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

Gene ID: 140564, updated on 12-Oct-2019

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
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; 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

Genomic context

See APOBEC3D in Genome Data Viewer
Location:
22q13.1
Exon count:
7
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 22 NC_000022.11 (39021127..39033277)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39417118..39435686)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3B Neighboring gene APOBEC3B antisense RNA 1 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3C Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3F Neighboring gene uncharacterized LOC107985563 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3G

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytidine deaminase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
deoxycytidine deaminase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
DNA cytosine deamination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA cytosine deamination IDA
Inferred from Direct Assay
more info
PubMed 
DNA demethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytidine deamination IEA
Inferred from Electronic Annotation
more info
 
cytidine to uridine editing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
defense response to virus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
defense response to virus IDA
Inferred from Direct Assay
more info
PubMed 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
negative regulation of single stranded viral RNA replication via double stranded DNA intermediate IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of single stranded viral RNA replication via double stranded DNA intermediate IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transposition IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transposition IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
P-body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
P-body IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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
NP_689639.2
XP_016884085.1

NCBI Reference Sequences (RefSeq)

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.

mRNA and Protein(s)

  1. NM_001363781.1NP_001350710.1  DNA dC->dU-editing enzyme APOBEC-3D isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL022318, BC017022, BX340829, CR456396, DA287097, DB121958
    Consensus CDS
    CCDS87027.1
    Related
    ENSP00000388017.2, ENST00000427494.6
    Conserved Domains (1) summary
    pfam08210
    Location:17199
    APOBEC_N; APOBEC-like N-terminal domain
  2. NM_152426.4NP_689639.2  DNA dC->dU-editing enzyme APOBEC-3D isoform 1

    See identical proteins and their annotated locations for NP_689639.2

    Status: REVIEWED

    Source sequence(s)
    AL022318, BC017022, BX340829, DA287097, DB121958, EU527884
    Consensus CDS
    CCDS46709.1
    UniProtKB/TrEMBL
    B2CML4
    Related
    ENSP00000216099.7, ENST00000216099.13
    Conserved Domains (1) summary
    pfam08210
    Location:213383
    APOBEC_N; APOBEC-like N-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p13 Primary Assembly

    Range
    39021127..39033277
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028596.2XP_016884085.1  DNA dC->dU-editing enzyme APOBEC-3D isoform X1

RNA

  1. XR_001755169.2 RNA Sequence

  2. XR_001755170.2 RNA Sequence

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