005 85 dbSNP
rs1246577799 85 dbSNP
rs773297580 87 dbSNP
rs949725500 95 dbSNP
rs981225913 98 dbSNP
rs903643638 100 dbSNP
rs1342340492 103 dbSNP
rs143206307 110 dbSNP
rs1234952464 111 dbSNP
rs1033342766 113 dbSNP
rs1367774082 114 dbSNP
rs1389020332 121 dbSNP
rs1437488359 124 dbSNP
rs924483250 126 dbSNP
rs1294119648 130 dbSNP
rs991667512 131 dbSNP
rs937177959 137 dbSNP
rs1326177769 144 dbSNP
rs1429705488 147 dbSNP
rs867007805 155 dbSNP
rs543635316 156 dbSNP
rs1388655300 160 dbSNP
rs1170846748 162 dbSNP
rs1024572801 163 dbSNP
rs1219584053 167 dbSNP
rs1280513249 168 dbSNP
rs1186468120 169 dbSNP
rs1054256281 171 dbSNP
rs563611902 173 dbSNP
rs1332873255 180 dbSNP
rs568625842 192 dbSNP
rs945995933 199 dbSNP
rs111892073 202 dbSNP
rs982993778 203 dbSNP
rs908613350 206 dbSNP
rs902532413 209 dbSNP
rs548715833 211 dbSNP
rs941466437 214 dbSNP
rs1009286414 215 dbSNP
rs559258427 218 dbSNP
rs921231392 223 dbSNP
rs900550323 225 dbSNP
rs1409338192 231 dbSNP
rs932654944 233 dbSNP
rs1051432121 241 dbSNP
rs1390487632 243 dbSNP
rs1162213577 244 dbSNP
rs996262390 245 dbSNP
rs1474018101 255 dbSNP
rs528174354 256 dbSNP
rs1042256045 262 dbSNP
rs952170165 264 dbSNP
rs1206612060 269 dbSNP
rs903607997 271 dbSNP
rs1288917887 274 dbSNP
rs551106709 276 dbSNP
rs1208235442 291 dbSNP
rs983720367 294 dbSNP
rs1015561308 302 dbSNP
rs1000529446 304 dbSNP
rs1227854321 308 dbSNP
rs143844000 308 dbSNP
rs534402324 308 dbSNP
rs543148031 308 dbSNP
rs1286640631 313 dbSNP
rs894785004 313 dbSNP
rs1349625224 315 dbSNP
rs1384808169 316 dbSNP
rs1401155731 318 dbSNP
rs1280419736 319 dbSNP
rs1354034029 323 dbSNP
rs1202824194 328 dbSNP
rs1409134207 330 dbSNP
rs1313770513 331 dbSNP
rs1409176468 332 dbSNP
rs1046561 333 dbSNP
rs1246102235 333 dbSNP
rs1323550708 334 dbSNP
rs1236924527 336 dbSNP
rs1260243891 338 dbSNP
rs1487889823 341 dbSNP
rs1217333535 343 dbSNP
rs1196438206 344 dbSNP
rs1265043396 344 dbSNP
rs1013270373 347 dbSNP
rs1484595849 352 dbSNP
rs1208355780 356 dbSNP
rs138536096 357 dbSNP
rs1414015225 358 dbSNP
rs1224780739 359 dbSNP
rs1425207223 368 dbSNP
rs971094273 382 dbSNP
rs1156240756 385 dbSNP
rs185299499 388 dbSNP
rs981474126 392 dbSNP
rs1273624686 403 dbSNP
rs374576318 404 dbSNP
rs1362710871 407 dbSNP
rs34131242 407 dbSNP
rs1420837016 410 dbSNP
rs1300656404 417 dbSNP
rs1326096893 422 dbSNP
rs1374007996 424 dbSNP
rs1385743584 430 dbSNP
rs1160627336 436 dbSNP
rs1024959279 442 dbSNP
rs1424362474 446 dbSNP
rs188172008 453 dbSNP
rs1462629141 462 dbSNP
rs572871638 463 dbSNP
rs989845810 464 dbSNP
rs971701251 468 dbSNP
rs1463731836 471 dbSNP
rs1354573948 475 dbSNP
rs1004787800 482 dbSNP
rs1311748458 485 dbSNP
rs1240756355 487 dbSNP
rs146779563 492 dbSNP
rs751424700 502 dbSNP
rs1345677743 504 dbSNP
rs1209098401 510 dbSNP
rs1237850231 530 dbSNP
