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

Summary

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 brain-derived neurotrophic factor receptor signaling pathway; long-term synaptic depression; and myeloid cell differentiation. Located in Golgi apparatus; neuronal dense core vesicle lumen; and sperm midpiece. Is active in several cellular components, including endoplasmic reticulum; mitochondrion; and neuronal cell body. 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, Nov 2024]
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

Location:: 19 A- B; 19 11.71 cM

Exon count:: 74

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	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_000085.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Analysis of Brain, Blood, and Testis Phenotypes Lacking the Vps13a Gene in C57BL/6N Mice.
Title: Analysis of Brain, Blood, and Testis Phenotypes Lacking the Vps13a Gene in C57BL/6N Mice.
chorein interacts with beta-adducin and beta-actin.
Title: Chorein, the protein responsible for chorea-acanthocytosis, interacts with β-adducin and β-actin.
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.
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)

Endonuclease-mediated (2)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BE687829 (e-PCR)
- UniSTS:209445

NoName (e-PCR)
- UniSTS:237900

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables molecular_function	ND No biological Data available more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within adult locomotory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in autophagy	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within autophagy	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within autophagy	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within brain-derived neurotrophic factor receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cell morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cellular response to osmotic stress	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chemokine production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within erythrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within exploration behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within flagellated sperm motility	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lipid transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within locomotory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within long-term synaptic depression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lysosomal protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in lysosomal protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within microglia differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within motor behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within multicellular organism growth	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuroinflammatory response	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within neuroinflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuromuscular process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuromuscular process controlling balance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron projection arborization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein retention in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within protein secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein targeting to vacuole	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of synaptic plasticity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to environmental enrichment	IMP Inferred from Mutant Phenotype 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 dense core granule	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in endosome membrane	ISO Inferred from Sequence Orthology more info
located_in endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in lipid droplet	ISO Inferred from Sequence Orthology more info
located_in lipid droplet	ISS Inferred from Sequence or Structural Similarity more info
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in lysosomal membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in mitochondria-associated endoplasmic reticulum membrane contact site	ISO Inferred from Sequence Orthology more info
located_in mitochondria-associated endoplasmic reticulum membrane contact site	ISS Inferred from Sequence or Structural Similarity more info
located_in mitochondrial membrane	ISO Inferred from Sequence Orthology more info
located_in mitochondrial membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in mitochondrial outer membrane	ISO Inferred from Sequence Orthology more info
located_in mitochondrial outer membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
is_active_in neuron projection	IDA Inferred from Direct Assay more info	PubMed
is_active_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
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

Names: chorea-acanthocytosis protein homolog; vacuolar protein sorting-associated protein 13A

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_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

Q3UQG7, Q3UX03, Q5DU08, Q5H8C4, Q80YV7, Q8C722

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: 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_000085.7 Reference GRCm39 C57BL/6J

Range

16592730..16758433 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011247256.3 → XP_011245558.1 intermembrane lipid transfer protein VPS13A 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
XM_006527126.4 → XP_006527189.1 intermembrane lipid transfer protein VPS13A 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
XM_036161609.1 → XP_036017502.1 intermembrane lipid transfer protein VPS13A 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