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VDR Gene

protein-coding   GIFtS: 74
GCID: GC12M048247

Vitamin D (1,25- Dihydroxyvitamin D3) Receptor

  See VDR-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Vitamin D (1,25- Dihydroxyvitamin D3) Receptor1 2
Nuclear Receptor Subfamily 1 Group I Member 12 3
1,25-Dihydroxyvitamin D3 Receptor2 3
NR1I12 3
Vitamin D Nuclear Receptor Variant 12
Vitamin D3 Receptor2

External Ids:    HGNC: 126791   Entrez Gene: 74212   Ensembl: ENSG000001114247   OMIM: 6017695   UniProtKB: P114733   

Export aliases for VDR gene to outside databases

Previous GC identifers: GC12M048134 GC12M047952 GC12M046521 GC12M045266


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for VDR Gene:
This gene encodes the nuclear hormone receptor for vitamin D3. This receptor also functions as a receptor for the
secondary bile acid lithocholic acid. The receptor belongs to the family of trans-acting transcriptional
regulatory factors and shows sequence similarity to the steroid and thyroid hormone receptors. Downstream targets
of this nuclear hormone receptor are principally involved in mineral metabolism though the receptor regulates a
variety of other metabolic pathways, such as those involved in the immune response and cancer. Mutations in this
gene are associated with type II vitamin D-resistant rickets. A single nucleotide polymorphism in the initiation
codon results in an alternate translation start site three codons downstream. Alternative splicing results in
multiple transcript variants encoding different proteins. (provided by RefSeq, Feb 2011)

GeneCards Summary for VDR Gene:
VDR (vitamin D (1,25- dihydroxyvitamin D3) receptor) is a protein-coding gene. Diseases associated with VDR include rickets, vitamin d-resistant, type iia, and vitamin d-dependent rickets type ii. GO annotations related to this gene include steroid hormone receptor activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is PPARD.

UniProtKB/Swiss-Prot: VDR_HUMAN, P11473
Function: Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the
expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association
with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC
complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for
VDR-promoter association. Plays a central role in calcium homeostasis

summary for VDR Gene:
Vitamin D receptors (VDRs) are members of the NR1I family, which also includes pregnane X (PXR) and
constitutive androstane (CAR) receptors, that form heterodimers with members of the retinoid X receptor
family. VDR is expressed in the intestine, thyroid and kidney and has a vital role in calcium homeostasis.
VDRs repress expression of 1alpha-hydroxylase (the proximal activator of 1,25(OH)2D3) and induce expression
of the 1,25(OH)2D3 inactivating enzyme CYP24. Also, it has recently been identified as an additional bile
acid receptor alongside FXR and may function to protect gut against the toxic and carcinogenic effects of
these endobiotics. Inherited mutations in the VDR gene leads to rickets, which is characterized by muscle
weakness, growth retardation, bone deformity and secondary hyperparathyroidism. The human gene encoding the
vitamin D receptor has been localized to chromosome 12q12-q14.

Gene Wiki entry for VDR (Calcitriol receptor) Gene

PharmGKB "VIP" summary for VDR


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000012.11  NT_029419.13  NC_018923.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the VDR gene promoter:
         PPAR-alpha   PPAR-gamma1   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVDR promoter sequence
   Search Chromatin IP Primers for VDR

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VDR


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12q13.11   Ensembl cytogenetic band:  12q13.11   HGNC cytogenetic band: 12q12-q14

VDR Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VDR gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M048247:  view genomic region     (about GC identifiers)

