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

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; 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

Location:: 22q13.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (38982347..38992779)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (39452733..39463200)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (39378352..39388784)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

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.
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.
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.
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.
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.
APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer.
Title: APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer.
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.
The APOBEC3B c.783delG Truncating Mutation Is Not Associated with an Increased Risk of Breast Cancer in the Polish Population.
Title: The APOBEC3B c.783delG Truncating Mutation Is Not Associated with an Increased Risk of Breast Cancer in the Polish Population.
APOBEC3B coordinates R-loop to promote replication stress and sensitize cancer cells to ATR/Chk1 inhibitors.
Title: APOBEC3B coordinates R-loop to promote replication stress and sensitize cancer cells to ATR/Chk1 inhibitors.
APOBEC3B stratifies ovarian clear cell carcinoma with distinct immunophenotype and prognosis.
Title: APOBEC3B stratifies ovarian clear cell carcinoma with distinct immunophenotype and prognosis.

Submit: New GeneRIF Correction See all GeneRIFs (164)

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 EBI GWAS CatalogPubMed

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

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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 deoxycytidine deaminase activity	IBA Inferred from Biological aspect of Ancestor more info
enables deoxycytidine 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 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 retrotransposon 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

EC 3.5.4.38

NP_004891.5

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.

mRNA and Protein(s)

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
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