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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

VDR Gene

protein-coding   GIFtS: 73
GCID: GC12M048247

vitamin D (1,25- dihydroxyvitamin D3) receptor
 Explore 232 diseases affiliated with
VDR via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for VDR    

Aliases
for VDR gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Vitamin D (1,25- Dihydroxyvitamin D3) Receptor1 2
NR1I11 2 3
Nuclear Receptor Subfamily 1 Group I Member 12 3
1,25-Dihydroxyvitamin D3 Receptor2 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


Summaries
for VDR gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for VDR:
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)

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:
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)

PharmGKB "VIP" summary for VDR


Genomic Views
for VDR gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000012.11  NC_018923.1  NT_029419.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the VDR gene promoter:
         PPAR-alpha   PPAR-gamma1   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: VDR promoter sequence
   Search SABiosciences Chromatin IP Primers for VDR

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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

Proteins
for VDR gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
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
Subcellular location: Nucleus
Caution: It is uncertain whether Met-1 or Met-4 is the initiator
Sequence caution: Sequence=AAP88938.1; Type=Erroneous gene model prediction;
6/34 PDB 3D structures from and Proteopedia for VDR (see all 34):
1DB1 (3D)        1IE8 (3D)        1IE9 (3D)        1KB2 (3D)        1KB4 (3D)        1KB6 (3D)    
Secondary accessions: B2R5Q1 Q5PSV3

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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P11473

    • VDR Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    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
    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 (see all 2): VDR
    OriGene Protein Over-expression Lysate (see all 3): VDR
    OriGene Custom Protein Services for VDR 
    GenScript Custom Purified and Recombinant Proteins Services for VDR
    Novus Biologicals VDR Proteins
    Novus Biologicals VDR Lysates
    Browse Sino Biological Recombinant Proteins
    ProSpec Recombinant Protein for VDR
    Uscn Proteins for VDR

    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA15589699
    GO:0005654nucleoplasm TAS--
    GO:0005720nuclear heterochromatin ----
    GO:0005792microsome ----
    GO:0005829cytosol ----


    VDR for ontologies           About GeneDecksing



    VDR Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of VDR
    R&D Systems Antibodies for VDR (VDR/NR1I1)
    OriGene Antibodies (see all 2): VDR
    OriGene Custom Antibody Services for VDR 
    GenScript Custom Superior Antibodies Services for VDR
    Novus Biologicals VDR Antibodies
    Abcam antibodies for VDR 
    Uscn Antibodies for VDR
    ThermoFisher Antibody for VDR

    Assay Products for VDR: 
    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Immunoassay Development
    Browse OriGene Fluorogenic Cell Assay Kits
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for VDR
    Browse Enzo Life Sciences for kits & assays
    Uscn ELISAs and CLIAs for VDR

    Protein Domains /
    Families
    for VDR gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    VDR for domains           About GeneDecksing

    5/6 InterPro domains/families (see all 6):
     IPR013088 Znf_NHR/GATA
     IPR008946 Nucl_hormone_rcpt_ligand-bd
     IPR000536 Nucl_hrmn_rcpt_lig-bd_core
     IPR001628 Znf_hrmn_rcpt
     IPR001723 Str_hrmn_rcpt

    Graphical View of Domain Structure for InterPro Entry P11473

    ProtoNet protein and cluster: P11473

    2 Blocks protein families:
    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


    Function
    for VDR gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         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

         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*

    miRNA
    Products:            		miRTarBase miRNAs that target VDR:
    hsa-mir-125b (MIRT001197)

    OriGene 3'-UTR Clone (see all 2): VDR
    Browse MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat VDR
    8/60 QIAGEN miScript miRNA 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:            		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for VDR (see all 7)
    OriGene shRNA RFP: VDR
    OriGene siRNA: VDR
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat VDR

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

    Clone
    Products:             		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for VDR (see all 4)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for VDR (see all 2)
    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)
    Browse Sino Biological Human cDNA Clones
    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
    Search LifeMap BioReagents cell lines for VDR

    In Situ Assay
    Products:       
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VDR

    Gene Ontology (GO): 5/11 molecular function terms (GO ID links to tree view) (see all 11):    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:0005499vitamin D binding ----


