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VDR (vitamin D receptor)

Identity

Alias (NCBI)NR1I1
PPP1R163
HGNC (Hugo) VDR
HGNC Alias symbNR1I1
PPP1R163
HGNC Alias nameprotein phosphatase 1, regulatory subunit 163
 1,25- dihydroxyvitamin D3 receptor
HGNC Previous namevitamin D (1,25- dihydroxyvitamin D3) receptor
LocusID (NCBI) 7421
Atlas_Id 45741
Location 12q13.11  [Link to chromosome band 12q13]
Location_base_pair Starts at 47841537 and ends at 47904994 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
LMBR1L (12q13.12) / VDR (12q13.11)VDR (12q13.11) / SLC1A5 (19q13.32)VDR (12q13.11) / VDR (12q13.11)
LMBR1L 12q13.12 / VDR 12q13.11

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 



External links

 

Nomenclature
HGNC (Hugo)VDR   12679
Cards
Entrez_Gene (NCBI)VDR    vitamin D receptor
AliasesNR1I1; PPP1R163
GeneCards (Weizmann)VDR
Ensembl hg19 (Hinxton)ENSG00000111424 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000111424 [Gene_View]  ENSG00000111424 [Sequence]  chr12:47841537-47904994 [Contig_View]  VDR [Vega]
ICGC DataPortalENSG00000111424
TCGA cBioPortalVDR
AceView (NCBI)VDR
Genatlas (Paris)VDR
SOURCE (Princeton)VDR
Genetics Home Reference (NIH)VDR
Genomic and cartography
GoldenPath hg38 (UCSC)VDR  -     chr12:47841537-47904994 -  12q13.11   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)VDR  -     12q13.11   [Description]    (hg19-Feb_2009)
GoldenPathVDR - 12q13.11 [CytoView hg19]  VDR - 12q13.11 [CytoView hg38]
ImmunoBaseENSG00000111424
Genome Data Viewer NCBIVDR [Mapview hg19]  
OMIM277440   601769   
Gene and transcription
Genbank (Entrez)AB307700 AF026260 AK024830 AK225844 AK299446
RefSeq transcript (Entrez)NM_000376 NM_001017535 NM_001017536 NM_001364085 NM_001374661 NM_001374662
Consensus coding sequences : CCDS (NCBI)VDR
Gene ExpressionVDR [ NCBI-GEO ]   VDR [ EBI - ARRAY_EXPRESS ]   VDR [ SEEK ]   VDR [ MEM ]
Gene Expression Viewer (FireBrowse)VDR [ Firebrowse - Broad ]
GenevisibleExpression of VDR in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)7421
GTEX Portal (Tissue expression)VDR
Human Protein AtlasENSG00000111424-VDR [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP11473   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP11473  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP11473
PhosPhoSitePlusP11473
Domaine pattern : Prosite (Expaxy)NR_LBD (PS51843)    NUCLEAR_REC_DBD_1 (PS00031)    NUCLEAR_REC_DBD_2 (PS51030)   
Domains : Interpro (EBI)DBD_VDR    NHR-like_dom_sf    Nucl_hrmn_rcpt_lig-bd    Nuclear_hrmn_rcpt    VitD_rcpt    Znf_hrmn_rcpt    Znf_NHR/GATA   
Domain families : Pfam (Sanger)Hormone_recep (PF00104)    zf-C4 (PF00105)   
Domain families : Pfam (NCBI)pfam00104    pfam00105   
Domain families : Smart (EMBL)HOLI (SM00430)  ZnF_C4 (SM00399)  
Conserved Domain (NCBI)VDR
PDB (RSDB)1DB1    1IE8    1IE9    1KB2    1KB4    1KB6    1S0Z    1S19    1TXI    1YNW    2HAM    2HAR    2HAS    2HB7    2HB8    3A2I    3A2J    3A3Z    3A40    3A78    3AUQ    3AUR    3AX8    3AZ1    3AZ2    3AZ3    3B0T    3CS4    3CS6    3KPZ    3M7R    3OGT    3P8X    3TKC    3VHW    3W0A    3W0C    3W0Y    3WGP    3WWR    3X31    3X36    4G2I    4ITE    4ITF    5GT4    5V39    5YSY    5YT2   
PDB Europe1DB1    1IE8    1IE9    1KB2    1KB4    1KB6    1S0Z    1S19    1TXI    1YNW    2HAM    2HAR    2HAS    2HB7    2HB8    3A2I    3A2J    3A3Z    3A40    3A78    3AUQ    3AUR    3AX8    3AZ1    3AZ2    3AZ3    3B0T    3CS4    3CS6    3KPZ    3M7R    3OGT    3P8X    3TKC    3VHW    3W0A    3W0C    3W0Y    3WGP    3WWR    3X31    3X36    4G2I    4ITE    4ITF    5GT4    5V39    5YSY    5YT2   
