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    Vps50 VPS50 subunit of EARP/GARPII complex [ Rattus norvegicus (Norway rat) ]

    Gene ID: 312083, updated on 2-Nov-2024

    Summary

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    Symbol
    Vps50provided by RGD
    Full Name
    VPS50 subunit of EARP/GARPII complexprovided by RGD
    Primary source
    RGD:1304751
    See related
    EnsemblRapid:ENSRNOG00000009894 AllianceGenome:RGD:1304751
    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
    Ccdc132; RGD1304751
    Summary
    Predicted to enable SNARE binding activity. Predicted to be involved in endocytic recycling. Located in membrane; perinuclear region of cytoplasm; and recycling endosome. Orthologous to human VPS50 (VPS50 subunit of EARP/GARPII complex). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 119.9), Kidney (RPKM 85.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Vps50 in Genome Data Viewer
    Location:
    4q13
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (32439101..32540299)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (31484424..31585617)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (28441255..28551784)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene sterile alpha motif domain containing 9 like Neighboring gene HEPACAM family member 2 Neighboring gene calcitonin receptor Neighboring gene microRNA 653 Neighboring gene microRNA 489

    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. A proposed clinical application of a model of CO2 laser radiation induced damage craters. Canestri F. J Med Eng Technol, 1988 May-Jun. PMID 3172165
    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. EARP is a multisubunit tethering complex involved in endocytic recycling. Schindler C, et al. Nat Cell Biol, 2015 May. PMID 25799061, Free PMC Article
    4. 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
    5. Large-scale proteomics and phosphoproteomics of urinary exosomes. Gonzales PA, et al. J Am Soc Nephrol, 2009 Feb. PMID 19056867, Free PMC Article

    See all (8) 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 SNARE binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables SNARE binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endocytic recycling IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within endocytic recycling ISO
    Inferred from Sequence Orthology
    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 protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IEA
    Inferred from Electronic Annotation
    more info
    		  
    NOT involved_in retrograde transport, endosome to Golgi ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT involved_in retrograde transport, endosome to Golgi ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of EARP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of EARP complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of EARP complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of EARP complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 recycling endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    syndetin
    Names
    EARP/GARPII complex subunit VPS50
    VPS50 EARP/GARPII complex subunit
    coiled-coil domain containing 132
    coiled-coil domain-containing protein 132
    coiled-coil domain-containing protein 132-like
    syndetin-like

    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_001173511.1 → NP_001166982.1  syndetin

      See identical proteins and their annotated locations for NP_001166982.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/Swiss-Prot
      F1LSG8
      UniProtKB/TrEMBL
      A0A8I6GK25
      Related
      ENSRNOP00000059003.1, ENSRNOT00000067087.4
      Conserved Domains (2) summary
      pfam10474
      Location:726 → 957
      DUF2451; Protein of unknown function C-terminus (DUF2451)
      pfam10475
      Location:54 → 345
      DUF2450; Protein of unknown function N-terminal domain (DUF2450)

    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_086022.1 Reference GRCr8

      Range
      32439101..32540299
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008762704.4 → XP_008760926.1  syndetin isoform X1

      UniProtKB/TrEMBL
      A0A8I6GK25
      Conserved Domains (2) summary
      pfam10474
      Location:725 → 956
      DUF2451; Protein of unknown function C-terminus (DUF2451)
      pfam10475
      Location:54 → 345
      DUF2450; Protein of unknown function N-terminal domain (DUF2450)

    2. XM_006236037.5 → XP_006236099.1  syndetin isoform X2

      UniProtKB/TrEMBL
      A0A8I6GK25
      Conserved Domains (2) summary
      pfam10474
      Location:724 → 955
      DUF2451; Protein of unknown function C-terminus (DUF2451)
      pfam10475
      Location:54 → 343
      DUF2450; Protein of unknown function N-terminal domain (DUF2450)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    F1LSG8.1 GenPept UniProtKB/Swiss-Prot:F1LSG8

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