miRTarBase - #MIRT520190


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pre-miRNA Information
pre-miRNA hsa-mir-4254   
Genomic Coordinates chr1: 31758660 - 31758735
Description Homo sapiens miR-4254 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4254
Sequence 44| GCCUGGAGCUACUCCACCAUCUC |66
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1415016281 1 dbSNP
rs564274475 8 dbSNP
rs12731294 9 dbSNP
rs780735773 13 dbSNP
rs1207241221 19 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol WBP2   
Synonyms GRAMD6, WBP-2
Description WW domain binding protein 2
Transcript NM_012478   
Expression
Putative miRNA Targets on WBP2
3'UTR of WBP2
(miRNA target sites are highlighted)		 
>WBP2|NM_012478|3'UTR
   1 GCCCTCCTGCCTCCCTGCCTCCCACCCTCATCTCTCTACCCTACCCCTCCCATCGGGGCTGTGCTGGGGCTTGGGGAGGG
  81 GAGGGGGCGCCTTGTTCTCCCTCCAGGTCTGATCATAAACAATTACCAGGAACTAGCATTGTGGGACATTAGGGCCCCCG
 161 GCCTCGGGAGAGGTGCCGCCCAGCTTCCCATGCCAGCCCGGAGCCCACAGTGCTGCCCAGCGTACCTCCCTCACCGTCTG
 241 GGGCTCTTCTGGGAGCACGGAGCATCCCCTGTTCCTGTTTCACTCTCAGCTTCTCCCCTCGAAGGGACTCTCTGGCCACC
 321 TCCTCCACCGCAGTCCAGCTCCCTCAGTCTGGCACCCACTGCTACACTCAGCCTCATGAGCCACTTCAGACCAGCCAGGT
 401 GTCTTCCCGGGCCCTGCCAGACCCTGCTCACATTCCCTCTGCTGGTCTGTGCTGGTCTCAGAAGGCCACCGCGCCCGCAT
 481 TCCACTCAGCCAGGGTCCAGCTGCAGCCCCCGCCACCCTTCCTTCCCTTCCCTGTCCTGGGTCATGTTGTTGCCACCCTG
 561 TGTGACTTTTGAAGCTGTAAAATGAGCTTCCAGGGCTTGGGTGGCGTCGGGGCAGGGCCGCCGAGGCTGGGAGGAAGCCC
 641 TTCTGCCTTTTGCTGGTGTTTCTGGAATTTGCTTTCCCTCACCTCTCACTTCCTTCTAGAAGGAGCTTCCTGACTGGAAC
 721 CAGAGAATGCATGTCTGTCCACTTGGTGGCTGCTGGGTGGGGCCGGGAACAAGGGCCCCTGACCCTGTGTGCTGGCCGGG
 801 ACCTGCCACCAGCCCCCCAGCCTGCTTCTTCCCCTTAAGCTTTGTGCCCCTGGATGCGCTAACATTCACTCTTGTTTGTC
 881 CCTGGACTGGCCATGAAGTGAGGAGATGGTTATTTAAAGAGAATTCCCTATTTATTTGACAAAAAATCCAGTTAATATAT
 961 TAATGTGAAATAAACCCTGTTTGCACCTCGATTTGTTTGCTGAAAATGTGAAATAGTAAAAATGAAATAACTGGA
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' cuCUACCACCUC--AUC------GAGGUCCg 5'
            |: || || |  | |      ||||||| 
Target 5' ggGGAGGGGGCGCCTTGTTCTCCCTCCAGGt 3'
 78 - 108 141.00 -22.80
2 
miRNA  3' cuCUACCACCU----CAUCGAGGUCCg 5'
            || | || |    | : :|||||| 
Target 5' ttGAAGCTGTAAAATGAGCTTCCAGGg 3'
 569 - 595 131.00 -13.34
3 
miRNA  3' cucuaccacCUCAUCGAGGUCcg 5'
                   |||   ||:|||  
Target 5' cagcctcatGAGCCACTTCAGac 3'
 369 - 391 110.00 -8.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26556040 40 COSMIC
