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

    Gene ID: 56433, updated on 21-Apr-2024

    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, Apr 2022]
    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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    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. 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
    4. 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
    5. Human homologues of yeast vacuolar protein sorting 29 and 35. Edgar AJ, et al. Biochem Biophys Res Commun, 2000 Nov 2. PMID 11062004

    See all (28) 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)
    • Gene trapped (1) 
    • Endonuclease-mediated (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 intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within 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
    		  
    Component Evidence Code Pubs
    located_in cytoplasm 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 intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    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 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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