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

Gene ID: 362199, updated on 13-Apr-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
Ensembl: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 enable ATP binding activity and kinase activity. 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, Apr 2022]
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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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, ENSRNOT00000011155.6
    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
    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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