Basic Information:

  VIRBase ID:  

VHID00428060

  Virus:  

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

  Host:  

Homo sapiens

  Confidence Score:  

0.5711

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      kshv-miR-K12-10b:  MIMAT0002180          TMED4:  NM_001303059     

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Interactor Information:

	Interactor1	Interactor2
Symbol	kshv-miR-K12-10b	TMED4
miRBase Accession/Entrez ID	MIMAT0002180	222068
Organism	Human gammaherpesvirus 8 (Kaposi's sarcoma herpesvirus, KSHV)	Homo sapiens
Category	miRNA	mRNA
Alias	-	ERS25//GMP25iso//HNLF//p24a3//p24alpha3

RNA Editing:

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	TMED4	chr7:44618327(-) A-I      3'UTR chr7:44618330(-) A-I      3'UTR chr7:44618341(-) A-I      3'UTR chr7:44618356(-) A-I      3'UTR chr7:44618365(-) A-I      3'UTR chr7:44618440(-) A-I      3'UTR chr7:44618459(-) A-I      3'UTR chr7:44618248(-) A-I      3'UTR chr7:44618321(-) A-I      3'UTR chr7:44618285(-) A-I      3'UTR chr7:44618317(-) A-I      3'UTR chr7:44618343(-) A-I      3'UTR chr7:44618427(-) A-I      3'UTR chr7:44618381(-) A-I      3'UTR chr7:44618299(-) A-I      3'UTR chr7:44618230(-) A-I      3'UTR chr7:44618282(-) A-I      3'UTR chr7:44618353(-) A-I      3'UTR chr7:44618308(-) A-I      3'UTR chr7:44618382(-) A-I      3'UTR chr7:44618378(-) A-I      3'UTR chr7:44618262(-) A-I      3'UTR chr7:44618273(-) A-I      3'UTR

Resource	Symbol	Editing Position	Change	SeqReg	exReg	PMID
DARNED	TMED4	chr7:44620289(-) A-I intron -    21960545 chr7:44619821(-) A-G intron -    22484847 chr7:44619833(-) A-G intron -    22484847 chr7:44619843(-) A-G intron -    22484847 chr7:44619885(-) A-G intron -    22484847 chr7:44619897(-) A-G intron -    22484847 chr7:44619911(-) A-G intron -    22484847 chr7:44620001(-) A-G intron -    22484847 chr7:44620289(-) A-G intron -    22484847 chr7:44620301(-) A-G intron -    22484847 chr7:44620302(-) A-G intron -    22484847 chr7:44620311(-) A-G intron -    22484847 chr7:44620381(-) A-G intron -    22484847 chr7:44620424(-) A-G intron -    22484847 chr7:44620470(-) A-G intron -    22484847 chr7:44620500(-) A-G intron -    22484847 chr7:44620508(-) A-G intron -    22484847 chr7:44620546(-) A-G intron -    22484847

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	TMED4	chr7:44617497-44617498(-) m6A 3'UTR       27773535 chr7:44617590-44617591(-) m6A 3'UTR       27773535 chr7:44617630-44617631(-) m6A 3'UTR       27773535 chr7:44617699-44617700(-) m6A 3'UTR       22575960 chr7:44617769-44617770(-) m6A 3'UTR       25456834//24981863//22575960 chr7:44617795-44617796(-) m6A 3'UTR       25456834//24981863//22575960 chr7:44617807-44617808(-) m6A 3'UTR       25456834//24981863//22575960 chr7:44618259-44618260(-) m6A 3'UTR       24209618 chr7:44619154-44619155(-) m6A CDS       27371828 chr7:44619509-44619510(-) m6A 3'UTR//exon//intron       27371828 chr7:44620108-44620109(-) m6A 3'UTR//exon//intron       27773535 chr7:44620126-44620127(-) m6A 3'UTR//exon//intron       27773535 chr7:44621334-44621335(-) m6A CDS//exon       27773535 chr7:44621657-44621658(-) m6A CDS//exon       24981863//27371828//27773536 chr7:44621696-44621697(-) m6A CDS//exon       24981863//27371828//27773536

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	TMED4	Cytosol HeLa-S3 cells     - Endoplasmic reticulum Human myelogenous leukemia cell line (K-562)     21613539 Exosome Blood     - Nucleolus K562 cells     - Nucleoplasm K562 cells     - Nucleus HCC cell line (HepG2)|HeLa-S3 cells     - Ribosome HEK-293 cells     22199352

Interaction Network (The top 100 interactions):

Interactor1: kshv-miR-K12-10b
Interactor2: TMED4

Evidence Support:

Weak-Evidence	PAR-CLIP
Prediction-Evidence	PARalyzer
Support Database	ViRBase

References:

PMID	22100165	Target region	3'UTR
Source	ViRBase	Interactor1 expression	None
Tissue or cell line	BC-3 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 S6B BC-3 derived 3'UTR clusters with seed matches to expressed miRNAs.