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Vps13b vacuolar protein sorting 13B [ Mus musculus (house mouse) ]

Gene ID: 666173, updated on 5-Mar-2024

Summary

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Official Symbol
Vps13bprovided by MGI
Official Full Name
vacuolar protein sorting 13Bprovided by MGI
Primary source
MGI:MGI:1916380
See related
Ensembl:ENSMUSG00000037646 AllianceGenome:MGI:1916380
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
Coh1; 4732488H20; D230005K13; 1810042B05Rik; 2310042E16Rik; C330002D13Rik
Summary
Predicted to act upstream of or within protein transport. Used to study Cohen syndrome and cataract. Human ortholog(s) of this gene implicated in Cohen syndrome. Orthologous to human VPS13B (vacuolar protein sorting 13 homolog B). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in subcutaneous fat pad adult (RPKM 3.3), testis adult (RPKM 2.8) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
15 B3.1; 15 14.46 cM
Exon count:
62
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (35371264..35931375)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (35371118..35931229)

Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_38341 Neighboring gene cDNA sequence BC048602 Neighboring gene RIKEN cDNA 4921515G04 gene Neighboring gene predicted gene, 33584 Neighboring gene STARR-seq mESC enhancer starr_38343 Neighboring gene STARR-seq mESC enhancer starr_38344 Neighboring gene predicted gene, 52228 Neighboring gene VISTA enhancer mm703 Neighboring gene predicted gene, 24771 Neighboring gene STARR-seq mESC enhancer starr_38346 Neighboring gene STARR-seq mESC enhancer starr_38347 Neighboring gene microRNA 599 Neighboring gene microRNA 875 Neighboring gene RIKEN cDNA 9130002K18 gene Neighboring gene nuclear receptor subfamily 2, group E, member 3 pseudogene Neighboring gene predicted gene, 41292 Neighboring gene STARR-seq mESC enhancer starr_38348 Neighboring gene STARR-seq mESC enhancer starr_38349 Neighboring gene STARR-seq mESC enhancer starr_38350 Neighboring gene STARR-seq mESC enhancer starr_38351 Neighboring gene cytochrome c oxidase subunit 6C Neighboring gene regulator of G-protein signalling 22 Neighboring gene heterogeneous nuclear ribonucleoprotein C 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
  • 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. Spatial Learning and Motor Deficits in Vacuolar Protein Sorting-associated Protein 13b (Vps13b) Mutant Mouse. Kim MJ, et al. Exp Neurobiol, 2019 Aug 31. PMID 31495077, Free PMC Article
  2. Cohen Syndrome-Associated Cataract Is Explained by VPS13B Functions in Lens Homeostasis and Is Modified by Additional Genetic Factors. Lhussiez V, et al. Invest Ophthalmol Vis Sci, 2020 Sep 1. PMID 32915983, Free PMC Article
  3. Expanded mutational spectrum in Cohen syndrome, tissue expression, and transcript variants of COH1. Seifert W, et al. Hum Mutat, 2009 Feb. PMID 19006247
  4. Vps13b is required for acrosome biogenesis through functions in Golgi dynamic and membrane trafficking. Da Costa R, et al. Cell Mol Life Sci, 2020 Feb. PMID 31218450
  5. SNAREs define targeting specificity of trafficking vesicles by combinatorial interaction with tethering factors. Koike S, et al. Nat Commun, 2019 Apr 8. PMID 30962439, Free PMC Article

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0532, MGC189855

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables lipid binding IEA
Inferred from Electronic Annotation
more info
  
enables molecular_function ND
No biological Data available
more info
  
enables phosphatidylinositol-3-phosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in Golgi organization ISO
Inferred from Sequence Orthology
more info
  
involved_in Golgi reassembly ISO
Inferred from Sequence Orthology
more info
  
involved_in acrosome assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in adipose tissue development ISO
Inferred from Sequence Orthology
more info
  
involved_in biological_process ND
No biological Data available
more info
  
involved_in central nervous system development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within lipid transport IEA
Inferred from Electronic Annotation
more info
  
involved_in maintenance of lens transparency IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nervous system development ISO
Inferred from Sequence Orthology
more info
  
involved_in slow endocytic recycling ISO
Inferred from Sequence Orthology
more info
  
involved_in vesicle-mediated transport ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
located_in Golgi membrane ISO
Inferred from Sequence Orthology
more info
  
located_in acrosomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cellular_component ND
No biological Data available
more info
  
located_in cis-Golgi network membrane ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum-Golgi intermediate compartment membrane ISO
Inferred from Sequence Orthology
more info
  
located_in endosome IEA
Inferred from Electronic Annotation
more info
  
located_in lysosome IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in trans-Golgi network membrane ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
intermembrane lipid transfer protein VPS13B
Names
cohen syndrome protein 1 homolog
vacuolar protein sorting-associated protein 13B

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_177151.4 → NP_796125.2  intermembrane lipid transfer protein VPS13B

    Status: VALIDATED

    Source sequence(s)
    AC121598, AC122241, AC144772, AC157521, AC166356
    Consensus CDS
    CCDS49592.1
    UniProtKB/Swiss-Prot
    E9QKX5, Q80TY5
    Related
    ENSMUSP00000045490.8, ENSMUST00000048646.9
    Conserved Domains (4) summary
    pfam06650
    Location:2605 → 2685
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:3705 → 3809
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:3 → 102
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16909
    Location:3557 → 3703
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

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_000081.7 Reference GRCm39 C57BL/6J

    Range
    35371264..35931375
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q80TY5.3 GenPept UniProtKB/Swiss-Prot:Q80TY5

Gene LinkOut

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