Apobec1 apolipoprotein B mRNA editing enzyme catalytic subunit 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Apobec1provided by RGD
Official Full Name: apolipoprotein B mRNA editing enzyme catalytic subunit 1provided by RGD
Primary source: RGD:2133
See related: Ensembl:ENSRNOG00000015411 AllianceGenome:RGD:2133
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: REPR; apobec-1
Summary: Enables several functions, including enzyme activator activity; hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines; and ribonucleoprotein complex binding activity. Involved in several processes, including cellular response to insulin stimulus; nucleic acid metabolic process; and positive regulation of mRNA modification. Located in cytoplasm and nucleus. Used to study familial hyperlipidemia and liver benign neoplasm. Biomarker of colon cancer and obesity. Orthologous to human APOBEC1 (apolipoprotein B mRNA editing enzyme catalytic subunit 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 59.5), Liver (RPKM 27.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q42

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (157472879..157500496, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (155800030..155828515, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (155386367..155414034, complement)

Chromosome 4 - NC_086022.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

To overcome this limitation, we developed a CRISPR-Cpf1-based BE by fusing the rat cytosine deaminase APOBEC1 to a catalytically inactive version of Lachnospiraceae bacterium Cpf1.
Title: Base editing with a Cpf1-cytidine deaminase fusion.
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.
Apobec-1 increased COX-2 expression and COX-2 mRNA stabilization in neurogenic cells, and failed to catalyze C-to-U editing of COX-2 mRNA
Title: Apobec-1 increases cyclooxygenase-2 and aggravates injury in oxygen-deprived neurogenic cells and middle cerebral artery occlusion rats.
It was found that rat APOBEC-1 overexpression had a hypermutation pattern similar to that of APOBEC-3s on its substrate apolipoprotein B mRNA.
Title: Hypermutation of ApoB mRNA by rat APOBEC-1 overexpression mimics APOBEC-3 hypermutation.
Taken together, these results demonstrate a model in which APOBEC1 induction during encephalitis in neurons may aid in thwarting HSV-1 infection.
Title: APOBEC1-mediated editing and attenuation of herpes simplex virus 1 DNA indicate that neurons have an antiviral role during herpes simplex encephalitis.
Editing by APOBEC-1 was studied in yeast using Gal4 linked to Gal80 via an apo B cassette (Gal4-C) or via a mouse Ig heavy chain gene variable region (Gal4-VH). APOBEC-1 induced C to U editing in ~15% of the Gal4-C transcripts, but did not affect Gal4-VH.
Title: The cytidine deaminases AID and APOBEC-1 exhibit distinct functional properties in a novel yeast selectable system.
observations allow speculation (i) that APOBEC-mediated C-to-U editing may contribute to the sequence variation of viruses that replicate entirely through RNA, and (ii) that additional cellular RNA substrates might exist for the APOBEC enzymes
Title: APOBEC-mediated editing of viral RNA.
may have roles in epigenetic reprogramming and cell plasticity
Title: Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming.

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	NAS Non-traceable Author Statement more info	PubMed
enables cytidine deaminase activity	IBA Inferred from Biological aspect of Ancestor more info
enables cytidine deaminase activity	IDA Inferred from Direct Assay more info	PubMed
enables cytidine deaminase activity	NAS Non-traceable Author Statement more info	PubMed
enables cytosine deaminase activity	IDA Inferred from Direct Assay more info	PubMed
enables enzyme activator activity	IDA Inferred from Direct Assay more info	PubMed
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables mRNA 3'-UTR AU-rich region binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribonucleoprotein complex 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	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA demethylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to insulin stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cytidine deamination	IEA Inferred from Electronic Annotation more info
involved_in cytidine metabolic process	IC Inferred by Curator 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	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cytidine to uridine editing	ISO Inferred from Sequence Orthology more info
involved_in cytidine to uridine editing	ISO Inferred from Sequence Orthology more info
involved_in defense response to virus	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within establishment of localization in cell	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lipoprotein biosynthetic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lipoprotein metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lipoprotein transport	ISO Inferred from Sequence Orthology more info
involved_in mRNA modification	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA modification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mRNA modification	ISO Inferred from Sequence Orthology more info
involved_in mRNA modification	ISO Inferred from Sequence Orthology more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mRNA stabilization	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation more info
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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression via chromosomal CpG island demethylation	ISO Inferred from Sequence Orthology 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 positive regulation of mRNA modification	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in response to calcium ion	IDA Inferred from Direct Assay more info	PubMed
involved_in response to ethanol	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to gamma radiation	ISO Inferred from Sequence Orthology more info
involved_in response to xenobiotic stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in response to zinc ion	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within triglyceride metabolic process	ISO Inferred from Sequence Orthology more info

