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
- 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
External Ids for APOBEC3D Gene
- HGNC: 17354
- Entrez Gene: 140564
- Ensembl: ENSG00000243811
- OMIM: 609900
- UniProtKB: Q96AK3
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
-
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 ENSG00000284554.
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.
No data available for CIViC summary , 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
- Elite enhancer and/or Elite enhancer-gene association
Download GeneHancer data dump
Enhancers around APOBEC3D on UCSC Golden Path with GeneCards custom track
Regulatory Element Products
Genomic Location for APOBEC3D Gene
- Chromosome:
- 22
- Start:
- 39,021,113 bp from pter
- End:
- 39,033,276 bp from pter
- Size:
- 12,164 bases
- Orientation:
- Plus strand
Genomic View for APOBEC3D Gene
Genes around APOBEC3D on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 22q13.1 by Ensembl
- 22q13.1 by Entrez Gene
- 22q13.1 by HGNC
APOBEC3D Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene 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
- 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.
Protein Expression for APOBEC3D Gene
Selected DME Specific Peptides for APOBEC3D Gene
- Q96AK3:
-
- CFLSWFC
- WLCYEVK
Post-translational modifications for APOBEC3D Gene
Other Protein References for APOBEC3D Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
- Novus Biologicals Antibodies for APOBEC3D
-
Abcam antibodies for APOBEC3D
- Invitrogen Antibodies for APOBEC3D
- antibodies-online Antibodies for APOBEC3D: See all 36
- GeneTex APOBEC3D antibody for APOBEC3D
Protein Products
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- antibodies-online Proteins for APOBEC3D: See all 3
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- Search GeneTex for Proteins for APOBEC3D
-
Abcam proteins for APOBEC3D
Assay Products
Domains & Families for APOBEC3D Gene
Gene Families for APOBEC3D Gene
Protein Domains for APOBEC3D Gene
Suggested Antigen Peptide Sequences for APOBEC3D Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
Q96AK3UniProtKB/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.
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
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0003824 | catalytic activity | IEA | -- |
| GO:0008270 | zinc ion binding | IEA | -- |
| GO:0016787 | hydrolase activity | IEA | -- |
| GO:0016814 | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines | IEA | -- |
| GO:0046872 | metal ion binding | IEA | -- |
Phenotypes for APOBEC3D Gene
- GenomeRNAi human phenotypes for APOBEC3D:
Animal Model Products
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-
-
ViGene Biosciences lentiviral particle packaged cDNA for APOBEC3D gene
-
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- Search ViGene Biosciences for APOBEC3D
CRISPR Products
-
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-
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miRNA for APOBEC3D Gene
- miRTarBase miRNAs that target APOBEC3D
miRNA Products
- Search ViGene Biosciences for APOBEC3D
Inhibitory RNA Products
- Origene RNAi, siRNA, and shRNA products in human, mouse, rat for APOBEC3D
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Clone Products
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-
VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Cell Line Products
-
Horizon Cell Lines for APOBEC3D
-
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-
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-
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Flow Cytometry 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.
| Compartment | Confidence |
|---|---|
| nucleus | 2 |
| cytosol | 2 |
| extracellular | 1 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000932 | P-body | IDA | 22915799 |
| GO:0005737 | cytoplasm | IEA,IDA | 21835787 |
Pathways & Interactions for APOBEC3D Gene
No Data Available
Interacting Proteins for APOBEC3D Gene
| Symbol | External ID(s) | Details |
|---|---|---|
| FN1 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0002376 | immune system process | IEA | -- |
| 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 | IEA,IDA | 21835787 |
No data available for Pathways by source and SIGNOR curated interactions for APOBEC3D Gene
Drugs & Compounds for APOBEC3D Gene
| Name | Synonyms | Role | CAS Number | PubChem IDs | PubMed IDs | |
|---|---|---|---|---|---|---|
| Ammonia |
|
7664-41-7 |
|
Transcripts for APOBEC3D Gene
mRNA/cDNA for APOBEC3D Gene
- (3) REFSEQ mRNAs :
- (3) Additional mRNA sequences :
- (2) Ensembl transcripts including schematic representations, and UCSC links where relevant :
Unigene Clusters for APOBEC3D Gene
CRISPR Products
-
OriGene CRISPR knockouts for APOBEC3D
-
Santa Cruz Biotechnology (SCBT) CRISPR for APOBEC3D
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miRNA Products
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Inhibitory RNA Products
- Origene RNAi, siRNA, and shRNA products in human, mouse, rat for APOBEC3D
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ViGene Biosciences ready-to-package AAV shRNAs for APOBEC3D gene
Clone Products
-
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- VectorBuilder custom plasmid, inducible vectors for APOBEC3D
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for APOBEC3D
-
VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Flow Cytometry Products
Expression 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).
