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    Vps13D Vacuolar protein sorting 13D [ Drosophila melanogaster (fruit fly) ]

    Gene ID: 39448, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Vps13Dprovided by FlyBase
    Official Full Name
    Vacuolar protein sorting 13Dprovided by FlyBase
    Primary source
    FLYBASE:FBgn0052113
    Locus tag
    Dmel_CG32113
    See related
    AllianceGenome:FB:FBgn0052113
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Drosophila melanogaster
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
    Also known as
    CG11002; CG11003; CG32113; Dmel\CG32113
    Summary
    Enables K63-linked polyubiquitin modification-dependent protein binding activity and ubiquitin binding activity. Involved in mitochondrion organization; mitophagy; and reticulophagy. Located in lysosome. Is expressed in adult head. Used to study autosomal recessive spinocerebellar ataxia 4. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 4. Orthologous to human VPS13D (vacuolar protein sorting 13 homolog D). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See Vps13D in Genome Data Viewer
    Location:
    69E1-69E2; 3-39 cM
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    Release 6.54 current Release 6 plus ISO1 MT (GCF_000001215.4) 3L NT_037436.4 (12755049..12768605)
    Release 5.57 previous assembly Release 5 (GCF_000001215.2) 3L NT_037436.3 (12748149..12761705)

    Chromosome 3L - NT_037436.4Genomic Context describing neighboring genes Neighboring gene uncharacterized protein Neighboring gene Kinesin light chain Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein Neighboring gene Huntingtin interacting protein 1 Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. An optimized temporally controlled Gal4 system in Drosophila reveals degeneration caused by adult-onset neuronal Vps13D knockdown. Rozich E, et al. Front Neurosci, 2023. PMID 37457002, Free PMC Article
    2. Mitochondrial fission, integrity and completion of mitophagy require separable functions of Vps13D in Drosophila neurons. Insolera R, et al. PLoS Genet, 2021 Aug. PMID 34383748, Free PMC Article
    3. Mutations in VPS13D lead to a new recessive ataxia with spasticity and mitochondrial defects. Seong E, et al. Ann Neurol, 2018 Jun. PMID 29604224, Free PMC Article
    4. Vmp1, Vps13D, and Marf/Mfn2 function in a conserved pathway to regulate mitochondria and ER contact in development and disease. Shen JL, et al. Curr Biol, 2021 Jul 26. PMID 34019822, Free PMC Article
    5. Vps13D functions in a Pink1-dependent and Parkin-independent mitophagy pathway. Shen JL, et al. J Cell Biol, 2021 Nov 1. PMID 34459871, Free PMC Article

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Mitochondrial fission, integrity and completion of mitophagy require separable functions of Vps13D in Drosophila neurons.
      Title: Mitochondrial fission, integrity and completion of mitophagy require separable functions of Vps13D in Drosophila neurons.
    2. VPS13D mutant cells possess phosphorylated DRP1 and mitochondrial fission factor (MFF) as well as DRP1 association with mitochondria, suggesting that VPS13D functions downstream of these known regulators of mitochondrial fission.
      Title: Vps13D Encodes a Ubiquitin-Binding Protein that Is Required for the Regulation of Mitochondrial Size and Clearance.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by FlyBase

    Function Evidence Code Pubs
    enables K63-linked polyubiquitin modification-dependent protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mitochondrion organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrion organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrion organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in mitophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein retention in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein targeting to vacuole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in reticulophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    vacuolar protein sorting 13D
    Names
    CG32113-PB
    Vps13D-PB

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NT_037436.4 Reference assembly

      Range
      12755049..12768605
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_168512.4 → NP_729825.2  vacuolar protein sorting 13D [Drosophila melanogaster]

      See identical proteins and their annotated locations for NP_729825.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9VU08
      Conserved Domains (5) summary
      pfam06650
      Location:2836 → 3113
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam12624
      Location:4 → 112
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16908
      Location:147 → 368
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16910
      Location:656 → 837
      VPS13_mid_rpt; Repeating coiled region of VPS13
      cl25572
      Location:3346 → 3802
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9VU08.3 Q9VU08

    Gene LinkOut

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