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    Abca13 ATP-binding cassette, sub-family A member 13 [ Mus musculus (house mouse) ]

    Gene ID: 268379, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Abca13provided by MGI
    Official Full Name
    ATP-binding cassette, sub-family A member 13provided by MGI
    Primary source
    MGI:MGI:2388707
    See related
    Ensembl:ENSMUSG00000004668 AllianceGenome:MGI:2388707
    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
    9830132L24; A930002G16Rik
    Summary
    Predicted to enable ATPase-coupled transmembrane transporter activity and lipid transporter activity. Involved in ceramide transport; positive regulation of cholesterol transport; and positive regulation of synaptic vesicle endocytosis. Located in intracellular vesicle. Is expressed in bone marrow; genitourinary system; and retina. Human ortholog(s) of this gene implicated in gastric adenocarcinoma. Orthologous to human ABCA13 (ATP binding cassette subfamily A member 13). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in kidney adult (RPKM 3.8) and liver E18 (RPKM 0.4) See more
    Orthologs
    human all
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    Genomic context

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    See Abca13 in Genome Data Viewer
    Location:
    11 A1; 11 6.13 cM
    Exon count:
    62
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (9141942..9634871)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (9191942..9684871)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_28553 Neighboring gene STARR-seq mESC enhancer starr_28555 Neighboring gene polymerase (RNA) II (DNA directed) polypeptide C pseudogene Neighboring gene uridine phosphorylase 1 Neighboring gene STARR-seq mESC enhancer starr_28556 Neighboring gene STARR-seq mESC enhancer starr_28557 Neighboring gene STARR-seq mESC enhancer starr_28558 Neighboring gene STARR-seq mESC enhancer starr_28559 Neighboring gene STARR-seq mESC enhancer starr_28560 Neighboring gene STARR-seq mESC enhancer starr_28561 Neighboring gene STARR-seq mESC enhancer starr_28562 Neighboring gene STARR-seq mESC enhancer starr_28564 Neighboring gene eukaryotic translation initiation factor 3, subunit 6, pseudogene 1 Neighboring gene STARR-seq mESC enhancer starr_28567 Neighboring gene STARR-seq mESC enhancer starr_28570 Neighboring gene STARR-seq mESC enhancer starr_28571 Neighboring gene STARR-seq mESC enhancer starr_28573 Neighboring gene STARR-seq mESC enhancer starr_28574 Neighboring gene STARR-seq mESC enhancer starr_28576 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data 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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    Related articles in PubMed

    1. The effects of neurological disorder-related codon variations of ABCA13 on the function of the ABC protein. Tomioka M, et al. Biosci Biotechnol Biochem, 2012. PMID 23221702
    2. Molecular structure and characterization of a novel murine ABC transporter, Abca13. Barros SA, et al. Gene, 2003 Mar 27. PMID 12706902
    3. ABCA13 dysfunction associated with psychiatric disorders causes impaired cholesterol trafficking. Nakato M, et al. J Biol Chem, 2021 Jan-Jun. PMID 33478937, Free PMC Article
    4. The human ATP binding cassette gene ABCA13, located on chromosome 7p12.3, encodes a 5058 amino acid protein with an extracellular domain encoded in part by a 4.8-kb conserved exon. Prades C, et al. Cytogenet Genome Res, 2002. PMID 12697998
    5. Rapid and Integrative Discovery of Retina Regulatory Molecules. Albrecht NE, et al. Cell Rep, 2018 Aug 28. PMID 30157441, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ABCA13 dysfunction associated with psychiatric disorders causes impaired cholesterol trafficking.
      Title: ABCA13 dysfunction associated with psychiatric disorders causes impaired cholesterol trafficking.
    2. T4031A replacement affects the function of ABCA13 in the brain
      Title: The effects of neurological disorder-related codon variations of ABCA13 on the function of the ABC protein.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3)  1 citation
    • Targeted (3) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables ABC-type transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATPase-coupled transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables lipid transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in ceramide transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in lipid transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of cholesterol transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of cholesterol transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of synaptic vesicle endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasmic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in intracellular vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in intracellular vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    ATP-binding cassette sub-family A member 13
    Names
    ATP-binding cassette transporter
    ATP-binding cassette, sub-family A (ABC1), member 13

    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)

    1. NM_178259.3 → NP_839990.2  ATP-binding cassette sub-family A member 13

      See identical proteins and their annotated locations for NP_839990.2

      Status: VALIDATED

      Source sequence(s)
      AL645994, AL663110, AL663114, AL669853
      Consensus CDS
      CCDS36110.1
      UniProtKB/Swiss-Prot
      Q5SSE9, Q80T20, Q8BHZ2, Q8CB91
      Related
      ENSMUSP00000040465.7, ENSMUST00000042740.13
      Conserved Domains (2) summary
      TIGR01257
      Location:3036 → 5019
      rim_protein; retinal-specific rim ABC transporter
      cd03263
      Location:4692 → 4919
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A

    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

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      9141942..9634871
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006514706.5 → XP_006514769.2  ATP-binding cassette sub-family A member 13 isoform X1

      Conserved Domains (1) summary
      TIGR01257
      Location:2205 → 4150
      rim_protein; retinal-specific rim ABC transporter
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5SSE9.1 GenPept UniProtKB/Swiss-Prot:Q5SSE9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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