Basic Information:

  VIRBase ID:  

VHID00446224

  Virus:  

Human gammaherpesvirus 8 (Kaposi's sarcoma herpesvirus, KSHV)

  Host:  

Homo sapiens

  Confidence Score:  

0.6743

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      kshv-miR-K12-9-3p:  MIMAT0002185          GEN1:  NM_001130009     

      *It may take a few minutes to display results.

Interactor Information:

	Interactor1	Interactor2
Symbol	kshv-miR-K12-9-3p	GEN1
miRBase Accession/Entrez ID	MIMAT0002185	348654
Organism	Human gammaherpesvirus 8 (Kaposi's sarcoma herpesvirus, KSHV)	Homo sapiens
Category	miRNA	mRNA
Alias	-	Gen

RNA Editing:

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	GEN1	chr2:17964540(+) A-I      3'UTR chr2:17960319(+) A-I      intronic chr2:17958318(+) A-I      intronic chr2:17958332(+) A-I      intronic chr2:17958381(+) A-I      intronic chr2:17958325(+) A-I      intronic chr2:17940006(+) A-I      intronic chr2:17937946(+) A-I      intronic chr2:17964454(+) A-I      3'UTR chr2:17940001(+) A-I      intronic chr2:17937955(+) A-I      intronic

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	GEN1	chr2:17935223-17935224(+) m6A 5'UTR//exon       24981863 chr2:17941327-17941328(+) m6A CDS       24981863 chr2:17942664-17942665(+) m6A CDS//exon       24981863 chr2:17961380-17961381(+) m6A CDS//exon       22608085 chr2:17961905-17961906(+) m6A CDS//exon       24981863//22608085 chr2:17961918-17961919(+) m6A CDS//exon       24981863//22608085 chr2:17961960-17961961(+) m6A CDS//exon       24284625//24981863//22608085 chr2:17962104-17962105(+) m6A CDS       24284625//24209618//24981863//27773535//22575960//22608085 chr2:17962125-17962126(+) m6A CDS       24284625//24209618//24981863//27773535//22575960//22608085 chr2:17962368-17962369(+) m6A CDS       24284625//24209618//24981863//22608085 chr2:17962403-17962404(+) m6A CDS       24284625//24981863//22608085 chr2:17962567-17962568(+) m6A CDS       24284625//24981863//22608085 chr2:17962679-17962680(+) m6A CDS       24284625//24209618//24981863//22608085 chr2:17962700-17962701(+) m6A CDS       24284625//24209618//24981863//22608085 chr2:17962718-17962719(+) m6A CDS       24284625//24209618//24981863//22608085 chr2:17962771-17962772(+) m6A CDS       24284625//24209618//24981863//22608085 chr2:17962785-17962786(+) m6A CDS       24284625//24209618//24981863//22608085 chr2:17962831-17962832(+) m6A CDS       24284625//24209618//24981863//22608085 chr2:17962875-17962876(+) m6A CDS       24284625//24209618//24981863//27773535//22575960//22608085 chr2:17962890-17962891(+) m6A CDS       24284625//24209618//24981863//27773535//22575960//22608085 chr2:17963026-17963027(+) m6A CDS       24284625//24209618//24981863//27773535//22608085 chr2:17963031-17963032(+) m6A CDS       24284625//24209618//24981863//27773535//22608085 chr2:17963053-17963054(+) m6A CDS       24284625//24209618//24981863//27773535//22608085 chr2:17963132-17963133(+) m6A CDS       24284625//24981863//22608085 chr2:17963184-17963185(+) m6A CDS       24284625//24981863//22608085 chr2:17963214-17963215(+) m6A 3'UTR       24981863//22608085 chr2:17963262-17963263(+) m6A 3'UTR       22608085 chr2:17963322-17963323(+) m6A 3'UTR       22608085 chr2:17964251-17964252(+) Y 3'UTR       26075521 chr2:17964902-17964903(+) m6A 3'UTR       24981863//27773535//22608085 chr2:17964984-17964985(+) m6A 