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Aliases for VDR Gene

Aliases for VDR Gene

  • Vitamin D (1,25- Dihydroxyvitamin D3) Receptor 2 3 5
  • Nuclear Receptor Subfamily 1 Group I Member 1 3 4
  • 1,25-Dihydroxyvitamin D3 Receptor 3 4
  • NR1I1 3 4
  • Protein Phosphatase 1, Regulatory Subunit 163 3
  • Vitamin D Nuclear Receptor Variant 1 3
  • Regulatory Subunit 163 2
  • Protein Phosphatase 1 2
  • Vitamin D Receptor 3
  • PPP1R163 3

External Ids for VDR Gene

Previous GeneCards Identifiers for VDR Gene

  • GC12M048247
  • GC12M048134
  • GC12M047952
  • GC12M046521
  • GC12M045266

Summaries for VDR Gene

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. Among its related pathways are Gene Expression and Nuclear receptors in lipid metabolism and toxicity. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and steroid hormone receptor activity. An important paralog of this gene is NR4A2.

UniProtKB/Swiss-Prot for VDR Gene

  • Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Recruited to promoters via its interaction with BAZ1B/WSTF which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.

Tocris Summary for VDR Gene

  • Vitamin D receptors (VDRs) are members of the NR1I family, which also includes pregnane X receptors (PXR) and constitutive androstane receptors (CAR). They form heterodimers with retinoid X receptor family members, and are expressed in the intestine, thyroid and kidney.

Gene Wiki entry for VDR Gene

PharmGKB "VIP" Summary for VDR Gene

No data available for fRNAdb sequence ontologies and piRNA Summary for VDR Gene

Genomics for VDR Gene

Regulatory Elements for VDR Gene

Genomic Location for VDR Gene

Chromosome:
12
Start:
47,841,537 bp from pter
End:
47,943,048 bp from pter
Size:
101,512 bases
Orientation:
Minus strand

Genomic View for VDR Gene

Genes around VDR on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VDR Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VDR Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VDR Gene

Proteins for VDR Gene

  • Protein details for VDR Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P11473-VDR_HUMAN
    Recommended name:
    Vitamin D3 receptor
    Protein Accession:
    P11473
    Secondary Accessions:
    • B2R5Q1
    • G3V1V9
    • Q5PSV3

    Protein attributes for VDR Gene

    Size:
    427 amino acids
    Molecular mass:
    48289 Da
    Quaternary structure:
    • 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. Interacts with IRX4, the interaction doesnt affect its transactivation activity.
    SequenceCaution:
    • Sequence=AAH60832.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAP88938.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for VDR Gene

    Alternative splice isoforms for VDR Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VDR Gene

Proteomics data for VDR Gene at MOPED

Post-translational modifications for VDR Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for VDR (VDR)

No data available for DME Specific Peptides for VDR Gene

Domains & Families for VDR Gene

Graphical View of Domain Structure for InterPro Entry

P11473

UniProtKB/Swiss-Prot:

VDR_HUMAN :
  • Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
  • Belongs to the nuclear hormone receptor family. NR1 subfamily.
Domain:
  • Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
  • Contains 1 nuclear receptor DNA-binding domain.
Family:
  • Belongs to the nuclear hormone receptor family. NR1 subfamily.
genes like me logo Genes that share domains with VDR: view

Function for VDR Gene

Molecular function for VDR Gene

GENATLAS Biochemistry:
vitamin D (1,25-dihydroxyvitamin D3) receptor,48kDa,nuclear steroid/thyroid hormone receptor superfamily,heterodimerizing with retinoic acid X receptors RXR*
UniProtKB/Swiss-Prot Function:
Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Recruited to promoters via its interaction with BAZ1B/WSTF which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.

Gene Ontology (GO) - Molecular Function for VDR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004879 RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding IEA --
GO:0005515 protein binding IPI 9632709
GO:0046965 retinoid X receptor binding IPI 17426122
GO:1902121 lithocholic acid binding IDA 12016314
genes like me logo Genes that share ontologies with VDR: view
genes like me logo Genes that share phenotypes with VDR: view

Human Phenotype Ontology for VDR Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VDR Gene

MGI Knock Outs for VDR:

Animal Model Products

Targeted motifs for VDR Gene
HOMER Transcription Factor Regulatory Elements motif VDR
  • Consensus sequence: NGAGGTCANNGAGTTCANNN Submotif: DR3 Cell Type: GM10855 GEO ID: GSE22484

