Basic Information:

  VIRBase ID:  

VHID00398613

  Virus:  

Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)

  Host:  

Homo sapiens

  Confidence Score:  

0.6040

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      ebv-miR-BART9-5p:  MIMAT0004816          RNF38:  NM_194332     

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Interactor Information:

	Interactor1	Interactor2
Symbol	ebv-miR-BART9-5p	RNF38
miRBase Accession/Entrez ID	MIMAT0004816	152006
Organism	Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)	Homo sapiens
Category	miRNA	mRNA
Alias	-	-

RNA Editing:

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	RNF38	chr9:36365503(-) A-I      intronic chr9:36369297(-) A-I      intronic chr9:36362255(-) A-I      intronic chr9:36378446(-) A-I      intronic chr9:36372940(-) A-I      intronic chr9:36369322(-) A-I      intronic chr9:36369327(-) A-I      intronic chr9:36369382(-) A-I      intronic chr9:36369422(-) A-I      intronic chr9:36369478(-) A-I      intronic chr9:36372928(-) A-I      intronic chr9:36378394(-) A-I      intronic chr9:36378383(-) A-I      intronic chr9:36371576(-) A-I      intronic chr9:36370810(-) A-I      intronic chr9:36346300(-) A-I      intronic chr9:36362308(-) A-I      intronic chr9:36346279(-) A-I      intronic chr9:36346275(-) A-I      intronic chr9:36369486(-) A-I      intronic chr9:36350018(-) A-I      intronic chr9:36347961(-) A-I      intronic chr9:36394031(-) A-I      intronic chr9:36394029(-) A-I      intronic chr9:36383318(-) A-I      intronic chr9:36350042(-) A-I      intronic chr9:36378445(-) A-I      intronic chr9:36346947(-) A-I      intronic chr9:36346392(-) A-I      intronic chr9:36346384(-) A-I      intronic chr9:36369456(-) A-I      intronic chr9:36361051(-) A-I      intronic chr9:36361040(-) A-I      intronic chr9:36361029(-) A-I      intronic chr9:36346343(-) A-I      intronic chr9:36341686(-) A-I      intronic chr9:36362759(-) A-I      intronic chr9:36361020(-) A-I      intronic chr9:36349954(-) A-I      intronic chr9:36365437(-) A-I      intronic chr9:36346406(-) A-I      intronic chr9:36346363(-) A-I      intronic chr9:36362231(-) A-I      intronic chr9:36362188(-) A-I      intronic chr9:36362097(-) A-I      intronic chr9:36361363(-) A-I      intronic chr9:36362763(-) A-I      intronic chr9:36361241(-) A-I      intronic chr9:36358925(-) A-I      intronic chr9:36365320(-) A-I      intronic chr9:36365361(-) A-I      intronic chr9:36362268(-) A-I      intronic chr9:36365441(-) A-I      intronic chr9:36349910(-) A-I      intronic chr9:36339244(-) A-I      3'UTR chr9:36367863(-) A-I      intronic chr9:36346391(-) A-I      intronic chr9:36397248(-) A-I      intronic chr9:36347079(-) A-I      intronic chr9:36350057(-) A-I      intronic chr9:36362272(-) A-I      intronic chr9:36370747(-) A-I      intronic chr9:36371581(-) A-I      intronic chr9:36346911(-) A-I      intronic chr9:36370757(-) A-I      intronic chr9:36365526(-) A-I      intronic chr9:36349860(-) A-I      intronic chr9:36348464(-) A-I      intronic chr9:36359900(-) A-I      intronic chr9:36365693(-) A-I      intronic chr9:36365381(-) A-I      intronic chr9:36362094(-) A-I      intronic chr9:36358969(-) A-I      intronic chr9:36365841(-) A-I      intronic chr9:36350065(-) A-I      intronic chr9:36362191(-) A-I      intronic chr9:36363939(-) A-I      intronic chr9:36341639(-) A-I      intronic chr9:36397249(-) A-I      intronic chr9:36346477(-) A-I      intronic chr9:36363209(-) A-I      intronic chr9:36370737(-) A-I      intronic chr9:36350019(-) A-I      intronic chr9:36346327(-) A-I      intronic chr9:36370854(-) A-I      intronic chr9:36340501(-) A-I      intronic chr9:36361281(-) A-I      intronic chr9:36371607(-) A-I      intronic chr9:36346311(-) A-I      intronic chr9:36346952(-) A-I      intronic chr9:36346313(-) A-I      intronic chr9:36374656(-) A-I      intronic chr9:36346461(-) A-I      intronic chr9:36346271(-) A-I      intronic chr9:36350066(-) A-I      intronic chr9:36349980(-) A-I      intronic chr9:36361234(-) A-I      intronic chr9:36362769(-) A-I      intronic chr9:36373191(-) A-I      intronic chr9:36346880(-) A-I      intronic chr9:36350087(-) A-I      intronic chr9:36365367(-) A-I      intronic chr9:36348456(-) A-I      intronic chr9:36361287(-) A-I      intronic chr9:36345152(-) A-I      intronic chr9:36370905(-) A-I      intronic chr9:36362197(-) A-I      intronic chr9:36346935(-) A-I      intronic chr9:36365483(-) A-I      intronic chr9:36365842(-) A-I      intronic chr9:36346438(-) A-I      intronic chr9:36346274(-) A-I      intronic chr9:36370646(-) A-I      intronic chr9:36346407(-) A-I      intronic chr9:36349948(-) A-I      intronic chr9:36350056(-) A-I      intronic chr9:36358956(-) A-I      intronic chr9:36365482(-) A-I      intronic chr9:36347054(-) A-I      intronic chr9:36347017(-) A-I      intronic chr9:36365384(-) A-I      intronic chr9:36374647(-) A-I      intronic chr9:36346299(-) A-I      intronic chr9:36347964(-) A-I      intronic chr9:36349953(-) A-I      intronic chr9:36378338(-) A-I      intronic chr9:36371608(-) A-I      intronic chr9:36374669(-) A-I      intronic chr9:36362771(-) A-I      intronic chr9:36365565(-) A-I      intronic chr9:36349944(-) A-I      intronic chr9:36373121(-) A-I      intronic chr9:36370652(-) A-I      intronic chr9:36347009(-) A-I      intronic chr9:36361432(-) A-I      intronic chr9:36365307(-) A-I      intronic chr9:36365496(-) A-I      intronic chr9:36371590(-) A-I      intronic chr9:36370846(-) A-I      intronic chr9:36346439(-) A-I      intronic chr9:36380500(-) A-I      intronic

