Basic Information:

  VIRBase ID:  

VHID00397416

  Virus:  

Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)

  Host:  

Homo sapiens

  Confidence Score:  

0.5711

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      ebv-miR-BART9-5p:  MIMAT0004816          TCF3:  NM_001351779     

      *It may take a few minutes to display results.

Interactor Information:

	Interactor1	Interactor2
Symbol	ebv-miR-BART9-5p	TCF3
miRBase Accession/Entrez ID	MIMAT0004816	6929
Organism	Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)	Homo sapiens
Category	miRNA	mRNA
Alias	-	AGM8//bHLHb21//E2A//E47//ITF1//p75//TCF-3//VDIR

RNA Editing:

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	TCF3	chr19:1634884(-) A-I      intronic chr19:1624283(-) A-I      intronic chr19:1641625(-) A-I      intronic chr19:1641629(-) A-I      intronic chr19:1640367(-) A-I      intronic chr19:1640659(-) A-I      intronic chr19:1641114(-) A-I      intronic chr19:1624905(-) A-I      intronic chr19:1641665(-) A-I      intronic chr19:1641703(-) A-I      intronic chr19:1641731(-) A-I      intronic chr19:1641066(-) A-I      intronic chr19:1637751(-) A-I      intronic chr19:1641000(-) A-I      intronic chr19:1637776(-) A-I      intronic chr19:1637796(-) A-I      intronic chr19:1637861(-) A-I      intronic chr19:1641646(-) A-I      intronic chr19:1641580(-) A-I      intronic chr19:1640746(-) A-I      intronic chr19:1641067(-) A-I      intronic chr19:1641037(-) A-I      intronic chr19:1625070(-) A-I      intronic chr19:1641670(-) A-I      intronic chr19:1637864(-) A-I      intronic chr19:1637906(-) A-I      intronic chr19:1638485(-) A-I      intronic chr19:1625102(-) A-I      intronic chr19:1624910(-) A-I      intronic chr19:1640353(-) A-I      intronic chr19:1643509(-) A-I      intronic chr19:1637742(-) A-I      intronic chr19:1640704(-) A-I      intronic chr19:1641065(-) A-I      intronic chr19:1642037(-) A-I      intronic chr19:1623591(-) A-I      intronic chr19:1640272(-) A-I      intronic chr19:1640345(-) A-I      intronic chr19:1641621(-) A-I      intronic chr19:1624920(-) A-I      intronic chr19:1624351(-) A-I      intronic chr19:1641524(-) A-I      intronic chr19:1643576(-) A-I      intronic chr19:1638479(-) A-I      intronic chr19:1638470(-) A-I      intronic chr19:1641707(-) A-I      intronic chr19:1639180(-) A-I      intronic chr19:1640982(-) A-I      intronic chr19:1640628(-) A-I      intronic chr19:1642743(-) A-I      intronic chr19:1641398(-) A-I      intronic chr19:1636363(-) A-I      intronic chr19:1643495(-) A-I      intronic chr19:1641786(-) A-I      intronic chr19:1638454(-) A-I      intronic chr19:1641865(-) A-I      intronic chr19:1640650(-) A-I      intronic chr19:1641622(-) A-I      intronic chr19:1638446(-) A-I      intronic chr19:1639244(-) A-I      intronic chr19:1625071(-) A-I      intronic chr19:1641724(-) A-I      intronic chr19:1643493(-) A-I      intronic chr19:1641519(-) A-I      intronic chr19:1640751(-) A-I      intronic chr19:1640370(-) A-I      intronic chr19:1637764(-) A-I      intronic chr19:1639236(-) A-I      intronic chr19:1637652(-) A-I      intronic chr19:1641623(-) A-I      intronic chr19:1641359(-) A-I      intronic chr19:1636392(-) A-I      intronic chr19:1636338(-) A-I      intronic chr19:1640945(-) A-I      intronic chr19:1641949(-) A-I      intronic chr19:1639237(-) A-I      intronic chr19:1624313(-) A-I      intronic chr19:1643348(-) A-I      intronic chr19:1639294(-) A-I      intronic chr19:1639220(-) A-I      intronic chr19:1636406(-) A-I      intronic chr19:1641399(-) A-I      intronic

