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    Vps9d1 VPS9 domain containing 1 [ Mus musculus (house mouse) ]

    Gene ID: 72325, updated on 8-May-2024

    Summary

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    Official Symbol
    Vps9d1provided by MGI
    Official Full Name
    VPS9 domain containing 1provided by MGI
    Primary source
    MGI:MGI:1914143
    See related
    Ensembl:ENSMUSG00000001062 AllianceGenome:MGI:1914143
    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
    5DOS1; Vsp9d1; 1300018I17Rik; 2410004N05Rik
    Summary
    Predicted to enable identical protein binding activity. Is expressed in several structures, including cardiovascular system; genitourinary system; gut; liver and biliary system; and nervous system. Orthologous to human VPS9D1 (VPS9 domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in whole brain E14.5 (RPKM 24.0), CNS E18 (RPKM 23.7) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Vps9d1 in Genome Data Viewer
    Location:
    8 E1; 8 72.09 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (123969095..123980961, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (123242356..123254222, complement)

    Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene spermatogenesis associated 33 Neighboring gene RIKEN cDNA 4933417D19 gene Neighboring gene cyclin dependent kinase 10 Neighboring gene spermatogenesis associated 2-like Neighboring gene zinc finger protein (C2H2 type) 276 Neighboring gene Fanconi anemia, complementation group A Neighboring gene STARR-positive B cell enhancer ABC_E8971 Neighboring gene STARR-seq mESC enhancer starr_22969 Neighboring gene STARR-seq mESC enhancer starr_22970 Neighboring gene spire type actin nucleation factor 2

    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. Genome-wide analysis of epigenomic alterations in fetal mouse forebrain after exposure to low doses of bisphenol A. Yaoi T, et al. Biochem Biophys Res Commun, 2008 Nov 21. PMID 18804091
    2. Impaired Spermatogenesis, Muscle, and Erythrocyte Function in U12 Intron Splicing-Defective Zrsr1 Mutant Mice. Horiuchi K, et al. Cell Rep, 2018 Apr 3. PMID 29617656
    3. Identification of 14-3-3epsilon substrates from embryonic murine brain. Ballif BA, et al. J Proteome Res, 2006 Sep. PMID 16944949
    4. A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. Yokoyama S, et al. Dev Cell, 2009 Dec. PMID 20059953, Free PMC Article
    5. The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Koscielny G, et al. Nucleic Acids Res, 2014 Jan. PMID 24194600, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (2) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables molecular_function ND
    No biological Data available
    more info
    		  
    enables small GTPase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in endocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    VPS9 domain-containing protein 1
    Names
    5-day ovary-specific transcript 1 protein
    VSP9 domain containing 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_001310661.1 → NP_001297590.1  VPS9 domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001297590.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK028751, AK032561, BC057621, BQ033590
      Consensus CDS
      CCDS80942.1
      UniProtKB/TrEMBL
      Q3U280
      Related
      ENSMUSP00000113634.2, ENSMUST00000118279.2
      Conserved Domains (1) summary
      pfam02204
      Location:528 → 644
      VPS9; Vacuolar sorting protein 9 (VPS9) domain

    2. NM_028200.2 → NP_082476.1  VPS9 domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_082476.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AK005046, AK028751, AK032561, BQ033590, BU053861
      Consensus CDS
      CCDS52698.1
      UniProtKB/Swiss-Prot
      Q6PFD1, Q8C190
      Related
      ENSMUSP00000113575.2, ENSMUST00000122363.8
      Conserved Domains (1) summary
      pfam02204
      Location:528 → 643
      VPS9; Vacuolar sorting protein 9 (VPS9) domain

    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_000074.7 Reference GRCm39 C57BL/6J

      Range
      123969095..123980961 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006531390.4 → XP_006531453.1  VPS9 domain-containing protein 1 isoform X1

      Conserved Domains (1) summary
      pfam02204
      Location:527 → 642
      VPS9; Vacuolar sorting protein 9 (VPS9) domain

    2. XM_030243787.2 → XP_030099647.1  VPS9 domain-containing protein 1 isoform X2

      Conserved Domains (1) summary
      pfam02204
      Location:316 → 431
      VPS9; Vacuolar sorting protein 9 (VPS9) domain

    3. XM_030243788.2 → XP_030099648.1  VPS9 domain-containing protein 1 isoform X2

      Conserved Domains (1) summary
      pfam02204
      Location:316 → 431
      VPS9; Vacuolar sorting protein 9 (VPS9) domain

    RNA

    1. XR_003947342.1 RNA Sequence

      Related
      ENSMUST00000155869.8

    2. XR_004934889.1 RNA Sequence

    3. XR_001778475.1 RNA Sequence

      Related
      ENSMUST00000146136.8

    4. XR_003947343.2 RNA Sequence

    5. XR_003947341.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8C190.1 GenPept UniProtKB/Swiss-Prot:Q8C190

    Gene LinkOut

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