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Aliases for APOBEC3D Gene

Aliases for APOBEC3D Gene

  • Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3D 2 3
  • Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3D 2 3 5
  • Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3E Pseudogene 2 3
  • A3D 3 4
  • Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3D (Putative) 2
  • Apolipoprotein B MRNA Editing Enzyme Catalytic Polypeptide Like 3D 3
  • Probable DNA DC->DU-Editing Enzyme APOBEC-3D 3
  • EC 3.5.4.- 4
  • APOBEC3DE 3
  • APOBEC3E 3
  • EC 3.5.4 63
  • ARP6 3

External Ids for APOBEC3D Gene

Previous HGNC Symbols for APOBEC3D Gene

  • APOBEC3E

Previous GeneCards Identifiers for APOBEC3D Gene

  • GC22U990236
  • GC22P036032
  • GC22P037660
  • GC22P037741
  • GC22P039380
  • GC22P022391
  • GC22P039411
  • GC22P039412
  • GC22P039414
  • GC22P039418

Summaries for APOBEC3D Gene

Entrez Gene Summary for APOBEC3D Gene

  • This gene is a member of the cytidine deaminase gene family. It is one of a group of related genes 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 and inhibit retroviruses, such as HIV, by deaminating cytosine residues in nascent retroviral cDNA. [provided by RefSeq, Jul 2008]

GeneCards Summary for APOBEC3D Gene

APOBEC3D (Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3D) is a Protein Coding gene. GO annotations related to this gene include hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines. An important paralog of this gene is AICDA.

UniProtKB/Swiss-Prot for APOBEC3D Gene

  • DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. Exhibits antiviral activity against vif-deficient HIV-1. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single-or double-stranded RNA. May inhibit the mobility of LTR and non-LTR retrotransposons.

Gene Wiki entry for APOBEC3D Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for APOBEC3D Gene

Genomics for APOBEC3D Gene

Regulatory Elements for APOBEC3D Gene

Enhancers for APOBEC3D Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around APOBEC3D on UCSC Golden Path with GeneCards custom track

Promoters for APOBEC3D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around APOBEC3D on UCSC Golden Path with GeneCards custom track

Genomic Location for APOBEC3D Gene

Chromosome:
22
Start:
39,014,363 bp from pter
End:
39,033,276 bp from pter
Size:
18,914 bases
Orientation:
Plus strand

Genomic View for APOBEC3D Gene

Genes around APOBEC3D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
APOBEC3D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for APOBEC3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for APOBEC3D Gene

Proteins for APOBEC3D Gene

  • Protein details for APOBEC3D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96AK3-ABC3D_HUMAN
    Recommended name:
    DNA dC->dU-editing enzyme APOBEC-3D
    Protein Accession:
    Q96AK3
    Secondary Accessions:
    • Q5JZ91
    • Q7Z2N2
    • Q7Z2N5
    • Q7Z2N6

    Protein attributes for APOBEC3D Gene

    Size:
    386 amino acids
    Molecular mass:
    46598 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22.

neXtProt entry for APOBEC3D Gene

Proteomics data for APOBEC3D Gene at MOPED

Selected DME Specific Peptides for APOBEC3D Gene

Post-translational modifications for APOBEC3D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for APOBEC3D Gene

Antibody Products

Domains & Families for APOBEC3D Gene

Suggested Antigen Peptide Sequences for APOBEC3D Gene

Graphical View of Domain Structure for InterPro Entry

Q96AK3

UniProtKB/Swiss-Prot:

ABC3D_HUMAN :
  • The CMP/dCMP deaminase domain 1 mediates RNA binding, RNA-dependent oligomerization and virion incorporation whereas the CMP/dCMP deaminase domain 2 confers deoxycytidine deaminase activity and substrate sequence specificity.
  • Belongs to the cytidine and deoxycytidylate deaminase family.
Domain:
  • The CMP/dCMP deaminase domain 1 mediates RNA binding, RNA-dependent oligomerization and virion incorporation whereas the CMP/dCMP deaminase domain 2 confers deoxycytidine deaminase activity and substrate sequence specificity.
  • Contains 2 CMP/dCMP-type deaminase domains.
Family:
  • Belongs to the cytidine and deoxycytidylate deaminase family.
genes like me logo Genes that share domains with APOBEC3D: view

Function for APOBEC3D Gene

Molecular function for APOBEC3D Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Cytidine + H(2)O = uridine + NH(3).
UniProtKB/Swiss-Prot EnzymeRegulation:
Antiviral activity is neutralized by the HIV-1 virion infectivity factor (VIF), that prevents its incorporation into progeny virions by both inhibiting its translation and/or by inducing its ubiquitination and subsequent degradation by the 26S proteasome.
UniProtKB/Swiss-Prot Function:
DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. Exhibits antiviral activity against vif-deficient HIV-1. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single-or double-stranded RNA. May inhibit the mobility of LTR and non-LTR retrotransposons.

