Apobec3 apolipoprotein B mRNA editing enzyme catalytic subunit 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Apobec3provided by RGD
Official Full Name: apolipoprotein B mRNA editing enzyme catalytic subunit 3provided by RGD
Primary source: RGD:1307800
See related: Ensembl:ENSRNOG00000016852 AllianceGenome:RGD:1307800
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Apobec3b; Apobec3f
Summary: Predicted to enable RNA binding activity; cytidine deaminase activity; and deoxycytidine deaminase activity. Predicted to be involved in several processes, including negative regulation of single stranded viral RNA replication via double stranded DNA intermediate; negative regulation of transposition; and nucleic acid metabolic process. Predicted to act upstream of or within hematopoietic progenitor cell differentiation; regulation of defense response to virus; and regulation of viral life cycle. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in P-body and nucleus. Orthologous to several human genes including APOBEC3D (apolipoprotein B mRNA editing enzyme catalytic subunit 3D) and APOBEC3F (apolipoprotein B mRNA editing enzyme catalytic subunit 3F). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 41.2), Thymus (RPKM 40.7) and 8 other tissues See more
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 7q34

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (113314196..113333306)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (111433789..111453032)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (121108108..121128346)

Chromosome 7 - NC_086025.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.

Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Gene Ontology Provided by RGD

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	ISO Inferred from Sequence Orthology more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
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 cytosine deamination	ISO Inferred from Sequence Orthology more info
involved_in DNA demethylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in clearance of foreign intracellular DNA	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within hematopoietic progenitor cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in negative regulation by host of viral genome replication	ISO Inferred from Sequence Orthology 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 negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of viral genome replication	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of defense response to virus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of viral life cycle	ISO Inferred from Sequence Orthology more info
involved_in retrotransposon silencing	ISO Inferred from Sequence Orthology more info
involved_in retrotransposon silencing	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in P-body	IBA Inferred from Biological aspect of Ancestor more info
located_in P-body	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
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

Go to the top of the page Help

Preferred Names: DNA dC->dU-editing enzyme APOBEC3

Names: apolipoprotein B editing complex 3; apolipoprotein B mRNA editing enzyme catalytic subunit 3B; apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B; apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F; probable DNA dC->dU-editing enzyme APOBEC3

NP_001028875.1

EC 3.5.4.38

XP_008763937.1

EC 3.5.4.38

XP_063119684.1

EC 3.5.4.38

XP_063119685.1

EC 3.5.4.38

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001033703.2 → NP_001028875.1 DNA dC->dU-editing enzyme APOBEC3

See identical proteins and their annotated locations for NP_001028875.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000007

UniProtKB/TrEMBL

F7EWS7, Q3T1K0

Related

ENSRNOP00000034183.5, ENSRNOT00000037134.6

Conserved Domains (3) summary

cd01283
Location:226 → 332

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:141 → 186

APOBEC_C; APOBEC-like C-terminal domain

pfam08210
Location:29 → 199

APOBEC_N; APOBEC-like N-terminal domain

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_086025.1 Reference GRCr8

Range

113314196..113333306

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063263614.1 → XP_063119684.1 DNA dC->dU-editing enzyme APOBEC3 isoform X1
XM_063263615.1 → XP_063119685.1 DNA dC->dU-editing enzyme APOBEC3 isoform X2
XM_008765715.4 → XP_008763937.1 DNA dC->dU-editing enzyme APOBEC3 isoform X3

UniProtKB/TrEMBL

F7EWS7

Conserved Domains (3) summary

cd01283
Location:203 → 309

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:118 → 163

APOBEC_C; APOBEC-like C-terminal domain

pfam08210
Location:11 → 176

APOBEC_N; APOBEC-like N-terminal domain