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 differen... See more...

Aliases for APOBEC1 Gene

Aliases for APOBEC1 Gene

  • Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 1 2 3 5
  • HEPR 2 3 4
  • Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide 1 2 3
  • Apolipoprotein B MRNA-Editing Enzyme 1 3 4
  • MRNA(Cytosine(6666)) Deaminase 1 3 4
  • C->U-Editing Enzyme APOBEC-1 3 4
  • APOBEC-1 2 3
  • CDAR1 2 3
  • BEDP 2 3
  • Apolipoprotein B MRNA Editing Enzyme Complex-1 3
  • EC 3.5.4.36 4
  • EC 3.5.4 51
  • APOBEC1 5

External Ids for APOBEC1 Gene

Previous GeneCards Identifiers for APOBEC1 Gene

  • GC12M007674
  • GC12M007970
  • GC12M007693
  • GC12M007801
  • GC12M007615

Summaries for APOBEC1 Gene

Entrez Gene Summary for APOBEC1 Gene

  • 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]

GeneCards Summary for APOBEC1 Gene

APOBEC1 (Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 1) is a Protein Coding gene. Diseases associated with APOBEC1 include Immunodeficiency With Hyper-Igm, Type 2 and Neurofibromatosis. Among its related pathways are Gene Expression and mRNA Editing- C to U Conversion. Gene Ontology (GO) annotations related to this gene include RNA binding and hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines. An important paralog of this gene is APOBEC3D.

UniProtKB/Swiss-Prot Summary for APOBEC1 Gene

  • Catalytic component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in the APOB mRNA. Also involved in CGA (Arg) to UGA (Stop) editing in the NF1 mRNA. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation.

Gene Wiki entry for APOBEC1 Gene

Additional gene information for APOBEC1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for APOBEC1 Gene

Genomics for APOBEC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for APOBEC1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J007665 Promoter/Enhancer 1.1 EPDnew Ensembl ENCODE 600.7 +3.6 3559 3.6 CTCF IKZF1 ZSCAN4 RXRB MAFF MAFK SAP130 RAD21 SPI1 ZNF654 APOBEC1 piR-57460-108 CD163
GH12J007693 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 0.4 -24.4 -24448 2.6 NFIC SPI1 NFIB ZNF18 ZNF664 NANOG MAX SP1 POU5F1 GDF3 piR-39701-009 APOBEC1
GH12J007637 Promoter/Enhancer 1.3 FANTOM5 ENCODE CraniofacialAtlas 0.3 +31.0 30956 3.7 SP1 CTCF ZNF143 PKNOX1 REST RAD21 TRIM22 SCRT2 RUNX3 ZNF444 piR-31470-103 piR-33735-019 ENSG00000219410 ZNF384 SCARNA12 GDF3 LAG3 DPPA3 SLC2A14 NANOG
GH12J007678 Enhancer 0.8 ENCODE 0.4 -7.0 -6951 0.2 CTCF IKZF1 DDX20 PKNOX1 MTA1 REST RAD21 DPF2 HDAC1 SOX6 MN298114-036 piR-57461-039 APOBEC1 piR-39701-009 GDF3
GH12J007677 Enhancer 0.7 ENCODE 0.4 -6.7 -6679 0.3 CTCF RAD21 ZNF766 CBFB GABPA SMC3 FOSL1 ARNT MNT NR2F1 MN298114-036 piR-57461-039 APOBEC1 piR-39701-009 GDF3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around APOBEC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for APOBEC1

Top Transcription factor binding sites by QIAGEN in the APOBEC1 gene promoter:
  • AP-1
  • Bach2
  • E47
  • FOXD3
  • FOXO1
  • FOXO1a
  • FOXO4
  • PPAR-gamma1
  • PPAR-gamma2
  • TBP

Genomic Locations for APOBEC1 Gene

Genomic Locations for APOBEC1 Gene
chr12:7,649,400-7,670,599
(GRCh38/hg38)
Size:
21,200 bases
Orientation:
Minus strand
chr12:7,801,996-7,818,502
(GRCh37/hg19)
Size:
16,507 bases
Orientation:
Minus strand

Genomic View for APOBEC1 Gene

Genes around APOBEC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
APOBEC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for APOBEC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for APOBEC1 Gene

Proteins for APOBEC1 Gene

  • Protein details for APOBEC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P41238-ABEC1_HUMAN
    Recommended name:
    C->U-editing enzyme APOBEC-1
    Protein Accession:
    P41238
    Secondary Accessions:
    • Q9UE64
    • Q9UM71