Start:
48,235,320 bp from pter      End:
48,336,831 bp from pter
Size:
101,512 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: VDR_HUMAN, P11473 (See protein sequence)
Recommended Name: Vitamin D3 receptor  
Size: 427 amino acids; 48289 Da
Subunit: Homodimer in the absence of bound vitamin D3. Heterodimer with RXRA after vitamin D3 binding. Interacts
with SMAD3. Interacts with MED1, NCOA1, NCOA2, NCOA3 and NCOA6 coactivators, leading to a strong increase of
transcription of target genes. Interacts (in a ligand-dependent manner) with BAZ1B/WSTF. Interacts with SNW1
Caution: It is uncertain whether Met-1 or Met-4 is the initiator
Sequence caution: Sequence=AAH60832.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=AAP88938.1; Type=Erroneous gene model prediction;
Selected PDB 3D structures from and Proteopedia for VDR (see all 41):
1DB1 (3D)        1IE8 (3D)        1IE9 (3D)        1KB2 (3D)        1KB4 (3D)        1KB6 (3D)    
Secondary accessions: B2R5Q1 G3V1V9 Q5PSV3
Alternative splicing: 2 isoforms:  P11473-1   P11473-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for VDR: NX_P11473

Explore proteomics data for VDR at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See VDR Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_000367.1  NP_001017535.1  NP_001017536.1  

    ENSEMBL proteins: 
     ENSP00000378734   ENSP00000449573   ENSP00000447173   ENSP00000449074   ENSP00000448659  
     ENSP00000449561   ENSP00000450105   ENSP00000229022   ENSP00000442145  
    Reactome Protein details: P11473

    VDR Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
    Browse R&D Systems for human recombinant proteins
    Enzo Life Sciences proteins for VDR
    OriGene Purified Proteins for VDR
    OriGene Protein Over-expression Lysate for VDR
    OriGene MassSpec for VDR
    OriGene Custom Protein Services for VDR
    GenScript Custom Purified and Recombinant Proteins Services for VDR
    Novus Biologicals VDR Proteins
    Novus Biologicals VDR Lysates
    Sino Biological Recombinant Protein for VDR
    Sino Biological Cell Lysate for VDR
    ProSpec Recombinant Protein for VDR
    Cloud-Clone Corp. Proteins for VDR

     
    Search eBioscience for Proteins for VDR 

     
    antibodies-online proteins for VDR (10 products) 

     
    antibodies-online peptides for VDR

    VDR Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of VDR
    R&D Systems Antibodies for VDR (VDR/NR1I1)
    Cell Signaling Technology (CST) Antibodies for VDR 
    OriGene Antibodies for VDR
    OriGene Custom Antibody Services for VDR
    Novus Biologicals VDR Antibodies
    Abcam antibodies for VDR
    Cloud-Clone Corp. Antibodies for VDR
    ThermoFisher Antibody for VDR
    antibodies-online antibodies for VDR (62 products) 

    VDR Assay Products:

    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for VDR
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for VDR
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for VDR
    Cloud-Clone Corp. CLIAs for VDR
    Search eBioscience for ELISAs for VDR 
    antibodies-online kits for VDR (16 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    NR: Nuclear hormone receptors

    IUPHAR Guide to PHARMACOLOGY protein family classification: Vitamin D receptor
    1I. Vitamin D receptor-like receptors

    Selected InterPro protein domains (see all 6):
     IPR008946 Nucl_hormone_rcpt_ligand-bd
     IPR001723 Str_hrmn_rcpt
     IPR000324 VitD_rcpt
     IPR013088 Znf_NHR/GATA
     IPR000536 Nucl_hrmn_rcpt_lig-bd_core

    Graphical View of Domain Structure for InterPro Entry P11473

    ProtoNet protein and cluster: P11473

    2 Blocks protein domains:
    IPB000324 Vitamin D receptor signature
    IPB001723 Steroid hormone receptor signature


    UniProtKB/Swiss-Prot: VDR_HUMAN, P11473
    Domain: Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal
    ligand-binding domain
    Similarity: Belongs to the nuclear hormone receptor family. NR1 subfamily
    Similarity: Contains 1 nuclear receptor DNA-binding domain


    Find genes that share domains with VDR           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: VDR_HUMAN, P11473
    Function: Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the
    expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association
    with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC
    complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for
    VDR-promoter association. Plays a central role in calcium homeostasis

