Basic Information:

  VIRBase ID:  

HHID00059789

  Virus:  

Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)

  Host:  

Homo sapiens

  Confidence Score:  

0.4752

  Interaction Type:  

Host-Host interaction

  Predicted Binding:

 

      hsa-miR-500a-3p:  MIMAT0002871          LIN54:  NM_001288996     

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Interactor Information:

	Interactor1	Interactor2
Symbol	hsa-miR-500a-3p	LIN54
miRBase Accession/Entrez ID	MIMAT0002871	132660
Organism	Homo sapiens	Homo sapiens
Category	miRNA	mRNA
Alias	-	CXCDC1//JC8.6//MIP120//TCX1

ncRNA SNP information:

Resource	Symbol	SNP ID	SNP Position	Ref/Alt
miRNASNP-v3	hsa-miR-500a-3p	rs782355787 chrX:50008482    A/G rs781884483 chrX:50008488    C/G rs782187953 chrX:50008486    AC/A rs782715546 chrX:50008487    C/T rs995124308 chrX:50008483    T/C

RNA Editing:

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	LIN54	chr4:83885470(-) A-I      intronic chr4:83880028(-) A-I      intronic chr4:83880030(-) A-I      intronic chr4:83928990(-) A-I      intronic chr4:83928875(-) A-I      intronic chr4:83928113(-) A-I      intronic chr4:83928063(-) A-I      intronic chr4:83927438(-) A-I      intronic chr4:83926696(-) A-I      intronic chr4:83926683(-) A-I      intronic chr4:83926670(-) A-I      intronic chr4:83926176(-) A-I      intronic chr4:83926145(-) A-I      intronic chr4:83925947(-) A-I      intronic chr4:83925943(-) A-I      intronic chr4:83925941(-) A-I      intronic chr4:83925848(-) A-I      intronic chr4:83925817(-) A-I      intronic chr4:83925711(-) A-I      intronic chr4:83925538(-) A-I      intronic chr4:83925530(-) A-I      intronic chr4:83925516(-) A-I      intronic chr4:83925489(-) A-I      intronic chr4:83924974(-) A-I      intronic chr4:83924449(-) A-I      intronic chr4:83924305(-) A-I      intronic chr4:83924304(-) A-I      intronic chr4:83924263(-) A-I      intronic chr4:83922243(-) A-I      intronic chr4:83922174(-) A-I      intronic chr4:83922138(-) A-I      intronic chr4:83921138(-) A-I      intronic chr4:83919463(-) A-I      intronic chr4:83917216(-) A-I      intronic chr4:83917215(-) A-I      intronic chr4:83917198(-) A-I      intronic chr4:83917186(-) A-I      intronic chr4:83917133(-) A-I      intronic chr4:83917054(-) A-I      intronic chr4:83916273(-) A-I      intronic chr4:83915844(-) A-I      intronic chr4:83915729(-) A-I      intronic chr4:83915058(-) A-I      intronic chr4:83914972(-) A-I      intronic chr4:83914909(-) A-I      intronic chr4:83914831(-) A-I      intronic chr4:83914765(-) A-I      intronic chr4:83914534(-) A-I      intronic chr4:83913625(-) A-I      intronic chr4:83906858(-) A-I      intronic chr4:83903655(-) A-I      intronic chr4:83903417(-) A-I      intronic chr4:83903171(-) A-I      intronic chr4:83880033(-) A-I      intronic chr4:83888332(-) A-I      intronic chr4:83888267(-) A-I      intronic chr4:83888232(-) A-I      intronic chr4:83887942(-) A-I      intronic chr4:83887900(-) A-I      intronic chr4:83887877(-) A-I      intronic chr4:83887869(-) A-I      intronic chr4:83887868(-) A-I      intronic chr4:83886088(-) A-I      intronic chr4:83885935(-) A-I      intronic chr4:83885916(-) A-I      intronic chr4:83885904(-) A-I      intronic chr4:83885379(-) A-I      intronic chr4:83885372(-) A-I      intronic chr4:83885368(-) A-I      intronic chr4:83885210(-) A-I      intronic chr4:83882985(-) A-I      intronic chr4:83882207(-) A-I      intronic chr4:83882011(-) A-I      intronic chr4:83882010(-) A-I      intronic chr4:83881653(-) A-I      intronic chr4:83881652(-) A-I      intronic chr4:83881555(-) A-I      