PDB (PDBSum)1DB1    1IE8    1IE9    1KB2    1KB4    1KB6    1S0Z    1S19    1TXI    1YNW    2HAM    2HAR    2HAS    2HB7    2HB8    3A2I    3A2J    3A3Z    3A40    3A78    3AUQ    3AUR    3AX8    3AZ1    3AZ2    3AZ3    3B0T    3CS4    3CS6    3KPZ    3M7R    3OGT    3P8X    3TKC    3VHW    3W0A    3W0C    3W0Y    3WGP    3WWR    3X31    3X36    4G2I    4ITE    4ITF    5GT4    5V39    5YSY    5YT2   
PDB (IMB)1DB1    1IE8    1IE9    1KB2    1KB4    1KB6    1S0Z    1S19    1TXI    1YNW    2HAM    2HAR    2HAS    2HB7    2HB8    3A2I    3A2J    3A3Z    3A40    3A78    3AUQ    3AUR    3AX8    3AZ1    3AZ2    3AZ3    3B0T    3CS4    3CS6    3KPZ    3M7R    3OGT    3P8X    3TKC    3VHW    3W0A    3W0C    3W0Y    3WGP    3WWR    3X31    3X36    4G2I    4ITE    4ITF    5GT4    5V39    5YSY    5YT2   
Structural Biology KnowledgeBase1DB1    1IE8    1IE9    1KB2    1KB4    1KB6    1S0Z    1S19    1TXI    1YNW    2HAM    2HAR    2HAS    2HB7    2HB8    3A2I    3A2J    3A3Z    3A40    3A78    3AUQ    3AUR    3AX8    3AZ1    3AZ2    3AZ3    3B0T    3CS4    3CS6    3KPZ    3M7R    3OGT    3P8X    3TKC    3VHW    3W0A    3W0C    3W0Y    3WGP    3WWR    3X31    3X36    4G2I    4ITE    4ITF    5GT4    5V39    5YSY    5YT2   
SCOP (Structural Classification of Proteins)1DB1    1IE8    1IE9    1KB2    1KB4    1KB6    1S0Z    1S19    1TXI    1YNW    2HAM    2HAR    2HAS    2HB7    2HB8    3A2I    3A2J    3A3Z    3A40    3A78    3AUQ    3AUR    3AX8    3AZ1    3AZ2    3AZ3    3B0T    3CS4    3CS6    3KPZ    3M7R    3OGT    3P8X    3TKC    3VHW    3W0A    3W0C    3W0Y    3WGP    3WWR    3X31    3X36    4G2I    4ITE    4ITF    5GT4    5V39    5YSY    5YT2   
CATH (Classification of proteins structures)1DB1    1IE8    1IE9    1KB2    1KB4    1KB6    1S0Z    1S19    1TXI    1YNW    2HAM    2HAR    2HAS    2HB7    2HB8    3A2I    3A2J    3A3Z    3A40    3A78    3AUQ    3AUR    3AX8    3AZ1    3AZ2    3AZ3    3B0T    3CS4    3CS6    3KPZ    3M7R    3OGT    3P8X    3TKC    3VHW    3W0A    3W0C    3W0Y    3WGP    3WWR    3X31    3X36    4G2I    4ITE    4ITF    5GT4    5V39    5YSY    5YT2   
SuperfamilyP11473
AlphaFold pdb e-kbP11473   
Human Protein Atlas [tissue]ENSG00000111424-VDR [tissue]
HPRD03463
Protein Interaction databases
DIP (DOE-UCLA)P11473
IntAct (EBI)P11473
BioGRIDVDR
STRING (EMBL)VDR
ZODIACVDR
Ontologies - Pathways
QuickGOP11473
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  negative regulation of transcription by RNA polymerase II  chromatin  cell morphogenesis  RNA polymerase II cis-regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  skeletal system development  DNA binding  DNA-binding transcription factor activity  nuclear receptor activity  nuclear receptor activity  nuclear receptor activity  protein binding  nucleus  nucleoplasm  nucleoplasm  cytosol  transcription initiation from RNA polymerase II promoter  calcium ion transport  cellular calcium ion homeostasis  multicellular organism development  lactation  zinc ion binding  negative regulation of cell population proliferation  positive regulation of gene expression  negative regulation of gene expression  negative regulation of keratinocyte proliferation  positive regulation of vitamin D 24-hydroxylase activity  cell differentiation  bile acid signaling pathway  lithocholic acid receptor activity  vitamin D metabolic process  receptor complex  positive regulation of keratinocyte differentiation  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  decidualization  retinoid X receptor binding  retinoid X receptor binding  intestinal absorption  positive regulation of apoptotic process involved in mammary gland involution  regulation of calcidiol 1-monooxygenase activity  mammary gland branching involved in pregnancy  vitamin D receptor signaling pathway  vitamin D receptor signaling pathway  vitamin D response element binding  vitamin D response element binding  RNA polymerase II transcription regulator complex  calcitriol binding  