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 pro... See more...

Aliases for NR1D1 Gene

Aliases for NR1D1 Gene

  • Nuclear Receptor Subfamily 1 Group D Member 1 2 3 4 5
  • V-ErbA-Related Protein 1 3 4
  • Rev-ErbA-Alpha 3 4
  • THRAL 3 4
  • EAR1 3 4
  • Nuclear Receptor Subfamily 1, Group D, Member 1 2
  • Nuclear Receptor Rev-ErbA-Alpha 3
  • Rev-ErbAalpha 3
  • REVERBalpha 3
  • REVERBA 3
  • THRA1 3
  • Ear-1 3
  • EAR-1 4
  • HRev 3
  • HREV 4

External Ids for NR1D1 Gene

Previous HGNC Symbols for NR1D1 Gene

  • THRAL

Previous GeneCards Identifiers for NR1D1 Gene

  • GC17M037844
  • GC17P040302
  • GC17M038159
  • GC17M038624
  • GC17M035502
  • GC17M038249
  • GC17M034042

Summaries for NR1D1 Gene

Entrez Gene Summary for NR1D1 Gene

  • 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]

GeneCards Summary for NR1D1 Gene

NR1D1 (Nuclear Receptor Subfamily 1 Group D Member 1) is a Protein Coding gene. Diseases associated with NR1D1 include Hypothyroidism, Congenital, Nongoitrous, 6 and Rem Sleep Behavior Disorder. Among its related pathways are Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha) and Circadian rythm related genes. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is NR1D2.

UniProtKB/Swiss-Prot Summary for NR1D1 Gene

  • Transcriptional repressor which coordinates circadian rhythm and metabolic pathways in a heme-dependent manner. Integral component of the complex transcription machinery that governs circadian rhythmicity and forms a critical negative limb of the circadian clock by directly repressing the expression of core clock components ARTNL/BMAL1, CLOCK and CRY1. Also regulates genes involved in metabolic functions, including lipid and bile acid metabolism, adipogenesis, gluconeogenesis and the macrophage inflammatory response. Acts as a receptor for heme which stimulates its interaction with the NCOR1/HDAC3 corepressor complex, enhancing transcriptional repression. Recognizes two classes of DNA response elements within the promoter of its target genes and can bind to DNA as either monomers or homodimers, depending on the nature of the response element. Binds as a monomer to a response element composed of the consensus half-site motif 5'-[A/G]GGTCA-3' preceded by an A/T-rich 5' sequence (RevRE), or as a homodimer to a direct repeat of the core motif spaced by two nucleotides (RevDR-2). Acts as a potent competitive repressor of ROR alpha (RORA) function and regulates the levels of its ligand heme by repressing the expression of PPARGC1A, a potent inducer of heme synthesis. Regulates lipid metabolism by repressing the expression of APOC3 and by influencing the activity of sterol response element binding proteins (SREBPs); represses INSIG2 which interferes with the proteolytic activation of SREBPs which in turn govern the rhythmic expression of enzymes with key functions in sterol and fatty acid synthesis. Regulates gluconeogenesis via repression of G6PC and PEPCK and adipocyte differentiation via repression of PPARG. Regulates glucagon release in pancreatic alpha-cells via the AMPK-NAMPT-SIRT1 pathway and the proliferation, glucose-induced insulin secretion and expression of key lipogenic genes in pancreatic-beta cells. Positively regulates bile acid synthesis by increasing hepatic expression of CYP7A1 via repression of NR0B2 and NFIL3 which are negative regulators of CYP7A1. Modulates skeletal muscle oxidative capacity by regulating mitochondrial biogenesis and autophagy; controls mitochondrial biogenesis and respiration by interfering with the STK11-PRKAA1/2-SIRT1-PPARGC1A signaling pathway. Represses the expression of SERPINE1/PAI1, an important modulator of cardiovascular disease and the expression of inflammatory cytokines and chemokines in macrophages. Represses gene expression at a distance in macrophages by inhibiting the transcription of enhancer-derived RNAs (eRNAs). Plays a role in the circadian regulation of body temperature and negatively regulates thermogenic transcriptional programs in brown adipose tissue (BAT); imposes a circadian oscillation in BAT activity, increasing body temperature when awake and depressing thermogenesis during sleep. In concert with NR2E3, regulates transcriptional networks critical for photoreceptor development and function. In addition to its activity as a repressor, can also act as a transcriptional activator. In the ovarian granulosa cells acts as a transcriptional activator of STAR which plays a role in steroid biosynthesis. In collaboration with SP1, activates GJA1 transcription in a heme-independent manner. Represses the transcription of CYP2B10, CYP4A10 and CYP4A14 (By similarity). Represses the transcription of CES2 (By similarity). Represses and regulates the circadian expression of TSHB in a NCOR1-dependent manner (By similarity). Negatively regulates the protein stability of NR3C1 and influences the time-dependent subcellular distribution of NR3C1, thereby affecting its transcriptional regulatory activity (By similarity). Plays a critical role in the circadian control of neutrophilic inflammation in the lung; under resting, non-stress conditions, acts as a rhythmic repressor to limit inflammatory activity whereas in the presence of inflammatory triggers undergoes ubiquitin-mediated degradation thereby relieving inhibition of the inflammatory response (By similarity). Plays a key role in the circadian regulation of microglial activation and neuroinflammation; suppresses microglial activation through the NF-kappaB pathway in the central nervous system (By similarity). Plays a role in the regulation of the diurnal rhythms of lipid and protein metabolism in the skeletal muscle via transcriptional repression of genes controlling lipid and amino acid metabolism in the muscle (By similarity).

