Detail Information

Basic Information:


  VIRBase ID:  

VHID00398357

  Virus:  

Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)

  Host:  

Homo sapiens

  Confidence Score:  

0.6002

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      ebv-miR-BART9-5p:           HSDL1:      

      *It may take a few minutes to display results.

Interactor Information:


Interactor1 Interactor2
Symbol ebv-miR-BART9-5p HSDL1
miRBase
Accession/Entrez ID		 MIMAT0004816 83693
Organism Human gammaherpesvirus 4 (Epstein-Barr virus, EPV) Homo sapiens
Category miRNA mRNA
Alias - SDR12C3

RNA Editing:


Resource Symbol Editing Position Change Genetic Region
RADAR HSDL1
chr16:84162375(-) A-I      intronic
chr16:84156203(-) A-I      3'UTR
chr16:84156229(-) A-I      3'UTR
chr16:84156184(-) A-I      3'UTR
chr16:84156236(-) A-I      3'UTR
chr16:84165567(-) A-I      intronic
chr16:84162381(-) A-I      intronic
chr16:84161025(-) A-I      intronic
chr16:84161750(-) A-I      intronic
chr16:84160913(-) A-I      intronic
chr16:84162495(-) A-I      intronic
chr16:84165558(-) A-I      intronic
chr16:84168045(-) A-I      intronic
chr16:84168055(-) A-I      intronic
chr16:84168674(-) A-I      intronic
chr16:84168134(-) A-I      intronic
chr16:84162473(-) A-I      intronic
chr16:84168645(-) A-I      intronic
chr16:84168665(-) A-I      intronic
chr16:84162490(-) A-I      intronic
chr16:84160844(-) A-I      intronic
chr16:84160959(-) A-I      intronic
chr16:84165565(-) A-I      intronic
chr16:84159586(-) A-I      intronic
chr16:84160893(-) A-I      intronic
chr16:84167251(-) A-I      intronic
chr16:84162355(-) A-I      intronic
chr16:84162736(-) A-I      intronic
chr16:84168036(-) A-I      intronic
chr16:84162743(-) A-I      intronic
chr16:84162585(-) A-I      intronic
chr16:84162342(-) A-I      intronic
chr16:84168203(-) A-I      intronic
chr16:84162380(-) A-I      intronic
chr16:84176130(-) A-I      intronic
chr16:84165187(-) A-I      intronic
chr16:84162731(-) A-I      intronic
chr16:84156039(-) A-I      3'UTR
chr16:84161633(-) A-I      intronic
chr16:84161772(-) A-I      intronic
chr16:84161886(-) A-I      intronic
chr16:84177557(-) A-I      intronic
chr16:84161782(-) A-I      intronic
chr16:84168204(-) A-I      intronic
chr16:84177496(-) A-I      intronic
chr16:84162441(-) A-I      intronic
chr16:84162467(-) A-I      intronic
chr16:84160984(-) A-I      intronic
chr16:84159645(-) A-I      intronic
chr16:84161093(-) A-I      intronic
chr16:84162492(-) A-I      intronic
chr16:84162819(-) A-I      intronic
chr16:84177405(-) A-I      intronic
chr16:84162805(-) A-I      intronic
chr16:84161731(-) A-I      intronic
chr16:84159519(-) A-I      intronic
chr16:84161024(-) A-I      intronic
chr16:84162451(-) A-I      intronic
chr16:84168135(-) A-I      intronic
chr16:84165186(-) A-I      intronic
chr16:84160885(-) A-I      intronic
chr16:84162477(-) A-I      intronic
chr16:84177584(-) A-I      intronic
chr16:84161855(-) A-I      intronic
chr16:84159596(-) A-I      intronic
chr16:84162797(-) A-I      intronic
chr16:84167277(-) A-I      intronic
chr16:84168625(-) A-I      intronic
chr16:84160917(-) A-I      intronic
chr16:84161837(-) A-I      intronic
chr16:84160988(-) A-I      intronic
chr16:84162506(-) A-I      intronic
chr16:84168594(-) A-I      intronic
chr16:84174034(-) A-I      intronic
chr16:84161649(-) A-I      intronic
chr16:84167083(-) A-I      intronic
chr16:84167152(-) A-I      intronic
chr16:84176108(-) A-I      intronic
chr16:84160998(-) A-I      intronic
chr16:84167248(-) A-I      intronic
chr16:84167971(-) A-I      intronic
chr16:84168065(-) A-I      intronic
chr16:84162491(-) A-I      intronic
chr16:84160989(-) A-I      intronic
chr16:84168775(-) A-I      intronic
chr16:84165513(-) A-I      intronic
chr16:84165258(-) A-I      intronic
chr16:84162396(-) A-I      intronic
chr16:84161636(-) A-I      intronic
chr16:84167271(-) A-I      intronic
chr16:84161825(-) A-I      intronic
chr16:84156208(-) A-I      3'UTR
chr16:84156127(-) A-I      3'UTR
chr16:84156101(-) A-I      3'UTR

