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APOBEC3B apolipoprotein B mRNA editing enzyme catalytic subunit 3B [ Homo sapiens (human) ]

Gene ID: 9582, updated on 21-Jan-2020

Summary

Official Symbol
APOBEC3Bprovided by HGNC
Official Full Name
apolipoprotein B mRNA editing enzyme catalytic subunit 3Bprovided by HGNC
Primary source
HGNC:HGNC:17352
See related
Ensembl:ENSG00000179750 MIM:607110
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
A3B; ARP4; ARCD3; PHRBNL; APOBEC1L; bK150C2.2; DJ742C19.2
Summary
This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes 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. It is thought that the proteins may be RNA editing enzymes and have roles in growth or cell cycle control. A hybrid gene results from the deletion of approximately 29.5 kb of sequence between this gene, APOBEC3B, and the adjacent gene APOBEC3A. The breakpoints of the deletion are within the two genes, so the deletion allele is predicted to have the promoter and coding region of APOBEC3A, but the 3' UTR of APOBEC3B. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]
Expression
Biased expression in bone marrow (RPKM 23.5), appendix (RPKM 8.8) and 12 other tissues See more
Orthologs

Genomic context

See APOBEC3B in Genome Data Viewer
Location:
22q13.1
Exon count:
8
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 22 NC_000022.11 (38982347..38992779)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39378352..39388784)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373033 Neighboring gene uncharacterized LOC107985562 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 apolipoprotein B mRNA editing enzyme catalytic subunit 3D

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?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 replication is inhibited by APOBEC3B and APOBEC3G in 293T cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag APOBEC3B may be incorporated into virions by HIV-1 Gag polyprotein PubMed
Vif vif HIV-1 Vif(HXB2) degrades APOBEC3B, and the Vif(HXB2) mutants E128K and F296K have a reduced ability to degrade APOBEC3B in cells PubMed
vif Both HIV-1 Vif(IIIB) and Vif(HXB2) induce polyubiquitination of APOBEC3B at position K63, but only Vif(HXB2) induces polyubiquitination of APOBEC3B at position K48 PubMed
vif Human APOBEC3B is able to inhibit HIV infectivity even in the presence of HIV-1 Vif by the G to A hypermutation PubMed
vif Vif(IIIB) induces A3A, A3B, and A3C emigration from the nucleus to the cytosol and thereby causes net increases in their cytosolic concentrations and anti-HIV-1 activities PubMed
vif Stress causes A3A, A3B, A3C, and A3F to co-localize efficiently with Vif(IIIB) and mRNA-PABP1 complexes in stress granules PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ21201

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
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 
deoxycytidine deaminase activity IMP
Inferred from Mutant Phenotype
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 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 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 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
DNA dC->dU-editing enzyme APOBEC-3B
Names
apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B
cytidine deaminase
phorbolin 2
phorbolin 3
phorbolin-1-related protein
phorbolin-2/3
probable DNA dC->dU-editing enzyme APOBEC-3B
NP_001257340.2
NP_004891.5

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_001270411.2NP_001257340.2  DNA dC->dU-editing enzyme APOBEC-3B isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site at the 5' end of a coding exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AL022318
    Consensus CDS
    CCDS58807.1
    Related
    ENSP00000385068.3, ENST00000407298.7
  2. NM_004900.5NP_004891.5  DNA dC->dU-editing enzyme APOBEC-3B isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AL022318
    Consensus CDS
    CCDS13982.1
    Related
    ENSP00000327459.3, ENST00000333467.4
    Conserved Domains (1) summary
    pfam08210
    Location:17187
    APOBEC_N; APOBEC-like N-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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
    38982347..38992779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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