APOBEC3D apolipoprotein B mRNA editing enzyme catalytic subunit 3D [Homo sapiens (human)] - Gene

Summary

Official Symbol: APOBEC3Dprovided by HGNC
Official Full Name: apolipoprotein B mRNA editing enzyme catalytic subunit 3Dprovided by HGNC
Primary source: HGNC:HGNC:17354
See related: Ensembl:ENSG00000243811 MIM:609900; AllianceGenome:HGNC:17354
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: A3D; A3DE; ARP6; APOBEC3E; APOBEC3DE
Summary: 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]
Expression: Broad expression in lymph node (RPKM 5.2), spleen (RPKM 4.6) and 22 other tissues See more
Orthologs: all
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Genomic context

Location:: 22q13.1

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (39021127..39033277)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (39491547..39503696)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (39417132..39429282)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Alternative splicing of APOBEC3D generates functional diversity and its role as a DNA mutator.
Title: Alternative splicing of APOBEC3D generates functional diversity and its role as a DNA mutator.
APOBEC3DE inhibits human LINE-1 retrotransposition.
Title: APOBEC3DE Inhibits LINE-1 Retrotransposition by Interacting with ORF1p and Influencing LINE Reverse Transcriptase Activity.
APOBEC3DE binds to itself, APOBEC3F, and APOBEC3G and antagonizes APOBEC3F and, to a lesser extent, APOBEC3G restriction of hepatitis B virus replication.
Title: APOBEC3DE Antagonizes Hepatitis B Virus Restriction Factors APOBEC3F and APOBEC3G.
These results indicate that APOBEC3 proteins can be copackaged and can comutate the same genomes, and can cooperate to inhibit HIV replication.
Title: APOBEC3 proteins can copackage and comutate HIV-1 genomes.
APOBEC3D/F and APOBEC3G fundamentally work as restriction factors against HIV-1 in vivo
Title: APOBEC3D and APOBEC3F potently promote HIV-1 diversification and evolution in humanized mouse model.
APOBEC3 deaminases upregulated by IFN-beta induce E2 hypermutation of HPV16 in cervical keratinocytes.
Title: APOBEC3 deaminases induce hypermutation in human papillomavirus 16 DNA upon beta interferon stimulation.
We found that two common novel polymorphisms in APOBEC3D decrease antiviral activity against HIV-1, and one polymorphism decreases activity against Alu retrotransposons in the human population.
Title: Identification and antiviral activity of common polymorphisms in the APOBEC3 locus in human populations.
The authors conclude that APOBEC3G exerts a greater restriction effect on HIV-1 than APOBEC3F and APOBEC3DE.
Title: APOBEC3G restricts HIV-1 to a greater extent than APOBEC3F and APOBEC3DE in human primary CD4+ T cells and macrophages.
endogenous levels of APOBEC3D, APOBEC3F, and APOBEC3G combine to restrict Vif-deficient HIV-1 and cause the hallmark dinucleotide hypermutation patterns in in the nonpermissive T cell line CEM2n
Title: Endogenous origins of HIV-1 G-to-A hypermutation and restriction in the nonpermissive T cell line CEM2n.
Distinct determinants in HIV-1 Vif and human APOBEC3 proteins are required for the suppression of diverse host anti-viral proteins.
Title: Distinct determinants in HIV-1 Vif and human APOBEC3 proteins are required for the suppression of diverse host anti-viral proteins.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vif	vif	Immunoblotting and crystal structure analyses reveal ten amino acids L268, F271, C272, I275, L276, S277, Y282, D302, F303, and H307 in APOBEC3D are involved in forming Vif-interaction interface	PubMed
	vif	CBF-beta-mediated increase of HIV-1 Vif steady-state levels results in decreased cellular levels of all Vif-sensitive APOBEC proteins (A3C, A3D, A3F, A3G, and A3H haplotype II)	PubMed
	vif	HIV-1 Vif inhibits human APOBEC3D encapsidation into HIV-1 virions and APOBEC3D-mediated GC-to-AC mutations in viral plus-strand DNA by triggering its proteasomal degradation	PubMed
	vif	Endogenous APOBEC3 proteins, particularly APOBEC3D, APOBEC3F, and APOBEC3G, can potently inhibit HIV-1 propagation in a mouse model by mutating 14DRMR17 and/or 40YRHHY44 motifs in Vif	PubMed
	vif	The LV portion of the Vif SLV/Ix4Yx9Y motif is required for optimal suppression of A3C or A3DE	PubMed
	vif	The antiviral activity of A3G to HIV-1 vif mutants NL4-3 40YRHHY44>A5 and NL4-3 14DRMR17>A4 with G-to-A hypermutations confers a greater restriction than the combined antiviral activity of A3F and A3DE in activated CD4+ T cells and macrophages	PubMed
	vif	HIV-1 Vif DR14/15AA and W79A mutants are less effective in reducing A3DE expression, compared to wild type Vif	PubMed
	vif	Human T cell line CEM.NKR clones display inhibition of HIV-1 replication although these clones retain low levels of A3DE, A3F, A3G, and A3H expression, suggesting that a novel restriction factor distinct from APOBEC3s exists in CEM.NKR cells	PubMed
	vif	Amino acid E289 in the EFLARH sequence of A3DE is critical for HIV-1 Vif-mediated degradation	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

RH65953 (e-PCR)
- UniSTS:55355

G18167 (e-PCR)
- UniSTS:43142

D11S3114 (e-PCR)
- UniSTS:152207

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables cytidine deaminase activity	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA cytosine deamination	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA cytosine deamination	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA demethylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in clearance of foreign intracellular DNA	IDA Inferred from Direct Assay more info	PubMed
involved_in cytidine deamination	IEA Inferred from Electronic Annotation more info
involved_in cytidine to uridine editing	IBA Inferred from Biological aspect of Ancestor more info
involved_in defense response to virus	IBA Inferred from Biological aspect of Ancestor more info
involved_in defense response to virus	IDA Inferred from Direct Assay more info	PubMed
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in P-body	IBA Inferred from Biological aspect of Ancestor more info
located_in P-body	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: DNA dC->dU-editing enzyme APOBEC-3D

Names: apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D; apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3E pseudogene; probable DNA dC->dU-editing enzyme APOBEC-3D

NP_001350710.1

EC 3.5.4.38

NP_689639.2

EC 3.5.4.38

XP_016884085.1

EC 3.5.4.38

XP_047297098.1

EC 3.5.4.38

XP_054181081.1

EC 3.5.4.38

XP_054181082.1

EC 3.5.4.38

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.