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    Vps52 VPS52 subunit of GARP complex [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25218, updated on 2-May-2024

    Summary

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    Official Symbol
    Vps52provided by RGD
    Official Full Name
    VPS52 subunit of GARP complexprovided by RGD
    Primary source
    RGD:3618
    See related
    Ensembl:ENSRNOG00000000470 AllianceGenome:RGD:3618
    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
    Also known as
    Are1; Sacm2l
    Summary
    Predicted to enable syntaxin binding activity. Predicted to be involved in Golgi to vacuole transport; endosomal transport; and lysosomal transport. Predicted to act upstream of or within ectodermal cell differentiation and embryonic ectodermal digestive tract development. 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. Orthologous to human VPS52 (VPS52 subunit of GARP complex). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Lung (RPKM 264.5), Thymus (RPKM 262.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Vps52 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (4922599..4933458, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (4920715..4931685, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (5431997..5441736, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene LOC224733l-1 pseudogene Neighboring gene RT1 class Ia, locus A1 Neighboring gene U6 spliceosomal RNA Neighboring gene ribosomal protein S18 Neighboring gene Beta-1,3-galactosyltransferase 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. Identification of a novel highly conserved gene in the centromeric part of the major histocompatibility complex. Walter L, et al. Genomics, 1998 Sep 15. PMID 9790748
    2. Molecular identification of t(w5): Vps52 promotes pluripotential cell differentiation through cell-cell interactions. Sugimoto M, et al. Cell Rep, 2012 Nov 29. PMID 23142660
    3. Characterization of the human GARP (Golgi associated retrograde protein) complex. Liewen H, et al. Exp Cell Res, 2005 May 15. PMID 15878329
    4. TSSC1 is novel component of the endosomal retrieval machinery. Gershlick DC, et al. Mol Biol Cell, 2016 Sep 15. PMID 27440922, Free PMC Article
    5. EARP is a multisubunit tethering complex involved in endocytic recycling. Schindler C, et al. Nat Cell Biol, 2015 May. PMID 25799061, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    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 
    enables syntaxin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables syntaxin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in Golgi to vacuole transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within ectodermal cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within embryonic ectodermal digestive tract development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endocytic recycling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endocytic recycling ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in lysosomal transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within lysosomal transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein targeting ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    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 EARP complex ISS
    Inferred from Sequence or Structural Similarity
    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 IEA
    Inferred from Electronic Annotation
    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 endosome membrane IEA
    Inferred from Electronic Annotation
    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
    		  
    is_active_in postsynapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in presynapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in recycling endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in recycling endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein 52 homolog
    Names
    SAC2 suppressor of actin mutations 2-like protein
    VPS52 GARP complex subunit
    vacuolar protein sorting 52 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_033097.2 → NP_149088.1  vacuolar protein sorting-associated protein 52 homolog

      See identical proteins and their annotated locations for NP_149088.1

      Status: VALIDATED

      Source sequence(s)
      BC166419
      UniProtKB/Swiss-Prot
      O55166
      UniProtKB/TrEMBL
      A0A8I6A724, B2GUV2
      Related
      ENSRNOP00000000549.3, ENSRNOT00000000549.6
      Conserved Domains (1) summary
      pfam04129
      Location:94 → 601
      Vps52; Vps52 / Sac2 family

    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_086038.1 Reference GRCr8

      Range
      4922599..4933458 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008772707.3 → XP_008770929.1  vacuolar protein sorting-associated protein 52 homolog isoform X1

      UniProtKB/TrEMBL
      A0A8I6A724
      Related
      ENSRNOP00000087040.1
      Conserved Domains (1) summary
      pfam04129
      Location:94 → 618
      Vps52; Vps52 / Sac2 family

    2. XM_063278973.1 → XP_063135043.1  vacuolar protein sorting-associated protein 52 homolog isoform X3

    3. XM_039098438.2 → XP_038954366.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

      UniProtKB/TrEMBL
      A0A8I6A724
      Conserved Domains (1) summary
      pfam04129
      Location:94 → 618
      Vps52; Vps52 / Sac2 family

    4. XM_039098440.2 → XP_038954368.1  vacuolar protein sorting-associated protein 52 homolog isoform X4

      Conserved Domains (1) summary
      cl19950
      Location:94 → 380
      Sec3_C; Exocyst complex component Sec3

    RNA

    1. XR_005497175.2 RNA Sequence

    2. XR_005497174.2 RNA Sequence

    3. XR_005497173.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O55166.2 GenPept UniProtKB/Swiss-Prot:O55166

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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