pre-miRNA Information
pre-miRNA hsa-mir-4480   
Genomic Coordinates chr10: 12578753 - 12578823
Description Homo sapiens miR-4480 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4480
Sequence 44| AGCCAAGUGGAAGUUACUUUA |64
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 1 10 + 12578796 23291724, 27587585 MiREDiBase
A-to-I 12 10 + 12578807 23291724, 27587585 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs929437808 7 dbSNP
rs1454494557 9 dbSNP
rs1345041659 17 dbSNP
rs561601367 21 dbSNP
Putative Targets

Gene Information
Gene Symbol PHLDA2   
Synonyms BRW1C, BWR1C, HLDA2, IPL, TSSC3
Description pleckstrin homology like domain family A member 2
Transcript NM_003311   
Expression
Putative miRNA Targets on PHLDA2
3'UTR of PHLDA2
(miRNA target sites are highlighted)
>PHLDA2|NM_003311|3'UTR
   1 GCCCGCCGCGGGCCATACGCTGGACGAGTCGGACCGAGGCTAGGACGTGGCCGGCGCTCTCCAGCCCTGCAGCAGAAGAA
  81 CTTCCCGTGCGCGCGGATCCTCGCTCCGTTGCACGGGCGCCTTAAGTTATTGGACTATCTAATATCTATGTATTTATTTC
 161 GCTGGTTCTTTGTAGTCACATATTTTATAGTCTTAATATCTTGTTTTTGCATCACTGTGCCCATTGCAAATAAATCACTT
 241 GGCCAGTTTGCTTTTCTACCATCCGGCTGTGGCTCAGTGAGACTCCTGCTGGGAGGGTGGAGGCCCAGGAATGGGCGGGC
 321 AGGACACCCTCATCCAGTCCTGCGGGGCTGGTGTGAAAGGCGCTGGGAACCGGCTTTGAATGAATAAATGAATCGTGTCA
 401 TCTGCAAAAAAAAAAAAAAAAA
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' auUUCAUUGAAGGUGAACCGa 5'
            || ||| |  |||||||| 
Target 5' gcAAATAAAT--CACTTGGCc 3'
226 - 244 159.00 -13.20
2
miRNA  3' auuuCAUUGAAGGUGAACCGa 5'
              | ::||   || |||| 
Target 5' gaccGAGGCTAGGACGTGGCc 3'
32 - 52 113.00 -9.80
3
miRNA  3' auuUCA--UUGAAGGUGAACCga 5'
             |||  :||| |::|| ||  
Target 5' ctcAGTGAGACTCCTGCTGGGag 3'
273 - 295 96.00 -10.80
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN29132576 128 COSMIC
COSN1131495 258 COSMIC
COSN6609073 275 COSMIC
COSN1528003 350 COSMIC
COSN26758018 605 COSMIC
COSN23988469 627 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs764245340 2 dbSNP
rs1199247133 7 dbSNP
rs1336135135 7 dbSNP
rs1248387213 8 dbSNP
rs925742769 10 dbSNP
rs1389631336 12 dbSNP
rs1198135911 13 dbSNP
rs558993627 15 dbSNP
rs780442733 16 dbSNP
rs945763216 17 dbSNP
rs1156540826 19 dbSNP
rs1383731760 23 dbSNP
rs1400507914 24 dbSNP
rs912924956 32 dbSNP
rs753174881 34 dbSNP
rs1481882880 38 dbSNP
rs1282782378 40 dbSNP
rs765490981 45 dbSNP
rs763184811 47 dbSNP
rs1266498514 49 dbSNP
rs200896318 50 dbSNP
rs1029443155 55 dbSNP
rs1466622116 57 dbSNP
rs979963482 62 dbSNP
rs1252394543 63 dbSNP
rs956298044 85 dbSNP
rs1179313553 88 dbSNP
rs1362869377 92 dbSNP
rs1472921329 96 dbSNP
rs1164261606 97 dbSNP
rs1435102479 98 dbSNP
rs952630860 106 dbSNP
rs1371661202 108 dbSNP
rs953068454 109 dbSNP
rs1031730513 113 dbSNP
rs1027753619 122 dbSNP
rs994911317 124 dbSNP
rs1245765507 128 dbSNP
rs897897368 128 dbSNP
rs904486227 129 dbSNP
rs1044455620 134 dbSNP
rs1483958082 139 dbSNP
rs550226914 146 dbSNP
rs896101035 153 dbSNP
rs929436877 154 dbSNP
rs1250523326 156 dbSNP
rs1189154392 158 dbSNP
rs538013101 165 dbSNP
rs752986329 174 dbSNP
rs1443193914 177 dbSNP
rs1163275680 184 dbSNP
rs1008847673 189 dbSNP
rs1432152082 194 dbSNP
