Aliases for APOBEC1 Gene
Aliases for APOBEC1 Gene
External Ids for APOBEC1 Gene
- HGNC: 604
- Entrez Gene: 339
- Ensembl: ENSG00000111701
- OMIM: 600130
- UniProtKB: P41238
Previous GeneCards Identifiers for APOBEC1 Gene
- GC12M007674
- GC12M007970
- GC12M007693
- GC12M007801
- GC12M007615
Summaries 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 Neurofibromatosis and Hypercholesterolemia, Familial. Among its related pathways are mRNA Editing- C to U Conversion and Gene Expression. 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 AICDA.
UniProtKB/Swiss-Prot 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.
No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for APOBEC1 Gene
Genomics for APOBEC1 Gene
Regulatory Elements for APOBEC1 Gene
Enhancers for APOBEC1 Gene
| GeneHancer Identifier | Enhancer Score | Enhancer Sources | Gene-Enhancer Score | TSS distance (kb) | Number of Genes Away | Size (kb) | Transcription Factor Binding Sites within enhancer | Gene Targets for Enhancer |
|---|---|---|---|---|---|---|---|---|
| GH12G007665 | 0.7 | ENCODE | 0.7 | +3.6 | 3560 | 3.6 | ELF3 CTCF SAP130 ZSCAN4 RAD21 RARA ZNF121 GATA3 FOS MAFK | APOBEC1 GC12M007647 |
| GH12G007677 | 1.2 | Ensembl ENCODE | 0.4 | -6.9 | -6929 | 0.8 | HDAC1 PKNOX1 TBL1XR1 ARNT RAD21 TCF12 ZNF766 GATA2 ELK1 ZNF654 | APOBEC1 GDF3 |
| GH12G007674 | 0.5 | Ensembl ENCODE | 0.7 | -4.9 | -4939 | 1.4 | DPPA3 APOBEC1 GDF3 | |
| GH12G007693 | 0.9 | Ensembl ENCODE | 0.3 | -24.4 | -24448 | 2.6 | NFIB MAX EP300 ZNF664 NFIC GATA2 BCL11A SMC3 POU5F1 ZNF18 | GDF3 APOBEC1 |
- Elite enhancer and/or Elite enhancer-gene association
Download GeneHancer data dump
Enhancers around APOBEC1 on UCSC Golden Path with GeneCards custom track
- Transcription factor binding sites by QIAGEN in the APOBEC1 gene promoter:
Regulatory Element Products
Genomic Location for APOBEC1 Gene
- Chromosome:
- 12
- Start:
- 7,649,400 bp from pter
- End:
- 7,670,599 bp from pter
- Size:
- 21,200 bases
- Orientation:
- Minus strand
Genomic View for APOBEC1 Gene
Genes around APOBEC1 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 12p13.31 by Ensembl
- 12p13.31 by Entrez Gene
- 12p13.31 by HGNC
APOBEC1 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene 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
- 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.
Protein Expression for APOBEC1 Gene
Selected DME Specific Peptides for APOBEC1 Gene
- P41238:
-
- SGVTIQIM
- NRQGLRDL
- CSITWFLSWSPCWECS
Post-translational modifications for APOBEC1 Gene
Other Protein References for APOBEC1 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
- EMD Millipore Complete listing of Mono and Polychlonal Antibodies for APOBEC1
-
Custom Antibody ServicesOriGene Antibodies for APOBEC1
- Novus Biologicals Antibodies for APOBEC1
- Invitrogen Antibodies for APOBEC1
- antibodies-online Antibodies for APOBEC1: See all 55
- GeneTex APOBEC1 antibody for APOBEC1
Protein Products
-
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- antibodies-online Proteins for APOBEC1: See all 8
- Search antibodies-online for peptides
- Search GeneTex for Proteins for APOBEC1
Assay Products
Domains & Families for APOBEC1 Gene
Gene Families for APOBEC1 Gene
Protein Domains for APOBEC1 Gene
Suggested Antigen Peptide Sequences for APOBEC1 Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
P41238- Family:
-
- Belongs to the cytidine and deoxycytidylate deaminase family.
Function for APOBEC1 Gene
Molecular function for APOBEC1 Gene
- GENATLAS Biochemistry:
- apolipoprotein B,mRNA editing component 1 (catalytic subunit),expressed in the small intestine and liver
- UniProtKB/Swiss-Prot CatalyticActivity:
- Cytosine(6666) in apolipoprotein B mRNA + H(2)O = uracil(6666) in apolipoprotein B mRNA + NH(3).
- 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.
