Detail Information

Basic Information:


  VIRBase ID:  

VHID00456956

  Virus:  

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

  Host:  

Homo sapiens

  Confidence Score:  

0.6040

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      kshv-miR-K12-6-3p:           LYSMD3:      

      *It may take a few minutes to display results.

Interactor Information:


Interactor1 Interactor2
Symbol kshv-miR-K12-6-3p LYSMD3
miRBase
Accession/Entrez ID		 MIMAT0002189 116068
Organism Human gammaherpesvirus 8 (Kaposi's sarcoma herpesvirus, KSHV) Homo sapiens
Category miRNA mRNA
Alias - -

RNA Editing:


Resource Symbol Editing Position Change Genetic Region
RADAR LYSMD3
chr5:89820968(-) A-I      NonSyn:Lys->Glu
chr5:89820969(-) A-I      Syn:Gly->Gly
chr5:89820966(-) A-I      Syn:Lys->Lys
chr5:89820681(-) A-I      intronic
chr5:89820682(-) A-I      intronic
chr5:89820477(-) A-I      intronic
chr5:89816480(-) A-I      intronic
chr5:89816624(-) A-I      intronic

RNA Modification:


Resource Symbol ModificationPosition Type Genomic Context PMID
RMBase LYSMD3
chr5:89814162-89814163(-) m6A 3'UTR       27773535
chr5:89814239-89814240(-) m6A 3'UTR       27773535
chr5:89814640-89814641(-) m6A 3'UTR//CDS       24284625//24209618//25456834//24981863//26404942//27773535//27371828//22608085
chr5:89814683-89814684(-) m6A 3'UTR//CDS       24284625//24209618//25456834//24981863//26404942//27773535//27371828//22608085
chr5:89814792-89814793(-) m6A 3'UTR//CDS       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr5:89814898-89814899(-) m6A 3'UTR//CDS//intron       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr5:89814918-89814919(-) m6A 3'UTR//CDS//intron       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr5:89814936-89814937(-) m6A 3'UTR//CDS//intron       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr5:89814951-89814952(-) m6A 3'UTR//CDS//intron       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr5:89814965-89814966(-) m6A 3'UTR//CDS//intron       24284625//24209618//25456834//24981863//28052920//27773535//27371828//22575960//22608085
chr5:89815014-89815015(-) m6A 3'UTR//CDS//intron       24284625//24209618//25456834//24981863//28052920//27773535//27371828//22575960//22608085
chr5:89815029-89815030(-) m6A 3'UTR//CDS//intron       24284625//24209618//24981863//28052920//27773535//27371828//22575960//22608085
chr5:89815049-89815050(-) m6A 3'UTR//CDS//intron       24284625//24209618//24981863//28052920//27773535//27371828//22575960//22608085
chr5:89815056-89815057(-) m6A 3'UTR//CDS//intron       24284625//24209618//24981863//28052920//27773535//27371828//22575960//22608085
chr5:89815062-89815063(-) m6A 3'UTR//CDS//intron       24284625//24209618//24981863//28052920//27773535//27371828//22575960//22608085
chr5:89815136-89815137(-) m6A CDS//intron       24284625//24209618//24981863//27773535//27371828//22608085
chr5:89815175-89815176(-) m6A CDS//intron       24284625//24981863//27773535//27371828//22608085
chr5:89815198-89815199(-) m6A CDS//intron       24284625//24981863//27773535//22608085
chr5:89815257-89815258(-) m6A 3'UTR//CDS//intron       24284625//27773535//22608085
chr5:89816208-89816209(-) m6A 3'UTR//intron       27773535//22608085
chr5:89816233-89816234(-) m6A 3'UTR//intron       27773535//22608085
chr5:89820932-89820933(-) m6A CDS       24284625//24981863//27773535//22608085
chr5:89820983-89820984(-) m6A CDS       24981863//27773535//27371828//22608085
chr5:89821020-89821021(-) m6A CDS       24981863//27773535//27371828//22608085
chr5:89822761-89822762(-) m6A 5'UTR//intron       27773535//27371828
chr5:89822784-89822785(-) m6A 5'UTR//intron       27773535//27371828
chr5:89825267-89825268(-) m6A 5'UTR       24981863//27371828
chr5:89825310-89825311(-) m6A 5'UTR       24981863//27371828
chr5:89825326-89825327(-) m6A 5'UTR       24981863//27371828
chr5:89825337-89825338(-) m6A 5'UTR       24981863//27371828

RNA Localization:


Resource Symbol Subcellular Localization Tissue or Cell Line PMID
RNALocate LYSMD3
Chromatin K562 cells     -
Exosome Blood     -
Nucleoplasm K562 cells     -
Nucleus HeLa-S3 cells|K562 cells     -

Interaction Network (The top 100 interactions):


Interactor1: kshv-miR-K12-6-3p
Interactor2: LYSMD3

Evidence Support:


Weak-Evidence PAR-CLIP
Prediction-Evidence cRep//miRanda//PARalyzer//Targetscan
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.

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