Basic Information:

  VIRBase ID:  

HHID00066037

  Virus:  

Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)

  Host:  

Homo sapiens

  Confidence Score:  

0.4752

  Interaction Type:  

Host-Host interaction

  Predicted Binding:

 

      hsa-miR-200c-5p:  MIMAT0004657          SMARCD1:  NM_003076     

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Interactor Information:

	Interactor1	Interactor2
Symbol	hsa-miR-200c-5p	SMARCD1
miRBase Accession/Entrez ID	MIMAT0004657	6602
Organism	Homo sapiens	Homo sapiens
Category	miRNA	mRNA
Alias	-	BAF60A//CRACD1//CSS11//Rsc6p

ncRNA SNP information:

Resource	Symbol	SNP ID	SNP Position	Ref/Alt
miRNASNP-v3	hsa-miR-200c-5p	rs1220589670 chr12:6963703    C/T rs1277597787 chr12:6963716    A/C rs372372905 chr12:6963719    G/A rs942672545 chr12:6963713    A/G rs1318673559 chr12:6963704    G/A

RNA Editing:

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	SMARCD1	chr12:50488761(+) A-I      intronic chr12:50486844(+) A-I      intronic chr12:50486871(+) A-I      intronic chr12:50491285(+) A-I      intronic chr12:50491078(+) A-I      intronic chr12:50487395(+) A-I      intronic chr12:50488681(+) A-I      intronic chr12:50491070(+) A-I      intronic chr12:50488764(+) A-I      intronic chr12:50491267(+) A-I      intronic chr12:50485079(+) A-I      intronic chr12:50486809(+) A-I      intronic chr12:50488680(+) A-I      intronic chr12:50487526(+) A-I      intronic chr12:50486820(+) A-I      intronic chr12:50487075(+) A-I      intronic chr12:50487161(+) A-I      intronic chr12:50486706(+) A-I      intronic chr12:50486758(+) A-I      intronic chr12:50487221(+) A-I      intronic chr12:50486794(+) A-I      intronic chr12:50487076(+) A-I      intronic chr12:50488720(+) A-I      intronic chr12:50487274(+) A-I      intronic chr12:50487640(+) A-I      intronic chr12:50485499(+) A-I      intronic chr12:50486879(+) A-I      intronic chr12:50486800(+) A-I      intronic chr12:50486107(+) A-I      intronic chr12:50491178(+) A-I      intronic chr12:50484792(+) A-I      intronic chr12:50487101(+) A-I      intronic chr12:50487735(+) A-I      intronic chr12:50486848(+) A-I      intronic chr12:50487692(+) A-I      intronic chr12:50486705(+) A-I      intronic chr12:50486542(+) A-I      intronic chr12:50486071(+) A-I      intronic chr12:50491072(+) A-I      intronic chr12:50491606(+) A-I      intronic chr12:50487223(+) A-I      intronic chr12:50486689(+) A-I      intronic chr12:50487098(+) A-I      intronic chr12:50486579(+) A-I      intronic chr12:50486934(+) A-I      intronic chr12:50486838(+) A-I      intronic chr12:50486595(+) A-I      intronic chr12:50486564(+) A-I      intronic chr12:50487072(+) A-I      intronic chr12:50487702(+) A-I      intronic chr12:50486574(+) A-I      intronic chr12:50487168(+) A-I      intronic chr12:50484814(+) A-I      intronic chr12:50487533(+) A-I      intronic chr12:50487367(+) A-I      intronic chr12:50487071(+) A-I      intronic chr12:50486760(+) A-I      intronic chr12:50491602(+) A-I      intronic chr12:50485149(+) A-I      intronic chr12:50487052(+) A-I      intronic

Resource	Symbol	Editing Position	Change	SeqReg	exReg	PMID
DARNED	SMARCD1	chr12:50491402(+) C-T intron -    22484847 chr12:50486564(+) A-G intron -    22484847 chr12:50486579(+) A-G intron -    22484847 chr12:50486758(+) A-G intron -    22484847 chr12:50486760(+) A-G intron -    22484847 chr12:50486838(+) A-G intron -    22484847 chr12:50487072(+) A-G intron -    22484847 chr12:50487161(+) A-G intron -    22484847

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	SMARCD1	chr12:50478957-50478958(+) m6A 5'UTR       24981863 chr12:50479066-50479067(+) m6A 5'UTR       24981863 chr12:50479248-50479249(+) m6A CDS//exon       24284625 chr12:50480071-50480072(+) m6A CDS//exon       24981863 chr12:50480124-50480125(+) m6A CDS//exon       24981863 chr12:50480546-50480547(+) m6A CDS//exon       24981863 chr12:50482332-50482333(+) m6A CDS//exon//intron       - chr12:50482377-50482378(+) m6A CDS//exon//intron       - chr12:50482382-50482383(+) m6A CDS//exon//intron       - chr12:50482388-50482389(+) m6A CDS//exon//intron       - chr12:50482403-50482404(+) m6A CDS//exon//intron       - chr12:50483171-50483172(+) m6A exon//intron       - chr12:50483184-50483185(+) m6A exon//intron       - chr12:50483675-50483676(+) m6A CDS       - chr12:50483693-50483694(+) m6A CDS       - chr12:50494083-50494084(+) m6A 3'UTR//exon       - chr12:50494171-50494172(+) m6A 3'UTR       -

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	hsa-miR-200c-5p	Exosome Breast milk|Cell lines|Epididymal epithelial cells|Osteoblast|Plasma|Primary glioblastoma neurosphere cells|Primary keratinocyte|Saliva|Serum|Urine     - Microvesicle Seminal plasma     23539611 Microvesicle Cell lines(GBM46|GBM8|HaCaT|K562|MCF-10A|MCF-7|MGG75)|Plasma|Primary glioblastoma neurosphere cells|Primary keratinocytes     -
	SMARCD1	Chromatin K562 cells     - Cytosol Human myelogenous leukemia cell line (K-562)     21613539 Cytosol HCC cell line (HepG2)     - Exosome Blood     - Nucleolus K562 cells     - Nucleoplasm K562 cells     - Nucleus HCC cell line (HepG2)|HeLa-S3 cells|K562 cells     -

Interaction Network (The top 100 interactions):

Interactor1: hsa-miR-200c-5p
Interactor2: SMARCD1

Evidence Support:

Weak-Evidence	PAR-CLIP
Support Database	ViRBase

References:

PMID	22291592	Target region	CDS
Source	ViRBase	Interactor1 expression	None
Tissue or cell line	EF3D-AGO2 cells//LCL35 cells//LCL-BAC cells//LCL-BAC-D1 cells//LCL-BAC-D3 cells	Interactor2 expression	None
Description	We identified 7, 827 miRNA-interaction sites in 3, 492 cellular 3'UTRs. 531 of these sites contained seed matches to viral miRNAs.Table S6: High confidence miRNA-interaction sites in 3'UTRs.