3'UTR       24981863//27773535//22608085 chr2:17964998-17964999(+) m6A 3'UTR       24981863//27773535//22608085 chr2:17965019-17965020(+) m6A 3'UTR       24209618//24981863//27773535//22608085 chr2:17965030-17965031(+) m6A 3'UTR       24209618//24981863//27773535//22608085 chr2:17965157-17965158(+) m6A 3'UTR       24284625//24981863//27773535//22575960//22608085 chr2:17965171-17965172(+) m6A 3'UTR       24284625//24981863//27773535//22575960//22608085 chr2:17965257-17965258(+) m6A 3'UTR       24284625//24209618//25456834//24981863//27773535//22575960//22608085 chr2:17965262-17965263(+) m6A 3'UTR       24284625//24209618//25456834//24981863//27773535//22575960//22608085 chr2:17965273-17965274(+) m6A 3'UTR       24284625//24209618//25456834//24981863//27773535//22575960//22608085 chr2:17965280-17965281(+) m6A 3'UTR       24284625//24209618//24981863//27773535//22575960//22608085 chr2:17965318-17965319(+) m6A 3'UTR       24284625//24209618//24981863//27773535//22575960//22608085 chr2:17965369-17965370(+) m6A 3'UTR       24284625//24209618//24981863//27773535//22575960//22608085 chr2:17965395-17965396(+) m6A 3'UTR       24284625//24209618//24981863//27773535//22575960//22608085 chr2:17965418-17965419(+) m6A 3'UTR       24284625//24209618//24981863//27773535//22575960//22608085 chr2:17965538-17965539(+) m6A 3'UTR       24981863//27773535//22608085 chr2:17965546-17965547(+) m6A 3'UTR       24981863//27773535//22608085 chr2:17965749-17965750(+) m6A 3'UTR       22608085 chr2:17965767-17965768(+) m6A 3'UTR       24981863//22608085 chr2:17965820-17965821(+) m6A 3'UTR       24981863//22608085 chr2:17965853-17965854(+) m6A 3'UTR       24981863//27773535//22608085 chr2:17965905-17965906(+) m6A 3'UTR       24981863//27773535//22608085 chr2:17965932-17965933(+) m6A 3'UTR       24981863//22608085 chr2:17966207-17966208(+) m6A 3'UTR       24981863 chr2:17966312-17966313(+) m6A 3'UTR       24981863 chr2:17966324-17966325(+) m6A 3'UTR       24981863 chr2:17966392-17966393(+) m6A 3'UTR       24981863 chr2:17966437-17966438(+) m6A 3'UTR       24981863

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	GEN1	Cytosol HCC cell line (HepG2)|K562 cells     - Exosome Blood     - Insoluble cytoplasm HCC cell line (HepG2)     - Membrane HCC cell line (HepG2)     - Nucleus Colon cancer cells     24393600 Nucleus HeLa-S3 cells|K562 cells     -

Interaction Network (The top 100 interactions):

Interactor1: kshv-miR-K12-9-3p
Interactor2: GEN1

Evidence Support:

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

References:

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

[2]PMID	22174674	Target region	None
Source	ViRBase//VIRmiRNA//VmiReg	Interactor1 expression	None
Tissue or cell line	EA.hy926 cells	Interactor2 expression	Downregulation
Description	As KSHV putative direct targets we extracted transcripts that were significantly down-regulated significantly in the replicate experiments, and which contained at least one seed-match to one of the KSHV miRNAs. We identified 704 putative direct targets in DG-75 cells (Figure 3B), and 980 putative direct targets in EA.hy926 cells (Figure 3C). A complete list of putative direct targets can be found in Dataset S2 for DG-75 cells and in Dataset S3 for EA.hy926 cells. The overlap between the two datasets contained 153 putative direct targets (Dataset S4).