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

General protein information

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

Names: Apolipoprotein B editing protein; apo B messenger RNA-editing protein; apolipoprotein B editing complex 1; apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1; apolipoprotein B mRNA-editing enzyme 1; mRNA(cytosine(6666)) deaminase 1

NP_037039.1

EC 3.5.4.36

XP_006237352.1

EC 3.5.4.36

XP_006237355.1

EC 3.5.4.36

XP_017447972.1

EC 3.5.4.36

XP_017447973.1

EC 3.5.4.36

XP_038963037.1

EC 3.5.4.36

XP_038963038.1

EC 3.5.4.36

XP_038963041.1

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_012907.2 → NP_037039.1 C->U-editing enzyme APOBEC-1

See identical proteins and their annotated locations for NP_037039.1

Status: PROVISIONAL

Source sequence(s)

BC085335

UniProtKB/Swiss-Prot

P38483

UniProtKB/TrEMBL

A0A8L2QAE9, A6ILF2

Related

ENSRNOP00000078194.1, ENSRNOT00000106242.1

Conserved Domains (1) summary

pfam18778
Location:17 → 186

NAD1; Novel AID APOBEC clade 1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

157472879..157500496 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039107113.2 → XP_038963041.1 C->U-editing enzyme APOBEC-1 isoform X2

UniProtKB/Swiss-Prot

P38483

UniProtKB/TrEMBL

A0A8L2QAE9, A6ILF2

Conserved Domains (1) summary

pfam18778
Location:17 → 186

NAD1; Novel AID APOBEC clade 1
XM_006237293.4 → XP_006237355.1 C->U-editing enzyme APOBEC-1 isoform X2

See identical proteins and their annotated locations for XP_006237355.1

UniProtKB/Swiss-Prot

P38483

UniProtKB/TrEMBL

A0A8L2QAE9, A6ILF2

Conserved Domains (1) summary

pfam18778
Location:17 → 186

NAD1; Novel AID APOBEC clade 1
XM_039107110.2 → XP_038963038.1 C->U-editing enzyme APOBEC-1 isoform X1

UniProtKB/TrEMBL

A0A8I5Y2I8, A0A8I6B1D0

Conserved Domains (1) summary

pfam18778
Location:87 → 256

NAD1; Novel AID APOBEC clade 1
XM_017592483.3 → XP_017447972.1 C->U-editing enzyme APOBEC-1 isoform X1

UniProtKB/TrEMBL

A0A8I5Y2I8, A0A8I6B1D0

Related

ENSRNOP00000094681.1

Conserved Domains (1) summary

pfam18778
Location:87 → 256

NAD1; Novel AID APOBEC clade 1
XM_006237290.4 → XP_006237352.1 C->U-editing enzyme APOBEC-1 isoform X2

See identical proteins and their annotated locations for XP_006237352.1

UniProtKB/Swiss-Prot

P38483

UniProtKB/TrEMBL

A0A8L2QAE9, A6ILF2

Conserved Domains (1) summary

pfam18778
Location:17 → 186

NAD1; Novel AID APOBEC clade 1
XM_017592484.3 → XP_017447973.1 C->U-editing enzyme APOBEC-1 isoform X2

UniProtKB/Swiss-Prot

P38483

UniProtKB/TrEMBL

A0A8L2QAE9, A6ILF2

Related

ENSRNOP00000077863.1

Conserved Domains (1) summary

pfam18778
Location:17 → 186

NAD1; Novel AID APOBEC clade 1
XM_039107109.2 → XP_038963037.1 C->U-editing enzyme APOBEC-1 isoform X1

UniProtKB/TrEMBL

A0A8I5Y2I8, A0A8I6B1D0

Conserved Domains (1) summary

pfam18778
Location:87 → 256

NAD1; Novel AID APOBEC clade 1