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    Vps53 VPS53 subunit of GARP complex [ Rattus norvegicus (Norway rat) ]

    Gene ID: 287535, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Vps53provided by RGD
    Official Full Name
    VPS53 subunit of GARP complexprovided by RGD
    Primary source
    RGD:1311391
    See related
    Ensembl:ENSRNOG00000006895 AllianceGenome:RGD:1311391
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1311391
    Summary
    Predicted to be involved in endocytic recycling and retrograde transport, endosome to Golgi. Predicted to act upstream of or within lysosomal transport. Predicted to be located in several cellular components, including Golgi apparatus; perinuclear region of cytoplasm; and recycling endosome. Predicted to be part of EARP complex and GARP complex. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 2E. Orthologous to human VPS53 (VPS53 subunit of GARP complex). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 36.1), Thymus (RPKM 34.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Vps53 in Genome Data Viewer
    Location:
    10q24
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (61418076..61536912, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (60919820..61038674, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (64218596..64341064, complement)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120095142 Neighboring gene refilin B Neighboring gene uncharacterized LOC103693391 Neighboring gene ribosomal protein L37-like 1 Neighboring gene TLC domain containing 3A Neighboring gene gem (nuclear organelle) associated protein 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. Characterization of the human GARP (Golgi associated retrograde protein) complex. Liewen H, et al. Exp Cell Res, 2005 May 15. PMID 15878329
    2. TSSC1 is novel component of the endosomal retrieval machinery. Gershlick DC, et al. Mol Biol Cell, 2016 Sep 15. PMID 27440922, Free PMC Article
    3. Dual roles of the mammalian GARP complex in tethering and SNARE complex assembly at the trans-golgi network. Pérez-Victoria FJ, et al. Mol Cell Biol, 2009 Oct. PMID 19620288, Free PMC Article
    4. EARP is a multisubunit tethering complex involved in endocytic recycling. Schindler C, et al. Nat Cell Biol, 2015 May. PMID 25799061, Free PMC Article
    5. The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles. Topalidou I, et al. PLoS Genet, 2016 May. PMID 27191843, Free PMC Article

    See all (7) 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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endocytic recycling ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within lysosomal transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein targeting to lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in vesicle-mediated cholesterol transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of EARP complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of GARP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of GARP complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in recycling endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in trans-Golgi network IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein 53 homolog
    Names
    VPS53 GARP complex subunit
    vacuolar protein sorting 53 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_001105813.1 → NP_001099283.1  vacuolar protein sorting-associated protein 53 homolog

      See identical proteins and their annotated locations for NP_001099283.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473948
      UniProtKB/TrEMBL
      A6HGU5, B4F763, D3ZPE5
      Related
      ENSRNOP00000010010.2, ENSRNOT00000010010.5
      Conserved Domains (1) summary
      pfam04100
      Location:40 → 453
      Vps53_N; Vps53-like, N-terminal

    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_086028.1 Reference GRCr8

      Range
      61418076..61536912 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039085521.2 → XP_038941449.1  vacuolar protein sorting-associated protein 53 homolog isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZUQ6
      Conserved Domains (1) summary
      pfam04100
      Location:13 → 371
      Vps53_N; Vps53-like, N-terminal
    Nucleotide Protein Strain
    Heading Accession and Version

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