Tocris Summary for NR1D1 Gene

  • Rev-Erb receptors are orphan nuclear receptors belonging to the NR1D receptor family. There are two types, Rev-Erbalpha and Rev-Erbbeta. They are important in the regulation of circadian rhythm, as well as lipid homeostasis and lipid metabolism.

Gene Wiki entry for NR1D1 Gene

Additional gene information for NR1D1 Gene

No data available for CIViC Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NR1D1 Gene

Genomics for NR1D1 Gene

GeneHancer (GH) Regulatory Elements for NR1D1 Gene

Promoters and enhancers for NR1D1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J040088 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 502.1 +5.4 5378 14.4 EP300 FOXK2 ZNF217 SIN3A NRF1 TCF12 MYC POLR2G USF1 SP1 NR1D1 MSL1 MED24 CDK12 GSDMA CCR7 THRA RPL19 CDC6 TOP2A
GH17J040102 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 502.1 -8.7 -8717 13.4 EP300 FOXK2 ZNF217 CTCF SIN3A NRF1 TCF12 MYC POLR2G USF1 NR1D1 MED1 SMARCE1 CDK12 MSL1 MED24 CASC3 THRA IGFBP4 RPL19
GH17J040062 Promoter/Enhancer 2.8 VISTA EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 3.2 +31.5 31508 15 HNRNPK EP300 CTCF TCF12 NRF1 ZNF300 POLR2G NCOR1 TEAD4 PHB2 THRA MED24 MED1 GSDMA SMARCE1 MSL1 RAPGEFL1 PSMD3 TCAP ORMDL3
GH17J040217 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 1.5 -118.7 -118734 3.5 HNRNPK ZBTB40 ZNF217 EP300 CTCF ZSCAN5C SIN3A NRF1 TCF12 USF1 WIPF2 SMARCE1 MED1 CDK12 RAPGEFL1 IGFBP4 ENSG00000266208 PGAP3 MSL1 RARA
GH17J039183 Enhancer 0.5 Ensembl 4.5 +917.4 917424 0.2 ZFHX2 ATF4 EGR2 ATF3 ATF7 NR2C1 MRPL45 NR1D1 lnc-ARL5C-3 LOC105371768 lnc-ARL5C-2 CACNB1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NR1D1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NR1D1

Top Transcription factor binding sites by QIAGEN in the NR1D1 gene promoter:
  • Arnt
  • Ik-2
  • LCR-F1
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4
  • PPAR-gamma1
  • YY1

