Detail Information

Basic Information:


  VIRBase ID:  

VHID00349112

  Virus:  

Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)

  Host:  

Homo sapiens

  Confidence Score:  

0.6787

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      ebv-miR-BART13-3p:           THUMPD1:      

      *It may take a few minutes to display results.

Interactor Information:


Interactor1 Interactor2
Symbol ebv-miR-BART13-3p THUMPD1
miRBase
Accession/Entrez ID		 MIMAT0003424 55623
Organism Human gammaherpesvirus 4 (Epstein-Barr virus, EPV) Homo sapiens
Category miRNA mRNA
Alias - Tan1

RNA Editing:


Resource Symbol Editing Position Change Genetic Region
RADAR THUMPD1
chr16:20750646(-) A-I      intronic
chr16:20750632(-) A-I      intronic
chr16:20750975(-) A-I      intronic
chr16:20750693(-) A-I      intronic
chr16:20750926(-) A-I      intronic
chr16:20750971(-) A-I      intronic
chr16:20751086(-) A-I      intronic
chr16:20751137(-) A-I      intronic
chr16:20751141(-) A-I      intronic
chr16:20751569(-) A-I      intronic
chr16:20751672(-) A-I      intronic
chr16:20752459(-) A-I      intronic
chr16:20750537(-) A-I      intronic
chr16:20750665(-) A-I      intronic
chr16:20750970(-) A-I      intronic
chr16:20752415(-) A-I      intronic
chr16:20751583(-) A-I      intronic
chr16:20750566(-) A-I      intronic
chr16:20751680(-) A-I      intronic
chr16:20752561(-) A-I      intronic
chr16:20750963(-) A-I      intronic
chr16:20750886(-) A-I      intronic
chr16:20750717(-) A-I      intronic
chr16:20750565(-) A-I      intronic
chr16:20750757(-) A-I      intronic
chr16:20751570(-) A-I      intronic
chr16:20752472(-) A-I      intronic
chr16:20750626(-) A-I      intronic
chr16:20750779(-) A-I      intronic
chr16:20750570(-) A-I      intronic
chr16:20750532(-) A-I      intronic
chr16:20750686(-) A-I      intronic
chr16:20750772(-) A-I      intronic
chr16:20750652(-) A-I      intronic
chr16:20751467(-) A-I      intronic
chr16:20750662(-) A-I      intronic
chr16:20751060(-) A-I      intronic
chr16:20750571(-) A-I      intronic
chr16:20750900(-) A-I      intronic
chr16:20750692(-) A-I      intronic
chr16:20750635(-) A-I      intronic
chr16:20751606(-) A-I      intronic
chr16:20751590(-) A-I      intronic
chr16:20750691(-) A-I      intronic
chr16:20750765(-) A-I      intronic
chr16:20750880(-) A-I      intronic
chr16:20752462(-) A-I      intronic
chr16:20751031(-) A-I      intronic
chr16:20750716(-) A-I      intronic
chr16:20751573(-) A-I      intronic
chr16:20750995(-) A-I      intronic
Resource Symbol Editing Position Change SeqReg exReg PMID
DARNED THUMPD1
chr16:20750565(-) A-G intron -    22484847
chr16:20750635(-) A-G intron -    22484847
chr16:20750691(-) A-G intron -    22484847
chr16:20751031(-) A-G intron -    22484847

RNA Modification:


