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

Gene ID: 9582, updated on 14-Nov-2024

Summary

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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; AllianceGenome:HGNC:17352
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
all
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Genomic context

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See APOBEC3B in Genome Data Viewer
Location:
22q13.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (38982347..38992779)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39452733..39463200)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39378352..39388784)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39359385-39360194 Neighboring gene uncharacterized LOC105373033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39361630-39362609 Neighboring gene uncharacterized LOC124905118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39370179-39370956 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13737 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:39380734-39381933 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39382500-39382695 Neighboring gene APOBEC3B antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:39394090-39394730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39406643-39407144 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr22:39409474-39410092 and GRCh37_chr22:39410093-39410710 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3C Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39415894-39416734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39417574-39418413 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3D Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39423978-39424906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39426361-39427157

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. APOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinoma. Cannataro VL, et al. Oncogene, 2019 May. PMID 30647454, Free PMC Article
  2. Enzyme cycling contributes to efficient induction of genome mutagenesis by the cytidine deaminase APOBEC3B. Adolph MB, et al. Nucleic Acids Res, 2017 Nov 16. PMID 28981865, Free PMC Article
  3. APOBEC3B edits HBV DNA and inhibits HBV replication during reverse transcription. Chen Y, et al. Antiviral Res, 2018 Jan. PMID 29129707
  4. In vivo and in vitro studies suggest a possible involvement of HPV infection in the early stage of breast carcinogenesis via APOBEC3B induction. Ohba K, et al. PLoS One, 2014. PMID 24858917, Free PMC Article
  5. Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. Shi K, et al. Sci Rep, 2017 Dec 12. PMID 29234087, Free PMC Article

See all (223) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genetic alteration of mRNA editing enzyme APOBEC3B in the pathogenesis of ovarian endometriosis.
    Title: Genetic alteration of mRNA editing enzyme APOBEC3B in the pathogenesis of ovarian endometriosis.
  2. New insights into ATR inhibition in muscle invasive bladder cancer: The role of apolipoprotein B mRNA editing catalytic subunit 3B.
    Title: New insights into ATR inhibition in muscle invasive bladder cancer: The role of apolipoprotein B mRNA editing catalytic subunit 3B.
  3. Action-at-a-distance mutations induced by 8-oxo-7,8-dihydroguanine are dependent on APOBEC3.
    Title: Action-at-a-distance mutations induced by 8-oxo-7,8-dihydroguanine are dependent on APOBEC3.
  4. Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry.
    Title: Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry.
  5. Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations.
    Title: Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations.
  6. The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance.
    Title: The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance.
  7. Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer.
    Title: Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer.
  8. Human APOBEC3B promotes tumor development in vivo including signature mutations and metastases.
    Title: Human APOBEC3B promotes tumor development in vivo including signature mutations and metastases.
  9. APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer.
    Title: APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer.
  10. Human cytomegalovirus mediates APOBEC3B relocalization early during infection through a ribonucleotide reductase-independent mechanism.
    Title: Human cytomegalovirus mediates APOBEC3B relocalization early during infection through a ribonucleotide reductase-independent mechanism.
Submit: New GeneRIF Correction See all GeneRIFs (167)

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

EBI GWAS Catalog

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

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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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

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ21201

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
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 cytidine deaminase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 clearance of foreign intracellular DNA IDA
Inferred from Direct Assay
more info
 PubMed 
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 transposable element silencing 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
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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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)

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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.

mRNA and Protein(s)

  1. NM_001270411.2 → NP_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
    UniProtKB/TrEMBL
    W0HJ78
    Related
    ENSP00000385068.3, ENST00000407298.7
    Conserved Domains (1) summary
    pfam18782
    Location:10 → 189
    NAD2; Novel AID APOBEC clade 2

  2. NM_004900.5 → NP_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
    UniProtKB/Swiss-Prot
    B0QYD2, O95618, Q20WL1, Q5IFJ4, Q7Z2N3, Q7Z6D6, Q9UE74, Q9UH17
    UniProtKB/TrEMBL
    W0HJ78
    Related
    ENSP00000327459.3, ENST00000333467.4
    Conserved Domains (1) summary
    pfam08210
    Location:17 → 187
    APOBEC_N; APOBEC-like N-terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    39452733..39463200
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UH17.1 GenPept UniProtKB/Swiss-Prot:Q9UH17

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