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    Vps11 VPS11 core subunit of CORVET and HOPS complexes [ Rattus norvegicus (Norway rat) ]

    Gene ID: 315600, updated on 6-Jun-2024

    Summary

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    Official Symbol
    Vps11provided by RGD
    Official Full Name
    VPS11 core subunit of CORVET and HOPS complexesprovided by RGD
    Primary source
    RGD:1308038
    See related
    Ensembl:ENSRNOG00000010733 AllianceGenome:RGD:1308038
    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 several functions, including protein-macromolecule adaptor activity; syntaxin binding activity; and ubiquitin protein ligase activity. Predicted to be involved in several processes, including negative regulation of intracellular estrogen receptor signaling pathway; positive regulation of intracellular transport; and vesicle organization. Predicted to act upstream of or within toxin transport. Predicted to be located in actin filament and endocytic vesicle. Predicted to be part of AP-3 adaptor complex; CORVET complex; and HOPS complex. Predicted to be active in endosome and presynaptic active zone. Predicted to colocalize with early endosome; late endosome; and lysosome. Human ortholog(s) of this gene implicated in hypomyelinating leukodystrophy 12. Orthologous to human VPS11 (VPS11 core subunit of CORVET and HOPS complexes). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Adrenal (RPKM 167.6), Brain (RPKM 144.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Vps11 in Genome Data Viewer
    Location:
    8q22
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (53580939..53595378, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (44684129..44698568, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (48677492..48692295, complement)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene H2A.X variant histone Neighboring gene hydroxymethylbilane synthase Neighboring gene hypoxia up-regulated 1 Neighboring gene solute carrier family 37 member 4

    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 ERM proteins interact with the HOPS complex to regulate the maturation of endosomes. Chirivino D, et al. Mol Biol Cell, 2011 Feb 1. PMID 21148287, Free PMC Article
    2. Molecular characterization of mammalian homologues of class C Vps proteins that interact with syntaxin-7. Kim BY, et al. J Biol Chem, 2001 Aug 3. PMID 11382755
    3. The interaction of mammalian Class C Vps with nSec-1/Munc18-a and syntaxin 1A regulates pre-synaptic release. Kim BY, et al. Biochem Biophys Res Commun, 2006 Nov 24. PMID 17027648
    4. 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
    5. 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

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 RGD

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein domain specific binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein-macromolecule adaptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables syntaxin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin protein ligase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endosomal vesicle fusion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endosome organization IBA
    Inferred from Biological aspect of Ancestor
    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 negative regulation of intracellular estrogen receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in organelle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of early endosome to late endosome transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of protein targeting to mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    involved_in protein ubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of organelle assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of protein stability ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    involved_in vacuole organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle docking involved in exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of AP-3 adaptor complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of CORVET complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of HOPS complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of HOPS complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in actin filament ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in autophagosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in clathrin-coated vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endocytic vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in late endosome ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in presynaptic active zone ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein 11 homolog
    Names
    VPS11 CORVET/HOPS core subunit
    vacuolar protein sorting 11 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_001108138.2 → NP_001101608.2  vacuolar protein sorting-associated protein 11 homolog

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      B5DF01, D3ZTB4
      Related
      ENSRNOP00000061998.2, ENSRNOT00000065456.2
      Conserved Domains (4) summary
      cd16688
      Location:820 → 863
      RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins
      pfam00637
      Location:411 → 536
      Clathrin; Region in Clathrin and VPS
      pfam12451
      Location:864 → 907
      VPS11_C; Vacuolar protein sorting protein 11 C terminal
      cl29593
      Location:142 → 292
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    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_086026.1 Reference GRCr8

      Range
      53580939..53595378 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063265432.1 → XP_063121502.1  vacuolar protein sorting-associated protein 11 homolog isoform X1

      UniProtKB/TrEMBL
      B5DF01, D3ZTB4

    2. XM_039081427.1 → XP_038937355.1  vacuolar protein sorting-associated protein 11 homolog isoform X2

      Conserved Domains (3) summary
      cd16688
      Location:458 → 501
      RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins
      pfam00637
      Location:49 → 174
      Clathrin; Region in Clathrin and VPS
      pfam12451
      Location:502 → 545
      VPS11_C; Vacuolar protein sorting protein 11 C terminal
    Nucleotide Protein Strain
    Heading Accession and Version

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