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Aliases for VPS29 Gene

Aliases for VPS29 Gene

  • Vacuolar Protein Sorting 29 Homolog (S. Cerevisiae) 2 3
  • Vesicle Protein Sorting 29 3 4
  • PEP11 Homolog 3 4
  • HVPS29 3 4
  • Vacuolar Protein Sorting-Associated Protein 29 3
  • Vacuolar Protein Sorting 29 (Yeast Homolog) 2
  • Vacuolar Sorting Protein VPS29/PEP11 3
  • Vacuolar Protein Sorting 29 (Yeast) 2
  • Retromer Protein 3
  • X 007 Protein 3
  • EC 3.1.3.3 63
  • PEP11 3
  • DC15 3
  • DC7 3

External Ids for VPS29 Gene

Previous GeneCards Identifiers for VPS29 Gene

  • GC12M109953
  • GC12M110725
  • GC12M110771
  • GC12M109341
  • GC12M109392
  • GC12M110929
  • GC12M107947

Summaries for VPS29 Gene

Entrez Gene Summary for VPS29 Gene

  • This gene belongs to a group of vacuolar protein sorting (VPS) genes that, when functionally impaired, disrupt the efficient delivery of vacuolar hydrolases. The protein encoded by this gene is a component of a large multimeric complex, termed the retromer complex, which is involved in retrograde transport of proteins from endosomes to the trans-Golgi network. This VPS protein may be involved in the formation of the inner shell of the retromer coat for retrograde vesicles leaving the prevacuolar compartment. Alternative splice variants encoding different isoforms and representing non-protein coding transcripts have been found for this gene. [provided by RefSeq, Aug 2013]

GeneCards Summary for VPS29 Gene

VPS29 (Vacuolar Protein Sorting 29 Homolog (S. Cerevisiae)) is a Protein Coding gene. Among its related pathways are Signaling by GPCR and beta-catenin independent WNT signaling. GO annotations related to this gene include phosphoserine phosphatase activity.

UniProtKB/Swiss-Prot for VPS29 Gene

  • Acts as component of the retromer cargo-selective complex (CSC). The CSC is believed to be the core functional component of retromer or respective retromer complex variants acting to prevent missorting of selected transmembrane cargo proteins into the lysosomal degradation pathway. The recruitment of the CSC to the endosomal membrane involves RAB7A and SNX3. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX3-retromer mediates the retrograde endosome-to-TGN transport of WLS distinct from the SNX-BAR retromer pathway. The SNX27-retromer is believed to be involved in endosome-to-plasma membrane trafficking and recycling of a broad spectrum of cargo proteins. The CSC seems to act as recruitment hub for other proteins, such as the WASH complex and TBC1D5. Required to regulate transcytosis of the polymeric immunoglobulin receptor (pIgR-pIgA) (Probable). Involved in GLUT1 endosome-to-plasma membrane trafficking; the function is dependent of association with ANKRD27 (PubMed:24856514).

Gene Wiki entry for VPS29 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS29 Gene

Genomics for VPS29 Gene

Regulatory Elements for VPS29 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for VPS29 Gene

Start:
110,491,097 bp from pter
End:
110,502,140 bp from pter
Size:
11,044 bases
Orientation:
Minus strand

Genomic View for VPS29 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for VPS29 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS29 Gene

Proteins for VPS29 Gene

  • Protein details for VPS29 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBQ0-VPS29_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 29
    Protein Accession:
    Q9UBQ0
    Secondary Accessions:
    • Q502Y5
    • Q6FIF8
    • Q6IAH3
    • Q9H0W0
    • Q9NRP1
    • Q9NRU7

    Protein attributes for VPS29 Gene

    Size:
    182 amino acids
    Molecular mass:
    20506 Da
    Quaternary structure:
    • Component of the heterotrimeric retromer cargo-selective complex (CSC), also described as vacuolar protein sorting subcomplex (VPS), formed by VPS26 (VPS26A or VPS26B), VPS29 and VPS35 (PubMed:11102511, PubMed:16737443, PubMed:17891154). The CSC has a highly elongated structure with VPS26 and VPS29 binding independently at opposite distal ends of VPS35 as central platform (By similarity). The CSC is believed to associate with variable sorting nexins to form functionally distinct retromer complex variants. The originally described retromer complex (also called SNX-BAR retromer) is a pentamer containing the CSC and a heterodimeric membrane-deforming subcomplex formed between SNX1 or SNX2 and SNX5 or SNX6 (also called SNX-BAR subcomplex); the respective CSC and SNX-BAR subcomplexes associate with low affinity. The CSC associates with SNX3 to form a SNX3-retromer complex. The CSC associates with SNX27, the WASH complex and the SNX-BAR subcomplex to form the SNX27-retromer complex (Probable). Interacts with VPS26A, VPS35, SNX1, SNX2, SNX27, KIAA0196, TBC1D5 (PubMed:11102511, PubMed:20923837, PubMed:23331060, PubMed:23563491). Interacts with VPS26B and ANKRD27 (By similarity).

