Basic Information:

  VIRBase ID:  

VHID00289397

  Virus:  

Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)

  Host:  

Homo sapiens

  Confidence Score:  

0.9523

  Interaction Type:  

Virus-Host interaction

  Predicted Binding:

 

      ebv-miR-BART1-5p:  MIMAT0000999          SP100:  NM_001080391     

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Interactor Information:

	Interactor1	Interactor2
Symbol	ebv-miR-BART1-5p	SP100
miRBase Accession/Entrez ID	MIMAT0000999	6672
Organism	Human gammaherpesvirus 4 (Epstein-Barr virus, EPV)	Homo sapiens
Category	miRNA	mRNA
Alias	-	lysp100b

RNA Editing:

Resource	Symbol	Editing Position	Change	Genetic Region
RADAR	SP100	chr2:231389471(+) A-I      intronic chr2:231389492(+) A-I      intronic chr2:231389494(+) A-I      intronic chr2:231389495(+) A-I      intronic chr2:231389502(+) A-I      intronic chr2:231389512(+) A-I      intronic chr2:231388556(+) A-I      intronic chr2:231383247(+) A-I      intronic chr2:231388503(+) A-I      intronic chr2:231387219(+) A-I      intronic chr2:231388545(+) A-I      intronic chr2:231389516(+) A-I      intronic chr2:231389517(+) A-I      intronic chr2:231389538(+) A-I      intronic chr2:231389552(+) A-I      intronic chr2:231389585(+) A-I      intronic chr2:231383226(+) A-I      intronic chr2:231393678(+) A-I      intronic chr2:231397724(+) A-I      intronic chr2:231388474(+) A-I      intronic chr2:231387630(+) A-I      intronic chr2:231387604(+) A-I      intronic chr2:231387425(+) A-I      intronic chr2:231382290(+) A-I      intronic chr2:231388143(+) A-I      intronic chr2:231365779(+) A-I      intronic chr2:231365778(+) A-I      intronic chr2:231365771(+) A-I      intronic chr2:231387353(+) A-I      intronic chr2:231383258(+) A-I      intronic chr2:231389287(+) A-I      intronic chr2:231388132(+) A-I      intronic chr2:231388135(+) A-I      intronic chr2:231389291(+) A-I      intronic chr2:231389013(+) A-I      intronic chr2:231389006(+) A-I      intronic chr2:231389005(+) A-I      intronic chr2:231389003(+) A-I      intronic chr2:231388991(+) A-I      intronic chr2:231388980(+) A-I      intronic chr2:231388589(+) A-I      intronic chr2:231388544(+) A-I      intronic chr2:231388153(+) A-I      intronic chr2:231383248(+) A-I      intronic chr2:231383254(+) A-I      intronic chr2:231388423(+) A-I      intronic chr2:231393685(+) A-I      intronic chr2:231393717(+) A-I      intronic chr2:231393732(+) A-I      intronic chr2:231383469(+) A-I      intronic chr2:231383472(+) A-I      intronic chr2:231383488(+) A-I      intronic chr2:231388509(+) A-I      intronic chr2:231383489(+) A-I      intronic chr2:231383504(+) A-I      intronic chr2:231383512(+) A-I      intronic chr2:231389208(+) A-I      intronic chr2:231389218(+) A-I      intronic chr2:231388463(+) A-I      intronic chr2:231388466(+) A-I      intronic chr2:231393670(+) A-I      intronic chr2:231389220(+) A-I      intronic chr2:231389232(+) A-I      intronic chr2:231389237(+) A-I      intronic chr2:231393658(+) A-I      intronic chr2:231389238(+) A-I      intronic chr2:231389239(+) A-I      intronic chr2:231389256(+) A-I      intronic chr2:231389467(+) A-I      intronic chr2:231389258(+) A-I      intronic chr2:231389265(+) A-I      intronic chr2:231389271(+) A-I      intronic chr2:231389279(+) A-I      intronic chr2:231388167(+) A-I      intronic chr2:231388149(+) A-I      intronic chr2:231388148(+) A-I      intronic chr2:231388127(+) A-I      intronic chr2:231387766(+) A-I      intronic chr2:231387765(+) A-I      intronic chr2:231387752(+) A-I      intronic chr2:231387739(+) A-I      intronic chr2:231387710(+) A-I      intronic chr2:231387695(+) A-I      