intronic chr4:83880538(-) A-I      intronic chr4:83880536(-) A-I      intronic chr4:83880532(-) A-I      intronic chr4:83880442(-) A-I      intronic chr4:83880416(-) A-I      intronic chr4:83880016(-) A-I      intronic chr4:83880002(-) A-I      intronic chr4:83879993(-) A-I      intronic chr4:83879988(-) A-I      intronic chr4:83879958(-) A-I      intronic chr4:83879948(-) A-I      intronic chr4:83877711(-) A-I      intronic chr4:83877692(-) A-I      intronic chr4:83877611(-) A-I      intronic chr4:83877610(-) A-I      intronic chr4:83877368(-) A-I      intronic chr4:83877331(-) A-I      intronic chr4:83877322(-) A-I      intronic chr4:83877207(-) A-I      intronic chr4:83876902(-) A-I      intronic chr4:83876392(-) A-I      intronic chr4:83875744(-) A-I      intronic chr4:83875738(-) A-I      intronic chr4:83874227(-) A-I      intronic chr4:83874162(-) A-I      intronic chr4:83855342(-) A-I      intronic chr4:83851341(-) A-I      intronic chr4:83851246(-) A-I      intronic chr4:83851215(-) A-I      intronic chr4:83851207(-) A-I      intronic chr4:83851162(-) A-I      intronic chr4:83851156(-) A-I      intronic chr4:83850907(-) A-I      intronic chr4:83850873(-) A-I      intronic chr4:83850847(-) A-I      intronic chr4:83850723(-) A-I      intronic chr4:83845407(-) A-I      intronic chr4:83845238(-) A-I      intronic chr4:83880037(-) A-I      intronic chr4:83887893(-) A-I      intronic chr4:83887927(-) A-I      intronic chr4:83887931(-) A-I      intronic chr4:83887940(-) A-I      intronic chr4:83887945(-) A-I      intronic chr4:83897860(-) A-I      intronic chr4:83845230(-) A-I      intronic chr4:83845206(-) A-I      intronic chr4:83844147(-) A-I      intronic chr4:83844107(-) A-I      intronic chr4:83844077(-) A-I      intronic chr4:83844076(-) A-I      intronic chr4:83844069(-) A-I      intronic chr4:83925305(-) A-I      intronic chr4:83874397(-) A-I      intronic chr4:83876448(-) A-I      intronic chr4:83876470(-) A-I      intronic chr4:83845260(-) A-I      intronic chr4:83881496(-) A-I      intronic chr4:83882031(-) A-I      intronic chr4:83882994(-) A-I      intronic chr4:83883026(-) A-I      intronic chr4:83845283(-) A-I      intronic chr4:83887941(-) A-I      intronic chr4:83888029(-) A-I      intronic chr4:83903576(-) A-I      intronic chr4:83903582(-) A-I      intronic chr4:83845294(-) A-I      intronic chr4:83845336(-) A-I      intronic chr4:83851218(-) A-I      intronic chr4:83875739(-) A-I      intronic chr4:83875740(-) A-I      intronic chr4:83875746(-) A-I      intronic chr4:83875748(-) A-I      intronic chr4:83880020(-) A-I      intronic chr4:83846372(-) A-I      3'UTR chr4:83846514(-) A-I      3'UTR chr4:83846550(-) A-I      3'UTR chr4:83846544(-) A-I      3'UTR chr4:83888310(-) A-I      intronic chr4:83877754(-) A-I      intronic chr4:83887807(-) A-I      intronic chr4:83913579(-) A-I      intronic chr4:83910152(-) A-I      intronic chr4:83885999(-) A-I      intronic chr4:83843955(-) A-I      intronic chr4:83845390(-) A-I      intronic chr4:83916227(-) A-I      intronic chr4:83874434(-) A-I      intronic chr4:83874310(-) A-I      intronic chr4:83903546(-) A-I      intronic chr4:83924906(-) A-I      intronic chr4:83920822(-) A-I      intronic chr4:83886069(-) A-I      intronic chr4:83885381(-) A-I      intronic chr4:83925822(-) A-I      intronic chr4:83851255(-) A-I      intronic chr4:83842743(-) A-I      intronic chr4:83903075(-) A-I      intronic chr4:83925316(-) A-I      intronic chr4:83850811(-) A-I      intronic chr4:83875685(-) A-I      intronic chr4:83914856(-) A-I      intronic chr4:83853727(-) A-I      