Basic Information:

  VIRBase ID:  

VHID00302943

  Virus:  

Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)

  Host:  

Homo sapiens

  Confidence Score:  

0.6040

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      ebv-miR-BART3-3p:  MIMAT0003411          POLR1D:  NM_152705     

      *It may take a few minutes to display results.

Interactor Information:

	Interactor1	Interactor2
Symbol	ebv-miR-BART3-3p	POLR1D
miRBase Accession/Entrez ID	MIMAT0003411	51082
Organism	Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)	Homo sapiens
Category	miRNA	mRNA
Alias	-	AC19//POLR1C//RPA16//RPA9//RPAC2//RPC16//RPO1-3//TCS2

RNA Editing:

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	POLR1D	chr13:28226297(+) A-I      intronic chr13:28226298(+) A-I      intronic chr13:28226305(+) A-I      intronic chr13:28226328(+) A-I      intronic chr13:28226339(+) A-I      intronic chr13:28226340(+) A-I      intronic chr13:28226418(+) A-I      intronic chr13:28226394(+) A-I      intronic chr13:28226381(+) A-I      intronic chr13:28228078(+) A-I      intronic chr13:28228196(+) A-I      intronic chr13:28228170(+) A-I      intronic chr13:28228163(+) A-I      intronic chr13:28228161(+) A-I      intronic chr13:28228158(+) A-I      intronic chr13:28228149(+) A-I      intronic chr13:28228143(+) A-I      intronic chr13:28228137(+) A-I      intronic chr13:28228119(+) A-I      intronic chr13:28228115(+) A-I      intronic chr13:28228113(+) A-I      intronic chr13:28228105(+) A-I      intronic chr13:28228097(+) A-I      intronic chr13:28228089(+) A-I      intronic chr13:28228087(+) A-I      intronic chr13:28228084(+) A-I      intronic chr13:28228060(+) A-I      intronic chr13:28227850(+) A-I      intronic chr13:28227848(+) A-I      intronic chr13:28227846(+) A-I      intronic chr13:28227813(+) A-I      intronic chr13:28227799(+) A-I      intronic chr13:28227798(+) A-I      intronic chr13:28227783(+) A-I      intronic chr13:28227753(+) A-I      intronic chr13:28227751(+) A-I      intronic chr13:28227730(+) A-I      intronic chr13:28227718(+) A-I      intronic chr13:28227717(+) A-I      intronic chr13:28227716(+) A-I      intronic chr13:28227706(+) A-I      intronic chr13:28225912(+) A-I      intronic chr13:28225903(+) A-I      intronic chr13:28225889(+) A-I      intronic chr13:28225886(+) A-I      intronic chr13:28225841(+) A-I      intronic chr13:28225840(+) A-I      intronic chr13:28225835(+) A-I      intronic chr13:28225834(+) A-I      intronic chr13:28225832(+) A-I      intronic chr13:28225830(+) A-I      intronic chr13:28225825(+) A-I      intronic chr13:28225817(+) A-I      intronic chr13:28225813(+) A-I      intronic chr13:28225811(+) A-I      intronic chr13:28225784(+) A-I      intronic chr13:28225783(+) A-I      intronic chr13:28225839(+) A-I      intronic chr13:28225922(+) A-I      intronic chr13:28225930(+) A-I      intronic chr13:28226272(+) A-I      intronic chr13:28226283(+) A-I      intronic chr13:28226290(+) A-I      intronic chr13:28226287(+) A-I      intronic chr13:28226289(+) A-I      intronic chr13:28226294(+) A-I      intronic chr13:28226300(+) A-I      intronic chr13:28226301(+) A-I      intronic chr13:28226302(+) A-I      intronic chr13:28226303(+) A-I      intronic chr13:28226308(+) A-I      intronic chr13:28226309(+) A-I      intronic chr13:28226332(+) A-I      intronic chr13:28226362(+) A-I      intronic chr13:28226370(+) A-I      intronic chr13:28226372(+) A-I      intronic chr13:28226378(+) A-I      intronic chr13:28226391(+) A-I      intronic chr13:28226393(+) A-I      intronic chr13:28226409(+) A-I      intronic chr13:28227642(+) A-I      intronic chr13:28227651(+) A-I      intronic chr13:28227652(+) A-I      intronic chr13:28227679(+) A-I      intronic chr13:28225935(+) A-I      intronic chr13:28225939(+) A-I      intronic chr13:28225940(+) A-I      intronic chr13:28225942(+) A-I      intronic chr13:28225954(+) A-I      intronic chr13:28227692(+) A-I      intronic chr13:28227704(+) A-I      intronic chr13:28225781(+) A-I      intronic chr13:28226851(+) A-I      intronic chr13:28225971(+) A-I      intronic chr13:28226251(+) A-I      intronic chr13:28227759(+) A-I      intronic chr13:28226266(+) A-I      intronic chr13:28226860(+) A-I      intronic chr13:28226864(+) A-I      intronic chr13:28226892(+) A-I      intronic chr13:28226896(+) A-I      intronic chr13:28227188(+) A-I      intronic chr13:28228159(+) A-I      intronic