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 ... See more...

Aliases for APOBEC3D Gene

Aliases for APOBEC3D Gene

  • Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3D 2 3 5
  • Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3E Pseudogene 2 3
  • Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3D 2 3
  • DNA DC->DU-Editing Enzyme APOBEC-3D 3 4
  • A3D 3 4
  • Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3D (Putative) 2
  • Probable DNA DC->DU-Editing Enzyme APOBEC-3D 3
  • EC 3.5.4.38 4
  • APOBEC3DE 3
  • APOBEC3E 3
  • EC 3.5.4 52
  • 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
  • GC22P039015

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. Among its related pathways are Human cytomegalovirus infection. Gene Ontology (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 ENSG00000284554.

UniProtKB/Swiss-Prot Summary 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

Additional gene information for APOBEC3D Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for APOBEC3D Gene

Genomics for APOBEC3D Gene

GeneHancer (GH) Regulatory Elements for APOBEC3D Gene

Promoters and enhancers for APOBEC3D Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22J039019 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 510.3 +0.4 402 3.4 ZIC2 ZNF263 AFF1 SKI TRIM25 NCOR1 SP2 ZBTB17 NFXL1 POLR2G APOBEC3C APOBEC3D HSALNG0135466 ENSG00000284554 piR-46491-001
GH22J039017 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE dbSUPER 514.8 -3.0 -3041 1.5 USF1 MITF POU5F1 POLR2A ZNF770 CTCF APOBEC3D APOBEC3C APOBEC3F ENSG00000284554 HSALNG0135466
GH22J039020 Promoter/Enhancer 0.5 EPDnew dbSUPER 500.7 -1.5 -1493 0.1 APOBEC3D HSALNG0135466 APOBEC3C ENSG00000284554
GH22J038174 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10 -842.3 -842304 8.7 ZNF217 TCF12 ZNF300 POLR2G USF1 SP1 NCOR1 RBAK GTF2E2 JUND PLA2G6 MAFF DDX17 TRIOBP PRDX3P1 TMEM184B ENSG00000228274 ANKRD54 ENSG00000230912 CBX6
GH22J039012 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 14.6 -6.6 -6635 3.8 CTCF POLR2G PHF8 ZIC2 POLR2A ZBTB11 AFF1 REST TOE1 MYC APOBEC3C ENSG00000284554 piR-33211-004 APOBEC3D APOBEC3G SNORD83A HSALNG0135466
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around APOBEC3D on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for APOBEC3D

Top Transcription factor binding sites by QIAGEN in the APOBEC3D gene promoter:
  • c-Myc
  • GR
  • GR-alpha
  • Max
  • Max1
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c
  • USF1
  • ZID

Genomic Locations for APOBEC3D Gene

Genomic Locations for APOBEC3D Gene
chr22:39,021,113-39,033,277
(GRCh38/hg38)
Size:
12,165 bases
Orientation:
Plus strand
chr22:39,410,368-39,429,281
(GRCh37/hg19)
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

Selected DME Specific Peptides for APOBEC3D Gene

Q96AK3:
  • CFLSWFC
  • WLCYEVK

Post-translational modifications for APOBEC3D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for APOBEC3D Gene

Domains & Families for APOBEC3D Gene

Gene Families for APOBEC3D Gene

Protein Domains for APOBEC3D Gene

Blocks:
  • Cytidine/deoxycytidylate deaminase, zinc-binding region
  • APOBEC-like, C-terminal
  • Heavy metal transport/detoxification protein
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for APOBEC3D Gene

GenScript: Design optimal peptide antigens:
  • Probable DNA dC->dU-editing enzyme APOBEC-3D (ABC3D_HUMAN)
  • HCG41704, isoform CRA_a (B2CML4_HUMAN)

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.
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 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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a 2'-deoxycytidine in a single-stranded DNA + H(+) + H2O = a 2'-deoxyuridine in a single-stranded DNA + NH4(+); Xref=Rhea:RHEA:50948, Rhea:RHEA-COMP:12846, Rhea:RHEA-COMP:12847, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:28938, ChEBI:CHEBI:85452, ChEBI:CHEBI:133902; EC=3.5.4.38;.
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.