intronic chr4:83881725(-) A-I      intronic chr4:83929794(-) A-I      intronic chr4:83888218(-) A-I      intronic chr4:83924965(-) A-I      intronic chr4:83877371(-) A-I      intronic chr4:83842869(-) A-I      intronic chr4:83925514(-) A-I      intronic chr4:83885476(-) A-I      intronic chr4:83888297(-) A-I      intronic chr4:83900978(-) A-I      intronic chr4:83921143(-) A-I      intronic chr4:83877211(-) A-I      intronic chr4:83885382(-) A-I      intronic chr4:83922082(-) A-I      intronic chr4:83925825(-) A-I      intronic chr4:83922919(-) A-I      intronic chr4:83885380(-) A-I      intronic chr4:83848178(-) A-I      3'UTR chr4:83846531(-) A-I      3'UTR chr4:83846542(-) A-I      3'UTR chr4:83846517(-) A-I      3'UTR chr4:83921079(-) A-I      intronic chr4:83913864(-) A-I      intronic chr4:83882101(-) A-I      intronic chr4:83850955(-) A-I      intronic chr4:83916226(-) A-I      intronic chr4:83888198(-) A-I      intronic chr4:83875667(-) A-I      intronic chr4:83922882(-) A-I      intronic chr4:83885271(-) A-I      intronic chr4:83900974(-) A-I      intronic chr4:83903092(-) A-I      intronic chr4:83877686(-) A-I      intronic chr4:83903649(-) A-I      intronic chr4:83886068(-) A-I      intronic chr4:83893332(-) A-I      intronic chr4:83885309(-) A-I      intronic chr4:83876434(-) A-I      intronic chr4:83921235(-) A-I      intronic chr4:83903104(-) A-I      intronic chr4:83925821(-) A-I      intronic chr4:83844026(-) A-I      intronic chr4:83874311(-) A-I      intronic chr4:83926660(-) A-I      intronic chr4:83925369(-) A-I      intronic chr4:83880092(-) A-I      intronic chr4:83904394(-) A-I      intronic chr4:83845166(-) A-I      intronic chr4:83878002(-) A-I      intronic chr4:83915754(-) A-I      intronic chr4:83925674(-) A-I      intronic chr4:83881751(-) A-I      intronic chr4:83842935(-) A-I      intronic chr4:83875610(-) A-I      intronic chr4:83850805(-) A-I      intronic chr4:83883334(-) A-I      intronic chr4:83921162(-) A-I      intronic chr4:83845226(-) A-I      intronic chr4:83850872(-) A-I      intronic chr4:83907452(-) A-I      intronic chr4:83915627(-) A-I      intronic chr4:83877145(-) A-I      intronic chr4:83914258(-) A-I      intronic chr4:83881996(-) A-I      intronic chr4:83881394(-) A-I      intronic chr4:83885332(-) A-I      intronic chr4:83903656(-) A-I      intronic chr4:83875735(-) A-I      intronic chr4:83926344(-) A-I      intronic chr4:83886002(-) A-I      intronic chr4:83903002(-) A-I      intronic chr4:83903079(-) A-I      intronic chr4:83903175(-) A-I      intronic chr4:83850837(-) A-I      intronic chr4:83885383(-) A-I      intronic chr4:83914908(-) A-I      intronic chr4:83850915(-) A-I      intronic chr4:83845287(-) A-I      intronic chr4:83843954(-) A-I      intronic chr4:83844004(-) A-I      intronic chr4:83903110(-) A-I      intronic chr4:83845266(-) A-I      intronic chr4:83925286(-) A-I      intronic chr4:83842183(-) A-I      intronic chr4:83881562(-) A-I      intronic chr4:83916853(-) A-I      intronic chr4:83844108(-) A-I      intronic chr4:83925745(-) A-I      intronic chr4:83885374(-) A-I      intronic chr4:83850695(-) A-I      intronic chr4:83881701(-) A-I      intronic chr4:83851253(-) A-I      intronic chr4:83850741(-) A-I      intronic chr4:83913705(-) A-I      intronic chr4:83874713(-) A-I      intronic chr4:83922246(-) A-I      intronic chr4:83921161(-) A-I      intronic chr4:83874309(-) A-I      intronic chr4:83925294(-) A-I      intronic chr4:83913706(-) A-I      intronic chr4:83842711(-) A-I      intronic chr4:83893270(-) A-I      intronic chr4:83877376(-) A-I      intronic

