Format

Send to:

Choose Destination

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

Gene ID: 9582, updated on 3-Jun-2018
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; Vega:OTTHUMG00000151085
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
See APOBEC3B in Genome Data Viewer
Location:
22q13.1
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 22 NC_000022.11 (38982399..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

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

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

  • Formation of the Editosome, organism-specific biosystem (from REACTOME)
    Formation of the Editosome, organism-specific biosystemThe editosome for C to U editing in mammals consist of a member of cytidine deaminase family of enzymes, apoB mRNA editig catalytic polypeptide 1 (APOBEC-1) and a complementing specificity factor (AC...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • mRNA Editing, organism-specific biosystem (from REACTOME)
    mRNA Editing, organism-specific biosystemAfter transcription, some RNA molecules are altered to contain bases not encoded in the genome. Most often this involves the editing or modification of one base to another, but in some organisms can ...
  • mRNA Editing: C to U Conversion, organism-specific biosystem (from REACTOME)
    mRNA Editing: C to U Conversion, organism-specific biosystemThe best characterized case of C to U editing is in the intestinal apolipoprotein B transcript, where the editing event creates a premature translation stop codon and consequently leads to a shorter ...
Products Interactant Other Gene Complex Source Pubs Description

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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
DNA demethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytidine to uridine editing 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 transposition IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
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

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_001270411.1NP_001257340.1  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)
    AK024854, AU098564, AY743217, BX114955, CT841510, U61083
    Consensus CDS
    CCDS58807.1
    UniProtKB/Swiss-Prot
    Q9UH17
    Related
    ENSP00000385068.3, OTTHUMP00000199090, ENST00000407298.7, OTTHUMT00000321235
    Conserved Domains (3) summary
    cd01283
    Location:8158
    cytidine_deaminase; Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on ...
    pfam05240
    Location:129174
    APOBEC_C; APOBEC-like C-terminal domain
    pfam08210
    Location:17187
    APOBEC_N; APOBEC-like N-terminal domain
  2. NM_004900.4NP_004891.4  DNA dC->dU-editing enzyme APOBEC-3B isoform a

    See identical proteins and their annotated locations for NP_004891.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AL022318, AU098564, AY743217, BX114955, U61083
    Consensus CDS
    CCDS13982.1
    UniProtKB/Swiss-Prot
    Q9UH17
    Related
    ENSP00000327459.3, OTTHUMP00000199088, ENST00000333467.3, OTTHUMT00000321233
    Conserved Domains (3) summary
    cd01283
    Location:8158
    cytidine_deaminase; Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on ...
    pfam05240
    Location:129174
    APOBEC_C; APOBEC-like C-terminal domain
    pfam08210
    Location:17187
    APOBEC_N; APOBEC-like N-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p12 Primary Assembly

    Range
    38982399..38992779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center