Resource Symbol ModificationPosition Type Genomic Context PMID
RMBase THUMPD1
chr16:20745520-20745521(-) m6A 3'UTR       24981863//22608085
chr16:20745569-20745570(-) m6A 3'UTR       24284625//24981863//22608085
chr16:20745577-20745578(-) m6A 3'UTR       24284625//24981863//22608085
chr16:20745604-20745605(-) m6A 3'UTR       24284625//24209618//24981863//22608085
chr16:20745616-20745617(-) m6A 3'UTR       24284625//24209618//24981863//22608085
chr16:20745754-20745755(-) m6A 3'UTR       -
chr16:20745792-20745793(-) m6A 3'UTR       -
chr16:20745797-20745798(-) m6A 3'UTR       -
chr16:20745845-20745846(-) m6A 3'UTR       -
chr16:20745932-20745933(-) m6A 3'UTR       27773535
chr16:20746008-20746009(-) m6A 3'UTR       27773535
chr16:20746024-20746025(-) m6A 3'UTR       27773535
chr16:20746173-20746174(-) m6A 3'UTR       24209618//24981863//27773535//22608085
chr16:20746229-20746230(-) m6A 3'UTR       24284625//24209618//24981863//26404942//27773535//22608085
chr16:20746287-20746288(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr16:20746295-20746296(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr16:20746402-20746403(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr16:20746422-20746423(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr16:20746472-20746473(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr16:20746480-20746481(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr16:20746563-20746564(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22575960//22608085
chr16:20746644-20746645(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//27773535//27371828//22575960//22608085
chr16:20746662-20746663(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//27773535//27371828//22575960//22608085
chr16:20746677-20746678(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//27773535//27371828//22575960//22608085
chr16:20746683-20746684(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//27773535//27371828//22575960//22608085
chr16:20746689-20746690(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//27773535//27371828//22575960//22608085
chr16:20746698-20746699(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//27773535//27371828//22575960//22608085
chr16:20746733-20746734(-) m6A 3'UTR       24284625//24209618//25456834//24981863//28052920//27773535//27371828//22608085
chr16:20746753-20746754(-) m6A 3'UTR       24284625//24981863//27773535//22608085
chr16:20746791-20746792(-) m6A 3'UTR       24284625//24981863//27773535//22608085
chr16:20746974-20746975(-) m6A 3'UTR       24284625//27773535//22608085
chr16:20747003-20747004(-) m6A 3'UTR       24284625//24981863//27773535//22608085
chr16:20747179-20747180(-) m6A 3'UTR       24284625//24981863//27773535//22608085
chr16:20747268-20747269(-) m6A 3'UTR       24284625//24981863//27773535//22608085
chr16:20747337-20747338(-) m6A 3'UTR       24284625//24981863//27773535//22575960//22608085
chr16:20747347-20747348(-) m6A 3'UTR       24284625//24981863//27773535//22575960//22608085
chr16:20747419-20747420(-) m6A 3'UTR       24284625//24981863//27773535//22608085
chr16:20747476-20747477(-) m6A 3'UTR       24284625//24209618//24981863//27773535//22608085
chr16:20747531-20747532(-) m6A 3'UTR       24284625//24209618//24981863//27773535//22608085
chr16:20747576-20747577(-) m6A 3'UTR       24284625//24209618//24981863//26404942//27773535//22608085
chr16:20747604-20747605(-) m6A 3'UTR       24284625//24209618//24981863//26404942//27773535//22608085
chr16:20747611-20747612(-) m6A 3'UTR       24284625//24209618//24981863//26404942//27773535//22608085
chr16:20747628-20747629(-) m6A 3'UTR       24284625//24209618//24981863//26404942//27773535//22608085
chr16:20747997-20747998(-) m6A 3'UTR//intron       24981863
chr16:20748116-20748117(-) m6A 3'UTR//intron       24981863//22608085
chr16:20748255-20748256(-) m6A CDS//exon       24284625//24209618//25456834//24981863//28052920//27773535//27371828//22608085
chr16:20748261-20748262(-) m6A CDS//exon       24284625//24209618//25456834//24981863//28052920//27773535//27371828//22608085
chr16:20748303-20748304(-) m6A CDS//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22608085
chr16:20748308-20748309(-) m6A CDS//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22608085
chr16:20748370-20748371(-) m6A CDS//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22608085
chr16:20748376-20748377(-) m6A CDS//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22608085
chr16:20748385-20748386(-) m6A CDS//exon       24284625//24209618//25456834//24981863//28052920//26404942//27773535//27371828//22608085
chr16:20748399-20748400(-) m6A CDS//exon       24284625//24209618//24981863//28052920//26404942//27773535//27371828//22608085
chr16:20749101-20749102(-) m6A 3'UTR//CDS//exon       24981863//27773535//22608085
chr16:20749109-20749110(-) m6A 3'UTR//CDS//exon       24981863//27773535//22608085
chr16:20749129-20749130(-) m6A 3'UTR//CDS//exon       24981863//27773535//22608085
chr16:20749140-20749141(-) m6A 3'UTR//CDS//exon       24981863//27773535//22608085
chr16:20749218-20749219(-) m6A 3'UTR//CDS//exon       24209618//27773535//22608085
chr16:20749233-20749234(-) m6A 3'UTR//CDS//exon       24209618//27773535//22608085
chr16:20750385-20750386(-) m6A CDS//exon       27773535
chr16:20753039-20753040(-) m6A CDS//exon       24981863//27371828
chr16:20753205-20753206(-) m6A 5'UTR       24981863
chr16:20753217-20753218(-) m6A 5'UTR       24981863

RNA Localization:


Resource Symbol Subcellular Localization Tissue or Cell Line PMID
RNALocate THUMPD1
Cytosol Human myelogenous leukemia cell line (K-562)     21613539
Cytosol K562 cells     -
Exosome Blood     -
Nucleoplasm K562 cells     -
Nucleus HCC cell line (HepG2)     -
Ribosome Colon cancer cells     24393600

Interaction Network (The top 100 interactions):


Interactor1: ebv-miR-BART13-3p
Interactor2: THUMPD1

Evidence Support:


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

References:


[1]PMID 22100165 Target region 3'UTR
Source RepTar//ViRBase//VIRmiRNA//VmiReg Interactor1 expression None
Tissue or cell line BC-1 cells Interactor2 expression Downregulation
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 22473208 Target region 3'UTR
Source RepTar//ViRBase//VIRmiRNA//VmiReg Interactor1 expression None
Tissue or cell line Jijoye cells Interactor2 expression None
Description Our HITS-CLIP data yield 1185 human 3'UTRs targeted by members of the miR-17~92 cluster in Jijoye cells. Comparison to the 1664 3'UTRs targeted by EBV miRNAs reveals 740 shared genes (44% of EBV targets and 62% of miR-17~92 targets; Figure 6B and Supplementary Table 7). Thus, EBV miRNAs co-target a majority of miR-17~92 regulated mRNAs, which are assigned to a variety of pathways, most notably regulating transcription, apoptosis, and the cell cycle (Figure 6C). Similarly, other abundant immunologically relevant miRNAs, 142-3p and miR-155, co-target with EBV miRNAs a large fraction of their Ago-bound 3'UTRs, representing ~60% of the targets for each of these host miRNAs (Supplementary Figure 5).

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