rs890723771 197 dbSNP
rs1395819201 198 dbSNP
rs1313578201 204 dbSNP
rs1301449772 212 dbSNP
rs1396638446 214 dbSNP
rs1336424984 220 dbSNP
rs1051091511 221 dbSNP
rs932181691 222 dbSNP
rs1218289147 223 dbSNP
rs1368082766 234 dbSNP
rs904715996 237 dbSNP
rs1043212129 240 dbSNP
rs781745396 243 dbSNP
rs567502188 244 dbSNP
rs549191436 249 dbSNP
rs1250308559 255 dbSNP
rs1201626732 258 dbSNP
rs1332824054 260 dbSNP
rs945817119 263 dbSNP
rs1183424333 268 dbSNP
rs1400274825 272 dbSNP
rs912978695 274 dbSNP
rs1056819 275 dbSNP
rs1168987638 280 dbSNP
rs10582 281 dbSNP
rs1466627573 287 dbSNP
rs200466299 289 dbSNP
rs927251341 294 dbSNP
rs980399477 296 dbSNP
rs952647134 299 dbSNP
rs1367055608 304 dbSNP
rs567045646 309 dbSNP
rs778967589 309 dbSNP
rs1294803839 314 dbSNP
rs551311316 315 dbSNP
rs1234791048 317 dbSNP
rs1260687322 318 dbSNP
rs972539111 319 dbSNP
rs932556576 321 dbSNP
rs962137480 324 dbSNP
rs1269579013 332 dbSNP
rs749978736 333 dbSNP
rs1466547546 334 dbSNP
rs1452832201 340 dbSNP
rs563296393 354 dbSNP
rs1179385722 358 dbSNP
rs1440216447 367 dbSNP
rs755113607 370 dbSNP
rs976653891 376 dbSNP
rs1008869086 377 dbSNP
rs954842364 386 dbSNP
rs1028979850 388 dbSNP
rs1160223953 389 dbSNP
rs1391050126 393 dbSNP
rs1194008217 405 dbSNP
rs996853997 407 dbSNP
rs532813465 415 dbSNP
rs1043280012 417 dbSNP
rs1031927996 420 dbSNP
rs1388421146 421 dbSNP
rs764789779 425 dbSNP
rs1209653267 465 dbSNP
rs891553052 468 dbSNP
rs1228415052 469 dbSNP
rs969243379 471 dbSNP
rs1056878668 473 dbSNP
rs562768788 474 dbSNP
rs1214175007 481 dbSNP
rs1260494593 485 dbSNP
rs1310783248 486 dbSNP
rs1240310966 488 dbSNP
rs1335681328 493 dbSNP
rs926982043 494 dbSNP
rs1414476936 496 dbSNP
rs115215816 510 dbSNP
rs753473745 511 dbSNP
rs919847567 513 dbSNP
rs1158165870 515 dbSNP
rs972550976 518 dbSNP
rs374662530 520 dbSNP
rs1035915954 521 dbSNP
rs558408518 523 dbSNP
rs1364824706 524 dbSNP
rs574012320 532 dbSNP
rs561861534 534 dbSNP
rs75881889 536 dbSNP
rs80068504 537 dbSNP
rs907976061 544 dbSNP
rs61871194 551 dbSNP
rs1159318790 552 dbSNP
rs1222829767 553 dbSNP
rs1306786944 555 dbSNP
rs987542507 561 dbSNP
rs954797418 565 dbSNP
rs540472597 567 dbSNP
rs1056832 568 dbSNP
rs1248561888 569 dbSNP
rs1290240448 572 dbSNP
rs996183042 572 dbSNP
rs114660250 576 dbSNP
rs1234662232 590 dbSNP
rs1425514247 595 dbSNP
rs1479802602 599 dbSNP
rs1176867718 600 dbSNP
rs553976538 604 dbSNP
rs1021845418 609 dbSNP
rs1384604238 610 dbSNP
rs1430316885 623 dbSNP
rs1038313904 628 dbSNP
rs1352230185 629 dbSNP
rs1187019212 632 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' auUUCAUUGAAGGUGAACCGa 5'
            || ||| |  |||||||| 
Target 5' -cAAAUAAAU--CACUUGGCc 3'
1 - 18
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 ENST00000314222.4 | 3UTR | CAAAUAAAUCACUUGGCCAGUUUG
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
117 hsa-miR-4480 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT056040 MLLT10 MLLT10, histone lysine methyltransferase DOT1L cofactor 2 2
MIRT091259 FXR1 FMR1 autosomal homolog 1 2 4
MIRT117347 MAPRE2 microtubule associated protein RP/EB family member 2 2 2
MIRT234960 ZNF439 zinc finger protein 439 2 4