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
- Elite partner
NURSA nuclear receptor signaling pathways regulating expression of APOBEC3D Gene:
APOBEC3DSOURCE GeneReport for Unigene cluster for APOBEC3D Gene:
Hs.658626mRNA Expression by UniProt/SwissProt for APOBEC3D Gene:
Q96AK3-ABC3D_HUMAN
Tissue specificity:
Expressed in lymphoid organs. Also detected in non-lymphoid tissues including lung.
Primer Products
-
OriGene qPCR primer pairs for APOBEC3D
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.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | APOBEC3D 34 |
|
||
| APOBEC3DE 35 |
|
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)
Paralogs for APOBEC3D Gene
Paralogs for APOBEC3D Gene
(9) SIMAP similar genes for APOBEC3D Gene using alignment to 1 proteins:
Pseudogenes.org Pseudogenes for APOBEC3D Gene
Variants for APOBEC3D Gene
| SNP ID | Clin | Chr 22 pos | Sequence Context | AA Info | Type |
|---|---|---|---|---|---|
| rs1000336007 | -- | 39,026,238(+) | CCGCT(C/T)CTCCT | intron-variant | |
| rs1000485119 | -- | 39,031,060(+) | ACTCC(A/G)GAGGC | intron-variant | |
| rs1000951953 | -- | 39,023,185(+) | ATCTC(A/G)GATCA | intron-variant | |
| rs1001185583 | -- | 39,029,492(+) | GTCTT(-/C)CGGAA | intron-variant, reference, frameshift-variant | |
| rs1001224052 | -- | 39,032,066(+) | TCCCC(A/G)GGAAG | intron-variant |
| 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 |
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
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
- 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 64
- 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 V.K. (J. Virol. 2013) 3 4 64
- 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 64
- Retroelements versus APOBEC3 family members: No great escape from the magnificent seven. (PMID: 22912627) Arias J.F. … Tokunaga K. (Front. Microbiol. 2012) 3 4 64
- HIV-1 replication and APOBEC3 antiviral activity are not regulated by P bodies. (PMID: 22915799) Phalora P.K. … Malim M.H. (J. Virol. 2012) 3 4 64
Products for APOBEC3D Gene
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- antibodies-online Antibodies for APOBEC3D: See all 36
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- antibodies-online Proteins for APOBEC3D: See all 3
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- GeneTex APOBEC3D antibody for APOBEC3D
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- ViGene Biosciences adenoviral particle packaged cDNA for APOBEC3D gene
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- Horizon Cell Lines for APOBEC3D
- Cyagen custom Knockout/knockin (KOKI) mouse models for APOBEC3D
- VectorBuilder custom plasmid, inducible vectors for APOBEC3D
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for APOBEC3D
- VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Sources for APOBEC3D Gene
- (1) GeneCards
- (2) HGNC
- (3) EntrezGene
- (4) Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) GO
- (12) TrEMBL
- (13) InterPro
- (14) ProtoNet
- (15) Blocks
- (16) MGI
- (17) IUBMB
- (18) KEGG
- (19) MINT
- (20) STRING
- (21) IntAct
- (22) Novoseek
- (23) PharmGKB
- (24) DrugBank
- (25) HMDB
- (26) UniGene
- (27) AceView
- (28) RNAdb
- (29) ASD
- (30) ECgene
- (31) GeneAnnot
- (32) CGAP SAGE
- (33) SOURCE
- (34) HomoloGene
- (35) PanEnsembl
- (36) euGenes
- (37) SGD
- (38) FlyBase
- (39) WormBase
- (40) Pseudogene
- (41) DGV
- (42) dbSNP
- (43) GenAtlas
- (44) GeneTests
- (45) HGMD
- (46) GAD
- (47) LSDB
- (48) BGMUT
- (49) HuGE
- (50) eBioscience
- (51) Atlas
- (52) Cell Signaling Technology
- (53) GenBank
- (54) H-invDB
- (55) HORDE
- (56) HUGE
- (57) IMGT
- (58) Leiden
- (59) MILLIPORE
- (60) miRBase
- (61) DME
- (62) NCBI
- (63) OriGene
- (64) PubMed
- (65) R&D Systems
- (66) TGDB
- (67) Tocris
- (68) Abcam
- (69) Novus
- (70) ProSpec
- (71) Sino Biological
- (72) GenScript
- (73) Qiagen
- (74) Cloud-Clone Corp.
- (75) Enzo Life Sciences
- (76) OCA
- (77) Proteopedia
- (78) MOPED
- (79) SPIRE
- (80) neXtProt
- (81) Reactome
- (82) GeneGo (Thomson Reuters)
- (83) fRNAdb
- (84) DISEASES
- (85) SIMAP
- (86) GenomeRNAi
- (87) LifeMap
- (88) miRTarBase
- (89) MalaCards
- (90) Invitrogen
- (91) BitterDB
- (92) Vector BioLabs
- (93) ESI-BIO
- (94) RefSeq
- (95) BioSystems
- (96) MaxQB
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