         Genatlas biochemistry entry for VDR:
    vitamin D (1,25-dihydroxyvitamin D3) receptor,48kDa,nuclear steroid/thyroid hormone receptor
    superfamily,heterodimerizing with retinoic acid X receptors RXR*

         Gene Ontology (GO): Selected molecular function terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IDA11891224
    GO:0003700contributes to sequence-specific DNA binding transcription factor activity IDA17426122
    GO:0003707steroid hormone receptor activity IEA--
    GO:0004879ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity ----
    GO:0005515protein binding IPI10409738
         
    Find genes that share ontologies with VDR           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for VDR:
     Increased cell death HMECs cel 

         Selected MGI mutant phenotypes (inferred from 10 alleles(MGI details for Vdr) (see all 19):
     behavior/neurological  cardiovascular system  cellular  craniofacial  digestive/alimentary 
     endocrine/exocrine gland  growth/size/body  hearing/vestibular/ear  hematopoietic system  homeostasis/metabolism 
     immune system  integument  limbs/digits/tail  mortality/aging  muscle 

    Find genes that share phenotypes with VDR           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for VDR: Vdrtm1.1Gcm Vdrtm1Tyam Vdrtm1Mbd Vdrtm1.2Sgcg Vdrtm1Ska Vdrtm1.1Pcn

       genOway: Develop your customized and physiologically relevant rodent model for VDR

    Transcription Factor Targeting: 
    Targeting motifs: HOMER Transcription Factor Regulatory Elements motif viewer 
                                          Consensus sequence:  NGAGGTCANNGAGTTCANNN 

    miRNA
    Products:
        
    miRTarBase miRNAs that target VDR:
    hsa-mir-27b-3p (MIRT006509), hsa-let-7a-5p (MIRT002080), hsa-mir-125b-5p (MIRT001197)

    Block miRNA regulation of human, mouse, rat VDR using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate VDR (see all 60):
    hsa-miR-548j hsa-miR-323-3p hsa-miR-302d hsa-miR-520e hsa-miR-765 hsa-miR-570 hsa-miR-372 hsa-miR-1184
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for VDR
    Predesigned siRNA for gene silencing in human, mouse, rat VDR

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for VDR

    Clone
    Products:
         
    OriGene clones in human, mouse for VDR (see all 13)
    OriGene ORF clones in mouse, rat for VDR
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 3): VDR (NM_001017536)
    Sino Biological Human cDNA Clone for VDR
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for VDR
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VDR

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for VDR
    Browse ESI BIO Cell Lines and PureStem Progenitors for VDR 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VDR


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    VDR_HUMAN, P11473: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytoskeleton2
    cytosol2
    extracellular2
    peroxisome2
    plasma membrane2

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005654nucleoplasm TAS--
    GO:0005730NOT nucleolus IDA--

    Find genes that share ontologies with VDR           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for VDR About   (see all 19)  
    See pathways by source

    SuperPathContained pathways About
    1Nuclear Receptor transcription pathway
    Nuclear Receptor transcription pathway0.67
    Nuclear Receptors0.67
    2Gene Expression
    Generic Transcription Pathway0.40
    Gene Expression0.40
    3Ca-dependent events
    Development Role of Activin A in cell differentiation and proliferation0.32
    4Vitamin D synthesis
    Vitamin D synthesis
    5Tuberculosis
    Tuberculosis


    Find genes that share SuperPaths with VDR           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for VDR
        Ca, cAMP and Lipid Signaling

    3 GeneGo (Thomson Reuters) Pathways for VDR
        Development Hedgehog and PTH signaling pathways in bone and cartilage development
    Transcription Role of VDR in regulation of genes involved in osteoporosis
    Development Role of Activin A in cell differentiation and proliferation

    Selected BioSystems Pathways for VDR (see all 10)
        Vitamin D synthesis
    Nuclear Receptors
    TGF-beta Receptor Signaling Pathway
    Ovarian Infertility Genes
    Nuclear receptors in lipid metabolism and toxicity