    VDR for ontologies           About GeneDecksing


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

    Animal Models:
         Mouse knock-outs for VDR: Vdrtm1.1Gcm Vdrtm1Tyam Vdrtm1Mbd Vdrtm1.2Sgcg Vdrtm1Ska
         15/19 MGI mutant phenotypes (inferred from 9 alleles) (MGI details for Vdr) (see all 19):
     behavior/neurological  cardiovascular system  cellular  craniofacial  digestive/alimentary 
     endocrine/exocrine gland  growth/size  hearing/vestibular/ear  hematopoietic system  homeostasis/metabolism 
     immune system  integument  limbs/digits/tail  mortality/aging  muscle 

    VDR for phenotypes           About GeneDecksing


    Pathways & Interactions
    for VDR gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways - 5/18 super-pathways (see all 18) About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Transcription_Role of VDR in regulation of genes involved in osteoporosis
    		Transcription_Role of VDR in regulation of genes involved in osteoporosis1.00
    		Transcription Role of VDR in regulation of genes involved in osteoporosis0.80
    2Development_Hedgehog and PTH signaling pathways in bone and cartilage development
    		Development_Hedgehog and PTH signaling pathways in bone and cartilage development1.00
    		Development Hedgehog and PTH signaling pathways in bone and cartilage development0.97
    3Nuclear Receptor transcription pathway
    		Nuclear Receptor transcription pathway1.00
    		Nuclear Receptors0.68
    4Generic Transcription Pathway
    		Generic Transcription Pathway1.00
    		Gene Expression0.46
    5PKA activation in glucagon signalling
    		Development_Role of Activin A in cell differentiation and proliferation0.33
    		Development Role of Activin A in cell differentiation and proliferation0.33

    Pathway sources
    See GeneCards unified pathways
    Show all pathways

    3 EMD Millipore Pathways for VDR
        Development Role of Activin A in cell differentiation and proliferation
    Development Hedgehog and PTH signaling pathways in bone and cartilage development
    Transcription Role of VDR in regulation of genes involved in osteoporosis


    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

    5/10 BioSystems Pathways for VDR (see all 10) 
        Nuclear Receptors
    Vitamin D synthesis
    TGF-beta Receptor Signaling Pathway
    Drug Induction of Bile Acid Pathway
    Ovarian Infertility Genes

    3        Reactome Pathways for VDR
        Generic Transcription Pathway
    Nuclear Receptor transcription pathway
    Gene Expression

    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


    VDR for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for VDR

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

    5/141 Interacting proteins for VDR (P114731, 2, 3 ENSP000002290224) via UniProtKB, MINT, STRING, and/or I2D (see all 141)
    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
    EP300Q094722, 3, ENSP000002632534MINT-7306489 MINT-7306512 MINT-7306501 I2D: score=1 STRING: ENSP00000263253
    EGR1P181462, ENSP000002399384MINT-7306489 MINT-7306512 MINT-7306501 STRING: ENSP00000239938
    About this table

    Gene Ontology (GO): 5/30 biological process terms (GO ID links to tree view) (see all 30):    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 ----
    GO:0006355regulation of transcription, DNA-dependent ----
    GO:0006367transcription initiation from RNA polymerase II promoter TAS--


    VDR for ontologies           About GeneDecksing



    Drugs & Compounds
    for VDR gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    VDR for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Enzo Life Sciences drugs & compounds for VDR

    Compounds for VDR available from Tocris Bioscience    About this table
    CompoundAction CAS #
    CalcipotriolVitamin D3 analog[112965-21-6]
    CalcifediolProhormone of calcitriol (Cat. No. 2551). Major circulating form of vitamin D[19356-17-3]
    ErcalcidiolMetabolite of vitamin D2[21343-40-8]
    CalcitriolVitamin D receptor (VDR) agonist[32222-06-3]
    Doxercalciferol Vitamin D2 analog, VDR agonist [54573-75-0]

    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--

    10/14 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

    10/96 Novoseek 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
    Drug/compound PharmGKB Annotation
    BisphosphonatesCA  
    CalciumCA  
    alendronateCA  
    clodronateCA  
    etidronic acidCA  
    raloxifeneCA  
    About this table

