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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

APOBEC3A Gene

protein-coding   GIFtS: 47
GCID: GC22P039348

apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like...

 Explore 6 diseases affiliated with
APOBEC3A via our new
 Human Malady Compendium 
Biological research products
for APOBEC3A
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3A1 2     Probable DNA DC->DU-Editing Enzyme APOBEC-3A2
PHRBN1 2 5     A3A3
ARP31 2     EC 3.5.4.-3
BK150C2.11     Phorbolin-13
Phorbolin 12     EC 3.5.48
Phorbolin-13     

External Ids:    HGNC: 173431   Entrez Gene: 2003152   Ensembl: ENSG000001283837   OMIM: 6071095   UniProtKB: P319413   

Export aliases for APOBEC3A gene to outside databases

Previous GC identifers: GC22P035968 GC22P037591 GC22P037596 GC22P037678 GC22Pr39368


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for APOBEC3A:
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)

UniProtKB/Swiss-Prot: ABC3A_HUMAN, P31941
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

Gene Wiki entry for APOBEC3A


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the APOBEC3A gene promoter:
         SRF   SRF (504 AA)   LCR-F1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidAPOBEC3A promoter sequence
   Search SABiosciences Chromatin IP Primers for APOBEC3A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat APOBEC3A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 22q13.1-q13.2   Ensembl cytogenetic band:  22q13.1   HGNC cytogenetic band: 22q13.1-q13.2

APOBEC3A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
APOBEC3A gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P039348:  view genomic region     (about GC identifiers)

Start:
39,348,746 bp from pter      End:
39,359,188 bp from pter
Size:
10,443 bases      Orientation:
plus strand

1 alternative location:
Chr22+,PATCHES 39,368,499-39,373,815     

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: ABC3A_HUMAN, P31941 (See protein sequence)
Recommended Name: DNA dC->dU-editing enzyme APOBEC-3A  
Size: 199 amino acids; 23012 Da
Cofactor: Zinc (By similarity)
Subunit: Interacts with EIF2C2/AGO2. Interacts with TRIB3 (via N-terminus)
Subcellular location: Nucleus. Cytoplasm
Miscellaneous: It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene
duplication, on chromosome 22
Secondary accessions: A0AVM1 Q12807 Q5JZ93 Q9UH18
Alternative initiation: 2 isoforms:  P31941-1   P31941-2   (Enzymatically active)

Explore the universe of human proteins at neXtProt for APOBEC3A: NX_P31941

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P31941

  • 3 DME Specific Peptides for APOBEC3A (P31941)
     FTSNFNN  PFQPWDGL  EHSQALSGRL 

    APOBEC3A Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001257335.1  NP_663745.1  

    ENSEMBL proteins: 
     ENSP00000384359   ENSP00000249116  

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    Uscn Proteins for APOBEC3A

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005737cytoplasm IDA--


    APOBEC3A for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for APOBEC3A


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    APOBEC3A for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR016193 Cytidine_deaminase-like
     IPR016192 APOBEC/CMP_deaminase_Zn-bd
     IPR007904 APOBEC_C

    Graphical View of Domain Structure for InterPro Entry P31941

    ProtoNet protein and cluster: P31941

    2 Blocks protein families:
    IPB002125 Cytidine/deoxycytidylate deaminase
    IPB007904 APOBEC-like


    UniProtKB/Swiss-Prot: ABC3A_HUMAN, P31941
    Similarity: Belongs to the cytidine and deoxycytidylate deaminase family
    Similarity: Contains 1 CMP/dCMP deaminase zinc-binding domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: ABC3A_HUMAN, P31941
    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
    Catalytic activity: Cytidine + H(2)O = uridine + NH(3)
    Induction: Up-regulated by interferon and CpG single-stranded DNA (at protein level)

    Enzyme Numbers (IUBMB): EC 3.5.42 EC 3.5.4.-1

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    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004126cytidine deaminase activity IMP--
    GO:0005515protein binding IPI--
    GO:0008270zinc ion binding IEA--
    GO:0047844deoxycytidine deaminase activity IMP--


    APOBEC3A for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for APOBEC3A

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for APOBEC3A (ENSP000002491164) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 5/9 biological process terms (GO ID links to tree view) (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0009972cytidine deamination IMP--
    GO:0010529negative regulation of transposition IDA--
    GO:0044356clearance of foreign intracellular DNA by conversion of DNA cytidine to uridine IDA--
    GO:0045071negative regulation of viral genome replication IDA16527742
    GO:0045087innate immune response IDA--


    APOBEC3A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    APOBEC3A for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for APOBEC3A
    1 Novoseek chemical compound relationship for APOBEC3A gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cytidine 84.7 3 16720547 (1), 10469298 (1), 20178977 (1)

    Search CenterWatch for drugs/clinical trials and news about APOBEC3A / ABC3A 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for APOBEC3A gene (2 alternative transcripts): 
    NM_001270406.1  NM_145699.3  

    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000495988 ENST00000402255 ENST00000488758 ENST00000249116(uc003awn.2 uc011aob.1 uc011aoc.1)


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    24/55 AceView cDNA sequences (see all 55):

    BI029063 BE644606 BI029065 BX114955 C00488 BU584024 CR456393 NM_004900 
    H79385 NM_145699 BU584432 BM687484 AW368715 BU727763 T71211 AK024854 
    BI030278 BC031803 AI761325 AA603662 BU178985 BM463931 CB218515 U03891 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    APOBEC3A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AATTGCAAGA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See APOBEC3A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for APOBEC3A

