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Aliases for APOBEC3A Gene

Aliases for APOBEC3A Gene

  • Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3A 2 3 5
  • Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3A 2 3
  • Phorbolin-1 3 4
  • A3A 3 4
  • Probable DNA DC->DU-Editing Enzyme APOBEC-3A 3
  • DNA DC->DU-Editing Enzyme APOBEC-3A 3
  • Phorbolin I 2
  • EC 3.5.4.- 4
  • BK150C2.1 3
  • EC 3.5.4 58
  • PHRBN 3
  • ARP3 3

External Ids for APOBEC3A Gene

Previous GeneCards Identifiers for APOBEC3A Gene

  • GC22P035968
  • GC22P037591
  • GC22P037596
  • GC22P037678
  • GC22P039348
  • GC22Pr39368

Summaries for APOBEC3A Gene

Entrez Gene Summary for APOBEC3A Gene

  • 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]

GeneCards Summary for APOBEC3A Gene

APOBEC3A (Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3A) is a Protein Coding gene. Among its related pathways are Formation of the Editosome and Gene Expression. GO annotations related to this gene include hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines and deoxycytidine deaminase activity. An important paralog of this gene is APOBEC3B.

UniProtKB/Swiss-Prot for APOBEC3A Gene

  • DNA deaminase (cytidine deaminase) with restriction activity against viruses, foreign DNA and mobility of retrotransposons. Exhibits antiviral activity against adeno-associated virus (AAV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons. Selectively targets single-stranded DNA and can deaminate both methylcytosine and cytosine in foreign DNA. Can induce somatic hypermutation in the nuclear and mitochondrial DNA. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.

Gene Wiki entry for APOBEC3A Gene

Additional gene information for APOBEC3A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for APOBEC3A Gene

Genomics for APOBEC3A Gene

Regulatory Elements for APOBEC3A Gene

Enhancers for APOBEC3A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH22H038941 1.8 FANTOM5 Ensembl ENCODE dbSUPER 24.3 -10.2 -10236 3 HDGF PKNOX1 TBL1XR1 BATF ZNF366 ATF7 ETV6 RUNX3 CREM IKZF2 APOBEC3A APOBEC3B JOSD1 SUN2 GTPBP1 DDX17 ENSG00000235209
GH22H038951 1.7 FANTOM5 Ensembl ENCODE dbSUPER 21 +0.7 690 4.9 HDGF CTCF PKNOX1 RELA RFX5 POLR2A STAT2 ZNF143 ATF7 IKZF2 APOBEC3B SUN2 APOBEC3A GTPBP1 APOBEC3B-AS1 DNAL4 JOSD1 APOBEC3D DDX17 LOC105373033
GH22H039308 2 FANTOM5 Ensembl ENCODE dbSUPER 14.9 +357.6 357593 4.3 HDGF PKNOX1 MLX ARNT ZFP64 SIN3A FEZF1 ZNF2 ZNF143 FOS DDX17 RPL3 SYNGR1 APOBEC3A ENSG00000230149 SNORD83B ENSG00000273076 ENSG00000272669 ENSG00000225450 TAB1
GH22H039266 1.8 FANTOM5 Ensembl ENCODE dbSUPER 15 +314.0 313989 1.5 HDGF PKNOX1 TBL1XR1 ZFP64 ARID4B BATF THRB EGR1 ZNF143 ATF7 SYNGR1 APOBEC3A ATF4 PDGFB GC22M042216
GH22H038966 1.6 FANTOM5 Ensembl ENCODE dbSUPER 15.2 +14.6 14608 2 HDAC1 CTCF PKNOX1 ATF1 CTBP1 ZNF547 ATF7 RUNX3 MAFK IKZF2 APOBEC3A GTPBP1 SUN2 APOBEC3B-AS1 JOSD1 DDX17 LOC105373033
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around APOBEC3A on UCSC Golden Path with GeneCards custom track

Genomic Locations for APOBEC3A Gene

Genomic Locations for APOBEC3A Gene
chr22:38,952,741-38,992,778
(GRCh38/hg38)
Size:
40,038 bases
Orientation:
Plus strand
chr22:39,348,746-39,359,188
(GRCh37/hg19)

Genomic View for APOBEC3A Gene

Genes around APOBEC3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
APOBEC3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for APOBEC3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for APOBEC3A Gene

Proteins for APOBEC3A Gene

  • Protein details for APOBEC3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P31941-ABC3A_HUMAN
    Recommended name:
    DNA dC->dU-editing enzyme APOBEC-3A
    Protein Accession:
    P31941
    Secondary Accessions:
    • A0AVM1
    • Q12807
    • Q5JZ93
    • Q9UH18

    Protein attributes for APOBEC3A Gene

    Size:
    199 amino acids
    Molecular mass:
    23012 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Interacts with AGO2. Interacts with TRIB3 (via N-terminus).
    Miscellaneous:
    • It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22.

