Basic Information:

  VIRBase ID:  

VHID00320696

  Virus:  

Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)

  Host:  

Homo sapiens

  Confidence Score:  

0.6743

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      ebv-miR-BART7-3p:  MIMAT0003416          SCFD1:  NM_001283032     

      *It may take a few minutes to display results.

Interactor Information:

	Interactor1	Interactor2
Symbol	ebv-miR-BART7-3p	SCFD1
miRBase Accession/Entrez ID	MIMAT0003416	23256
Organism	Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)	Homo sapiens
Category	miRNA	mRNA
Alias	-	C14orf163//RA410//SLY1//SLY1P//STXBP1L2

RNA Editing:

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	SCFD1	chr14:31150312(+) A-I      intronic chr14:31117927(+) A-I      intronic chr14:31161205(+) A-I      intronic chr14:31178588(+) A-I      intronic chr14:31147231(+) A-I      intronic chr14:31111420(+) A-I      intronic chr14:31123868(+) A-I      intronic chr14:31147229(+) A-I      intronic chr14:31174791(+) A-I      intronic chr14:31123801(+) A-I      intronic chr14:31173484(+) A-I      intronic chr14:31163726(+) A-I      intronic chr14:31161211(+) A-I      intronic chr14:31149880(+) A-I      intronic chr14:31193706(+) A-I      intronic chr14:31163699(+) A-I      intronic chr14:31163653(+) A-I      intronic chr14:31161212(+) A-I      intronic chr14:31147320(+) A-I      intronic chr14:31147287(+) A-I      intronic chr14:31112120(+) A-I      intronic chr14:31147146(+) A-I      intronic chr14:31147145(+) A-I      intronic chr14:31147101(+) A-I      intronic chr14:31127851(+) A-I      intronic chr14:31111499(+) A-I      intronic chr14:31111433(+) A-I      intronic chr14:31101186(+) A-I      intronic chr14:31101179(+) A-I      intronic chr14:31098973(+) A-I      intronic chr14:31149901(+) A-I      intronic chr14:31098972(+) A-I      intronic chr14:31098967(+) A-I      intronic chr14:31098950(+) A-I      intronic chr14:31098936(+) A-I      intronic chr14:31098853(+) A-I      intronic chr14:31098848(+) A-I      intronic chr14:31098835(+) A-I      intronic chr14:31153481(+) A-I      intronic chr14:31146496(+) A-I      intronic chr14:31123760(+) A-I      intronic chr14:31125114(+) A-I      intronic chr14:31123766(+) A-I      intronic chr14:31123805(+) A-I      intronic chr14:31173406(+) A-I      intronic chr14:31096791(+) A-I      intronic chr14:31202691(+) A-I      intronic chr14:31202579(+) A-I      intronic chr14:31184787(+) A-I      intronic chr14:31123733(+) A-I      intronic chr14:31163769(+) A-I      intronic chr14:31123622(+) A-I      intronic chr14:31184656(+) A-I      intronic chr14:31101134(+) A-I      intronic chr14:31169759(+) A-I      intronic chr14:31163741(+) A-I      intronic chr14:31150372(+) A-I      intronic chr14:31163806(+) A-I      intronic chr14:31163826(+) A-I      intronic chr14:31150177(+) A-I      intronic chr14:31163696(+) A-I      intronic chr14:31101133(+) A-I      intronic chr14:31147211(+) A-I      intronic chr14:31174727(+) A-I      intronic chr14:31173405(+) A-I      intronic chr14:31173513(+) A-I      intronic chr14:31143808(+) A-I      intronic chr14:31202682(+) A-I      intronic chr14:31195164(+) A-I      intronic chr14:31195160(+) A-I      intronic chr14:31147235(+) A-I      intronic chr14:31173451(+) A-I      intronic chr14:31163676(+) A-I      intronic chr14:31202772(+) A-I      intronic chr14:31184626(+) A-I      intronic chr14:31147216(+) A-I      intronic chr14:31118011(+) A-I      intronic chr14:31163737(+) A-I      intronic chr14:31184599(+) A-I      intronic chr14:31202802(+) A-I      intronic chr14:31125072(+) A-I      intronic chr14:31163757(+) A-I      intronic chr14:31127782(+) A-I      intronic chr14:31096782(+) A-I      intronic chr14:31163818(+) A-I      intronic chr14:31150280(+) A-I      intronic chr14:31111394(+) A-I      intronic chr14:31143834(+) A-I      intronic chr14:31178648(+) A-I      intronic chr14:31163617(+) A-I      intronic chr14:31184679(+) A-I      intronic chr14:31178686(+) A-I      intronic chr14:31149857(+) A-I      intronic chr14:31163623(+) A-I      intronic chr14:31174722(+) A-I      intronic chr14:31180673(+) A-I      intronic chr14:31111349(+) A-I      intronic chr14:31117876(+) A-I      intronic chr14:31147175(+) A-I      intronic chr14:31127657(+) A-I      intronic chr14:31180542(+) A-I      intronic chr14:31112144(+) A-I      intronic chr14:31153469(+) A-I      intronic chr14:31153452(+) A-I      intronic chr14:31194261(+) A-I      intronic chr14:31153405(+) A-I      intronic chr14:31163624(+) A-I      intronic chr14:31123800(+) A-I      intronic chr14:31163831(+) A-I      intronic chr14:31096894(+) A-I      intronic chr14:31163773(+) A-I      intronic

