EuRBPDB

Note: to get the extension of tumor abbreviations.

Cancer Related Information
Basic Information

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
25355878	APOBEC3A functions as a restriction factor of human papillomavirus.	J Virol	2015 Jan	Warren CJ	doi: 10.1128/JVI.02383-14
27155849	Analysis of APOBEC3A/3B germline deletion polymorphism in breast, cervical and oral cancers from South India and its impact on miRNA regulation.	Tumour Biol	2016 Sep	Revathidevi S	-
23977391	Human APOBEC3A isoforms translocate to the nucleus and induce DNA double strand breaks leading to cell stress and death.	PLoS One	2013 Aug 20	Mussil B	doi: 10.1371/journal.pone.0073641
23599896	DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis.	Elife	2013 Apr 16	Taylor BJ	doi: 10.7554/eLife.00534.
26320772	Impact of functional germline variants and a deletion polymorphism in APOBEC3A and APOBEC3B on breast cancer risk and survival in a Swedish study population.	J Cancer Res Clin Oncol	2016 Jan	Gohler S	doi: 10.1007/s00432-015-2038-7
24728294	Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer.	Nat Genet	2014 May	Nik-Zainal S	doi: 10.1038/ng.2955
28825669	Roles of APOBEC3A and APOBEC3B in Human Papillomavirus Infection and Disease Progression.	Viruses	2017 Aug 21	Warren CJ	doi: 10.3390/v9080233.

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq	RBD
BLCA	chr22	38961401	Silent	novel	L63L	0.59
BLCA	chr22	38962508	Silent	novel	*200*	0.31
BLCA	chr22	38957676	5'UTR	novel		0.25
BLCA	chr22	38959611	Silent	novel	L33L	0.06
BRCA	chr22	38961433	Missense_Mutation	NA	R74H	0.3
BRCA	chr22	38961433	Missense_Mutation	novel	R74L	0.13
BRCA	chr22	38961386	Splice_Site	NA	X59_splice	0.6
COAD	chr22	38962253	Intron	novel		0.33
COAD	chr22	38962630	3'UTR	novel		0.07
COAD	chr22	38961674	Silent	novel	T154T	0.57
COAD	chr22	38961580	Missense_Mutation	rs150243518	R123H	0.48	APOBEC_N
COAD	chr22	38962682	3'UTR	novel		0.31
COAD	chr22	38962507	Nonstop_Mutation	novel	200Rext7	0.15
COAD	chr22	38962182	Missense_Mutation	NA	A185V	0.32	APOBEC_N
COAD	chr22	38961594	Missense_Mutation	rs374922066	R128C	0.47	APOBEC_N
COAD	chr22	38962700	3'UTR	novel		0.32
GBM	chr22	38959647	Silent	rs193155851	S45S	0.34
GBM	chr22	38961608	Silent	rs141631289	Y132Y	0.8
HNSC	chr22	38962508	Silent	novel	*200*	0.13
LIHC	chr22	38961500	Missense_Mutation	novel	I96M	0.68
LUAD	chr22	38962622	3'UTR	novel		0.48
LUAD	chr22	38959556	Missense_Mutation	NA	P15Q	0.12
LUAD	chr22	38961572	Silent	rs764951988	V120V	0.26
LUAD	chr22	38959684	Missense_Mutation	novel	Q58K	0.41
LUAD	chr22	38962097	Splice_Site	NA	X157_splice	0.51
LUSC	chr22	38961653	Silent	novel	G147G	0.09
LUSC	chr22	38957574	5'UTR	novel		0.67
OV	chr22	38962658	3'UTR	novel		0.35
OV	chr22	38957713	Missense_Mutation	NA	G8R	0.55
SKCM	chr22	38961464	Silent	rs540617000	L84L	0.41
SKCM	chr22	38959608	Nonsense_Mutation	novel	Y32*	0.69
SKCM	chr22	38957674	5'UTR	novel		0.17
SKCM	chr22	38961644	Silent	novel	R144R	0.37
SKCM	chr22	38961678	Missense_Mutation	NA	D156N	0.08	APOBEC_N
SKCM	chr22	38961485	Silent	novel	R91R	0.29
SKCM	chr22	38961486	Missense_Mutation	novel	V92I	0.29
SKCM	chr22	38959618	Missense_Mutation	NA	E36K	0.16
SKCM	chr22	38962632	3'UTR	novel		0.24
SKCM	chr22	38959591	Missense_Mutation	novel	G27R	0.48
SKCM	chr22	38962502	Missense_Mutation	novel	G198E	0.23
UCEC	chr22	38961428	Missense_Mutation	novel	E72D	0.82
UCEC	chr22	38962638	3'UTR	novel		0.33
UCEC	chr22	38961413	Silent	rs752263105	Y67Y	0.53
UCEC	chr22	38962525	3'UTR	novel		0.06
UCEC	chr22	38961454	Missense_Mutation	novel	S81Y	0.39
UCEC	chr22	38959647	Silent	rs193155851	S45S	0.31
UCEC	chr22	38957665	5'UTR	novel		0.41
UCEC	chr22	38962102	Missense_Mutation	novel	F158L	0.36	APOBEC_N
UCEC	chr22	38962580	3'UTR	novel		0.35
UCEC	chr22	38957605	5'UTR	novel		0.43
UCEC	chr22	38962567	3'UTR	novel		0.4

