Apobec1 apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Apobec1provided by MGI
Official Full Name: apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1provided by MGI
Primary source: MGI:MGI:103298
See related: Ensembl:ENSMUSG00000040613 AllianceGenome:MGI:103298
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Cdar1; APOBEC-1
Summary: Enables mRNA 3'-UTR AU-rich region binding activity. Involved in DNA demethylation and negative regulation of DNA methylation-dependent heterochromatin assembly. Acts upstream of or within several processes, including RNA modification; lipoprotein transport; and mRNA stabilization. Predicted to be active in cytoplasm and nucleus. Is expressed in early conceptus and genitourinary system. Orthologous to human APOBEC1 (apolipoprotein B mRNA editing enzyme catalytic subunit 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in mammary gland adult (RPKM 5.7), spleen adult (RPKM 5.4) and 25 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 F1; 6 57.68 cM

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (122554751..122579995, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (122577792..122603024, complement)

Chromosome 6 - NC_000072.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

At an experimental level mouse APOBEC1 is remarkable among 12 mammalian A1 enzymes in that it represents a source of somatic mutations in mouse genome, potentially fueling oncogenesis.
Title: Mouse APOBEC1 cytidine deaminase can induce somatic mutations in chromosomal DNA.
APOBEC1-mediated RNA editing occurs within brain microglia cells and is key to maintaining their resting status. Apobec1-/- mice display age-related signs of CNS neurodegeneration.
Title: Loss of APOBEC1 RNA-editing function in microglia exacerbates age-related CNS pathophysiology.
Here, we show that partial loss of either APOBEC1 complementation factor (A1CF), the RNA-binding cofactor of APOBEC1 in RNA editing, or Argonaute 2 (AGO2), a key factor in the biogenesis of certain noncoding RNAs, modulates risk for TGCTs and testicular abnormalities in both parent-of-origin and conventional genetic manners.
Title: Parent-of-origin effects of A1CF and AGO2 on testicular germ-cell tumors, testicular abnormalities, and fertilization bias.
substantial rearrangement/duplication of transgene elements is present, and transgene integration was accompanied by the deletion of a 19,500 bp fragment of genomic DNA that contains the promoter, exon 1 and part of intron 1 of the APOBEC1 complementation factor (A1cf) gene, as well as several elements that are predicted to regulate chromosomal architecture
Title: Chromosomal mapping of the αMHC-MerCreMer transgene in mice reveals a large genomic deletion.
The observations demonstrate that A1CF does not act as the APOBEC1 complementation factor in vivo under normal physiological conditions and suggest new roles for A1CF, specifically within the male adult kidney.
Title: APOBEC1 complementation factor (A1CF) is dispensable for C-to-U RNA editing in vivo.
Apobec-1-dependent C-to-U RNA editing exerts broad functional effects in a tissue-specific manner.
Title: Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver.
RBM47 and APOBEC1 constitute the basic machinery for C to U RNA editing.
Title: C to U RNA editing mediated by APOBEC1 requires RNA-binding protein RBM47.
In contrast to in vitro results, APOBEC1 neither inhibited nor significantly drove the molecular evolution of Friend retrovirus in wild type or APOBEC1 knockout mice.
Title: Reassessment of murine APOBEC1 as a retrovirus restriction factor in vivo.
Individual genetic variability at the Apobec1 locus results in differential rates of C-to-U(T) editing in murine macrophages; with mouse strains expressing mostly a truncated alternative transcript isoform of Apobec1 exhibiting lower rates of editing.
Title: The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages.
The transgenic rescue of intestinal apobec-1 expression restores C-to-U RNA editing of apoB mRNA in vivo, including the canonical site at position 6666 and also at approximately 20 other newly identified downstream sites present in WT mice.
Title: Intestine-specific expression of Apobec-1 rescues apolipoprotein B RNA editing and alters chylomicron production in Apobec1 -/- mice.

Submit: New GeneRIF Correction See all GeneRIFs (21)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (2)
Targeted (4) 1 citation
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

