NR1D1 protein expression summary - The Human Protein Atlas

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NR1D1

SUMMARY

TISSUE

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GENERAL INFORMATIONⁱ General description of the gene and encoded protein(s) using information from HGNC and Ensembl, as well as predictions made as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Gene name according to HGNC.	NR1D1 (ear-1, hRev, Rev-ErbAalpha, THRA1, THRAL)
Gene description	Nuclear receptor subfamily 1 group D member 1
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcribed from this gene as defined by Ensembl.	1
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
	SHOW MORE

TISSUE ATLASⁱ

RNA tissue specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA, GTEX and FANTOM5. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. Read more	Low tissue specificity
RNA tissue distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA, GTEX and FANTOM5. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Protein expressionⁱ A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation. "Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile. Read more	Cytoplasmic expression most tissues.

CELL ATLASⁱ

Main locationⁱ The main location is characterized by presence in all tested cell lines and/or increased intensity compared to other locations. It is highlighted in the illustration to the right. If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively.	Localized to the Nuclear bodies
Summaryⁱ Show complete data for human cells assay. The location(s) are highlighted in the illustration on the right.	Localized to the nuclear bodies.
RNA cell specificityⁱ The cell lines in the Human Protein Atlas have been analyzed by RNA-seq to estimate the transcript abundance of each protein-coding gene. The RNA-seq data was then used to classify all genes according to their cell line-specific expression into one of six different categories, defined based on the total set of all NX values in all analyzed cell lines. Read more	Cell line enhanced (Karpas-707)
RNA cell distributionⁱ Classification of genes according to distribution of their RNA expression among the cell lines within the HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many

PATHOLOGY ATLASⁱ

Melanoma p<0.001

Cancer expression specificity (RNA)ⁱ Specificity of RNA expression in 17 cancer types is categorized as either cancer enriched, group enriched, cancer enhanced, low cancer specificity and not detected. Read more	Low cancer specificity
Cancer expression distribution (RNA)ⁱ Distribution of RNA expression in 17 cancer types is categorized as either detected in single, detected in some, detected in many, detected in all, or not detected. Read more	Detected in all
Prognostic summary	Prognostic marker in melanoma (favourable) and colorectal cancer (unfavourable)

BRAIN ATLAS

	Human brain	Pig brain	Mouse brain
Regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analyzed brain samples, grouped into 10 main brain regions and calculated for the three different species. The human brain expression profile is based on a combination of data from GTEX and FANTOM5. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low region specificity	Low region specificity	Low region specificity
Regional distributionⁱ The regional distribution category is based on mRNA expression detected above cut off or not in the analyzed brain samples, grouped into 10 main brain regions and calculated for the three different species. The human brain expression is based on a combination of data from GTEX and FANTOM5. The distribution categories include: detected in all, detected in many, detected in some, detected in single and not detected. The classification rules are the same used for the tissue distribution category. Read more	Detected in all	Detected in all	Detected in all

BLOOD ATLAS

RNA blood cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Cell type enhanced (MAIT T-cell)
RNA blood cell type distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many
Blood-based immunoassayⁱ The blood-based immunoassay category applies to actively secreted proteins and is based on plasma or serum protein concentrations established with enzyme-linked immunosorbent assays, compiled from a literature search. The categories include: detected and not detected, where detection refers to a concentration found in the literature search. Read more	Not analysed since only proteins predicted to be actively secreted to blood is analysed here
Mass spectrometry:ⁱ Detection or not of the gene in blood, based on spectral count estimations from a publicly available mass spectrometry-based plasma proteomics data set obtained from the PeptideAtlas.	Not detected

