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 PLCB3   
Synonyms -
Description phospholipase C beta 3
Transcript NM_000932   
Other Transcripts NM_001184883   
Expression
Putative miRNA Targets on PLCB3
3'UTR of PLCB3
(miRNA target sites are highlighted)
>PLCB3|NM_000932|3'UTR
   1 ACTGGCTGAGCGAGGTGGCCACAGGGCCAGGGCGGGCGCTGGGTGGAGGGCAGGAGGCAATGACACTAATGCTTTTTTTT
  81 TTTTTTTTTAACTTTTTATCTAGAAATTTTATTTTTTTAAACCCGGGGCAAGTACCTCAGCTAACTCCCTTCATCCTCCT
 161 GGGGCCCCTCCTTCCTGCCCTCAGTCTTAGGTTAGGGCCTTGGTCAGGGCTTTGCTCCCTGTGACACCCACACCCTCGAG
 241 CTAGCAGCGTCTCCTCCCTTCCCCGGGAGAGCTGGCTGGAGACTTGGAGCTCCGGGAAGTAGGAGTCACATTTTTTTCTC
 321 TATTCTTTGGGGATTTTTTTTACATGAATAAAAGTGGATTTCAGGGACCCTGTGTGCAGTGTGATTTGGGGTGACAGGAC
 401 TCTGGGCCCTAAGTTTCCTCATCTATAAAATGGACTTTGGGCATTTGGTGGGGTTGAGGTCACGCCTCCAGCCAAGGGCT
 481 GCTGGGTTGAACCTGAGCTTGCCCTGCCGAGTCTGCTGAGCTTCCGTGGCCTTCTGCTTGTGCCCTCTGCCCCCAAGCCG
 561 CTGTTCCTGTTCCCCCATCCCCATGACTTTCGTCTCTCCGAGGCTCTCCCTGTTCTCTCTTTTCTGAGGCTCAGGCCTCT
 641 GCTTCAGGAAGCCTTCCCTGCCCCGCTTCCTGTGGCCTGATATGACCCAAACGCCTAGTATCTTCCGCTGGGGCTGCTCT
 721 GGGCCCCCGACAGGCAGTTGACTCTATCAGGTGATGGATCGGCCAGGGTGGAGCAGGGCAGCTCAGAACCTGCCCAACAC
 801 CGGGGGACCTGGGTCTTCAGAAATAGGTGGGCAGTAGGCCTGCCTGTGACTCTGGGGGAAGGGAAGTGGACAGTCACAGA
 881 CACGCAGGGGCTGGGCCACCCAGCATCCCCTCATCCCTGTGAGGGAGATGTTATGCCTGTTTTACAGATGAGGAGACTGA
 961 GGCCCGGAGCCATCTGTCGTGTGCTAGGCCACAGCTAAGTCAAGACGTCCTGACCTGGAGGCAGGGCAGGCCTGGACCCT
1041 CCGTGGTGGACTGTCTTCAGCCAGCCTGGACCTGTCCCATGCCTCAAGACCAGCGAAAAGTGGCAGAGAGCCCACAGTGC
1121 GGGCTCCAGGGCGGGGCTGGGCTCGCAGCAGGGTCGGCTTGGCACCTCTTCAAGGCCTCTCCCAGCTTCCTGGCTCTTCC
1201 CAGGCTGCCCGCCTGCATCCCTCCTCCAGGGGAAGGCGGCCTCTTATCTGGGCTTATCTCCTGCCAATTGAGTATCTTCT
1281 TTGCTTTGTTTTTGCTGCAGCCTCAGGCAAACAGATGGGGTGGGGAGGCCAGGGAAACAGGCTCCGGAGTAGGGCCCTCC
1361 TCCCTCAGGGTCAATGCAATGGCCCCAGACTTCCTCACTTCTTCTGTGGGACGCTGCCCTATCCCCCAGTTCTGCTCACT
1441 CCAGTGTATTCCGTATCTAGGCTCCTCAGCAGCCAACTCCCACCTTCCTGACTCTAGCTGGTGTCCACTGAGGGACACAC
1521 TCCAAGTCAGTTCCCAGGTCCTCAAATACCAGCTGAATGTCTAACTTCTGGGTGTGACATTCCAGCCCCTAGAAGCCTGG
1601 CCTCTGCTGCTCCCCTGTCCTTCCATGGGTCCACTCCTCCTTGCGCCGGGGGGGATGACCCTCACCTCACCTTCCGGTCG
1681 CAGCTCTAGCTGCCTCCTCCCTGAAGCCCTCTCTGACTGCCCTGCCGATTCCGGGCCCTCGGGAGCTTCCGCGAGCAGGG
1761 CCGTGGCGCAATGCATCTCTGTGCCCGGCACCAAGAACCGGCCCGGGTTATAGGGGGCGCCAATAAATCTTTCTGGAACG
1841 GAGCCCCCGCTCTGTCCGGGTCCCCGCATGAAGCCTCAGTTTCCAGCGACCGCGCT
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' cgcAGCAGGGTCGGCTTGGCa 3'
1144 - 1164 138.00 -12.10
2
miRNA  3' auUUCAUUGAAG---GUGAACCGa 5'
            ||  :||||:   ||:||||: 
Target 5' aaAATGGACTTTGGGCATTTGGTg 3'
427 - 450 127.00 -9.70
3
miRNA  3' auUUCAUUGA-AGGUGAACCga 5'
            |: |::||    ||||||  
Target 5' agAGCTGGCTGGAGACTTGGag 3'
268 - 289 123.00 -11.60
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1216802719 3 dbSNP
rs1003963230 5 dbSNP
rs1294101055 8 dbSNP
rs1401397412 10 dbSNP
rs764965705 12 dbSNP
rs902736763 13 dbSNP
rs1247196156 19 dbSNP
rs1291972047 27 dbSNP
rs1450426490 31 dbSNP
rs771857036 32 dbSNP
rs772917896 33 dbSNP
rs570600975 34 dbSNP
rs766564841 35 dbSNP
rs139556115 38 dbSNP
rs1388259755 39 dbSNP
rs1320254253 45 dbSNP
rs1448578986 45 dbSNP
rs1163976054 46 dbSNP
rs539868645 52 dbSNP
rs1312709663 55 dbSNP
rs543413428 58 dbSNP
rs1287401058 61 dbSNP
rs1407418618 68 dbSNP
rs533215507 71 dbSNP
rs1157281831 73 dbSNP
