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VPS54 VPS54, GARP complex subunit [ Homo sapiens (human) ]

Gene ID: 51542, updated on 12-May-2016
Official Symbol
VPS54provided by HGNC
Official Full Name
VPS54, GARP complex subunitprovided by HGNC
Primary source
HGNC:HGNC:18652
See related
Ensembl:ENSG00000143952 HPRD:10302; MIM:614633; Vega:OTTHUMG00000152627
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
WR; HCC8; SLP-8p; VPS54L; hVps54L; PPP1R164
Summary
This gene encodes for a protein that in yeast forms part of a trimeric vacuolar-protein-sorting complex that is required for retrograde transport of proteins from prevacuoles to the late Golgi compartment. As in yeast, mammalian Vps54 proteins contain a coiled-coil region and dileucine motifs. Alternative splicing results in multiple transcript variants encoding different isoforms [provided by RefSeq, Jul 2008]
Orthologs
Location:
2p13-p14
Exon count:
25
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 2 NC_000002.12 (63892150..64019080, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (64119280..64246526, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374766 Neighboring gene UDP-glucose pyrophosphorylase 2 Neighboring gene uncharacterized LOC105374765 Neighboring gene uncharacterized LOC105374767 Neighboring gene pellino E3 ubiquitin protein ligase 1 Neighboring gene long intergenic non-protein coding RNA 309

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystem (from REACTOME)
    Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystemThe mammalian Golgi complex, a central hub of both anterograde and retrograde trafficking, is a ribbon of stacked cisterna with biochemically distinct compartments (reviewed in Glick and Nakano, 2009...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Retrograde transport at the Trans-Golgi-Network, organism-specific biosystem (from REACTOME)
    Retrograde transport at the Trans-Golgi-Network, organism-specific biosystemThe trans-Golgi network is the docking site for retrograde cargo from the endolysosomal system and the plasma membrane. Typical cargo includes recycling resident TGN proteins such as TGOLN2 (also kn...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
syntaxin binding IBA
Inferred from Biological aspect of Ancestor
more info
 
Process Evidence Code Pubs
Golgi to vacuole transport IBA
Inferred from Biological aspect of Ancestor
more info
 
growth IEA
Inferred from Electronic Annotation
more info
 
homeostasis of number of cells within a tissue IEA
Inferred from Electronic Annotation
more info
 
lysosomal transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
musculoskeletal movement IEA
Inferred from Electronic Annotation
more info
 
neurofilament cytoskeleton organization IEA
Inferred from Electronic Annotation
more info
 
protein transport IEA
Inferred from Electronic Annotation
more info
 
retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
 
retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
GARP complex IDA
Inferred from Direct Assay
more info
PubMed 
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network membrane TAS
Traceable Author Statement
more info
 
Preferred Names
vacuolar protein sorting-associated protein 54
Names
VPS54 GARP complex subunit
hepatocellular carcinoma protein 8
protein phosphatase 1, regulatory subunit 164
tumor antigen HOM-HCC-8
tumor antigen SLP-8p
vacuolar protein sorting 54 homolog

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.

Genomic

  1. NG_042277.1 RefSeqGene

    Range
    5001..131548
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001005739.1NP_001005739.1  vacuolar protein sorting-associated protein 54 isoform 2

    See identical proteins and their annotated locations for NP_001005739.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in one of the 5' coding exons compared to transcript variant 1, resulting in a shorter isoform (2) compared to isoform 1.
    Source sequence(s)
    AK002205, AL514510, AW452246, BC030275, BC041868
    Consensus CDS
    CCDS46302.1
    UniProtKB/Swiss-Prot
    Q9P1Q0
    Related
    ENSP00000386980, OTTHUMP00000202090, ENST00000409558, OTTHUMT00000327063
    Conserved Domains (1) summary
    pfam07928
    Location:723857
    Vps54; Vps54-like protein
  2. NM_016516.2NP_057600.2  vacuolar protein sorting-associated protein 54 isoform 1

    See identical proteins and their annotated locations for NP_057600.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AF102177, AK002205, AL514510, AW452246, BC030275, BC041868
    Consensus CDS
    CCDS33208.1
    UniProtKB/Swiss-Prot
    Q9P1Q0
    Related
    ENSP00000272322, OTTHUMP00000202089, ENST00000272322, OTTHUMT00000327062
    Conserved Domains (1) summary
    pfam07928
    Location:735869
    Vps54; Vps54-like protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p2 Primary Assembly

    Range
    63892150..64019080 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006712029.2XP_006712092.1  

    Related
    ENSP00000346499, OTTHUMP00000202091, ENST00000354504, OTTHUMT00000327064
    Conserved Domains (1) summary
    pfam07928
    Location:699833
    Vps54; Vps54-like protein
  2. XM_011532903.1XP_011531205.1  

    Conserved Domains (1) summary
    pfam10475
    Location:207331
    DUF2450; Protein of unknown function N-terminal domain (DUF2450)

RNA

  1. XR_244939.3 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018913.2 Alternate CHM1_1.1

    Range
    64049942..64176502 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)