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
PCPG	DEL	0.3333	0.044123
THCA	DEL	0.1563	0.046486
THYM	DEL	0.0813	0.063154

Survival Analysis

Cancer	P-value	Q-value
SARC	0.033	Kaplan-Meier Survival Analysis
MESO	0.018	Kaplan-Meier Survival Analysis
SKCM	0.0017	Kaplan-Meier Survival Analysis
PCPG	0.038	Kaplan-Meier Survival Analysis
CESC	0.017	Kaplan-Meier Survival Analysis
UCEC	0.0077	Kaplan-Meier Survival Analysis
DLBC	0.028	Kaplan-Meier Survival Analysis
CHOL	0.038	Kaplan-Meier Survival Analysis
UVM	0.017	Kaplan-Meier Survival Analysis
OV	0.0011	Kaplan-Meier Survival Analysis

Drugs

Cell lines and drugs in GSE70138 or GSE92742

Description

RBDs

Literatures

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000128383 (Gene tree)
Gene ID: 200315
Gene Symbol: APOBEC3A
Alias: ARP3|PHRBN
Full Name: apolipoprotein B mRNA editing enzyme catalytic subunit 3A
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Plus strand
Length: 40,038 bases
Position: chr22:38,952,741-38,992,778
Accession: 17343
RBP type: canonical RBP
Summary: This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1. The protein encoded by this gene lacks the zinc binding activity of other family members. The protein plays a role in immunity, by restricting transmission of foreign DNA such as viruses. One mechanism of foreign DNA restriction is deamination of foreign double-stranded DNA cytidines to uridines, which leads to DNA degradation. However, other mechanisms are also thought to be involved, as anti-viral effect is not dependent on deaminase activity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]

RNA binding domains(RBDs)

Protein ID	Domain	Pfam ID	E-value	Domain number	Total number
ENSP00000249116	APOBEC_N	PF08210.11	5e-47	1	1
ENSP00000384359	APOBEC_N	PF08210.11	5e-47	1	1
ENSP00000481904	APOBEC_N	PF08210.11	5e-47	1	1
ENSP00000249116	APOBEC_C	PF05240.14	3.9e-30	1	1
ENSP00000384359	APOBEC_C	PF05240.14	3.9e-30	1	1
ENSP00000481904	APOBEC_C	PF05240.14	3.9e-30	1	1

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
24163103	Structural determinants of human APOBEC3A enzymatic and nucleic acid binding properties.	Nucleic Acids Res	2014 Jan	Mitra M	doi: 10.1093/nar/gkt945
30679582	A panel of eGFP reporters for single base editing by APOBEC-Cas9 editosome complexes.	Sci Rep	2019 Jan 24	Martin AS	doi: 10.1038/s41598-018-36739-9.

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000402255	APOBEC3A-202	1478	-	ENSP00000384359	199 (aa)	-	P31941
ENST00000249116	APOBEC3A-201	1444	-	ENSP00000249116	199 (aa)	-	P31941
ENST00000495988	APOBEC3A-204	566	-	-	- (aa)	-	-
ENST00000618553	APOBEC3A-205	1103	-	ENSP00000481904	199 (aa)	-	P31941
ENST00000488758	APOBEC3A-203	344	-	-	- (aa)	-	-

Gene Model

Click here to download ENSG00000128383's gene model file

Pathways

Pathway ID	Pathway Name	Source
hsa05170	Human immunodeficiency virus 1 infection	KEGG

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000128383	Breast Neoplasms	4E-6	27354352

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000128383	rs12628403	22	38962032	C	Breast cancer	27354352	[1.09-1.25]	1.17	EFO_0000305
ENSG00000128383	rs12628403	22	38962032	?	Mean corpuscular hemoglobin	30595370			EFO_0004527