    Three dimensional structures from OCA and Proteopedia for APOBEC3A Gene

    Alternative splice isoforms for APOBEC3A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for APOBEC3A Gene

Selected DME Specific Peptides for APOBEC3A Gene

P31941:
  • EHSQALSGRL
  • FTSNFNN
  • PFQPWDGL

Post-translational modifications for APOBEC3A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for APOBEC3A Gene

Domains & Families for APOBEC3A Gene

Gene Families for APOBEC3A Gene

Suggested Antigen Peptide Sequences for APOBEC3A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P31941

UniProtKB/Swiss-Prot:

ABC3A_HUMAN :
  • Belongs to the cytidine and deoxycytidylate deaminase family.
Family:
  • Belongs to the cytidine and deoxycytidylate deaminase family.
genes like me logo Genes that share domains with APOBEC3A: view

Function for APOBEC3A Gene

Molecular function for APOBEC3A Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Cytidine + H(2)O = uridine + NH(3).
UniProtKB/Swiss-Prot Function:
DNA deaminase (cytidine deaminase) with restriction activity against viruses, foreign DNA and mobility of retrotransposons. Exhibits antiviral activity against adeno-associated virus (AAV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons. Selectively targets single-stranded DNA and can deaminate both methylcytosine and cytosine in foreign DNA. Can induce somatic hypermutation in the nuclear and mitochondrial DNA. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.
UniProtKB/Swiss-Prot Induction:
Up-regulated by interferon and CpG single-stranded DNA (at protein level).

Enzyme Numbers (IUBMB) for APOBEC3A Gene

Phenotypes From GWAS Catalog for APOBEC3A Gene

Gene Ontology (GO) - Molecular Function for APOBEC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0004126 cytidine deaminase activity IMP 20062055
GO:0005515 protein binding IPI 22915799
GO:0008270 zinc ion binding IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with APOBEC3A: view
genes like me logo Genes that share phenotypes with APOBEC3A: view

Animal Model Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for APOBEC3A Gene

Localization for APOBEC3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for APOBEC3A Gene

Nucleus. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for APOBEC3A gene
Compartment Confidence
nucleus 5
cytosol 3
extracellular 2
plasma membrane 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for APOBEC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 16527742
GO:0005737 cytoplasm IDA,IEA 16527742
genes like me logo Genes that share ontologies with APOBEC3A: view

Pathways & Interactions for APOBEC3A Gene

genes like me logo Genes that share pathways with APOBEC3A: view

Pathways by source for APOBEC3A Gene

Interacting Proteins for APOBEC3A Gene

Gene Ontology (GO) - Biological Process for APOBEC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009972 cytidine deamination IEA --
GO:0010529 negative regulation of transposition IDA 16527742
GO:0044356 clearance of foreign intracellular DNA by conversion of DNA cytidine to uridine IDA 20062055
GO:0045071 negative regulation of viral genome replication IDA 16527742
GO:0045087 innate immune response IDA,IEA 21123384
genes like me logo Genes that share ontologies with APOBEC3A: view

No data available for SIGNOR curated interactions for APOBEC3A Gene

Drugs & Compounds for APOBEC3A Gene

(4) Drugs for APOBEC3A Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Ammonia Approved Pharma 0
Water Approved Pharma 0
Cytidine Experimental Pharma 0
Uridine Experimental Pharma 0
genes like me logo Genes that share compounds with APOBEC3A: view

Transcripts for APOBEC3A Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for APOBEC3A Gene

No ASD Table

Relevant External Links for APOBEC3A Gene

GeneLoc Exon Structure for
APOBEC3A
ECgene alternative splicing isoforms for
APOBEC3A

Expression for APOBEC3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for APOBEC3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for APOBEC3A Gene

This gene is overexpressed in Whole Blood (x41.2) and Minor Salivary Gland (x5.0).

Protein differential expression in normal tissues from HIPED for APOBEC3A Gene

This gene is overexpressed in Cervix (47.4), Heart (8.4), Monocytes (6.8), and Spleen (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for APOBEC3A Gene



Protein tissue co-expression partners for APOBEC3A Gene

NURSA nuclear receptor signaling pathways regulating expression of APOBEC3A Gene:

APOBEC3A

mRNA Expression by UniProt/SwissProt for APOBEC3A Gene:

P31941-ABC3A_HUMAN
Tissue specificity: Expressed in peripheral leukocytes with higher expression in CD14-positive phagocytic cells. Highly expressed in keratinocytes and in periphery blood monocytes. Also detected in non-lymphoid tissues including lung and adipose tissues. Found at high levels in colorectal adenocarcinoma, Burkitts lymphoma and chronic myelogenous leukemia.