chr13:28228165(+) A-I      intronic chr13:28227175(+) A-I      intronic chr13:28228193(+) A-I      intronic chr13:28223128(+) A-I      intronic chr13:28226856(+) A-I      intronic chr13:28226744(+) A-I      intronic chr13:28227298(+) A-I      intronic chr13:28227225(+) A-I      intronic chr13:28231588(+) A-I      intronic chr13:28226750(+) A-I      intronic chr13:28227136(+) A-I      intronic chr13:28226855(+) A-I      intronic chr13:28228169(+) A-I      intronic chr13:28226900(+) A-I      intronic chr13:28228200(+) A-I      intronic chr13:28227299(+) A-I      intronic chr13:28228179(+) A-I      intronic chr13:28228127(+) A-I      intronic chr13:28228100(+) A-I      intronic chr13:28228101(+) A-I      intronic chr13:28228162(+) A-I      intronic chr13:28228052(+) A-I      intronic chr13:28227141(+) A-I      intronic chr13:28228099(+) A-I      intronic chr13:28227162(+) A-I      intronic chr13:28226924(+) A-I      intronic chr13:28227177(+) A-I      intronic chr13:28226999(+) A-I      intronic chr13:28226932(+) A-I      intronic chr13:28228134(+) A-I      intronic chr13:28228166(+) A-I      intronic chr13:28226753(+) A-I      intronic chr13:28228120(+) A-I      intronic chr13:28227305(+) A-I      intronic chr13:28227011(+) A-I      intronic chr13:28228197(+) A-I      intronic chr13:28228132(+) A-I      intronic chr13:28227117(+) A-I      intronic chr13:28226314(+) A-I      intronic chr13:28227220(+) A-I      intronic chr13:28225819(+) A-I      intronic chr13:28226385(+) A-I      intronic chr13:28226275(+) A-I      intronic chr13:28225816(+) A-I      intronic chr13:28228245(+) A-I      intronic chr13:28227811(+) A-I      intronic chr13:28227761(+) A-I      intronic chr13:28227016(+) A-I      intronic chr13:28227249(+) A-I      intronic chr13:28227137(+) A-I      intronic chr13:28227116(+) A-I      intronic chr13:28226919(+) A-I      intronic chr13:28226943(+) A-I      intronic chr13:28226758(+) A-I      intronic chr13:28225910(+) A-I      intronic chr13:28225943(+) A-I      intronic chr13:28227237(+) A-I      intronic chr13:28227806(+) A-I      intronic chr13:28228064(+) A-I      intronic chr13:28228133(+) A-I      intronic chr13:28225895(+) A-I      intronic chr13:28227106(+) A-I      intronic chr13:28228220(+) A-I      intronic chr13:28228091(+) A-I      intronic chr13:28227201(+) A-I      intronic chr13:28226866(+) A-I      intronic chr13:28226854(+) A-I      intronic chr13:28226842(+) A-I      intronic chr13:28227202(+) A-I      intronic chr13:28228096(+) A-I      intronic chr13:28227240(+) A-I      intronic chr13:28227269(+) A-I      intronic chr13:28226399(+) A-I      intronic chr13:28228212(+) A-I      intronic chr13:28227725(+) A-I      intronic chr13:28227140(+) A-I      intronic chr13:28227015(+) A-I      intronic chr13:28226273(+) A-I      intronic chr13:28226948(+) A-I      intronic chr13:28228230(+) A-I      intronic chr13:28228080(+) A-I      intronic chr13:28225969(+) A-I      intronic chr13:28227653(+) A-I      intronic chr13:28226797(+) A-I      intronic chr13:28226916(+) A-I      intronic chr13:28226887(+) A-I      intronic chr13:28226274(+) A-I      intronic chr13:28227273(+) A-I      intronic chr13:28226374(+) A-I      intronic chr13:28227165(+) A-I      intronic chr13:28225775(+) A-I      intronic chr13:28226848(+) A-I      intronic chr13:28225826(+) A-I      intronic chr13:28226845(+) A-I      intronic chr13:28226806(+) A-I      intronic chr13:28232225(+) A-I      intronic chr13:28227223(+) A-I      intronic chr13:28210724(+) A-I      intronic chr13:28227792(+) A-I      intronic chr13:28225913(+) A-I      intronic chr13:28227645(+) A-I      intronic chr13:28225961(+) A-I      intronic chr13:28227774(+) A-I      intronic chr13:28227789(+) A-I      intronic chr13:28226925(+) A-I      intronic chr13:28227277(+) A-I      intronic chr13:28228118(+) A-I      intronic chr13:28226459(+) A-I      intronic chr13:28228090(+) A-I      intronic chr13:28228180(+) A-I      intronic chr13:28227153(+) A-I      intronic chr13:28228189(+) A-I      intronic chr13:28226938(+) A-I      intronic chr13:28227693(+) A-I      intronic chr13:28228044(+) A-I      intronic chr13:28227760(+) A-I      intronic chr13:28225797(+) A-I      intronic chr13:28228108(+) A-I      intronic chr13:28227853(+) A-I      intronic chr13:28225894(+) A-I      intronic chr13:28226886(+) A-I      intronic chr13:28227793(+) A-I      intronic chr13:28227795(+) A-I      intronic

