Basic Information:

  VIRBase ID:  

VHID00305348

  Virus:  

Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)

  Host:  

Homo sapiens

  Confidence Score:  

0.6055

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      ebv-miR-BART4-5p:  MIMAT0003412          SNX1:  NM_148955     

      *It may take a few minutes to display results.

Interactor Information:

	Interactor1	Interactor2
Symbol	ebv-miR-BART4-5p	SNX1
miRBase Accession/Entrez ID	MIMAT0003412	6642
Organism	Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)	Homo sapiens
Category	miRNA	mRNA
Alias	-	HsT17379//VPS5

RNA Editing:

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	SNX1	chr15:64432862(+) A-I      3'UTR chr15:64434476(+) A-I      3'UTR chr15:64411802(+) A-I      intronic chr15:64407896(+) A-I      intronic chr15:64434339(+) A-I      3'UTR chr15:64434312(+) A-I      3'UTR chr15:64432857(+) A-I      3'UTR chr15:64432801(+) A-I      3'UTR chr15:64401080(+) A-I      intronic chr15:64396724(+) A-I      intronic chr15:64402863(+) A-I      intronic chr15:64411421(+) A-I      intronic chr15:64400138(+) A-I      intronic chr15:64402725(+) A-I      intronic chr15:64402720(+) A-I      intronic chr15:64391974(+) A-I      intronic chr15:64411595(+) A-I      intronic chr15:64402713(+) A-I      intronic chr15:64393133(+) A-I      intronic chr15:64393263(+) A-I      intronic chr15:64401824(+) A-I      intronic chr15:64427391(+) A-I      intronic chr15:64390739(+) A-I      intronic chr15:64391808(+) A-I      intronic chr15:64401904(+) A-I      intronic chr15:64401887(+) A-I      intronic chr15:64396546(+) A-I      intronic chr15:64392091(+) A-I      intronic chr15:64392140(+) A-I      intronic chr15:64401873(+) A-I      intronic chr15:64393108(+) A-I      intronic chr15:64401890(+) A-I      intronic chr15:64409870(+) A-I      intronic chr15:64427434(+) A-I      intronic chr15:64392145(+) A-I      intronic chr15:64401872(+) A-I      intronic chr15:64392146(+) A-I      intronic chr15:64401775(+) A-I      intronic chr15:64401732(+) A-I      intronic chr15:64412990(+) A-I      intronic chr15:64401728(+) A-I      intronic chr15:64401451(+) A-I      intronic chr15:64411586(+) A-I      intronic chr15:64401393(+) A-I      intronic chr15:64390834(+) A-I      intronic chr15:64397363(+) A-I      intronic chr15:64427421(+) A-I      intronic chr15:64397314(+) A-I      intronic chr15:64397184(+) A-I      intronic chr15:64412565(+) A-I      intronic chr15:64396913(+) A-I      intronic chr15:64391975(+) A-I      intronic chr15:64392613(+) A-I      intronic chr15:64397054(+) A-I      intronic chr15:64411472(+) A-I      intronic chr15:64401025(+) A-I      intronic chr15:64401927(+) A-I      intronic chr15:64392029(+) A-I      intronic chr15:64396964(+) A-I      intronic chr15:64396999(+) A-I      intronic chr15:64427837(+) A-I      intronic chr15:64396850(+) A-I      intronic chr15:64396810(+) A-I      intronic chr15:64412589(+) A-I      intronic chr15:64396679(+) A-I      intronic chr15:64396908(+) A-I      intronic chr15:64396663(+) A-I      intronic chr15:64411479(+) A-I      intronic chr15:64396963(+) A-I      intronic chr15:64396657(+) A-I      intronic chr15:64412895(+) A-I      intronic chr15:64396611(+) A-I      intronic chr15:64396923(+) A-I      intronic chr15:64390804(+) A-I      intronic chr15:64392623(+) A-I      intronic chr15:64417801(+) A-I      intronic chr15:64392076(+) A-I      intronic chr15:64417788(+) A-I      intronic chr15:64396551(+) A-I      intronic chr15:64401825(+) A-I      intronic chr15:64412974(+) A-I      intronic chr15:64396516(+) A-I      intronic chr15:64395095(+) A-I      intronic chr15:64427538(+) A-I      intronic chr15:64412955(+) A-I      intronic chr15:64395092(+) A-I      intronic chr15:64400932(+) A-I      intronic