Basic Information:

  VIRBase ID:  

HHID00060992

  Virus:  

Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)

  Host:  

Homo sapiens

  Confidence Score:  

0.4752

  Interaction Type:  

Host-Host interaction

  Predicted Binding:

 

      hsa-miR-548a-3p:  MIMAT0003251          RAPGEF2:  NM_001351726     

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Interactor Information:

	Interactor1	Interactor2
Symbol	hsa-miR-548a-3p	RAPGEF2
miRBase Accession/Entrez ID	MIMAT0003251	9693
Organism	Homo sapiens	Homo sapiens
Category	miRNA	mRNA
Alias	-	CNrasGEF//nRap GEP//NRAPGEP//PDZ-GEF1//PDZGEF1//RA-GEF//RA-GEF-1//RAGEF//Rap-GEP

ncRNA SNP information:

Resource	Symbol	SNP ID	SNP Position	Ref/Alt
miRNASNP-v3	hsa-miR-548a-3p	rs1164461265 chr6:18571854    A/G rs1165672383 chr6:18571864    G/C rs1367516995 chr6:18571852    G/A rs1452081761 chr6:18571844    C/T rs1456125774 chr6:18571853    C/A rs371324260 chr6:18571856    T/TTAC rs745784846 chr6:18571855    AT/A rs753232100 chr6:18571865    C/T rs765730274 chr6:18571860    T/G rs1029034755 chr6:135239228    G/T rs1178036684 chr6:135239234    A/T rs1395774538 chr6:135239235    C/T rs373439066 chr6:135239231    A/C rs373439066 chr6:135239231    A/G rs1181589874 chr8:104484390    G/T rs1328816266 chr8:104484397    C/T rs552025667 chr8:104484394    T/C rs746672467 chr8:104484389    A/T rs766393197 chr8:104484388    A/G rs769687902 chr8:104484405    G/A rs769687902 chr8:104484405    G/T rs1177955102 chr6:18571847    A/G rs1178800173 chr6:18571851    G/C rs1236087532 chr6:18571849    C/A rs1236087532 chr6:18571849    C/T rs1441316829 chr6:18571850    T/C rs1441316829 chr6:18571850    T/G rs970024181 chr6:18571848    A/T rs1252922886 chr6:135239223    A/T rs1309130208 chr8:104484401    T/A rs1375898875 chr8:104484398    C/G rs745714043 chr8:104484402    T/A rs776399840 chr8:104484399    A/G

RNA Editing:

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	RAPGEF2	chr4:160202592(+) A-I      intronic chr4:160202702(+) A-I      intronic chr4:160202729(+) A-I      intronic chr4:160205956(+) A-I      intronic chr4:160212565(+) A-I      intronic chr4:160212648(+) A-I      intronic chr4:160255421(+) A-I      intronic chr4:160256833(+) A-I      intronic chr4:160255511(+) A-I      intronic chr4:160256828(+) A-I      intronic chr4:160256830(+) A-I      intronic chr4:160258813(+) A-I      intronic chr4:160202621(+) A-I      intronic chr4:160202644(+) A-I      intronic chr4:160202657(+) A-I      intronic chr4:160202661(+) A-I      intronic chr4:160202672(+) A-I      intronic chr4:160258997(+) A-I      intronic chr4:160269142(+) A-I      intronic chr4:160218240(+) A-I      intronic chr4:160158216(+) A-I      intronic chr4:160159066(+) A-I      intronic chr4:160159095(+) A-I      intronic chr4:160173391(+) A-I      intronic chr4:160175041(+) A-I      intronic chr4:160175784(+) A-I      intronic chr4:160175886(+) A-I      intronic chr4:160175896(+) A-I      intronic chr4:160175900(+) A-I      intronic chr4:160175942(+) A-I      intronic chr4:160175962(+) A-I      intronic chr4:160244965(+) A-I      intronic chr4:160174999(+) A-I      intronic chr4:160278256(+) A-I      intronic chr4:160277973(+) A-I      intronic chr4:160212541(+) A-I      intronic chr4:160244971(+) A-I      intronic chr4:160173347(+) A-I      intronic chr4:160205995(+) A-I      intronic chr4:160205972(+) A-I      intronic chr4:160158896(+) A-I      intronic chr4:160206042(+) A-I      intronic chr4:160159039(+) A-I      intronic chr4:160255505(+) A-I      intronic chr4:160155639(+) A-I      intronic chr4:160158302(+) A-I      intronic chr4:160256840(+) A-I      intronic chr4:160202646(+) A-I      intronic chr4:160254391(+) A-I      intronic chr4:160269117(+) A-I      intronic chr4:160159072(+) A-I      intronic chr4:160256824(+) A-I      intronic chr4:160174935(+) A-I      intronic chr4:160158969(+) A-I      intronic chr4:160175953(+) A-I      intronic chr4:160202273(+) A-I      intronic chr4:160202703(+) A-I      intronic chr4:160256834(+) A-I      intronic chr4:160255425(+) A-I      intronic chr4:160255475(+) A-I      intronic chr4:160159076(+) A-I      intronic chr4:160158949(+) A-I      intronic chr4:160202283(+) A-I      intronic chr4:160175890(+) A-I      intronic chr4:160202305(+) A-I      intronic chr4:160158253(+) A-I      intronic chr4:160242628(+) A-I      intronic chr4:160202327(+) A-I      intronic chr4:160202645(+) A-I      intronic chr4:160278257(+) A-I      intronic chr4:160222283(+) A-I      intronic chr4:160158901(+) A-I      intronic chr4:160159055(+) A-I      intronic chr4:160254258(+) A-I      intronic chr4:160158950(+) A-I      intronic

