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

Gene ID: 176377, updated on 4-Jan-2025

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, Jan 2025]
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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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