intronic chr2:231387679(+) A-I      intronic chr2:231387669(+) A-I      intronic chr2:231387663(+) A-I      intronic chr2:231387659(+) A-I      intronic chr2:231387656(+) A-I      intronic chr2:231387647(+) A-I      intronic chr2:231387483(+) A-I      intronic chr2:231387477(+) A-I      intronic chr2:231387464(+) A-I      intronic chr2:231387394(+) A-I      intronic chr2:231387388(+) A-I      intronic chr2:231387385(+) A-I      intronic chr2:231387365(+) A-I      intronic chr2:231387304(+) A-I      intronic chr2:231387284(+) A-I      intronic chr2:231387278(+) A-I      intronic chr2:231387268(+) A-I      intronic chr2:231387259(+) A-I      intronic chr2:231387247(+) A-I      intronic chr2:231387243(+) A-I      intronic chr2:231382388(+) A-I      intronic chr2:231382386(+) A-I      intronic chr2:231382334(+) A-I      intronic chr2:231382315(+) A-I      intronic chr2:231377255(+) A-I      intronic chr2:231377130(+) A-I      intronic chr2:231376694(+) A-I      intronic chr2:231376682(+) A-I      intronic chr2:231376681(+) A-I      intronic chr2:231376646(+) A-I      intronic chr2:231376603(+) A-I      intronic chr2:231366687(+) A-I      intronic chr2:231366683(+) A-I      intronic chr2:231365877(+) A-I      intronic chr2:231365867(+) A-I      intronic chr2:231360219(+) A-I      intronic chr2:231360195(+) A-I      intronic chr2:231360174(+) A-I      intronic chr2:231343669(+) A-I      intronic chr2:231343640(+) A-I      intronic chr2:231343636(+) A-I      intronic chr2:231342514(+) A-I      intronic chr2:231326680(+) A-I      intronic chr2:231326599(+) A-I      intronic chr2:231326430(+) A-I      intronic chr2:231326409(+) A-I      intronic chr2:231293419(+) A-I      intronic chr2:231293348(+) A-I      intronic chr2:231293339(+) A-I      intronic chr2:231293315(+) A-I      intronic chr2:231293297(+) A-I      intronic chr2:231293287(+) A-I      intronic chr2:231293275(+) A-I      intronic chr2:231293227(+) A-I      intronic chr2:231292902(+) A-I      intronic chr2:231292858(+) A-I      intronic chr2:231292850(+) A-I      intronic chr2:231292835(+) A-I      intronic chr2:231292705(+) A-I      intronic chr2:231292674(+) A-I      intronic chr2:231292668(+) A-I      intronic chr2:231292049(+) A-I      intronic chr2:231292042(+) A-I      intronic chr2:231292034(+) A-I      intronic chr2:231292018(+) A-I      intronic chr2:231292016(+) A-I      intronic chr2:231291981(+) A-I      intronic chr2:231291980(+) A-I      intronic chr2:231291977(+) A-I      intronic chr2:231366701(+) A-I      intronic chr2:231401949(+) A-I      intronic chr2:231401899(+) A-I      intronic chr2:231401894(+) A-I      intronic chr2:231401893(+) A-I      intronic chr2:231401859(+) A-I      intronic chr2:231401753(+) A-I      intronic chr2:231401745(+) A-I      intronic chr2:231401744(+) A-I      intronic chr2:231401723(+) A-I      intronic chr2:231400359(+) A-I      intronic chr2:231399078(+) A-I      intronic chr2:231398968(+) A-I      intronic chr2:231398967(+) A-I      intronic chr2:231398943(+) A-I      intronic chr2:231398922(+) A-I      intronic chr2:231398876(+) A-I      intronic chr2:231398867(+) A-I      intronic chr2:231397778(+) A-I      intronic chr2:231397770(+) A-I      intronic chr2:231397757(+) A-I      intronic chr2:231397679(+) A-I      intronic chr2:231397670(+) A-I      intronic chr2:231397662(+) A-I      intronic chr2:231397599(+) A-I      intronic chr2:231389050(+) A-I      intronic chr2:231389021(+) A-I      intronic chr2:231389020(+) A-I      intronic chr2:231388986(+) A-I      intronic chr2:231388983(+) A-I      intronic chr2:231388977(+) A-I      intronic chr2:231388964(+) A-I      intronic chr2:231388956(+) A-I      intronic