miRTarBase - #MIRT574099


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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 VASN   
Synonyms SLITL2
Description vasorin
Transcript NM_138440   
Expression
Putative miRNA Targets on VASN
3'UTR of VASN
(miRNA target sites are highlighted)		 
>VASN|NM_138440|3'UTR
   1 GCCAGAGAGAGACAGGGCAGCTGGGGCCGGGCTCTCAGCCAGTGAGATGGCCAGCCCCCTCCTGCTGCCACACCACGTAA
  81 GTTCTCAGTCCCAACCTCGGGGATGTGTGCAGACAGGGCTGTGTGACCACAGCTGGGCCCTGTTCCCTCTGGACCTCGGT
 161 CTCCTCATCTGTGAGATGCTGTGGCCCAGCTGACGAGCCCTAACGTCCCCAGAACCGAGTGCCTATGAGGACAGTGTCCG
 241 CCCTGCCCTCCGCAACGTGCAGTCCCTGGGCACGGCGGGCCCTGCCATGTGCTGGTAACGCATGCCTGGGCCCTGCTGGG
 321 CTCTCCCACTCCAGGCGGACCCTGGGGGCCAGTGAAGGAAGCTCCCGGAAAGAGCAGAGGGAGAGCGGGTAGGCGGCTGT
 401 GTGACTCTAGTCTTGGCCCCAGGAAGCGAAGGAACAAAAGAAACTGGAAAGGAAGATGCTTTAGGAACATGTTTTGCTTT
 481 TTTAAAATATATATATATTTATAAGAGATCCTTTCCCATTTATTCTGGGAAGATGTTTTTCAAACTCAGAGACAAGGACT
 561 TTGGTTTTTGTAAGACAAACGATGATATGAAGGCCTTTTGTAAGAAAAAATAAAAGATGAAGTGTGTTTAAAAAAAAAAA
 641 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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' cucuACCACCUCA-----UCGAGGUCCg 5'
              || |||: |     | ||||||| 
Target 5' gcccTGCTGGGCTCTCCCA-CTCCAGGc 3'
 310 - 336 146.00 -20.60
2 
miRNA  3' cucuacCACCU-CAUCGAGGUCCg 5'
                ||| | | |||||| || 
Target 5' gggccaGTGAAGGAAGCTCCCGGa 3'
 346 - 369 129.00 -16.10
3 
miRNA  3' cuCUACCACCUCAUCGAGGUCcg 5'
            |: ||  | ||: |||:||  
Target 5' taGGCGGCTGTGTGACTCTAGtc 3'
 390 - 412 121.00 -14.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN18739987 27 COSMIC
COSN23405894 74 COSMIC
COSN30175612 129 COSMIC
COSN30120150 168 COSMIC
COSN31544913 275 COSMIC
COSN17976595 279 COSMIC
COSN30169846 326 COSMIC
COSN15626908 393 COSMIC
COSN30111696 395 COSMIC
COSN31543546 417 COSMIC
COSN30137777 467 COSMIC
COSN30528633 487 COSMIC
COSN30111125 489 COSMIC
COSN30128444 499 COSMIC
COSN31530239 508 COSMIC
COSN30132556 512 COSMIC
COSN31519197 537 COSMIC
COSN15626909 558 COSMIC
COSN20112566 571 COSMIC
COSN30126226 581 COSMIC
COSN15626910 620 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1246248490 3 dbSNP
rs764588101 6 dbSNP
rs1218223137 7 dbSNP
rs1337908029 9 dbSNP
rs774877419 12 dbSNP
rs927766231 12 dbSNP
rs1291165739 14 dbSNP
rs760292195 14 dbSNP
rs1273409576 15 dbSNP
rs868070989 16 dbSNP
rs1483179609 17 dbSNP
rs1033253536 21 dbSNP
rs1253534170 22 dbSNP
rs935220934 22 dbSNP
rs754144001 27 dbSNP
rs1188210362 29 dbSNP
rs537529255 30 dbSNP
rs1213831092 32 dbSNP
rs752244621 37 dbSNP
rs1453305397 40 dbSNP
rs1359618322 49 dbSNP
rs1447383432 50 dbSNP
rs1431050002 54 dbSNP
rs1358043496 55 dbSNP
rs1445262519 57 dbSNP
rs1300798284 60 dbSNP
rs1024731035 62 dbSNP
rs1379356463 72 dbSNP
rs557206727 77 dbSNP
rs1164788847 78 dbSNP
rs540601047 78 dbSNP
rs893690478 84 dbSNP
rs180928330 87 dbSNP
rs1039321554 95 dbSNP
rs980627203 99 dbSNP
rs926440512 100 dbSNP
rs1490815633 103 dbSNP
rs937849375 104 dbSNP
rs545745967 108 dbSNP
rs1219130859 109 dbSNP
rs1292332685 110 dbSNP
rs984024070 113 dbSNP
rs997877325 116 dbSNP
rs116096591 117 dbSNP
rs890614352 123 dbSNP
rs1344554887 126 dbSNP
rs1256670293 128 dbSNP
rs1005085548 129 dbSNP
rs1015515378 140 dbSNP
rs963623904 145 dbSNP
rs1294592478 146 dbSNP
rs995105135 154 dbSNP
rs145570618 158 dbSNP
rs1023628932 159 dbSNP
rs1265767552 160 dbSNP
rs1174558338 161 dbSNP
rs1481419466 162 dbSNP
rs1269731688 180 dbSNP
rs1478378453 182 dbSNP
rs1176501682 188 dbSNP
rs939949437 195 dbSNP
rs1036668600 196 dbSNP
rs1205029418 199 dbSNP