calcitriol binding  lithocholic acid binding  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  negative regulation of transcription by RNA polymerase II  chromatin  cell morphogenesis  RNA polymerase II cis-regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  skeletal system development  DNA binding  DNA-binding transcription factor activity  nuclear receptor activity  nuclear receptor activity  nuclear receptor activity  protein binding  nucleus  nucleoplasm  nucleoplasm  cytosol  transcription initiation from RNA polymerase II promoter  calcium ion transport  cellular calcium ion homeostasis  multicellular organism development  lactation  zinc ion binding  negative regulation of cell population proliferation  positive regulation of gene expression  negative regulation of gene expression  negative regulation of keratinocyte proliferation  positive regulation of vitamin D 24-hydroxylase activity  cell differentiation  bile acid signaling pathway  lithocholic acid receptor activity  vitamin D metabolic process  receptor complex  positive regulation of keratinocyte differentiation  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  decidualization  retinoid X receptor binding  retinoid X receptor binding  intestinal absorption  positive regulation of apoptotic process involved in mammary gland involution  regulation of calcidiol 1-monooxygenase activity  mammary gland branching involved in pregnancy  vitamin D receptor signaling pathway  vitamin D receptor signaling pathway  vitamin D response element binding  vitamin D response element binding  RNA polymerase II transcription regulator complex  calcitriol binding  calcitriol binding  lithocholic acid binding  
Pathways : BIOCARTAControl of Gene Expression by Vitamin D Receptor [Genes]    Nuclear Receptors in Lipid Metabolism and Toxicity [Genes]   
Pathways : KEGGEndocrine and other factor-regulated calcium reabsorption    Mineral absorption    Tuberculosis   
NDEx NetworkVDR
Atlas of Cancer Signalling NetworkVDR
Wikipedia pathwaysVDR
Orthology - Evolution
OrthoDB7421
GeneTree (enSembl)ENSG00000111424
Phylogenetic Trees/Animal Genes : TreeFamVDR
Homologs : HomoloGeneVDR
Homology/Alignments : Family Browser (UCSC)VDR
Gene fusions - Rearrangements
Fusion : MitelmanLMBR1L/VDR [12q13.12/12q13.11]  
Fusion : QuiverVDR
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerVDR [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)VDR
dbVarVDR
ClinVarVDR
MonarchVDR
1000_GenomesVDR 
Exome Variant ServerVDR
GNOMAD BrowserENSG00000111424
Varsome BrowserVDR
ACMGVDR variants
VarityP11473
Genomic Variants (DGV)VDR [DGVbeta]
DECIPHERVDR [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisVDR 
Mutations
ICGC Data PortalVDR 
TCGA Data PortalVDR 
Broad Tumor PortalVDR
OASIS PortalVDR [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICVDR  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DVDR
Mutations and Diseases : HGMDVDR
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaVDR
DgiDB (Drug Gene Interaction Database)VDR
DoCM (Curated mutations)VDR
CIViC (Clinical Interpretations of Variants in Cancer)VDR
Cancer3DVDR
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM277440    601769   
Orphanet12173   
DisGeNETVDR
MedgenVDR
Genetic Testing Registry VDR
NextProtP11473 [Medical]
GENETestsVDR
Target ValidationVDR
Huge Navigator VDR [HugePedia]
ClinGenVDR
Clinical trials, drugs, therapy
MyCancerGenomeVDR
Protein Interactions : CTDVDR
Pharm GKB GenePA37301
Pharm GKB PathwaysPA2025   
PharosP11473
Clinical trialVDR
Miscellaneous
canSAR (ICR)VDR
HarmonizomeVDR
DataMed IndexVDR
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXVDR
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Oct 4 15:37:58 CEST 2021

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