Genomic Locations for NR1D1 Gene

Genomic Locations for NR1D1 Gene
chr17:40,092,784-40,100,725
(GRCh38/hg38)
Size:
7,942 bases
Orientation:
Minus strand
chr17:38,249,037-38,256,978
(GRCh37/hg19)
Size:
7,942 bases
Orientation:
Minus strand

Genomic View for NR1D1 Gene

Genes around NR1D1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NR1D1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NR1D1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NR1D1 Gene

Proteins for NR1D1 Gene

  • Protein details for NR1D1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P20393-NR1D1_HUMAN
    Recommended name:
    Nuclear receptor subfamily 1 group D member 1
    Protein Accession:
    P20393
    Secondary Accessions:
    • Q0P5Z4
    • Q15304

    Protein attributes for NR1D1 Gene

    Size:
    614 amino acids
    Molecular mass:
    66805 Da
    Quaternary structure:
    • Binds DNA as a monomer or a homodimer (PubMed:9660968). Interacts with C1D, NR2E3 and SP1 (By similarity). Interacts with OPHN1 (via C-terminus) (PubMed:21874017). Interacts with ZNHIT1 (PubMed:17892483). Interacts with PER2; the interaction associates PER2 to ARNTL promoter region (PubMed:22170608). Interacts with CRY1 (PubMed:22170608). Interacts with CCAR2 (PubMed:23398316). Interacts with SIAH2 (PubMed:26392558). Interacts with CDK1 (By similarity). Interacts with FBXW7 (PubMed:27238018). Interacts with HUWE1 (PubMed:20534529). Interacts with NR0B2 (By similarity). Interacts with NFIL3 (By similarity). Interacts (via domain NR LBD) with HSP90AA1 and HSP90AB1 (By similarity).

    Three dimensional structures from OCA and Proteopedia for NR1D1 Gene

neXtProt entry for NR1D1 Gene

Post-translational modifications for NR1D1 Gene

  • Ubiquitinated, leading to its proteasomal degradation (PubMed:16484495, PubMed:23398316, PubMed:20534529). Ubiquitinated by SIAH2; leading to its proteasomal degradation (PubMed:26392558). Ubiquitinated by the SCF(FBXW7) complex when phosphorylated by CDK1 leading to its proteasomal degradation (By similarity). Rapidly ubiquitinated in response to inflammatory triggers and sumoylation is a prerequisite to its ubiquitination (By similarity).
  • Sumoylated by UBE2I, desumoylated by SENP1, and sumoylation is a prerequisite to its ubiquitination.
  • Phosphorylated by CSNK1E; phosphorylation enhances its cytoplasmic localization.
  • Undergoes lysosome-mediated degradation in a time-dependent manner in the liver.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NR1D1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NR1D1 Gene

Domains & Families for NR1D1 Gene

Gene Families for NR1D1 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Nuclear receptors
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for NR1D1 Gene

Blocks:
  • Steroid hormone receptor signature
  • Vitamin D receptor signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NR1D1 Gene

GenScript: Design optimal peptide antigens:
  • Nuclear receptor Rev-ErbA-alpha (F1D8S3_HUMAN)
  • V-erbA-related protein 1 (NR1D1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P20393

UniProtKB/Swiss-Prot:

NR1D1_HUMAN :
  • Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
  • Belongs to the nuclear hormone receptor family. NR1 subfamily.
Domain:
  • Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
Family:
  • Belongs to the nuclear hormone receptor family. NR1 subfamily.
genes like me logo Genes that share domains with NR1D1: view