Resource	Symbol	Editing Position	Change	SeqReg	exReg	PMID
DARNED	LIN54	chr4:83850695(-) A-G intron -    22484847 chr4:83850837(-) A-G intron -    22484847 chr4:83850872(-) A-G intron -    22484847 chr4:83850915(-) A-G intron -    22484847 chr4:83850953(-) A-G intron -    22484847 chr4:83851222(-) A-G intron -    22484847 chr4:83851253(-) A-G intron -    22484847 chr4:83851255(-) A-G intron -    22484847 chr4:83874311(-) A-G intron -    22484847 chr4:83875705(-) C-T intron -    22484847 chr4:83875735(-) A-G intron -    22484847 chr4:83877226(-) A-G intron -    22484847 chr4:83877230(-) A-G intron -    22484847 chr4:83877371(-) A-G intron -    22484847 chr4:83877376(-) A-G intron -    22484847 chr4:83877377(-) A-G intron -    22484847 chr4:83877754(-) A-G intron -    22484847 chr4:83881394(-) A-G intron -    22484847 chr4:83881659(-) A-G intron -    22484847 chr4:83882101(-) A-G intron -    22484847 chr4:83882210(-) A-G intron -    22484847 chr4:83882987(-) A-G intron -    22484847 chr4:83883107(-) A-G intron -    22484847 chr4:83885271(-) A-G intron -    22484847 chr4:83885293(-) A-G intron -    22484847 chr4:83885309(-) A-G intron -    22484847 chr4:83885332(-) A-G intron -    22484847 chr4:83885371(-) A-G intron -    22484847 chr4:83885374(-) A-G intron -    22484847 chr4:83885380(-) A-G intron -    22484847 chr4:83885381(-) A-G intron -    22484847 chr4:83885382(-) A-G intron -    22484847 chr4:83885383(-) A-G intron -    22484847 chr4:83885957(-) A-G intron -    22484847 chr4:83885999(-) A-G intron -    22484847 chr4:83886002(-) A-G intron -    22484847 chr4:83886012(-) A-G intron -    22484847 chr4:83886068(-) A-G intron -    22484847 chr4:83886069(-) A-G intron -    22484847 chr4:83888218(-) A-G intron -    22484847 chr4:83888296(-) A-G intron -    22484847 chr4:83888297(-) A-G intron -    22484847 chr4:83888310(-) A-G intron -    22484847 chr4:83893270(-) A-G intron -    22484847 chr4:83903079(-) A-G intron -    22484847 chr4:83903092(-) A-G intron -    22484847 chr4:83903103(-) A-G intron -    22484847 chr4:83903158(-) A-G intron -    22484847 chr4:83903175(-) A-G intron -    22484847 chr4:83903649(-) A-G intron -    22484847 chr4:83903656(-) A-G intron -    22484847 chr4:83906831(-) A-G intron -    22484847 chr4:83907452(-) A-G intron -    22484847 chr4:83910152(-) A-G intron -    22484847 chr4:83912297(-) A-G intron -    22484847 chr4:83913705(-) A-G intron -    22484847 chr4:83913706(-) A-G intron -    22484847 chr4:83914856(-) A-G intron -    22484847 chr4:83914908(-) A-G intron -    22484847 chr4:83915845(-) C-G intron -    22484847 chr4:83921143(-) A-G intron -    22484847 chr4:83921161(-) A-G intron -    22484847 chr4:83921170(-) A-G intron -    22484847 chr4:83922246(-) A-G intron -    22484847 chr4:83924447(-) A-G intron -    22484847 chr4:83924906(-) A-G intron -    22484847 chr4:83925473(-) T-C intron -    22484847 chr4:83925514(-) A-G intron -    22484847 chr4:83925745(-) A-G intron -    22484847 chr4:83925822(-) A-G intron -    22484847 chr4:83926344(-) A-G intron -    22484847 chr4:83926660(-) A-G intron -    22484847 chr4:83926669(-) A-G intron -    22484847 chr4:83926695(-) A-G intron -    22484847 chr4:83929794(-) A-G intron -    22484847

