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    vps-39 CNH domain-containing protein;Vacuolar protein sorting-associated protein 39 homolog [ Caenorhabditis elegans ]

    Gene ID: 179902, updated on 9-Dec-2024

    Summary

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    Official Symbol
    vps-39
    Official Full Name
    CNH domain-containing protein;Vacuolar protein sorting-associated protein 39 homolog
    Primary source
    WormBase:WBGene00011625
    Locus tag
    CELE_T08G5.5
    See related
    AllianceGenome:WB:WBGene00011625
    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
    Predicted to be involved in autophagy and endosomal vesicle fusion. Predicted to be located in late endosome membrane and lysosomal membrane. Predicted to be part of HOPS complex. Predicted to be active in cytoplasm and membrane. Orthologous to human VPS39 (VPS39 subunit of HOPS complex). [provided by Alliance of Genome Resources, Dec 2024]
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    Genomic context

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    See vps-39 in Genome Data Viewer
    Location:
    chromosome: V
    Exon count:
    10
    Sequence:
    Chromosome: V; NC_003283.11 (14034323..14038378, complement)

    Chromosome V - NC_003283.11Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene pseudo Neighboring gene INSulin related Neighboring gene pseudo Neighboring gene ncRNA Neighboring gene C2H2-type domain-containing protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003283.11

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. CUTI-1: A novel tetraspan protein involved in C. elegans CUTicle formation and epithelial integrity. Fritz JA, et al. PLoS One, 2009. PMID 19357781, Free PMC Article
    2. Human GABARAP can restore autophagosome biogenesis in a C. elegans lgg-1 mutant. Jenzer C, et al. Autophagy, 2014 Oct 1. PMID 25126728, Free PMC Article
    3. The C. elegans LC3 acts downstream of GABARAP to degrade autophagosomes by interacting with the HOPS subunit VPS39. Manil-Ségalen M, et al. Dev Cell, 2014 Jan 13. PMID 24374177
    4. Lysosome biogenesis mediated by vps-18 affects apoptotic cell degradation in Caenorhabditis elegans. Xiao H, et al. Mol Biol Cell, 2009 Jan. PMID 18923146, Free PMC Article
    5. Caenorhabditis elegans SAND-1 is essential for RAB-7 function in endosomal traffic. Poteryaev D, et al. EMBO J, 2007 Jan 24. PMID 17203072, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Interacts with LGG-1 and LGG-2 during allophagy.
      Title: The C. elegans LC3 acts downstream of GABARAP to degrade autophagosomes by interacting with the HOPS subunit VPS39.
    Submit: New GeneRIF Correction

    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 autophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endosomal vesicle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of HOPS complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in late 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
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    CNH domain-containing protein;Vacuolar protein sorting-associated protein 39 homolog
    NP_001041163.1
    • Confirmed by transcript evidence
    NP_001041164.1
    • Confirmed by transcript evidence
    NP_001123010.1
    • Confirmed by transcript evidence
    NP_001360569.1
    • 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_003283.11 Reference assembly

      Range
      14034323..14038378 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001047699.5 → NP_001041164.1  Vacuolar protein sorting-associated protein 39 homolog [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001041164.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A8JJR1, Q1ZXS5, Q9XUQ4
      Conserved Domains (3) summary
      pfam00780
      Location:21 → 303
      CNH; CNH domain
      pfam10366
      Location:471 → 576
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:811 → 919
      Vps39_2; Vacuolar sorting protein 39 domain 2

    2. NM_001129538.6 → NP_001123010.1  Vacuolar protein sorting-associated protein 39 homolog [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001123010.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q1ZXS5
      Conserved Domains (5) summary
      pfam00637
      Location:598 → 736
      Clathrin; Region in Clathrin and VPS
      pfam00780
      Location:21 → 303
      CNH; CNH domain
      pfam04556
      Location:318 → 384
      DpnII; DpnII restriction endonuclease
      pfam10366
      Location:468 → 573
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:805 → 913
      Vps39_2; Vacuolar sorting protein 39 domain 2

    3. NM_001373154.2 → NP_001360569.1  CNH domain-containing protein [Caenorhabditis elegans]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A486WXM5
      Conserved Domains (3) summary
      pfam00780
      Location:21 → 303
      CNH; CNH domain
      pfam10366
      Location:468 → 573
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:808 → 916
      Vps39_2; Vacuolar sorting protein 39 domain 2

    4. NM_001047698.5 → NP_001041163.1  Vacuolar protein sorting-associated protein 39 homolog [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001041163.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q1ZXS5
      Conserved Domains (5) summary
      pfam00637
      Location:601 → 739
      Clathrin; Region in Clathrin and VPS
      pfam00780
      Location:21 → 303
      CNH; CNH domain
      pfam04556
      Location:318 → 384
      DpnII; DpnII restriction endonuclease
      pfam10366
      Location:471 → 576
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:808 → 916
      Vps39_2; Vacuolar sorting protein 39 domain 2
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q1ZXS5.1

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