    UniProtKB/Swiss-Prot: ABC3A_HUMAN, P31941
    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, Burkitt's lymphoma and chronic myelogenous
    leukemia

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for APOBEC3A gene from 1/6 species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia APOBEC16
    --
    25(a)
    possible ortholog
    3(98130519-98131040)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for APOBEC3A gene
    APOBEC3G2  APOBEC3D2  APOBEC3F2  APOBEC12  APOBEC22  APOBEC3B2  APOBEC3C2  AICDA2  
    APOBEC3H2  
    11 SIMAP similar genes for APOBEC3A using alignment to 2 protein entries:     ABC3A_HUMAN (see all proteins):
    APOBEC3B    APOBEC3G    AID    AICDA    APOBEC3F    APOBEC3C
    APOBEC2    APOBEC3D    APOBEC3DE    APOBEC3H    bK150C2.9

    APOBEC3A for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for APOBEC3A
    PGOHUM00000259961


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/188 NCBI SNPs in APOBEC3A are shown (see all 188    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs734199171,2
    C,--22323559(+) TGTCCC/TTGTCC 1 -- int12Minor allele frequency- T:0.04WA 120
    rs1138197421,2
    C,--22323801(+) AGTGAT/CCTCCC 1 -- int12Minor allele frequency- C:0.07CSA WA 120
    rs97544481,2
    --22327060(+) CAGACA/GCCAGC 1 -- int1 ese30--------
    rs97544401,2
    --22327074(+) GCAGTA/GTGCTC 1 -- int10--------
    rs72863171,2
    C,--22327209(+) aacacA/Ggtgaa 1 -- int1 ese30--------
    rs1132977731,2
    C,F,--22327219(+) AACCCC/TGTCTC 1 -- int12Minor allele frequency- T:0.50WA NA 4
    rs1121570581,2
    C,F,--22327470(+) TTATGG/CTCAAT 1 -- int12Minor allele frequency- C:0.50WA CSA 4
    rs39859501,2
    C,--22327774(+) TCACTC/TACAGA 1 -- int11Minor allele frequency- T:0.50WA 2
    rs96110541,2
    H--39351618(+) AGTGAG/CACTGT 3 -- us2k14Minor allele frequency- C:0.00NS EA 420
    rs1385871431,2
    --39351744(+) TCTCTC/TCTCTC 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for APOBEC3A (39348746 - 39359188 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 8 variations for APOBEC3A
         8 CNVs: 32467 103175 67891 0549 38981 36029 7349 36030

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    APOBEC3A for disorders           About GeneDecksing

    OMIM gene information: 607109    OMIM disorders: --

    6 diseases for APOBEC3A:    About MalaCards
    albinism    psoriasis    hepatitis b    hepatitis
    immunodeficiency    hepatitis b virus infection

    1 Novoseek disease relationship for APOBEC3A gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    psoriasis 45.7 1 10469298 (1)

    Human Genome Epidemiology (HuGE) Navigator: APOBEC3A (2 documents)

    Export disorders for APOBEC3A gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for APOBEC3A gene, integrated from 9 sources (see all 49):
    (articles sorted by number of sources associating them with APOBEC3A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Psoriasis upregulated phorbolin-1 shares structural but not functional similarity to the mRNA-editing protein apobec-1. (PubMed id 10469298)1, 2, 3, 9 Madsen P.P.... Celis J.E. (1999)
    2. An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22. (PubMed id 11863358)1, 2, 3 Jarmuz A....Navaratnam N. (2002)
    3. APOBEC3A is a potent inhibitor of adeno-associated virus and retrotransposons. (PubMed id 16527742)1, 2, 9 Chen H....Weitzman M.D. (2006)
    4. Human Tribbles 3 protects nuclear DNA from cytidine deamination by APOBEC3A. (PubMed id 22977230)1, 2 Aynaud M.M.... Vartanian J.P. (2012)
    5. APOBEC3A, APOBEC3B, and APOBEC3H haplotype 2 restrict human T-lymphotropic virus type 1. (PubMed id 22457529)1, 2 Ooms M....Munk C. (2012)
    6. APOBEC3A can activate the DNA damage response and cau se cell-cycle arrest. (PubMed id 21460793)1, 2 Landry S....Weitzman M.D. (2011)
    7. Structure-function analyses point to a polynucleotide -accommodating groove essential for APOBEC3A restriction activities. (PubMed id 21123384)1, 2 Bulliard Y....Trono D. (2011)
    8. Innate immune signaling induces high levels of TC-spe cific deaminase activity in primary monocyte-derived cells through expression o f APOBEC3A isoforms. (PubMed id 20615867)1, 2 Thielen B.K....Lingappa J.R. (2010)
    9. APOBEC3 proteins mediate the clearance of foreign DNA from human cells. (PubMed id 20062055)1, 2 Stenglein M.D....Harris R.S. (2010)
    10. Deaminase-independent inhibition of parvoviruses by t he APOBEC3A cytidine deaminase. (PubMed id 19461882)1, 2 Narvaiza I....Weitzman M.D. (2009)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 200315 HGNC: 17343 AceView: APOBEC3BandAPOBEC3A Ensembl:ENSG00000128383 euGenes: HUgn200315
    ECgene: APOBEC3A H-InvDB: APOBEC3A

    (According to HUGE)
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