    1 Reactome Pathway for VDR
        Nuclear Receptor transcription pathway

    1 PharmGKB Pathway for VDR
        Etoposide Pathway, Pharmacokinetics/Pharmacodynamics

    3 Kegg Pathways  (Kegg details for VDR):
        Endocrine and other factor-regulated calcium reabsorption
    Mineral absorption
    Tuberculosis

        Pathway & Disease-focused RT2 Profiler PCR Arrays including VDR: 
              Osteogenesis in human mouse rat
              Estrogen Receptor Signaling in human mouse rat
              Stem Cell Transcription Factors in human mouse rat
              Nuclear Receptors & Coregulators in human mouse rat
              Adipogenesis in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for VDR

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for VDR (P114731, 2, 3 ENSP000002290224) via UniProtKB, MINT, STRING, and/or I2D (see all 159)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HRO435932, 3, ENSP000003708264MINT-18209 I2D: score=3 STRING: ENSP00000370826
    SNW1Q135731, 3, ENSP000002615314EBI-286357,EBI-632715 I2D: score=2 STRING: ENSP00000261531
    TP53P046371, 3, ENSP000002693054EBI-286357,EBI-366083 I2D: score=2 STRING: ENSP00000269305
    RXRBP287023, ENSP000003638124I2D: score=3 STRING: ENSP00000363812
    ENSG00000206289P287023I2D: score=3 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 27):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IDA17426122
    GO:0000902cell morphogenesis IMP17223341
    GO:0001501skeletal system development IEA--
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0006367transcription initiation from RNA polymerase II promoter TAS--

    Find genes that share ontologies with VDR           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Enzo Life Sciences drugs & compounds for VDR
      Browse compounds at ApexBio 

    Compounds for VDR available from Tocris Bioscience    About this table
    CompoundAction CAS #
    EB 1089Vitamin D receptor (VDR) agonist[134404-52-7]
    CalcipotriolVitamin D3 analog[112965-21-6]
    AlfacalcidolProdrug of vitamin D3 (Cat. No. 4156)[41294-56-8]
    CalcifediolProhormone of calcitriol (Cat. No. 2551). Major circulating form of vitamin D[19356-17-3]
    CalcitriolVitamin D receptor (VDR) agonist[32222-06-3]

    5 HMDB Compounds for VDR    About this table
    CompoundSynonyms CAS #PubMed Ids
    Calcidiol25-Hydroxyvitamin D3 (see all 11)19356-17-3--
    Calcitriol(3b,5Z,7E)-9,10-Secocholesta-5,7,10(19)-trienetriol (see all 19)32222-06-3--
    CalciumCa (see all 2)7440-70-2--
    Ergocalciferol(+)-Vitamin D2 (see all 72)50-14-6--
    Vitamin D3(+)-Vitamin D3 (see all 32)67-97-0--

    Selected DrugBank Compounds for VDR (see all 14)    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    ErgocalciferolSynthetic Vitamin D (see all 2)50-14-6targetagonist20525913 17207992 18290715 17218095 17440943 11752352 17519354 20091647 16949927
    Dihydrotachysterol-- 67-96-9targetagonist20525913 17139284 11752352 8380156 17016423 1336906
    Paricalcitol-- 131918-61-1targetagonist16076355 17139284 11752352 17016423 20204178 19494617
    Alfacalcidol1-hydroxycholecalciferol (see all 3)41294-56-8targetagonist15503649 11752352 20435140
    Calcipotriol-- 112965-21-6targetantagonist17139284 11752352 17016423
    Cholecalciferol(+)-vitamin D3 (see all 5)67-97-0targetagonist15503649 11752352 20435140
    1alpha,25-Dihydroxyl-20-Epi-22-Oxa-24,26,27-Trihomovitamin D3-- --target--17139284 17016423
    CalcidiolCalcifediol (see all 4)19356-17-3targetagonist15503649 11752352
    Calcitriol1,25-(OH)2D3 (see all 2)32222-06-3targetantagonist15503649 11752352
    Seocalcitol(5Z,7E,22E,24E)-(1S,3R)-26,27-dimethyl-24a-homo-9,10-seco-5,7,10(19),22,24-cholestapentaene-1,3,25-triol (see all 4)134404-52-7target--17139284 17016423

