miRTarBase - #MIRT464897


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pre-miRNA Information
pre-miRNA hsa-mir-4259   
Genomic Coordinates chr1: 159899979 - 159900079
Description Homo sapiens miR-4259 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4259
Sequence 70| CAGUUGGGUCUAGGGGUCAGGA |91
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1237551241 4 dbSNP
rs772339482 8 dbSNP
rs1314022637 15 dbSNP
rs1414601728 19 dbSNP
rs746067692 20 dbSNP
rs779101228 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol UBALD1   
Synonyms FAM100A, PP11303
Description UBA like domain containing 1
Transcript NM_145253   
Expression
Putative miRNA Targets on UBALD1
3'UTR of UBALD1
(miRNA target sites are highlighted)		 
>UBALD1|NM_145253|3'UTR
   1 GGGAGGCCCCTCCCCCCTCCCGGAGGCCAGGACCCCGTGGGGCGGGGGAGAGGACGTCTCTGCGGGCCCCCTTCACCCCT
  81 TTTCTGTCTGCACCCCTTGTTCCCCGGAGCCCTGGAGGGGAGAGCGCGGACTCTAGCCAGGCAGGGACACGTCTGGTGCC
 161 AGAACACGCAGCTGCCCACACGCAAGGTCATGGCCCCAGCGGCCCCGGCACATGGAGTGGTTCAGAGCGGCCTGGGTGCC
 241 TGGCGGACAGAACTTCAGAGACCACGCAGCCTTCCTTCGAAGACGCACCTGCCCAGCCCAGCCCAGGGGTGCCGTGGAGG
 321 ACCACCCTGGCGGAGACATTGCTGATCCCTGGCTTGGAGCTCCTTGGGGGCCGGCAGGCCTCGACCCCCACCCTAGGGAA
 401 TGCAGAGCCTCTCCGCATGTGTGCGCGTGGCCGTGTCTGTGTATTTCTACGTGTGTCGCTCTTCAGAAGCAACCTAGTTC
 481 CTGGGGCAGCTGGACTTTGCATGTTAGTGTGAGCCCCCAGCCCCCTGCCCGCCGCCCCCTCCCCAGGGCCCTGCCTCCTC
 561 CCCACCCCCTCGTCAGCCAGCGTTGCTGTTCCTTGCAGAGAAAAGGATTGTGGGAAACTCCAGGACTCTTCCCACCGCCT
 641 CCCAGCGCCTGCCTGCTGGGGCTGCCTGCATGCCTCCCCTGCACCTGGGGGTACCCGCATCCACTTCCTTTCCCCCTTTT
 721 AACAAAAGAGAAGAACGAATTCCAAACCACAAAAAAAAAAAAAAAAA
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' aggacUGG--GGAUCUGGGUUGac 5'
               |||  || || ||||:|  
Target 5' gacgcACCTGCCCAG-CCCAGCcc 3'
 282 - 304 118.00 -19.90
2 
miRNA  3' aggacugGGGAUCUGGGUUGac 5'
                 :| |:| ||||:|  
Target 5' cgcaaggTCATGGCCCCAGCgg 3'
 181 - 202 115.00 -15.00
3 
miRNA  3' aggacUGG-GGAUCUGGGUUGac 5'
               ||| |||   ||||:|  
Target 5' ttcccACCGCCT---CCCAGCgc 3'
 629 - 648 114.00 -16.40
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31961162 168 COSMIC
COSN8232566 175 COSMIC
COSN20078478 236 COSMIC
COSN26123331 266 COSMIC
COSN31539907 415 COSMIC
COSN6645845 426 COSMIC
COSN30538666 621 COSMIC
COSN15001626 659 COSMIC
COSN30169381 663 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs766229180 1 dbSNP
rs936122052 4 dbSNP
rs962533059 6 dbSNP
rs1235676972 12 dbSNP
rs1294503600 12 dbSNP
rs762464861 13 dbSNP
rs1270076967 15 dbSNP
rs372905090 16 dbSNP
rs772516296 17 dbSNP
rs746251587 18 dbSNP
rs747552005 18 dbSNP
rs774856515 20 dbSNP
rs771357717 21 dbSNP
rs200303724 22 dbSNP
rs1363929489 25 dbSNP
rs777899930 29 dbSNP
rs1434862620 32 dbSNP
rs756301232 33 dbSNP
rs748315853 36 dbSNP
rs781420679 37 dbSNP
rs1431763669 40 dbSNP
rs201775709 41 dbSNP
rs139182752 43 dbSNP
rs758308812 44 dbSNP
rs1433447551 48 dbSNP
rs1317633373 55 dbSNP
rs746291942 56 dbSNP
rs971012697 63 dbSNP
rs961902289 64 dbSNP
rs1167525763 66 dbSNP
rs1018763770 67 dbSNP
rs1178923654 71 dbSNP