    Search CenterWatch for drugs/clinical trials and news about VDR 

    Transcripts
    for VDR gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    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

    miRNA
    Products:             		 OriGene 3'-UTR Clone (see all 2): VDR
    Browse OriGene MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat VDR
    8/60 QIAGEN miScript miRNA 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:             		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for VDR (see all 7)
    OriGene shRNA RFP: VDR
    OriGene siRNA: VDR
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat VDR
    Clone
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    Additional cDNA 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 

    24/209 AceView cDNA sequences (see all 209):

    BC060832 AI276169 AI764972 BC033465 AI304806 BM908433 AI222526 BM855050 
    BM764797 BF594290 BX482193 AW351784 AW139900 BM746741 M65208 BE858037 
    BF588580 CA771271 AI142972 BM783434 BE045545 AW517434 AA009969 AI087278 

    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

    Expression
    for VDR gene

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    VDR expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GTGGCGCAAG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    VDR expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    10/32 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 32) 
    Tissue Anatomical Compartment CellCategory (developmental path)
    HeartLeft VentricleCardiomyocytesMyocardium
    BoneAutopod Growth PlateHypertrophic ChondrocytesBone, Cartilage
    BoneAutopod PeriosteumEndochondral OsteoblastsBone
    BoneAutopod PeriosteumEndochondral OsteocytesBone
    BoneCervical VertebraeEndochondral OsteoblastsBone
    BoneCervical VertebraeEndochondral OsteocytesBone
    BoneCervical VertebraeHypertrophic ChondrocytesBone, Cartilage
    BoneLumbar VertebraeEndochondral OsteoblastsBone
    BoneLumbar VertebraeEndochondral OsteocytesBone
    BoneLumbar VertebraeHypertrophic ChondrocytesBone, Cartilage
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See VDR Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for VDR

    SOURCE GeneReport for Unigene cluster: Hs.524368
        SABiosciences Expression via Pathway-Focused 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

    Primer
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    In Situ
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    Orthologs
    for VDR gene

    (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)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for VDR gene from 6/19 species (see all 19)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves VDR1 vitamin D (1,25- dihydroxyvitamin D3) receptor 77.24(n)
    80.09(a)    		   395988  NM_205098.1  NP_990429.1 
    lizard
    (Anolis carolinensis)    		 Reptilia VDR6
    NR1I36
    		 --
    		 78(a)
    38(a)
    		 1 ↔ 1
    possible ortholog
    		 2(66244772-66300913)
    AAWZ02038821(3849-9082)
    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 Hr961 Hormone receptor-like in 96 49.37(n)
    34.6(a)    		   42993  NM_079769.2  NP_524493.1 
    worm
    (Caenorhabditis elegans)    		 Secernentea nhr-486
    nhr-86
    (see all 3)    		 Nuclear hormone receptor family member nhr-8
    (see all 3)    		 9(a)
    13(a)
    (see all 3)    		 possible ortholog
    possible ortholog
    (see all 3)    		 X(15708153-15716345)
    IV(7710977-7714670)


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

    Paralogs
    for VDR gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for VDR gene
    NR4A32  NR4A12  NR1I22  RARG2  NR1I32  THRB2  RARA2  NR1H22  
    NR4A22  NR1H42  RARB2  THRA2  NR1H32  
    18/62 SIMAP similar genes for VDR using alignment to 9 protein entries:     VDR_HUMAN (see all proteins) (see all similar genes):
    NR1i1    NR1I1    RORA    NR1F1    NR1F2    RORB
    NR1F3    RORC    NR5A2    ESRRA    ESRRB    PPARG
    NR1C3    NR5A1    HNF4G    NR2A3    NR1D2    NR2B3

    VDR for paralogs           About GeneDecksing



    Genomic Variants
    for VDR gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    UniProtKB/Swiss-Prot: VDR_HUMAN, P11473
    Polymorphism: Genetic variations in VDR may determine Mycobacterium tuberculosis susceptibility [MIM:607948]


