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    vps18 VPS18 core subunit of CORVET and HOPS complexes [ Danio rerio (zebrafish) ]

    Gene ID: 100005887, updated on 9-Dec-2024

    Summary

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    Official Symbol
    vps18provided by ZNC
    Official Full Name
    VPS18 core subunit of CORVET and HOPS complexesprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-020419-33
    See related
    Ensembl:ENSDARG00000070433 AllianceGenome:ZFIN:ZDB-GENE-020419-33
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    chunp6929; wu:fj35h10; hm:zehl0587
    Summary
    Predicted to enable protein-macromolecule adaptor activity. Acts upstream of or within several processes, including apical protein localization; endosome to pigment granule transport; and notochord cell vacuolation. Predicted to be located in late endosome membrane and lysosomal membrane. Predicted to be part of HOPS complex. Predicted to be active in endosome. Used to study cholestasis. Orthologous to human VPS18 (VPS18 core subunit of CORVET and HOPS complexes). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See vps18 in Genome Data Viewer
    Location:
    chromosome: 20
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 20 NC_007131.7 (28354269..28361557, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 20 NC_007131.6 (28455179..28462467, complement)

    Chromosome 20 - NC_007131.7Genomic Context describing neighboring genes Neighboring gene ChaC, cation transport regulator homolog 1 (E. coli) Neighboring gene INO80 complex ATPase subunit Neighboring gene ras homolog family member V Neighboring gene phosphatidylinositol glycan anchor biosynthesis, class H

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. The zebrafish mutant vps18 as a model for vesicle-traffic related hypopigmentation diseases. Maldonado E, et al. Pigment Cell Res, 2006 Aug. PMID 16827750
    2. A genetic screen in zebrafish identifies the mutants vps18, nf2 and foie gras as models of liver disease. Sadler KC, et al. Development, 2005 Aug. PMID 16000385
    3. Notochord vacuoles are lysosome-related organelles that function in axis and spine morphogenesis. Ellis K, et al. J Cell Biol, 2013 Mar 4. PMID 23460678, Free PMC Article
    4. Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development. Golling G, et al. Nat Genet, 2002 Jun. PMID 12006978
    5. Genetic characterization and in vivo image analysis of novel zebrafish Danio rerio pigment mutants. Hsu CC, et al. J Fish Biol, 2013 May. PMID 23639161

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A deficiency of Vps18 in zebrafish larvae results in hepatomegaly and skin hypopigmentation.
      Title: The zebrafish mutant vps18 as a model for vesicle-traffic related hypopigmentation diseases.
    2. Mutation of the class C vacuolar protein sorting gene vps18 results in hepatomegaly associated with large, vesicle-filled hepatocytes.
      Title: A genetic screen in zebrafish identifies the mutants vps18, nf2 and foie gras as models of liver disease.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC103535, MGC173734

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein-macromolecule adaptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within apical protein localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within bile acid and bile salt transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endosome to lysosome transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within endosome to lysosome transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within endosome to pigment granule transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within eye pigmentation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lysosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within notochord cell vacuolation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within optokinetic behavior IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in organelle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within pigment granule maturation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vesicle docking involved in exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of HOPS complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosomal membrane 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
    		  

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein 18 homolog
    Names
    vacuolar protein sorting 18 homolog
    vacuolar protein sorting protein 18

    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_173245.2 → NP_775352.2  vacuolar protein sorting-associated protein 18 homolog

      See identical proteins and their annotated locations for NP_775352.2

      Status: PROVISIONAL

      Source sequence(s)
      BC086828
      UniProtKB/Swiss-Prot
      P59015, Q5SPB8
      UniProtKB/TrEMBL
      B7ZVV5
      Related
      ENSDARP00000094129.3, ENSDART00000103352.4
      Conserved Domains (3) summary
      smart00299
      Location:641 → 768
      CLH; Clathrin heavy chain repeat homology
      pfam00637
      Location:618 → 743
      Clathrin; Region in Clathrin and VPS
      pfam05131
      Location:291 → 435
      Pep3_Vps18; Pep3/Vps18/deep orange family

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007131.7 Reference GRCz11 Primary Assembly

      Range
      28354269..28361557 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P59015.2 GenPept UniProtKB/Swiss-Prot:P59015

    Gene LinkOut

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