    Selected IUPHAR Ligands for VDR (Vitamin D receptor) (see all 12)    About this table
    LigandTypeActionAffinityPubmed IDs
    KH1060
    AgonistAgonist10.18573413
    2MD
    AgonistAgonist109804706
    EB1089
    AgonistAgonist9.578573413 1472092
    calcipotriol
    AgonistAgonist9.37976510
    1,25-dihydroxyvitamin D3
    AgonistAgonist8.9 - 9.217976510 12089348
    TV-02H
    AgonistAgonist8.57976510
    ZK159222
    AntagonistAntagonist7.5411094341 12901907
    calcitriol-26,23-lactone
    AgonistAgonist7.56572492
    LG190178
    AgonistAgonist6.8210322128
    3-keto-lithocholic acid
    AgonistAgonist6.5412016314

    Selected Novoseek inferred chemical compound relationships for VDR gene (see all 96)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    vitamin d 98.5 6294 17644135 (14), 11918709 (11), 9751364 (10), 19931640 (10) (see all 99)
    1,25 dihydroxy vitamin d3 96 520 8807569 (6), 17520689 (5), 1849039 (5), 9579411 (4) (see all 99)
    calcitriol 95.2 546 7737990 (6), 18556746 (6), 15861036 (5), 18216322 (4) (see all 99)
    apai 94.6 197 16100768 (3), 17704996 (3), 10491209 (3), 8806247 (2) (see all 99)
    eb 1089 87.3 32 15569516 (3), 9099905 (2), 9831892 (2), 18082637 (2) (see all 18)
    25-hydroxyvitamin d 86.5 78 10696983 (3), 14969396 (3), 15911240 (2), 19615888 (2) (see all 48)
    paricalcitol 86.3 39 12813173 (3), 17687191 (2), 18525004 (2), 16076355 (2) (see all 22)
    kh 1060 80.3 13 10677578 (4), 15615532 (1), 7981122 (1), 11344298 (1) (see all 5)
    1alpha-hydroxyvitamin d5 79 2 17130524 (1), 10762752 (1)
    apal 74.8 13 15977460 (3), 10758594 (1), 11579931 (1), 19758194 (1) (see all 6)

    6 PharmGKB related drug/compound annotations for VDR gene    About this table
    Drug/compound PharmGKB Annotation
    BisphosphonatesCA  
    CalciumCA  
    alendronateCA  
    clodronateCA  
    etidronic acidCA  
    raloxifeneCA  



    Find genes that share compounds with VDR           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for VDR gene (3 alternative transcripts): 
    NM_000376.2  NM_001017535.1  NM_001017536.1  

    Unigene Cluster for VDR:

    Vitamin D (1,25- dihydroxyvitamin D3) receptor
    Hs.524368  [show with all ESTs]
    Unigene Representative Sequence: NM_001017536
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000395324 ENST00000549336 ENST00000550325 ENST00000547065 ENST00000546653
    ENST00000550314 ENST00000548664 ENST00000229022(uc001rqm.3 uc001rqn.3 uc001rql.3 uc010slq.2)
    ENST00000535672
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    hsa-miR-548j hsa-miR-323-3p hsa-miR-302d hsa-miR-520e hsa-miR-765 hsa-miR-570 hsa-miR-372 hsa-miR-1184
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    Additional mRNA sequence: 

    AB307700.1 AF026260.1 AK024830.1 AK225844.1 AK299446.1 AK309587.1 AK312267.1 BC033465.1 
    BC060832.1 HQ692836.1 J03258.1 M65208.1 X67482.1 