COSN31483076 54 COSMIC
COSN30139699 88 COSMIC
COSN31482995 101 COSMIC
COSN30752051 109 COSMIC
COSN25234701 172 COSMIC
COSN25242878 173 COSMIC
COSN6549322 236 COSMIC
COSN28974925 274 COSMIC
COSN30027236 473 COSMIC
COSN20619412 815 COSMIC
COSN30540833 852 COSMIC
COSN31566914 857 COSMIC
COSN1201353 858 COSMIC
COSN9673967 977 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1235895512 2 dbSNP
rs987121524 10 dbSNP
rs1337136606 11 dbSNP
rs1454580887 18 dbSNP
rs1407512235 19 dbSNP
rs774862579 20 dbSNP
rs553245181 23 dbSNP
rs770918318 25 dbSNP
rs1374255694 30 dbSNP
rs1167885651 31 dbSNP
rs1333666636 37 dbSNP
rs1309879752 38 dbSNP
rs1427497922 41 dbSNP
rs1261541177 42 dbSNP
rs1184586211 44 dbSNP
rs1463081603 45 dbSNP
rs1241811155 46 dbSNP
rs1354166758 48 dbSNP
rs1230022431 53 dbSNP
rs908605311 54 dbSNP
rs182026710 55 dbSNP
rs1253081093 57 dbSNP
rs777978881 59 dbSNP
rs114129161 62 dbSNP
rs1315523035 63 dbSNP
rs1247875484 66 dbSNP
rs748341225 67 dbSNP
rs922545264 69 dbSNP
rs1336036888 72 dbSNP
rs112525741 73 dbSNP
rs779735968 77 dbSNP
rs558160216 79 dbSNP
rs750335308 85 dbSNP
rs1385436458 87 dbSNP
rs968920843 87 dbSNP
rs376221037 89 dbSNP
rs765288135 94 dbSNP
rs1164393713 97 dbSNP
rs757175524 101 dbSNP
rs753392530 119 dbSNP
rs569387245 126 dbSNP
rs760348887 132 dbSNP
rs1377109088 137 dbSNP
rs1395598512 139 dbSNP
rs915096513 141 dbSNP
rs73997645 147 dbSNP
rs1449923849 151 dbSNP
rs1421095440 154 dbSNP
rs767786307 155 dbSNP
rs768255229 159 dbSNP
rs1030736735 160 dbSNP
rs767226716 160 dbSNP
rs536050054 165 dbSNP
rs1480458235 166 dbSNP
rs1292808943 167 dbSNP
rs1224961933 168 dbSNP
rs1357018615 170 dbSNP
rs1314039167 175 dbSNP
rs1239756218 176 dbSNP
rs774573008 177 dbSNP
rs970413602 178 dbSNP
rs1254895619 179 dbSNP
rs1390286274 180 dbSNP
rs1365603059 194 dbSNP
rs1216132408 198 dbSNP
rs563642327 199 dbSNP
rs547311902 200 dbSNP
rs1364113706 201 dbSNP
rs748961284 207 dbSNP
rs9899283 221 dbSNP
rs995765452 222 dbSNP
rs1404582250 231 dbSNP
rs563775025 235 dbSNP
rs1038516233 236 dbSNP
rs1356839742 242 dbSNP
rs1005662730 243 dbSNP
rs756588099 258 dbSNP
rs940211614 262 dbSNP
rs886159916 266 dbSNP
rs1413794728 270 dbSNP
rs35922446 270 dbSNP
rs887216340 270 dbSNP
rs1051527718 271 dbSNP
rs1201400869 274 dbSNP
rs1047127213 277 dbSNP
rs1487512319 284 dbSNP
rs1196546679 287 dbSNP