chr2:231388951(+) A-I      intronic chr2:231388928(+) A-I      intronic chr2:231388924(+) A-I      intronic chr2:231388888(+) A-I      intronic chr2:231388887(+) A-I      intronic chr2:231388873(+) A-I      intronic chr2:231388863(+) A-I      intronic chr2:231388862(+) A-I      intronic chr2:231388808(+) A-I      intronic chr2:231388794(+) A-I      intronic chr2:231388793(+) A-I      intronic chr2:231388600(+) A-I      intronic chr2:231388599(+) A-I      intronic chr2:231388576(+) A-I      intronic chr2:231388569(+) A-I      intronic chr2:231388536(+) A-I      intronic chr2:231388533(+) A-I      intronic chr2:231388530(+) A-I      intronic chr2:231388526(+) A-I      intronic chr2:231388525(+) A-I      intronic chr2:231388517(+) A-I      intronic chr2:231388504(+) A-I      intronic chr2:231388501(+) A-I      intronic chr2:231388485(+) A-I      intronic chr2:231388477(+) A-I      intronic chr2:231388473(+) A-I      intronic chr2:231388472(+) A-I      intronic chr2:231388465(+) A-I      intronic chr2:231388464(+) A-I      intronic chr2:231388462(+) A-I      intronic chr2:231388374(+) A-I      intronic chr2:231388172(+) A-I      intronic chr2:231399033(+) A-I      intronic chr2:231376661(+) A-I      intronic chr2:231398859(+) A-I      intronic chr2:231398868(+) A-I      intronic chr2:231376850(+) A-I      intronic chr2:231398950(+) A-I      intronic chr2:231399010(+) A-I      intronic chr2:231398970(+) A-I      intronic chr2:231366637(+) A-I      intronic chr2:231376633(+) A-I      intronic chr2:231398971(+) A-I      intronic chr2:231398935(+) A-I      intronic chr2:231389019(+) A-I      intronic chr2:231398964(+) A-I      intronic chr2:231387321(+) A-I      intronic chr2:231388369(+) A-I      intronic chr2:231292799(+) A-I      intronic chr2:231397576(+) A-I      intronic chr2:231376630(+) A-I      intronic chr2:231376601(+) A-I      intronic chr2:231333545(+) A-I      intronic chr2:231293232(+) A-I      intronic chr2:231398956(+) A-I      intronic chr2:231398994(+) A-I      intronic chr2:231399023(+) A-I      intronic chr2:231388414(+) A-I      intronic chr2:231388568(+) A-I      intronic chr2:231342530(+) A-I      intronic chr2:231376605(+) A-I      intronic chr2:231292886(+) A-I      intronic chr2:231377144(+) A-I      intronic chr2:231365703(+) A-I      intronic chr2:231397625(+) A-I      intronic chr2:231341685(+) A-I      intronic chr2:231330740(+) A-I      intronic chr2:231387343(+) A-I      intronic chr2:231382271(+) A-I      intronic chr2:231387345(+) A-I      intronic chr2:231357957(+) A-I      intronic chr2:231397758(+) A-I      intronic chr2:231292861(+) A-I      intronic chr2:231293431(+) A-I      intronic chr2:231382359(+) A-I      intronic chr2:231341674(+) A-I      intronic chr2:231387257(+) A-I      intronic chr2:231375248(+) A-I      intronic chr2:231399006(+) A-I      intronic chr2:231382369(+) A-I      intronic chr2:231343600(+) A-I      intronic chr2:231342527(+) A-I      intronic chr2:231387370(+) A-I      intronic chr2:231388438(+) A-I      intronic chr2:231398974(+) A-I      intronic chr2:231293364(+) A-I      intronic chr2:231341714(+) A-I      intronic chr2:231376765(+) A-I      intronic chr2:231387465(+) A-I      intronic chr2:231382408(+) A-I      intronic chr2:231382333(+) A-I      intronic chr2:231397596(+) A-I      intronic chr2:231292736(+) A-I      intronic chr2:231366688(+) A-I      intronic chr2:231376711(+) A-I      intronic chr2:231382419(+) A-I      intronic chr2:231333337(+) A-I      intronic chr2:231388124(+) A-I      intronic chr2:231366632(+) A-I      intronic chr2:231382206(+) A-I      intronic chr2:231376856(+) A-I      intronic chr2:231376651(+) A-I      intronic

Resource	Symbol	Editing Position	Change	SeqReg	exReg	PMID
DARNED	SP100	chr2:231377610(+) A-I intron -    22327324 chr2:231387257(+) A-I intron -    22327324 chr2:231388568(+) A-I intron -    22327324 chr2:231389250(+) A-I intron -    22327324 chr2:231389470(+) A-I intron -    22327324 chr2:231389580(+) A-I intron -    22327324 chr2:231389584(+) A-I intron -    22327324 chr2:231389587(+) A-I intron -    22327324 chr2:231389592(+) A-I intron -    22327324 chr2:231397596(+) A-I intron -    22327324 chr2:231398974(+) A-I intron -    22028664   //22327324 chr2:231399000(+) A-I intron -    22028664   //22327324 chr2:231398859(+) A-I intron -    22028664 chr2:231398868(+) A-I intron -    22028664 chr2:231398935(+) A-I intron -    22028664 chr2:231398950(+) A-I intron -    22028664 chr2:231398956(+) A-I intron -    22028664 chr2:231398964(+) A-I intron -    22028664 chr2:231398970(+) A-I intron -    22028664 chr2:231398971(+) A-I intron -    22028664 chr2:231398994(+) A-I intron -    22028664 chr2:231399010(+) A-I intron -    22028664 chr2:231399023(+) A-I intron -    22028664 chr2:231399033(+) A-I intron -    22028664 chr2:231378559(+) A-I intron -    21960545 chr2:231378565(+) A-I intron -    21960545 chr2:231381523(+) A-I intron -    21960545 chr2:231382827(+) A-I intron -    21960545 chr2:231383447(+) A-I intron -    21960545 chr2:231383512(+) A-I intron -    21960545 chr2:231350947(+) C-T intron -    22484847 chr2:231377610(+) A-G intron -    22484847 chr2:231378559(+) A-G intron -    22484847 chr2:231292060(+) A-G intron -    22484847 chr2:231292691(+) A-G intron -    22484847 chr2:231292736(+) A-G intron -    22484847 chr2:231292760(+) A-G intron -    22484847 chr2:231292799(+) A-G intron -    22484847 chr2:231292825(+) A-G intron -    22484847 chr2:231292861(+) A-G intron -    22484847 chr2:231292886(+) A-G intron -    22484847 chr2:231292894(+) A-G intron -    22484847 chr2:231293364(+) A-G intron -    22484847 chr2:231293431(+) A-G intron -    22484847 chr2:231329644(+) C-T intron -    22484847 chr2:231329756(+) T-G intron -    22484847 chr2:231337142(+) C-A intron -    22484847 chr2:231341654(+) T-C intron -    22484847 chr2:231341674(+) A-G intron -    22484847 chr2:231341685(+) A-G intron -    22484847 chr2:231341714(+) A-G intron -    22484847 chr2:231342527(+) A-G intron -    22484847 chr2:231342529(+) A-G intron -    22484847 chr2:231342530(+) A-G intron -    22484847 chr2:231343600(+) A-G intron -    22484847 chr2:231357957(+) A-G intron -    22484847 chr2:231365696(+) A-G intron -    22484847 chr2:231365703(+) A-G intron -    22484847 chr2:231365834(+) A-G intron -    22484847 chr2:231365836(+) A-G intron -    22484847 chr2:231366632(+) A-G intron -    22484847 chr2:231366637(+) A-G intron -    22484847 chr2:231366688(+) A-G intron -    22484847 chr2:231376601(+) A-G intron -    22484847 chr2:231376605(+) A-G intron -    22484847 chr2:231376630(+) A-G intron -    22484847 chr2:231376633(+) A-G intron -    22484847 chr2:231376651(+) A-G intron -    22484847 chr2:231376661(+) A-G intron -    22484847 chr2:231376711(+) A-G intron -    22484847 chr2:231376789(+) C-T intron -    22484847 chr2:231376850(+) A-G intron -    22484847 chr2:231377144(+) A-G intron -    22484847 chr2:231377246(+) A-C intron -    22484847 chr2:231382206(+) A-G intron -    22484847 chr2:231382208(+) A-G intron -    22484847 chr2:231382271(+) A-G intron -    22484847 chr2:231382333(+) A-G intron -    22484847 chr2:231382359(+) A-G intron -    22484847 chr2:231382408(+) A-G intron -    22484847 chr2:231382419(+) A-G intron -    22484847

