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    VPS54 VPS54 subunit of GARP complex [ Sus scrofa (pig) ]

    Gene ID: 100621212, updated on 17-Aug-2024

    Summary

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    Official Symbol
    VPS54provided by VGNC
    Official Full Name
    VPS54 subunit of GARP complexprovided by VGNC
    Primary source
    VGNC:VGNC:94862
    See related
    Ensembl:ENSSSCG00000027509
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Sus scrofa
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Suina; Suidae; Sus
    Expression
    Ubiquitous expression in liver (RPKM 23.3), psoas major muscle (RPKM 19.5) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See VPS54 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    106 current Sscrofa11.1 (GCF_000003025.6) 3 NC_010445.4 (77856093..77978194)
    105 previous assembly Sscrofa10.2 (GCF_000003025.5) 3 NC_010445.3 (81716210..81780374)

    Chromosome 3 - NC_010445.4Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC110259999 Neighboring gene pellino E3 ubiquitin protein ligase 1 Neighboring gene proline-rich protein HaeIII subfamily 1-like Neighboring gene UDP-glucose pyrophosphorylase 2 Neighboring gene nucleoplasmin-2 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Transcriptome data used for gene annotation Transcriptome data used for gene annotation
    • Description: Nine kinds of tissues and a mixture of multiple tissues were sequenced for genome annotation
    • BioProject: PRJNA311523
    • Publication: PMID 27646534
    • Analysis date: Thu Dec 14 17:10:49 2017

    Bibliography

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    Related articles in PubMed

    1. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
    2. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables syntaxin binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi to vacuole transport IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in retrograde transport, endosome to Golgi IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of GARP complex IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein 54
    Names
    VPS54, GARP complex subunit

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: Sus scrofa 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 Sscrofa11.1 Primary Assembly

    Genomic

    1. NC_010445.4 Reference Sscrofa11.1 Primary Assembly

      Range
      77856093..77978194
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021087458.1 → XP_020943117.1  vacuolar protein sorting-associated protein 54 isoform X1

      UniProtKB/TrEMBL
      A0A0B8RVD6, A0A286ZL70, A0A4X1WB22, A0A8D1C776, A0A8D1HRQ3
      Conserved Domains (1) summary
      pfam07928
      Location:737 → 867
      Vps54; Vps54-like protein

    2. XM_021087460.1 → XP_020943119.1  vacuolar protein sorting-associated protein 54 isoform X2

      UniProtKB/TrEMBL
      A0A480PKZ3, A0A8D1C776
      Conserved Domains (1) summary
      pfam07928
      Location:725 → 855
      Vps54; Vps54-like protein

    3. XM_021087462.1 → XP_020943121.1  vacuolar protein sorting-associated protein 54 isoform X3

      UniProtKB/TrEMBL
      A0A480TLG6, A0A4X1WC89, A0A5G2RHB5, A0A8D1XUJ6
      Related
      ENSSSCP00000074549.1, ENSSSCT00000073694.1
      Conserved Domains (1) summary
      pfam07928
      Location:634 → 764
      Vps54; Vps54-like protein

    4. XM_021087459.1 → XP_020943118.1  vacuolar protein sorting-associated protein 54 isoform X1

      UniProtKB/TrEMBL
      A0A0B8RVD6, A0A286ZL70, A0A4X1WB22, A0A8D1C776, A0A8D1HRQ3
      Related
      ENSSSCP00000032215.1, ENSSSCT00000054111.3
      Conserved Domains (1) summary
      pfam07928
      Location:737 → 867
      Vps54; Vps54-like protein

    RNA

    1. XR_002342640.1 RNA Sequence

    2. XR_002342639.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version

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