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VDR vitamin D receptor [ Homo sapiens (human) ]

Gene ID: 7421, updated on 18-Nov-2018

Summary

Official Symbol
VDRprovided by HGNC
Official Full Name
vitamin D receptorprovided by HGNC
Primary source
HGNC:HGNC:12679
See related
Ensembl:ENSG00000111424 MIM:601769; Vega:OTTHUMG00000169890
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NR1I1; PPP1R163
Summary
This gene encodes vitamin D3 receptor, which is a member of the nuclear hormone receptor superfamily of ligand-inducible transcription factors. This receptor also functions as a receptor for the secondary bile acid, lithocholic acid. Downstream targets of vitamin D3 receptor are principally involved in mineral metabolism, though this receptor regulates a variety of other metabolic pathways, such as those involved in 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. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. A recent study provided evidence for translational readthrough in this gene, and expression of an additional C-terminally extended isoform via the use of an alternative in-frame translation termination codon. [provided by RefSeq, Jun 2018]
Expression
Broad expression in small intestine (RPKM 24.6), duodenum (RPKM 24.1) and 14 other tissues See more
Orthologs

Genomic context

See VDR in Genome Data Viewer
Location:
12q13.11
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (47841537..47905031, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (48235320..48298814, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 48 member 1 Neighboring gene histone deacetylase 7 Neighboring gene long intergenic non-protein coding RNA 2354 Neighboring gene transmembrane protein 106C Neighboring gene uncharacterized LOC105369752 Neighboring gene collagen type II alpha 1 chain

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Postmenopausal osteoporosis
MedGen: C0029458 OMIM: 166710 GeneReviews: Not available
Compare labs
Vitamin D-dependent rickets, type 2
MedGen: C0342646 OMIM: 277440 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of vitamin D (1,25- dihydroxyvitamin D3) receptor (VDR) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp160 and gp120 contain alpha-N-acetylgalactosaminidase (Nagalase) activity, which deglycosylates serum vitamin D3-binding protein (Gc protein) PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Direct p53 effectors, organism-specific biosystem (from Pathway Interaction Database)
    Direct p53 effectors, organism-specific biosystem
    Direct p53 effectors
  • Drug Induction of Bile Acid Pathway, organism-specific biosystem (from WikiPathways)
    Drug Induction of Bile Acid Pathway, organism-specific biosystem
    Drug Induction of Bile Acid Pathway
  • Endocrine and other factor-regulated calcium reabsorption, organism-specific biosystem (from KEGG)
    Endocrine and other factor-regulated calcium reabsorption, organism-specific biosystemCalcium (Ca2+) is essential for numerous physiological functions including intracellular signalling processes, neuronal excitability, muscle contraction and bone formation. Therefore, its homeostasis...
  • Endocrine and other factor-regulated calcium reabsorption, conserved biosystem (from KEGG)
    Endocrine and other factor-regulated calcium reabsorption, conserved biosystemCalcium (Ca2+) is essential for numerous physiological functions including intracellular signalling processes, neuronal excitability, muscle contraction and bone formation. Therefore, its homeostasis...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • Mineral absorption, organism-specific biosystem (from KEGG)
    Mineral absorption, organism-specific biosystemMinerals are one of the five fundamental groups of nutrients needed to sustain life. Of the minerals, calcium plays innumerable roles in our bodies, serving as a main component of bone as well as an ...
  • Mineral absorption, conserved biosystem (from KEGG)
    Mineral absorption, conserved biosystemMinerals are one of the five fundamental groups of nutrients needed to sustain life. Of the minerals, calcium plays innumerable roles in our bodies, serving as a main component of bone as well as an ...
  • Nuclear Receptor transcription pathway, organism-specific biosystem (from REACTOME)
    Nuclear Receptor transcription pathway, organism-specific biosystemA classic example of bifunctional transcription factors is the family of Nuclear Receptor (NR) proteins. These are DNA-binding transcription factors that bind certain hormones, vitamins, and other s...
  • Nuclear Receptors, organism-specific biosystem (from WikiPathways)
    Nuclear Receptors, organism-specific biosystemNuclear receptors are a class of proteins found within the interior of cells that are responsible for sensing the presence of steroid and thyroid hormones and certain other molecules. In response, th...
  • Nuclear Receptors in Lipid Metabolism and Toxicity, organism-specific biosystem (from WikiPathways)
    Nuclear Receptors in Lipid Metabolism and Toxicity, organism-specific biosystemNuclear receptors are transcription factors that are activated upon binding to its ligands. Initially, they had been classified as classic endocrine nuclear hormone receptors and orphan receptors. Ho...
  • Ovarian Infertility Genes, organism-specific biosystem (from WikiPathways)
    Ovarian Infertility Genes, organism-specific biosystemOvarian bottleneck genes associated with infertility. A valuable approach to the study of infertility is the comparison of mutations of individual human and mouse genes associated with infertility ph...
  • RXR and RAR heterodimerization with other nuclear receptor, organism-specific biosystem (from Pathway Interaction Database)
    RXR and RAR heterodimerization with other nuclear receptor, organism-specific biosystem
    RXR and RAR heterodimerization with other nuclear receptor
  • Regulation of nuclear SMAD2/3 signaling, organism-specific biosystem (from Pathway Interaction Database)
    Regulation of nuclear SMAD2/3 signaling, organism-specific biosystem
    Regulation of nuclear SMAD2/3 signaling
  • Retinoic acid receptors-mediated signaling, organism-specific biosystem (from Pathway Interaction Database)
    Retinoic acid receptors-mediated signaling, organism-specific biosystem
    Retinoic acid receptors-mediated signaling
  • Tuberculosis, organism-specific biosystem (from KEGG)
    Tuberculosis, organism-specific biosystemTuberculosis, or TB, is an infectious disease caused by Mycobacterium tuberculosis. One third of the world's population is thought to be infected with TB. About 90% of those infected result in latent...
  • Tuberculosis, conserved biosystem (from KEGG)
    Tuberculosis, conserved biosystemTuberculosis, or TB, is an infectious disease caused by Mycobacterium tuberculosis. One third of the world's population is thought to be infected with TB. About 90% of those infected result in latent...
  • Vitamin D Metabolism, organism-specific biosystem (from WikiPathways)
    Vitamin D Metabolism, organism-specific biosystemPhotochemical synthesis of vitamin D3 (cholecalciferol, D3) occurs cutaneously where pro-vitamin D3 (7-dehydrocholesterol) is converted to pre-vitamin D3 (pre-D3) in response to ultraviolet B (sunlig...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcitriol binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcitriol binding IDA
Inferred from Direct Assay
more info
PubMed 
calcitriol binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
lithocholic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
lithocholic acid receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
nuclear receptor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
nuclear receptor transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
retinoid X receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
retinoid X receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
signaling receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
steroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
 
transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
vitamin D binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
contributes_to vitamin D response element binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
contributes_to vitamin D response element binding IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
animal organ morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bile acid signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
calcium ion transport IEA
Inferred from Electronic Annotation
more info
 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular calcium ion homeostasis IEA
Inferred from Electronic Annotation
more info
 
decidualization IEP
Inferred from Expression Pattern
more info
PubMed 
intestinal absorption IEA
Inferred from Electronic Annotation
more info
 
lactation IEA
Inferred from Electronic Annotation
more info
 
mammary gland branching involved in pregnancy IEA
Inferred from Electronic Annotation
more info
 
multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of keratinocyte proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of apoptotic process involved in mammary gland involution IEA
Inferred from Electronic Annotation
more info
 
positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of keratinocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of vitamin D 24-hydroxylase activity IDA
Inferred from Direct Assay
more info
PubMed 
regulation of calcidiol 1-monooxygenase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
skeletal system development IEA
Inferred from Electronic Annotation
more info
 
steroid hormone mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
vitamin D metabolic process TAS
Traceable Author Statement
more info
 
vitamin D receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
vitamin D receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
RNA polymerase II transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II transcription factor complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
receptor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
vitamin D3 receptor
Names
1,25-dihydroxyvitamin D3 receptor
nuclear receptor subfamily 1 group I member 1
protein phosphatase 1, regulatory subunit 163
vitamin D (1,25- dihydroxyvitamin D3) receptor
vitamin D nuclear receptor variant 1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008731.1 RefSeqGene

    Range
    5001..68495
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000376.2NP_000367.1  vitamin D3 receptor isoform VDRA

