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

    Gene ID: 666173, updated on 27-Nov-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
    Enables phosphatidylinositol-3-phosphate binding activity. Involved in acrosome assembly; central nervous system development; and maintenance of lens transparency. Acts upstream of or within several processes, including dentate gyrus development; head morphogenesis; and social behavior. Located in acrosomal membrane. 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, Nov 2024]
    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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    See Vps13b in Genome Data Viewer
    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. Exploring the pathological mechanisms underlying Cohen syndrome. Vacca F, et al. Front Neurosci, 2024. PMID 39010945, Free PMC Article
    2. 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
    3. 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
    4. Expanded mutational spectrum in Cohen syndrome, tissue expression, and transcript variants of COH1. Seifert W, et al. Hum Mutat, 2009 Feb. PMID 19006247
    5. 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, Free PMC Article

    See all (31) 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 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 organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in Golgi reassembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in Golgi reassembly ISS
    Inferred from Sequence or Structural Similarity
    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 adipose tissue development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within brain development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in central nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within dentate gyrus development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within head morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in maintenance of lens transparency IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within memory 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 muscle organ development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nervous system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nervous system development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in slow endocytic recycling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in slow endocytic recycling ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within social behavior IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vesicle-mediated transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in vesicle-mediated transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi membrane 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 cis-Golgi network membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum-Golgi intermediate compartment membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum-Golgi intermediate compartment membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in recycling endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in trans-Golgi network membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in trans-Golgi network membrane ISS
    Inferred from Sequence or Structural Similarity
    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

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

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