Enzyme Numbers (IUBMB) for APOBEC1 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0003723 | RNA binding | TAS | 7736571 |
| GO:0003729 | mRNA binding | IEA | -- |
| GO:0003824 | catalytic activity | IEA | -- |
| GO:0004126 | cytidine deaminase activity | TAS | -- |
| GO:0004131 | cytosine deaminase activity | IEA | -- |
Phenotypes for APOBEC1 Gene
- MGI mutant phenotypes for APOBEC1:
- inferred from 4 alleles
- GenomeRNAi human phenotypes for APOBEC1:
Animal Models for APOBEC1 Gene
Animal Model Products
-
Taconic Biosciences Mouse Models for APOBEC1
-
ViGene Biosciences lentiviral particle packaged cDNA for APOBEC1 gene
-
ViGene Biosciences ready-to-package AAV shRNAs for APOBEC1 gene
- Search ViGene Biosciences for APOBEC1
CRISPR Products
-
OriGene CRISPR knockouts for APOBEC1
-
Santa Cruz Biotechnology (SCBT) CRISPR for APOBEC1
- GenScript: Design CRISPR guide RNA sequences for APOBEC1
miRNA Products
- Search ViGene Biosciences for APOBEC1
Inhibitory RNA Products
- Origene shRNA, siRNA, and RNAi products in human, mouse, rat for APOBEC1
- Browse OriGene Inhibitory RNA Products For APOBEC1
-
ViGene Biosciences ready-to-package AAV shRNAs for APOBEC1 gene
Clone Products
-
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Cell Line Products
-
Horizon Cell Lines for APOBEC1
-
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-
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-
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Flow Cytometry Products
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.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| extracellular | 2 |
| cytosol | 2 |
| peroxisome | 1 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005634 | nucleus | IEA | -- |
| GO:0005654 | nucleoplasm | TAS | -- |
| GO:0005737 | cytoplasm | IEA,IDA | 22580899 |
Pathways & Interactions for APOBEC1 Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | mRNA Editing- C to U Conversion |
.82
|
|
| 2 | Gene Expression |
.48
|
|
Pathways by source for APOBEC1 Gene
4 Reactome pathways for APOBEC1 Gene
Interacting Proteins 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 | -- |
No data available for SIGNOR curated interactions for APOBEC1 Gene
Transcripts for APOBEC1 Gene
mRNA/cDNA for APOBEC1 Gene
- (3) REFSEQ mRNAs :
- (14) Additional mRNA sequences :
- (67) Selected AceView cDNA sequences:
- (2) Ensembl transcripts including schematic representations, and UCSC links where relevant :
Unigene Clusters for APOBEC1 Gene
CRISPR Products
-
OriGene CRISPR knockouts for APOBEC1
-
Santa Cruz Biotechnology (SCBT) CRISPR for APOBEC1
- GenScript: Design CRISPR guide RNA sequences for APOBEC1
miRNA Products
- Search ViGene Biosciences for APOBEC1
Inhibitory RNA Products
- Origene shRNA, siRNA, and RNAi products in human, mouse, rat for APOBEC1
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-
ViGene Biosciences ready-to-package AAV shRNAs for APOBEC1 gene
Clone Products
-
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Flow Cytometry Products
Expression for APOBEC1 Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
- Spleen (Hematopoietic System)
- Blood (Cardiovascular System)
-
Pancreas (Endocrine System)
- Duct Cells Pancreatic Ducts
-
Epithelial Cells
- Duct Cells Pancreatic Ducts
-
Colon (Gastrointestinal Tract)
-
Stomach (Gastrointestinal Tract)
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, PaxDb, and MOPED for APOBEC1 Gene
NURSA nuclear receptor signaling pathways regulating expression of APOBEC1 Gene:
APOBEC1SOURCE GeneReport for Unigene cluster for APOBEC1 Gene:
Hs.560mRNA 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(4.3)
Primer Products
-
OriGene qPCR primer pairs and template standards for APOBEC1
-
OriGene qPCR primer pairs for APOBEC1
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.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | APOBEC1 34 35 |
|
||
| dog (Canis familiaris) |
Mammalia | APOBEC1 34 35 |
|
||
| cow (Bos Taurus) |
Mammalia | APOBEC1 34 35 |
|
||
| mouse (Mus musculus) |
Mammalia | Apobec1 34 16 35 |
|
||
| rat (Rattus norvegicus) |
Mammalia | Apobec1 34 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | APOBEC1 35 |
|
OneToOne | |
| platypus (Ornithorhynchus anatinus) |
Mammalia | APOBEC1 35 |
|
OneToOne | |
| lizard (Anolis carolinensis) |
Reptilia | APOBEC1 35 |