    Protein attributes for APOBEC1 Gene

    Size:
    236 amino acids
    Molecular mass:
    28192 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Homodimer. Part of the apolipoprotein B mRNA editing complex with A1CF. Found in a complex with CELF2/CUGBP2 and A1CF. Interacts with HNRPAB and SYNCRIP.

neXtProt entry for APOBEC1 Gene

Selected DME Specific Peptides for APOBEC1 Gene

P41238:
  • SGVTIQIM
  • NRQGLRDL
  • CSITWFLSWSPCWECS

Post-translational modifications for APOBEC1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for APOBEC1 Gene

Domains & Families for APOBEC1 Gene

Gene Families for APOBEC1 Gene

Protein Domains for APOBEC1 Gene

InterPro:
Blocks:
  • Cytidine/deoxycytidylate deaminase, zinc-binding region
  • APOBEC-like, C-terminal
ProtoNet:

Suggested Antigen Peptide Sequences for APOBEC1 Gene

GenScript: Design optimal peptide antigens:
  • HEPR (ABEC1_HUMAN)
  • APOBEC1 protein (Q4VB33_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P41238

UniProtKB/Swiss-Prot:

ABEC1_HUMAN :
  • Belongs to the cytidine and deoxycytidylate deaminase family.
Family:
  • Belongs to the cytidine and deoxycytidylate deaminase family.
genes like me logo Genes that share domains with APOBEC1: view

Function for APOBEC1 Gene

Molecular function for APOBEC1 Gene

UniProtKB/Swiss-Prot Function:
Catalytic component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in the APOB mRNA. Also involved in CGA (Arg) to UGA (Stop) editing in the NF1 mRNA. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=cytidine(6666) in apoB mRNA + H(+) + H2O = NH4(+) + uridine(6666) in apoB mRNA; Xref=Rhea:RHEA:21772, Rhea:RHEA-COMP:13888, Rhea:RHEA-COMP:13889, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:28938, ChEBI:CHEBI:65315, ChEBI:CHEBI:82748; EC=3.5.4.36; Evidence={ECO:0000269|PubMed:11727199};.
GENATLAS Biochemistry:
apolipoprotein B,mRNA editing component 1 (catalytic subunit),expressed in the small intestine and liver

Enzyme Numbers (IUBMB) for APOBEC1 Gene

Phenotypes From GWAS Catalog for APOBEC1 Gene

Gene Ontology (GO) - Molecular Function for APOBEC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding TAS,IBA 21873635
GO:0003729 mRNA binding IEA --
GO:0003824 catalytic activity IEA --
GO:0004126 cytidine deaminase activity TAS --
GO:0004131 cytosine deaminase activity IEA --
genes like me logo Genes that share ontologies with APOBEC1: view
genes like me logo Genes that share phenotypes with APOBEC1: view

Animal Models for APOBEC1 Gene

MGI Knock Outs for APOBEC1:

Animal Model Products

  • Taconic Biosciences Mouse Models for APOBEC1

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for APOBEC1

No data available for Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for APOBEC1 Gene

Localization for APOBEC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for APOBEC1 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for APOBEC1 gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for APOBEC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IBA 21873635
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IBA,IDA 22580899
genes like me logo Genes that share ontologies with APOBEC1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for APOBEC1 Gene

Pathways & Interactions for APOBEC1 Gene

PathCards logo

SuperPathways for APOBEC1 Gene

genes like me logo Genes that share pathways with APOBEC1: view

Pathways by source for APOBEC1 Gene

Gene Ontology (GO) - Biological Process for APOBEC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006396 RNA processing TAS 7736571
GO:0006397 mRNA processing IEA --
GO:0006629 lipid metabolic process TAS 8078915
GO:0006641 triglyceride metabolic process IEA --
GO:0006970 response to osmotic stress IEA --
genes like me logo Genes that share ontologies with APOBEC1: view

No data available for SIGNOR curated interactions for APOBEC1 Gene

Drugs & Compounds for APOBEC1 Gene

(6) Drugs for APOBEC1 Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Zinc chloride Approved, Investigational Pharma Target, cofactor, chelator 0
Zinc sulfate, unspecified form Approved, Experimental Pharma Target, cofactor, chelator 0

(2) Additional Compounds for APOBEC1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with APOBEC1: view

Transcripts for APOBEC1 Gene

mRNA/cDNA for APOBEC1 Gene

3 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for APOBEC1

Alternative Splicing Database (ASD) splice patterns (SP) for APOBEC1 Gene

No ASD Table

Relevant External Links for APOBEC1 Gene

GeneLoc Exon Structure for
APOBEC1

Expression for APOBEC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for APOBEC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for APOBEC1 Gene

This gene is overexpressed in Small Intestine - Terminal Ileum (x43.6) and Colon - Transverse (x7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for APOBEC1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for APOBEC1

SOURCE GeneReport for Unigene cluster for APOBEC1 Gene:

Hs.560

mRNA Expression by UniProt/SwissProt for APOBEC1 Gene:

P41238-ABEC1_HUMAN
Tissue specificity: Expressed exclusively in the small intestine.

