Basic Information:

  VIRBase ID:  

VHID00444622

  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-K12-9-3p:  MIMAT0002185          ATF3:  NM_001674     

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Interactor Information:

	Interactor1	Interactor2
Symbol	kshv-miR-K12-9-3p	ATF3
miRBase Accession/Entrez ID	MIMAT0002185	467
Organism	Human gammaherpesvirus 8 (Kaposi's sarcoma herpesvirus, KSHV)	Homo sapiens
Category	miRNA	mRNA
Alias	-	-

RNA Editing:

Resource	Symbol	Editing Position
Lncediting	ATF3	chr1: 212787266

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	ATF3	chr1:212789196(+) A-I      intronic chr1:212789732(+) A-I      intronic chr1:212789778(+) A-I      intronic chr1:212789231(+) A-I      intronic chr1:212789849(+) A-I      intronic chr1:212789916(+) A-I      intronic chr1:212788888(+) A-I      intronic chr1:212789719(+) A-I      intronic chr1:212788919(+) A-I      intronic chr1:212789066(+) A-I      intronic chr1:212745183(+) A-I      intronic chr1:212788911(+) A-I      intronic chr1:212787266(+) A-I      ncRNA chr1:212789217(+) A-I      intronic chr1:212789116(+) A-I      intronic chr1:212789101(+) A-I      intronic chr1:212789025(+) A-I      intronic chr1:212789232(+) A-I      intronic chr1:212789042(+) A-I      intronic chr1:212788966(+) A-I      intronic chr1:212753840(+) A-I      intronic chr1:212787786(+) A-I      intronic chr1:212788942(+) A-I      intronic chr1:212789199(+) A-I      intronic chr1:212789088(+) A-I      intronic chr1:212787744(+) A-I      intronic

Resource	Symbol	Editing Position	Change	SeqReg	exReg	PMID
DARNED	ATF3	chr1:212787266(+) A-I intron -    19478186   //21960545 chr1:212789217(+) A-G intron -    22484847

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	ATF3	chr1:212782216-212782217(+) m6A 5'UTR//exon//intron       24981863 chr1:212788514-212788515(+) m6A 5'UTR//CDS//exon//intron       27773535 chr1:212788572-212788573(+) m6A CDS//exon//intron       24981863//27773535 chr1:212791541-212791542(+) m6A CDS//exon//intron       24981863//27773535 chr1:212791660-212791661(+) m6A exon//intron       27773535//22608085 chr1:212791970-212791971(+) m6A exon//intron       24981863 chr1:212792107-212792108(+) m6A exon//intron       25456834//24981863 chr1:212792731-212792732(+) m6A 3'UTR//CDS//exon       24209618//24981863//22608085 chr1:212792834-212792835(+) m6A 3'UTR//CDS//exon       24284625//24209618//24981863//26404942//27773535//22608085 chr1:212792853-212792854(+) m6A 3'UTR//CDS//exon       24284625//24209618//24981863//26404942//27773535//22608085 chr1:212792882-212792883(+) m6A 3'UTR//CDS//exon       24284625//24209618//24981863//26404942//27773535//22608085 chr1:212792956-212792957(+) m6A 3'UTR//exon       24284625//25456834//24981863//26404942//27773535//22608085 chr1:212793015-212793016(+) m6A 3'UTR//exon       24284625//24981863//26404942//22608085 chr1:212793084-212793085(+) m6A 3'UTR//exon       24284625//24981863//22608085 chr1:212793206-212793207(+) m6A 3'UTR//exon       24284625//24981863 chr1:212793322-212793323(+) m6A 3'UTR//exon       24284625//24209618//24981863//27773535 chr1:212793408-212793409(+) m6A 3'UTR//exon       24284625//24981863//27773535 chr1:212793573-212793574(+) m6A 3'UTR//exon       24284625 chr1:212793637-212793638(+) m6A 3'UTR//exon       24284625

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	ATF3	Chromatin K562 cells     - Cytoplasm Human hepatoma cell line (HepG2)     16109718 Cytosol Human myelogenous leukemia cell line (K-562)     21613539 Exosome Blood     - Nucleoplasm K562 cells     - Nucleus HCC cell line (HepG2)|HeLa-S3 cells     -

Interaction Network (The top 100 interactions):

Interactor1: kshv-miR-K12-9-3p
Interactor2: ATF3

Evidence Support:

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

References:

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.