rs1264505806 289 dbSNP
rs932933097 289 dbSNP
rs1320110911 290 dbSNP
rs550176503 290 dbSNP
rs530397624 291 dbSNP
rs561452743 292 dbSNP
rs934043220 293 dbSNP
rs1398858554 296 dbSNP
rs922629367 298 dbSNP
rs1384219374 300 dbSNP
rs541523808 300 dbSNP
rs535566573 301 dbSNP
rs573036204 304 dbSNP
rs1359727753 308 dbSNP
rs1417607061 309 dbSNP
rs1476201030 314 dbSNP
rs947320267 318 dbSNP
rs1040085565 319 dbSNP
rs11645 322 dbSNP
rs1332464379 323 dbSNP
rs1234650950 324 dbSNP
rs942645133 328 dbSNP
rs769156097 329 dbSNP
rs981501525 330 dbSNP
rs1488413742 331 dbSNP
rs970151184 337 dbSNP
rs1269470422 339 dbSNP
rs1446816895 343 dbSNP
rs1291157992 346 dbSNP
rs1022962798 347 dbSNP
rs1216109958 348 dbSNP
rs995937567 349 dbSNP
rs1336210861 364 dbSNP
rs745449945 376 dbSNP
rs1364320845 383 dbSNP
rs956525202 387 dbSNP
rs1362283312 392 dbSNP
rs891302540 394 dbSNP
rs1440981633 396 dbSNP
rs923721824 408 dbSNP
rs1051474967 409 dbSNP
rs1410516217 413 dbSNP
rs1242797949 414 dbSNP
rs1308083363 416 dbSNP
rs997256916 419 dbSNP
rs1271683242 422 dbSNP
rs981867059 429 dbSNP
rs1468994892 435 dbSNP
rs566670076 438 dbSNP
rs1236605162 439 dbSNP
rs1459211544 440 dbSNP
rs1180279108 442 dbSNP
rs1326433358 442 dbSNP
rs1462955170 448 dbSNP
rs1023319314 455 dbSNP
rs1012298128 470 dbSNP
rs550509677 471 dbSNP
rs1392355461 472 dbSNP
rs559283070 473 dbSNP
rs79220087 476 dbSNP
rs1005708594 477 dbSNP
rs887284315 483 dbSNP
rs1298391365 484 dbSNP
rs914473625 485 dbSNP
rs1394620793 492 dbSNP
rs1053450667 493 dbSNP
rs1336037499 500 dbSNP
rs1475256301 502 dbSNP
rs1256159824 507 dbSNP
rs11549519 508 dbSNP
rs577193245 510 dbSNP
rs141368308 511 dbSNP
rs867443806 517 dbSNP
rs1039734850 519 dbSNP
rs538262690 521 dbSNP
rs575663220 522 dbSNP
rs970098947 523 dbSNP
rs757844270 527 dbSNP
rs528896853 532 dbSNP
rs1192306445 533 dbSNP
rs942675067 534 dbSNP
rs1420927483 535 dbSNP
rs1466719598 537 dbSNP
rs893760806 541 dbSNP
rs1170758574 544 dbSNP
rs1358176730 545 dbSNP
rs1304897661 546 dbSNP
rs1356661549 547 dbSNP
rs916010103 548 dbSNP
rs538879663 553 dbSNP
rs535566952 555 dbSNP
rs1215210398 559 dbSNP
rs1274619264 560 dbSNP
rs1300890848 564 dbSNP
rs1310616500 577 dbSNP
rs1015807968 579 dbSNP
rs1212460917 589 dbSNP
rs1004476199 592 dbSNP
rs1215878052 596 dbSNP
rs1485874772 596 dbSNP
rs1260907408 601 dbSNP
rs567100427 605 dbSNP
rs935204003 606 dbSNP
rs1029831392 608 dbSNP
rs997039117 609 dbSNP