Enzyme Numbers (IUBMB) for APOBEC3D Gene

Gene Ontology (GO) - Molecular Function for APOBEC3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
genes like me logo Genes that share ontologies with APOBEC3D: view
genes like me logo Genes that share phenotypes with APOBEC3D: view

Animal Model Products

CRISPR Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for APOBEC3D Gene

Localization for APOBEC3D Gene

Subcellular locations from UniProtKB/Swiss-Prot for APOBEC3D Gene

Cytoplasm. Cytoplasm, P-body.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for APOBEC3D Gene COMPARTMENTS Subcellular localization image for APOBEC3D gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1

No data available for Gene Ontology (GO) - Cellular Components for APOBEC3D Gene

Pathways & Interactions for APOBEC3D Gene

SuperPathways for APOBEC3D Gene

No Data Available

Interacting Proteins for APOBEC3D Gene

Gene Ontology (GO) - Biological Process for APOBEC3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010529 negative regulation of transposition IDA 20062055
GO:0045869 negative regulation of single stranded viral RNA replication via double stranded DNA intermediate IDA 21835787
GO:0070383 DNA cytosine deamination IDA 21835787
genes like me logo Genes that share ontologies with APOBEC3D: view

No data available for Pathways by source and SIGNOR curated interactions for APOBEC3D Gene

Drugs & Compounds for APOBEC3D Gene

(2) Drugs for APOBEC3D Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Cytidine Experimental Pharma 0
Uridine Experimental Pharma 0

(2) Additional Compounds for APOBEC3D Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Ammonia
  • Ammonia anhydrous
  • Ammonia inhalant
  • Ammonia solution strong [usan]
  • Ammonia water
  • Ammoniak
7664-41-7
Water
  • Dihydrogen oxide
  • Steam
7732-18-5
genes like me logo Genes that share compounds with APOBEC3D: view

Transcripts for APOBEC3D Gene

mRNA/cDNA for APOBEC3D Gene

(4) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for APOBEC3D Gene

Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for APOBEC3D Gene

No ASD Table

Relevant External Links for APOBEC3D Gene

GeneLoc Exon Structure for
APOBEC3D
ECgene alternative splicing isoforms for
APOBEC3D

Expression for APOBEC3D Gene

mRNA expression in normal human tissues for APOBEC3D Gene

mRNA differential expression in normal tissues according to GTEx for APOBEC3D Gene

This gene is overexpressed in Whole Blood (x5.9) and Spleen (x5.6).

Protein differential expression in normal tissues from HIPED for APOBEC3D Gene

This gene is overexpressed in Peripheral blood mononuclear cells (42.2), Heart (16.2), and Blymphocyte (10.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for APOBEC3D Gene



SOURCE GeneReport for Unigene cluster for APOBEC3D Gene Hs.658626

mRNA Expression by UniProt/SwissProt for APOBEC3D Gene

Q96AK3-ABC3D_HUMAN
Tissue specificity: Expressed in lymphoid organs. Also detected in non-lymphoid tissues including lung.
genes like me logo Genes that share expression patterns with APOBEC3D: view

Protein tissue co-expression partners for APOBEC3D Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for APOBEC3D Gene

Orthologs for APOBEC3D Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for APOBEC3D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia APOBEC3D 35
  • 96.37 (n)
  • 90.93 (a)
APOBEC3DE 36
  • 91 (a)
OneToOne
Species with no ortholog for APOBEC3D:
  • 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)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • 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 APOBEC3D Gene

ENSEMBL:
Gene Tree for APOBEC3D (if available)
TreeFam:
Gene Tree for APOBEC3D (if available)

Paralogs for APOBEC3D Gene

(9) SIMAP similar genes for APOBEC3D Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for APOBEC3D Gene

genes like me logo Genes that share paralogs with APOBEC3D: view

Variants for APOBEC3D Gene

Sequence variations from dbSNP and Humsavar for APOBEC3D Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs2142834 -- 39,022,608(+) GGGCC(C/T)GAGCT intron-variant, upstream-variant-2KB
rs2179234 -- 39,022,731(+) CCCAG(A/G)GCCGT intron-variant, upstream-variant-2KB
rs7289668 -- 39,024,607(+) GGGCC(C/T)GCGAG intron-variant
rs34074269 -- 39,024,596(+) GCAAC(C/T)TTCCA intron-variant
rs34108294 -- 39,032,590(+) AAATC(-/T)TTTTT utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for APOBEC3D Gene

Variant ID Type Subtype PubMed ID
nsv915079 CNV Gain 21882294
nsv915080 CNV Loss 21882294
nsv915081 CNV Gain 21882294
nsv915082 CNV Gain 21882294
nsv834196 CNV Loss 17160897
nsv915083 CNV Loss 21882294
esv2724241 CNV Deletion 23290073
esv2724242 CNV Deletion 23290073
esv2724243 CNV Deletion 23290073
esv2676044 CNV Deletion 23128226
esv22523 CNV Gain 19812545
nsv915084 CNV Loss 21882294

Variation tolerance for APOBEC3D Gene

Residual Variation Intolerance Score: 66.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.37; 27.11% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for APOBEC3D Gene

HapMap Linkage Disequilibrium report
APOBEC3D
Human Gene Mutation Database (HGMD)
APOBEC3D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for APOBEC3D Gene

Disorders for APOBEC3D Gene

Relevant External Links for APOBEC3D

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
APOBEC3D

No disorders were found for APOBEC3D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for APOBEC3D Gene

Publications for APOBEC3D Gene

  1. 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 67
  2. The assembly of Vif ubiquitin E3 ligase for APOBEC3 degradation. (PMID: 25408426) Kim D.Y. (Arch. Pharm. Res. 2015) 3
  3. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3
  4. Multiple APOBEC3 restriction factors for HIV-1 and one Vif to rule them all. (PMID: 24189052) Desimmie B.A. … Pathak V.K. (J. Mol. Biol. 2014) 3
  5. APOBEC3 deaminases induce hypermutation in human papillomavirus 16 DNA upon beta interferon stimulation. (PMID: 24227842) Wang Z. … Muramatsu M. (J. Virol. 2014) 3

Products for APOBEC3D Gene

Sources for APOBEC3D Gene

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