Resource	Symbol	Editing Position	Change	SeqReg	exReg	PMID
DARNED	SCFD1	chr14:31163617(+) A-G intron -    22484847 chr14:31163696(+) A-G intron -    22484847 chr14:31163741(+) A-G intron -    22484847 chr14:31163757(+) A-G intron -    22484847 chr14:31163818(+) A-G intron -    22484847 chr14:31184774(+) C-A intron -    22484847

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	SCFD1	chr14:31091601-31091602(+) m6A 5'UTR//CDS       24981863 chr14:31097459-31097460(+) m6A CDS//exon//intron       24209618 chr14:31097472-31097473(+) m6A CDS//exon//intron       24209618 chr14:31107395-31107396(+) m6A 3'UTR//5'UTR//CDS//intron       27773535 chr14:31112545-31112546(+) m6A 3'UTR//CDS//exon       27773535 chr14:31112559-31112560(+) m6A 3'UTR//CDS//exon       27773535 chr14:31112569-31112570(+) m6A 3'UTR//CDS//exon       27773535 chr14:31118765-31118766(+) m6A 3'UTR//CDS//exon       27773535 chr14:31119772-31119773(+) m6A 3'UTR//CDS//exon       27773535 chr14:31119777-31119778(+) m6A 3'UTR//CDS//exon       27773535 chr14:31119784-31119785(+) m6A 3'UTR//CDS//exon       27773535 chr14:31119813-31119814(+) m6A 3'UTR//CDS//exon       27773535 chr14:31122729-31122730(+) m6A 3'UTR//CDS//exon       27773535 chr14:31139474-31139475(+) m6A 3'UTR//CDS//exon       27773535 chr14:31139510-31139511(+) m6A 3'UTR//CDS//exon       27773535 chr14:31139529-31139530(+) m6A 3'UTR//CDS//exon       27773535 chr14:31139543-31139544(+) m6A 3'UTR//CDS//exon       27773535 chr14:31139589-31139590(+) m6A 3'UTR//CDS//exon       27773535 chr14:31142498-31142499(+) m6A 3'UTR//CDS//exon       27773535 chr14:31143131-31143132(+) m6A 3'UTR//CDS//exon       27773535 chr14:31144201-31144202(+) m6A 3'UTR//CDS//exon       27773535 chr14:31144219-31144220(+) m6A 3'UTR//CDS//exon       27773535 chr14:31144261-31144262(+) m6A 3'UTR//CDS//exon       27773535 chr14:31185154-31185155(+) m6A 3'UTR//CDS//exon       27773535 chr14:31185178-31185179(+) m6A 3'UTR//CDS//exon       27773535 chr14:31188533-31188534(+) m6A 3'UTR//CDS//exon       27773535 chr14:31190915-31190916(+) m6A exon//intron       27773535 chr14:31190950-31190951(+) m6A exon//intron       27773535 chr14:31191817-31191818(+) m6A exon//intron       27773535 chr14:31204000-31204001(+) m6A 3'UTR//CDS//exon       27773535 chr14:31204009-31204010(+) m6A 3'UTR//CDS//exon       27773535 chr14:31204037-31204038(+) Y 3'UTR//CDS//exon       26075521 chr14:31204060-31204061(+) m6A 3'UTR//CDS//exon       27773535 chr14:31204805-31204806(+) m6A 3'UTR//CDS//exon       27773535 chr14:31204824-31204825(+) m6A 3'UTR//exon       27773535 chr14:31204988-31204989(+) m6A 3'UTR//exon       27773535

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	ebv-miR-BART7-3p	Exosome Jurkat-derived T cell line (J77cl20)     21505438
	SCFD1	Chromatin K562 cells     - Cytosol Human myelogenous leukemia cell line (K-562)     21613539 Cytosol HCC cell line (HepG2)|HeLa-S3 cells     - Exosome Blood     - Insoluble cytoplasm HCC cell line (HepG2)     - Nucleoplasm K562 cells     - Nucleus HCC cell line (HepG2)|HeLa-S3 cells     - Ribosome HEK-293 cells     22199352

Interaction Network (The top 100 interactions):

Interactor1: ebv-miR-BART7-3p
Interactor2: SCFD1

Evidence Support:

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

References:

[1]PMID	22100165	Target region	3'UTR
Source	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	ViRBase//VIRmiRNA//VmiReg	Interactor1 expression	None
Tissue or cell line	Jijoye cells	Interactor2 expression	Downregulation
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).