Vdr vitamin D receptor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vdrprovided by RGD
Official Full Name: vitamin D receptorprovided by RGD
Primary source: RGD:3959
See related: EnsemblRapid:ENSRNOG00000054420 AllianceGenome:RGD:3959
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Nr1i1
Summary: Enables calcitriol binding activity; nuclear receptor activity; and sequence-specific DNA binding activity. Involved in several processes, including cellular response to amyloid-beta; negative regulation of bone trabecula formation; and positive regulation of parathyroid hormone secretion. Located in several cellular components, including T-tubule; chromatin; and nuclear lumen. Used to study vitamin D-dependent rickets type 2A. Biomarker of retinal degeneration and secondary hyperparathyroidism. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); carcinoma (multiple); liver disease (multiple); lung disease (multiple); and melanoma (multiple). Orthologous to human VDR (vitamin D receptor). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 182.4), Lung (RPKM 16.2) and 3 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q36

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (130864764..130916757, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (128987981..129037677, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (139344452..139394138, complement)

Chromosome 7 - NC_086025.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

1,25-D3 ameliorates ischemic brain injury by alleviating endoplasmic reticulum stress and ferroptosis: Involvement of vitamin D receptor and p53 signaling.
Title: 1,25-D3 ameliorates ischemic brain injury by alleviating endoplasmic reticulum stress and ferroptosis: Involvement of vitamin D receptor and p53 signaling.
VDR regulates mitochondrial function as a protective mechanism against renal tubular cell injury in diabetic rats.
Title: VDR regulates mitochondrial function as a protective mechanism against renal tubular cell injury in diabetic rats.
1,25D/VDR inhibits pancreatic beta cell ferroptosis by downregulating FOXO1 expression in diabetes mellitus.
Title: 1,25D/VDR inhibits pancreatic β cell ferroptosis by downregulating FOXO1 expression in diabetes mellitus.
VDR Regulates BNP Promoting Neurite Growth and Survival of Cochlear Spiral Ganglion Neurons through cGMP-PKG Signaling Pathway.
Title: VDR Regulates BNP Promoting Neurite Growth and Survival of Cochlear Spiral Ganglion Neurons through cGMP-PKG Signaling Pathway.
Vitamin D receptor absence does not enhance intestinal tumorigenesis in ApcPirc/+rats.
Title: Vitamin D receptor absence does not enhance intestinal tumorigenesis in ApcPirc/+rats.
Calcipotriol attenuates liver fibrosis through the inhibition of vitamin D receptor-mediated NF-kappaB signaling pathway.
Title: Calcipotriol attenuates liver fibrosis through the inhibition of vitamin D receptor-mediated NF-κB signaling pathway.
Influence of Stress on the Vitamin D-Vitamin D Receptor System, Macrophages, and the Local Inflammatory Milieu in Endometriosis.
Title: Influence of Stress on the Vitamin D-Vitamin D Receptor System, Macrophages, and the Local Inflammatory Milieu in Endometriosis.
Vitamin D attenuates cerebral artery remodeling through VDR/AMPK/eNOS dimer phosphorylation pathway after subarachnoid hemorrhage in rats.
Title: Vitamin D attenuates cerebral artery remodeling through VDR/AMPK/eNOS dimer phosphorylation pathway after subarachnoid hemorrhage in rats.
Inhibition of vitamin D receptor exerts a protective role in high-level glucose induced retinal ganglion cell damage by activating the STAT3 pathway.
Title: Vitamin D receptor regulates high-level glucose induced retinal ganglion cell damage through STAT3 pathway.
This study demonstrated that decreased expression of VDR may play a role in age-related intervertebral disc degeneration in rats and that activation of VDR ameliorates oxidative stress-induced apoptosis in annulus fibrosus cells by preserving mitochondrial functions.
Title: Age-dependent expression of the vitamin D receptor and the protective effect of vitamin D receptor activation on H(2)O(2)-induced apoptosis in rat intervertebral disc cells.