RNA Modification:

Resource	Symbol	ModificationPosition	Type	Genomic Context	PMID
RMBase	SP100	chr2:231305239-231305240(+) m6A 5'UTR//intron       24209618 chr2:231305266-231305267(+) m6A 5'UTR//intron       24209618 chr2:231307665-231307666(+) m6A CDS       24209618 chr2:231314263-231314264(+) m6A exon//intron       24981863 chr2:231314297-231314298(+) m6A CDS//exon       24981863 chr2:231314319-231314320(+) m6A CDS//exon       24981863 chr2:231314324-231314325(+) m6A CDS//exon       24981863 chr2:231314388-231314389(+) m6A CDS//exon       24981863 chr2:231314396-231314397(+) m6A CDS//exon       24981863 chr2:231314896-231314897(+) m6A CDS//exon       24981863 chr2:231338124-231338125(+) m6A CDS//exon       24981863 chr2:231339126-231339127(+) m6A CDS//exon       24981863//27773535 chr2:231339145-231339146(+) m6A CDS//exon       24981863//27773535 chr2:231358530-231358531(+) m6A exon//intron       24981863//27773535 chr2:231358602-231358603(+) m6A exon//intron       24981863 chr2:231358619-231358620(+) m6A exon//intron       24981863 chr2:231363187-231363188(+) m6A CDS//exon       24981863//27773535 chr2:231363200-231363201(+) m6A CDS//exon       24981863//27773535 chr2:231367799-231367800(+) m6A CDS       24981863//27773535 chr2:231369000-231369001(+) m6A CDS//exon       24981863 chr2:231371019-231371020(+) m6A CDS//exon       24981863 chr2:231379800-231379801(+) m6A intron       - chr2:231379828-231379829(+) m6A CDS//intron       - chr2:231379887-231379888(+) m6A CDS//intron       24981863 chr2:231379936-231379937(+) m6A CDS//intron       24981863 chr2:231380120-231380121(+) m6A CDS//intron       - chr2:231380318-231380319(+) m6A CDS//intron       24981863//27773535 chr2:231380435-231380436(+) m6A 3'UTR//intron       24981863 chr2:231380448-231380449(+) m6A 3'UTR//intron       24981863 chr2:231380470-231380471(+) m6A 3'UTR//intron       24981863 chr2:231407749-231407750(+) m6A 3'UTR//exon       24981863 chr2:231407793-231407794(+) m6A 3'UTR//exon       24981863 chr2:231408540-231408541(+) m6A 3'UTR//exon       24981863 chr2:231408585-231408586(+) m6A 3'UTR//exon       24981863 chr2:231408619-231408620(+) m6A 3'UTR//exon       24981863 chr2:231408647-231408648(+) m6A 3'UTR//exon       24981863 chr2:231408684-231408685(+) m6A 3'UTR//exon       24981863 chr2:231408693-231408694(+) m6A 3'UTR//exon       24981863 chr2:231408717-231408718(+) m6A 3'UTR//exon       24981863 chr2:231408752-231408753(+) m6A 3'UTR//exon       24981863 chr2:231408770-231408771(+) m6A 3'UTR//exon       24981863