rs1368748587 612 dbSNP
rs923773951 613 dbSNP
rs546863686 620 dbSNP
rs751934996 622 dbSNP
rs1362966726 623 dbSNP
rs1431602705 624 dbSNP
rs1365763528 626 dbSNP
rs916304418 644 dbSNP
rs539611393 646 dbSNP
rs1348385096 647 dbSNP
rs1239109578 661 dbSNP
rs1228192576 664 dbSNP
rs1448601989 669 dbSNP
rs1356479899 681 dbSNP
rs1215886513 689 dbSNP
rs1245689384 694 dbSNP
rs570831935 698 dbSNP
rs1487209925 702 dbSNP
rs778306566 705 dbSNP
rs1295698218 709 dbSNP
rs963371921 731 dbSNP
rs1015848420 733 dbSNP
rs1395275131 737 dbSNP
rs1439509338 741 dbSNP
rs758886234 743 dbSNP
rs1366036249 752 dbSNP
rs191539132 762 dbSNP
rs376041204 764 dbSNP
rs1348271651 765 dbSNP
rs561797709 765 dbSNP
rs1044286 770 dbSNP
rs1045530370 776 dbSNP
rs1326876645 776 dbSNP
rs1445791238 777 dbSNP
rs948570277 779 dbSNP
rs879221372 781 dbSNP
rs765566078 797 dbSNP
rs1224326222 798 dbSNP
rs1289027749 800 dbSNP
rs915973390 802 dbSNP
rs1214975489 807 dbSNP
rs1025780248 817 dbSNP
rs759524898 818 dbSNP
rs1225025627 819 dbSNP
rs901279856 822 dbSNP
rs1470710489 833 dbSNP
rs1163238921 837 dbSNP
rs767545607 840 dbSNP
rs1412224905 844 dbSNP
rs1489918031 848 dbSNP
rs755076514 849 dbSNP
rs11549524 853 dbSNP
rs530436062 857 dbSNP
rs941336850 858 dbSNP
rs1399838966 859 dbSNP
rs753961333 862 dbSNP
rs567957403 864 dbSNP
rs1421970329 867 dbSNP
rs1442619608 868 dbSNP
rs1255308273 874 dbSNP
rs1376829814 874 dbSNP
rs528354084 877 dbSNP
rs1273197106 880 dbSNP
rs1186631222 884 dbSNP
rs1216976315 887 dbSNP
rs893821835 891 dbSNP
rs1274652478 892 dbSNP
rs1224276199 893 dbSNP
rs1187234035 898 dbSNP
rs1053749338 908 dbSNP
rs982818353 909 dbSNP
rs2880 924 dbSNP
rs1296582552 928 dbSNP
rs1423078286 938 dbSNP
rs1441721267 942 dbSNP
rs1464107978 946 dbSNP
rs35810342 947 dbSNP
rs1169904791 956 dbSNP
rs1029947068 957 dbSNP
rs1410349719 965 dbSNP
rs902403055 979 dbSNP
rs1376337748 983 dbSNP
rs1046256165 986 dbSNP
rs187152539 987 dbSNP
rs1293818699 989 dbSNP
rs949225185 990 dbSNP
rs964563695 993 dbSNP
rs181726619 994 dbSNP
rs1433198258 995 dbSNP
rs1394872749 997 dbSNP
rs1285991754 1010 dbSNP
rs990983427 1013 dbSNP
rs1339590416 1021 dbSNP
rs545692295 1031 dbSNP
rs908900726 1032 dbSNP
rs113767977 1036 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 23558.0
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 GSM1065667. RNA binding protein: AGO1. Condition:4-thiouridine ...

