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 RTN2   
Synonyms NSP2, NSPL1, NSPLI, SPG12
Description reticulon 2
Transcript NM_005619   
Other Transcripts NM_206900 , NM_206901   
Expression
Putative miRNA Targets on RTN2
3'UTR of RTN2
(miRNA target sites are highlighted)
>RTN2|NM_005619|3'UTR
   1 GAACGGTGTCTCTGCCCGCAGGACGCCTGCCCCCAGCCCCCGCAGCCCTCTGGCCCCCTCCATCTCTTGTCCGTTCCCAC
  81 CCACCCCCCTCCTCGGCCCGAGCCTTTTCCCGGTGGGTGTCAGGATCACTCCCACTAGGGACTCTGCGCTAATTACCTGA
 161 GCGACCAGGACTACATTTCCCAAGAGGCTCTGCTCCAGGAGTCCAGGAAAGACGAGGCACCTTGGCCGCGGGGCCTGCTG
 241 GGACTTGTAGTTGCCTAGACAGGGCACCACCCTGCACTTCCGGACCCGCCGCTGGAGGCGCCGTGAGGCGTTGGTGTCTC
 321 CTGGATGCTACTAGCCCCAACGCCGGGGCTTTGCATGGGGCCCAGGGGAGGCCTGAGCTTGGATTTACACTGTAATAAAG
 401 ACTCCTGTGGAAAACCCGAG
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' gaaagacgaggcacCTTGGCc 3'
207 - 227 120.00 -9.10
2
miRNA  3' auUUC-AUUGAAGGUGAACCga 5'
            |:| | ||| ||||| ||  
Target 5' tcAGGATCACTCCCACTAGGga 3'
120 - 141 115.00 -10.80
3
miRNA  3' auUUCAUUGAAGGUGAACCga 5'
            ::| ::| |  :|||||  
Target 5' agGGGAGGCCTGAGCTTGGat 3'
364 - 384 111.00 -9.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
329546 51 ClinVar
329545 148 ClinVar
329544 217 ClinVar
329543 270 ClinVar
329542 300 ClinVar
329541 344 ClinVar
COSN30152961 1 COSMIC
COSN30524657 3 COSMIC
COSN30149351 50 COSMIC
COSN30482512 60 COSMIC
COSN30482551 61 COSMIC
COSN31487197 66 COSMIC
COSN24713365 83 COSMIC
COSN30531486 87 COSMIC
COSN31510161 88 COSMIC
COSN26993540 96 COSMIC
COSN30516986 134 COSMIC
COSN30531027 158 COSMIC
COSN15014264 183 COSMIC
COSN31550448 238 COSMIC
COSN22148847 245 COSMIC
COSN6145359 245 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs369143999 4 dbSNP
rs1335155521 5 dbSNP
rs755030115 6 dbSNP
rs751576259 7 dbSNP
rs766619556 10 dbSNP
rs758567861 12 dbSNP
rs750623233 13 dbSNP
rs761978138 14 dbSNP
rs199639693 16 dbSNP
rs1187972024 17 dbSNP
rs1343960277 21 dbSNP
rs1229095983 26 dbSNP
rs1447967034 29 dbSNP
rs1482017437 30 dbSNP
rs1201641964 31 dbSNP
rs1256501203 32 dbSNP
rs202169598 33 dbSNP
rs1214721874 36 dbSNP
rs762231590 37 dbSNP
rs777060551 38 dbSNP
rs764602378 39 dbSNP
rs760266287 41 dbSNP
rs774608454 45 dbSNP
rs775096446 47 dbSNP
rs1227021540 48 dbSNP
rs569611116 51 dbSNP
rs1467711622 54 dbSNP
rs1173225703 55 dbSNP
rs946661374 57 dbSNP
rs1384276914 69 dbSNP
rs906459972 73 dbSNP
rs1281450558 76 dbSNP
rs1046452631 78 dbSNP
rs767502543 80 dbSNP
rs915067102 81 dbSNP
rs1207559386 82 dbSNP
rs1310362456 83 dbSNP
rs1234855899 86 dbSNP
rs947758738 87 dbSNP
rs1052244215 88 dbSNP
rs935185376 89 dbSNP
rs1193359883 94 dbSNP
rs549990311 103 dbSNP
rs1435442244 109 dbSNP
rs537688582 109 dbSNP
rs867080931 110 dbSNP
rs981493296 112 dbSNP
rs1363333759 124 dbSNP
rs1451661325 129 dbSNP
rs1221437919 131 dbSNP
rs971419840 137 dbSNP
rs529811709 145 dbSNP
rs936435150 147 dbSNP
rs886054503 148 dbSNP
rs377322841 150 dbSNP
rs977626476 152 dbSNP
rs1388449711 153 dbSNP
rs915931311 156 dbSNP
rs1334680804 158 dbSNP
rs967583321 161 dbSNP
rs1438943382 163 dbSNP
rs750675243 164 dbSNP
rs1319898298 166 dbSNP