Resource	Symbol	Editing Position	Change	SeqReg	exReg	PMID
DARNED	TCF3	chr19:1614330(-) A-I intron -    22327324 chr19:1624176(-) G-A intron -    22484847 chr19:1638446(-) A-G intron -    22484847 chr19:1640345(-) A-G intron -    22484847 chr19:1641622(-) A-G intron -    22484847 chr19:1641623(-) A-G intron -    22484847 chr19:1641660(-) A-G intron -    22484847 chr19:1641707(-) A-G intron -    22484847 chr19:1643493(-) A-G intron -    22484847 chr19:1643495(-) A-G intron -    22484847

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	TCF3	chr19:1609343-1609344(-) m6A 3'UTR       24981863//27773535 chr19:1609378-1609379(-) m6A 3'UTR       24284625//24981863//27773535 chr19:1609493-1609494(-) m6A 3'UTR       24284625//27773535 chr19:1609509-1609510(-) m6A 3'UTR       24284625//27773535 chr19:1609564-1609565(-) m6A 3'UTR       24284625//27773535 chr19:1609639-1609640(-) m6A 3'UTR//intron       24284625 chr19:1609767-1609768(-) m6A 3'UTR//intron       24284625 chr19:1609808-1609809(-) m6A 3'UTR//intron       24284625 chr19:1609830-1609831(-) m6A 3'UTR//intron       24284625 chr19:1609860-1609861(-) m6A 3'UTR//intron       24284625 chr19:1609925-1609926(-) m6A 3'UTR//intron       24284625 chr19:1610022-1610023(-) m6A 3'UTR//intron       24284625 chr19:1610203-1610204(-) m6A 3'UTR//intron       24284625//27773536 chr19:1610261-1610262(-) m6A 3'UTR//intron       24284625//27371828//27773536 chr19:1610380-1610381(-) m6A 3'UTR//intron       24284625//25456834//24981863//27371828//27773536//22608085 chr19:1610438-1610439(-) m6A 3'UTR//intron       24284625//25456834//24981863//27773535//27371828//27773536//22608085 chr19:1610477-1610478(-) m6A 3'UTR//intron       24284625//24209618//25456834//24981863//27773535//27371828//27773536//22608085 chr19:1610496-1610497(-) m6A 3'UTR//intron       24284625//24209618//25456834//24981863//27773535//27371828//27773536//22608085 chr19:1610527-1610528(-) m6A 3'UTR//intron       24284625//24209618//25456834//24981863//27773535//27371828//27773536//22608085 chr19:1610536-1610537(-) m6A 3'UTR//intron       24284625//24209618//25456834//24981863//27773535//27371828//27773536//22608085 chr19:1610563-1610564(-) m6A 3'UTR//intron       24284625//24209618//25456834//24981863//27773535//27371828//27773536//22608085 chr19:1610585-1610586(-) m6A 3'UTR//intron       24284625//24209618//25456834//24981863//27371828 chr19:1610622-1610623(-) m6A 3'UTR//intron       24284625//24209618//25456834//24981863//27371828 chr19:1610759-1610760(-) m6A 3'UTR//intron       24284625//25456834//24981863 chr19:1610893-1610894(-) m6A 3'UTR//intron       24209618 chr19:1610904-1610905(-) m6A 3'UTR//intron       24209618//24981863//27773535 chr19:1610952-1610953(-) m6A 3'UTR//intron       24981863//27773535 chr19:1610963-1610964(-) m6A 3'UTR//intron       24981863//27773535 chr19:1611016-1611017(-) m6A 3'UTR//intron       24981863//27773535 chr19:1611180-1611181(-) m6A 3'UTR//intron       24284625//27773535//22608085 chr19:1611251-1611252(-) m6A 3'UTR//intron       24284625//24981863//27773535//22608085 chr19:1611280-1611281(-) m6A 3'UTR//intron       24284625//24981863//27773535//22608085 chr19:1611339-1611340(-) m6A 3'UTR//intron       