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 PPDPF   
Synonyms C20orf149, dJ697K14.9, exdpf
Description pancreatic progenitor cell differentiation and proliferation factor
Transcript NM_024299   
Expression
Putative miRNA Targets on PPDPF
3'UTR of PPDPF
(miRNA target sites are highlighted)
>PPDPF|NM_024299|3'UTR
   1 CCTGAGCGGTTACCACCAGCCCCAGGCCTGCGGAGGCGCTAGTCCACCAGAGCCCCTCCCCGCCCCTCTCCCCACTCCGC
  81 ATCCCTCGCCCCCCTCCCCACCTCCCACCCCCCACCCTGTAAACTAGGCGGCTGCAGCAAGCAGACCTTCGCATCAACAC
 161 AGCAGACACCAAAAACCAGTGAGAGCCCCGCTCTCTACCGCCCGGCCCCAGCACTCGCTAGCTTTCCTGACACCTGGAAC
 241 TGTGCACCTGGCACCAAGCGGAAAATAAACTCCAAGCAGCCAGTAGCCCCGAAAAAAAAAAAAAAAAAA
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' auuuCAUUGA-AGGUGAACCGa 5'
              | |||| | ||| |||| 
Target 5' acctGGAACTGTGCACCTGGCa 3'
232 - 253 129.00 -9.90
2
miRNA  3' auuuCAUUGAAGGUGAACCGa 5'
              ||||     ||| ||| 
Target 5' ccctGTAA-----ACTAGGCg 3'
115 - 130 112.00 -5.60
3
miRNA  3' auuucauugaaGGUGAACCGa 5'
                     |||||  || 
Target 5' cgcccctctccCCACTCCGCa 3'
61 - 81 86.00 -6.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26990006 5 COSMIC
COSN30519389 9 COSMIC
COSN31784965 32 COSMIC
COSN20053373 80 COSMIC
COSN1252202 104 COSMIC
COSN30631495 114 COSMIC
COSN30532298 284 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1273745320 1 dbSNP
rs1348208274 3 dbSNP
rs765173465 3 dbSNP
rs988831075 4 dbSNP
rs776086297 5 dbSNP
rs769356807 9 dbSNP
rs777124295 14 dbSNP
rs1160918821 19 dbSNP
rs554285189 20 dbSNP
rs1411116518 23 dbSNP
rs1380142978 24 dbSNP
rs1199984342 25 dbSNP
rs1265468371 26 dbSNP
rs764765966 27 dbSNP
rs750122035 29 dbSNP
rs1486196450 31 dbSNP
rs762312285 32 dbSNP
rs1352859348 33 dbSNP
rs1464505040 38 dbSNP
rs1328346428 45 dbSNP
rs1303943216 47 dbSNP
rs1288085395 50 dbSNP
rs1355169033 51 dbSNP
rs1235081778 53 dbSNP
rs1329027376 56 dbSNP
rs1399133290 57 dbSNP
rs765918277 58 dbSNP
rs1301352197 59 dbSNP
rs1230519742 61 dbSNP
rs1354988535 61 dbSNP
rs752152135 62 dbSNP
rs751136137 63 dbSNP
rs757923802 64 dbSNP
rs1336940058 65 dbSNP
rs1361973024 65 dbSNP
rs1212706554 66 dbSNP
rs763894685 67 dbSNP
rs754893938 68 dbSNP
rs781153703 70 dbSNP
rs1360420794 72 dbSNP
rs1205956564 73 dbSNP
rs1173547275 74 dbSNP
rs751250456 74 dbSNP
rs752455609 75 dbSNP
rs1485105347 76 dbSNP
rs755964227 77 dbSNP
rs757733692 79 dbSNP
rs1139147 80 dbSNP
rs1477149031 81 dbSNP
rs1167871058 82 dbSNP
rs758345734 84 dbSNP
rs1411739032 85 dbSNP
rs1478262497 86 dbSNP
rs781671539 86 dbSNP
rs1265514042 87 dbSNP
rs780279220 87 dbSNP
rs1214513997 88 dbSNP
rs1201967411 89 dbSNP
rs1487935605 89 dbSNP
rs747145499 89 dbSNP
rs1375132390 90 dbSNP
rs1372689888 91 dbSNP
rs769265128 93 dbSNP
rs777318539 94 dbSNP
rs746193239 95 dbSNP
rs756607218 95 dbSNP
rs748422172 96 dbSNP
rs1340479955 97 dbSNP
rs1357105495 97 dbSNP
rs1428325263 98 dbSNP
rs770207409 99 dbSNP
rs1400586980 100 dbSNP