Evidence on tissue expression from TISSUES for APOBEC3A Gene

  • Skin(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with APOBEC3A: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for APOBEC3A Gene

Orthologs for APOBEC3A Gene

This gene was present in the common ancestor of mammals.

Orthologs for APOBEC3A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia APOBEC3A 33 34
  • 98.75 (n)
cow
(Bos Taurus)
Mammalia APOBEC3A 33 34
  • 66.67 (n)
dog
(Canis familiaris)
Mammalia APOBEC3A 33
  • 65.38 (n)
-- 34
  • 46 (a)
ManyToMany
-- 34
  • 30 (a)
ManyToMany
Species where no ortholog for APOBEC3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for APOBEC3A Gene

ENSEMBL:
Gene Tree for APOBEC3A (if available)
TreeFam:
Gene Tree for APOBEC3A (if available)

Paralogs for APOBEC3A Gene

(10) SIMAP similar genes for APOBEC3A Gene using alignment to 2 proteins:

Pseudogenes.org Pseudogenes for APOBEC3A Gene

genes like me logo Genes that share paralogs with APOBEC3A: view

Variants for APOBEC3A Gene

Sequence variations from dbSNP and Humsavar for APOBEC3A Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs1000213836 -- 38,960,249(+) GAGAG(A/G)CCAGG intron-variant
rs1000706253 -- 38,955,854(+) TCTTT(A/G)TCATC upstream-variant-2KB
rs1000924375 -- 38,961,754(+) GAAAG(A/G)CCTTG intron-variant
rs1001254289 -- 38,958,881(+) GTGCT(A/G)CCTCC intron-variant
rs1001421218 -- 38,957,523(+) AGCTG(A/G)AGAAG utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for APOBEC3A Gene

Variant ID Type Subtype PubMed ID
nsv9907 CNV loss 18304495
nsv979675 CNV duplication 23825009
nsv964630 OTHER complex 23825009
nsv829221 CNV loss 20364138
nsv589021 CNV loss 21841781
nsv3627 CNV deletion 18451855
nsv198 CNV deletion 15895083
nsv1056597 CNV loss 25217958
esv3647746 CNV loss 21293372
esv3568392 CNV loss 25503493
esv33846 CNV gain+loss 17666407
esv29947 CNV loss 18421352
esv28999 CNV loss 19812545
esv2763703 CNV loss 21179565
esv2760711 CNV loss 21179565
esv2724238 CNV deletion 23290073
esv2604392 CNV loss 19546169
esv2495318 CNV deletion 19546169
dgv833e199 CNV deletion 23128226
dgv770n67 CNV loss 20364138
dgv4569n100 CNV loss 25217958
dgv4568n100 CNV loss 25217958
dgv36n47 CNV loss 21111241
dgv172n111 CNV deletion 26073780

Variation tolerance for APOBEC3A Gene

Residual Variation Intolerance Score: 86.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.60; 12.90% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for APOBEC3A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
APOBEC3A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for APOBEC3A Gene

Disorders for APOBEC3A Gene

Relevant External Links for APOBEC3A

Genetic Association Database (GAD)
APOBEC3A
Human Genome Epidemiology (HuGE) Navigator
APOBEC3A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
APOBEC3A

No disorders were found for APOBEC3A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for APOBEC3A Gene

Publications for APOBEC3A Gene

  1. Psoriasis upregulated phorbolin-1 shares structural but not functional similarity to the mRNA-editing protein apobec-1. (PMID: 10469298) Madsen P … Celis JE (The Journal of investigative dermatology 1999) 2 3 4 22 60
  2. APOBEC3A is a potent inhibitor of adeno-associated virus and retrotransposons. (PMID: 16527742) Chen H … Weitzman MD (Current biology : CB 2006) 3 4 22 60
  3. An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22. (PMID: 11863358) Jarmuz A … Navaratnam N (Genomics 2002) 2 3 4 60
  4. APOBEC3A, APOBEC3B, and APOBEC3H haplotype 2 restrict human T-lymphotropic virus type 1. (PMID: 22457529) Ooms M … Münk C (Journal of virology 2012) 3 4 60
  5. Human Tribbles 3 protects nuclear DNA from cytidine deamination by APOBEC3A. (PMID: 22977230) Aynaud MM … Vartanian JP (The Journal of biological chemistry 2012) 3 4 60

Products for APOBEC3A Gene

Sources for APOBEC3A Gene

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