Submit: New GeneRIF Correction See all GeneRIFs (77)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Vdr (e-PCR), detects polymorphism
- UniSTS:144750

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
contributes_to DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables bile acid nuclear receptor activity	IEA Inferred from Electronic Annotation more info
enables bile acid nuclear receptor activity	ISO Inferred from Sequence Orthology more info
enables calcitriol binding	IDA Inferred from Direct Assay more info	PubMed
enables calcitriol binding	IEA Inferred from Electronic Annotation more info
enables calcitriol binding	ISO Inferred from Sequence Orthology more info
enables lithocholic acid binding	IEA Inferred from Electronic Annotation more info
enables lithocholic acid binding	ISO Inferred from Sequence Orthology more info
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables nuclear receptor activity	ISO Inferred from Sequence Orthology more info
enables nuclear retinoid X receptor binding	IEA Inferred from Electronic Annotation more info
enables nuclear retinoid X receptor binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables vitamin D binding	IDA Inferred from Direct Assay more info	PubMed
enables vitamin D binding	IMP Inferred from Mutant Phenotype more info	PubMed
contributes_to vitamin D response element binding	IBA Inferred from Biological aspect of Ancestor more info
enables vitamin D response element binding	IEA Inferred from Electronic Annotation more info
contributes_to vitamin D response element binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within animal organ morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in apoptotic process involved in mammary gland involution	IEA Inferred from Electronic Annotation more info
acts_upstream_of apoptotic process involved in mammary gland involution	ISO Inferred from Sequence Orthology more info
involved_in apoptotic signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in calcium ion transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within calcium ion transport	ISO Inferred from Sequence Orthology more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cell morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cellular response to amyloid-beta	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to vitamin D	IEP Inferred from Expression Pattern more info	PubMed
involved_in decidualization	IEA Inferred from Electronic Annotation more info
involved_in decidualization	ISO Inferred from Sequence Orthology more info
involved_in heart development	IEP Inferred from Expression Pattern more info	PubMed
involved_in intestinal absorption	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within intestinal absorption	ISO Inferred from Sequence Orthology more info
involved_in intracellular calcium ion homeostasis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within intracellular calcium ion homeostasis	ISO Inferred from Sequence Orthology more info
involved_in lactation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lactation	ISO Inferred from Sequence Orthology more info
involved_in mRNA transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in mRNA transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in mammary gland branching involved in pregnancy	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mammary gland branching involved in pregnancy	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of bone trabecula formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of keratinocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of keratinocyte proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of ossification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in nuclear receptor-mediated bile acid signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in nuclear receptor-mediated bile acid signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in phosphate ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in phosphate ion transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of apoptotic process involved in mammary gland involution	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of apoptotic process involved in mammary gland involution	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of keratinocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of keratinocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of parathyroid hormone secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of vitamin D 24-hydroxylase activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of vitamin D receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of vitamin D receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of calcidiol 1-monooxygenase activity	ISO Inferred from Sequence Orthology more info
involved_in regulation of calcium ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed
involved_in response to aldosterone	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to bile acid	IEA Inferred from Electronic Annotation more info
involved_in response to bile acid	ISO Inferred from Sequence Orthology more info
involved_in response to calcium ion	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to estradiol	IEP Inferred from Expression Pattern more info	PubMed
involved_in retinoic acid receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in retinoic acid receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in skeletal system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within skeletal system development	ISO Inferred from Sequence Orthology more info
involved_in vitamin D receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in vitamin D receptor signaling pathway	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	IEA Inferred from Electronic Annotation more info
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
located_in T-tubule	IDA Inferred from Direct Assay more info	PubMed
located_in caveola	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	IEA Inferred from Electronic Annotation more info
is_active_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in dense fibrillar component	IDA Inferred from Direct Assay more info	PubMed
located_in euchromatin	IDA Inferred from Direct Assay more info	PubMed
located_in heterochromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear matrix	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of receptor complex	IEA Inferred from Electronic Annotation more info
part_of receptor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: vitamin D3 receptor

Names: 1,25-dihydroxyvitamin D3 receptor; nuclear receptor subfamily 1 group I member 1; vitamin D (1,25- dihydroxyvitamin D3) receptor

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

NM_017058.2 → NP_058754.2 vitamin D3 receptor

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000007

UniProtKB/Swiss-Prot

P13053

UniProtKB/TrEMBL

A6KC47, G3V744

Related

ENSRNOP00000111704.1, ENSRNOT00000122258.1

Conserved Domains (2) summary

cd06933
Location:124 → 422

NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily

cd06955
Location:16 → 122

NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers