Apobec3 apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Apobec3provided by MGI
Official Full Name: apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3provided by MGI
Primary source: MGI:MGI:1933111
See related: Ensembl:ENSMUSG00000009585 AllianceGenome:MGI:1933111
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: Arp3; Rfv3; Cem15; Apobec; Gm20117
Summary: Predicted to enable several functions, including hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines; identical protein binding activity; and zinc ion binding activity. Involved in negative regulation of transposition and negative regulation of viral genome replication. Acts upstream of or within hematopoietic progenitor cell differentiation; regulation of defense response to virus; and regulation of viral life cycle. Located in cytoplasm. Is expressed in several structures, including alimentary system; brain; genitourinary system; heart; and sensory organ. Orthologous to several human genes including APOBEC3F (apolipoprotein B mRNA editing enzyme catalytic subunit 3F). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in spleen adult (RPKM 21.8), mammary gland adult (RPKM 13.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 15 E1; 15 37.85 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	15	NC_000081.7 (79774620..79802419)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	15	NC_000081.6 (79892058..79918218)

Chromosome 15 - NC_000081.7 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?

Direct inhibition of human APOBEC3 deaminases by HIV-1 Vif independent of the proteolysis pathway.
Title: Direct inhibition of human APOBEC3 deaminases by HIV-1 Vif independent of the proteolysis pathway.
The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance.
Title: The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance.
Distinctive High Expression of Antiretroviral APOBEC3 Protein in Mouse Germinal Center B Cells.
Title: Distinctive High Expression of Antiretroviral APOBEC3 Protein in Mouse Germinal Center B Cells.
Multifaceted HIV-1 Vif interactions with human E3 ubiquitin ligase and APOBEC3s.
Title: Multifaceted HIV-1 Vif interactions with human E3 ubiquitin ligase and APOBEC3s.
Molecular analysis of gamma1, gamma3, and alpha class switch recombination junctions in APOBEC3-deficient mice using high-throughput sequencing.
Title: Molecular analysis of γ1, γ3, and α class switch recombination junctions in APOBEC3-deficient mice using high-throughput sequencing.
Structural perspectives on HIV-1 Vif and APOBEC3 restriction factor interactions.
Title: Structural perspectives on HIV-1 Vif and APOBEC3 restriction factor interactions.
Murine Leukemia Virus P50 Protein Counteracts APOBEC3 by Blocking Its Packaging.
Title: Murine Leukemia Virus P50 Protein Counteracts APOBEC3 by Blocking Its Packaging.
APOBEC3 regulates keratinocyte differentiation and expression of Notch3.
Title: APOBEC3 regulates keratinocyte differentiation and expression of Notch3.
Impact of Suboptimal APOBEC3G Neutralization on the Emergence of HIV Drug Resistance in Humanized Mice.
Title: Impact of Suboptimal APOBEC3G Neutralization on the Emergence of HIV Drug Resistance in Humanized Mice.
we report the first parallel, comparative analysis of site selection of APOBEC3 deamination using six of the seven purified APOBEC3 proteins (i.e. A3A, A3B, A3C, A3F, A3G and A3H haplotype II) and oligonucleotides having 5'TC3' or 5'CT3' dinucleotide target sites and variable flanking bases within diverse DNA secondary structures.
Title: Deamination hotspots among APOBEC3 family members are defined by both target site sequence context and ssDNA secondary structure.

Submit: New GeneRIF Correction See all GeneRIFs (57)

Variation

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Alleles

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

Spontaneous (1) 1 citation
Gene trapped (1) 1 citation
Targeted (1) 1 citation
Not Applicable (1) 1 citation
Endonuclease-mediated (6)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Apobec3 (e-PCR), detects polymorphism
- UniSTS:506735

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables catalytic activity	IEA Inferred from Electronic Annotation 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 deoxycytidine deaminase activity	IBA Inferred from Biological aspect of Ancestor more info
enables deoxycytidine deaminase activity	ISO Inferred from Sequence Orthology more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables identical protein 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 zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA cytosine deamination	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA demethylation	IBA Inferred from Biological aspect of Ancestor 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
acts_upstream_of_or_within hematopoietic progenitor cell differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within immune system process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within innate immune response	IEA Inferred from Electronic Annotation 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 viral genome replication	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of defense response to virus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of viral life cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrotransposon silencing	IDA Inferred from Direct Assay more info	PubMed