rs962879913 533 dbSNP
rs974125881 534 dbSNP
rs1362540223 541 dbSNP
rs945860482 545 dbSNP
rs954012411 550 dbSNP
rs986850299 553 dbSNP
rs1358082949 559 dbSNP
rs1332031304 564 dbSNP
rs1436542145 572 dbSNP
rs1439828532 574 dbSNP
rs1395407898 578 dbSNP
rs549939790 587 dbSNP
rs1160945020 589 dbSNP
rs1167708839 589 dbSNP
rs759314956 591 dbSNP
rs1289128502 598 dbSNP
rs139935493 602 dbSNP
rs1187387202 604 dbSNP
rs1177171134 610 dbSNP
rs945350428 612 dbSNP
rs1042697054 617 dbSNP
rs1440270921 619 dbSNP
rs1486271209 623 dbSNP
rs944728742 624 dbSNP
rs1297866165 638 dbSNP
rs925080885 639 dbSNP
rs1040818710 643 dbSNP
rs536111709 653 dbSNP
rs767243172 663 dbSNP
rs1449029998 666 dbSNP
rs936521008 667 dbSNP
rs192747351 674 dbSNP
rs1290931548 677 dbSNP
rs1368621830 677 dbSNP
rs996283177 681 dbSNP
rs1416145825 683 dbSNP
rs572359788 684 dbSNP
rs1307419691 693 dbSNP
rs1279060184 704 dbSNP
rs1427568412 707 dbSNP
rs887956633 709 dbSNP
rs1313799346 710 dbSNP
rs1005425290 714 dbSNP
rs1411956202 715 dbSNP
rs1190117466 716 dbSNP
rs1013656464 719 dbSNP
rs545876059 720 dbSNP
rs1475614707 723 dbSNP
rs752297363 724 dbSNP
rs1201980603 728 dbSNP
rs755752964 734 dbSNP
rs183507323 756 dbSNP
rs1046104961 759 dbSNP
rs1457961754 760 dbSNP
rs1252284798 769 dbSNP
rs1179920563 774 dbSNP
rs558325924 776 dbSNP
rs1291103031 795 dbSNP
rs188169139 804 dbSNP
rs1355607278 806 dbSNP
rs1192342255 816 dbSNP
rs1287583524 818 dbSNP
rs1427670319 821 dbSNP
rs1408609456 822 dbSNP
rs6047890 832 dbSNP
rs1034459530 838 dbSNP
rs142800891 845 dbSNP
rs1015867694 847 dbSNP
rs1180597999 850 dbSNP
rs563459869 850 dbSNP
rs962849559 856 dbSNP
rs73572500 858 dbSNP
rs1487750422 861 dbSNP
rs1215191330 862 dbSNP
rs1323894020 875 dbSNP
rs1334847899 877 dbSNP
rs1266975987 889 dbSNP
rs1393921426 895 dbSNP
rs1236312560 899 dbSNP
rs1307699556 903 dbSNP
rs1028399989 906 dbSNP
rs1368526735 924 dbSNP
rs914295112 930 dbSNP
rs967193835 950 dbSNP
rs1441953700 955 dbSNP
rs1387934262 957 dbSNP
rs752955443 961 dbSNP
rs542858627 972 dbSNP
rs1212547731 977 dbSNP
rs1277358395 983 dbSNP
rs756526310 985 dbSNP
rs1431747223 986 dbSNP
rs912524662 995 dbSNP
rs538374451 996 dbSNP
rs978004424 997 dbSNP
rs1247071624 998 dbSNP
rs528128129 1006 dbSNP
rs115623645 1008 dbSNP
rs1261179104 1010 dbSNP
rs1039603111 1017 dbSNP
rs564666167 1021 dbSNP
rs921943855 1023 dbSNP
rs1424790301 1024 dbSNP
rs931939898 1029 dbSNP
rs1316589514 1032 dbSNP
rs1383987304 1033 dbSNP
rs1385786311 1034 dbSNP
rs916321795 1038 dbSNP
rs949125591 1039 dbSNP
rs1049180704 1040 dbSNP
rs530493281 1054 dbSNP
rs1449311475 1068 dbSNP
rs753365032 1073 dbSNP
rs1190594843 1079 dbSNP
rs1004975429 1083 dbSNP
rs758866968 1085 dbSNP
rs907355778 1091 dbSNP
rs184674478 1101 dbSNP
rs1034540277 1106 dbSNP
rs958379381 1110 dbSNP
rs1011164846 1124 dbSNP