rs1257227169 72 dbSNP
rs1024073662 79 dbSNP
rs1418063246 83 dbSNP
rs1176256669 91 dbSNP
rs1396438418 93 dbSNP
rs1434980446 98 dbSNP
rs570916237 102 dbSNP
rs551109400 105 dbSNP
rs1050736208 106 dbSNP
rs531376975 112 dbSNP
rs569011345 113 dbSNP
rs1054284128 114 dbSNP
rs1000557402 117 dbSNP
rs1374127535 119 dbSNP
rs1390832625 123 dbSNP
rs1307219144 124 dbSNP
rs548947233 125 dbSNP
rs767299066 126 dbSNP
rs1484049849 127 dbSNP
rs781367725 128 dbSNP
rs1251762713 137 dbSNP
rs946121722 144 dbSNP
rs879474929 147 dbSNP
rs931995121 151 dbSNP
rs917429390 153 dbSNP
rs1314687590 154 dbSNP
rs1226368191 165 dbSNP
rs1378409219 167 dbSNP
rs1431855146 168 dbSNP
rs1057298053 169 dbSNP
rs937621195 172 dbSNP
rs1465584730 174 dbSNP
rs923244157 175 dbSNP
rs927573675 176 dbSNP
rs1396836912 178 dbSNP
rs1040875328 179 dbSNP
rs984331975 181 dbSNP
rs371326966 182 dbSNP
rs1365775469 187 dbSNP
rs376614137 192 dbSNP
rs529185881 193 dbSNP
rs940765585 196 dbSNP
rs1307037371 198 dbSNP
rs908063795 199 dbSNP
rs984968459 200 dbSNP
rs952311758 201 dbSNP
rs961820763 202 dbSNP
rs368508873 204 dbSNP
rs1420733698 205 dbSNP
rs560019884 206 dbSNP
rs980321424 207 dbSNP
rs971071020 210 dbSNP
rs1322980684 219 dbSNP
rs841183 226 dbSNP
rs532782410 228 dbSNP
rs955809395 229 dbSNP
rs1295111817 234 dbSNP
rs1335402982 237 dbSNP
rs1484079936 238 dbSNP
rs563813137 239 dbSNP
rs1287166435 242 dbSNP
rs1249641185 244 dbSNP
rs1216118657 245 dbSNP
rs1243054368 258 dbSNP
rs1033299745 262 dbSNP
rs1488203961 263 dbSNP
rs544275858 265 dbSNP
rs953295131 266 dbSNP
rs1475839441 272 dbSNP
rs1162686461 279 dbSNP
rs1411780698 284 dbSNP
rs1431160294 286 dbSNP
rs1160194089 287 dbSNP
rs1359644202 289 dbSNP
rs1028886112 290 dbSNP
rs999990706 292 dbSNP
rs889585560 293 dbSNP
rs1355965728 295 dbSNP
rs1000041518 301 dbSNP
rs1374972149 302 dbSNP
rs1223984001 304 dbSNP
rs1214855299 307 dbSNP
rs1284794428 307 dbSNP
rs1351060220 307 dbSNP
rs904559770 308 dbSNP
rs1041682353 310 dbSNP
rs1028207187 311 dbSNP
rs751598535 313 dbSNP
rs1010315923 314 dbSNP
rs1219136013 320 dbSNP
rs998032745 322 dbSNP
rs895892586 327 dbSNP
rs901873031 329 dbSNP
rs184874522 330 dbSNP
rs1418130488 331 dbSNP
rs841182 332 dbSNP
rs1435091140 340 dbSNP
rs1230087554 343 dbSNP
rs886522565 347 dbSNP
rs1049573008 353 dbSNP
rs930806405 364 dbSNP
rs542102146 366 dbSNP
rs11641419 367 dbSNP
rs1442216358 368 dbSNP
rs374995189 372 dbSNP
rs916938182 373 dbSNP
rs863499 376 dbSNP
rs1236102508 379 dbSNP
rs971718457 382 dbSNP
rs539808451 383 dbSNP
rs1200373498 388 dbSNP
rs1394122863 389 dbSNP
rs988491232 393 dbSNP
rs1160570375 394 dbSNP
rs1237664914 399 dbSNP
rs369831248 402 dbSNP
rs1438032398 408 dbSNP
rs1195810640 409 dbSNP
rs955856813 414 dbSNP
rs1477543518 415 dbSNP
rs1032768011 420 dbSNP
rs1170600163 422 dbSNP
rs1398495404 424 dbSNP
rs978449694 425 dbSNP
rs570879570 426 dbSNP
rs1028096163 427 dbSNP
rs998088529 430 dbSNP
rs953253033 432 dbSNP
rs901083486 433 dbSNP
rs1342023372 440 dbSNP
rs1219833776 441 dbSNP
rs1257502711 443 dbSNP
rs1019403205 448 dbSNP
rs557418374 450 dbSNP