Resource	Symbol	Editing Position	Change	SeqReg	exReg	PMID
DARNED	POLR1D	chr13:28225775(+) A-I intron -    15258596 chr13:28225816(+) A-I intron -    15258596   //21960545 chr13:28225894(+) A-I intron -    15258596 chr13:28225895(+) A-I intron -    15258596   //22327324 chr13:28227305(+) A-I intron -    22327324 chr13:28227761(+) A-I intron -    22327324 chr13:28227792(+) A-I intron -    22327324 chr13:28228052(+) A-I intron -    22028664 chr13:28228064(+) A-I intron -    22028664 chr13:28228080(+) A-I intron -    22028664 chr13:28228090(+) A-I intron -    22028664 chr13:28228091(+) A-I intron -    22028664 chr13:28228096(+) A-I intron -    22028664 chr13:28228099(+) A-I intron -    22028664 chr13:28228100(+) A-I intron -    22028664 chr13:28228101(+) A-I intron -    22028664 chr13:28228108(+) A-I intron -    22028664 chr13:28228118(+) A-I intron -    22028664 chr13:28228120(+) A-I intron -    22028664 chr13:28228127(+) A-I intron -    22028664 chr13:28228132(+) A-I intron -    22028664 chr13:28228133(+) A-I intron -    22028664 chr13:28228134(+) A-I intron -    22028664 chr13:28228162(+) A-I intron -    22028664 chr13:28228166(+) A-I intron -    22028664 chr13:28228169(+) A-I intron -    22028664 chr13:28228179(+) A-I intron -    22028664   //21960545 chr13:28228180(+) A-I intron -    22028664 chr13:28228189(+) A-I intron -    22028664 chr13:28228193(+) A-I intron -    22028664 chr13:28228197(+) A-I intron -    22028664 chr13:28228200(+) A-I intron -    22028664 chr13:28228212(+) A-I intron -    22028664 chr13:28228220(+) A-I intron -    22028664 chr13:28227645(+) A-I intron -    21960545 chr13:28227653(+) A-I intron -    21960545 chr13:28225817(+) A-I intron -    21960545 chr13:28225775(+) A-G intron -    22484847 chr13:28225816(+) A-G intron -    22484847 chr13:28225819(+) A-G intron -    22484847 chr13:28225894(+) A-G intron -    22484847 chr13:28225895(+) A-G intron -    22484847 chr13:28225910(+) A-G intron -    22484847 chr13:28225913(+) A-G intron -    22484847 chr13:28227725(+) A-G intron -    22484847 chr13:28227760(+) A-G intron -    22484847 chr13:28227761(+) A-G intron -    22484847 chr13:28227792(+) A-G intron -    22484847 chr13:28227795(+) A-G intron -    22484847 chr13:28226842(+) A-G intron -    22484847 chr13:28226845(+) A-G intron -    22484847 chr13:28226919(+) A-G intron -    22484847 chr13:28226943(+) A-G intron -    22484847 chr13:28226948(+) A-G intron -    22484847 chr13:28227137(+) A-G intron -    22484847 chr13:28227299(+) A-G intron -    22484847 chr13:28227305(+) A-G intron -    22484847 chr13:28210724(+) A-G intron -    22484847 chr13:28225969(+) A-G intron -    22484847 chr13:28226273(+) A-G intron -    22484847 chr13:28226274(+) A-G intron -    22484847 chr13:28226314(+) A-G intron -    22484847 chr13:28227645(+) A-G intron -    22484847 chr13:28227653(+) A-G intron -    22484847 chr13:28227693(+) A-G intron -    22484847

