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Aliases for VDR Gene

Aliases for VDR Gene

  • Vitamin D (1,25- Dihydroxyvitamin D3) Receptor 2 3
  • 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 D3 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 Retinoic acid receptors-mediated signaling and Gene Expression. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and steroid hormone receptor activity. An important paralog of this gene is NR1I2.

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 (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 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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for VDR Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Other Protein References for VDR Gene

Antibody Products

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

No data available for DME Specific Peptides for VDR Gene

Domains for VDR Gene

Gene Families for VDR Gene

HGNC:
  • NR :Nuclear hormone receptors
IUPHAR :

Graphical View of Domain Structure for InterPro Entry

P11473

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
  • 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:0003677 DNA binding IDA 11891224
GO:0003700 contributes_to sequence-specific DNA binding transcription factor activity IDA 17426122
GO:0003707 steroid hormone receptor activity IEA --
GO:0004879 ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity --
GO:0005515 protein binding IPI 10409738
genes like me logo Genes that share ontologies with VDR: view
genes like me logo Genes that share phenotypes with VDR: view

Animal Models for VDR Gene

MGI Knock Outs for VDR:

Animal Model Products

CRISPR Products

miRNA for VDR Gene

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

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VDR

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targeting 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 2
cytosol 2
extracellular 2
peroxisome 2
plasma membrane 2

Gene Ontology (GO) - Cellular Components for VDR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 15589699
GO:0005654 nucleoplasm TAS --
GO:0043235 receptor complex IDA 17426122
GO:0090575 RNA polymerase II transcription factor complex IDA 17426122
genes like me logo Genes that share ontologies with VDR: view

Pathways for VDR Gene

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

PCR Array Products

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 --
GO:0006355 regulation of transcription, DNA-templated --
genes like me logo Genes that share ontologies with VDR: view

Compounds for VDR Gene

(5) Tocris Compounds for VDR Gene

Compound Action Cas Number
Alfacalcidol Prodrug of vitamin D3 (Cat. No. 4156) [41294-56-8]
Calcifediol Prohormone of calcitriol (Cat. No. 2551). Major circulating form of vitamin D [19356-17-3]
Calcipotriol Vitamin D3 analog [112965-21-6]
Calcitriol Vitamin D receptor (VDR) agonist [32222-06-3]
EB 1089 Vitamin D receptor (VDR) agonist [134404-52-7]

(5) HMDB Compounds for VDR Gene

Compound Synonyms Cas Number PubMed IDs
Calcidiol
  • 25-Hydroxyvitamin D3
19356-17-3
Calcitriol
  • (3b,5Z,7E)-9,10-Secocholesta-5,7,10(19)-trienetriol
32222-06-3
Calcium
  • Ca
7440-70-2
Ergocalciferol
  • (+)-Vitamin D2
50-14-6
Vitamin D3
  • (+)-Vitamin D3
67-97-0

(12) IUPHAR Ligand for VDR Gene

Ligand Type Action Affinity Pubmed IDs
KH1060 Agonist Agonist 10.1
2MD Agonist Agonist 10
EB1089 Agonist Agonist 9.57
calcipotriol Agonist Agonist 9.3
1,25-dihydroxyvitamin D3 Agonist Agonist 9.21
TV-02H Agonist Agonist 8.5
ZK159222 Antagonist Antagonist 7.54
calcitriol-26,23-lactone Agonist Agonist 7.5
LG190178 Agonist Agonist 6.82
lithocholic acid Agonist Agonist 5.05
3-keto-lithocholic acid Agonist Agonist 4.8
TEI-9647 Antagonist Antagonist

(96) Novoseek inferred chemical compound relationships for VDR Gene

Compound -log(P) Hits PubMed IDs
vitamin d 98.5 408
1,25 dihydroxy vitamin d3 96 190
calcitriol 95.2 178
apai 94.6 119
eb 1089 87.3 24

(6) PharmGKB related drug/compound annotations for VDR Gene

Drug/compound Annotation
alendronate CA
Bisphosphonates CA
Calcium CA
clodronate CA
etidronic acid CA
raloxifene CA
genes like me logo Genes that share compounds with VDR: view

Transcripts for VDR Gene

Unigene Clusters for VDR Gene

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

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VDR

Primer Products

Flow Cytometry Products

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 (6.5) and Skin - Not Sun Exposed (Suprapubic) (4.5).

Integrated Proteomics: protein expression 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 expressions with VDR: view

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt 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
chimpanzee
(Pan troglodytes)
Mammalia VDR 35
  • 93.1 (n)
  • 91.13 (a)
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
oppossum
(Monodelphis domestica)
Mammalia VDR 36
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VDR 36
  • 45 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vdr 35
  • 87.16 (n)
  • 90.31 (a)
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
African clawed frog
(Xenopus laevis)
Amphibia vdr-A 35
tropical clawed frog
(Silurana tropicalis)
Amphibia vdr 35
  • 67.54 (n)
  • 74.52 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.668 35
zebrafish
(Danio rerio)
Actinopterygii vdr 35
VDR (1 of 2) 36
  • 67 (a)
OneToMany
vdra 35
  • 70.32 (n)
  • 71.33 (a)
vdrb 36
  • 71 (a)
OneToMany
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

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 MAF
rs9729 -- 47,842,840(-) TCATT(A/C/G)AGGAA utr-variant-3-prime
rs12088 -- 47,842,905(-) GTATT(C/G)GTCCA utr-variant-3-prime
rs731236 -- 47,844,974(-) CTGAT(C/T)GAGGC synonymous-codon, reference
rs739837 -- 47,844,438(+) ACTTA(G/T)GCAGC utr-variant-3-prime
rs757343 -- 47,845,892(-) CCCTT(A/G)ACCTC intron-variant

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

Variant ID Type Subtype PubMed ID
esv8233 CNV Gain 19470904

Relevant External Links for VDR Gene

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

Disorders for VDR Gene

(2) OMIM Diseases for VDR Gene (601769)

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.

(96) Novoseek inferred disease relationships for VDR Gene

Disease -log(P) Hits PubMed IDs
hvdrr 92.5 62
rickets 83.6 77
hyperparathyroidism secondary 82.7 49
vitamin d deficiency 82.4 26
osteoporosis 77.4 136

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

Publications for VDR Gene

  1. 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 23 48
  2. 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 48
  3. Variation in the vitamin D receptor gene is associated with multiple sclerosis in an Australian population. (PMID: 16076630) Tajouri L. … Lea R.A. (J. Neurogenet. 2005) 3 23 48
  4. Associations between polymorphisms in the vitamin D receptor and breast cancer risk. (PMID: 16214913) Chen W.Y. … Hankinson S.E. (Cancer Epidemiol. Biomarkers Prev. 2005) 3 23 48
  5. Meta-analysis of vitamin D receptor polymorphisms and pulmonary tuberculosis risk. (PMID: 16229232) Lewis S.J. … Davey Smith G. (Int. J. Tuberc. Lung Dis. 2005) 3 23 48

Products for VDR Gene

Sources for VDR Gene

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