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    vps-53 Vacuolar protein sorting-associated protein 53 homolog [ Caenorhabditis elegans ]

    Gene ID: 176377, updated on 9-Dec-2024

    Summary

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    Official Symbol
    vps-53
    Official Full Name
    Vacuolar protein sorting-associated protein 53 homolog
    Primary source
    WormBase:WBGene00011502
    Locus tag
    CELE_T05G5.8
    See related
    AllianceGenome:WB:WBGene00011502
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Caenorhabditis elegans (strain: Bristol N2)
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
    Summary
    Involved in positive regulation of locomotion involved in locomotory behavior; regulation of brood size; and regulation of dense core granule transport. Located in perikaryon and perinuclear region of cytoplasm. Part of GARP complex. Is expressed in body wall musculature; intestine; neurons; and pharynx. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 2E. Orthologous to human VPS53 (VPS53 subunit of GARP complex). [provided by Alliance of Genome Resources, Dec 2024]
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    Genomic context

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    See vps-53 in Genome Data Viewer
    Location:
    chromosome: III
    Exon count:
    6
    Sequence:
    Chromosome: III; NC_003281.10 (9753675..9757514, complement)

    Chromosome III - NC_003281.10Genomic Context describing neighboring genes Neighboring gene Uncharacterized protein Neighboring gene Dephospho-CoA kinase Neighboring gene putative enoyl-CoA hydratase, mitochondrial Neighboring gene GRIP and coiled-coil domain-containing protein 2 Neighboring gene Regulator of microtubule dynamics protein 1 Neighboring gene ncRNA Neighboring gene ncRNA

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003281.10

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The Caenorhabditis elegans GARP complex contains the conserved Vps51 subunit and is required to maintain lysosomal morphology. Luo L, et al. Mol Biol Cell, 2011 Jul 15. PMID 21613545, Free PMC Article
    2. The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles. Topalidou I, et al. PLoS Genet, 2016 May. PMID 27191843, Free PMC Article
    3. Amino acid and protein specificity of protein fatty acylation in C. elegans. Zhang B, et al. Proc Natl Acad Sci U S A, 2024 Jan 30. PMID 38252833, Free PMC Article
    4. EPIC: software toolkit for elution profile-based inference of protein complexes. Hu LZ, et al. Nat Methods, 2019 Aug. PMID 31308550, Free PMC Article
    5. OrthoList: a compendium of C. elegans genes with human orthologs. Shaye DD, et al. PLoS One, 2011. PMID 21647448, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by WormBase

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of dense core granule transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of dense core granule transport IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in positive regulation of dense core granule transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of locomotion involved in locomotory behavior IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in positive regulation of locomotion involved in locomotory behavior IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of brood size IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of GARP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of GARP complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of GARP complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of GARP complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perikaryon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    Vacuolar protein sorting-associated protein 53 homolog
    NP_001255027.2
    • Confirmed by transcript evidence
    NP_001255028.2
    • Confirmed by transcript evidence

    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. NC_003281.10 Reference assembly

      Range
      9753675..9757514 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001268098.3 → NP_001255027.2  Vacuolar protein sorting-associated protein 53 homolog [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001255027.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      E5QCF9, P34561
      Conserved Domains (1) summary
      pfam04100
      Location:30 → 390
      Vps53_N; Vps53-like, N-terminal

    2. NM_001268099.4 → NP_001255028.2  Vacuolar protein sorting-associated protein 53 homolog [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001255028.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      P34561
      Conserved Domains (1) summary
      pfam04100
      Location:1 → 166
      Vps53_N; Vps53-like, N-terminal
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P34561.4

    Gene LinkOut

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    Chemical Information
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