rs567358509 184 dbSNP
rs781226645 189 dbSNP
rs952419394 190 dbSNP
rs12104 198 dbSNP
rs547149523 200 dbSNP
rs1174968403 202 dbSNP
rs987851819 211 dbSNP
rs1027922832 213 dbSNP
rs1250408262 214 dbSNP
rs886054502 217 dbSNP
rs1184433950 218 dbSNP
rs1174690348 219 dbSNP
rs1478768054 220 dbSNP
rs1162860796 228 dbSNP
rs761612900 231 dbSNP
rs962213225 232 dbSNP
rs1018668451 235 dbSNP
rs1464992054 238 dbSNP
rs1029433165 243 dbSNP
rs1289698490 245 dbSNP
rs1249778533 248 dbSNP
rs1008693109 254 dbSNP
rs1310079268 257 dbSNP
rs111496259 258 dbSNP
rs888781748 260 dbSNP
rs994921989 262 dbSNP
rs1245946907 263 dbSNP
rs1441615765 263 dbSNP
rs1050543796 265 dbSNP
rs1038744348 266 dbSNP
rs943143539 269 dbSNP
rs527298509 270 dbSNP
rs893691642 271 dbSNP
rs1252630859 272 dbSNP
rs1485361718 273 dbSNP
rs1180356807 276 dbSNP
rs531587034 277 dbSNP
rs1425371936 279 dbSNP
rs1052317599 281 dbSNP
rs890095914 284 dbSNP
rs564911299 285 dbSNP
rs906430482 286 dbSNP
rs1370664242 289 dbSNP
rs545000793 290 dbSNP
rs927839202 299 dbSNP
rs532093070 300 dbSNP
rs774021825 302 dbSNP
rs1295324237 303 dbSNP
rs563132390 309 dbSNP
rs894798474 310 dbSNP
rs1053899308 320 dbSNP
rs543207340 321 dbSNP
rs1229203645 324 dbSNP
rs991875564 325 dbSNP
rs796215268 327 dbSNP
rs952092179 330 dbSNP
rs1208068483 332 dbSNP
rs1239494586 332 dbSNP
rs1335314045 334 dbSNP
rs923688947 335 dbSNP
rs1043017 338 dbSNP
rs1041876514 339 dbSNP
rs1447385764 342 dbSNP
rs375889892 344 dbSNP
rs1360253784 345 dbSNP
rs1413478538 348 dbSNP
rs560649063 349 dbSNP
rs920811326 353 dbSNP
rs972313599 357 dbSNP
rs1801948 360 dbSNP
rs1336512736 365 dbSNP
rs527810528 370 dbSNP
rs1408594411 373 dbSNP
rs1019158542 380 dbSNP
rs1448307050 388 dbSNP
rs1319422347 394 dbSNP
rs1363492082 404 dbSNP
rs1437694417 407 dbSNP
rs1299042650 415 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions LCL-BAC-D2
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 GSM1133252. RNA binding protein: AGO2. Condition:Untreated ...

- Majoros WH; Lekprasert P; Mukherjee N; et al., 2013, Nature methods.

Article - Majoros WH; Lekprasert P; Mukherjee N; et al.
- Nature methods, 2013
High-throughput sequencing has opened numerous possibilities for the identification of regulatory RNA-binding events. Cross-linking and immunoprecipitation of Argonaute proteins can pinpoint a microRNA (miRNA) target site within tens of bases but leaves the identity of the miRNA unresolved. A flexible computational framework, microMUMMIE, integrates sequence with cross-linking features and reliably identifies the miRNA family involved in each binding event. It considerably outperforms sequence-only approaches and quantifies the prevalence of noncanonical binding modes.
LinkOut: [PMID: 23708386]
CLIP-seq Support 1 for dataset GSM1133252
Method / RBP PAR-CLIP / AGO2
Cell line / Condition LCL-BAC-D2 / Untreated
Location of target site ENST00000245923.4 | 3UTR | UUGGCAUUGGGCCUGG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23708386 / GSE46611
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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