rs537537204 451 dbSNP
rs1049191959 457 dbSNP
rs371247558 458 dbSNP
rs906057935 469 dbSNP
rs1196425550 480 dbSNP
rs1374635624 489 dbSNP
rs1475684062 490 dbSNP
rs1044574538 492 dbSNP
rs950317340 501 dbSNP
rs917508566 504 dbSNP
rs1420813073 511 dbSNP
rs1327051010 515 dbSNP
rs1389515634 518 dbSNP
rs1384737647 519 dbSNP
rs1328632048 526 dbSNP
rs938726679 526 dbSNP
rs113786484 527 dbSNP
rs1233372089 528 dbSNP
rs1332279501 530 dbSNP
rs928620403 531 dbSNP
rs1194668194 534 dbSNP
rs895763228 536 dbSNP
rs749946004 537 dbSNP
rs980063398 540 dbSNP
rs568508079 543 dbSNP
rs1453111162 545 dbSNP
rs1330263442 546 dbSNP
rs1283758764 549 dbSNP
rs1476164297 550 dbSNP
rs764898113 551 dbSNP
rs1406697093 552 dbSNP
rs1035795108 553 dbSNP
rs1348484454 554 dbSNP
rs1307358887 556 dbSNP
rs1326266009 559 dbSNP
rs1397342663 560 dbSNP
rs1287082406 564 dbSNP
rs761420427 566 dbSNP
rs1048591513 568 dbSNP
rs776355520 569 dbSNP
rs549115103 571 dbSNP
rs1339032114 572 dbSNP
rs897419319 572 dbSNP
rs989432355 576 dbSNP
rs934354070 581 dbSNP
rs1037249844 582 dbSNP
rs940389239 582 dbSNP
rs1354683728 585 dbSNP
rs1198361927 587 dbSNP
rs1215573946 588 dbSNP
rs1283649271 595 dbSNP
rs1486598025 596 dbSNP
rs529088034 614 dbSNP
rs1302413336 616 dbSNP
rs1231723572 618 dbSNP
rs978506888 621 dbSNP
rs1421484794 623 dbSNP
rs953784951 624 dbSNP
rs1028148342 627 dbSNP
rs1225062452 635 dbSNP
rs561306633 636 dbSNP
rs376854414 637 dbSNP
rs1359074583 639 dbSNP
rs1015519866 641 dbSNP
rs978555751 645 dbSNP
rs1004509173 646 dbSNP
rs759893817 647 dbSNP
rs950771315 651 dbSNP
rs1239757405 653 dbSNP
rs1466219331 660 dbSNP
rs750285221 663 dbSNP
rs1349868832 665 dbSNP
rs1210577115 668 dbSNP
rs1027643524 673 dbSNP
rs767241537 674 dbSNP
rs1331038988 675 dbSNP
rs1020160666 676 dbSNP
rs905943145 683 dbSNP
rs1044458642 685 dbSNP
rs1405536989 687 dbSNP
rs989110536 691 dbSNP
rs1177435009 696 dbSNP
rs1014430551 697 dbSNP
rs895941139 698 dbSNP
rs1182961068 705 dbSNP
rs1401173181 716 dbSNP
rs960080202 717 dbSNP
rs1373476948 728 dbSNP
rs1036086502 733 dbSNP
rs570454594 736 dbSNP
rs1310349691 737 dbSNP
rs1229578882 741 dbSNP
rs533087503 742 dbSNP
rs761585050 747 dbSNP
rs774624173 748 dbSNP
rs1042698128 749 dbSNP
rs1456978119 750 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
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 GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' aggacugggGAUCU---GGGUUGAc 5'
                   ||| |   ||||||| 
Target 5' ---------CUACACCCCCCAACUu 3'
 		1 - 16
Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
CLIP-seq Support 1 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000590965.1 | 3UTR | cuacaccccccaacuucccug
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
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
40 hsa-miR-4259 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT074403 TNRC6A trinucleotide repeat containing 6A 2 2
MIRT082380 HNRNPUL1 heterogeneous nuclear ribonucleoprotein U like 1 2 6
MIRT224489 NDRG1 N-myc downstream regulated 1 2 2
MIRT227807 GTF3C4 general transcription factor IIIC subunit 4 2 2
