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

Gene ID: 179902, updated on 2-Nov-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, Nov 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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