GENE INFORMATIONⁱ 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	NR1D1 (HGNC Symbol)
Synonyms	ear-1, hRev, Rev-ErbAalpha, THRA1, THRAL
Description	Nuclear receptor subfamily 1 group D member 1 (HGNC Symbol)
Entrez gene summary	This gene encodes a transcription factor that is a member of the nuclear receptor subfamily 1. The encoded protein is a ligand-sensitive transcription factor that negatively regulates the expression of core clock proteins. In particular this protein represses the circadian clock transcription factor aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL). This protein may also be involved in regulating genes that function in metabolic, inflammatory and cardiovascular processes. [provided by RefSeq, Jan 2013]
Chromosome	17
Cytoband	q21.1
Chromosome location (bp)	40092787 - 40100725
Protein evidence	Evidence at protein level (all genes)
Protein classⁱ Protein class(es) of the gene product according to selected gene lists. List of protein classes.	Nuclear receptors Predicted intracellular proteins Transcription factors
Ensembl	ENSG00000126368 (version 92.38)
Entrez gene	9572
UniProt	P20393 (UniProt - Evidence at protein level)
neXtProt	NX_P20393
Antibodypedia	NR1D1 antibodies

PROTEIN BROWSERⁱ

NR1D1-201

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.
Splice variant	UniProt	Protein class	Gene ontology	Length & mass	Signal peptide (predicted)	Transmembrane regions (predicted)
NR1D1-201 ENSP00000246672 ENST00000246672	P20393 [Direct mapping] Nuclear receptor subfamily 1 group D member 1 F1D8S3 [Target identity:100%; Query identity:100%] Nuclear receptor Rev-ErbA-alpha; Nuclear receptor subfamily 1, group D, member 1 Show all	Nuclear receptors Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Transcription factors Zinc-coordinating DNA-binding domains Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Peptideatlas) Show all	GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000790 [nuclear chromatin] GO:0000977 [RNA polymerase II regulatory region sequence-specific DNA binding] GO:0000978 [RNA polymerase II proximal promoter sequence-specific DNA binding] GO:0000981 [RNA polymerase II transcription factor activity, sequence-specific DNA binding] GO:0001046 [core promoter sequence-specific DNA binding] GO:0001078 [transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding] GO:0001222 [transcription corepressor binding] GO:0003677 [DNA binding] GO:0003700 [DNA binding transcription factor activity] GO:0003707 [steroid hormone receptor activity] GO:0003714 [transcription corepressor activity] GO:0004879 [nuclear receptor activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005737 [cytoplasm] GO:0005978 [glycogen biosynthetic process] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006367 [transcription initiation from RNA polymerase II promoter] GO:0007623 [circadian rhythm] GO:0008270 [zinc ion binding] GO:0010498 [proteasomal protein catabolic process] GO:0010871 [negative regulation of receptor biosynthetic process] GO:0016604 [nuclear body] GO:0019216 [regulation of lipid metabolic process] GO:0020037 [heme binding] GO:0030154 [cell differentiation] GO:0030425 [dendrite] GO:0030522 [intracellular receptor signaling pathway] GO:0032922 [circadian regulation of gene expression] GO:0034144 [negative regulation of toll-like receptor 4 signaling pathway] GO:0035947 [regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter] GO:0042752 [regulation of circadian rhythm] GO:0042995 [cell projection] GO:0043197 [dendritic spine] GO:0043401 [steroid hormone mediated signaling pathway] GO:0043565 [sequence-specific DNA binding] GO:0044212 [transcription regulatory region DNA binding] GO:0044321 [response to leptin] GO:0045598 [regulation of fat cell differentiation] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0046872 [metal ion binding] GO:0048511 [rhythmic process] GO:0060086 [circadian temperature homeostasis] GO:0061178 [regulation of insulin secretion involved in cellular response to glucose stimulus] GO:0061469 [regulation of type B pancreatic cell proliferation] GO:0070859 [positive regulation of bile acid biosynthetic process] GO:0071222 [cellular response to lipopolysaccharide] GO:2000188 [regulation of cholesterol homeostasis] Show all	614 aa 66.8 kDa	No	0

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The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg foundation.