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

Gene ID: 100034394, updated on 2-Nov-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, Nov 2024]
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
RS_2024_08 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (40379761..40687805)
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 si:ch211-120e1.1 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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: GCF_000002035.6-RS_2024_08

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
    40379761..40687805
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017352306.3 → 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_017352308.3 → 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_017352307.3 → XP_017207796.1  syndetin isoform X2

    UniProtKB/TrEMBL
    A0A8M6YUM6
Nucleotide Protein Strain
Heading Accession and Version

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