rs900871692 204 dbSNP
rs542184040 205 dbSNP
rs758024548 206 dbSNP
rs928104912 208 dbSNP
rs1305736781 210 dbSNP
rs957016383 214 dbSNP
rs1177551392 217 dbSNP
rs562289074 218 dbSNP
rs1359256923 220 dbSNP
rs1418689182 221 dbSNP
rs889939816 226 dbSNP
rs1000293207 231 dbSNP
rs1334920066 233 dbSNP
rs113649657 234 dbSNP
rs183726419 240 dbSNP
rs564071007 241 dbSNP
rs1417223334 242 dbSNP
rs138013996 252 dbSNP
rs1010911907 253 dbSNP
rs1177718065 254 dbSNP
rs1220906350 256 dbSNP
rs946627616 257 dbSNP
rs753600129 258 dbSNP
rs1353139873 262 dbSNP
rs1214688096 264 dbSNP
rs1259628678 266 dbSNP
rs746612767 267 dbSNP
rs971842385 270 dbSNP
rs1001600891 271 dbSNP
rs546576737 272 dbSNP
rs1488816761 274 dbSNP
rs770965791 275 dbSNP
rs142609070 277 dbSNP
rs933696127 278 dbSNP
rs112850548 279 dbSNP
rs1016698015 284 dbSNP
rs1451640213 289 dbSNP
rs952120490 290 dbSNP
rs1347071134 292 dbSNP
rs549035207 295 dbSNP
rs1159129613 296 dbSNP
rs569017239 300 dbSNP
rs1395125866 301 dbSNP
rs886827152 303 dbSNP
rs537698143 313 dbSNP
rs1004372198 320 dbSNP
rs909707379 324 dbSNP
rs1260540808 328 dbSNP
rs780912089 332 dbSNP
rs1486540312 337 dbSNP
rs1260827172 338 dbSNP
rs1438610210 355 dbSNP
rs1036508165 358 dbSNP
rs3169377 359 dbSNP
rs1359408496 363 dbSNP
rs1290038582 365 dbSNP
rs1248549345 367 dbSNP
rs1341450271 368 dbSNP
rs1295072777 374 dbSNP
rs557936357 387 dbSNP
rs570572289 388 dbSNP
rs1298922425 396 dbSNP
rs539561722 412 dbSNP
rs973103291 413 dbSNP
rs1423920244 419 dbSNP
rs562946315 421 dbSNP
rs995070798 422 dbSNP
rs1165413837 424 dbSNP
rs1458165633 428 dbSNP
rs1372323513 430 dbSNP
rs1023933310 436 dbSNP
rs552924712 436 dbSNP
rs373338738 438 dbSNP
rs969370558 441 dbSNP
rs1361999282 447 dbSNP
rs1198147884 453 dbSNP
rs1490325913 460 dbSNP
rs745853542 465 dbSNP
rs1290137580 469 dbSNP
rs933682658 472 dbSNP
rs542496359 481 dbSNP
rs910949282 484 dbSNP
rs1309552432 487 dbSNP
rs778962433 487 dbSNP
rs956791907 487 dbSNP
rs1404344755 491 dbSNP
rs1438495145 496 dbSNP
rs562089503 500 dbSNP
rs988646305 505 dbSNP
rs935755636 506 dbSNP
rs1054519564 507 dbSNP
rs769769767 515 dbSNP
rs1304838505 521 dbSNP
rs1387306202 526 dbSNP
rs566388955 533 dbSNP
rs1463195724 536 dbSNP
rs774336577 536 dbSNP
rs1423969286 546 dbSNP
rs1175270817 561 dbSNP
rs1238141552 563 dbSNP
rs1010485313 566 dbSNP
rs200210521 570 dbSNP
rs1201614958 571 dbSNP
rs1046426315 581 dbSNP
rs921212658 582 dbSNP
rs1354604610 585 dbSNP
rs1227981298 586 dbSNP
rs1459376349 590 dbSNP
rs1288139919 591 dbSNP
rs555829386 593 dbSNP
rs1222938605 596 dbSNP
rs1050745005 599 dbSNP
rs1285331467 607 dbSNP
rs1233845479 620 dbSNP
rs1456834178 623 dbSNP
rs1335170177 625 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 GSM545212. RNA binding protein: AGO1. Condition:Control ...

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

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]
CLIP-seq Support 1 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_138440 | 3UTR | UCCCACUCCAGGCGGACCCUGGGGGCCAGUGAAGGAAGCUCCCGGAAAGAGCAGAGGGAGAGCGGGUAGGCGGCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM545212
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / Control
Location of target site ENST00000304735.3 | 3UTR | UCACUGCCUGCUUUCCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
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 -0.354 0.32 -0.600 0.2 4 Click to see details
THCA -0.354 0.32 -0.600 0.2 4 Click to see details
THCA -0.354 0.32 -0.600 0.2 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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