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for VDR Gene

Localization for VDR Gene

Subcellular locations from UniProtKB/Swiss-Prot for VDR Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VDR Gene COMPARTMENTS Subcellular localization image for VDR gene
Compartment Confidence
nucleus 5
cytoskeleton 3
cytosol 3
extracellular 2
peroxisome 2
plasma membrane 2
endoplasmic reticulum 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for VDR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0090575 RNA polymerase II transcription factor complex IDA 17426122
genes like me logo Genes that share ontologies with VDR: view

Pathways & Interactions for VDR Gene

genes like me logo Genes that share pathways with VDR: view

SIGNOR curated interactions for VDR Gene

Is activated by:

Gene Ontology (GO) - Biological Process for VDR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IDA 17426122
GO:0000902 cell morphogenesis IMP 17223341
GO:0001501 skeletal system development IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006367 transcription initiation from RNA polymerase II promoter TAS --
genes like me logo Genes that share ontologies with VDR: view

Drugs & Compounds for VDR Gene

(81) Drugs for VDR Gene - From: DrugBank, HMDB, Novoseek, ApexBio, DGIdb, Tocris, PharmGKB, and IUPHAR

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcitriol Approved Nutra antagonist, Target TNF-α and IL-1β production inhibitor, Vitamin D receptor (VDR) agonist 161
Calcipotriol Approved Pharma Agonist, antagonist, Target Vitamin D3 analog 0
Paricalcitol Approved, Investigational Pharma agonist, Target 0
Alfacalcidol Approved Nutra Target, agonist Bone resorption inhibitor 43
Cholecalciferol Approved Nutra Target, agonist Fat-soluble secosteroids 799,792

(53) Additional Compounds for VDR Gene - From: Novoseek, IUPHAR, and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
EB 1089
134404-52-7
EB1089
Agonist
KH1060
Agonist
TEI-9647
Antagonist
TV-02H
Agonist

(5) Tocris Compounds for VDR Gene

Compound Action Cas Number
Calcipotriol Vitamin D3 analog 112965-21-6
Calcitriol Vitamin D receptor (VDR) agonist 32222-06-3
Doxercalciferol Vitamin D2 analog, VDR agonist 54573-75-0
EB 1089 Vitamin D receptor (VDR) agonist 134404-52-7
Ercalcitriol Active metabolite of vitamin D2 60133-18-8

(6) ApexBio Compounds for VDR Gene

Compound Action Cas Number
Alfacalcidol Bone resorption inhibitor 41294-56-8
Calcifediol Major circulating form of vitamin D3 19356-17-3
Calcitriol TNF-α and IL-1β production inhibitor 32222-06-3
Doxercalciferol Vitamin D receptor activator 54573-75-0
Lithocholic Acid Activator of vitamin D receptor,PXR and FXR 434-13-9
Vitamin D3 Fat-soluble secosteroids 67-97-0
genes like me logo Genes that share compounds with VDR: view

Drug Products

Transcripts for VDR Gene

Unigene Clusters for VDR Gene

Vitamin D (1,25- dihydroxyvitamin D3) receptor:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for VDR Gene

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

Relevant External Links for VDR Gene

GeneLoc Exon Structure for
VDR
ECgene alternative splicing isoforms for
VDR

Expression for VDR Gene

mRNA expression in normal human tissues for VDR Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VDR Gene

This gene is overexpressed in Colon - Transverse (x6.5) and Skin - Not Sun Exposed (Suprapubic) (x4.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for VDR Gene



SOURCE GeneReport for Unigene cluster for VDR Gene Hs.524368

genes like me logo Genes that share expression patterns with VDR: view

In Situ Assay Products

No data available for Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for VDR Gene

Orthologs for VDR Gene

This gene was present in the common ancestor of animals.

Orthologs for VDR Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia VDR 35
  • 89.49 (n)
  • 90.82 (a)
VDR 36
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VDR 35
  • 91.1 (n)
  • 92.74 (a)
VDR 36
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vdr 35
  • 86.1 (n)
  • 87.68 (a)
Vdr 16
Vdr 36
  • 89 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia VDR 35
  • 93.1 (n)
  • 91.13 (a)
rat
(Rattus norvegicus)
Mammalia Vdr 35
  • 87.16 (n)
  • 90.31 (a)
oppossum
(Monodelphis domestica)
Mammalia VDR 36
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VDR 36
  • 45 (a)
OneToOne
chicken
(Gallus gallus)
Aves VDR 35
  • 76.83 (n)
  • 79.91 (a)
VDR 36
  • 78 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VDR 36
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vdr 35
  • 67.54 (n)
  • 74.52 (a)
African clawed frog
(Xenopus laevis)
Amphibia vdr-A 35
zebrafish
(Danio rerio)
Actinopterygii vdr 35
vdra 35
  • 70.32 (n)
  • 71.33 (a)
VDR (1 of 2) 36
  • 67 (a)
OneToMany
vdrb 36
  • 71 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.668 35
fruit fly
(Drosophila melanogaster)
Insecta EcR 36
  • 14 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 23 (a)
OneToMany
Species with no ortholog for VDR:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for VDR Gene