UniSTS:224890 (e-PCR)
- UniSTS:224890

Apobec1 (e-PCR), detects polymorphism
- UniSTS:496783

RH127292 (e-PCR)
- UniSTS:209818

Homology

Orthologs from Annotation Pipeline: 212 organisms have orthologs with human gene Apobec1
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables catalytic activity	IEA Inferred from Electronic Annotation more info
enables cytidine deaminase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables cytidine deaminase activity	ISO Inferred from Sequence Orthology more info
enables cytosine deaminase activity	ISO Inferred from Sequence Orthology more info
enables enzyme activator activity	ISO Inferred from Sequence Orthology more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables mRNA 3'-UTR AU-rich region binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables ribonucleoprotein complex binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA cytosine deamination	ISO Inferred from Sequence Orthology more info
involved_in DNA demethylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in DNA demethylation	IDA Inferred from Direct Assay more info	PubMed
involved_in cytidine to uridine editing	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in cytidine to uridine editing	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cytidine to uridine editing	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cytidine to uridine editing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cytidine to uridine editing	ISO Inferred from Sequence Orthology more info
involved_in defense response to virus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of localization in cell	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within lipoprotein biosynthetic process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within lipoprotein metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lipoprotein transport	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within mRNA modification	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within mRNA modification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA modification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mRNA stabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA methylation-dependent heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of triglyceride metabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of DNA demethylation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of mRNA modification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell population proliferation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in response to calcium ion	ISO Inferred from Sequence Orthology more info
involved_in response to ethanol	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to gamma radiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to osmotic stress	ISO Inferred from Sequence Orthology more info
involved_in response to xenobiotic stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within triglyceride metabolic process	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
part_of apolipoprotein B mRNA editing enzyme complex	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
part_of mRNA editing complex	NAS Non-traceable Author Statement more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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

Names: apolipoprotein B editing complex 1; mRNA(cytosine(6666)) deaminase 1

NP_001127863.1

EC 3.5.4.36

NP_112436.1

EC 3.5.4.36

XP_006505464.1

EC 3.5.4.36

XP_011239461.1

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_001134391.2 → NP_001127863.1 C->U-editing enzyme APOBEC-1 isoform a

See identical proteins and their annotated locations for NP_001127863.1

Status: VALIDATED

Source sequence(s)

AC158651

Consensus CDS

CCDS20498.1

UniProtKB/Swiss-Prot

P51908, Q99L67

UniProtKB/TrEMBL

Q3U9G8

Related

ENSMUSP00000108204.2, ENSMUST00000112585.8

Conserved Domains (1) summary

pfam18774
Location:26 → 159

APOBEC4_like; APOBEC4-like -AID/APOBEC-deaminase
NM_001409467.1 → NP_001396396.1 C->U-editing enzyme APOBEC-1 isoform a

Status: VALIDATED

Source sequence(s)

AC158651

UniProtKB/Swiss-Prot

Q99L67

UniProtKB/TrEMBL

Q3U9G8
NM_001409468.1 → NP_001396397.1 C->U-editing enzyme APOBEC-1 isoform a

Status: VALIDATED

Source sequence(s)

AC158651

UniProtKB/Swiss-Prot

Q99L67

UniProtKB/TrEMBL

Q3U9G8
NM_001409469.1 → NP_001396398.1 C->U-editing enzyme APOBEC-1 isoform a

Status: VALIDATED

Source sequence(s)

AC158651

UniProtKB/Swiss-Prot

Q99L67

UniProtKB/TrEMBL

Q3U9G8
NM_001409470.1 → NP_001396399.1 C->U-editing enzyme APOBEC-1 isoform a

Status: VALIDATED

Source sequence(s)

AC158651

UniProtKB/Swiss-Prot

Q99L67

UniProtKB/TrEMBL

Q3U9G8
NM_001409471.1 → NP_001396400.1 C->U-editing enzyme APOBEC-1 isoform b

Status: VALIDATED

Source sequence(s)

AC158651
NM_031159.4 → NP_112436.1 C->U-editing enzyme APOBEC-1 isoform a

See identical proteins and their annotated locations for NP_112436.1

Status: VALIDATED

Source sequence(s)

AC158651

Consensus CDS

CCDS20498.1

UniProtKB/Swiss-Prot

P51908, Q99L67

UniProtKB/TrEMBL

Q3U9G8

Related

ENSMUSP00000108205.2, ENSMUST00000112586.8

Conserved Domains (1) summary

pfam18774
Location:26 → 159

APOBEC4_like; APOBEC4-like -AID/APOBEC-deaminase

RNA

NR_176849.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC158651
NR_176850.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC158651

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000072.7 Reference GRCm39 C57BL/6J

Range

122554751..122579995 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011241159.4 → XP_011239461.1 C->U-editing enzyme APOBEC-1 isoform X1

UniProtKB/Swiss-Prot

P51908

UniProtKB/TrEMBL

Q3U9G8

Conserved Domains (1) summary

pfam18774
Location:26 → 159

APOBEC4_like; APOBEC4-like -AID/APOBEC-deaminase
XM_006505401.4 → XP_006505464.1 C->U-editing enzyme APOBEC-1 isoform X1

UniProtKB/Swiss-Prot

P51908

UniProtKB/TrEMBL

Q3U9G8

Conserved Domains (1) summary

pfam18774
Location:26 → 159

APOBEC4_like; APOBEC4-like -AID/APOBEC-deaminase