Resource	Symbol	Editing Position	Change	SeqReg	exReg	PMID
DARNED	RAPGEF2	chr4:160189367(+) A-G intron -    21725310 chr4:160202273(+) A-G intron -    22484847 chr4:160202283(+) A-G intron -    22484847 chr4:160202645(+) A-G intron -    22484847 chr4:160202646(+) A-G intron -    22484847 chr4:160202703(+) A-G intron -    22484847 chr4:160202712(+) A-G intron -    22484847 chr4:160205972(+) A-G intron -    22484847 chr4:160205995(+) A-G intron -    22484847 chr4:160206042(+) A-G intron -    22484847 chr4:160212541(+) A-G intron -    22484847 chr4:160222283(+) A-G intron -    22484847 chr4:160255423(+) A-G intron -    22484847 chr4:160255425(+) A-G intron -    22484847 chr4:160255505(+) A-G intron -    22484847 chr4:160255566(+) A-G intron -    22484847 chr4:160255567(+) A-G intron -    22484847 chr4:160256824(+) A-G intron -    22484847 chr4:160256908(+) A-G intron -    22484847 chr4:160269102(+) G-T intron -    22484847

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	RAPGEF2	chr4:160235770-160235771(+) m6A CDS//exon       24981863 chr4:160235790-160235791(+) m6A CDS//exon       24981863 chr4:160235824-160235825(+) m1A CDS//exon       26863410 chr4:160235827-160235828(+) m6A CDS//exon       24981863 chr4:160235863-160235864(+) m6A CDS//exon       24981863 chr4:160235875-160235876(+) m6A CDS//exon       24981863 chr4:160235890-160235891(+) m6A CDS//exon       24981863 chr4:160235904-160235905(+) m6A CDS//exon       24981863 chr4:160244614-160244615(+) m6A CDS       27773535 chr4:160244719-160244720(+) m6A CDS       24981863//27773535 chr4:160244748-160244749(+) m6A CDS       24981863//27773535 chr4:160247821-160247822(+) m6A exon//intron       24981863 chr4:160251064-160251065(+) m6A CDS//exon       24981863//27773535 chr4:160251110-160251111(+) m6A CDS//exon       24981863//27773535//22575960 chr4:160251119-160251120(+) m6A CDS//exon       24981863//27773535//22575960 chr4:160251129-160251130(+) m6A CDS//exon       24981863//27773535//22575960 chr4:160251135-160251136(+) m6A CDS//exon       24981863//27773535//22575960 chr4:160251146-160251147(+) m6A CDS//exon       24981863//27773535//22575960 chr4:160253788-160253789(+) m6A CDS       24981863//27773535 chr4:160253814-160253815(+) m6A CDS       24981863//27773535 chr4:160253840-160253841(+) m6A CDS       24981863 chr4:160262729-160262730(+) m6A CDS       27773535//22608085 chr4:160262740-160262741(+) m6A CDS       27773535//22608085 chr4:160262746-160262747(+) m6A CDS       27773535//22608085 chr4:160262856-160262857(+) m6A CDS       24284625//24981863//22608085 chr4:160262874-160262875(+) m6A CDS       24284625//24981863//22608085 chr4:160262904-160262905(+) m6A CDS       24981863//22608085 chr4:160262917-160262918(+) m6A CDS       24981863//22608085 chr4:160262965-160262966(+) m6A CDS       24981863 chr4:160267981-160267982(+) m6A CDS       24981863 chr4:160268079-160268080(+) m6A CDS       24981863 chr4:160274030-160274031(+) m6A CDS//exon       