Basic Information:

  VIRBase ID:  

VHID00317235

  Virus:  

Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)

  Host:  

Homo sapiens

  Confidence Score:  

0.6002

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      ebv-miR-BART6-3p:  MIMAT0003415          HMG20A:  NM_018200     

      *It may take a few minutes to display results.

Interactor Information:

	Interactor1	Interactor2
Symbol	ebv-miR-BART6-3p	HMG20A
miRBase Accession/Entrez ID	MIMAT0003415	10363
Organism	Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)	Homo sapiens
Category	miRNA	mRNA
Alias	-	HMGX1//HMGXB1

RNA Editing:

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	HMG20A	chr15:77768759(+) A-I      intronic chr15:77758545(+) A-I      intronic chr15:77772911(+) A-I      intronic chr15:77772909(+) A-I      intronic chr15:77772861(+) A-I      intronic chr15:77764890(+) A-I      intronic chr15:77757838(+) A-I      intronic chr15:77764681(+) A-I      intronic chr15:77729938(+) A-I      intronic chr15:77730076(+) A-I      intronic chr15:77757369(+) A-I      intronic chr15:77764721(+) A-I      intronic chr15:77757877(+) A-I      intronic chr15:77764782(+) A-I      intronic chr15:77757867(+) A-I      intronic chr15:77768561(+) A-I      intronic chr15:77757769(+) A-I      intronic chr15:77757757(+) A-I      intronic chr15:77757583(+) A-I      intronic chr15:77764783(+) A-I      intronic chr15:77764807(+) A-I      intronic chr15:77768659(+) A-I      intronic chr15:77768662(+) A-I      intronic chr15:77768667(+) A-I      intronic chr15:77768716(+) A-I      intronic chr15:77772694(+) A-I      intronic chr15:77758459(+) A-I      intronic chr15:77757958(+) A-I      intronic chr15:77772898(+) A-I      intronic chr15:77757425(+) A-I      intronic chr15:77757401(+) A-I      intronic chr15:77757373(+) A-I      intronic chr15:77758638(+) A-I      intronic chr15:77764717(+) A-I      intronic chr15:77757557(+) A-I      intronic chr15:77757999(+) A-I      intronic chr15:77757998(+) A-I      intronic chr15:77758465(+) A-I      intronic chr15:77772727(+) A-I      intronic chr15:77758677(+) A-I      intronic chr15:77758712(+) A-I      intronic chr15:77758713(+) A-I      intronic chr15:77757497(+) A-I      intronic chr15:77768668(+) A-I      intronic chr15:77764774(+) A-I      intronic chr15:77757831(+) A-I      intronic chr15:77757972(+) A-I      intronic chr15:77742495(+) A-I      intronic chr15:77742606(+) A-I      intronic chr15:77758547(+) A-I      intronic chr15:77753263(+) A-I      intronic chr15:77757392(+) A-I      intronic chr15:77757864(+) A-I      intronic chr15:77758513(+) A-I      intronic chr15:77764756(+) A-I      intronic chr15:77742602(+) A-I      intronic chr15:77764820(+) A-I      intronic chr15:77721436(+) A-I      intronic chr15:77772535(+) A-I      intronic chr15:77768670(+) A-I      intronic chr15:77758537(+) A-I      intronic chr15:77757807(+) A-I      intronic chr15:77764792(+) A-I      intronic chr15:77757971(+) A-I      intronic chr15:77764680(+) A-I      intronic chr15:77757863(+) A-I      intronic chr15:77772537(+) A-I      intronic chr15:77757799(+) A-I      intronic chr15:77757400(+) A-I      intronic chr15:77768707(+) A-I      intronic chr15:77758576(+) A-I      intronic chr15:77758508(+) A-I      intronic chr15:77757959(+) A-I      intronic chr15:77758624(+) A-I      intronic chr15:77721201(+) A-I      intronic chr15:77758544(+) A-I      intronic

Resource	Symbol	Editing Position	Change	SeqReg	exReg	PMID
DARNED	HMG20A	chr15:77757863(+) A-I intron -    22327324 chr15:77757864(+) A-I intron -    22327324 chr15:77758513(+) A-I intron -    22327324