    9 DOTS entries:

    DT.453125  DT.95169917  DT.100746083  DT.121152042  DT.91733040  DT.100754577  DT.100754579  DT.121152020 
    DT.91733061 

    Selected AceView cDNA sequences (see all 209):

    BC033465 AI140037 AA009969 AW517434 CD365843 M65208 BM746741 AW351784 
    BM783434 CA770971 BC060832 X67482 AI764972 BM462824 AI276169 CA771271 
    AI087232 BE045545 AI087278 AF026260 BF588580 BM764797 AW139900 BX482193 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for VDR    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10
    SP1:                    -     -                                                                     
    SP2:                          -                                                                     
    SP3:                    -     -     -                                                               
    SP4:                                                                                                


    ECgene alternative splicing isoforms for VDR

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    VDR expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTGGCGCAAG
    VDR Expression
    About this image


    VDR expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Kidney (Urinary System)    fully expand to see all 5 entries
             Distal Tubule Cells Distal Tubule
             Proximal Tubule
     
     Heart (Cardiovascular System)
             Cardiomyocytes Left Ventricle
     
     Bone (Muscoskeletal System)    fully expand to see all 3 entries
             Chondrocytes Zeugopod Epiphyseal End
             Zeugopod Growth Plate
     
     Epithelial Cells
             Distal Tubule Cells Distal Tubule
     
     Gut Tube (Gastrointestinal Tract)
             Foregut
    VDR Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VDR Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.524368
        Pathway & Disease-focused RT2 Profiler PCR Arrays including VDR: 
              Osteogenesis in human mouse rat
              Estrogen Receptor Signaling in human mouse rat
              Stem Cell Transcription Factors in human mouse rat
              Nuclear Receptors & Coregulators in human mouse rat
              Adipogenesis in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for VDR gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vdr1 , 5 vitamin D receptor1, 5 86.1(n)1
    87.68(a)1
      15 (53.85 cM)5
    223371  NM_009504.41  NP_033530.21 
     978544255 
    chicken
    (Gallus gallus)
    Aves VDR1 vitamin D (1,25- dihydroxyvitamin D3) receptor 76.83(n)
    79.91(a)
      395988  NM_205098.1  NP_990429.1 
    lizard
    (Anolis carolinensis)
    Reptilia VDR6
    vitamin D (1,25- dihydroxyvitamin D3) receptor
    74(a)
    1 ↔ 1
    2(66240756-66352726)
    African clawed frog
    (Xenopus laevis)
    Amphibia vdr-A2 vitamin D (1,25- dihydroxyvitamin D3) receptor 76.55(n)    U91846.1 
    zebrafish
    (Danio rerio)
    Actinopterygii vdr2 vitamin D receptor 79.44(n)   30076  AF164512.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta EcR6
    Ecdysone receptor
    14(a)
    1 → many
    2R(1975378-2056592)


    ENSEMBL Gene Tree for VDR (if available)
    TreeFam Gene Tree for VDR (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for VDR gene
    PPARD2  RARG2  NR1I22  PPARA2  THRB2  RARA2  NR1H42  NR1D22  
    RARB2  RORA2  RORB2  RORC2  NR1D12  NR1I32  PPARG2  NR1H22  
    THRA2  NR1H32  
    Selected SIMAP similar genes for VDR using alignment to 11 protein entries:     VDR_HUMAN (see all proteins) (see all similar genes):
    NR1i1    NR1I1    RORA    NR1F1    NR1F2    RORB
    NR1F3    RORC    NR5A2    ESRRA    ESRRB    NR5A1
    PPARG    NR2A3    HNF4G    NR2B3    THRB    NR2A1

    Find genes that share paralogs with VDR           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Polymorphic Variants from UniProtKB/Swiss-Prot
    VDR_HUMAN, P11473: Genetic variations in VDR may determine Mycobacterium tuberculosis susceptibility [MIM:607948]


