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    vps39 VPS39 subunit of HOPS complex [ Danio rerio (zebrafish) ]

    Gene ID: 567078, updated on 4-Jan-2025

    Summary

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    Official Symbol
    vps39provided by ZNC
    Official Full Name
    VPS39 subunit of HOPS complexprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-080530-2
    See related
    Ensembl:ENSDARG00000074471 AllianceGenome:ZFIN:ZDB-GENE-080530-2
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    lbk; vam6
    Summary
    Acts upstream of or within developmental pigmentation; eye development; and vesicle-mediated transport. Is expressed in brain; digestive system; head; and integument. Orthologous to human VPS39 (VPS39 subunit of HOPS complex). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    human mouse all
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    Genomic context

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    See vps39 in Genome Data Viewer
    Location:
    chromosome: 17
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 17 NC_007128.7 (50073970..50113486)
    105 previous assembly GRCz10 (GCF_000002035.5) 17 NC_007128.6 (49994882..50034417)

    Chromosome 17 - NC_007128.7Genomic Context describing neighboring genes Neighboring gene zgc:100951 Neighboring gene zgc:173816 Neighboring gene UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16 Neighboring gene Jun dimerization protein 2a

    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 lbk/vam6 resembles human multisystemic disorders caused by aberrant trafficking of endosomal vesicles. Schonthaler HB, et al. Development, 2008 Jan. PMID 18077594
    2. Nxhl Controls Angiogenesis by Targeting VE-PTP Through Interaction With Nucleolin. Luo H, et al. Front Cell Dev Biol, 2021. PMID 34733844, Free PMC Article
    3. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, Free PMC Article
    4. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The present study provides the first phenotypic description of a lack of vam6 gene function in a multicellular organism.
      Title: The zebrafish mutant lbk/vam6 resembles human multisystemic disorders caused by aberrant trafficking of endosomal vesicles.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Process Evidence Code Pubs
    acts_upstream_of_or_within developmental pigmentation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within eye development 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 intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    vam6/Vps39-like protein
    Names
    vacuolar protein sorting 39 homolog
    vesicle fusion protein

    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_001113540.2 → NP_001107012.2  vam6/Vps39-like protein

      Status: VALIDATED

      Source sequence(s)
      CU655820, CU928140, EF446162
      UniProtKB/TrEMBL
      A0A8N1YZ39, B0EXK3
      Related
      ENSDARP00000100792.2, ENSDART00000113644.4
      Conserved Domains (4) summary
      pfam00637
      Location:579 → 734
      Clathrin; Region in Clathrin and VPS
      pfam10366
      Location:448 → 550
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:760 → 868
      Vps39_2; Vacuolar sorting protein 39 domain 2
      cl02434
      Location:20 → 278
      CNH; CNH domain

    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_007128.7 Reference GRCz11 Primary Assembly

      Range
      50073970..50113486
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005158918.5 → XP_005158975.1  vam6/Vps39-like protein isoform X1

      UniProtKB/TrEMBL
      A0A8M2B5G7, B0EXK3
      Conserved Domains (4) summary
      pfam00637
      Location:578 → 733
      Clathrin; Region in Clathrin and VPS
      pfam10366
      Location:447 → 549
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:759 → 867
      Vps39_2; Vacuolar sorting protein 39 domain 2
      cl02434
      Location:20 → 277
      CNH; CNH domain
    Nucleotide Protein Strain
    Heading Accession and Version

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