rs780546121 100 dbSNP
rs772672824 101 dbSNP
rs1215826434 102 dbSNP
rs1466383347 102 dbSNP
rs1277551969 103 dbSNP
rs762660932 104 dbSNP
rs1211114042 107 dbSNP
rs1425993209 108 dbSNP
rs766076741 108 dbSNP
rs1281966500 109 dbSNP
rs1487532838 110 dbSNP
rs1192841815 112 dbSNP
rs1243216287 113 dbSNP
rs1476667847 114 dbSNP
rs773826665 115 dbSNP
rs1394526683 117 dbSNP
rs914624558 118 dbSNP
rs1236876076 120 dbSNP
rs1255713408 121 dbSNP
rs1175782680 125 dbSNP
rs1358813005 127 dbSNP
rs1398742979 128 dbSNP
rs1317301041 130 dbSNP
rs1345772048 131 dbSNP
rs536659900 136 dbSNP
rs1043574532 139 dbSNP
rs910407745 140 dbSNP
rs1392093929 142 dbSNP
rs950302313 142 dbSNP
rs1234337189 143 dbSNP
rs981905962 144 dbSNP
rs1414714063 147 dbSNP
rs1348031697 149 dbSNP
rs1204976305 150 dbSNP
rs1285391334 151 dbSNP
rs943267119 152 dbSNP
rs1212344057 157 dbSNP
rs1252865675 158 dbSNP
rs1454788279 161 dbSNP
rs1040262762 165 dbSNP
rs1195503166 168 dbSNP
rs1378711482 169 dbSNP
rs1469803114 170 dbSNP
rs1157846805 171 dbSNP
rs1458868444 175 dbSNP
rs1235992235 178 dbSNP
rs1163160596 180 dbSNP
rs901774378 182 dbSNP
rs928936403 184 dbSNP
rs1047394393 186 dbSNP
rs887521334 187 dbSNP
rs1005965475 188 dbSNP
rs1226071823 189 dbSNP
rs1354903381 196 dbSNP
rs1314882757 198 dbSNP
rs1241345318 200 dbSNP
rs902146109 201 dbSNP
rs999246929 203 dbSNP
rs375504345 204 dbSNP
rs1350666991 205 dbSNP
rs554975036 207 dbSNP
rs1325631048 210 dbSNP
rs576260827 212 dbSNP
rs1412978072 215 dbSNP
rs1003468013 217 dbSNP
rs1007158423 218 dbSNP
rs1407505830 221 dbSNP
rs1177741972 222 dbSNP
rs1018104339 227 dbSNP
rs1035924904 233 dbSNP
rs956281814 234 dbSNP
rs1248055186 235 dbSNP
rs543662969 249 dbSNP
rs558512366 253 dbSNP
rs1416188086 255 dbSNP
rs1021672541 256 dbSNP
rs1450481414 257 dbSNP
rs1286094645 258 dbSNP
rs1356433827 260 dbSNP
rs968768975 268 dbSNP
rs576966927 274 dbSNP
rs985571674 281 dbSNP
rs540756643 283 dbSNP
rs139707650 286 dbSNP
rs758274578 286 dbSNP
rs1434414853 287 dbSNP
rs1253071015 288 dbSNP
rs911309208 289 dbSNP
rs1339948223 291 dbSNP
rs1204576900 292 dbSNP
rs867495774 294 dbSNP
rs909987510 298 dbSNP
rs1189157362 300 dbSNP
rs943192893 302 dbSNP
rs559010603 305 dbSNP
rs992108184 314 dbSNP
rs917418629 320 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293S
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in GSM1084079. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep2_AbnovaAb ...

- Karginov FV; Hannon GJ, 2013, Genes & development.

Article - Karginov FV; Hannon GJ
- Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
CLIP-seq Support 1 for dataset GSM1084079
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep2_AbnovaAb
Location of target site ENST00000370179.3 | 3UTR | AAACGUGGUGAAACCCCGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
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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