RNA Modification:


Resource Symbol ModificationPosition Type Genomic Context PMID
RMBase HSDL1
chr16:84156296-84156297(-) m6A 3'UTR//exon       27773535
chr16:84156366-84156367(-) m6A 3'UTR//exon       27773535
chr16:84156431-84156432(-) m6A 3'UTR//exon       24284625//27773535
chr16:84156441-84156442(-) m6A 3'UTR//exon       27773535
chr16:84156459-84156460(-) m6A 3'UTR//exon//intron       27773535
chr16:84156484-84156485(-) m6A 3'UTR//exon//intron       27773535
chr16:84156625-84156626(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//27773535//27371828//22608085
chr16:84156725-84156726(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//27773535//27371828//22608085
chr16:84156834-84156835(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//27773535//27371828//22608085
chr16:84156854-84156855(-) m6A 3'UTR//exon       24284625//24209618//24981863//27773535//27371828//22608085
chr16:84156900-84156901(-) m6A 3'UTR//exon       24284625//24209618//24981863//27773535//27371828//22608085
chr16:84156916-84156917(-) Y 3'UTR//exon       26075521
chr16:84157003-84157004(-) m6A 3'UTR//exon       24284625//27773535//22608085
chr16:84157026-84157027(-) m6A 3'UTR//exon       24284625//22608085
chr16:84157077-84157078(-) m6A 3'UTR//exon       24284625//22608085
chr16:84157104-84157105(-) m6A 3'UTR//exon       24284625
chr16:84158066-84158067(-) m6A 3'UTR//exon       24981863//22608085
chr16:84158098-84158099(-) m6A 3'UTR//exon       24284625//24981863//22608085
chr16:84158167-84158168(-) m6A 3'UTR//exon       24284625//24981863//22608085
chr16:84158193-84158194(-) m6A 3'UTR//exon       24981863//22608085
chr16:84158280-84158281(-) Y CDS       26075521
chr16:84163726-84163727(-) m6A CDS       24284625//24209618//24981863//27371828//22608085
chr16:84163741-84163742(-) m6A CDS       24284625//24209618//24981863//27371828//22608085
chr16:84163753-84163754(-) m6A CDS       24284625//24209618//24981863//27371828//22608085
chr16:84163831-84163832(-) m6A CDS//intron       24284625//24209618//24981863//27371828//22608085
chr16:84163882-84163883(-) m6A CDS//intron       24284625//24209618//24981863//27371828//22608085
chr16:84163901-84163902(-) m6A CDS//intron       24284625//24209618//24981863//27371828//22608085
chr16:84163927-84163928(-) m6A CDS//intron       24209618//24981863//22608085
chr16:84164593-84164594(-) m6A exon//intron       24209618
chr16:84164614-84164615(-) m6A exon//intron       24209618
chr16:84169162-84169163(-) m6A 5'UTR//exon       24284625//24209618//25456834//27371828//27773536
chr16:84172892-84172893(-) m6A 5'UTR//intron       24284625//24209618//25456834//27371828//27773536
chr16:84177930-84177931(-) m6A 5'UTR//intron       -
chr16:84177935-84177936(-) m6A 5'UTR//intron       -
chr16:84178026-84178027(-) m6A 5'UTR//intron       24981863
chr16:84178700-84178701(-) m6A 5'UTR//exon       24981863
chr16:84178713-84178714(-) m6A 5'UTR//exon       24981863

RNA Localization:


Resource Symbol Subcellular Localization Tissue or Cell Line PMID
RNALocate HSDL1
Chromatin K562 cells     -
Cytoplasm Nasopharyngeal carcinoma cells     20498841
Cytosol HCC cell line (HepG2)     -
Exosome Blood     -
Insoluble cytoplasm HCC cell line (HepG2)     -
Nucleolus K562 cells     -
Nucleoplasm K562 cells     -
Nucleus Nasopharyngeal carcinoma cells     20498841
Nucleus HeLa-S3 cells|K562 cells     -
Ribosome Colon cancer cells     24393600

Interaction Network (The top 100 interactions):


Interactor1: ebv-miR-BART9-5p
Interactor2: HSDL1

Evidence Support:


Weak-Evidence PAR-CLIP
Prediction-Evidence miRanda//PARalyzer//Targetscan
Support Database ViRBase//VIRmiRNA//VmiReg

References:


PMID 22100165 Target region 3'UTR
Source ViRBase//VIRmiRNA//VmiReg Interactor1 expression None
Tissue or cell line BC-1 cells Interactor2 expression Downregulation
Description 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.Clusters with seed matches to expressed miRNAs were considered candidate target sites. Of the clusters mapping to human 3'UTRs, 69% (BC-1) and 70% (BC-3) had seed matches to expressed miRNAs (Tables S6).Table S6A BC-1 derived 3'UTR clusters with seed matches to expressed miRNAs.

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