    Three dimensional structures from OCA and Proteopedia for VPS29 Gene

    Alternative splice isoforms for VPS29 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS29 Gene

Proteomics data for VPS29 Gene at MOPED

Post-translational modifications for VPS29 Gene

  • Ubiquitination at Lys30 and Lys50
  • Modification sites at PhosphoSitePlus

Other Protein References for VPS29 Gene

Antibody Products

Domains for VPS29 Gene

Suggested Antigen Peptide Sequences for VPS29 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UBQ0

UniProtKB/Swiss-Prot:

VPS29_HUMAN :
  • Q9UBQ0
Family:
  • Belongs to the VPS29 family.
genes like me logo Genes that share domains with VPS29: view

No data available for Gene Families for VPS29 Gene

Function for VPS29 Gene

Molecular function for VPS29 Gene

UniProtKB/Swiss-Prot Function:
Acts as component of the retromer cargo-selective complex (CSC). The CSC is believed to be the core functional component of retromer or respective retromer complex variants acting to prevent missorting of selected transmembrane cargo proteins into the lysosomal degradation pathway. The recruitment of the CSC to the endosomal membrane involves RAB7A and SNX3. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX3-retromer mediates the retrograde endosome-to-TGN transport of WLS distinct from the SNX-BAR retromer pathway. The SNX27-retromer is believed to be involved in endosome-to-plasma membrane trafficking and recycling of a broad spectrum of cargo proteins. The CSC seems to act as recruitment hub for other proteins, such as the WASH complex and TBC1D5. Required to regulate transcytosis of the polymeric immunoglobulin receptor (pIgR-pIgA) (Probable). Involved in GLUT1 endosome-to-plasma membrane trafficking; the function is dependent of association with ANKRD27 (PubMed:24856514).

Enzyme Numbers (IUBMB) for VPS29 Gene

Gene Ontology (GO) - Molecular Function for VPS29 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004647 phosphoserine phosphatase activity --
GO:0005515 protein binding IPI 11102511
GO:0008270 zinc ion binding IBA --
GO:0008565 contributes_to protein transporter activity IBA --
GO:0046872 metal ion binding --
genes like me logo Genes that share ontologies with VPS29: view

Phenotypes for VPS29 Gene

GenomeRNAi human phenotypes for VPS29:
genes like me logo Genes that share phenotypes with VPS29: view

Animal Model Products

miRNA for VPS29 Gene

miRTarBase miRNAs that target VPS29

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VPS29

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for VPS29 Gene

Localization for VPS29 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS29 Gene

Cytoplasm. Membrane; Peripheral membrane protein. Endosome membrane; Peripheral membrane protein. Early endosome. Late endosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VPS29 Gene COMPARTMENTS Subcellular localization image for VPS29 gene
Compartment Confidence
endosome 5
cytosol 3
mitochondrion 2
nucleus 2
golgi apparatus 1
lysosome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for VPS29 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA --
GO:0005768 endosome IDA --
GO:0005769 early endosome IEA --
GO:0005770 late endosome IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with VPS29: view

Pathways for VPS29 Gene

genes like me logo Genes that share pathways with VPS29: view

Pathways by source for VPS29 Gene

Gene Ontology (GO) - Biological Process for VPS29 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IBA --
GO:0015031 protein transport --
GO:0016311 dephosphorylation --
GO:0042147 retrograde transport, endosome to Golgi IBA --
GO:1990126 retrograde transport, endosome to plasma membrane IMP 24856514
genes like me logo Genes that share ontologies with VPS29: view

Transcripts for VPS29 Gene

Unigene Clusters for VPS29 Gene

Vacuolar protein sorting 29 homolog (S. cerevisiae):
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VPS29

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS29 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c · 6d ^ 7a · 7b · 7c ^ 8a · 8b
SP1: - - - - - - -
SP2: - - - - - -
SP3: - - - - - - - -
SP4: - - - - - - -
SP5: - - -
SP6:
SP7: - - - -
SP8:
SP9: - - -
SP10:

Relevant External Links for VPS29 Gene

GeneLoc Exon Structure for
VPS29
ECgene alternative splicing isoforms for
VPS29

Expression for VPS29 Gene

mRNA expression in normal human tissues for VPS29 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, MOPED, and MaxQB for VPS29 Gene

SOURCE GeneReport for Unigene cluster for VPS29 Gene Hs.600114

mRNA Expression by UniProt/SwissProt for VPS29 Gene

Q9UBQ0-VPS29_HUMAN
Tissue specificity: Ubiquitous. Highly expressed in heart, lung, placenta, spleen, peripheral blood leukocytes, thymus, colon skeletal muscle, kidney and brain
genes like me logo Genes that share expressions with VPS29: view

Expression partners for VPS29 Gene

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and Protein differential expression in normal tissues for VPS29 Gene

