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Aliases for APOBEC3D Gene

Aliases for APOBEC3D Gene

  • Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3D 2 3
  • 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
  • Probable DNA DC->DU-Editing Enzyme APOBEC-3D 3
  • 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 Polypeptide-Like 3D) is a Protein Coding gene. Diseases associated with APOBEC3D include hiv-1. 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

Genomic Location for APOBEC3D Gene

Start:
39,014,363 bp from pter
End:
39,039,681 bp from pter
Size:
25,319 bases
Orientation:
Plus strand

Genomic View for APOBEC3D Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Domains for APOBEC3D Gene

Gene Families for APOBEC3D Gene

HGNC:
  • APOBEC :Apolipoprotein B mRNA editing enzymes

Suggested Antigen Peptide Sequences for APOBEC3D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96AK3

UniProtKB/Swiss-Prot:

ABC3D_HUMAN :
  • Q96AK3
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 --
GO:0008270 zinc ion binding IEA --
GO:0016814 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines IEA --
genes like me logo Genes that share ontologies with APOBEC3D: view

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for APOBEC3D

In Situ Assay Products

Flow Cytometry Products

No data available for Phenotypes , Animal Models , miRNA , Transcription Factor Targeting 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 4
cytosol 2
extracellular 1

Gene Ontology (GO) - Cellular Components for APOBEC3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 cytoplasmic mRNA processing body IDA 22915799
GO:0005737 cytoplasm IDA 21835787
genes like me logo Genes that share ontologies with APOBEC3D: view

Pathways 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:0008152 metabolic process --
GO:0010529 negative regulation of transposition IDA 20062055
GO:0045087 innate immune response IEA --
GO:0045869 negative regulation of single stranded viral RNA replication via double stranded DNA intermediate IDA 21835787
GO:0051607 defense response to virus IDA 21835787
genes like me logo Genes that share ontologies with APOBEC3D: view

No data available for Pathways by source for APOBEC3D Gene

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:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for APOBEC3D

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for APOBEC3D
  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

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 (5.9) and Spleen (5.6).

Integrated Proteomics: protein expression 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 expressions with APOBEC3D: view

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

Selected 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 MAF
rs1139726 -- 39,020,059(+) tccaa(A/G)tgctg upstream-variant-2KB
rs1139727 -- 39,019,867(+) atggc(A/G)caatc upstream-variant-2KB
rs1139728 -- 39,019,900(+) tcccg(A/G)gttta upstream-variant-2KB
rs1139729 -- 39,019,905(+) agttt(A/G)agcga upstream-variant-2KB
rs1139730 -- 39,019,906(+) gttta(A/G)gcgat upstream-variant-2KB

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

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

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for APOBEC3D Gene including...

Search for APOBEC3D Gene in MalaCards »
genes like me logo Genes that share disorders with APOBEC3D: view

No data available for UniProtKB/Swiss-Prot 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
  2. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I. … Wright H. (Nature 1999) 3 4
  3. APOBEC3 proteins mediate the clearance of foreign DNA from human cells. (PMID: 20062055) Stenglein M.D. … Harris R.S. (Nat. Struct. Mol. Biol. 2010) 3 4
  4. Human and rhesus APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H demonstrate a conserved capacity to restrict Vif-deficient HIV-1. (PMID: 21835787) Hultquist J.F. … Harris R.S. (J. Virol. 2011) 3 4
  5. Endogenous origins of HIV-1 G-to-A hypermutation and restriction in the nonpermissive T cell line CEM2n. (PMID: 22807680) Refsland E.W. … Harris R.S. (PLoS Pathog. 2012) 3 4

Products for APOBEC3D Gene

Sources for APOBEC3D Gene

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