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Vps29 VPS29 retromer complex component [ Mus musculus (house mouse) ]

Gene ID: 56433, updated on 13-Jan-2025

Summary

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Official Symbol
Vps29provided by MGI
Official Full Name
VPS29 retromer complex componentprovided by MGI
Primary source
MGI:MGI:1928344
See related
Ensembl:ENSMUSG00000029462 AllianceGenome:MGI:1928344
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
PEP11; 2010015D08Rik
Summary
Predicted to enable metal ion binding activity. Predicted to be involved in endocytic recycling; intracellular protein transport; and retrograde transport, endosome to Golgi. Predicted to act upstream of or within Golgi to vacuole transport. Part of retromer complex. Is expressed in cranial ganglion; dorsal root ganglion; and gonad. Orthologous to human VPS29 (VPS29 retromer complex component). [provided by Alliance of Genome Resources, Jan 2025]
Expression
Ubiquitous expression in CNS E18 (RPKM 27.9), placenta adult (RPKM 22.1) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Vps29 in Genome Data Viewer
Location:
5 F; 5 62.32 cM
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (122492391..122503047)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (122354328..122364984)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 1700112N08 gene Neighboring gene STARR-seq mESC enhancer starr_14278 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:122738438-122738621 Neighboring gene PTC7 protein phosphatase homolog Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:122760748-122760949 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:122761679-122761976 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:122767369-122767570 Neighboring gene RAD9 checkpoint clamp component B Neighboring gene STARR-positive B cell enhancer ABC_E2761 Neighboring gene STARR-seq mESC enhancer starr_14283 Neighboring gene family with sequence similarity 216, member A Neighboring gene GPN-loop GTPase 3 Neighboring gene predicted gene, 32853 Neighboring gene STARR-positive B cell enhancer ABC_E4787 Neighboring gene STARR-positive B cell enhancer ABC_E8077 Neighboring gene actin related protein 2/3 complex, subunit 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. The Vps35 D620N mutation linked to Parkinson's disease disrupts the cargo sorting function of retromer. Follett J, et al. Traffic, 2014 Feb. PMID 24152121
  2. Identification of novel retromer complexes in the mouse testis. Kim E, et al. Biochem Biophys Res Commun, 2008 Oct 10. PMID 18656452
  3. Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer assembly. Collins BM, et al. Nat Struct Mol Biol, 2005 Jul. PMID 15965486
  4. Human homologues of yeast vacuolar protein sorting 29 and 35. Edgar AJ, et al. Biochem Biophys Res Commun, 2000 Nov 2. PMID 11062004
  5. Endosomal recruitment of the WASH complex: active sequences and mutations impairing interaction with the retromer. Helfer E, et al. Biol Cell, 2013 May. PMID 23331060

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. These results suggest that mouse Vps26b-Vps29-Vps35 retromer complex is implicated in the transport of sortilin from endosomes to the trans-Golgi network.
    Title: Implication of mouse Vps26b-Vps29-Vps35 retromer complex in sortilin trafficking.
  2. Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer assembly.
    Title: Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer assembly.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (4) 
  • Gene trapped (1) 

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within Golgi to vacuole transport ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in endocytic recycling ISO
Inferred from Sequence Orthology
more info
  
involved_in endocytic recycling ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrograde transport, endosome to Golgi IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
is_active_in endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endosome ISO
Inferred from Sequence Orthology
more info
  
located_in endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
  
part_of retromer complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of retromer complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of retromer complex ISO
Inferred from Sequence Orthology
more info
  
part_of retromer, cargo-selective complex IEA
Inferred from Electronic Annotation
more info
  
part_of retromer, cargo-selective complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
vacuolar protein sorting-associated protein 29
Names
vacuolar protein sorting 29
vacuolar sorting protein 29
vesicle protein sorting 29
NP_001334382.1
NP_001346155.1
NP_062754.1

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_001347453.2 → NP_001334382.1  vacuolar protein sorting-associated protein 29 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC113285
    Consensus CDS
    CCDS84954.1
    UniProtKB/Swiss-Prot
    Q9QZ88
    Related
    ENSMUSP00000113525.2, ENSMUST00000118830.8
    Conserved Domains (1) summary
    cd07394
    Location:6 → 183
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain

  2. NM_001359226.1 → NP_001346155.1  vacuolar protein sorting-associated protein 29 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
    Source sequence(s)
    AC113285
    Conserved Domains (1) summary
    cd07394
    Location:11 → 188
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain

  3. NM_019780.2 → NP_062754.1  vacuolar protein sorting-associated protein 29 isoform 2

    See identical proteins and their annotated locations for NP_062754.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC113285
    Consensus CDS
    CCDS39256.1
    UniProtKB/Swiss-Prot
    Q3UCZ0, Q9D107, Q9QZ88
    Related
    ENSMUSP00000121020.2, ENSMUST00000155671.8
    Conserved Domains (1) summary
    cd07394
    Location:2 → 179
    MPP_Vps29; Homo sapiens Vps29 and related proteins, metallophosphatase domain

RNA

  1. NR_152872.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC113285

  2. NR_152873.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC113285

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    122492391..122503047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9QZ88.1 GenPept UniProtKB/Swiss-Prot:Q9QZ88

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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