24284625//24981863//27773535//22608085 chr19:1611359-1611360(-) m6A 3'UTR//intron       24284625//24981863//27773535//27371828//22575960//22608085 chr19:1611364-1611365(-) m6A 3'UTR//intron       24284625//24981863//27773535//27371828//22575960//22608085 chr19:1611421-1611422(-) m6A 3'UTR//intron       24284625//25456834//24981863//27773535//27371828//27773536//22575960//22608085 chr19:1611634-1611635(-) m6A 3'UTR//intron       24284625//25456834//24981863//27773535//27371828//27773536//22575960 chr19:1611775-1611776(-) m6A 3'UTR//CDS//exon       24284625//27773535//27371828//27773536//22575960 chr19:1611841-1611842(-) m6A 3'UTR//CDS//exon       24284625//27773535//27371828//27773536//22575960 chr19:1612268-1612269(-) m6A 3'UTR//CDS//intron       24284625//24209618//27773535//27371828//27773536//22575960 chr19:1612279-1612280(-) m6A 3'UTR//CDS//intron       24284625//24209618//27773535//27371828//27773536//22575960 chr19:1612387-1612388(-) m6A 3'UTR//CDS//intron       24284625//24209618//24981863//27773535//27371828//22575960 chr19:1612396-1612397(-) m6A 3'UTR//CDS//intron       24284625//24209618//24981863//27773535//27371828//22575960 chr19:1615303-1615304(-) m6A 3'UTR//CDS//exon//intron       24284625//24209618//24981863//27773535//27371828 chr19:1615341-1615342(-) m6A 3'UTR//CDS//exon//intron       24284625//24209618//24981863//28052920//27773535//27371828 chr19:1615346-1615347(-) m6A 3'UTR//CDS//exon//intron       24284625//24209618//24981863//28052920//27773535//27371828 chr19:1615688-1615689(-) m6A CDS//exon       24209618//25456834//24981863//27371828//27773536 chr19:1615715-1615716(-) m1A CDS//exon       26863196//26863410 chr19:1615750-1615751(-) m6A CDS//exon       24209618//25456834//24981863//27773535//27371828//27773536//22575960 chr19:1619273-1619274(-) m6A CDS//intron       24284625//27773536 chr19:1619456-1619457(-) m6A CDS//exon//intron       - chr19:1621178-1621179(-) m6A CDS//exon       24284625//27773536 chr19:1622350-1622351(-) m6A CDS       24284625//27773535//22575960 chr19:1622388-1622389(-) m6A CDS       24284625//27773535//22575960 chr19:1625637-1625638(-) m6A CDS       24284625//22575960 chr19:1632043-1632044(-) m6A CDS//intron       24284625 chr19:1632049-1632050(-) m6A CDS//intron       24284625 chr19:1632394-1632395(-) m6A CDS//intron       24284625//27773536 chr19:1650185-1650186(-) m6A CDS       24284625//24209618//27773536 chr19:1650209-1650210(-) m6A CDS       24284625//24209618//27773536 chr19:1650242-1650243(-) m6A CDS       24284625//24209618//27773536

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	TCF3	Chromatin K562 cells     - Cytosol Human myelogenous leukemia cell line (K-562)     21613539 Cytosol HeLa-S3 cells|K562 cells     - Exosome Blood     - Nucleolus K562 cells     - Nucleoplasm K562 cells     - Nucleus HCC cell line (HepG2)|K562 cells     - Ribosome HEK-293 cells     22199352

Interaction Network (The top 100 interactions):

Interactor1: ebv-miR-BART9-5p
Interactor2: TCF3

Evidence Support:

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

References:

PMID	22100165	Target region	3'UTR
Source	ViRBase//VIRmiRNA	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.