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APOBEC3A apolipoprotein B mRNA editing enzyme catalytic subunit 3A [ Homo sapiens (human) ]

Gene ID: 200315, updated on 27-Nov-2024

Summary

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Official Symbol
APOBEC3Aprovided by HGNC
Official Full Name
apolipoprotein B mRNA editing enzyme catalytic subunit 3Aprovided by HGNC
Primary source
HGNC:HGNC:17343
See related
Ensembl:ENSG00000128383 MIM:607109; AllianceGenome:HGNC:17343
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
A3A; ARP3; PHRBN; bK150C2.1
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]
Expression
Biased expression in bone marrow (RPKM 38.8), appendix (RPKM 13.8) and 5 other tissues See more
Orthologs
all
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Genomic context

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See APOBEC3A in Genome Data Viewer
Location:
22q13.1
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (38957609..38963184)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39427986..39433575)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39353614..39359189)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39260057-39260936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39260937-39261814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39261933-39262744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13734 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13735 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13736 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:39268427-39268977 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:39269364-39270563 Neighboring gene chromobox 6 Neighboring gene uncharacterized LOC105373032 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63270 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63315 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63367 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_63385 and experimental_63387 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39332328-39333149 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39345610-39346460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39350327-39351206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39359385-39360194 Neighboring gene uncharacterized LOC105373033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39361630-39362609 Neighboring gene uncharacterized LOC124905118

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. APOBEC3A Expression in Penile Squamous Cell Carcinoma. Heller M, et al. Pathobiology, 2018. PMID 29166639
  2. Heat-Induced Editing of HPV Genes to Clear Mucocutaneous Warts? Piguet V. J Invest Dermatol, 2017 Apr. PMID 28340680
  3. NMR-based method of small changes reveals how DNA mutator APOBEC3A interacts with its single-stranded DNA substrate. Harjes S, et al. Nucleic Acids Res, 2017 May 19. PMID 28369637, Free PMC Article
  4. Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity. Kouno T, et al. Nat Commun, 2017 Apr 28. PMID 28452355, Free PMC Article
  5. APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA. Schutsky EK, et al. Nucleic Acids Res, 2017 Jul 27. PMID 28472485, Free PMC Article

See all (161) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Her2 amplification, Rel-A, and Bach1 can influence APOBEC3A expression in breast cancer cells.
    Title: Her2 amplification, Rel-A, and Bach1 can influence APOBEC3A expression in breast cancer cells.
  2. The cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis.
    Title: The cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis.
  3. The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress.
    Title: The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress.
  4. Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry.
    Title: Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry.
  5. Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations.
    Title: Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations.
  6. Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer.
    Title: Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer.
  7. Mitochondrial double-stranded RNA triggers induction of the antiviral DNA deaminase APOBEC3A and nuclear DNA damage.
    Title: Mitochondrial double-stranded RNA triggers induction of the antiviral DNA deaminase APOBEC3A and nuclear DNA damage.
  8. Unraveling the Enzyme-Substrate Properties for APOBEC3A-Mediated RNA Editing.
    Title: Unraveling the Enzyme-Substrate Properties for APOBEC3A-Mediated RNA Editing.
  9. Therapy-induced APOBEC3A drives evolution of persistent cancer cells.
    Title: Therapy-induced APOBEC3A drives evolution of persistent cancer cells.
  10. The role of APOBEC3A in cervical cancer development and progression: A retrospective study.
    Title: The role of APOBEC3A in cervical cancer development and progression: A retrospective study.
Submit: New GeneRIF Correction See all GeneRIFs (127)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci.
EBI GWAS Catalog
Genome-wide association study identifies multiple loci associated with bladder cancer risk.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat Microarray analysis indicates HIV-1 Tat upregulates the expression of many proteins, including Phorbolin I, in immature dendritic cells, an effect that likely facilitates the expansion of HIV-1 infection PubMed
Vif vif Vif(IIIB) induces A3A, A3B, and A3C emigration from the nucleus to the cytosol and thereby causes net increases in their cytosolic concentrations and anti-HIV-1 activities PubMed
vif HIV-1 Vif reduces cellular expression and packaging of A3G-3A chimera PubMed
vif Stress causes A3A, A3B, A3C, and A3F to co-localize efficiently with Vif(IIIB) and mRNA-PABP1 complexes in stress granules PubMed
Vpr vpr HIV-1 Vpr upregulates the gene expression of APOBEC3A in human monocyte-derived dendritic cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cytidine deaminase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cytidine deaminase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables cytidine deaminase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in DNA cytosine deamination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in clearance of foreign intracellular DNA IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cytidine to uridine editing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in defense response to virus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in defense response to virus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in innate immune response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of viral genome replication IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of gene expression via chromosomal CpG island demethylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in transposable element silencing IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in P-body IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
DNA dC->dU-editing enzyme APOBEC-3A
Names
apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A
phorbolin-1
probable DNA dC->dU-editing enzyme APOBEC-3A
NP_001257335.1
NP_663745.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001270406.2 → NP_001257335.1  DNA dC->dU-editing enzyme APOBEC-3A isoform b

    See identical proteins and their annotated locations for NP_001257335.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site at the 5' end of a coding exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AL022318, BC144146, BI029063
    UniProtKB/TrEMBL
    A0A0K0MJ25, B7ZLZ1
    Conserved Domains (3) summary
    cd01283
    Location:10 → 102
    cytidine_deaminase; Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on ...
    pfam05240
    Location:116 → 161
    APOBEC_C; APOBEC-like C-terminal domain
    pfam08210
    Location:10 → 173
    APOBEC_N; APOBEC-like N-terminal domain

  2. NM_145699.4 → NP_663745.1  DNA dC->dU-editing enzyme APOBEC-3A isoform a

    See identical proteins and their annotated locations for NP_663745.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AL022318, BC126416, BI029063, DB322320, U03891
    Consensus CDS
    CCDS13981.1
    UniProtKB/Swiss-Prot
    A0AVM1, P31941, Q12807, Q5JZ93, Q9UH18
    UniProtKB/TrEMBL
    A0A0K0MJ25, A0A0K0MJ49
    Related
    ENSP00000249116.2, ENST00000249116.7
    Conserved Domains (1) summary
    pfam08210
    Location:18 → 191
    APOBEC_N; APOBEC-like N-terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    38957609..38963184
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    39427986..39433575
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P31941.3 GenPept UniProtKB/Swiss-Prot:P31941

Gene LinkOut

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