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

Gene ID: 287535, updated on 18-Sep-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
EnsemblRapid: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 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 IDA
Inferred from Direct Assay
more info
 PubMed 
located_in recycling endosome ISO
Inferred from Sequence Orthology
more info
  
located_in trans-Golgi network IDA
Inferred from Direct Assay
more info
 PubMed 

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
    ENSRNOP00000096750.2, ENSRNOT00000116582.2
    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
    Related
    ENSRNOP00000081957.2, ENSRNOT00000099955.2
    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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