|
OneToOne |
- Species where no ortholog for APOBEC1 was found in the sources mined by GeneCards:
-
- A. gosspyii yeast (Ashbya 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 squirt (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)
Paralogs for APOBEC1 Gene
Variants for APOBEC1 Gene
| SNP ID | Clin | Chr 12 pos | Sequence Context | AA Info | Type |
|---|---|---|---|---|---|
| rs1000086155 | -- | 7,663,265(+) | CTGGA(C/T)GGTAG | intron-variant | |
| rs1000349979 | -- | 7,668,035(+) | TAAAA(A/G)TCTTG | intron-variant | |
| rs1000408388 | -- | 7,654,366(+) | ATCCA(C/T)AGTTC | intron-variant | |
| rs1000439946 | -- | 7,662,868(+) | GACCT(-/GCAATGGAGGGAGATGA)GCAAT | intron-variant | |
| rs1000926561 | -- | 7,656,993(+) | ATTTT(C/T)AGTTT | intron-variant |
| 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 |
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)
Relevant External Links 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
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| neurofibromatosis |
|
|
| hypercholesterolemia, familial |
|
|
| immunodeficiency with hyper-igm, type 2 |
|
|
Search APOBEC1 in MalaCards
View complete list of genes associated with diseases
Relevant External Links for APOBEC1
No data available for UniProtKB/Swiss-Prot and Genatlas for APOBEC1 Gene
Publications for APOBEC1 Gene
- Investigation of the Lith6 candidate genes APOBEC1 and PPARG in human gallstone disease. (PMID: 17696929) Schafmayer C. … Tepel J. (Liver Int. 2007) 3 22 46 64
- 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 N.O. (Am. J. Hum. Genet. 2002) 3 4 22 64
- Human apolipoprotein B RNA editing deaminase gene (APOBEC1). (PMID: 9479499) Fujino T. … Scott J. (Genomics 1998) 3 4 22 64
- Molecular cloning of a human small intestinal apolipoprotein B mRNA editing protein. (PMID: 8208612) Hadjiagapiou C. … Davidson N.O. (Nucleic Acids Res. 1994) 3 4 22 64
- 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 B.B. (Arterioscler. Thromb. Vasc. Biol. 2012) 3 4 64
Products for APOBEC1 Gene
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- antibodies-online Antibodies for APOBEC1: See all 55
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- ViGene Biosciences adenoviral particle packaged cDNA for APOBEC1 gene
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- VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
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- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Sources for APOBEC1 Gene
- (1) GeneCards
- (2) HGNC
- (3) EntrezGene
- (4) Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) GO
- (12) TrEMBL
- (13) InterPro
- (14) ProtoNet
- (15) Blocks
- (16) MGI
- (17) IUBMB
- (18) KEGG
- (19) MINT
- (20) STRING
- (21) IntAct
- (22) Novoseek
- (23) PharmGKB
- (24) DrugBank
- (25) HMDB
- (26) UniGene
- (27) AceView
- (28) RNAdb
- (29) ASD
- (30) ECgene
- (31) GeneAnnot
- (32) CGAP SAGE
- (33) SOURCE
- (34) HomoloGene
- (35) PanEnsembl
- (36) euGenes
- (37) SGD
- (38) FlyBase
- (39) WormBase
- (40) Pseudogene
- (41) DGV
- (42) dbSNP
- (43) GenAtlas
- (44) GeneTests
- (45) HGMD
- (46) GAD
- (47) LSDB
- (48) BGMUT
- (49) HuGE
- (50) eBioscience
- (51) Atlas
- (52) Cell Signaling Technology
- (53) GenBank
- (54) H-invDB
- (55) HORDE
- (56) HUGE
- (57) IMGT
- (58) Leiden
- (59) MILLIPORE
- (60) miRBase
- (61) DME
- (62) NCBI
- (63) OriGene
- (64) PubMed
- (65) R&D Systems
- (66) TGDB
- (67) Tocris
- (68) Abcam
- (69) Novus
- (70) ProSpec
- (71) Sino Biological
- (72) GenScript
- (73) Qiagen
- (74) Cloud-Clone Corp.
- (75) Enzo Life Sciences
- (76) OCA
- (77) Proteopedia
- (78) MOPED
- (79) SPIRE
- (80) neXtProt
- (81) Reactome
- (82) GeneGo (Thomson Reuters)
- (83) fRNAdb
- (84) DISEASES
- (85) SIMAP
- (86) GenomeRNAi
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- (98) BioGPS
- (99) Illumina
- (100) COMPARTMENTS
- (101) HOMER
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- (103) ApexBio
- (104) Addgene
- (105) antibodies-online
- (106) CYP
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- (109) TreeFam
- (110) PathCards
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- (112) GeneTex
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- (141) ENCODE
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- (154) TISSUES
- (155) Gene ORGANizer