rs1166633503 73 dbSNP
rs1298630180 73 dbSNP
rs1411471351 73 dbSNP
rs1461828439 73 dbSNP
rs570819056 73 dbSNP
rs1473587117 88 dbSNP
rs1408852164 90 dbSNP
rs1242036775 91 dbSNP
rs1266818867 92 dbSNP
rs1249023457 93 dbSNP
rs1490417220 93 dbSNP
rs1204126262 98 dbSNP
rs903615967 99 dbSNP
rs1483961325 101 dbSNP
rs7395760 104 dbSNP
rs1000288474 112 dbSNP
rs1022750001 120 dbSNP
rs1422111107 125 dbSNP
rs1167030915 126 dbSNP
rs1386052459 130 dbSNP
rs1429355248 148 dbSNP
rs1327893534 158 dbSNP
rs1441342741 165 dbSNP
rs189413585 166 dbSNP
rs1028386339 176 dbSNP
rs1455546777 182 dbSNP
rs1345799384 191 dbSNP
rs753820893 194 dbSNP
rs1443472435 201 dbSNP
rs1427827018 202 dbSNP
rs1194858063 203 dbSNP
rs1449190173 216 dbSNP
rs1246606808 227 dbSNP
rs34190960 227 dbSNP
rs968441266 228 dbSNP
rs1302750682 234 dbSNP
rs117423477 238 dbSNP
rs1208780427 238 dbSNP
rs1309983331 244 dbSNP
rs1305476355 245 dbSNP
rs924397063 249 dbSNP
rs562553902 252 dbSNP
rs1364114565 257 dbSNP
rs1295152166 259 dbSNP
rs762198591 265 dbSNP
rs918106976 266 dbSNP
rs1464588352 272 dbSNP
rs961292988 279 dbSNP
rs1174769934 286 dbSNP
rs1429680601 292 dbSNP
rs949646080 294 dbSNP
rs1045343917 295 dbSNP
rs954078202 309 dbSNP
rs1180949542 311 dbSNP
rs1236781534 311 dbSNP
rs1481967623 311 dbSNP
rs926604405 312 dbSNP
rs1281853085 313 dbSNP
rs531412078 323 dbSNP
rs1211439939 326 dbSNP
rs1341350796 329 dbSNP
rs1272469531 331 dbSNP
rs1229296297 332 dbSNP
rs1312217264 334 dbSNP
rs985491412 334 dbSNP
rs545182560 335 dbSNP
rs1357373989 336 dbSNP
rs1183607923 339 dbSNP
rs946805052 344 dbSNP
rs1042537488 346 dbSNP
rs924108648 359 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions BC-3
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 GSM796039. RNA binding protein: AGO2. Condition:4-Thiouridine ...

- Gottwein E; Corcoran DL; Mukherjee N; et al., 2011, Cell host & microbe.

Article - Gottwein E; Corcoran DL; Mukherjee N; et al.
- Cell host & microbe, 2011
Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus (KSHV) and frequently also harbors Epstein-Barr virus (EBV). The expression of KSHV- and EBV-encoded microRNAs (miRNAs) in PELs suggests a role for these miRNAs in latency and lymphomagenesis. Using PAR-CLIP, a technology which allows the direct and transcriptome-wide identification of miRNA targets, we delineate the target sites for all viral and cellular miRNAs expressed in PEL cell lines. The resulting data set revealed that KSHV miRNAs directly target more than 2000 cellular mRNAs, including many involved in pathways relevant to KSHV pathogenesis. Moreover, 58% of these mRNAs are also targeted by EBV miRNAs, via distinct binding sites. In addition to a known viral analog of cellular miR-155, we show that KSHV encodes a viral miRNA that mimics cellular miR-142-3p function. In summary, this study identifies an extensive list of KSHV miRNA targets, which are likely to influence viral replication and pathogenesis.
LinkOut: [PMID: 22100165]
CLIP-seq Support 1 for dataset GSM796039
Method / RBP PAR-CLIP / AGO2
Cell line / Condition BC-3 / 4-Thiouridine
Location of target site ENST00000540288.1 | 3UTR | UUGGCACCUCUUCAAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22100165 / GSE32109
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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