miRTarBase - #MIRT442609


—
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 MRC1   
Synonyms CD206, CLEC13D, CLEC13DL, MMR, MRC1L1, bA541I19.1, hMR
Description mannose receptor C-type 1
Transcript NM_002438   
Expression
Putative miRNA Targets on MRC1
3'UTR of MRC1
(miRNA target sites are highlighted)		 
>MRC1|NM_002438|3'UTR
   1 TACCTCAATGCGATTCTGAGATATTTGAATTTCATAAAATTGTAACTGAAATTTAAAATTTTTAGTTCAATGTGATTGTT
  81 TTCTTTAAAATGAGTACTGAATTGTACTGGTCTGTCCTTTTTTCCTTTGCCTAATTGAAGAAATAATTGCTTGTTTTCTA
 161 GCCTGGCAAGATATTTTCATAAAAGAGGGATAACAATGCTGATTACTACCTTTTAAAATATTTTAGATAAATGCACAGCA
 241 CCACAGCACCACATCTAAGCATTAGTGATGGGTAGCTGATGTCAGCTTCATGTGGATTTTAAGCACTCTAGAAACAATGA
 321 AGCTTCTTGGCATATTTTAAGGAGCTCCCAAAATGTGTTACCTATTAAATTGTAACTCAGCAAGTAGAAGACCATTTGAA
 401 AAGTCAGGTACAAATTTCCTCAAGTGGCATAAAAATGTAGTCAGTTTTCTCTTTTACCAGTTTTTATTTCCACTCCAATT
 481 ATTTAGAACTTTATTTGTACATGTGCAGAAGAATAAGGCAGCTGAGAATCTTGTTTCCCCCAAGAGAGTTTTACAGGCTG
 561 AGTGTTGCAAATGTGTTCTTTGTCCTGTTATATGTATATCAGGAATACAAGGATGTGAAATAAAACTGTAAATTTGCATA
 641 ACTGGATGTACTTAGATAATGTGAAATAAACATTAAAGACAAGGTCTATTTTTAATAAAAAAAAAAAAAAA
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' caATGAAGCTT---CTTGGCa 3'
 315 - 332 127.00 -8.80
2 
miRNA  3' auUUCAU-UGAAGGUGAACcga 5'
            ||||| |   |||:|||   
Target 5' gcAAGTAGAAGACCATTTGaaa 3'
 380 - 401 107.00 -10.82
3 
miRNA  3' auuucAUUGAAGG-UGAACCGa 5'
               |: :|||: :| |||| 
Target 5' ttgctTGTTTTCTAGCCTGGCa 3'
 147 - 168 104.00 -6.80
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26585390 28 COSMIC
COSN26553594 565 COSMIC
COSN8639447 618 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1370269855 2 dbSNP
rs983864140 9 dbSNP
rs908326124 10 dbSNP
rs939663198 12 dbSNP
rs1179961528 13 dbSNP
rs992909774 18 dbSNP
rs1483873952 46 dbSNP
rs1252289908 56 dbSNP
rs917143258 63 dbSNP
rs1487339853 73 dbSNP
rs1266663914 87 dbSNP
rs1221599378 105 dbSNP
rs948655015 110 dbSNP
rs1044312360 112 dbSNP
rs925777999 119 dbSNP
rs935873708 144 dbSNP
rs1053130629 160 dbSNP
rs1283122653 163 dbSNP
rs1403306182 166 dbSNP
rs1393202896 172 dbSNP
rs1453094164 177 dbSNP
rs891879082 180 dbSNP
rs1156786314 187 dbSNP
rs1473564093 188 dbSNP
rs1412430898 195 dbSNP
rs1198470215 200 dbSNP
rs1431251614 205 dbSNP
rs1008866736 211 dbSNP
rs1485227535 212 dbSNP
rs1265762808 215 dbSNP
rs1211124189 233 dbSNP
rs1040791815 235 dbSNP
rs1330480044 247 dbSNP
rs1262889248 249 dbSNP
rs900730476 260 dbSNP
rs1333219290 275 dbSNP
rs1302159362 284 dbSNP
rs996417639 291 dbSNP
rs1027941938 293 dbSNP
rs1359938994 295 dbSNP
rs1322720538 305 dbSNP
rs1458720789 307 dbSNP
rs1389349692 321 dbSNP
rs952187895 322 dbSNP
rs1464298711 324 dbSNP
rs1379170709 326 dbSNP
rs1199119616 331 dbSNP
rs1005056554 340 dbSNP
rs1427627843 348 dbSNP
rs1245638632 351 dbSNP
rs1190000177 354 dbSNP
rs1464971891 363 dbSNP
rs1243026349 365 dbSNP
rs1199246936 373 dbSNP
rs1015307410 380 dbSNP
rs1257012538 381 dbSNP
rs961430921 393 dbSNP
rs992481441 394 dbSNP
rs1299891466 395 dbSNP
rs1435853384 398 dbSNP
rs1382133637 399 dbSNP
rs1335938686 402 dbSNP
rs981 406 dbSNP
rs1394279265 409 dbSNP
rs1404083628 414 dbSNP
rs941 417 dbSNP
rs1461156388 429 dbSNP
rs1387889810 433 dbSNP
rs1170123093 435 dbSNP
rs1449466456 436 dbSNP
rs1384084438 445 dbSNP
rs1444700009 452 dbSNP
rs535043250 452 dbSNP
rs969727135 472 dbSNP
rs1195635915 476 dbSNP
rs1482291130 477 dbSNP
rs1276954512 478 dbSNP
rs979983272 478 dbSNP
rs1229429778 490 dbSNP
rs1358806556 491 dbSNP
rs1282568756 500 dbSNP
rs1242482633 501 dbSNP
rs1342248343 503 dbSNP
rs1334777686 508 dbSNP
rs925913692 511 dbSNP
rs1408945822 518 dbSNP
rs1368472454 522 dbSNP
rs935799234 539 dbSNP
rs1430072293 541 dbSNP
rs1384068576 544 dbSNP
rs1369502097 545 dbSNP
rs1474046510 545 dbSNP
rs1181726356 549 dbSNP
rs1254492005 560 dbSNP
rs1206134894 564 dbSNP
rs1490260129 574 dbSNP
rs1287789371 576 dbSNP
rs1211666593 577 dbSNP
rs1284638702 578 dbSNP
rs1227719480 579 dbSNP
rs1348377695 591 dbSNP
rs1410020398 592 dbSNP
rs1348993066 593 dbSNP
rs1321200861 610 dbSNP
rs1406560996 612 dbSNP
rs1053371090 622 dbSNP
rs1158484877 624 dbSNP
rs1456179761 626 dbSNP
rs913288804 635 dbSNP
rs1414612738 641 dbSNP
rs1183418589 651 dbSNP
rs1480328772 657 dbSNP
rs1245165328 661 dbSNP
rs1201281973 685 dbSNP
rs944805636 687 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 ENST00000239761.3 | 3UTR | UUGGCAUAUUUUAAG
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)

Error report submission