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	LIN54	chr4:83848320-83848321(-) m6A 3'UTR//intron       27773535 chr4:83848391-83848392(-) m6A 3'UTR//intron       27773535 chr4:83848435-83848436(-) m6A 3'UTR//intron       27773535 chr4:83848458-83848459(-) m6A 3'UTR//intron       27773535 chr4:83848776-83848777(-) m6A 3'UTR//intron       27773535 chr4:83848810-83848811(-) m6A 3'UTR//intron       27773535 chr4:83848825-83848826(-) m6A 3'UTR//intron       27773535 chr4:83848841-83848842(-) m6A 3'UTR//intron       27773535 chr4:83848863-83848864(-) m6A 3'UTR//intron       27773535 chr4:83849138-83849139(-) m6A 3'UTR//intron       24284625//24209618//24981863//27773535//22575960//22608085 chr4:83849176-83849177(-) m6A 3'UTR//intron       24284625//24209618//25456834//24981863//27773535//27371828//22575960//22608085 chr4:83849199-83849200(-) m6A 3'UTR//intron       24284625//24209618//25456834//24981863//27773535//27371828//22575960//22608085 chr4:83849226-83849227(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//27773535//27371828//22575960//22608085 chr4:83849239-83849240(-) m6A 3'UTR//exon       24284625//24209618//25456834//24981863//27773535//27371828//22575960//22608085 chr4:83849378-83849379(-) m6A 3'UTR//CDS       24284625//24209618//25456834//24981863//27773535//27371828//22575960//22608085 chr4:83852140-83852141(-) m6A 3'UTR//CDS       27773535 chr4:83852177-83852178(-) m6A 3'UTR//CDS       27773535 chr4:83852225-83852226(-) m6A 3'UTR//CDS       27773535 chr4:83860877-83860878(-) m6A 3'UTR//CDS       27773535 chr4:83861044-83861045(-) m6A 3'UTR//CDS       27773535 chr4:83867430-83867431(-) m6A 3'UTR//CDS//intron       27773535 chr4:83891523-83891524(-) m6A 3'UTR//CDS//intron       27773535 chr4:83891580-83891581(-) m6A CDS//intron       27773535 chr4:83891592-83891593(-) m6A CDS//intron       27773535 chr4:83900065-83900066(-) m6A CDS//intron       27773535 chr4:83900069-83900070(-) m6A CDS//intron       27773535 chr4:83900096-83900097(-) m6A CDS//intron       27773535 chr4:83905321-83905322(-) m6A CDS//exon//intron       27773535 chr4:83905336-83905337(-) m6A CDS//exon//intron       27773535 chr4:83905412-83905413(-) m6A CDS//exon//intron       24981863//27773535//22608085 chr4:83905586-83905587(-) m6A CDS//exon//intron       24284625//24209618//24981863//27773535//22575960//22608085 chr4:83905595-83905596(-) m6A CDS//exon//intron       24284625//24209618//24981863//27773535//22575960//22608085 chr4:83905603-83905604(-) m6A CDS//exon//intron       24284625//24209618//24981863//27773535//22575960//22608085 chr4:83905616-83905617(-) m6A CDS//exon//intron       24284625//24209618//24981863//27773535//22575960//22608085 chr4:83905630-83905631(-) m6A CDS//exon//intron       24284625//24209618//24981863//27773535//22575960//22608085 chr4:83905644-83905645(-) m6A CDS//exon//intron       24284625//24209618//24981863//27773535//22575960//22608085 chr4:83905681-83905682(-) m6A CDS//exon//intron       24284625//24209618//24981863//27773535//22575960//22608085 chr4:83905694-83905695(-) m6A CDS//exon//intron       24284625//24209618//24981863//27773535//22575960//22608085 chr4:83905721-83905722(-) m6A CDS//exon//intron       24284625//24209618//24981863//27773535//22575960//22608085 chr4:83905805-83905806(-) m6A CDS//exon//intron       24284625//24981863//27773535//22608085 chr4:83905868-83905869(-) m6A CDS//exon//intron       24284625//24981863//27773535//22608085 chr4:83905873-83905874(-) m6A CDS//intron       24284625//24981863//27773535//22608085 chr4:83905944-83905945(-) m6A CDS//intron       24284625//24209618//24981863//27773535//22608085 chr4:83934043-83934044(-) m6A 5'UTR//exon       24209618

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	hsa-miR-500a-3p	Exosome B cell line (Raji)|Primary dendritic cells     21505438 Exosome Brain tissue     23382797 Exosome Plasma     23663360 Exosome Human mast cell line (HMC-1)     24009880 Exosome Breast milk|Cell lines|Epididymal epithelial cells|Osteoblast|Plasma|Primary glioblastoma neurosphere cells|Primary keratinocyte|Saliva|Serum|Urine     - Microvesicle Plasma     23077538 Microvesicle Seminal plasma     23539611 Microvesicle Colon cancer cell line (LIM1863)|Fibroblasts|Mesenchymal stem cells|Urine     - Mitochondrion Cell line (HEK-293|HeLa)     22984580
	LIN54	Exosome Blood     - Nucleolus K562 cells     - Nucleoplasm K562 cells     - Nucleus HCC cell line (HepG2)     -

Interaction Network (The top 100 interactions):

Interactor1: hsa-miR-500a-3p
Interactor2: LIN54

Evidence Support:

Weak-Evidence	PAR-CLIP
Support Database	ViRBase

References:

PMID	22291592	Target region	3'UTR
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.