Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

VDR (vitamin D (1,25- dihydroxyvitamin D3) receptor)

Identity

Other namesNR1I1
HGNC (Hugo) VDR
LocusID (NCBI) 7421
Location 12q13.11
Location_base_pair Starts at 48235320 and ends at 48298814 bp from pter ( according to hg19-Feb_2009)
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  7421  vitamin D (1,25- dihydroxyvitamin D3) receptor
GeneCards (Weizmann)VDR
Ensembl (Hinxton)ENSG00000111424 [Gene_View]  chr12:48235320-48298814 [Contig_View]  VDR [Vega]
ICGC DataPortalENSG00000111424
cBioPortalVDR
AceView (NCBI)VDR
Genatlas (Paris)VDR
WikiGenes7421
SOURCE (Princeton)NM_000376 NM_001017535 NM_001017536
Genomic and cartography
GoldenPath (UCSC)VDR  -  12q13.11   chr12:48235320-48298814 -  12q13.11   [Description]    (hg19-Feb_2009)
EnsemblVDR - 12q13.11 [CytoView]
Mapping of homologs : NCBIVDR [Mapview]
OMIM166710   277440   601769   
Gene and transcription
Genbank (Entrez)AB307700 AF026260 AK024830 AK225844 AK299446
RefSeq transcript (Entrez)NM_000376 NM_001017535 NM_001017536
RefSeq genomic (Entrez)AC_000144 NC_000012 NC_018923 NG_008731 NT_029419 NW_001838057 NW_004929384
Consensus coding sequences : CCDS (NCBI)VDR
Cluster EST : UnigeneHs.524368 [ NCBI ]
CGAP (NCI)Hs.524368
Alternative Splicing : Fast-db (Paris)GSHG0007412
Alternative Splicing GalleryENSG00000111424
Gene ExpressionVDR [ NCBI-GEO ]     VDR [ SEEK ]   VDR [ MEM ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP11473 (Uniprot)
NextProtP11473  [Medical]
With graphics : InterProP11473
Splice isoforms : SwissVarP11473 (Swissvar)
Domaine pattern : Prosite (Expaxy)NUCLEAR_REC_DBD_1 (PS00031)    NUCLEAR_REC_DBD_2 (PS51030)   
Domains : Interpro (EBI)Nucl_hormone_rcpt_ligand-bd [organisation]   Nucl_hrmn_rcpt_lig-bd_core [organisation]   Str_hrmn_rcpt [organisation]   VitD_rcpt [organisation]   Znf_hrmn_rcpt [organisation]   Znf_NHR/GATA [organisation]  
Related proteins : CluSTrP11473
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)  
DMDM Disease mutations7421
Blocks (Seattle)P11473
PDB (SRS)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    4G2I   
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    4G2I   
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    4G2I   
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    4G2I   
Human Protein AtlasENSG00000111424 [gene] [tissue] [antibody] [cell] [cancer]
Peptide AtlasP11473
HPRD03463
IPIIPI00005716   IPI01012259   IPI00443026   IPI00976483   IPI01021765   IPI01021623   IPI01021431   IPI01022572   
Protein Interaction databases
DIP (DOE-UCLA)P11473
IntAct (EBI)P11473
FunCoupENSG00000111424
BioGRIDVDR
InParanoidP11473
Interologous Interaction database P11473
IntegromeDBVDR
STRING (EMBL)VDR
Ontologies - Pathways
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  cell morphogenesis  skeletal system development  DNA binding  sequence-specific DNA binding transcription factor activity  steroid hormone receptor activity  protein binding  nucleus  nucleoplasm  transcription initiation from RNA polymerase II promoter  calcium ion transport  cellular calcium ion homeostasis  signal transduction  lactation  zinc ion binding  negative regulation of cell proliferation  calcitriol receptor activity  organ morphogenesis  gene expression  positive regulation of gene expression  negative regulation of keratinocyte proliferation  positive regulation of vitamin D 24-hydroxylase activity  bile acid signaling pathway  lithocholic acid receptor activity  sequence-specific DNA binding  positive regulation of keratinocyte differentiation  negative regulation of transcription, DNA-dependent  positive regulation of transcription from RNA polymerase II promoter  decidualization  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 response element binding  calcitriol binding  lithocholic acid binding  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  cell morphogenesis  skeletal system development  DNA binding  sequence-specific DNA binding transcription factor activity  steroid hormone receptor activity  protein binding  nucleus  nucleoplasm  transcription initiation from RNA polymerase II promoter  calcium ion transport  cellular calcium ion homeostasis  signal transduction  lactation  zinc ion binding  negative regulation of cell proliferation  calcitriol receptor activity  organ morphogenesis  gene expression  positive regulation of gene expression  negative regulation of keratinocyte proliferation  positive regulation of vitamin D 24-hydroxylase activity  bile acid signaling pathway  lithocholic acid receptor activity  sequence-specific DNA binding  positive regulation of keratinocyte differentiation  negative regulation of transcription, DNA-dependent  positive regulation of transcription from RNA polymerase II promoter  decidualization  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 response element 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   
Protein Interaction DatabaseVDR
Wikipedia pathwaysVDR
Gene fusion - rearrangments
Polymorphisms : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)VDR
snp3D : Map Gene to Disease7421
SNP (GeneSNP Utah)VDR
SNP : HGBaseVDR
Genetic variants : HAPMAPVDR
Exome VariantVDR
1000_GenomesVDR 
ICGC programENSG00000111424 
Somatic Mutations in Cancer : COSMICVDR 
CONAN: Copy Number AnalysisVDR 
Mutations and Diseases : HGMDVDR
Genomic VariantsVDR  VDR [DGVbeta]
dbVarVDR
ClinVarVDR
Pred. of missensesPolyPhen-2  SIFT(SG)  SIFT(JCVI)  Align-GVGD  MutAssessor  Mutanalyser  
Pred. splicesGeneSplicer  Human Splicing Finder  MaxEntScan  
Diseases
OMIM166710    277440    601769   
MedgenVDR
GENETestsVDR
Disease Genetic AssociationVDR
Huge Navigator VDR [HugePedia]  VDR [HugeCancerGEM]
General knowledge
Homologs : HomoloGeneVDR
Homology/Alignments : Family Browser (UCSC)VDR
Phylogenetic Trees/Animal Genes : TreeFamVDR
Chemical/Protein Interactions : CTD7421
Chemical/Pharm GKB GenePA37301
Clinical trialVDR
Cancer Resource (Charite)ENSG00000111424
Other databases
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
CoreMineVDR
iHOPVDR
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

Contributor(s)

Written09-2002Dessen P, Le Minor S
Updated12-2013Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Fri Jul 11 17:25:35 CEST 2014

Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.