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vps53 VPS53 subunit of GARP complex [ Danio rerio (zebrafish) ]

Gene ID: 492817, updated on 2-Nov-2024

Summary

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Official Symbol
vps53provided by ZNC
Official Full Name
VPS53 subunit of GARP complexprovided by ZNC
Primary source
ZFIN:ZDB-GENE-041114-199
See related
Ensembl:ENSDARG00000069324 AllianceGenome:ZFIN:ZDB-GENE-041114-199
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
wu:fb77d11; zgc:103741
Summary
Predicted to be involved in retrograde transport, endosome to Golgi. Predicted to be located in Golgi apparatus and endosome membrane. Predicted to be part of 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, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See vps53 in Genome Data Viewer
Location:
chromosome: 15
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 15 NC_007126.7 (25100722..25153352, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 15 NC_007126.6 (25165457..25218088, complement)

Chromosome 15 - NC_007126.7Genomic Context describing neighboring genes Neighboring gene exonuclease 5 Neighboring gene refilin B Neighboring gene uncharacterized LOC137487753 Neighboring gene info solute carrier family 35 member F2, like Neighboring gene MAX network transcriptional repressor a

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. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, Free PMC Article
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
  4. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
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 GARP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of GARP complex IEA
Inferred from Electronic Annotation
more info
  
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
located_in endosome IEA
Inferred from Electronic Annotation
more info
  
located_in endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
vacuolar protein sorting-associated protein 53 homolog
Names
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_001007458.2 → NP_001007459.2  vacuolar protein sorting-associated protein 53 homolog

    Status: VALIDATED

    Source sequence(s)
    BX908796
    UniProtKB/TrEMBL
    A0A8M1N3K3, F6P6T6
    Related
    ENSDARP00000072558.4, ENSDART00000078095.4
    Conserved Domains (2) summary
    pfam04100
    Location:39 → 451
    Vps53_N; Vps53-like, N-terminal
    pfam16854
    Location:691 → 775
    VPS53_C; Vacuolar protein sorting-associated protein 53 C-terminus

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_007126.7 Reference GRCz11 Primary Assembly

    Range
    25100722..25153352 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005157580.5 → XP_005157637.1  vacuolar protein sorting-associated protein 53 homolog isoform X1

    UniProtKB/TrEMBL
    A0A8M2B4E9, E7FAG0
    Related
    ENSDARP00000110309.1, ENSDART00000122184.4
    Conserved Domains (2) summary
    pfam04100
    Location:39 → 452
    Vps53_N; Vps53-like, N-terminal
    pfam16854
    Location:692 → 776
    VPS53_C; Vacuolar protein sorting-associated protein 53 C-terminus

Reference GRCz11 ALT_DRER_TU_2

Genomic

  1. NW_018395323.1 Reference GRCz11 ALT_DRER_TU_2

    Range
    437709..490335 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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