MIRT441356 ZNF75A zinc finger protein 75a 2 2
MIRT441426 STXBP2 syntaxin binding protein 2 2 2
MIRT441455 ZNF488 zinc finger protein 488 2 4
MIRT441524 ZBTB10 zinc finger and BTB domain containing 10 2 2
MIRT441576 EXOC5 exocyst complex component 5 2 2
MIRT441597 ABCB5 ATP binding cassette subfamily B member 5 2 6
MIRT441610 ATP13A4 ATPase 13A4 2 2
MIRT441698 CIT citron rho-interacting serine/threonine kinase 2 2
MIRT441714 FGF9 fibroblast growth factor 9 2 2
MIRT441784 MAPK8 mitogen-activated protein kinase 8 2 4
MIRT441795 EXOSC2 exosome component 2 2 2
MIRT441868 RNASEL ribonuclease L 2 2
MIRT441900 SLC9A8 solute carrier family 9 member A8 2 6
MIRT441919 FAM217B family with sequence similarity 217 member B 2 2
MIRT441928 C1orf109 chromosome 1 open reading frame 109 2 2
MIRT441938 RIMKLB ribosomal modification protein rimK like family member B 2 2
MIRT442157 DPY19L1 dpy-19 like C-mannosyltransferase 1 2 2
MIRT442172 AZF1 azoospermia factor 1 2 2
MIRT442208 IRS1 insulin receptor substrate 1 2 2
MIRT442237 DDX19A DEAD-box helicase 19A 2 2
MIRT442366 ZC3HAV1L zinc finger CCCH-type containing, antiviral 1 like 2 2
MIRT442572 SDC1 syndecan 1 2 2
MIRT442604 ZNF391 zinc finger protein 391 2 2
MIRT442609 MRC1 mannose receptor C-type 1 2 2
MIRT442647 POP4 POP4 homolog, ribonuclease P/MRP subunit 2 2
MIRT442658 OIP5 Opa interacting protein 5 2 6
MIRT442686 COX15 COX15, cytochrome c oxidase assembly homolog 2 2
MIRT442773 JAG1 jagged 1 2 2
MIRT442785 CHD8 chromodomain helicase DNA binding protein 8 2 2
MIRT442895 PLCB3 phospholipase C beta 3 2 2
MIRT442941 C17orf105 chromosome 17 open reading frame 105 2 2
MIRT442959 SGCD sarcoglycan delta 2 2
MIRT442998 EDAR ectodysplasin A receptor 2 2
MIRT443017 C21orf91 chromosome 21 open reading frame 91 2 2
MIRT443064 CASP5 caspase 5 2 2
MIRT443069 ABLIM1 actin binding LIM protein 1 2 2
MIRT443208 VPS36 vacuolar protein sorting 36 homolog 2 2
MIRT443237 ANKRD26 ankyrin repeat domain 26 2 2
MIRT443253 A1CF APOBEC1 complementation factor 2 2
MIRT443329 JUN Jun proto-oncogene, AP-1 transcription factor subunit 2 2
MIRT443333 NRAS NRAS proto-oncogene, GTPase 2 2
MIRT443349 STX7 syntaxin 7 2 2
MIRT443452 CLIC5 chloride intracellular channel 5 2 2
MIRT443547 GPR35 G protein-coupled receptor 35 2 2
MIRT443616 AVPR1A arginine vasopressin receptor 1A 2 2
MIRT443626 CPSF2 cleavage and polyadenylation specific factor 2 2 2
MIRT443730 ALPK3 alpha kinase 3 2 2
MIRT443786 ST13 ST13, Hsp70 interacting protein 2 2
MIRT443852 RGS6 regulator of G protein signaling 6 2 2
MIRT445483 KLF5 Kruppel like factor 5 2 2
MIRT471105 PHLDA2 pleckstrin homology like domain family A member 2 2 2
MIRT472329 NETO2 neuropilin and tolloid like 2 2 4
MIRT472391 NDRG3 NDRG family member 3 2 2
MIRT473522 MAX MYC associated factor X 2 2
MIRT473874 MAFK MAF bZIP transcription factor K 2 6
MIRT476021 GTF2A1 general transcription factor IIA subunit 1 2 2
MIRT478320 DDN dendrin 2 2
MIRT492049 TNFSF9 TNF superfamily member 9 2 2
MIRT494851 ANKRD24 ankyrin repeat domain 24 2 2
MIRT494991 TSSC1 EARP complex and GARP complex interacting protein 1 2 2