    10/1357 NCBI SNPs in VDR are shown (see all 1357)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 12 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1219097931,2
    		Cpathogenic45290760(-) CTGCCG/AGCTCA 6 /Q /R mis11Minor allele frequency- A:0.00NA 4552
    rs115741441,2
    		C,H,--45265894(-) TATGCC/TGATGC 3 -- ds50015Minor allele frequency- T:0.00NS EA 600
    rs115741411,2
    		C,F,H,--45266078(-) AAACTG/CTGCTC 3 -- ds500120Minor allele frequency- C:0.03NS EA NA CSA WA 1812
    rs782918851,2
    		--45266217(+) AGGACA/TATGTA 3 -- ds50011Minor allele frequency- T:0.01WA 118
    rs115741401,2
    		C,H--45266290(-) GAGCAA/GTGCCA 3 -- ds50015Minor allele frequency- G:0.00NS EA 594
    rs577403041,2
    		C,--45266311(+) TTCTGT/CCAAAT 3 -- ds50012Minor allele frequency- C:0.15WA 120
    rs115741391,2
    		C,F,--45266603(-) AAGCGA/TGGTCA 3 -- ut3110Minor allele frequency- T:0.04NS NA WA 14404
    rs731098351,2
    		--45266745(+) CAAATA/GTCTAT 3 -- ut310--------
    rs115741381,2
    		C,F,H,--45266750(-) GTGAAA/GTAGAC 3 -- ut3112Minor allele frequency- G:0.06NS EA NA WA 1392
    rs28535631,2
    		C,F,A,H,--45266786(-) AAAAGG/ATCATC 3 -- ut31 ese3 trp329Minor allele frequency- A:0.09NS EA NA WA CSA 3700

    HapMap Linkage Disequilibrium report for VDR (48235320 - 48336831 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for VDR
         1 Indel: 60087
    Human Gene Mutation Database (HGMD): VDR

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    Disorders / Diseases
    for VDR gene

    (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
    VDR for disorders           About GeneDecksing

    OMIM gene information: 601769   
    OMIM disorders: 277440  166710  
    UniProtKB/Swiss-Prot: VDR_HUMAN, P11473
  • Defects in VDR are the cause of rickets vitamin D-dependent type 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

    20/232 diseases for VDR (see all 232):    About MalaCards
    rickets, vitamin d-resistant, type iia    htlv-1 associated myelopathy/tropical spastic paraparesis    ossification of posterior longitudinal ligament of spine    vitamin d-dependent rickets type ii
    rickets    htlv-1 associated myelopathy    secondary hyperparathyroidism    hyperparathyroidism
    hypercalciuria, absorptive    spinal stenosis    tropical spastic paraparesis    osteoporosis, involutional
    atrichia with papular lesions    relapsing-remitting multiple sclerosis    lumbar disc degeneration    thyroiditis
    congenital ichthyosiform erythroderma    spastic paraparesis    hypersensitivity reaction type ii disease    lumbar disc disease

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

    10/96 Novoseek 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

    Publications
    for VDR gene

    (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)
    About This Section

    PubMed articles for VDR gene, integrated from 9 sources (see all 2494):
    (articles sorted by number of sources associating them with VDR)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. 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. (1996)
    2. [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. (2003)
    3. 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. (2001)
    4. 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. (1997)
    5. 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. (1994)
    6. Association of vitamin D receptor gene polymorphism with sporadic breast cancer in Taiwanese patients. (PubMed id 12150447)1, 4, 9 Hou M.F....Huang T.J. (2002)
    7. Single nucleotide polymorphism screening and association analysis--exclusion of integrin beta 7 and vitamin D receptor (chromosome 12q) as candidate genes for asthma. (PubMed id 15663557)1, 4, 9 Vollmert C....Wjst M. (2004)
    8. Association of the vitamin D receptor genotype with bone metastases in breast cancer patients. (PubMed id 12566913)1, 4, 9 Schondorf T....Gohring U.J. (2003)
    9. [Association of the vitamin D receptor gene start codon polymorphism with vitamin D deficiency rickets] (PubMed id 14746673)1, 4, 9 Lu H.J....Zhou L.F. (2003)
    10. Vitamin D receptor gene polymorphisms are associated with breast cancer risk in a UK Caucasian population. (PubMed id 11461072)1, 4, 9 Bretherton-Watt D....Colston K.W. (2001)

    External Searches for VDR gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing VDR gene

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

    Other Databases showing VDR gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing VDR gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for VDR Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/VDR
    NIEHS-SNPshttp://egp.gs.washington.edu/data/vdr/
    SHMPDhttp://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=VDR

    Intellectual Property
    for VDR gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		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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    About This Section

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