U.S. flag

An official website of the United States government

Links from GEO Profiles

    • Showing Current items.

    Vdr vitamin D receptor [ Rattus norvegicus (Norway rat) ]

    Gene ID: 24873, updated on 9-Dec-2024

    Summary

    Official Symbol
    Vdrprovided by RGD
    Official Full Name
    vitamin D receptorprovided by RGD
    Primary source
    RGD:3959
    See related
    EnsemblRapid:ENSRNOG00000054420 AllianceGenome:RGD:3959
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Nr1i1
    Summary
    Enables calcitriol binding activity; nuclear receptor activity; and sequence-specific DNA binding activity. Involved in several processes, including cellular response to amyloid-beta; negative regulation of bone trabecula formation; and positive regulation of parathyroid hormone secretion. Located in several cellular components, including T-tubule; chromatin; and nuclear lumen. Used to study vitamin D-dependent rickets type 2A. Biomarker of retinal degeneration and secondary hyperparathyroidism. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); carcinoma (multiple); liver disease (multiple); lung disease (multiple); and melanoma (multiple). Orthologous to human VDR (vitamin D receptor). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 182.4), Lung (RPKM 16.2) and 3 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Vdr in Genome Data Viewer
    Location:
    7q36
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (130864764..130916757, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (128987981..129037677, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (139344452..139394138, complement)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene histone deacetylase 7 Neighboring gene uncharacterized LOC108351548 Neighboring gene uncharacterized LOC103692974 Neighboring gene transmembrane protein 106C Neighboring gene collagen type II alpha 1 chain

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding  
    contributes_to DNA-binding transcription factor activity  
    enables DNA-binding transcription factor activity PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables bile acid nuclear receptor activity  
    enables bile acid nuclear receptor activity  
    enables calcitriol binding PubMed 
    enables calcitriol binding  
    enables calcitriol binding  
    enables lithocholic acid binding  
    enables lithocholic acid binding  
    enables nuclear receptor activity  
    enables nuclear receptor activity PubMed 
    enables nuclear receptor activity  
    enables nuclear retinoid X receptor binding  
    enables nuclear retinoid X receptor binding  
    enables protein binding PubMed 
    enables sequence-specific DNA binding PubMed 
    enables vitamin D binding PubMed 
    enables vitamin D binding PubMed 
    contributes_to vitamin D response element binding  
    enables vitamin D response element binding  
    contributes_to vitamin D response element binding  
    enables zinc ion binding  
    Items 1 - 25 of 65
    Process Evidence Code Pubs
    acts_upstream_of_or_within animal organ morphogenesis  
    involved_in apoptotic process involved in mammary gland involution  
    acts_upstream_of apoptotic process involved in mammary gland involution  
    involved_in apoptotic signaling pathway PubMed 
    involved_in calcium ion transport  
    acts_upstream_of_or_within calcium ion transport  
    involved_in cell differentiation  
    involved_in cell morphogenesis  
    involved_in cell morphogenesis  
    involved_in cellular response to amyloid-beta PubMed 
    involved_in cellular response to vitamin D PubMed 
    involved_in decidualization  
    involved_in decidualization  
    involved_in heart development PubMed 
    involved_in intestinal absorption  
    acts_upstream_of_or_within intestinal absorption  
    involved_in intracellular calcium ion homeostasis  
    acts_upstream_of_or_within intracellular calcium ion homeostasis  
    involved_in lactation  
    acts_upstream_of_or_within lactation  
    involved_in mRNA transcription by RNA polymerase II  
    involved_in mRNA transcription by RNA polymerase II  
    involved_in mammary gland branching involved in pregnancy  
    acts_upstream_of_or_within mammary gland branching involved in pregnancy  
    acts_upstream_of_or_within negative regulation of DNA-templated transcription  
    involved_in negative regulation of bone trabecula formation PubMed 
    involved_in negative regulation of cell population proliferation  
    involved_in negative regulation of keratinocyte proliferation  
    involved_in negative regulation of keratinocyte proliferation  
    involved_in negative regulation of ossification PubMed 
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in nuclear receptor-mediated bile acid signaling pathway  
    involved_in nuclear receptor-mediated bile acid signaling pathway  
    involved_in phosphate ion transmembrane transport  
    involved_in phosphate ion transmembrane transport  
    involved_in positive regulation of apoptotic process involved in mammary gland involution  
    acts_upstream_of_or_within positive regulation of apoptotic process involved in mammary gland involution  
    involved_in positive regulation of gene expression  
    involved_in positive regulation of gene expression  
    involved_in positive regulation of keratinocyte differentiation  
    involved_in positive regulation of keratinocyte differentiation  
    involved_in positive regulation of parathyroid hormone secretion PubMed 
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of vitamin D 24-hydroxylase activity  
    involved_in positive regulation of vitamin D receptor signaling pathway  
    involved_in positive regulation of vitamin D receptor signaling pathway  
    acts_upstream_of_or_within regulation of DNA-templated transcription  
    involved_in regulation of calcidiol 1-monooxygenase activity  
    involved_in regulation of calcium ion transport PubMed 
    involved_in regulation of transcription by RNA polymerase II PubMed 
    involved_in response to aldosterone PubMed 
    involved_in response to bile acid  
    involved_in response to bile acid  
    involved_in response to calcium ion PubMed 
    involved_in response to estradiol PubMed 
    involved_in retinoic acid receptor signaling pathway  
    involved_in retinoic acid receptor signaling pathway  
    involved_in skeletal system development  
    acts_upstream_of_or_within skeletal system development  
    involved_in vitamin D receptor signaling pathway  
    involved_in vitamin D receptor signaling pathway  
    Items 1 - 25 of 65
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex  
    part_of RNA polymerase II transcription regulator complex  
    located_in T-tubule PubMed 
    located_in caveola PubMed 
    located_in chromatin  
    is_active_in chromatin  
    located_in cytosol  
    located_in cytosol  
    located_in dense fibrillar component PubMed 
    located_in euchromatin PubMed 
    located_in heterochromatin PubMed 
    located_in nuclear matrix PubMed 
    located_in nucleoplasm  
    located_in nucleoplasm  
    is_active_in nucleus  
    is_active_in nucleus  
    located_in nucleus  
    located_in perinuclear region of cytoplasm PubMed 
    part_of receptor complex  
    part_of receptor complex  

    General protein information

    Preferred Names
    vitamin D3 receptor
    Names
    1,25-dihydroxyvitamin D3 receptor
    nuclear receptor subfamily 1 group I member 1
    vitamin D (1,25- dihydroxyvitamin D3) receptor

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_017058.2NP_058754.2  vitamin D3 receptor

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/Swiss-Prot
      P13053
      UniProtKB/TrEMBL
      A6KC47, G3V744
      Related
      ENSRNOP00000111704.1, ENSRNOT00000122258.1
      Conserved Domains (2) summary
      cd06933
      Location:124422
      NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
      cd06955
      Location:16122
      NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers

    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_086025.1 Reference GRCr8

      Range
      130864764..130916757 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063263005.1XP_063119075.1  vitamin D3 receptor isoform X1

    External link. Please review our privacy policy.