Detail Information

Basic Information:


  VIRBase ID:  

VHID00465218

  Virus:  

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

  Host:  

Homo sapiens

  Confidence Score:  

0.6791

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      kshv-miR-K12-4-3p:           CDC42SE1:      

      *It may take a few minutes to display results.

Interactor Information:


Interactor1 Interactor2
Symbol kshv-miR-K12-4-3p CDC42SE1
miRBase
Accession/Entrez ID		 MIMAT0002192 56882
Organism Human gammaherpesvirus 8 (Kaposi's sarcoma herpesvirus, KSHV) Homo sapiens
Category miRNA mRNA
Alias - SCIP1//SPEC1

RNA Editing:


Resource Symbol Editing Position Change Genetic Region
RADAR CDC42SE1
chr1:151023728(-) A-I      3'UTR
chr1:151023752(-) A-I      3'UTR
chr1:151023750(-) A-I      3'UTR
chr1:151023753(-) A-I      3'UTR
chr1:151023714(-) A-I      3'UTR
chr1:151023715(-) A-I      3'UTR
chr1:151023707(-) A-I      3'UTR
chr1:151023699(-) A-I      3'UTR
chr1:151023691(-) A-I      3'UTR
chr1:151023690(-) A-I      3'UTR
Resource Symbol Editing Position Change SeqReg exReg PMID
DARNED CDC42SE1
chr1:151026399(-) T-C intron -    22484847

RNA Modification:


Resource Symbol ModificationPosition Type Genomic Context PMID
RMBase CDC42SE1
chr1:151024854-151024855(-) m6A 3'UTR//exon       26404942
chr1:151024894-151024895(-) m6A 3'UTR//exon       26404942
chr1:151025278-151025279(-) m6A 3'UTR//exon       24284625//27773535
chr1:151025349-151025350(-) m6A 3'UTR//exon       24284625//24209618//24981863//26404942//27773535//22608085
chr1:151025451-151025452(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr1:151025458-151025459(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr1:151025466-151025467(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr1:151025521-151025522(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr1:151025553-151025554(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr1:151025605-151025606(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr1:151025662-151025663(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr1:151025714-151025715(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr1:151025729-151025730(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr1:151025786-151025787(-) m6A 3'UTR//exon       24284625//24209618//24981863//27773535//27371828//22575960//22608085
chr1:151026759-151026760(-) m6A CDS//exon       24284625//24209618//27773535//27371828
chr1:151027500-151027501(-) m6A CDS//exon       24209618//27773535//27371828
chr1:151027560-151027561(-) m6A CDS//exon       24209618//27773535//27371828
chr1:151027574-151027575(-) m6A CDS//exon       24209618//27773535//27371828
chr1:151027598-151027599(-) m1A CDS//exon       26863410
chr1:151027628-151027629(-) m6A exon//intron       24209618//27773535//27371828
chr1:151027672-151027673(-) m6A exon//intron       27773535
chr1:151028185-151028186(-) m6A CDS//exon       22575960
chr1:151028207-151028208(-) m6A 5'UTR//exon       22575960
chr1:151028218-151028219(-) m6A 5'UTR//exon       22575960
chr1:151028237-151028238(-) m6A 5'UTR//exon       22575960
chr1:151028268-151028269(-) m6A 5'UTR//exon       22575960
chr1:151028316-151028317(-) m6A 5'UTR//exon       22575960
chr1:151028334-151028335(-) m6A 5'UTR//exon       24284625
chr1:151028386-151028387(-) m6A 5'UTR//exon       24284625
chr1:151028449-151028450(-) m6A 5'UTR//exon       24284625
chr1:151029165-151029166(-) m6A 5'UTR//exon//intron       24284625//24981863
chr1:151029175-151029176(-) m6A 5'UTR//exon//intron       24284625//24981863
chr1:151029210-151029211(-) m6A 5'UTR//exon//intron       24284625//24981863
chr1:151029247-151029248(-) m6A 5'UTR//exon//intron       24981863
chr1:151039729-151039730(-) m6A 5'UTR       -
chr1:151039792-151039793(-) m6A 5'UTR       24981863
chr1:151040835-151040836(-) m6A 5'UTR       24981863//22608085
chr1:151042765-151042766(-) m6A 5'UTR       22608085

RNA Localization:


Resource Symbol Subcellular Localization Tissue or Cell Line PMID
RNALocate CDC42SE1
Chromatin K562 cells     -
Cytosol Human myelogenous leukemia cell line (K-562)     21613539
Exosome Blood     -
Nucleolus K562 cells     -
Nucleoplasm K562 cells     -
Nucleus HeLa-S3 cells|K562 cells     -
Ribosome HEK-293 cells     22199352
Ribosome Colon cancer cells     24393600

Related Drug Information:


Resource Symbol Drug Name PubChem ID
RNAactDrug kshv-miR-K12-4-3p
Panobinostat       6918837
Nilotinib       644241
Irinotecan       60838
Topotecan       60700
l-685,458       5479543
Palbociclib       5330286
Dovitinib       135398510
Crizotinib       11626560
Nvp-aew541       11476171
Pha-665752       10461815

Interaction Network (The top 100 interactions):


Interactor1: kshv-miR-K12-4-3p
Interactor2: CDC42SE1

Evidence Support:


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

References:


[1]PMID 22100165 Target region 3'UTR
Source RepTar//ViRBase//VmiReg Interactor1 expression None
Tissue or cell line BC-1 cells//BC-3 cells//BJAB 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 RepTar//ViRBase//VmiReg Interactor1 expression None
Tissue or cell line DG-75 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).

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