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    Vps52 VPS52 GARP complex subunit [ Mus musculus (house mouse) ]

    Gene ID: 224705, updated on 8-May-2024

    Summary

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    Official Symbol
    Vps52provided by MGI
    Official Full Name
    VPS52 GARP complex subunitprovided by MGI
    Primary source
    MGI:MGI:1330304
    See related
    Ensembl:ENSMUSG00000024319 AllianceGenome:MGI:1330304
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    ARE1; SAC2; tclw5; Sacm2l; D130068D18; D430041K17Rik
    Summary
    Predicted to enable syntaxin binding activity. Acts 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. Is expressed in several structures, including brain; genitourinary system; heart; hemolymphoid system gland; and liver. Orthologous to human VPS52 (VPS52 subunit of GARP complex). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in adrenal adult (RPKM 27.3), thymus adult (RPKM 23.9) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Vps52 in Genome Data Viewer
    Location:
    17 B1; 17 17.98 cM
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (34174753..34186012)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (33955779..33967038)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E8668 Neighboring gene UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4 Neighboring gene ribosomal protein S18 Neighboring gene STARR-positive B cell enhancer ABC_E3199 Neighboring gene predicted gene, 23111 Neighboring gene histocompatibility 2, K region locus 2 Neighboring gene STARR-positive B cell enhancer ABC_E2483 Neighboring gene STARR-seq mESC enhancer starr_42421 Neighboring gene predicted gene, 53998

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. The Vps52 subunit of the GARP and EARP complexes is a novel Arf6-interacting protein that negatively regulates neurite outgrowth of hippocampal neurons. Ibuchi K, et al. Brain Res, 2020 Oct 15. PMID 32473257
    2. Genome-wide analysis of epigenomic alterations in fetal mouse forebrain after exposure to low doses of bisphenol A. Yaoi T, et al. Biochem Biophys Res Commun, 2008 Nov 21. PMID 18804091
    3. Studies of the Genetic Variability in Wild Populations of House Mice. I. Analysis of Seven Alleles at Locus T. Dunn LC, et al. Genetics, 1956 May. PMID 17247632, Free PMC Article
    4. The GARP Complex Is Involved in Intracellular Cholesterol Transport via Targeting NPC2 to Lysosomes. Wei J, et al. Cell Rep, 2017 Jun 27. PMID 28658628
    5. 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

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Vps52 subunit of the GARP and EARP complexes is a novel Arf6-interacting protein that negatively regulates neurite outgrowth of hippocampal neurons.
      Title: The Vps52 subunit of the GARP and EARP complexes is a novel Arf6-interacting protein that negatively regulates neurite outgrowth of hippocampal neurons.
    2. The Vps52 was responsible for the tw5 mutation, and revealed development-specific functions of this gene, which was formerly thought to be solely involved in retrograde endocytic transport.
      Title: Molecular identification of t(w5): Vps52 promotes pluripotential cell differentiation through cell-cell interactions.
    Submit: New GeneRIF Correction

    Phenotypes

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    Associated conditions

    Description Tests
    t-complex lethal w5
    GeneReviews: Not available

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    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 MGI

    Function Evidence Code Pubs
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within embryonic ectodermal digestive tract development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 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
    		 PubMed 
    involved_in protein targeting IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within 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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of EARP complex ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    part_of GARP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of GARP complex ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in postsynapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in presynapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in recycling endosome ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein 52 homolog
    Names
    vacuolar protein sorting 52

    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_001357329.1 → NP_001344258.1  vacuolar protein sorting-associated protein 52 homolog isoform 2

      Status: VALIDATED

      Source sequence(s)
      BE945926, CR974462
      UniProtKB/TrEMBL
      A0A068BGT0, Q3V3A4
      Conserved Domains (1) summary
      pfam04129
      Location:1 → 476
      Vps52; Vps52 / Sac2 family

    2. NM_001357330.1 → NP_001344259.1  vacuolar protein sorting-associated protein 52 homolog isoform 3

      Status: VALIDATED

      Source sequence(s)
      BE945926, CR974462
      Conserved Domains (1) summary
      cl19950
      Location:1 → 349
      Sec3_C; Exocyst complex component Sec3

    3. NM_001379410.1 → NP_001366339.1  vacuolar protein sorting-associated protein 52 homolog isoform 4

      Status: VALIDATED

      Source sequence(s)
      CR974462
      UniProtKB/TrEMBL
      A0A068BGT0
      Conserved Domains (1) summary
      pfam04129
      Location:94 → 606
      Vps52; Vps52 / Sac2 family

    4. NM_001379411.1 → NP_001366340.1  vacuolar protein sorting-associated protein 52 homolog isoform 5

      Status: VALIDATED

      Source sequence(s)
      CR974462
      Conserved Domains (1) summary
      cl19950
      Location:1 → 354
      Sec3_C; Exocyst complex component Sec3

    5. NM_172620.4 → NP_766208.2  vacuolar protein sorting-associated protein 52 homolog isoform 1

      See identical proteins and their annotated locations for NP_766208.2

      Status: VALIDATED

      Source sequence(s)
      AK051732, AK052523, BE945926, CR974462
      Consensus CDS
      CCDS37574.1
      UniProtKB/Swiss-Prot
      Q6P4N7, Q8BQ15, Q8C754, Q9QWT6, Q9QWV2
      UniProtKB/TrEMBL
      A0A068BGT0
      Related
      ENSMUSP00000025178.10, ENSMUST00000025178.17
      Conserved Domains (1) summary
      pfam04129
      Location:94 → 601
      Vps52; Vps52 / Sac2 family

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000083.7 Reference GRCm39 C57BL/6J

      Range
      34174753..34186012
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030249706.1 → XP_030105566.1  vacuolar protein sorting-associated protein 52 homolog isoform X1

      UniProtKB/TrEMBL
      A0A068BGT0, Q3V3A4
      Conserved Domains (1) summary
      pfam04129
      Location:1 → 481
      Vps52; Vps52 / Sac2 family

    RNA

    1. XR_001782066.2 RNA Sequence

    2. XR_003952110.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8C754.1 GenPept UniProtKB/Swiss-Prot:Q8C754

    Gene LinkOut

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

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