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	POLR1D	chr13:28195022-28195023(+) m6A 5'UTR//exon       24284625//24209618//25456834//24981863//27371828//22608085 chr13:28195066-28195067(+) m6A 5'UTR//exon       24284625//24209618//25456834//24981863//27371828//27773536//22608085 chr13:28195104-28195105(+) m6A 5'UTR//exon       24284625//25456834//24981863//27371828//27773536//22608085 chr13:28195144-28195145(+) m6A 5'UTR//exon       24284625//24209618//25456834//24981863//27371828//27773536//22608085 chr13:28195271-28195272(+) m6A 5'UTR//exon//intron       24284625//24209618//25456834//24981863//22608085 chr13:28195504-28195505(+) m6A 5'UTR//exon//intron       24284625//24209618//25456834//24981863//22608085 chr13:28195694-28195695(+) m6A 5'UTR//exon//intron       25456834//24981863//22608085 chr13:28196067-28196068(+) m6A 5'UTR//exon//intron       24284625//22575960 chr13:28196108-28196109(+) m6A 5'UTR//intron       24284625//27773535//22575960//22608085 chr13:28197030-28197031(+) m6A 5'UTR//CDS//intron       24284625//24209618//24981863//26404942//27773535//22608085 chr13:28197057-28197058(+) m6A CDS//intron       24284625//24209618//24981863//26404942//27773535//22608085 chr13:28197087-28197088(+) m6A CDS//intron       24284625//24209618//24981863//26404942//27773535//22608085 chr13:28197095-28197096(+) m6A CDS//intron       24284625//24209618//24981863//26404942//27773535//22608085 chr13:28197127-28197128(+) m6A CDS//intron       24284625//24209618//24981863//26404942//27773535//22608085 chr13:28197169-28197170(+) m6A CDS//intron       24284625//24209618//24981863//26404942//27773535//22608085 chr13:28197192-28197193(+) Y CDS//intron       26075521 chr13:28197240-28197241(+) m6A CDS//intron       24284625//24209618//25456834//24981863//26404942//27773535//22575960//22608085 chr13:28197343-28197344(+) m6A CDS//intron       24284625//24209618//25456834//24981863//26404942//27773535//22575960//22608085 chr13:28197411-28197412(+) m6A 3'UTR//intron       24284625//24209618//24981863//26404942//27773535//22575960//22608085 chr13:28197448-28197449(+) m6A 3'UTR//intron       24284625//24981863//27773535//22608085 chr13:28197546-28197547(+) m6A 3'UTR//intron       24284625//22608085 chr13:28197585-28197586(+) m6A 3'UTR//intron       22608085 chr13:28222444-28222445(+) m6A exon//intron       - chr13:28222468-28222469(+) m6A exon//intron       - chr13:28222530-28222531(+) m6A 5'UTR//CDS//exon       - chr13:28222558-28222559(+) m6A 5'UTR//CDS//exon       - chr13:28222570-28222571(+) m6A 5'UTR//CDS//exon       24284625//27773535 chr13:28222578-28222579(+) m6A CDS//exon       24284625//27773535 chr13:28224190-28224191(+) m6A CDS//intron       24284625//27773535 chr13:28224201-28224202(+) m6A CDS//intron       24284625//27773535 chr13:28224222-28224223(+) m6A 3'UTR//intron       24284625//27773535 chr13:28224266-28224267(+) m6A 3'UTR//intron       - chr13:28224643-28224644(+) m6A 3'UTR//intron       24284625//25456834//24981863//22608085 chr13:28224672-28224673(+) m6A 3'UTR//intron       24284625//25456834//24981863//22608085 chr13:28224678-28224679(+) m6A 3'UTR//intron       24284625//25456834//24981863//22608085 chr13:28224739-28224740(+) m6A 3'UTR//intron       24284625//24981863//22608085 chr13:28224744-28224745(+) m6A 3'UTR//intron       