    Selected SNPs for VDR (see all 1677)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0046654
    Rickets vitamin D-dependent 2A (VDDR2A)4--see VAR_0046652 H Q mis40--------
    VAR_0046564
    Rickets vitamin D-dependent 2A (VDDR2A)4--see VAR_0046562 G D mis40--------
    VAR_0046644
    Rickets vitamin D-dependent 2A (VDDR2A)4--see VAR_0046642 R L mis40--------
    VAR_0046664
    Rickets vitamin D-dependent 2A (VDDR2A)4--see VAR_0046662 I S mis40--------
    VAR_0046574
    Rickets vitamin D-dependent 2A (VDDR2A)4--see VAR_0046572 H Q mis40--------
    VAR_0046634
    Rickets vitamin D-dependent 2A (VDDR2A)4--see VAR_0046632 R Q mis40--------
    VAR_0046674
    Rickets vitamin D-dependent 2A (VDDR2A)4--see VAR_0046672 R C mis40--------
    VAR_0046624
    Rickets vitamin D-dependent 2A (VDDR2A)4--see VAR_0046622 R Q mis40--------
    VAR_0046584
    Rickets vitamin D-dependent 2A (VDDR2A)4--see VAR_0046582 K E mis40--------
    VAR_0046604
    Rickets vitamin D-dependent 2A (VDDR2A)4--see VAR_0046602 F I mis40--------

    HapMap Linkage Disequilibrium report for VDR (48235320 - 48336831 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for VDR:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv8233CNV Gain19470904

    Human Gene Mutation Database (HGMD): VDR
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing VDR
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 601769   
    OMIM disorders: 277440  166710  
    UniProtKB/Swiss-Prot: VDR_HUMAN, P11473
  • Rickets vitamin D-dependent 2A (VDDR2A) [MIM:277440]: A disorder of vitamin D metabolism resulting in
    severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to
    rickets. Note=The disease is caused by mutations affecting the gene represented in this entry

  • Selected diseases for VDR (see all 22):    
    About MalaCards
    rickets, vitamin d-resistant, type iia    vitamin d-dependent rickets type ii    osteoporosis, involutional    atrichia with papular lesions
    rickets    osteoporosis    hyperparathyroidism    hypercalciuria, absorptive
    campylobacteriosis    multidrug-resistant tuberculosis    caveolinopathies    lumbar disc disease
    syringomyelia    spondylosis    lead poisoning    degenerative disc disease
    intervertebral disc disease    tuberculosis    dentinogenesis imperfecta    spinal stenosis

    18 diseases from the University of Copenhagen DISEASES database for VDR:
    Rickets     Osteoporosis     Hyperparathyroidism     X-linked hypophosphatemia
    Hypercalcemia     Alopecia     Kidney disease     Prostate cancer
    Osteomalacia     Psoriasis     Tuberculosis     Diabetes mellitus
    Hyperphosphatemia     Hypophosphatemia     Colorectal cancer     Breast cancer
    Multiple sclerosis     Hypersensitivity reaction type II disease

    Find genes that share disorders with VDR           About GenesLikeMe

    Selected Novoseek inferred disease relationships for VDR gene (see all 96)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hvdrr 92.5 100 17106204 (4), 9005998 (3), 15190891 (3), 17071612 (3) (see all 36)
    rickets 83.6 128 14746673 (3), 19815438 (3), 17202743 (3), 11092401 (3) (see all 55)
    hyperparathyroidism secondary 82.7 71 8807569 (2), 12234290 (2), 12771291 (2), 9844148 (2) (see all 45)
    vitamin d deficiency 82.4 33 14746673 (3), 16083553 (2), 16613705 (2), 10696983 (1) (see all 22)
    osteoporosis 77.4 240 9656208 (4), 14527203 (3), 9069156 (3), 10322698 (3) (see all 99)
    hypercalcemia 69.5 16 11033842 (3), 16528410 (2), 18180267 (2), 11562285 (1) (see all 11)
    vitamin d-dependent rickets, type ii 69 8 11344183 (2), 19921089 (2), 9275211 (1), 9702072 (1)
    parathyroid hyperplasia 67.9 11 11780466 (1), 18216322 (1), 16076355 (1), 8397225 (1) (see all 8)
    rickets hypophosphatemic 67.2 41 16753019 (4), 18827005 (3), 11386849 (2), 12612432 (2) (see all 21)
    hypercalciuria 66.9 23 10232686 (1), 10491744 (1), 15141345 (1), 16775452 (1) (see all 14)