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

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]
CLIP-seq Support 1 for dataset GSM1065667
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_6
Location of target site ENST00000254806.3 | 3UTR | GUUCUCCCUCCAGGUCUGAUCAUAAACAAUUACCAGGAACUAGCAUUGUGGGACAUUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
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
THCA -0.627 0.19 -0.800 0.1 4 Click to see details
THCA -0.627 0.19 -0.800 0.1 4 Click to see details
THCA -0.627 0.19 -0.800 0.1 4 Click to see details
57 hsa-miR-4254 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT061595 BTG2 BTG anti-proliferation factor 2 2 4
MIRT306302 ABCC5 ATP binding cassette subfamily C member 5 2 2
MIRT353697 ACTR2 ARP2 actin related protein 2 homolog 2 2
MIRT442351 RAB6B RAB6B, member RAS oncogene family 2 2
MIRT448535 RIMS4 regulating synaptic membrane exocytosis 4 2 2
MIRT449881 CYP3A5 cytochrome P450 family 3 subfamily A member 5 2 2
MIRT457644 ZNF69 zinc finger protein 69 2 2
MIRT458620 TRIM72 tripartite motif containing 72 2 2
MIRT470963 PKM pyruvate kinase, muscle 2 2
MIRT476285 GMFB glia maturation factor beta 2 10
MIRT477615 EFNA3 ephrin A3 2 2
MIRT482761 TMEM126B transmembrane protein 126B 2 2
MIRT492535 PSMD11 proteasome 26S subunit, non-ATPase 11 2 2
MIRT502995 CCDC71L coiled-coil domain containing 71 like 2 8
MIRT508467 HOXB6 homeobox B6 2 4
MIRT520190 WBP2 WW domain binding protein 2 2 2
MIRT525117 PRKD2 protein kinase D2 2 2
MIRT525773 SOD2 superoxide dismutase 2 2 2
MIRT526411 TFAM transcription factor A, mitochondrial 2 2
MIRT528152 AGTPBP1 ATP/GTP binding protein 1 2 2
MIRT534111 SOGA3 SOGA family member 3 2 2
MIRT538026 DNAJC10 DnaJ heat shock protein family (Hsp40) member C10 2 2
MIRT539288 ANGEL2 angel homolog 2 2 2
MIRT541103 RAF1 Raf-1 proto-oncogene, serine/threonine kinase 2 2
MIRT550999 SUOX sulfite oxidase 2 2
MIRT562165 HOXA13 homeobox A13 2 2
MIRT570122 CACNG8 calcium voltage-gated channel auxiliary subunit gamma 8 2 2
MIRT571104 DENND4B DENN domain containing 4B 2 2
MIRT574099 VASN vasorin 2 2
MIRT611153 ZNF486 zinc finger protein 486 2 2
MIRT612252 STX1B syntaxin 1B 2 4
MIRT614808 RIOK3 RIO kinase 3 2 2
MIRT622153 SORBS2 sorbin and SH3 domain containing 2 2 2
MIRT624286 CRCP CGRP receptor component 2 2
MIRT624875 ABCC12 ATP binding cassette subfamily C member 12 2 2
MIRT627479 STRN striatin 2 2
MIRT641273 AMDHD2 amidohydrolase domain containing 2 2 2
MIRT645622 TSPAN6 tetraspanin 6 2 2
MIRT650226 SIGLEC9 sialic acid binding Ig like lectin 9 2 2
MIRT657507 HBEGF heparin binding EGF like growth factor 2 2
MIRT660811 AHCY adenosylhomocysteinase 2 2
MIRT667439 METTL14 methyltransferase like 14 2 2
MIRT693744 ACACA acetyl-CoA carboxylase alpha 2 2
MIRT697852 UBE2Z ubiquitin conjugating enzyme E2 Z 2 2
MIRT698719 SUMO2 small ubiquitin-like modifier 2 2 2
MIRT699980 RREB1 ras responsive element binding protein 1 2 2
MIRT700689 POLR3D RNA polymerase III subunit D 2 2
MIRT703267 GNL3L G protein nucleolar 3 like 2 2
MIRT703787 FAM102B family with sequence similarity 102 member B 2 2
MIRT711277 SDR9C7 short chain dehydrogenase/reductase family 9C member 7 2 2
MIRT711863 TRAF2 TNF receptor associated factor 2 2 2
MIRT712451 KHNYN KH and NYN domain containing 2 2
MIRT714449 UBXN2A UBX domain protein 2A 2 2
MIRT718846 SNX20 sorting nexin 20 2 2
MIRT721333 IFNAR2 interferon alpha and beta receptor subunit 2 2 2
MIRT723315 PRKCH protein kinase C eta 2 2
MIRT736659 CYP2B6 cytochrome P450 family 2 subfamily B member 6 1 0
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-4254 Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-4254 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4254 Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-4254 Sunitinib 5329102 NSC750690 approved sensitive tissue
hsa-miR-4254 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4254 Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)
hsa-miR-4254 Cisplatin 5460033 NSC119875 approved resistant cell line (OVSAHO)

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