chr15:64390713(+) A-I      intronic chr15:64412825(+) A-I      intronic chr15:64390839(+) A-I      intronic chr15:64395078(+) A-I      intronic chr15:64397029(+) A-I      intronic chr15:64393248(+) A-I      intronic chr15:64412502(+) A-I      intronic chr15:64390664(+) A-I      intronic chr15:64390830(+) A-I      intronic chr15:64411910(+) A-I      intronic chr15:64392523(+) A-I      intronic chr15:64393091(+) A-I      intronic chr15:64391766(+) A-I      intronic chr15:64391771(+) A-I      intronic chr15:64411883(+) A-I      intronic chr15:64411868(+) A-I      intronic chr15:64411864(+) A-I      intronic chr15:64411582(+) A-I      intronic chr15:64391955(+) A-I      intronic chr15:64390823(+) A-I      intronic chr15:64393066(+) A-I      intronic chr15:64427397(+) A-I      intronic chr15:64411673(+) A-I      intronic chr15:64391972(+) A-I      intronic chr15:64392679(+) A-I      intronic chr15:64401314(+) A-I      intronic chr15:64411418(+) A-I      intronic chr15:64392615(+) A-I      intronic chr15:64390721(+) A-I      intronic chr15:64411361(+) A-I      intronic chr15:64392598(+) A-I      intronic chr15:64402670(+) A-I      intronic chr15:64434318(+) A-I      3'UTR chr15:64434379(+) A-I      3'UTR chr15:64434455(+) A-I      3'UTR chr15:64432805(+) A-I      3'UTR chr15:64432900(+) A-I      3'UTR chr15:64434468(+) A-I      3'UTR chr15:64434373(+) A-I      3'UTR chr15:64432886(+) A-I      3'UTR chr15:64432909(+) A-I      3'UTR chr15:64432826(+) A-I      3'UTR chr15:64432924(+) A-I      3'UTR chr15:64432882(+) A-I      3'UTR chr15:64434323(+) A-I      3'UTR chr15:64432838(+) A-I      3'UTR chr15:64434509(+) A-I      3'UTR chr15:64434377(+) A-I      3'UTR chr15:64432984(+) A-I      3'UTR chr15:64434260(+) A-I      3'UTR chr15:64432876(+) A-I      3'UTR chr15:64434266(+) A-I      3'UTR chr15:64432839(+) A-I      3'UTR chr15:64434378(+) A-I      3'UTR chr15:64390638(+) A-I      intronic chr15:64411674(+) A-I      intronic chr15:64390745(+) A-I      intronic chr15:64401780(+) A-I      intronic chr15:64392108(+) A-I      intronic chr15:64411382(+) A-I      intronic chr15:64390797(+) A-I      intronic chr15:64428071(+) A-I      intronic chr15:64394599(+) A-I      intronic chr15:64401996(+) A-I      intronic chr15:64412888(+) A-I      intronic chr15:64407085(+) A-I      intronic chr15:64390665(+) A-I      intronic chr15:64401907(+) A-I      intronic chr15:64392185(+) A-I      intronic chr15:64401108(+) A-I      intronic chr15:64412886(+) A-I      intronic chr15:64413019(+) A-I      intronic chr15:64401386(+) A-I      intronic chr15:64412571(+) A-I      intronic chr15:64390810(+) A-I      intronic chr15:64390646(+) A-I      intronic chr15:64411503(+) A-I      intronic chr15:64391753(+) A-I      intronic chr15:64401405(+) A-I      intronic chr15:64391980(+) A-I      intronic chr15:64401162(+) A-I      intronic chr15:64427337(+) A-I      intronic chr15:64394524(+) A-I      intronic chr15:64390798(+) A-I      intronic chr15:64405837(+) A-I      intronic chr15:64392060(+) A-I      intronic chr15:64391800(+) A-I      intronic chr15:64401848(+) A-I      intronic chr15:64411878(+) A-I      intronic chr15:64401320(+) A-I      intronic chr15:64412893(+) A-I      intronic chr15:64393103(+) A-I      intronic chr15:64412960(+) A-I      intronic chr15:64401500(+) A-I      intronic chr15:64391748(+) A-I      intronic chr15:64411695(+) A-I      intronic chr15:64392085(+) A-I      intronic chr15:64393275(+) A-I      intronic chr15:64417407(+) A-I      intronic chr15:64411700(+) A-I      intronic chr15:64402737(+) A-I      intronic chr15:64412526(+) A-I      intronic chr15:64400205(+) A-I      intronic chr15:64412833(+) A-I      intronic chr15:64401064(+) A-I      intronic chr15:64411843(+) A-I      intronic chr15:64427511(+) A-I      intronic