RNA Localization:

Resource	Symbol	Subcellular Localization	Tissue or Cell Line	PMID
RNALocate	SP100	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 K562 cells     - Ribosome Colon cancer cells     24393600

Related Drug Information:

Resource	Symbol	Drug Name	PubChem ID
RNAactDrug	ebv-miR-BART1-5p	Panobinostat       6918837 Irinotecan       60838 Topotecan       60700 l-685,458       5479543 Palbociclib       5330286 Dovitinib       135398510 Crizotinib       11626560

Interaction Network (The top 100 interactions):

Interactor1: ebv-miR-BART1-5p
Interactor2: SP100

Evidence Support:

Strong-Evidence	Dual luciferase reporter assay//Luciferase reporter assay
Weak-Evidence	PAR-CLIP
Prediction-Evidence	miRanda//PARalyzer//PITA
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	None
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	23170179	Target region	3'UTR
Source	ViRBase	Interactor1 expression	Downregulation
Tissue or cell line	EF3D-AGO2 cells//LCL35 cells//LCL-BAC cells//LCL-BAC-D1 cells//LCL-BAC-D3 cells	Interactor2 expression	None
Description	For each of them, direct interactions between 3'UTR and EBV miRNAs were confirmed by luciferase assay but no functional assay has been performed so far (Table 2).Table 2 Validated targets from high-throughput studies. Shown are cellular targets identified by photoactivatable ribonucleoside enhanced crosslinking and immunoprecipitation (PAR-CLIP), High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) or RNA immunoprecipitation and microarray (RIP-Chip) techniques. Validation of these targets was done using luciferase reporter assays.

[3]PMID	23342366	Target region	3'UTR
Source	ViRBase//VIRmiRNA//VmiReg	Interactor1 expression	Downregulation
Tissue or cell line	EF3D-AGO2 cells//LCL35 cells//LCL-BAC cells//LCL-BAC-D1 cells//LCL-BAC-D3 cells	Interactor2 expression	None
Description	On the other hand, EBV miRNAs repress cellular proteins, which include p53 up-regulated modulator of apoptosis (PUMA), DICER1, and BIM [96,97,98] (Table 2).

[4]PMID	22291592	Target region	3'UTR
Source	ViRBase//VIRmiRNA//VmiReg	Interactor1 expression	None
Tissue or cell line	293T cells//Lymphoblastoid cells	Interactor2 expression	Downregulation
Description	Of the 12 PAR-CLIP-identified target 3'UTRs tested against EBV miRNAs, 11 3'UTRs (BACH1, CLEC2D, CLIP1, DAZAP2, KDM4B, LY75, OTUD1, PDE7A, PELI1, SP100, ZNF451) resulted in luciferase inhibition following ectopic viral miRNA expression (Figure S3).