    Genatlas disease: VDR
    rickets,vitamin D-dependent,type II,with alopecia

    Genetic Association Database (GAD): VDR
    Human Genome Epidemiology (HuGE) Navigator: VDR (797 documents)

    Export disorders for VDR gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for VDR gene, integrated from 10 sources (see all 2626):
    (articles sorted by number of sources associating them with VDR)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Vitamin D receptor (VDR) gene polymorphisms and haplotypes, interactions with plasma 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D, and prostate cancer risk. (PubMed id 17440943)1, 4, 7, 9 Mikhak B....Giovannucci E. (Prostate 2007)
    2. Promoter and 3'-untranslated-region haplotypes in the vitamin D receptor gene predispose to osteoporotic fracture: the Rotterdam study. (PubMed id 16252240)1, 2, 4, 9 Fang Y....Uitterlinden A.G. (Am. J. Hum. Genet. 2005)
    3. Plasma 1,25 dihydroxy vitamin D3 level and expression of vitamin d receptor and cathelicidin in pulmonary tuberculosis. (PubMed id 19219539)1, 4, 9 Selvaraj P....Alagarasu K. (J. Clin. Immunol. 2009)
    4. A novel mutation in the deoxyribonucleic acid-binding domain of the vitamin D receptor causes hereditary 1,25-dihydroxyvitamin D-resistant rickets. (PubMed id 8675579)1, 2, 9 Lin U.-T.... Feldman D. (J. Clin. Endocrinol. Metab. 1996)
    5. [The influence of hormonal replacement therapy on bone density in postmenopausal women depending on polymorphism of vitamin D receptor (VDR) and estrogen receptor (ER) genes]. (PubMed id 15552843)1, 4, 9 Brodowska A. (Ann Acad Med Stetin 2003)
    6. The vitamin D receptor genotype predisposes to the development of calcific aortic valve stenosis. (PubMed id 11359741)1, 4, 9 Ortlepp J.R....Hanrath P. (Heart 2001)
    7. The bone mass density in postmenopausal women using hormonal replacement therapy in relation to polymorphism in vitamin D receptor and estrogen receptor genes. (PubMed id 19903038)1, 4, 9 Brodowska A....Nawrocka-Rutkowska J. (Gynecol. Endocrinol. 2009)
    8. Hereditary vitamin D resistant rickets caused by a novel mutation in the vitamin D receptor that results in decreased affinity for hormone and cellular hyporesponsiveness. (PubMed id 9005998)1, 2, 9 Malloy P.J....Feldman D. (J. Clin. Invest. 1997)
    9. Two mutations causing vitamin D resistant rickets: modelling on the basis of steroid hormone receptor DNA-binding domain crystal structures. (PubMed id 7828346)1, 2, 9 Rut A.R....O'Riordan J.L.H. (Clin. Endocrinol. (Oxf.) 1994)
    10. Genotypes of vitamin D and estrogen receptors in pre and perimenopausal women from Cordoba, Argentina. (PubMed id 17408018)1, 4, 9 Ulla M....Tolosa de Talamoni N. (Medicina (B Aires) 2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 7421 HGNC: 12679 AceView: VDR Ensembl:ENSG00000111424 euGenes: HUgn7421
    ECgene: VDR Kegg: 7421 H-InvDB: VDR

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for VDR Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=VDR[genesymbol]
    NIEHS-SNPshttp://egp.gs.washington.edu/data/vdr/
    SHMPDhttp://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=VDR

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for VDR gene:
    Search GeneIP for patents involving VDR

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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