Evidence on tissue expression from TISSUES for APOBEC1 Gene

  • Intestine(4.8)
  • Blood(4.4)
  • Liver(2.1)
genes like me logo Genes that share expression patterns with APOBEC1: view

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for APOBEC1 Gene

Orthologs for APOBEC1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for APOBEC1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia APOBEC1 30 31
  • 99.29 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia APOBEC1 30 31
  • 83.05 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia APOBEC1 30 31
  • 80.23 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Apobec1 30 17 31
  • 77.34 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Apobec1 30
  • 76.61 (n)
Oppossum
(Monodelphis domestica)
Mammalia APOBEC1 31
  • 67 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia APOBEC1 31
  • 44 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia APOBEC1 31
  • 39 (a)
OneToOne
Species where no ortholog for APOBEC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for APOBEC1 Gene

ENSEMBL:
Gene Tree for APOBEC1 (if available)
TreeFam:
Gene Tree for APOBEC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for APOBEC1: view image

Paralogs for APOBEC1 Gene

(3) SIMAP similar genes for APOBEC1 Gene using alignment to 2 proteins:

  • ABEC1_HUMAN
  • Q4VB33_HUMAN
genes like me logo Genes that share paralogs with APOBEC1: view

Variants for APOBEC1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for APOBEC1 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs12820011 - p.Arg236Lys
rs2302515 - p.Met80Ile

Additional dbSNP identifiers (rs#s) for APOBEC1 Gene

Structural Variations from Database of Genomic Variants (DGV) for APOBEC1 Gene

Variant ID Type Subtype PubMed ID
dgv1350n100 CNV loss 25217958
dgv178n27 CNV loss 19166990
dgv263n67 CNV gain 20364138
dgv5e196 CNV duplication 17116639
esv3580096 CNV loss 25503493
nsv1036408 CNV loss 25217958
nsv521149 CNV loss 19592680
nsv521241 CNV loss 19592680
nsv557272 CNV loss 21841781
nsv557273 CNV loss 21841781
nsv826213 CNV gain 20364138
nsv826216 CNV gain 20364138

Variation tolerance for APOBEC1 Gene

Residual Variation Intolerance Score: 85.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.93; 35.95% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for APOBEC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
APOBEC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for APOBEC1 Gene

Disorders for APOBEC1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for APOBEC1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
immunodeficiency with hyper-igm, type 2
  • higm2
neurofibromatosis
  • central neurofibromatosis
immunodeficiency with hyper-igm, type 1
  • higm1
immune deficiency disease
  • primary immunodeficiency disease
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for APOBEC1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with APOBEC1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for APOBEC1 Gene

Publications for APOBEC1 Gene

  1. Investigation of the Lith6 candidate genes APOBEC1 and PPARG in human gallstone disease. (PMID: 17696929) Schafmayer C … Tepel J (Liver international : official journal of the International Association for the Study of the Liver 2007) 3 23 41
  2. C-->U editing of neurofibromatosis 1 mRNA occurs in tumors that express both the type II transcript and apobec-1, the catalytic subunit of the apolipoprotein B mRNA-editing enzyme. (PMID: 11727199) Mukhopadhyay D … Davidson NO (American journal of human genetics 2002) 3 4 23
  3. Human apolipoprotein B RNA editing deaminase gene (APOBEC1). (PMID: 9479499) Fujino T … Scott J (Genomics 1998) 3 4 23
  4. Molecular cloning of a human small intestinal apolipoprotein B mRNA editing protein. (PMID: 8208612) Hadjiagapiou C … Davidson NO (Nucleic acids research 1994) 3 4 23
  5. Proprotein convertase subtilisin/kexin type 9 interacts with apolipoprotein B and prevents its intracellular degradation, irrespective of the low-density lipoprotein receptor. (PMID: 22580899) Sun H … Teng BB (Arteriosclerosis, thrombosis, and vascular biology 2012) 3 4

Products for APOBEC1 Gene

Sources for APOBEC1 Gene