rs995668330 1136 dbSNP
rs1341275925 1137 dbSNP
rs1028537200 1151 dbSNP
rs570191338 1152 dbSNP
rs1021333613 1159 dbSNP
rs529564186 1161 dbSNP
rs889952246 1162 dbSNP
rs1312125972 1165 dbSNP
rs1220060472 1172 dbSNP
rs967564718 1179 dbSNP
rs1377791691 1186 dbSNP
rs977193242 1187 dbSNP
rs1314083575 1193 dbSNP
rs1429447196 1194 dbSNP
rs1394788334 1211 dbSNP
rs150607885 1213 dbSNP
rs1476200430 1215 dbSNP
rs1373338833 1216 dbSNP
rs566236348 1220 dbSNP
rs975756886 1224 dbSNP
rs921144601 1225 dbSNP
rs931979308 1228 dbSNP
rs14181 1230 dbSNP
rs190528845 1233 dbSNP
rs1032206421 1245 dbSNP
rs957981806 1246 dbSNP
rs990700758 1255 dbSNP
rs558164311 1259 dbSNP
rs769152727 1276 dbSNP
rs1231513528 1283 dbSNP
rs940795360 1284 dbSNP
rs1216603329 1289 dbSNP
rs1294370816 1295 dbSNP
rs1409776044 1306 dbSNP
rs775264314 1308 dbSNP
rs34756351 1323 dbSNP
rs1331262312 1337 dbSNP
rs1264329277 1339 dbSNP
rs1396766746 1342 dbSNP
rs1489504830 1342 dbSNP
rs374936391 1342 dbSNP
rs571794160 1346 dbSNP
rs1163838250 1349 dbSNP
rs1186040442 1350 dbSNP
rs1419401395 1350 dbSNP
rs1036436171 1351 dbSNP
rs115121514 1352 dbSNP
rs1473262086 1361 dbSNP
rs181752957 1366 dbSNP
rs2031 1368 dbSNP
rs757993576 1370 dbSNP
rs75572491 1374 dbSNP
rs1037407286 1378 dbSNP
rs894694975 1379 dbSNP
rs542446075 1385 dbSNP
rs1011774706 1390 dbSNP
rs1273910585 1394 dbSNP
rs931511612 1395 dbSNP
rs553265754 1401 dbSNP
rs1158036838 1408 dbSNP
rs902828275 1411 dbSNP
rs1050011332 1417 dbSNP
rs999026413 1420 dbSNP
rs1324728012 1421 dbSNP
rs1019338261 1422 dbSNP
rs371945893 1428 dbSNP
rs965592484 1433 dbSNP
rs1395972120 1437 dbSNP
rs1164982728 1443 dbSNP
rs1399658220 1445 dbSNP
rs748344908 1450 dbSNP
rs889930321 1451 dbSNP
rs1394284507 1454 dbSNP
rs975211740 1455 dbSNP
rs1191926380 1462 dbSNP
rs139209694 1474 dbSNP
rs1019677136 1476 dbSNP
rs1445411814 1480 dbSNP
rs149967120 1485 dbSNP
rs1224834791 1487 dbSNP
rs1344709383 1491 dbSNP
rs984020819 1499 dbSNP
rs909242076 1512 dbSNP
rs1326252176 1515 dbSNP
rs940673724 1516 dbSNP
rs958040446 1519 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
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 GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection ...

- Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ucccggggaggcGAGGAGGAGGGAa 5'
                      ||:| ||||||| 
Target 5' ------------CUUCCCCUCCCUc 3'
 		1 - 13
Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 85364.0
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 GSM1065669. RNA binding protein: AGO1. Condition:4-thiouridine ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ucccggggaggcGAGGAGGAGGGAa 5'
                      ||:| ||||||| 
Target 5' ------------CUUCCCCUCCCUc 3'
 		1 - 13
Article - Memczak S; Jens M; Elefsinioti A; Torti F; et al.
- Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
Experimental Support 3 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions MCF7
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 SRR1045082. RNA binding protein: AGO2. Condition:Untreated ...

- Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology.

Article - Farazi TA; Ten Hoeve JJ; Brown M; et al.
- Genome biology, 2014
BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
LinkOut: [PMID: 24398324]
CLIP-seq Support 1 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000382352.3 | 3UTR | CUUCCCCUCCCUCAUUUAAUUUGCUGCUUUUAAUCUACGUGGUCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1065669
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_8
Location of target site ENST00000382352.3 | 3UTR | CUUCCCCUCCCUCAUUUAAUUUGCUGCUUUUAAUCUACG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset SRR1045082
Method / RBP PAR-CLIP / AGO2
Cell line / Condition MCF7 / Untreated
Location of target site ENST00000382352.3 | 3UTR | CUCUUCCCCUCCCUCAUUUAAUUUGCUGCUUUUAAUCUACG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24398324 / SRX388831
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
206 hsa-miR-4739 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT057839 SLC30A7 solute carrier family 30 member 7 2 2
MIRT059680 CRTC2 CREB regulated transcription coactivator 2 2 2
MIRT083284 ZCCHC3 zinc finger CCHC-type containing 3 2 6
MIRT117523 MIDN midnolin 2 2
MIRT125598 SCD stearoyl-CoA desaturase 2 2
MIRT158424 TNRC6B trinucleotide repeat containing 6B 2 4
MIRT180896 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT183522 BTG2 BTG anti-proliferation factor 2 2 4
MIRT197842 DCAF7 DDB1 and CUL4 associated factor 7 2 2
MIRT227610 ZBTB34 zinc finger and BTB domain containing 34 2 2
MIRT260049 JUN Jun proto-oncogene, AP-1 transcription factor subunit 2 2
MIRT266231 PEX11B peroxisomal biogenesis factor 11 beta 2 2
MIRT267389 TMEM138 transmembrane protein 138 2 2
MIRT284431 CAPN15 calpain 15 2 2
MIRT293023 ZNF566 zinc finger protein 566 2 2
MIRT318024 CENPQ centromere protein Q 2 2
MIRT339336 SESN2 sestrin 2 2 2
MIRT445769 CCND3 cyclin D3 2 2
MIRT451026 MYH14 myosin heavy chain 14 2 8
MIRT451436 TJP3 tight junction protein 3 2 4
MIRT451704 C1RL complement C1r subcomponent like 2 2
MIRT451968 TMPRSS5 transmembrane protease, serine 5 2 2
MIRT452008 FKBP5 FK506 binding protein 5 2 2
MIRT452471 SORCS2 sortilin related VPS10 domain containing receptor 2 2 2
MIRT452720 DTHD1 death domain containing 1 2 2
MIRT453490 PITPNM3 PITPNM family member 3 2 2
MIRT454314 ZNF134 zinc finger protein 134 2 2
MIRT454401 NRG4 neuregulin 4 2 2
MIRT454498 SLC29A1 solute carrier family 29 member 1 (Augustine blood group) 2 2
MIRT454839 POLR2J3 RNA polymerase II subunit J3 2 2
MIRT455147 TBC1D25 TBC1 domain family member 25 2 2
MIRT455887 KIF2C kinesin family member 2C 2 2
MIRT456138 SAMD10 sterile alpha motif domain containing 10 2 2
MIRT456165 TTF2 transcription termination factor 2 2 2
MIRT457167 MXRA7 matrix remodeling associated 7 2 2
MIRT457444 NOL10 nucleolar protein 10 2 2
MIRT457571 ZNF34 zinc finger protein 34 2 2
MIRT457632 UPK3BL uroplakin 3B like 1 2 2
MIRT458748 CES2 carboxylesterase 2 2 2
MIRT459493 CCL11 C-C motif chemokine ligand 11 2 2
MIRT459936 HHIP hedgehog interacting protein 2 4
