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RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue/cell line enriched, group enriched, tissue/cell line enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for The Cancer Genome Atlas (TCGA) data from cancer tissues and internally generated Human Protein Atlas (HPA) data from normal tissues and cell lines.
TCGA (cancer tissue):
Expressed in all
HPA (cell line):
Cell line enhanced (HDLM-2, U-937)
HPA (normal tissue):
Tissue enhanced (parathyroid gland)
Protein evidencei
Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.
Evidence at protein level
IMMUNOHISTOCHEMISTRY DATA RELIABILITY
Reliability score - normal tissuesi
Reliability score (score description), divided into Enhanced, Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between antibody staining pattern, available RNA-Seq and gene/protein characterization data, as well as similarity between independent antibodies targeting the same protein.
Kaplan-Meier plots for all cancers where high expression of this gene has significant (p<0.001) association with patient survival are shown in this summary. Whether the prognosis is favourable or unfavourable is indicated in brackets. Each Kaplan-Meier plot is clickable and redirects to a detailed page that includes individual expression and survival data for patients with the selected cancer.
RNA expression overview shows RNA-seq data from The Cancer Genome Atlas (TCGA).
TCGA dataseti
RNA-seq data in 17 cancer types are reported as median FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA). RNA cancer tissue category is calculated based on mRNA expression levels across all 17 cancer tissues and include: cancer tissue enriched, cancer group enriched, cancer tissue enhanced, expressed in all, mixed and not detected. To access cancer specific RNA and prognostic data, click on the cancer name. The cancer types are color-coded according to which type of normal organ the cancer originates from.
Antibody staining in 20 different cancers is summarized by a selection of four standard cancer tissue samples representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional fifth image can be added as a complement. The assay and annotation is described here. Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset.
Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.
Gene name
VDR (HGNC Symbol)
Synonyms
NR1I1, PPP1R163
Description
Vitamin D (1,25- dihydroxyvitamin D3) receptor (HGNC Symbol)
Entrez gene summary
This gene encodes the nuclear hormone receptor for vitamin D3. This receptor also functions as a receptor for the secondary bile acid lithocholic acid. The receptor belongs to the family of trans-acting transcriptional regulatory factors and shows sequence similarity to the steroid and thyroid hormone receptors. Downstream targets of this nuclear hormone receptor are principally involved in mineral metabolism though the receptor regulates a variety of other metabolic pathways, such as those involved in the 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. Alternative splicing results in multiple transcript variants encoding different proteins. [provided by RefSeq, Feb 2011]
The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.
At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.
Under the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more).
The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (read more).
If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.
Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.
VDR-001
VDR-002
VDR-004
VDR-006
VDR-007
VDR-008
VDR-201
PROTEIN INFORMATIONi
The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.
The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.
The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.
The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Nuclear receptors Transporters Predicted intracellular proteins Transcription factors Zinc-coordinating DNA-binding domains Disease related genes FDA approved drug targets Small molecule drugs Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000902 [cell morphogenesis] GO:0003677 [DNA binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0003707 [steroid hormone receptor activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006367 [transcription initiation from RNA polymerase II promoter] GO:0007165 [signal transduction] GO:0008270 [zinc ion binding] GO:0008285 [negative regulation of cell proliferation] GO:0008434 [calcitriol receptor activity] GO:0010628 [positive regulation of gene expression] GO:0010839 [negative regulation of keratinocyte proliferation] GO:0010980 [positive regulation of vitamin D 24-hydroxylase activity] GO:0038183 [bile acid signaling pathway] GO:0038186 [lithocholic acid receptor activity] GO:0043235 [receptor complex] GO:0043401 [steroid hormone mediated signaling pathway] GO:0043565 [sequence-specific DNA binding] GO:0045618 [positive regulation of keratinocyte differentiation] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0046697 [decidualization] GO:0046872 [metal ion binding] GO:0046965 [retinoid X receptor binding] GO:0060558 [regulation of calcidiol 1-monooxygenase activity] GO:0070561 [vitamin D receptor signaling pathway] GO:0070644 [vitamin D response element binding] GO:0090575 [RNA polymerase II transcription factor complex] GO:1902098 [calcitriol binding] GO:1902121 [lithocholic acid binding]
