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

Gene ID: 72325, updated on 27-Nov-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 guanyl-nucleotide exchange factor activity; identical protein binding activity; and small GTPase binding activity. Predicted to be involved in vesicle-mediated transport. Predicted to be active in cytosol and endocytic vesicle. 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, Nov 2024]
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 (21) 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 guanyl-nucleotide exchange factor activity IEA
Inferred from Electronic Annotation
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

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