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    Vps39 VPS39 subunit of HOPS complex [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362199, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Vps39provided by RGD
    Official Full Name
    VPS39 subunit of HOPS complexprovided by RGD
    Primary source
    RGD:1304858
    See related
    EnsemblRapid:ENSRNOG00000008316 AllianceGenome:RGD:1304858
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to be involved in endocytic recycling; lysosomal transport; and vesicle fusion. Predicted to be located in late endosome membrane and lysosomal membrane. Predicted to be part of AP-3 adaptor complex and lysosomal 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]
    Expression
    Biased expression in Brain (RPKM 128.1), Heart (RPKM 115.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Vps39 in Genome Data Viewer
    Location:
    3q35
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (127721076..127758658, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (107266846..107304884, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (112087213..112125307, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene phospholipase A2 group IVD Neighboring gene phospholipase A2, group IVF Neighboring gene ribosomal protein S25, pseudogene 11 Neighboring gene transmembrane protein 87A Neighboring gene glucosidase, alpha; neutral C Neighboring gene uncharacterized LOC108350445 Neighboring gene calpain 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. The HOPS proteins hVps41 and hVps39 are required for homotypic and heterotypic late endosome fusion. Pols MS, et al. Traffic, 2013 Feb. PMID 23167963
    2. The HOPS complex mediates autophagosome-lysosome fusion through interaction with syntaxin 17. Jiang P, et al. Mol Biol Cell, 2014 Apr. PMID 24554770, Free PMC Article
    3. Structural basis of Vps33A recruitment to the human HOPS complex by Vps16. Graham SC, et al. Proc Natl Acad Sci U S A, 2013 Aug 13. PMID 23901104, Free PMC Article
    4. Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome Fusion with Endosomes and Autophagosomes. Wartosch L, et al. Traffic, 2015 Jul. PMID 25783203, Free PMC Article
    5. Mammalian CORVET is required for fusion and conversion of distinct early endosome subpopulations. Perini ED, et al. Traffic, 2014 Dec. PMID 25266290

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in autophagosome-lysosome fusion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in autophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endocytic recycling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endosomal vesicle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endosomal vesicle fusion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endosome to lysosome transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in late endosome to lysosome transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of AP-3 adaptor complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of HOPS complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in late endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of lysosomal HOPS complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosomal membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    vam6/Vps39-like protein
    Names
    VPS39 HOPS complex subunit
    Vam6
    vacuolar protein sorting 39 homolog

    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_001012186.2 → NP_001012186.2  vam6/Vps39-like protein

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      E9PT04
      Related
      ENSRNOP00000011155.5, ENSRNOT00000011155.7
      Conserved Domains (5) summary
      smart00299
      Location:584 → 735
      CLH; Clathrin heavy chain repeat homology
      pfam00637
      Location:588 → 735
      Clathrin; Region in Clathrin and VPS
      pfam10366
      Location:449 → 551
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:761 → 868
      Vps39_2; Vacuolar sorting protein 39 domain 2
      cl02434
      Location:20 → 280
      CNH; CNH domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      127721076..127758658 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006234782.5 → XP_006234844.1  vam6/Vps39-like protein isoform X1

      UniProtKB/TrEMBL
      A0A0G2KA50
      Related
      ENSRNOP00000075259.2, ENSRNOT00000085132.3
      Conserved Domains (5) summary
      smart00299
      Location:595 → 746
      CLH; Clathrin heavy chain repeat homology
      pfam00637
      Location:599 → 746
      Clathrin; Region in Clathrin and VPS
      pfam10366
      Location:460 → 562
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:772 → 879
      Vps39_2; Vacuolar sorting protein 39 domain 2
      cl02434
      Location:20 → 291
      CNH; CNH domain

    2. XM_039105457.2 → XP_038961385.1  vam6/Vps39-like protein isoform X2

      UniProtKB/TrEMBL
      E9PT04
      Conserved Domains (4) summary
      pfam10366
      Location:426 → 528
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:738 → 846
      Vps39_2; Vacuolar sorting protein 39 domain 2
      cl02434
      Location:46 → 257
      CNH; CNH domain
      cl26078
      Location:565 → 712
      Clathrin; Region in Clathrin and VPS
    Nucleotide Protein Strain
    Heading Accession and Version

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