Nuclear receptors Transporters Predicted intracellular proteins Transcription factors Zinc-coordinating DNA-binding domains Disease related genes FDA approved drug targets Small molecule drugs Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000902 [cell morphogenesis] GO:0001501 [skeletal system development] GO:0003677 [DNA binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0003707 [steroid hormone receptor activity] GO:0004879 [RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006367 [transcription initiation from RNA polymerase II promoter] GO:0006816 [calcium ion transport] GO:0006874 [cellular calcium ion homeostasis] GO:0007165 [signal transduction] GO:0007275 [multicellular organism development] GO:0007595 [lactation] GO:0008270 [zinc ion binding] GO:0008285 [negative regulation of cell proliferation] GO:0008434 [calcitriol receptor activity] GO:0009887 [animal organ morphogenesis] GO:0010628 [positive regulation of gene expression] GO:0010839 [negative regulation of keratinocyte proliferation] GO:0010980 [positive regulation of vitamin D 24-hydroxylase activity] GO:0038183 [bile acid signaling pathway] GO:0038186 [lithocholic acid receptor activity] GO:0043235 [receptor complex] GO:0043401 [steroid hormone mediated signaling pathway] GO:0043565 [sequence-specific DNA binding] GO:0045618 [positive regulation of keratinocyte differentiation] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0046697 [decidualization] GO:0046872 [metal ion binding] GO:0046965 [retinoid X receptor binding] GO:0050892 [intestinal absorption] GO:0060058 [positive regulation of apoptotic process involved in mammary gland involution] GO:0060558 [regulation of calcidiol 1-monooxygenase activity] GO:0060745 [mammary gland branching involved in pregnancy] GO:0070561 [vitamin D receptor signaling pathway] GO:0070644 [vitamin D response element binding] GO:0090575 [RNA polymerase II transcription factor complex] GO:1902098 [calcitriol binding] GO:1902121 [lithocholic acid binding]
Nuclear receptors Transporters Predicted intracellular proteins Transcription factors Zinc-coordinating DNA-binding domains Disease related genes FDA approved drug targets Small molecule drugs Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000902 [cell morphogenesis] GO:0003677 [DNA binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0003707 [steroid hormone receptor activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006367 [transcription initiation from RNA polymerase II promoter] GO:0007165 [signal transduction] GO:0008270 [zinc ion binding] GO:0008285 [negative regulation of cell proliferation] GO:0008434 [calcitriol receptor activity] GO:0010628 [positive regulation of gene expression] GO:0010839 [negative regulation of keratinocyte proliferation] GO:0010980 [positive regulation of vitamin D 24-hydroxylase activity] GO:0038183 [bile acid signaling pathway] GO:0038186 [lithocholic acid receptor activity] GO:0043235 [receptor complex] GO:0043401 [steroid hormone mediated signaling pathway] GO:0043565 [sequence-specific DNA binding] GO:0045618 [positive regulation of keratinocyte differentiation] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0046697 [decidualization] GO:0046872 [metal ion binding] GO:0046965 [retinoid X receptor binding] GO:0060558 [regulation of calcidiol 1-monooxygenase activity] GO:0070561 [vitamin D receptor signaling pathway] GO:0070644 [vitamin D response element binding] GO:0090575 [RNA polymerase II transcription factor complex] GO:1902098 [calcitriol binding] GO:1902121 [lithocholic acid binding]
Nuclear receptors Transporters Predicted intracellular proteins Transcription factors Zinc-coordinating DNA-binding domains Disease related genes FDA approved drug targets Small molecule drugs Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000902 [cell morphogenesis] GO:0003677 [DNA binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0003707 [steroid hormone receptor activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006367 [transcription initiation from RNA polymerase II promoter] GO:0007165 [signal transduction] GO:0008270 [zinc ion binding] GO:0008285 [negative regulation of cell proliferation] GO:0008434 [calcitriol receptor activity] GO:0010628 [positive regulation of gene expression] GO:0010839 [negative regulation of keratinocyte proliferation] GO:0010980 [positive regulation of vitamin D 24-hydroxylase activity] GO:0038183 [bile acid signaling pathway] GO:0038186 [lithocholic acid receptor activity] GO:0043235 [receptor complex] GO:0043401 [steroid hormone mediated signaling pathway] GO:0043565 [sequence-specific DNA binding] GO:0045618 [positive regulation of keratinocyte differentiation] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0046697 [decidualization] GO:0046872 [metal ion binding] GO:0046965 [retinoid X receptor binding] GO:0060558 [regulation of calcidiol 1-monooxygenase activity] GO:0070561 [vitamin D receptor signaling pathway] GO:0070644 [vitamin D response element binding] GO:0090575 [RNA polymerase II transcription factor complex] GO:1902098 [calcitriol binding] GO:1902121 [lithocholic acid binding]
The Human Protein Atlas project is funded
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