MIRT293253 DR1 down-regulator of transcription 1 2 2
MIRT455060 MEN1 menin 1 2 2
MIRT459206 RCE1 Ras converting CAAX endopeptidase 1 2 2
MIRT464866 UBB ubiquitin B 2 8
MIRT464897 UBALD1 UBA like domain containing 1 2 2
MIRT467210 SPRY4 sprouty RTK signaling antagonist 4 2 2
MIRT467749 SLC36A1 solute carrier family 36 member 1 2 2
MIRT470565 POU2F1 POU class 2 homeobox 1 2 2
MIRT473523 MAX MYC associated factor X 2 2
MIRT474955 KCTD10 potassium channel tetramerization domain containing 10 2 4
MIRT478575 CTNND1 catenin delta 1 2 2
MIRT479952 CBX4 chromobox 4 2 6
MIRT486151 SIX5 SIX homeobox 5 2 6
MIRT488836 MRRF mitochondrial ribosome recycling factor 2 2
MIRT489466 MSC musculin 2 2
MIRT498922 SRCAP Snf2 related CREBBP activator protein 2 2
MIRT501166 SLC10A7 solute carrier family 10 member 7 2 6
MIRT504195 FAM127B retrotransposon Gag like 8A 2 2
MIRT507342 FAM168A family with sequence similarity 168 member A 2 2
MIRT512629 GPX1 glutathione peroxidase 1 2 4
MIRT514365 UBBP4 ubiquitin B pseudogene 4 2 6
MIRT523321 H3F3B H3 histone family member 3B 2 2
MIRT529793 AP4S1 adaptor related protein complex 4 sigma 1 subunit 2 2
MIRT544301 TSPYL1 TSPY like 1 2 2
MIRT552985 VAT1 vesicle amine transport 1 2 2
MIRT562785 LIMA1 LIM domain and actin binding 1 2 2
MIRT653090 SSR3 signal sequence receptor subunit 3 2 2
MIRT661985 DSN1 DSN1 homolog, MIS12 kinetochore complex component 2 4
MIRT666982 PHAX phosphorylated adaptor for RNA export 2 2
MIRT683255 WFDC6 WAP four-disulfide core domain 6 2 2
MIRT684051 FOLR1 folate receptor 1 2 2
MIRT686137 B4GALT7 beta-1,4-galactosyltransferase 7 2 2
MIRT688435 DNAL1 dynein axonemal light chain 1 2 2
MIRT698391 TMED2 transmembrane p24 trafficking protein 2 2 2
MIRT698819 STK38 serine/threonine kinase 38 2 2
MIRT715754 HSD11B1L hydroxysteroid 11-beta dehydrogenase 1 like 2 2
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-4259 Cisplatin 5460033 NSC119875 approved resistant High Pancreatic Cancer cell line (BxPC-3)
hsa-miR-4259 Fluorouracil 3385 NSC19893 approved sensitive High Pancreatic Cancer cell line (PATU8988)
hsa-miR-4259 Paclitaxel 36314 NSC125973 approved resistant High Non-Small Cell Lung Cancer cell line (A549)
hsa-miR-4259 Imatinib 5291 NSC743414 approved resistant High Chronic Myelogenous Leukemia cell line (K562)
hsa-miR-4259 Temozolomide 5394 NSC362856 approved resistant High Glioblastoma cell line (U251)
hsa-mir-4259 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-miR-4259 Temozolomide 5394 NSC362856 approved sensitive cell line (U251)
hsa-miR-4259 Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-4259 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4259 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-4259 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)
hsa-miR-4259 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4259 Docetaxel+Cisplatin+5-Fluorouracil resistant tissue (hypopharyngeal squamous cell carcinoma)

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