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000128383's network

* RBP PPI network refers to all genes directly bind to RBP

Orthologs

Ensembl ID	Gene Symbol	Coverage	Identiy	Ortholog	Gene Symbol	Coverage	Identiy	Species
ENSG00000128383	APOBEC3A	96	56.701	ENSCJAG00000012500	-	96	56.701	Callithrix_jacchus
ENSG00000128383	APOBEC3A	100	56.931	ENSTSYG00000035593	-	100	56.931	Carlito_syrichta
ENSG00000128383	APOBEC3A	95	67.876	ENSCCAG00000027450	-	96	67.876	Cebus_capucinus
ENSG00000128383	APOBEC3A	100	81.683	ENSCATG00000013527	-	100	81.683	Cercocebus_atys
ENSG00000128383	APOBEC3A	95	79.365	ENSCSAG00000006445	-	76	79.365	Chlorocebus_sabaeus
ENSG00000128383	APOBEC3A	72	76.871	ENSCSAG00000018401	-	70	76.871	Chlorocebus_sabaeus
ENSG00000128383	APOBEC3A	100	83.417	ENSCANG00000030513	-	100	83.417	Colobus_angolensis_palliatus
ENSG00000128383	APOBEC3A	96	87.047	ENSGGOG00000006721	APOBEC3B	98	87.047	Gorilla_gorilla
ENSG00000128383	APOBEC3A	100	80.693	ENSMFAG00000008980	APOBEC3A	100	80.693	Macaca_fascicularis
ENSG00000128383	APOBEC3A	95	83.854	ENSMMUG00000004015	-	98	83.854	Macaca_mulatta
ENSG00000128383	APOBEC3A	100	81.188	ENSMMUG00000042504	APOBEC3A	100	81.188	Macaca_mulatta
ENSG00000128383	APOBEC3A	95	76.596	ENSMNEG00000043211	-	93	76.596	Macaca_nemestrina
ENSG00000128383	APOBEC3A	96	80.311	ENSMLEG00000004809	-	98	80.311	Mandrillus_leucophaeus
ENSG00000128383	APOBEC3A	100	90.955	ENSNLEG00000015215	-	100	90.955	Nomascus_leucogenys
ENSG00000128383	APOBEC3A	96	90.674	ENSPPAG00000009288	APOBEC3B	98	90.674	Pan_paniscus
ENSG00000128383	APOBEC3A	99	95.960	ENSPTRG00000014384	APOBEC3B	99	95.960	Pan_troglodytes
ENSG00000128383	APOBEC3A	100	79.703	ENSPANG00000006941	APOBEC3B	100	79.703	Papio_anubis
ENSG00000128383	APOBEC3A	96	83.420	ENSPPYG00000011831	-	98	83.420	Pongo_abelii
ENSG00000128383	APOBEC3A	77	59.615	ENSPCOG00000017606	-	98	59.615	Propithecus_coquereli
ENSG00000128383	APOBEC3A	100	82.915	ENSRBIG00000042829	-	100	85.027	Rhinopithecus_bieti
ENSG00000128383	APOBEC3A	100	82.915	ENSRROG00000028773	APOBEC3G	100	85.027	Rhinopithecus_roxellana

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0003723	RNA binding	21873635.	IBA	Function
GO:0004126	cytidine deaminase activity	21873635.	IBA	Function
GO:0004126	cytidine deaminase activity	16527742.21123384.	IDA	Function
GO:0004126	cytidine deaminase activity	20062055.	IMP	Function
GO:0005515	protein binding	22915799.24557838.	IPI	Function
GO:0005634	nucleus	21873635.	IBA	Component
GO:0005634	nucleus	16527742.21123384.21835787.	IDA	Component
GO:0005737	cytoplasm	21873635.	IBA	Component
GO:0005737	cytoplasm	16527742.21123384.21835787.	IDA	Component
GO:0008270	zinc ion binding	-	IEA	Function
GO:0009972	cytidine deamination	-	IEA	Process
GO:0010529	negative regulation of transposition	16527742.20062055.21123384.	IDA	Process
GO:0016554	cytidine to uridine editing	21873635.	IBA	Process
GO:0044356	clearance of foreign intracellular DNA by conversion of DNA cytidine to uridine	20062055.	IDA	Process
GO:0045071	negative regulation of viral genome replication	16527742.	IDA	Process
GO:0045087	innate immune response	21123384.	IDA	Process
GO:0047844	deoxycytidine deaminase activity	22457529.	IMP	Function
GO:0051607	defense response to virus	21123384.22457529.	IDA	Process
GO:0070383	DNA cytosine deamination	16527742.21123384.	IDA	Process
GO:0070383	DNA cytosine deamination	20062055.	IMP	Process
GO:0071466	cellular response to xenobiotic stimulus	20062055.	IDA	Process
GO:0080111	DNA demethylation	21873635.	IBA	Process
GO:0080111	DNA demethylation	21496894.	IDA	Process

EuRBPDB

Note: to get the extension of tumor abbreviations.

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742

Description

RBDs

Literatures

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Orthologs

Gene Ontology

Note: Click here to get the extension of tumor abbreviations.

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742

Note: to get the extension of tumor abbreviations.