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Vps13a vacuolar protein sorting 13A [ Mus musculus (house mouse) ]

Gene ID: 271564, updated on 5-Jan-2023

Summary

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Official Symbol
Vps13aprovided by MGI
Official Full Name
vacuolar protein sorting 13Aprovided by MGI
Primary source
MGI:MGI:2444304
See related
Ensembl:ENSMUSG00000046230 AllianceGenome:MGI:2444304
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
Chac; Chorein; mKIAA0986; 4930425F11; 9930023P20; 4930516E05Rik; 4930543C13Rik; D330038K10Rik
Summary
Acts upstream of or within several processes, including flagellated sperm motility; social behavior; and sperm mitochondrion organization. Located in Golgi apparatus; neuronal dense core vesicle lumen; and sperm midpiece. Is expressed in central nervous system; retina; and thymus primordium. Used to study choreaacanthocytosis. Human ortholog(s) of this gene implicated in choreaacanthocytosis and choreatic disease. Orthologous to human VPS13A (vacuolar protein sorting 13 homolog A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis adult (RPKM 4.2), cortex adult (RPKM 2.3) and 23 other tissues See more
Orthologs
human all
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Genomic context

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See Vps13a in Genome Data Viewer
Location:
19; 19 A- B
Exon count:
74
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (16592730..16758433, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (16615366..16781071, complement)

Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene guanine nucleotide binding protein, alpha 14 Neighboring gene nuclear import 7 pseudogene Neighboring gene predicted gene, 41811 Neighboring gene predicted gene, 32256 Neighboring gene forkhead box B2 Neighboring gene predicted gene, 32341

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
  • 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. Phenotypic abnormalities in a chorea-acanthocytosis mouse model are modulated by strain background. Sakimoto H, et al. Biochem Biophys Res Commun, 2016 Mar 25. PMID 26921443
  2. Chorein deficiency leads to upregulation of gephyrin and GABA(A) receptor. Kurano Y, et al. Biochem Biophys Res Commun, 2006 Dec 15. PMID 17070500
  3. Mouse model of chorea-acanthocytosis exhibits male infertility caused by impaired sperm motility as a result of ultrastructural morphological abnormalities in the mitochondrial sheath in the sperm midpiece. Nagata O, et al. Biochem Biophys Res Commun, 2018 Sep 5. PMID 29928881
  4. Brain-specific transcript variants of 5' and 3' ends of mouse VPS13A and VPS13C. Mizuno E, et al. Biochem Biophys Res Commun, 2007 Feb 23. PMID 17196930
  5. A gene-targeted mouse model for chorea-acanthocytosis. Tomemori Y, et al. J Neurochem, 2005 Feb. PMID 15686477

See all (30) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. chorein interacts with beta-adducin and beta-actin.
    Title: Chorein, the protein responsible for chorea-acanthocytosis, interacts with β-adducin and β-actin.
  2. Mouse CHAC cDNA sequence and the exon-intron structures of the CHAC disease gene are identified and a CHAC model mouse produced by a gene-targeting technique.
    Title: A gene-targeted mouse model for chorea-acanthocytosis.
  3. Brain-specific variants of VPS13A may be involved in the brain-specific pathology of chorea-acanthocytosis.
    Title: Brain-specific transcript variants of 5' and 3' ends of mouse VPS13A and VPS13C.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (3)  1 citation
  • Endonuclease-mediated (2) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0986

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in autophagy IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
acts_upstream_of_or_within autophagy ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within flagellated sperm motility IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within lipid transport IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within locomotory behavior IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in lysosomal protein catabolic process ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within nervous system development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein retention in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in protein targeting to vacuole IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
acts_upstream_of_or_within social behavior IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within sperm mitochondrion organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in dense core granule IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum membrane ISO
Inferred from Sequence Orthology
more info
  
located_in endosome IEA
Inferred from Electronic Annotation
more info
  
located_in endosome membrane ISO
Inferred from Sequence Orthology
more info
  
is_active_in extrinsic component of membrane IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in extrinsic component of membrane ISO
Inferred from Sequence Orthology
more info
  
located_in lipid droplet ISO
Inferred from Sequence Orthology
more info
  
located_in lysosomal membrane ISO
Inferred from Sequence Orthology
more info
  
located_in lysosome IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondria-associated endoplasmic reticulum membrane ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrial membrane ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrial outer membrane ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  
located_in neuronal dense core vesicle lumen IDA
Inferred from Direct Assay
more info
 PubMed 
located_in sperm midpiece IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
intermembrane lipid transfer protein VPS13A; vacuolar protein sorting-associated protein 13A
Names
chorea-acanthocytosis protein homolog

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_173028.4 → NP_766616.2  intermembrane lipid transfer protein VPS13A

    See identical proteins and their annotated locations for NP_766616.2

    Status: VALIDATED

    Source sequence(s)
    AB115421, AC125185, AK076578, BC062130, BE687829
    Consensus CDS
    CCDS37929.1
    UniProtKB/Swiss-Prot
    Q5H8C4, Q8C722
    UniProtKB/TrEMBL
    Q6P6M9
    Related
    ENSMUSP00000068716.7, ENSMUST00000068156.8
    Conserved Domains (7) summary
    COG5043
    Location:4 → 2005
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2202 → 2445
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:2938 → 3017
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4 → 113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:142 → 371
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:2758 → 2935
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:568 → 791
    VPS13_mid_rpt; Repeating coiled region of VPS13

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000085.7 Reference GRCm39 C57BL/6J

    Range
    16592730..16758433 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011247256.3 → XP_011245558.1  vacuolar protein sorting-associated protein 13A isoform X1

    Conserved Domains (4) summary
    COG5043
    Location:4 → 2005
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2202 → 2445
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:142 → 371
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:2758 → 2935
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

  2. XM_006527126.4 → XP_006527189.1  vacuolar protein sorting-associated protein 13A isoform X2

    UniProtKB/Swiss-Prot
    Q5H8C4
    Conserved Domains (4) summary
    COG5043
    Location:4 → 2005
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2202 → 2445
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:142 → 371
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:2758 → 2935
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

  3. XM_036161609.1 → XP_036017502.1  vacuolar protein sorting-associated protein 13A isoform X3

    UniProtKB/TrEMBL
    A0A286YCT3
    Related
    ENSMUSP00000153129.2, ENSMUST00000224149.2
    Conserved Domains (3) summary
    COG5043
    Location:4 → 2005
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2202 → 2336
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam16908
    Location:142 → 371
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5H8C4.1 GenPept UniProtKB/Swiss-Prot:Q5H8C4

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