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

Gene ID: 224705, updated on 2-Nov-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. Involved in protein targeting and vesicle-mediated cholesterol transport. Acts upstream of or within ectodermal cell differentiation and embryonic ectodermal digestive tract development. Is active in postsynapse and presynapse. 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, Nov 2024]
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 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. Gene mapping within the T/t complex of the mouse. I. t-Lethal genes are nonallelic. Artzt K, et al. Cell, 1982 Mar. PMID 7074682
  5. 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

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 IEA
Inferred from Electronic Annotation
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 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
 PubMed 
involved_in protein targeting IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 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 endosome membrane IEA
Inferred from Electronic Annotation
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
  
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
  
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
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

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