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    vps50 VPS50 EARP/GARPII complex subunit [ Danio rerio (zebrafish) ]

    Gene ID: 100034394, updated on 27-Mar-2024

    Summary

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    Official Symbol
    vps50provided by ZNC
    Official Full Name
    VPS50 EARP/GARPII complex subunitprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-060503-325
    See related
    Ensembl:ENSDARG00000002880 AllianceGenome:ZFIN:ZDB-GENE-060503-325
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    ccdc132; si:ch211-128d6.1; si:ch211-287b5.1; si:ch211-77k19.1
    Summary
    Predicted to enable SNARE binding activity. Predicted to be involved in endocytic recycling. Predicted to act upstream of or within retrograde transport, endosome to Golgi. Predicted to be part of EARP complex. Is expressed in head and heart. Orthologous to human VPS50 (VPS50 subunit of EARP/GARPII complex). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See vps50 in Genome Data Viewer
    Location:
    chromosome: 19
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (40379766..40686033)
    105 previous assembly GRCz10 (GCF_000002035.5) 19 NC_007130.6 (40792648..41099264)

    Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 133 member B Neighboring gene HEPACAM family member 2 Neighboring gene calcitonin receptor Neighboring gene microRNA 489 Neighboring gene tissue factor pathway inhibitor 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. The rare mutation in the endosome-associated recycling protein gene VPS50 is associated with human neural tube defects. Shi Z, et al. Mol Cytogenet, 2019. PMID 30828385, Free PMC Article
    2. Calcitonin receptor family evolution and fishing for function using in silico promoter analysis. Martins R, et al. Gen Comp Endocrinol, 2014 Dec 1. PMID 24815885
    3. Zebrafish Collagen Type I: Molecular and Biochemical Characterization of the Major Structural Protein in Bone and Skin. Gistelinck C, et al. Sci Rep, 2016 Feb 15. PMID 26876635, Free PMC Article
    4. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Lo J, et al. Genome Res, 2003 Mar. PMID 12618376, Free PMC Article
    5. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables SNARE binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within endocytic recycling IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within retrograde transport, endosome to Golgi IEA
    Inferred from Electronic Annotation
    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
    		  

    General protein information

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    Preferred Names
    syndetin
    Names
    coiled-coil domain containing 132

    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_001365104.1 → NP_001352033.1  syndetin isoform 1

      Status: VALIDATED

      Source sequence(s)
      BX936336, CABZ01060509, CABZ01060512, CABZ01060513, CABZ01060514, CT027724
      UniProtKB/TrEMBL
      A0A8M6Z2H2
      Conserved Domains (2) summary
      pfam10474
      Location:752 → 983
      DUF2451; Protein of unknown function C-terminus (DUF2451)
      pfam10475
      Location:54 → 345
      Vps54_N; Vacuolar-sorting protein 54, of GARP complex

    2. NM_001365105.1 → NP_001352034.1  syndetin isoform 2

      Status: VALIDATED

      Source sequence(s)
      BX936336, CABZ01060509, CABZ01060512, CABZ01060513, CABZ01060514, CT027724
      UniProtKB/TrEMBL
      A0A8M6YWH5, F1R0A4
      Conserved Domains (2) summary
      pfam10474
      Location:727 → 958
      DUF2451; Protein of unknown function C-terminus (DUF2451)
      pfam10475
      Location:54 → 345
      Vps54_N; Vacuolar-sorting protein 54, of GARP complex

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007130.7 Reference GRCz11 Primary Assembly

      Range
      40379766..40686033
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017352306.2 → XP_017207795.1  syndetin isoform X1

      UniProtKB/TrEMBL
      A0A8M6Z2H2
      Conserved Domains (2) summary
      pfam10474
      Location:752 → 983
      DUF2451; Protein of unknown function C-terminus (DUF2451)
      pfam10475
      Location:54 → 345
      Vps54_N; Vacuolar-sorting protein 54, of GARP complex

    2. XM_017352308.2 → XP_017207797.1  syndetin isoform X3

      UniProtKB/TrEMBL
      A0A8M6YWH5, F1R0A4
      Related
      ENSDARP00000101077.2, ENSDART00000110699.4
      Conserved Domains (2) summary
      pfam10474
      Location:727 → 958
      DUF2451; Protein of unknown function C-terminus (DUF2451)
      pfam10475
      Location:54 → 345
      Vps54_N; Vacuolar-sorting protein 54, of GARP complex

    3. XM_017352307.2 → XP_017207796.1  syndetin isoform X2

      UniProtKB/TrEMBL
      A0A8M6YUM6

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018395058.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      34364..205405
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021473351.1 → XP_021329026.1  syndetin isoform X4

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018395059.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      6447..51178
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021473352.1 → XP_021329027.1  syndetin isoform X5

    Nucleotide Protein Strain
    Heading Accession and Version

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