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 CHD8   
Synonyms AUTS18, HELSNF1
Description chromodomain helicase DNA binding protein 8
Transcript NM_001170629   
Other Transcripts NM_020920   
Expression
Putative miRNA Targets on CHD8
3'UTR of CHD8
(miRNA target sites are highlighted)
>CHD8|NM_001170629|3'UTR
   1 AGCCCCAGCATGGGCCCCATTGCTTGGGCGGCTGCTGTATTTTCATTTACTCTGGCCCTTGGACTATGGAAACGTGGGAG
  81 GGGCAGGGGAGATGTGGGGAAGTCCAGGACTCCAGGAGGTGAAAAGGAAAAAAAAAAAAAAATGTACCTGATTGCTCCCA
 161 ATTATGAGAGGATTGGGTGGGCAGGGGAACTCCTAAAATAATACATGACCACTTCCTCATTTCTGGGGAAGGAAAGGAGA
 241 CTAGAGCAGCTGGTGTGCTCACCCCTCCCTAGTCACCTCCATTAACCACAGACTATGTAGCGCTGGCCCTAGCCTCTGGC
 321 AGAGCCTGTTCCTGGCCGAACTGTGGATACAGCTGGAGGGTCAGGAACTGTTACCTTCTTTCCCCTTGGCATTAATAAAT
 401 TTAAGTTAATCCTTTTCCAAAAAAAAAAAAAAAAAAAAAAAAA
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' ttaccttcTTTCCCCTTGGCa 3'
371 - 391 129.00 -12.80
2
miRNA  3' auuuCAUUGAAG---GUGA-ACCGa 5'
              ||| :|||   :||| |||| 
Target 5' tgctGTATTTTCATTTACTCTGGCc 3'
33 - 57 125.00 -8.80
3
miRNA  3' auuucauugaaGGUGAACCga 5'
                     :::|||||  
Target 5' catgggccccaTTGCTTGGgc 3'
9 - 29 106.00 -8.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
1183346 143 ClinVar
1194978 148 ClinVar
COSN30723407 29 COSMIC
COSN30581936 87 COSMIC
COSN1165639 128 COSMIC
COSN1165647 140 COSMIC
COSN25563943 170 COSMIC
COSN25752224 178 COSMIC
COSN30163502 302 COSMIC
COSN26565714 336 COSMIC
COSN31479579 365 COSMIC
COSN31608772 412 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1207287151 5 dbSNP
rs965429372 10 dbSNP
rs1184833248 12 dbSNP
rs1476454860 17 dbSNP
rs1019253397 18 dbSNP
rs754091661 20 dbSNP
rs1220817255 24 dbSNP
rs765051321 29 dbSNP
rs577177637 30 dbSNP
rs776047392 37 dbSNP
rs951126946 38 dbSNP
rs1026516741 45 dbSNP
rs1316862010 49 dbSNP
rs1270512544 50 dbSNP
rs1394521283 59 dbSNP
rs557336181 63 dbSNP
rs933334289 66 dbSNP
rs1393449879 74 dbSNP
rs1438491668 77 dbSNP
rs1340339457 80 dbSNP
rs1299706051 83 dbSNP
rs923338975 88 dbSNP
rs1296768543 95 dbSNP
rs899437695 98 dbSNP
rs1357951579 108 dbSNP
rs1360782022 119 dbSNP
rs1302070259 120 dbSNP
rs1455984898 121 dbSNP
rs1369672042 127 dbSNP
rs1165449724 128 dbSNP
rs1272199378 128 dbSNP
rs1468304630 139 dbSNP
rs78304393 141 dbSNP
rs78520772 142 dbSNP
rs1212238033 143 dbSNP
rs1371394659 143 dbSNP
rs370612022 143 dbSNP
rs75170206 143 dbSNP
rs1002437560 144 dbSNP
rs1055398493 144 dbSNP
rs1165884095 144 dbSNP
rs1459632582 145 dbSNP
rs1322331963 147 dbSNP
rs538945835 148 dbSNP
rs1022172884 153 dbSNP
rs1316200004 158 dbSNP
rs1284399583 159 dbSNP
rs1195598239 166 dbSNP
rs1332269096 173 dbSNP
rs1488458436 179 dbSNP
rs1262882554 180 dbSNP
rs1351924843 183 dbSNP
rs1264248920 184 dbSNP
rs990342770 185 dbSNP
rs766590617 186 dbSNP
rs376559942 189 dbSNP
rs760799895 192 dbSNP
rs1257022528 193 dbSNP
rs971065489 206 dbSNP
rs1474350027 211 dbSNP
rs773863893 226 dbSNP
rs993853333 240 dbSNP
rs913987421 241 dbSNP
rs1452843510 253 dbSNP
rs1176283883 260 dbSNP
rs543340734 262 dbSNP
rs1404302048 269 dbSNP
rs898246870 270 dbSNP
rs1311750249 271 dbSNP
rs1222344658 277 dbSNP
rs1317861639 291 dbSNP
rs1411264223 297 dbSNP
rs1276792056 300 dbSNP
rs1038575381 301 dbSNP
rs1006757078 302 dbSNP
rs553509091 303 dbSNP
rs1220854861 312 dbSNP
rs889696479 317 dbSNP
rs1341506803 319 dbSNP
rs1211599118 321 dbSNP
rs1300226421 331 dbSNP
rs936496371 336 dbSNP
rs921065792 337 dbSNP
rs1051039407 338 dbSNP
rs933911075 342 dbSNP
rs1392386217 347 dbSNP
rs189392324 349 dbSNP
rs767858164 351 dbSNP
rs1172998476 364 dbSNP
rs1464600687 367 dbSNP
rs1398036351 373 dbSNP
rs1431145247 379 dbSNP
rs1298369640 385 dbSNP
rs1041745365 389 dbSNP
rs946090893 390 dbSNP
rs1391139941 407 dbSNP
rs1305308857 408 dbSNP
rs1172731288 412 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 GSM796040. 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 GSM796040
Method / RBP PAR-CLIP / AGO2
Cell line / Condition BC-3 / 4-Thiouridine
Location of target site ENST00000430710.3 | 3UTR | UUGGCAUUAAUAAAUU
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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