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

Paralogs for VDR Gene

Paralogs for VDR Gene

genes like me logo Genes that share paralogs with VDR: view

Variants for VDR Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for VDR Gene

P11473-VDR_HUMAN
Genetic variations in VDR may determine Mycobacterium tuberculosis susceptibility [MIM:607948].

Sequence variations from dbSNP and Humsavar for VDR Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
VAR_004656 Rickets vitamin D-dependent 2A (VDDR2A)
VAR_004657 Rickets vitamin D-dependent 2A (VDDR2A)
VAR_004658 Rickets vitamin D-dependent 2A (VDDR2A)
VAR_004659 Rickets vitamin D-dependent 2A (VDDR2A)
VAR_004660 Rickets vitamin D-dependent 2A (VDDR2A)

Structural Variations from Database of Genomic Variants (DGV) for VDR Gene

Variant ID Type Subtype PubMed ID
esv8233 CNV Gain 19470904

Variation tolerance for VDR Gene

Residual Variation Intolerance Score: 42.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.50; 29.20% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VDR Gene

HapMap Linkage Disequilibrium report
VDR
Human Gene Mutation Database (HGMD)
VDR

Disorders for VDR Gene

MalaCards: The human disease database

(56) MalaCards diseases for VDR Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
rickets, vitamin d-resistant, type iia
  • vitamin d-dependent rickets type ii
vitamin d-dependent rickets type ii
  • rickets-alopecia syndrome
osteoporosis
  • osteoporosis, postmenopausal, susceptibility
rickets
  • active rickets
calcium metabolism disease
  • calcium metabolism disorders
- elite association - COSMIC cancer census association via MalaCards
Search VDR in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VDR_HUMAN
  • 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. {ECO:0000269 PubMed:1652893, ECO:0000269 PubMed:2177843, ECO:0000269 PubMed:2849209, ECO:0000269 PubMed:7828346, ECO:0000269 PubMed:8106618, ECO:0000269 PubMed:8381803, ECO:0000269 PubMed:8392085, ECO:0000269 PubMed:8675579, ECO:0000269 PubMed:8961271, ECO:0000269 PubMed:9005998}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for VDR Gene

rickets,vitamin D-dependent,type II,with alopecia

Relevant External Links for VDR

Genetic Association Database (GAD)
VDR
Human Genome Epidemiology (HuGE) Navigator
VDR
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VDR
genes like me logo Genes that share disorders with VDR: view

Publications for VDR Gene

  1. Vitamin D receptor (VDR) gene polymorphisms and haplotypes, interactions with plasma 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D, and prostate cancer risk. (PMID: 17440943) Mikhak B. … Giovannucci E. (Prostate 2007) 3 23 25 26
  2. Promoter and 3'-untranslated-region haplotypes in the vitamin D receptor gene predispose to osteoporotic fracture: the Rotterdam study. (PMID: 16252240) Fang Y. … Uitterlinden A.G. (Am. J. Hum. Genet. 2005) 3 4 48 67
  3. New acquisitions in therapy of secondary hyperparathyroidism in chronic kidney disease and peritoneal dialysis patients: role of vitamin D receptor activators. (PMID: 19494617) Brancaccio D. … Gallieni M. (Contrib Nephrol 2009) 23 25 26
  4. Transgenic expression of the human Vitamin D receptor (hVDR) in the duodenum of VDR-null mice attenuates the age-dependent decline in calcium absorption. (PMID: 17207992) Marks H.D. … Peleg S. (J. Steroid Biochem. Mol. Biol. 2007) 23 25 26
  5. The 1alpha,25-dihydroxy Vitamin D3 receptor preferentially recruits the coactivator SRC-1 during up-regulation of the osteocalcin gene. (PMID: 17218095) Carvallo L. … Montecino M. (J. Steroid Biochem. Mol. Biol. 2007) 23 25 26

Products for VDR Gene

Sources for VDR Gene

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