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	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	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
part_of ribonucleoprotein complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA dC->dU-editing enzyme APOBEC-3

Names: apolipoprotein B editing complex 3; apolipoprotein B mRNA-editing complex 3; recovery from Friend virus 3

NP_001153887.1

EC 3.5.4.38

NP_001333970.1

EC 3.5.4.38

NP_084531.2

EC 3.5.4.38

XP_006521616.1

EC 3.5.4.38

XP_017172295.1

EC 3.5.4.38

XP_017172297.1

EC 3.5.4.38

XP_036015533.1

EC 3.5.4.38

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_001160415.1 → NP_001153887.1 DNA dC->dU-editing enzyme APOBEC-3 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AC113595

Consensus CDS

CCDS49669.1

UniProtKB/Swiss-Prot

H3BJL0, Q8C7L0, Q8C8V7, Q99J72

UniProtKB/TrEMBL

E9QMH1

Related

ENSMUSP00000105249.4, ENSMUST00000109620.10

Conserved Domains (3) summary

cd01283
Location:35 → 141

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:137 → 182

APOBEC_C; APOBEC-like C-terminal domain

pfam08210
Location:26 → 195

APOBEC_N; APOBEC-like N-terminal domain
NM_001347041.1 → NP_001333970.1 DNA dC->dU-editing enzyme APOBEC-3 isoform 3

Status: VALIDATED

Source sequence(s)

AC113595

Consensus CDS

CCDS84179.1

UniProtKB/TrEMBL

Q3TI69

Related

ENSMUSP00000023054.8, ENSMUST00000023054.14

Conserved Domains (2) summary

pfam18772
Location:1 → 99

APOBEC2

pfam18782
Location:102 → 264

NAD2; Novel AID APOBEC clade 2
NM_030255.3 → NP_084531.2 DNA dC->dU-editing enzyme APOBEC-3 isoform 2

See identical proteins and their annotated locations for NP_084531.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region, compared to variant 1. The encoded isoform (2)is shorter than isoform 1.

Source sequence(s)

AA288216, AK049256, AK153719, BY228556

Consensus CDS

CCDS27654.1

UniProtKB/TrEMBL

B5T0I9, Q3U5C5

Related

ENSMUSP00000132391.2, ENSMUST00000165537.8

Conserved Domains (3) summary

cd01283
Location:35 → 141

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:137 → 182

APOBEC_C; APOBEC-like C-terminal domain

pfam08210
Location:26 → 195

APOBEC_N; APOBEC-like N-terminal domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000081.7 Reference GRCm39 C57BL/6J

Range

79774620..79802419

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036159640.1 → XP_036015533.1 DNA dC->dU-editing enzyme APOBEC-3 isoform X2

UniProtKB/TrEMBL

Q3TI69

Conserved Domains (2) summary

pfam18772
Location:1 → 99

APOBEC2

pfam18782
Location:102 → 264

NAD2; Novel AID APOBEC clade 2
XM_017316808.3 → XP_017172297.1 DNA dC->dU-editing enzyme APOBEC-3 isoform X2

UniProtKB/TrEMBL

Q3TI69

Conserved Domains (2) summary

pfam18772
Location:1 → 99

APOBEC2

pfam18782
Location:102 → 264

NAD2; Novel AID APOBEC clade 2
XM_017316806.3 → XP_017172295.1 DNA dC->dU-editing enzyme APOBEC-3 isoform X1

UniProtKB/TrEMBL

B5T0I9

Related

ENSMUSP00000135079.2, ENSMUST00000177098.8

Conserved Domains (2) summary

pfam18772
Location:32 → 209

APOBEC2

pfam18782
Location:212 → 374

NAD2; Novel AID APOBEC clade 2
XM_006521553.5 → XP_006521616.1 DNA dC->dU-editing enzyme APOBEC-3 isoform X3

Conserved Domains (1) summary

pfam18782
Location:54 → 216

NAD2; Novel AID APOBEC clade 2