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VPS52 VPS52 subunit of GARP complex [ Homo sapiens (human) ]

Gene ID: 6293, updated on 17-Jun-2019

Summary

Official Symbol
VPS52provided by HGNC
Official Full Name
VPS52 subunit of GARP complexprovided by HGNC
Primary source
HGNC:HGNC:10518
See related
Ensembl:ENSG00000223501 MIM:603443
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
ARE1; SAC2; SACM2L; dJ1033B10.5
Summary
This gene encodes a protein that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and late endosomes, back to the trans-Golgi network. This gene is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
Expression
Ubiquitous expression in thyroid (RPKM 15.7), testis (RPKM 14.8) and 25 other tissues See more
Orthologs

Genomic context

See VPS52 in Genome Data Viewer
Location:
6p21.32
Exon count:
23
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (33250272..33271965, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33218049..33239723, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene zinc finger protein 70 pseudogene 1 Neighboring gene uncharacterized LOC105375022 Neighboring gene HLA complex group 25 Neighboring gene ribosomal protein S18 Neighboring gene beta-1,3-galactosyltransferase 4 Neighboring gene WD repeat domain 46

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • RP5-1033B10, DKFZp547I194

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rab GTPase binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
syntaxin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
syntaxin binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Golgi to vacuole transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ectodermal cell differentiation IEA
Inferred from Electronic Annotation
more info
 
embryonic ectodermal digestive tract development IEA
Inferred from Electronic Annotation
more info
 
endocytic recycling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endocytic recycling IMP
Inferred from Mutant Phenotype
more info
PubMed 
lysosomal transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lysosomal transport IDA
Inferred from Direct Assay
more info
PubMed 
protein transport IEA
Inferred from Electronic Annotation
more info
 
retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
EARP complex IDA
Inferred from Direct Assay
more info
PubMed 
GARP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
 
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
recycling endosome IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
vacuolar protein sorting-associated protein 52 homolog
Names
SAC2 suppressor of actin mutations 2-like protein
VPS52, GARP complex subunit
vacuolar protein sorting 52 homolog

NCBI Reference Sequences (RefSeq)

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_001289174.2NP_001276103.1  vacuolar protein sorting-associated protein 52 homolog isoform 2

    See identical proteins and their annotated locations for NP_001276103.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, initiates translation at an alternate start codon and lacks an alternate exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK093057, AK299563, BQ022405
    UniProtKB/TrEMBL
    B4DS44
    Conserved Domains (1) summary
    pfam04129
    Location:27534
    Vps52; Vps52 / Sac2 family
  2. NM_001289175.1NP_001276104.1  vacuolar protein sorting-associated protein 52 homolog isoform 3

    See identical proteins and their annotated locations for NP_001276104.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 3, which is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AK001725, AK093057, AK297935, AK299563, BQ022405, DC395438
    UniProtKB/Swiss-Prot
    Q8N1B4
    UniProtKB/TrEMBL
    A0A1U9X8S4, B3KMF7, B4DS44
    Conserved Domains (1) summary
    pfam04129
    Location:1476
    Vps52; Vps52 / Sac2 family
  3. NM_001289176.1NP_001276105.1  vacuolar protein sorting-associated protein 52 homolog isoform 4

    See identical proteins and their annotated locations for NP_001276105.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 4, which is shorter than isoform 1.
    Source sequence(s)
    AK001725, AK093057, AK299563, BQ022405, DC395438
    UniProtKB/Swiss-Prot
    Q8N1B4
    UniProtKB/TrEMBL
    B3KMF7, B4DS44
    Conserved Domains (1) summary
    cl19950
    Location:1412
    Sec3_C; Exocyst complex component Sec3
  4. NM_022553.6NP_072047.4  vacuolar protein sorting-associated protein 52 homolog isoform 1

    See identical proteins and their annotated locations for NP_072047.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK001725, BC040114, DC400338
    Consensus CDS
    CCDS4770.2
    UniProtKB/Swiss-Prot
    Q8N1B4
    UniProtKB/TrEMBL
    B3KMF7, Q4VXZ2
    Related
    ENSP00000409952.2, ENST00000445902.3
    Conserved Domains (1) summary
    pfam04129
    Location:94601
    Vps52; Vps52 / Sac2 family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    33250272..33271965 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011178.1XP_016866667.1  vacuolar protein sorting-associated protein 52 homolog isoform X3

    UniProtKB/Swiss-Prot
    Q8N1B4
    UniProtKB/TrEMBL
    A0A1U9X8S4
    Conserved Domains (1) summary
    pfam04129
    Location:1476
    Vps52; Vps52 / Sac2 family
  2. XM_011514799.1XP_011513101.1  vacuolar protein sorting-associated protein 52 homolog isoform X3

    See identical proteins and their annotated locations for XP_011513101.1

    Conserved Domains (1) summary
    pfam04129
    Location:27534
    Vps52; Vps52 / Sac2 family
  3. XM_011514797.1XP_011513099.1  vacuolar protein sorting-associated protein 52 homolog isoform X3

    See identical proteins and their annotated locations for XP_011513099.1

    Conserved Domains (1) summary
    pfam04129
    Location:27534
    Vps52; Vps52 / Sac2 family
  4. XM_011514798.2XP_011513100.1  vacuolar protein sorting-associated protein 52 homolog isoform X3

    See identical proteins and their annotated locations for XP_011513100.1

    Conserved Domains (1) summary
    pfam04129
    Location:27534
    Vps52; Vps52 / Sac2 family
  5. XM_024446519.1XP_024302287.1  vacuolar protein sorting-associated protein 52 homolog isoform X3

    Conserved Domains (1) summary
    pfam04129
    Location:1476
    Vps52; Vps52 / Sac2 family
  6. XM_017011177.2XP_016866666.1  vacuolar protein sorting-associated protein 52 homolog isoform X1

  7. XM_017011179.2XP_016866668.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    4661769..4683446 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

    Range
    4493784..4515479 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

    Range
    4669733..4671435 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    Range
    4686254..4707927 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    Range
    4444672..4466382 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    4698976..4720646 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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