APOBEC1 apolipoprotein B mRNA editing enzyme catalytic subunit 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: APOBEC1provided by HGNC
Official Full Name: apolipoprotein B mRNA editing enzyme catalytic subunit 1provided by HGNC
Primary source: HGNC:HGNC:604
See related: Ensembl:ENSG00000111701 MIM:600130; AllianceGenome:HGNC:604
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: APO1; BEDP; HEPR; CDAR1; APOBEC-1
Summary: This gene encodes a member of the cytidine deaminase enzyme family. The encoded protein forms a multiple-protein editing holoenzyme with APOBEC1 complementation factor (ACF) and APOBEC1 stimulating protein (ASP). This holoenzyme is involved in the editing of C-to-U nucleotide bases in apolipoprotein B and neurofibromatosis-1 mRNAs. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2015]
Expression: Biased expression in duodenum (RPKM 22.2), small intestine (RPKM 18.5) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.31

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (7649400..7670599, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (7663658..7684886, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (7801996..7823195, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Identification of RBM46 as a novel APOBEC1 cofactor for C-to-U RNA-editing activity.
Title: Identification of RBM46 as a novel APOBEC1 cofactor for C-to-U RNA-editing activity.
APOBEC mutagenesis is a common process in normal human small intestine.
Title: APOBEC mutagenesis is a common process in normal human small intestine.
The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness.
Title: The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness.
Harnessing A3G for efficient and selective C-to-T conversion at C-rich sequences.
Title: Harnessing A3G for efficient and selective C-to-T conversion at C-rich sequences.
APOBEC1 cytosine deaminase activity on single-stranded DNA is suppressed by replication protein A.
Title: APOBEC1 cytosine deaminase activity on single-stranded DNA is suppressed by replication protein A.
Our findings propose APOBEC1 and isoform b as the potential endogenous mutators implicated in cancer in-frame indels and pave the way for their use as novel prognostic tumor markers.
Title: Pancancer analysis identifies prognostic high-APOBEC1 expression level implicated in cancer in-frame insertions and deletions.
Luciferase-fused 3' untranslated region of human Dickkopf1 activity was highly upregulated in A1CF-overexpressed MCF7 cells, but this upregulation can be inhibited by mutating conserved binding motifs of Dickkopf1 3' untranslated region. A1CF played a crucial role in cell migration and survival through affecting 3' untranslated region of Dickkopf1 to upregulate its expression in MCF7 cells.
Title: Apobec-1 complementation factor regulates cell migration and apoptosis through Dickkopf1 by acting on its 3' untranslated region in MCF7 cells.
AICDA/APOBEC family of cytidine deaminases is significant in innate immunity, as it restricts numerous viruses, including HBV, through hypermutationdependent and independent mechanisms. (Review)
Title: Associations between activation-induced cytidine deaminase/apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like cytidine deaminase expression, hepatitis B virus (HBV) replication and HBV-associated liver disease (Review).
Results show that expression of APOBEC1 induces a mutator phenotype in 2 different cellular models.
Title: The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas.
An APOBEC-mediated mutational signature in 47% of 192 tumors suggests that APOBEC-catalyzed deamination provides a source of DNA damage in esophageal squamous cell carcinoma.
Title: Genomic analyses reveal mutational signatures and frequently altered genes in esophageal squamous cell carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (26)

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

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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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat downregulates APOBEC1 in HEK 293T cells	PubMed
nucleocapsid	gag	Human APOBEC1 is encapsidated into HIV-1 virions via its interaction with NC, but exhibits no inhibition of the infectivity of both wild-type and DeltaVif HIV-1	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	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	IC Inferred by Curator more info	PubMed
enables cytidine deaminase activity	TAS Traceable Author Statement more info
enables mRNA 3'-UTR AU-rich region binding	IEA Inferred from Electronic Annotation more info
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 chromosomal 5-methylcytosine DNA demethylation pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in cytidine to uridine editing	IBA Inferred from Biological aspect of Ancestor more info
involved_in cytidine to uridine editing	IDA Inferred from Direct Assay more info	PubMed
involved_in cytidine to uridine editing	TAS Traceable Author Statement more info
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
involved_in lipid metabolic process	TAS Traceable Author Statement more info	PubMed
involved_in lipoprotein biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in lipoprotein transport	IEA Inferred from Electronic Annotation more info
involved_in mRNA modification	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA stabilization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of triglyceride metabolic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression via chromosomal CpG island demethylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in response to gamma radiation	IEA Inferred from Electronic Annotation more info
involved_in triglyceride metabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of apolipoprotein B mRNA editing enzyme complex	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of mRNA editing complex	NAS Non-traceable Author Statement more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IC Inferred by Curator more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: C->U-editing enzyme APOBEC-1

Names: apolipoprotein B mRNA editing enzyme complex-1; apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1; apolipoprotein B mRNA-editing enzyme 1; mRNA(cytosine(6666)) deaminase 1

NP_001291495.1

EC 3.5.4.36

NP_001635.2

EC 3.5.4.36

NP_005880.2

EC 3.5.4.36

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_001304566.1 → NP_001291495.1 C->U-editing enzyme APOBEC-1 isoform a

See identical proteins and their annotated locations for NP_001291495.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AC006927, AI380263, L26234, U72891

Consensus CDS

CCDS8579.1

UniProtKB/Swiss-Prot

P41238, Q9UE64, Q9UM71

UniProtKB/TrEMBL

Q4VB33

Conserved Domains (2) summary

cd01283
Location:33 → 105

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:125 → 177

APOBEC_C; APOBEC-like C-terminal domain
NM_001644.5 → NP_001635.2 C->U-editing enzyme APOBEC-1 isoform a

See identical proteins and their annotated locations for NP_001635.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AC006927, AI380263, BC144708, U72891

Consensus CDS

CCDS8579.1

UniProtKB/Swiss-Prot

P41238, Q9UE64, Q9UM71

UniProtKB/TrEMBL

Q4VB33

Related

ENSP00000229304.4, ENST00000229304.5

Conserved Domains (2) summary

cd01283
Location:33 → 105

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:125 → 177

APOBEC_C; APOBEC-like C-terminal domain
NM_005889.4 → NP_005880.2 C->U-editing enzyme APOBEC-1 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate internal exon compared to variant 1, which causes translation initiation at a downstream AUG. The resulting isoform (b) is shorter at the N-terminus compared to isoform a.

Source sequence(s)

AC006927, AI380263, BC144708, U72891

UniProtKB/Swiss-Prot

P41238

Conserved Domains (2) summary

cd01283
Location:12 → 60

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:80 → 132

APOBEC_C; APOBEC-like C-terminal domain