24284625//24981863//22608085 chr13:28224814-28224815(+) m6A 3'UTR//intron       24284625//24981863//22608085 chr13:28224824-28224825(+) m6A 3'UTR//intron       24284625//24981863//22608085 chr13:28224847-28224848(+) m6A 3'UTR//intron       - chr13:28224854-28224855(+) m6A 3'UTR//intron       - chr13:28225229-28225230(+) m6A 3'UTR//intron       - chr13:28225265-28225266(+) m6A 3'UTR//intron       - chr13:28225294-28225295(+) m6A 3'UTR//intron       - chr13:28225329-28225330(+) m6A 3'UTR//intron       - chr13:28225392-28225393(+) m6A 3'UTR//intron       - chr13:28225399-28225400(+) m6A 3'UTR//intron       - chr13:28225473-28225474(+) m6A 3'UTR//intron       - chr13:28239878-28239879(+) m6A 3'UTR//CDS//exon       24284625//24209618//25456834//24981863//27773535//27371828//22608085 chr13:28239905-28239906(+) m6A 3'UTR//CDS//exon       24284625//24209618//25456834//24981863//27773535//27371828//22608085 chr13:28239912-28239913(+) m6A 3'UTR//CDS//exon       24284625//24209618//25456834//24981863//27773535//27371828//22608085 chr13:28239933-28239934(+) m6A 3'UTR//CDS//exon       24284625//24209618//25456834//24981863//27773535//27371828//22608085 chr13:28239965-28239966(+) m6A 3'UTR//CDS//exon       24284625//24209618//25456834//24981863//27773535//27371828//22608085 chr13:28239975-28239976(+) m6A 3'UTR//CDS//exon       24284625//24209618//25456834//24981863//27773535//27371828//22608085 chr13:28240058-28240059(+) m6A 3'UTR//CDS//exon       24284625//24209618//25456834//24981863//22608085 chr13:28240097-28240098(+) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//22608085 chr13:28240176-28240177(+) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//26404942//22608085 chr13:28240270-28240271(+) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//22608085 chr13:28240325-28240326(+) m6A 3'UTR//exon       25456834//24981863//22608085 chr13:28240372-28240373(+) m6A 3'UTR//exon       - chr13:28241221-28241222(+) m6A 3'UTR       24981863 chr13:28241231-28241232(+) m6A 3'UTR       24981863 chr13:28241334-28241335(+) m6A 3'UTR       24981863 chr13:28241374-28241375(+) m6A 3'UTR       24981863

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	POLR1D	Cytosol HCC cell line (HepG2)     - Endoplasmic reticulum Human myelogenous leukemia cell line (K-562)     21613539 Exosome Blood     - Membrane K562 cells     - Nucleolus K562 cells     - Ribosome Colon cancer cells     24393600

Interaction Network (The top 100 interactions):

Interactor1: ebv-miR-BART3-3p
Interactor2: POLR1D

Evidence Support:

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

References:

[1]PMID	22100165	Target region	3'UTR
Source	RepTar//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.

[2]PMID	22291592	Target region	3'UTR
Source	RepTar//ViRBase//VIRmiRNA//VmiReg	Interactor1 expression	None
Tissue or cell line	EF3D-AGO2 cells//LCL35 cells//LCL-BAC cells//LCL-BAC-D1 cells//LCL-BAC-D3 cells	Interactor2 expression	Downregulation
Description	We identified 7,827 miRNA-interaction sites in 3,492 cellular 3'UTRs. 531 of these sites contained seed matches to viral miRNAs.Table S6: High confidence miRNA-interaction sites in 3'UTRs.We identified an additional 2,972 CDS miRNA-interaction sites present in at least two libraries, 89.7% of which could be assigned to a miRNA (Table S7).