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    Vps9d1 VPS9 domain containing 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 307923, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Vps9d1provided by RGD
    Official Full Name
    VPS9 domain containing 1provided by RGD
    Primary source
    RGD:1565149
    See related
    EnsemblRapid:ENSRNOG00000028904 AllianceGenome:RGD:1565149
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1565149
    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. Orthologous to human VPS9D1 (VPS9 domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 48.2), Adrenal (RPKM 43.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Vps9d1 in Genome Data Viewer
    Location:
    19q12
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (68185517..68199469, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (51276998..51290726, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (56040527..56054199, complement)

    Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene spermatogenesis associated 33 Neighboring gene cyclin-dependent kinase 10 Neighboring gene spermatogenesis associated 2-like Neighboring gene zinc finger protein (C2H2 type) 276 Neighboring gene FA complementation group A Neighboring gene small nucleolar RNA SNORD43

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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 small GTPase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    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
    RBSC-thyroid hormone receptor associated-like polypeptide

    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_001107440.3 → NP_001100910.2  VPS9 domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001100910.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      B2RYG3, F1MAA8
      Conserved Domains (2) summary
      pfam02204
      Location:526 → 641
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      cl00299
      Location:13 → 81
      MIT; MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar ...

    2. NM_001414938.1 → NP_001401867.1  VPS9 domain-containing protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      A6IZX4
      Related
      ENSRNOP00000039540.5, ENSRNOT00000051945.5

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086037.1 Reference GRCr8

      Range
      68185517..68199469 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063278070.1 → XP_063134140.1  VPS9 domain-containing protein 1 isoform X2

    2. XM_063278069.1 → XP_063134139.1  VPS9 domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8J8XTW6

    3. XM_039097784.2 → XP_038953712.1  VPS9 domain-containing protein 1 isoform X2

      Conserved Domains (1) summary
      pfam02204
      Location:490 → 605
      VPS9; Vacuolar sorting protein 9 (VPS9) domain

    4. XM_039097782.2 → XP_038953710.1  VPS9 domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8J8XTW6
      Conserved Domains (1) summary
      pfam02204
      Location:491 → 606
      VPS9; Vacuolar sorting protein 9 (VPS9) domain

    5. XM_039097787.2 → XP_038953715.1  VPS9 domain-containing protein 1 isoform X3

      Conserved Domains (1) summary
      pfam02204
      Location:362 → 477
      VPS9; Vacuolar sorting protein 9 (VPS9) domain

    RNA

    1. XR_005496656.2 RNA Sequence

    2. XR_005496657.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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