chr15:64393116(+) A-I      intronic chr15:64394516(+) A-I      intronic chr15:64401806(+) A-I      intronic chr15:64392529(+) A-I      intronic chr15:64402784(+) A-I      intronic chr15:64427456(+) A-I      intronic chr15:64391730(+) A-I      intronic chr15:64390821(+) A-I      intronic chr15:64390251(+) A-I      intronic chr15:64390660(+) A-I      intronic chr15:64393236(+) A-I      intronic chr15:64393121(+) A-I      intronic chr15:64401474(+) A-I      intronic chr15:64411349(+) A-I      intronic chr15:64412968(+) A-I      intronic chr15:64413028(+) A-I      intronic chr15:64412919(+) A-I      intronic chr15:64392705(+) A-I      intronic chr15:64411583(+) A-I      intronic chr15:64405469(+) A-I      intronic chr15:64401113(+) A-I      intronic chr15:64427745(+) A-I      intronic chr15:64407849(+) A-I      intronic chr15:64396552(+) A-I      intronic chr15:64401492(+) A-I      intronic chr15:64411335(+) A-I      intronic chr15:64390734(+) A-I      intronic chr15:64395131(+) A-I      intronic chr15:64394546(+) A-I      intronic chr15:64393029(+) A-I      intronic chr15:64393184(+) A-I      intronic chr15:64392652(+) A-I      intronic chr15:64428000(+) A-I      intronic chr15:64392793(+) A-I      intronic chr15:64412973(+) A-I      intronic chr15:64401067(+) A-I      intronic chr15:64393053(+) A-I      intronic chr15:64411803(+) A-I      intronic chr15:64411621(+) A-I      intronic chr15:64392551(+) A-I      intronic chr15:64401425(+) A-I      intronic chr15:64412601(+) A-I      intronic chr15:64412929(+) A-I      intronic chr15:64411342(+) A-I      intronic chr15:64401315(+) A-I      intronic chr15:64401846(+) A-I      intronic chr15:64411696(+) A-I      intronic chr15:64393186(+) A-I      intronic chr15:64411800(+) A-I      intronic chr15:64427824(+) A-I      intronic chr15:64402735(+) A-I      intronic chr15:64409725(+) A-I      intronic chr15:64401896(+) A-I      intronic chr15:64411504(+) A-I      intronic chr15:64390637(+) A-I      intronic chr15:64393104(+) A-I      intronic chr15:64401997(+) A-I      intronic chr15:64401408(+) A-I      intronic chr15:64401355(+) A-I      intronic chr15:64392094(+) A-I      intronic chr15:64401093(+) A-I      intronic chr15:64427835(+) A-I      intronic chr15:64393269(+) A-I      intronic chr15:64390631(+) A-I      intronic chr15:64427737(+) A-I      intronic chr15:64392695(+) A-I      intronic chr15:64411679(+) A-I      intronic chr15:64393182(+) A-I      intronic chr15:64401394(+) A-I      intronic chr15:64409844(+) A-I      intronic chr15:64411682(+) A-I      intronic chr15:64401461(+) A-I      intronic chr15:64411376(+) A-I      intronic chr15:64411456(+) A-I      intronic chr15:64411395(+) A-I      intronic chr15:64392546(+) A-I      intronic chr15:64394043(+) A-I      intronic chr15:64427458(+) A-I      intronic chr15:64391990(+) A-I      intronic chr15:64396919(+) A-I      intronic chr15:64411573(+) A-I      intronic chr15:64426534(+) A-I      intronic chr15:64427746(+) A-I      intronic chr15:64396859(+) A-I      intronic chr15:64432922(+) A-I      3'UTR chr15:64434282(+) A-I      3'UTR chr15:64434514(+) A-I      3'UTR chr15:64434356(+) A-I      3'UTR chr15:64434447(+) A-I      3'UTR chr15:64434442(+) A-I      3'UTR chr15:64434329(+) A-I      3'UTR chr15:64433045(+) A-I      3'UTR chr15:64434332(+) A-I      3'UTR chr15:64433036(+) A-I      3'UTR chr15:64432844(+) A-I      3'UTR chr15:64434391(+) A-I      3'UTR chr15:64434419(+) A-I      3'UTR chr15:64433046(+) A-I      3'UTR chr15:64434502(+) A-I      3'UTR chr15:64433018(+) A-I      3'UTR chr15:64432863(+) A-I      3'UTR chr15:64432883(+) A-I      3'UTR chr15:64432949(+) A-I      3'UTR chr15:64434452(+) A-I      3'UTR chr15:64434315(+) A-I      3'UTR chr15:64432948(+) A-I      3'UTR chr15:64432969(+) A-I      3'UTR

