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

Gene ID: 339, updated on 4-Nov-2018

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; Vega:OTTHUMG00000141288
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
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

Genomic context

See APOBEC1 in Genome Data Viewer
Location:
12p13.31
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (7649400..7670599, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (7801996..7823195, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene clathrin light chain A pseudogene Neighboring gene nucleolar protein interacting with the FHA domain of MKI67 pseudogene 3 Neighboring gene growth differentiation factor 3 Neighboring gene developmental pluripotency associated 3

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • 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 ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
AU-rich element binding IEA
Inferred from Electronic Annotation
more info
 
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 
cytidine deaminase activity TAS
Traceable Author Statement
more info
 
cytosine deaminase activity IEA
Inferred from Electronic Annotation
more info
 
enzyme activator activity IEA
Inferred from Electronic Annotation
more info
 
mRNA binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IEA
Inferred from Electronic Annotation
more info
 
ribonucleoprotein complex binding IEA
Inferred from Electronic Annotation
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
DNA cytosine deamination IEA
Inferred from Electronic Annotation
more info
 
DNA demethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA demethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA processing TAS
Traceable Author Statement
more info
PubMed 
cellular response to insulin stimulus IEA
Inferred from Electronic Annotation
more info
 
cytidine deamination IEA
Inferred from Electronic Annotation
more info
 
cytidine to uridine editing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytidine to uridine editing TAS
Traceable Author Statement
more info
 
defense response to virus IEA
Inferred from Electronic Annotation
more info
 
lipid metabolic process TAS
Traceable Author Statement
more info
PubMed 
lipoprotein biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
lipoprotein transport IEA
Inferred from Electronic Annotation
more info
 
mRNA modification IEA
Inferred from Electronic Annotation
more info
 
mRNA processing IEA
Inferred from Electronic Annotation
more info
 
mRNA stabilization IEA
Inferred from Electronic Annotation
more info
 
negative regulation of methylation-dependent chromatin silencing ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of triglyceride metabolic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of catalytic activity IEA
Inferred from Electronic Annotation
more info
 
positive regulation of mRNA modification IEA
Inferred from Electronic Annotation
more info
 
regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
response to calcium ion IEA
Inferred from Electronic Annotation
more info
 
response to ethanol IEA
Inferred from Electronic Annotation
more info
 
response to gamma radiation IEA
Inferred from Electronic Annotation
more info
 
response to osmotic stress IEA
Inferred from Electronic Annotation
more info
 
response to zinc ion IEA
Inferred from Electronic Annotation
more info
 
triglyceride metabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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
NP_001635.2
NP_005880.2

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_001304566.1NP_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
    Conserved Domains (2) summary
    cd01283
    Location:33105
    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:125177
    APOBEC_C; APOBEC-like C-terminal domain
  2. NM_001644.4NP_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)
    AI380263, BC144708, U72891
    Consensus CDS
    CCDS8579.1
    UniProtKB/Swiss-Prot
    P41238
    Related
    ENSP00000229304.4, OTTHUMP00000180598, ENST00000229304.4, OTTHUMT00000280523
    Conserved Domains (2) summary
    cd01283
    Location:33105
    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:125177
    APOBEC_C; APOBEC-like C-terminal domain
  3. NM_005889.3NP_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)
    AI380263, BC144708, U72891
    UniProtKB/Swiss-Prot
    P41238
    Conserved Domains (2) summary
    cd01283
    Location:1260
    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:80132
    APOBEC_C; APOBEC-like C-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_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    7649400..7670599 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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