Orthologs for VPS29 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS29 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia VPS29 35
  • 95.47 (n)
  • 100 (a)
VPS29 36
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS29 35
  • 96.01 (n)
  • 100 (a)
VPS29 36
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vps29 35
  • 90.19 (n)
  • 100 (a)
Vps29 16
Vps29 36
  • 99 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia VPS29 35
  • 99.69 (n)
  • 99.53 (a)
VPS29 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps29 35
  • 91.11 (n)
  • 99.44 (a)
oppossum
(Monodelphis domestica)
Mammalia VPS29 36
  • 99 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS29 36
  • 97 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS29 35
  • 85.33 (n)
  • 97.28 (a)
VPS29 36
  • 95 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 85 (a)
OneToMany
-- 36
  • 97 (a)
OneToMany
-- 36
  • 90 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.3938 35
vps29 35
  • 82.41 (n)
  • 97.78 (a)
zebrafish
(Danio rerio)
Actinopterygii vps29 35
  • 79.07 (n)
  • 96.67 (a)
wufb06g05 35
vps29 36
  • 96 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9310 35
fruit fly
(Drosophila melanogaster)
Insecta CG4764 37
  • 83 (a)
CG4764 35
  • 70.93 (n)
  • 83.89 (a)
CG4764 36
  • 83 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002338 35
  • 70 (n)
  • 86.67 (a)
worm
(Caenorhabditis elegans)
Secernentea ZK1128.8 37
  • 60 (a)
vps-29 35
  • 61.51 (n)
  • 59.67 (a)
vps-29 36
  • 57 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS29 36
  • 29 (a)
OneToOne
VPS29 38
thale cress
(Arabidopsis thaliana)
eudicotyledons MAG1 35
  • 62.06 (n)
  • 65.75 (a)
barley
(Hordeum vulgare)
Liliopsida Hv.3466 35
rice
(Oryza sativa)
Liliopsida Os.10198 35
Os02g0265400 35
  • 62.04 (n)
  • 65 (a)
corn
(Zea mays)
Liliopsida Zm.8987 35
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8907 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.866 36
  • 76 (a)
OneToOne
Species with no ortholog for VPS29:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VPS29 Gene

ENSEMBL:
Gene Tree for VPS29 (if available)
TreeFam:
Gene Tree for VPS29 (if available)

Paralogs for VPS29 Gene

Selected SIMAP similar genes for VPS29 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with VPS29: view

No data available for Paralogs for VPS29 Gene

Variants for VPS29 Gene

Sequence variations from dbSNP and Humsavar for VPS29 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type MAF
rs1063335 -- 110,493,181(-) AAAAT(C/T)GGTCT synonymous-codon, reference, intron-variant, nc-transcript-variant
rs1063336 -- 110,493,169(-) ATCCA(C/T)GGACA synonymous-codon, reference, intron-variant, nc-transcript-variant
rs1063337 -- 110,493,151(-) ATTCC(A/G)TGGGG reference, synonymous-codon, intron-variant, nc-transcript-variant
rs1063338 -- 110,493,142(-) GGAGA(C/T)ATGGC synonymous-codon, reference, intron-variant, nc-transcript-variant
rs1063339 -- 110,493,123(-) CCCTG(C/T)TGCAG synonymous-codon, reference, intron-variant, nc-transcript-variant

Structural Variations from Database of Genomic Variants (DGV) for VPS29 Gene

Variant ID Type Subtype PubMed ID
nsv826512 CNV Loss 20364138

Relevant External Links for VPS29 Gene

HapMap Linkage Disequilibrium report
VPS29

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS29 Gene

Disorders for VPS29 Gene

No disorders were found for VPS29 Gene.

No data available for MalaCards , OMIM , UniProtKB/Swiss-Prot , University of Copenhagen DISEASES , Novoseek inferred disease relationships , Genatlas and External Links for VPS29 Gene

Publications for VPS29 Gene

  1. Human homologues of yeast vacuolar protein sorting 29 and 35. (PMID: 11062004) Edgar A.J. … Polak J.M. (Biochem. Biophys. Res. Commun. 2000) 2 3 4 23
  2. Crystal structure of human vacuolar protein sorting protein 29 reveals a phosphodiesterase/nuclease-like fold and two protein-protein interaction sites. (PMID: 15788412) Wang D. … Liu P. (J. Biol. Chem. 2005) 3 4 23
  3. The human Vps29 retromer component is a metallo-phosphoesterase for a cation-independent mannose 6-phosphate receptor substrate peptide. (PMID: 16737443) Damen E. … van Leeuwen J.E.M. (Biochem. J. 2006) 3 4 23
  4. Membrane recruitment of the cargo-selective retromer subcomplex is catalysed by the small GTPase Rab7 and inhibited by the Rab-GAP TBC1D5. (PMID: 19531583) Seaman M.N. … Bright N. (J. Cell. Sci. 2009) 3 23
  5. Human orthologs of yeast vacuolar protein sorting proteins Vps26, 29, and 35: assembly into multimeric complexes. (PMID: 11102511) Renfrew Haft C. … Taylor S.I. (Mol. Biol. Cell 2000) 3 4

Products for VPS29 Gene

Sources for VPS29 Gene

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