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    VDR vitamin D receptor [ Homo sapiens (human) ]

    Gene ID: 7421, updated on 13-May-2024

    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; AllianceGenome:HGNC:12679
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    12q13.11
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (47841537..47904994, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (47802918..47866398, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (48235320..48298777, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902926 Neighboring gene histone deacetylase 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6267 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:48211237-48211897 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:48212615-48213188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4402 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4403 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:48214527-48215448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6269 Neighboring gene long intergenic non-protein coding RNA 2354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48236992-48237565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48237566-48238138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48239663-48240164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48262276-48262776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48276324-48276836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6273 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48329073-48329573 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:48353651-48354181 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:48367908-48368120 Neighboring gene transmembrane protein 106C Neighboring gene uncharacterized LOC105369752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48375074-48375619 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Vitamin D-dependent rickets type II with alopecia
    MedGen: C0342646 OMIM: 277440 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 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 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
     
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables calcitriol binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables calcitriol binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables lithocholic acid binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables nuclear retinoid X receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables nuclear retinoid X receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    contributes_to vitamin D response element binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    contributes_to vitamin D response element binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in apoptotic process involved in mammary gland involution IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in bile acid signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in calcium ion transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in decidualization IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in intestinal absorption IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intracellular calcium ion homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lactation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mRNA transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mRNA transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mammary gland branching involved in pregnancy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in multicellular organism development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of keratinocyte proliferation 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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in phosphate ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of apoptotic process involved in mammary gland involution IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of bone mineralization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of keratinocyte differentiation 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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of vitamin D 24-hydroxylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of vitamin D receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of vitamin D receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of calcidiol 1-monooxygenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in response to bile acid IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in skeletal system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in vitamin D receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in vitamin D receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of RNA polymerase II transcription regulator complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of RNA polymerase II transcription regulator complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of 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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      5038..68495
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000376.3NP_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, BC060832, BM908433, BQ002808, CF138099, J03258
      Consensus CDS
      CCDS8757.1
      UniProtKB/Swiss-Prot
      B2R5Q1, G3V1V9, P11473, Q5PSV3
      UniProtKB/TrEMBL
      B6ZGT0, F1D8P8
      Related
      ENSP00000449573.2, ENST00000549336.6
      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_001017535.2NP_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
      Consensus CDS
      CCDS8757.1
      UniProtKB/Swiss-Prot
      B2R5Q1, G3V1V9, P11473, Q5PSV3
      UniProtKB/TrEMBL
      B6ZGT0, 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. NM_001017536.2NP_001017536.1  vitamin D3 receptor isoform VDRB1

      See identical proteins and their annotated locations for NP_001017536.1

      Status: REVIEWED

      Source sequence(s)
      AC004466, BC060832, BM685276
      Consensus CDS
      CCDS55820.1
      UniProtKB/TrEMBL
      B6ZGT0
      Related
      ENSP00000447173.1, ENST00000550325.5
      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_001364085.2NP_001351014.1  vitamin D3 receptor isoform VDRAx

      Status: REVIEWED

      Source sequence(s)
      AC004466, AC121338
      Consensus CDS
      CCDS91689.1
      UniProtKB/TrEMBL
      A0A5K1VW50, B6ZGT0
      Related
      ENSP00000229022.5, ENST00000229022.9
      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
    5. NM_001374661.1NP_001361590.1  vitamin D3 receptor isoform VDRA

      Status: REVIEWED

      Source sequence(s)
      AC004466, AC121338
      Consensus CDS
      CCDS8757.1
      UniProtKB/Swiss-Prot
      B2R5Q1, G3V1V9, P11473, Q5PSV3
      UniProtKB/TrEMBL
      B6ZGT0, 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
    6. NM_001374662.1NP_001361591.1  vitamin D3 receptor isoform VDRA

      Status: REVIEWED

      Source sequence(s)
      AC004466, AC121338
      Consensus CDS
      CCDS8757.1
      UniProtKB/Swiss-Prot
      B2R5Q1, G3V1V9, P11473, Q5PSV3
      UniProtKB/TrEMBL
      B6ZGT0, 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

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      47841537..47904994 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047429500.1XP_047285456.1  vitamin D3 receptor isoform X2

      UniProtKB/Swiss-Prot
      B2R5Q1, G3V1V9, P11473, Q5PSV3
      UniProtKB/TrEMBL
      F1D8P8
    2. XM_024449178.2XP_024304946.1  vitamin D3 receptor isoform X1

      UniProtKB/TrEMBL
      B6ZGT0
      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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      47802918..47866398 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373132.1XP_054229107.1  vitamin D3 receptor isoform X2

      UniProtKB/Swiss-Prot
      B2R5Q1, G3V1V9, P11473, Q5PSV3
      UniProtKB/TrEMBL
      F1D8P8
    2. XM_054373131.1XP_054229106.1  vitamin D3 receptor isoform X1