MIRT460104 GNG3 G protein subunit gamma 3 2 2
MIRT460154 ASB16 ankyrin repeat and SOCS box containing 16 2 2
MIRT460195 PCYT1A phosphate cytidylyltransferase 1, choline, alpha 2 2
MIRT460324 SH3RF1 SH3 domain containing ring finger 1 2 2
MIRT460665 IGFBP4 insulin like growth factor binding protein 4 2 2
MIRT460703 RNF157 ring finger protein 157 2 2
MIRT460898 UBE2S ubiquitin conjugating enzyme E2 S 2 2
MIRT461581 SCO1 SCO1, cytochrome c oxidase assembly protein 2 4
MIRT461825 SNAP23 synaptosome associated protein 23 2 2
MIRT462041 FAAH fatty acid amide hydrolase 2 2
MIRT462119 AKR7A2 aldo-keto reductase family 7 member A2 2 2
MIRT462467 GCDH glutaryl-CoA dehydrogenase 2 2
MIRT462811 NTN1 netrin 1 2 2
MIRT463339 ZFHX3 zinc finger homeobox 3 2 2
MIRT463452 ZC3HAV1L zinc finger CCCH-type containing, antiviral 1 like 2 2
MIRT463928 WNT3 Wnt family member 3 2 2
MIRT464274 VCL vinculin 2 2
MIRT465378 TPM3 tropomyosin 3 2 6
MIRT465558 TOB2 transducer of ERBB2, 2 2 2
MIRT466363 THBS1 thrombospondin 1 2 2
MIRT467363 SP2 Sp2 transcription factor 2 2
MIRT467781 SLC2A4 solute carrier family 2 member 4 2 2
MIRT467826 SLC29A2 solute carrier family 29 member 2 2 2
MIRT468112 SH3TC2 SH3 domain and tetratricopeptide repeats 2 2 2
MIRT468733 SDC4 syndecan 4 2 2
MIRT469178 RNF111 ring finger protein 111 2 2
MIRT469577 RARA retinoic acid receptor alpha 2 2
MIRT470790 PNPLA6 patatin like phospholipase domain containing 6 2 2
MIRT471177 PHB2 prohibitin 2 2 2
MIRT471325 PGAM4 phosphoglycerate mutase family member 4 2 2
MIRT471398 PDPR pyruvate dehydrogenase phosphatase regulatory subunit 2 2
MIRT471548 PAX5 paired box 5 2 2
MIRT471848 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT472229 NGFR nerve growth factor receptor 2 2
MIRT472548 NACC1 nucleus accumbens associated 1 2 2
MIRT473115 MLXIP MLX interacting protein 2 2
MIRT473212 MINK1 misshapen like kinase 1 2 2
MIRT473590 MAT2A methionine adenosyltransferase 2A 2 2
MIRT474184 LETMD1 LETM1 domain containing 1 2 2
MIRT474671 KLF13 Kruppel like factor 13 2 2
MIRT474854 KHSRP KH-type splicing regulatory protein 2 2
MIRT475152 IP6K1 inositol hexakisphosphate kinase 1 2 2
MIRT475390 ICOSLG inducible T-cell costimulator ligand 2 2
MIRT475587 HMGXB4 HMG-box containing 4 2 2
MIRT475773 HDLBP high density lipoprotein binding protein 2 2
MIRT477060 FAM210A family with sequence similarity 210 member A 2 2
MIRT477397 ENTPD7 ectonucleoside triphosphate diphosphohydrolase 7 2 2
MIRT478335 DDN dendrin 2 2
MIRT478609 CTDSP2 CTD small phosphatase 2 2 3
MIRT479135 CNBP CCHC-type zinc finger nucleic acid binding protein 2 4
MIRT480106 CALR calreticulin 2 2
MIRT480416 C19orf47 chromosome 19 open reading frame 47 2 2
MIRT480461 C11orf84 chromosome 11 open reading frame 84 2 4
MIRT481268 ATXN7L3 ataxin 7 like 3 2 2
MIRT481413 ASXL1 additional sex combs like 1, transcriptional regulator 2 2
MIRT481743 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT482159 AK2 adenylate kinase 2 2 2
MIRT482317 AGO2 argonaute 2, RISC catalytic component 2 2
MIRT482398 AEN apoptosis enhancing nuclease 2 2
MIRT483346 CHRDL1 chordin like 1 2 8
MIRT483596 SLC26A9 solute carrier family 26 member 9 2 2
MIRT483634 NAV2 neuron navigator 2 2 2
MIRT483750 ALDH9A1 aldehyde dehydrogenase 9 family member A1 2 2
MIRT484085 SUGT1 SGT1 homolog, MIS12 kinetochore complex assembly cochaperone 2 4
MIRT484225 SUMO1 small ubiquitin-like modifier 1 2 6
MIRT484296 AIP aryl hydrocarbon receptor interacting protein 2 4
MIRT484374 GATA6 GATA binding protein 6 2 12
MIRT484395 ZNF710 zinc finger protein 710 2 4
MIRT484446 RAB7A RAB7A, member RAS oncogene family 2 4
MIRT484590 HACE1 HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 2 2
MIRT484626 SIX3 SIX homeobox 3 2 6
MIRT484737 ABCC6 ATP binding cassette subfamily C member 6 2 4
MIRT484861 ZNF70 zinc finger protein 70 2 4
MIRT486701 GLYR1 glyoxylate reductase 1 homolog 2 2
MIRT486803 PARP11 poly(ADP-ribose) polymerase family member 11 2 2
MIRT487059 C10orf55 chromosome 10 open reading frame 55 2 2
MIRT487077 CLASP1 cytoplasmic linker associated protein 1 2 4
MIRT487148 NCOR2 nuclear receptor corepressor 2 2 2
MIRT487625 C20orf96 chromosome 20 open reading frame 96 2 2
MIRT487710 CDK14 cyclin dependent kinase 14 2 2
MIRT487853 CLSTN1 calsyntenin 1 2 4
MIRT487970 IQSEC2 IQ motif and Sec7 domain 2 2 2
MIRT488138 GPR107 G protein-coupled receptor 107 2 2
MIRT488208 MAT1A methionine adenosyltransferase 1A 2 2
MIRT488363 PAX2 paired box 2 2 2
MIRT488593 ST7L suppression of tumorigenicity 7 like 2 2
MIRT488985 REXO2 RNA exonuclease 2 2 2
MIRT489068 STARD3 StAR related lipid transfer domain containing 3 2 2
MIRT489177 ANKRD45 ankyrin repeat domain 45 2 4
MIRT489327 GNB1L G protein subunit beta 1 like 2 2
MIRT489423 TUBB2A tubulin beta 2A class IIa 2 2
MIRT489808 KRT80 keratin 80 2 4
MIRT489868 ATP2A3 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3 2 2
MIRT489922 RTKN rhotekin 2 2
MIRT490159 TMEM63C transmembrane protein 63C 2 2
MIRT490312 HOXB13 homeobox B13 2 2
MIRT490771 SRCIN1 SRC kinase signaling inhibitor 1 2 2
MIRT490904 BARHL1 BarH like homeobox 1 2 6
MIRT491072 ACVR1B activin A receptor type 1B 2 4
MIRT491242 KCNA5 potassium voltage-gated channel subfamily A member 5 2 2
MIRT491456 HOXB5 homeobox B5 2 2
MIRT492893 NFIX nuclear factor I X 2 2
MIRT492923 NFAT5 nuclear factor of activated T-cells 5 2 2
MIRT494021 DUSP9 dual specificity phosphatase 9 2 2
MIRT494046 DUSP7 dual specificity phosphatase 7 2 4
MIRT494190 CNOT6L CCR4-NOT transcription complex subunit 6 like 2 2
MIRT494721 ARHGAP31 Rho GTPase activating protein 31 2 2
MIRT494819 AKAP11 A-kinase anchoring protein 11 2 2
MIRT494909 UCP2 uncoupling protein 2 2 2
MIRT495262 CCDC108 cilia and flagella associated protein 65 2 2
MIRT495511 RGS6 regulator of G protein signaling 6 2 2
MIRT496604 TAGLN transgelin 2 2
MIRT498276 POFUT1 protein O-fucosyltransferase 1 2 2
MIRT499031 MAG myelin associated glycoprotein 2 2
MIRT499816 LONRF3 LON peptidase N-terminal domain and ring finger 3 2 2
MIRT500457 ZFP36L1 ZFP36 ring finger protein like 1 2 2
MIRT502340 GIGYF1 GRB10 interacting GYF protein 1 2 4
MIRT503646 POLR2F RNA polymerase II subunit F 2 4
MIRT508000 BCL2L13 BCL2 like 13 2 4
MIRT510802 SEPT2 septin 2 2 6
MIRT511040 NRF1 nuclear respiratory factor 1 2 2
MIRT512930 UBL4A ubiquitin like 4A 2 2
MIRT532005 ACTR2 ARP2 actin related protein 2 homolog 2 2
MIRT539926 DUSP28 dual specificity phosphatase 28 2 2
MIRT553376 TRIM44 tripartite motif containing 44 2 2
MIRT568790 VPS37D VPS37D, ESCRT-I subunit 2 2
MIRT568827 TRIM67 tripartite motif containing 67 2 2
MIRT568876 LY6H lymphocyte antigen 6 family member H 2 2
MIRT568912 ATP6V1B1 ATPase H+ transporting V1 subunit B1 2 2
MIRT569993 TMEM184A transmembrane protein 184A 2 2
MIRT570225 SLC27A1 solute carrier family 27 member 1 2 2
MIRT570490 THRA thyroid hormone receptor, alpha 2 2
MIRT570541 RPH3A rabphilin 3A 2 2
MIRT570587 OTUD7B OTU deubiquitinase 7B 2 2
MIRT573681 HES6 hes family bHLH transcription factor 6 2 2
MIRT576457 Itga11 integrin alpha 11 2 3
MIRT608254 ITGA11 integrin subunit alpha 11 2 3
MIRT609751 FAM198A family with sequence similarity 198 member A 2 2
MIRT610860 ARSA arylsulfatase A 2 2
MIRT627528 SRP19 signal recognition particle 19 2 4
MIRT627895 OLFML2A olfactomedin like 2A 2 2
MIRT629785 PTDSS2 phosphatidylserine synthase 2 2 2
MIRT647051 C1QTNF6 C1q and TNF related 6 2 2
MIRT649532 GTF3C3 general transcription factor IIIC subunit 3 2 2
MIRT661455 MORC4 MORC family CW-type zinc finger 4 2 2
MIRT667859 IPCEF1 interaction protein for cytohesin exchange factors 1 2 2
MIRT668824 CYLD CYLD lysine 63 deubiquitinase 2 2
MIRT669492 ARL4C ADP ribosylation factor like GTPase 4C 2 2
MIRT670166 SLC29A4 solute carrier family 29 member 4 2 2
MIRT670929 DESI1 desumoylating isopeptidase 1 2 2
MIRT674655 NKRF NFKB repressing factor 2 2
MIRT681452 CIITA class II major histocompatibility complex transactivator 2 2
MIRT681766 CDKAL1 CDK5 regulatory subunit associated protein 1 like 1 2 2
MIRT682033 AGXT2 alanine--glyoxylate aminotransferase 2 2 4
MIRT684821 BRIX1 BRX1, biogenesis of ribosomes 2 2
MIRT686009 NEK4 NIMA related kinase 4 2 2
MIRT691758 IKBKG inhibitor of nuclear factor kappa B kinase subunit gamma 2 2
MIRT701938 MLLT1 MLLT1, super elongation complex subunit 2 2
MIRT702794 IFNAR2 interferon alpha and beta receptor subunit 2 2 2
MIRT705706 ANKFY1 ankyrin repeat and FYVE domain containing 1 2 2
MIRT713377 STK35 serine/threonine kinase 35 2 2
MIRT714792 ATP6V1A ATPase H+ transporting V1 subunit A 2 2
MIRT715003 TSPAN11 tetraspanin 11 2 2
MIRT722688 RRM2 ribonucleotide reductase regulatory subunit M2 2 2
MIRT755868 ITGA10 integrin subunit alpha 10 3 1
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-4 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4739 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-miR-4739 Fluorouracil 3385 NSC19893 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-miR-4739 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (SW1990)
hsa-miR-4739 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (SW1990)
hsa-miR-4739 Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-4739 Cisplatin 5460033 NSC119875 approved resistant High Pancreatic Cancer cell line (BxPC-3)
hsa-miR-4739 Dabrafenib 44462760 NSC764134 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-4739 Vemurafenib 42611257 NSC761431 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-mir-4739 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-mir-4739 Ceritinib 57379345 NSC776422 approved sensitive cell line (H3122)
hsa-miR-4739 Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-4739 Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-4739 Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-4739 Leuprorelin/Goserelin + Bicalutamide resistant tissue (prostate cancer)
hsa-miR-4739 Ceritinib 57379345 NSC776422 approved sensitive cell line (H3122)

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