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	HMG20A	chr15:77712775-77712776(+) m6A 5'UTR       25456834 chr15:77712829-77712830(+) m6A 5'UTR       25456834 chr15:77713193-77713194(+) m6A 5'UTR//intron       24981863//27773535//22608085 chr15:77713301-77713302(+) m6A 5'UTR//exon//intron       24981863//22608085 chr15:77750756-77750757(+) m6A 5'UTR//CDS//exon//intron       - chr15:77756710-77756711(+) m6A 5'UTR//CDS//exon       27773535 chr15:77756767-77756768(+) m6A exon//intron       24981863//27773535 chr15:77759483-77759484(+) m6A 5'UTR//CDS//intron       24284625//24981863 chr15:77759494-77759495(+) m6A 5'UTR//CDS//intron       24284625//24981863 chr15:77759555-77759556(+) m6A 3'UTR//CDS       24284625//24981863//27773535 chr15:77759573-77759574(+) m6A 3'UTR//CDS       24981863//27773535 chr15:77759627-77759628(+) m6A 3'UTR//CDS       24981863//27773535 chr15:77759645-77759646(+) m6A 3'UTR//CDS       24981863//27773535 chr15:77763270-77763271(+) m6A 3'UTR//CDS       24981863//27773535 chr15:77763298-77763299(+) m6A 3'UTR//CDS       24981863//27773535 chr15:77763304-77763305(+) m6A 3'UTR//CDS       24981863//27773535 chr15:77763317-77763318(+) m6A 3'UTR//CDS       24981863//27773535 chr15:77763347-77763348(+) m6A CDS       24981863 chr15:77763354-77763355(+) m6A CDS       24981863 chr15:77769902-77769903(+) m6A CDS       24981863 chr15:77769960-77769961(+) m6A CDS       24981863 chr15:77770803-77770804(+) m6A CDS//exon       24284625//24981863//22608085 chr15:77771531-77771532(+) m6A CDS//exon       24284625//24981863//22608085 chr15:77771544-77771545(+) m6A CDS//exon       24284625//24981863//22608085 chr15:77771565-77771566(+) m6A CDS//exon       24284625//24981863//26404942//22608085 chr15:77771601-77771602(+) m6A CDS//exon       24284625//24981863//26404942//22608085 chr15:77771610-77771611(+) m6A CDS//exon       24284625//24981863//26404942//22608085 chr15:77771640-77771641(+) m6A CDS//exon       24284625//24981863//26404942//27773535//22608085 chr15:77771724-77771725(+) m6A 3'UTR//intron       24284625//24981863//22608085 chr15:77771744-77771745(+) m6A 3'UTR//intron       24284625//24981863//22608085 chr15:77771766-77771767(+) m6A 3'UTR//intron       24284625//24981863//22608085 chr15:77771777-77771778(+) m6A 3'UTR//intron       24284625//24981863//22608085 chr15:77775319-77775320(+) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//22608085 chr15:77775383-77775384(+) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//26404942//22608085 chr15:77775655-77775656(+) m6A 3'UTR//exon       24284625//24209618//24981863//22608085 chr15:77775679-77775680(+) m6A 3'UTR//exon       24284625//24209618//24981863//22608085 chr15:77775802-77775803(+) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//22575960//22608085 chr15:77775850-77775851(+) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//22575960//22608085 chr15:77777366-77777367(+) m6A 3'UTR//exon       24284625 chr15:77777386-77777387(+) m6A 3'UTR//exon       24284625

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	HMG20A	Chromatin K562 cells     - Cytosol HCC cell line (HepG2)     - Exosome Blood     - Nucleoplasm K562 cells     - Nucleus HeLa-S3 cells|K562 cells     - Ribosome Colon cancer cells     24393600

Interaction Network (The top 100 interactions):

Interactor1: ebv-miR-BART6-3p
Interactor2: HMG20A

Evidence Support:

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

References:

PMID	22100165	Target region	3'UTR
Source	RepTar//ViRBase//VIRmiRNA//VmiReg	Interactor1 expression	None
Tissue or cell line	BC-1 cells	Interactor2 expression	None
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.