Resource	Symbol	Editing Position	Change	SeqReg	exReg	PMID
DARNED	SNX1	chr15:64390251(+) A-I intron -    15342557 chr15:64390631(+) A-I intron -    15342557 chr15:64390646(+) A-I intron -    15342557 chr15:64390660(+) A-I intron -    15342557 chr15:64390665(+) A-I intron -    15342557 chr15:64390797(+) A-I intron -    15342557 chr15:64390810(+) A-I intron -    15342557 chr15:64390821(+) A-I intron -    15342557 chr15:64401451(+) A-I intron -    22327324 chr15:64411395(+) A-I intron -    22327324 chr15:64434329(+) A-I intron -    22327324 chr15:64394043(+) A-I intron -    21960545 chr15:64394488(+) A-I intron -    21960545 chr15:64394516(+) A-I intron -    21960545 chr15:64433036(+) A-G intron -    21725310 chr15:64394043(+) A-G intron -    22484847 chr15:64394516(+) A-G intron -    22484847 chr15:64394524(+) A-G intron -    22484847 chr15:64394546(+) A-G intron -    22484847 chr15:64391748(+) A-G intron -    22484847 chr15:64393103(+) A-G intron -    22484847 chr15:64396859(+) A-G intron -    22484847 chr15:64401451(+) A-G intron -    22484847 chr15:64401890(+) A-G intron -    22484847 chr15:64405837(+) A-G intron -    22484847 chr15:64409844(+) A-G intron -    22484847 chr15:64409870(+) A-G intron -    22484847 chr15:64411376(+) A-G intron -    22484847 chr15:64411395(+) A-G intron -    22484847 chr15:64411695(+) A-G intron -    22484847 chr15:64411696(+) A-G intron -    22484847 chr15:64411700(+) A-G intron -    22484847 chr15:64432839(+) A-G intron -    22484847 chr15:64432844(+) A-G intron -    22484847 chr15:64434329(+) A-G intron -    22484847 chr15:64434356(+) A-G intron -    22484847 chr15:64434373(+) A-G intron -    22484847 chr15:64434442(+) A-G intron -    22484847 chr15:64434447(+) A-G intron -    22484847 chr15:64434502(+) A-G intron -    22484847 chr15:64434514(+) A-G intron -    22484847