24284625 chr4:160274041-160274042(+) m6A CDS//exon       24284625 chr4:160274713-160274714(+) m6A CDS//exon       24284625//24981863//22575960//22608085 chr4:160274840-160274841(+) m6A CDS       24284625//24209618//24981863//26404942//27773535//22575960//22608085 chr4:160274916-160274917(+) m6A CDS       24284625//24209618//24981863//26404942//27773535//22575960//22608085 chr4:160274983-160274984(+) m6A CDS       24284625//24209618//24981863//26404942//27773535//22608085 chr4:160275022-160275023(+) Y CDS       26075521 chr4:160275036-160275037(+) m6A CDS       24284625//24981863//27773535//22608085 chr4:160277107-160277108(+) m6A CDS       24284625 chr4:160277115-160277116(+) m6A CDS       24284625 chr4:160277226-160277227(+) m6A CDS       24284625 chr4:160277245-160277246(+) m6A CDS       24284625 chr4:160279272-160279273(+) m6A CDS       24284625//25456834//24981863//22608085 chr4:160279298-160279299(+) m6A 3'UTR       24284625//25456834//24981863//22608085 chr4:160279370-160279371(+) m6A 3'UTR       24284625//24209618//25456834//24981863//22575960//22608085 chr4:160279392-160279393(+) m6A 3'UTR       24284625//24209618//25456834//24981863//22575960//22608085 chr4:160279503-160279504(+) m6A 3'UTR       24284625//24209618//25456834//24981863//22575960//22608085 chr4:160279727-160279728(+) m6A 3'UTR       24981863//27773535//22608085 chr4:160279758-160279759(+) m6A 3'UTR       24981863//27773535//22608085 chr4:160279768-160279769(+) m6A 3'UTR       24981863//27773535//22608085 chr4:160280407-160280408(+) m6A 3'UTR       24284625 chr4:160280443-160280444(+) m6A 3'UTR       24284625//24981863 chr4:160280474-160280475(+) m6A 3'UTR       24284625//24981863//22608085 chr4:160280484-160280485(+) m6A 3'UTR       24284625//24981863//22608085 chr4:160280521-160280522(+) m6A 3'UTR       24284625//24981863//22608085 chr4:160280656-160280657(+) m6A 3'UTR       24284625//24981863//22608085 chr4:160280706-160280707(+) m6A 3'UTR       24284625//24981863//22608085 chr4:160280958-160280959(+) m6A 3'UTR       24981863 chr4:160280979-160280980(+) m6A 3'UTR       24981863

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	hsa-miR-548a-3p	Exosome Pooled sera     27278097 Exosome Breast milk|Cell lines|Epididymal epithelial cells|Osteoblast|Plasma|Primary glioblastoma neurosphere cells|Primary keratinocyte|Saliva|Serum|Urine     - Microvesicle Follicular fluid     23666971 Microvesicle Cell lines(GBM46|GBM8|HaCaT|K562|MCF-10A|MCF-7|MGG75)|Plasma|Primary glioblastoma neurosphere cells|Primary keratinocytes     -
	RAPGEF2	Chromatin K562 cells     - Cytosol Human myelogenous leukemia cell line (K-562)     21613539 Cytosol HCC cell line (HepG2)|K562 cells     - Exosome Blood     - Nucleoplasm K562 cells     - Nucleus HCC cell line (HepG2)|HeLa-S3 cells|K562 cells     -

Interaction Network (The top 100 interactions):

Interactor1: hsa-miR-548a-3p
Interactor2: RAPGEF2

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.