Enzyme Numbers (IUBMB) for APOBEC3D Gene

Phenotypes From GWAS Catalog for APOBEC3D Gene

Gene Ontology (GO) - Molecular Function for APOBEC3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA 21873635
GO:0003824 catalytic activity IEA --
GO:0004126 cytidine deaminase activity IBA 21873635
GO:0008270 zinc ion binding IEA --
GO:0016787 hydrolase 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

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for APOBEC3D

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
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 APOBEC3D gene
Compartment Confidence
nucleus 4
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for APOBEC3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IDA 22915799
GO:0005634 nucleus IBA 21873635
GO:0005737 cytoplasm IBA,IDA 21835787
genes like me logo Genes that share ontologies with APOBEC3D: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for APOBEC3D Gene

Pathways & Interactions for APOBEC3D Gene

PathCards logo

SuperPathways for APOBEC3D Gene

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

Pathways by source for APOBEC3D Gene

1 KEGG pathway for APOBEC3D Gene

Gene Ontology (GO) - Biological Process for APOBEC3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002376 immune system process IEA --
GO:0009972 cytidine deamination IEA --
GO:0010529 negative regulation of transposition IDA,IBA 20062055
GO:0016554 cytidine to uridine editing IBA 21873635
GO:0045087 innate immune response IEA --
genes like me logo Genes that share ontologies with APOBEC3D: view

No data available for SIGNOR curated interactions for APOBEC3D Gene

Drugs & Compounds for APOBEC3D Gene

(4) Drugs for APOBEC3D Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Ammonia Approved Pharma 0
Cytarabine Approved, Experimental, Investigational Pharma 1324
Water Approved Pharma 0
Uridine Experimental, Investigational Pharma 0
genes like me logo Genes that share compounds with APOBEC3D: view

Transcripts for APOBEC3D Gene

mRNA/cDNA for APOBEC3D Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for APOBEC3D

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

No ASD Table

Relevant External Links for APOBEC3D Gene

GeneLoc Exon Structure for
APOBEC3D

Expression for APOBEC3D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for APOBEC3D Gene



Protein tissue co-expression partners for APOBEC3D Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for APOBEC3D

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

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 30
  • 96.37 (n)
APOBEC3DE 31
  • 91 (a)
OneToOne
Species where no ortholog for APOBEC3D 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)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for APOBEC3D: view image

Paralogs for APOBEC3D Gene

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

  • ABC3D_HUMAN

Pseudogenes.org Pseudogenes for APOBEC3D Gene

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

Variants for APOBEC3D Gene

Additional dbSNP identifiers (rs#s) for APOBEC3D Gene

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

Variant ID Type Subtype PubMed ID
esv22523 CNV gain 19812545
esv2676044 CNV deletion 23128226
esv2724241 CNV deletion 23290073
esv2724242 CNV deletion 23290073
esv2724243 CNV deletion 23290073
esv2763703 CNV loss 21179565
esv3647751 CNV gain 21293372
esv3647753 CNV gain 21293372
esv3647755 CNV loss 21293372
esv3647756 CNV gain 21293372
nsv834196 CNV loss 17160897
nsv962794 CNV duplication 23825009

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)

Additional Variant Information for APOBEC3D Gene

Human Gene Mutation Database (HGMD)
APOBEC3D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
APOBEC3D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for APOBEC3D Gene

Disorders for APOBEC3D Gene

Additional Disease Information for 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 54
  2. APOBEC3G restricts HIV-1 to a greater extent than APOBEC3F and APOBEC3DE in human primary CD4+ T cells and macrophages. (PMID: 23097438) Chaipan C … Pathak VK (Journal of virology 2013) 3 4 54
  3. HIV-1 replication and APOBEC3 antiviral activity are not regulated by P bodies. (PMID: 22915799) Phalora PK … Malim MH (Journal of virology 2012) 3 4 54
  4. Retroelements versus APOBEC3 family members: No great escape from the magnificent seven. (PMID: 22912627) Arias JF … Tokunaga K (Frontiers in microbiology 2012) 3 4 54
  5. Endogenous origins of HIV-1 G-to-A hypermutation and restriction in the nonpermissive T cell line CEM2n. (PMID: 22807680) Refsland EW … Harris RS (PLoS pathogens 2012) 3 4 54

Products for APOBEC3D Gene

Sources for APOBEC3D Gene