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	SNX1	chr15:64388209-64388210(+) m1A 5'UTR//intron       26863196//26863410 chr15:64388250-64388251(+) m6A CDS//intron       24284625 chr15:64388310-64388311(+) m6A CDS//intron       - chr15:64388324-64388325(+) m6A CDS//intron       - chr15:64388345-64388346(+) m6A CDS//intron       - chr15:64404776-64404777(+) m6A 5'UTR//CDS       - chr15:64404853-64404854(+) Am 5'UTR//CDS       - chr15:64407898-64407899(+) m6A 3'UTR//5'UTR//intron       - chr15:64410339-64410340(+) m6A 3'UTR//5'UTR//CDS//intron       - chr15:64410377-64410378(+) m6A 3'UTR//5'UTR//CDS//intron       - chr15:64411000-64411001(+) m6A 3'UTR//5'UTR//CDS//intron       27773535 chr15:64422138-64422139(+) m6A 3'UTR//CDS//intron       24981863//22575960 chr15:64429075-64429076(+) m6A 3'UTR//CDS//intron       24284625//27773535 chr15:64429084-64429085(+) m6A 3'UTR//CDS//intron       24284625//27773535 chr15:64429107-64429108(+) m6A 3'UTR//CDS//intron       24284625//27773535 chr15:64429820-64429821(+) m6A 3'UTR//intron       24284625//24981863//22575960 chr15:64429827-64429828(+) m6A 3'UTR//intron       24284625//24981863//22575960 chr15:64429888-64429889(+) m6A 3'UTR//intron       24284625//24981863//22575960 chr15:64429918-64429919(+) m6A 3'UTR//intron       24284625//24981863//22575960 chr15:64430039-64430040(+) m6A 3'UTR//intron       26404942//27773535 chr15:64430131-64430132(+) m6A 3'UTR//intron       27773535 chr15:64433689-64433690(+) m6A 3'UTR//intron       - chr15:64433703-64433704(+) m6A 3'UTR//intron       24981863 chr15:64433715-64433716(+) m6A 3'UTR//intron       24981863 chr15:64433728-64433729(+) m6A 3'UTR//intron       24981863 chr15:64434149-64434150(+) m6A 3'UTR//intron       24981863 chr15:64434157-64434158(+) m6A 3'UTR//intron       24981863 chr15:64434619-64434620(+) m6A 3'UTR//intron       24209618//24981863 chr15:64434716-64434717(+) m6A 3'UTR//intron       24981863 chr15:64434880-64434881(+) m6A 3'UTR//intron       24981863 chr15:64434936-64434937(+) m6A 3'UTR//intron       24981863//22608085 chr15:64434941-64434942(+) m6A 3'UTR//intron       24981863//22608085 chr15:64435095-64435096(+) m6A 3'UTR//intron       24284625//25456834//24981863//22608085 chr15:64435142-64435143(+) m6A 3'UTR//intron       24284625//25456834//24981863//22608085 chr15:64435247-64435248(+) m6A 3'UTR//intron       24284625//25456834//24981863//22575960//22608085 chr15:64435256-64435257(+) m6A 3'UTR//intron       24284625//25456834//24981863//22608085 chr15:64435354-64435355(+) m6A 3'UTR//intron       24284625//25456834//24981863//22608085 chr15:64435364-64435365(+) m6A 3'UTR//intron       24284625//25456834//24981863//22608085 chr15:64435417-64435418(+) m6A 3'UTR//intron       25456834//24981863 chr15:64435449-64435450(+) m6A 3'UTR//intron       25456834//24981863//22608085 chr15:64435479-64435480(+) m6A 3'UTR//intron       24981863//22608085 chr15:64435485-64435486(+) m6A 3'UTR//intron       24981863//22608085 chr15:64435579-64435580(+) m6A 3'UTR//intron       24981863//22608085 chr15:64435637-64435638(+) m6A 3'UTR//intron       24284625//24981863//22608085 chr15:64435720-64435721(+) m6A 3'UTR//intron       24284625//24981863 chr15:64435783-64435784(+) m6A 3'UTR//intron       24981863 chr15:64435982-64435983(+) m6A 3'UTR//intron       24981863//22608085 chr15:64436017-64436018(+) m6A 3'UTR//intron       24981863//27773535//22608085 chr15:64436079-64436080(+) m6A 3'UTR//intron       24981863//27773535//22608085

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	SNX1	Chromatin K562 cells     - Cytoplasm Nasopharyngeal carcinoma cells     20498841 Cytoplasm Nasopharyngeal carcinoma cells     20498841 Cytoplasm Nasopharyngeal carcinoma cells     20498841 Cytosol Human myelogenous leukemia cell line (K-562)     21613539 Cytosol K562 cells     - Exosome Blood     - Membrane HCC cell line (HepG2)     - Nucleolus K562 cells     - Nucleoplasm K562 cells     - Nucleus Nasopharyngeal carcinoma cells     20498841 Nucleus Nasopharyngeal carcinoma cells     20498841 Nucleus Nasopharyngeal carcinoma cells     20498841 Nucleus HCC cell line (HepG2)|HeLa-S3 cells|K562 cells     - Ribosome HEK-293 cells     22199352 Ribosome Colon cancer cells     24393600

Interaction Network (The top 100 interactions):

Interactor1: ebv-miR-BART4-5p
Interactor2: SNX1

Evidence Support:

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

References:

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.