    See identical proteins and their annotated locations for NP_000367.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes two isoforms, which result from the use of alternative in-frame translation termination codons. The shorter isoform (VDRA, also known as VDR) results from translation termination at the upstream UGA stop codon, while the longer isoform (VDRAx, also known as VDRx) results from UGA stop codon readthrough to the downstream UGA termination codon. This RefSeq represents the shorter isoform (VDRA). Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AC004466, AC121338, BC060832, BM908433, BQ002808, CF138099, J03258
    Consensus CDS
    CCDS8757.1
    UniProtKB/Swiss-Prot
    P11473
    UniProtKB/TrEMBL
    F1D8P8
    Related
    ENSP00000449573.1, OTTHUMP00000242392, ENST00000549336.5, OTTHUMT00000406434
    Conserved Domains (2) summary
    cd06933
    Location:124426
    NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
    cd06955
    Location:16122
    NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
  2. NM_001017535.1NP_001017535.1  vitamin D3 receptor isoform VDRA

    See identical proteins and their annotated locations for NP_001017535.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an additional 5' non-coding exon compared to variant 1. Variants 1 and 2 encode the same isoform (VDRA).
    Source sequence(s)
    AC004466, AC121338, BC060832, BM908433, BQ002808, BX355584, CF138099, J03258
    Consensus CDS
    CCDS8757.1
    UniProtKB/Swiss-Prot
    P11473
    UniProtKB/TrEMBL
    F1D8P8
    Related
    ENSP00000229022.3, ENST00000229022.7
    Conserved Domains (2) summary
    cd06933
    Location:124426
    NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
    cd06955
    Location:16122
    NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
  3. NM_001017536.1NP_001017536.1  vitamin D3 receptor isoform VDRB1

    See identical proteins and their annotated locations for NP_001017536.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) is alternatively spliced at the 5' end, resulting in translation initiation at an in-frame upstream start codon, compared to variant 1. The encoded isoform (VDRB1) has a longer and distinct N-terminus compared to isoform VDRA.
    Source sequence(s)
    AC004466, BC060832, BM685276, DA721726
    Consensus CDS
    CCDS55820.1
    UniProtKB/Swiss-Prot
    P11473
    Related
    ENSP00000447173.1, OTTHUMP00000242393, ENST00000550325.5, OTTHUMT00000406435
    Conserved Domains (2) summary
    cd06933
    Location:174476
    NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
    cd06955
    Location:66172
    NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
  4. NM_001364085.1NP_001351014.1  vitamin D3 receptor isoform VDRAx

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes two isoforms, which result from the use of alternative in-frame translation termination codons. The shorter isoform (VDRA, also known as VDR) results from translation termination at the upstream UGA stop codon, while the longer isoform (VDRAx, also known as VDRx) results from UGA stop codon readthrough to the downstream UGA termination codon. This RefSeq represents the longer, C-terminally extended isoform (VDRAx). As the UGA stop codon has been reported to specify several alternative amino acids (tryptophan, cysteine, arginine and serine), its location in the longer isoform is denoted by an 'X'.
    Source sequence(s)
    AC004466, AK312267, BC060832, BQ002808, DA721726
    Conserved Domains (2) summary
    cd06933
    Location:124426
    NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
    cd06955
    Location:16122
    NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    47841537..47905031 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006719587.3XP_006719650.1  vitamin D3 receptor isoform X2

    See identical proteins and their annotated locations for XP_006719650.1

    UniProtKB/Swiss-Prot
    P11473
    UniProtKB/TrEMBL
    F1D8P8
    Conserved Domains (2) summary
    cd06933
    Location:124426
    NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
    cd06955
    Location:16122
    NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
  2. XM_011538720.2XP_011537022.1  vitamin D3 receptor isoform X2

    See identical proteins and their annotated locations for XP_011537022.1

    UniProtKB/Swiss-Prot
    P11473
    UniProtKB/TrEMBL
    F1D8P8
    Conserved Domains (2) summary
    cd06933
    Location:124426
    NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
    cd06955
    Location:16122
    NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
  3. XM_024449178.1XP_024304946.1  vitamin D3 receptor isoform X1

    Conserved Domains (2) summary
    cd06933
    Location:147449
    NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
    cd06955
    Location:39145
    NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
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