Resource	Symbol	Editing Position	Change	SeqReg	exReg	PMID
DARNED	RNF38	chr9:36346949(-) A-I intron -    22327324 chr9:36346274(-) A-G intron -    22484847 chr9:36346299(-) A-G intron -    22484847 chr9:36346313(-) A-G intron -    22484847 chr9:36346407(-) A-G intron -    22484847 chr9:36346438(-) A-G intron -    22484847 chr9:36346439(-) A-G intron -    22484847 chr9:36346477(-) A-G intron -    22484847 chr9:36346880(-) A-G intron -    22484847 chr9:36346912(-) A-G intron -    22484847 chr9:36346949(-) A-G intron -    22484847 chr9:36347884(-) A-G intron -    22484847 chr9:36349860(-) A-G intron -    22484847 chr9:36350019(-) A-G intron -    22484847 chr9:36350057(-) A-G intron -    22484847 chr9:36350087(-) A-G intron -    22484847 chr9:36365565(-) A-G intron -    22484847 chr9:36365681(-) C-A intron -    22484847 chr9:36371581(-) A-G intron -    22484847

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	RNF38	chr9:36339631-36339632(-) m6A 3'UTR       24981863 chr9:36339680-36339681(-) m6A 3'UTR       24981863 chr9:36339692-36339693(-) m6A 3'UTR       24981863 chr9:36353286-36353287(-) m6A CDS       27773535 chr9:36353298-36353299(-) m6A CDS       27773535 chr9:36356316-36356317(-) m6A CDS       27773535 chr9:36357804-36357805(-) m6A CDS//exon       27773535 chr9:36357926-36357927(-) m6A CDS//exon       27773535 chr9:36369857-36369858(-) m6A CDS//exon       27773535//27371828 chr9:36372552-36372553(-) m6A CDS//intron       27371828 chr9:36376097-36376098(-) m6A 5'UTR//CDS//exon       24981863//27773535 chr9:36390506-36390507(-) m6A 5'UTR//CDS//exon//intron       27773535

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	RNF38	Cytosol HCC cell line (HepG2)|K562 cells     - Exosome Blood     - Nucleus HCC cell line (HepG2)|HeLa-S3 cells|K562 cells     - Ribosome-free cytosol Colon cancer cells     24393600

Interaction Network (The top 100 interactions):

Interactor1: ebv-miR-BART9-5p
Interactor2: RNF38

Evidence Support:

Weak-Evidence	PAR-CLIP
Prediction-Evidence	miRanda//PARalyzer//PITA//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.