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    Vps53 VPS53 GARP complex subunit [ Mus musculus (house mouse) ]

    Gene ID: 68299, updated on 9-Dec-2024

    Summary

    Official Symbol
    Vps53provided by MGI
    Official Full Name
    VPS53 GARP complex subunitprovided by MGI
    Primary source
    MGI:MGI:1915549
    See related
    Ensembl:ENSMUSG00000017288 AllianceGenome:MGI:1915549
    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
    Hccs1; 2010002A08Rik; 2310040I21Rik; 3100002B05Rik
    Summary
    Involved in protein targeting to lysosome and vesicle-mediated cholesterol transport. Predicted to be located in several cellular components, including perinuclear region of cytoplasm; recycling endosome; and trans-Golgi network. 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, Dec 2024]
    Expression
    Ubiquitous expression in CNS E18 (RPKM 8.3), cerebellum adult (RPKM 8.2) and 28 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Vps53 in Genome Data Viewer
    Location:
    11 B5; 11 45.92 cM
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (75937052..76070464, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (76046226..76179638, complement)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_30012 Neighboring gene ligand of ATE1 Neighboring gene refilin B Neighboring gene STARR-seq mESC enhancer starr_30013 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:75920753-75920862 Neighboring gene predicted gene, 46252 Neighboring gene TLC domain containing 3A Neighboring gene STARR-positive B cell enhancer ABC_E8426 Neighboring gene gem nuclear organelle associated protein 4

    Genomic regions, transcripts, and products

    Expression

    • 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

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Gene trapped (1) 
    • Targeted (3)  1 citation

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: Glod4

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    involved_in endocytic recycling ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in endocytic recycling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within lysosomal transport ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    involved_in protein targeting to lysosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 retrograde transport, endosome to Golgi ISS
    Inferred from Sequence or Structural Similarity
    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 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
    PubMed 
    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
    PubMed 
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    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
    PubMed 
    located_in recycling endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in trans-Golgi network ISO
    Inferred from Sequence Orthology
    more info
    PubMed 

    General protein information

    Preferred Names
    vacuolar protein sorting-associated protein 53 homolog

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001364738.1NP_001351667.1  vacuolar protein sorting-associated protein 53 homolog isoform 2

      Status: VALIDATED

      Source sequence(s)
      AK008026, AK009586, AL591129
      Related
      ENSMUST00000140886.3
      Conserved Domains (1) summary
      pfam04100
      Location:4061
      Vps53_N; Vps53-like, N-terminal
    2. NM_026664.4NP_080940.2  vacuolar protein sorting-associated protein 53 homolog isoform 1

      See identical proteins and their annotated locations for NP_080940.2

      Status: VALIDATED

      Source sequence(s)
      AK009586, AK033495
      Consensus CDS
      CCDS25060.1
      UniProtKB/Swiss-Prot
      Q8C7U0, Q8CCB4, Q8CIA1, Q9CX82, Q9D6T7
      UniProtKB/TrEMBL
      Q3TJT1, Q3TLZ3, Q3TX19, Q3UDN2
      Related
      ENSMUSP00000061317.5, ENSMUST00000056601.11
      Conserved Domains (1) summary
      pfam04100
      Location:40453
      Vps53_N; Vps53-like, N-terminal

    RNA

    1. NR_157296.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AK009586, CA325661
      Related
      ENSMUST00000129256.2

    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_000077.7 Reference GRCm39 C57BL/6J

      Range
      75937052..76070464 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)