MIRT495034 RASSF2 Ras association domain family member 2 2 2
MIRT495111 NOL10 nucleolar protein 10 2 2
MIRT495113 TRADD TNFRSF1A associated via death domain 2 2
MIRT495131 METTL24 methyltransferase like 24 2 2
MIRT495147 STAC2 SH3 and cysteine rich domain 2 2 2
MIRT495297 NUP54 nucleoporin 54 2 2
MIRT495341 RTN2 reticulon 2 2 2
MIRT495347 ATP5S ATP synthase, H+ transporting, mitochondrial Fo complex subunit s (factor B) 2 2
MIRT496682 DUSP18 dual specificity phosphatase 18 2 2
MIRT496743 TGFBR1 transforming growth factor beta receptor 1 2 2
MIRT496841 KCNIP2 potassium voltage-gated channel interacting protein 2 2 2
MIRT496852 GPAM glycerol-3-phosphate acyltransferase, mitochondrial 2 2
MIRT496889 FOXP1 forkhead box P1 2 2
MIRT496922 CLMN calmin 2 2
MIRT496990 TMEM231 transmembrane protein 231 2 2
MIRT497002 SNAP25 synaptosome associated protein 25 2 2
MIRT497058 C6orf223 chromosome 6 open reading frame 223 2 2
MIRT500529 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta 2 6
MIRT506048 PPP6C protein phosphatase 6 catalytic subunit 2 4
MIRT512163 CD164 CD164 molecule 2 6
MIRT527051 RDH13 retinol dehydrogenase 13 2 2
MIRT532282 TNFSF14 TNF superfamily member 14 2 2
MIRT534083 SPRY4 sprouty RTK signaling antagonist 4 2 2
MIRT534605 RNASEH1 ribonuclease H1 2 4
MIRT539509 ACSS3 acyl-CoA synthetase short chain family member 3 2 2
MIRT543069 ARID4B AT-rich interaction domain 4B 2 2
MIRT544233 CCBL2 kynurenine aminotransferase 3 2 2
MIRT544686 ZNF224 zinc finger protein 224 2 4
MIRT546269 TMEM30A transmembrane protein 30A 2 4
MIRT559069 C19orf47 chromosome 19 open reading frame 47 2 2
MIRT562768 RMI2 RecQ mediated genome instability 2 2 2
MIRT563974 HCFC1 host cell factor C1 2 2
MIRT564086 NSA2 NSA2, ribosome biogenesis homolog 2 2
MIRT564525 PDXP pyridoxal phosphatase 2 2
MIRT564613 ZNF703 zinc finger protein 703 2 2
MIRT566252 PTBP1 polypyrimidine tract binding protein 1 2 2
MIRT614420 ZNF440 zinc finger protein 440 2 2
MIRT618789 MTHFR methylenetetrahydrofolate reductase 2 2
MIRT619160 PPDPF pancreatic progenitor cell differentiation and proliferation factor 2 2
MIRT641778 ZDHHC7 zinc finger DHHC-type containing 7 2 4
MIRT653680 SLC25A36 solute carrier family 25 member 36 2 2
MIRT657861 GJD2 gap junction protein delta 2 2 2
MIRT660879 ADCYAP1R1 ADCYAP receptor type I 2 2
MIRT668781 DAAM1 dishevelled associated activator of morphogenesis 1 2 4
MIRT688559 DCAF16 DDB1 and CUL4 associated factor 16 2 2
MIRT695393 WDR41 WD repeat domain 41 2 2
MIRT698680 TCEA1 transcription elongation factor A1 2 2
MIRT700974 PDIA6 protein disulfide isomerase family A member 6 2 2
MIRT705055 C5orf15 chromosome 5 open reading frame 15 2 2
MIRT705864 AFF1 AF4/FMR2 family member 1 2 2
MIRT710586 CDCA4 cell division cycle associated 4 2 2
MIRT713904 IGF2R insulin like growth factor 2 receptor 2 2
MIRT717133 SKI SKI proto-oncogene 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-4480 Cisplatin 5460033 NSC119875 approved sensitive cell line (CIS)
hsa-miR-4480 Cisplatin 5460033 NSC119875 approved resistant cell line (A549)

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