Function for NR1D1 Gene

Molecular function for NR1D1 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional repressor which coordinates circadian rhythm and metabolic pathways in a heme-dependent manner. Integral component of the complex transcription machinery that governs circadian rhythmicity and forms a critical negative limb of the circadian clock by directly repressing the expression of core clock components ARTNL/BMAL1, CLOCK and CRY1. Also regulates genes involved in metabolic functions, including lipid and bile acid metabolism, adipogenesis, gluconeogenesis and the macrophage inflammatory response. Acts as a receptor for heme which stimulates its interaction with the NCOR1/HDAC3 corepressor complex, enhancing transcriptional repression. Recognizes two classes of DNA response elements within the promoter of its target genes and can bind to DNA as either monomers or homodimers, depending on the nature of the response element. Binds as a monomer to a response element composed of the consensus half-site motif 5'-[A/G]GGTCA-3' preceded by an A/T-rich 5' sequence (RevRE), or as a homodimer to a direct repeat of the core motif spaced by two nucleotides (RevDR-2). Acts as a potent competitive repressor of ROR alpha (RORA) function and regulates the levels of its ligand heme by repressing the expression of PPARGC1A, a potent inducer of heme synthesis. Regulates lipid metabolism by repressing the expression of APOC3 and by influencing the activity of sterol response element binding proteins (SREBPs); represses INSIG2 which interferes with the proteolytic activation of SREBPs which in turn govern the rhythmic expression of enzymes with key functions in sterol and fatty acid synthesis. Regulates gluconeogenesis via repression of G6PC and PEPCK and adipocyte differentiation via repression of PPARG. Regulates glucagon release in pancreatic alpha-cells via the AMPK-NAMPT-SIRT1 pathway and the proliferation, glucose-induced insulin secretion and expression of key lipogenic genes in pancreatic-beta cells. Positively regulates bile acid synthesis by increasing hepatic expression of CYP7A1 via repression of NR0B2 and NFIL3 which are negative regulators of CYP7A1. Modulates skeletal muscle oxidative capacity by regulating mitochondrial biogenesis and autophagy; controls mitochondrial biogenesis and respiration by interfering with the STK11-PRKAA1/2-SIRT1-PPARGC1A signaling pathway. Represses the expression of SERPINE1/PAI1, an important modulator of cardiovascular disease and the expression of inflammatory cytokines and chemokines in macrophages. Represses gene expression at a distance in macrophages by inhibiting the transcription of enhancer-derived RNAs (eRNAs). Plays a role in the circadian regulation of body temperature and negatively regulates thermogenic transcriptional programs in brown adipose tissue (BAT); imposes a circadian oscillation in BAT activity, increasing body temperature when awake and depressing thermogenesis during sleep. In concert with NR2E3, regulates transcriptional networks critical for photoreceptor development and function. In addition to its activity as a repressor, can also act as a transcriptional activator. In the ovarian granulosa cells acts as a transcriptional activator of STAR which plays a role in steroid biosynthesis. In collaboration with SP1, activates GJA1 transcription in a heme-independent manner. Represses the transcription of CYP2B10, CYP4A10 and CYP4A14 (By similarity). Represses the transcription of CES2 (By similarity). Represses and regulates the circadian expression of TSHB in a NCOR1-dependent manner (By similarity). Negatively regulates the protein stability of NR3C1 and influences the time-dependent subcellular distribution of NR3C1, thereby affecting its transcriptional regulatory activity (By similarity). Plays a critical role in the circadian control of neutrophilic inflammation in the lung; under resting, non-stress conditions, acts as a rhythmic repressor to limit inflammatory activity whereas in the presence of inflammatory triggers undergoes ubiquitin-mediated degradation thereby relieving inhibition of the inflammatory response (By similarity). Plays a key role in the circadian regulation of microglial activation and neuroinflammation; suppresses microglial activation through the NF-kappaB pathway in the central nervous system (By similarity). Plays a role in the regulation of the diurnal rhythms of lipid and protein metabolism in the skeletal muscle via transcriptional repression of genes controlling lipid and amino acid metabolism in the muscle (By similarity).
GENATLAS Biochemistry:
nuclear receptor subfamily 1,group D,member 1,partially overlapping THRA (exon for THRA2) on the opposite strand

Phenotypes From GWAS Catalog for NR1D1 Gene

Gene Ontology (GO) - Molecular Function for NR1D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IBA 21873635
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 19955433
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA,IMP 8622974
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS 19274049
GO:0001222 transcription corepressor binding IMP 18006707
genes like me logo Genes that share ontologies with NR1D1: view
genes like me logo Genes that share phenotypes with NR1D1: view

Animal Models for NR1D1 Gene

MGI Knock Outs for NR1D1:

Animal Model Products

miRNA for NR1D1 Gene

miRTarBase miRNAs that target NR1D1
Targeted motifs for NR1D1 Gene
HOMER Transcription Factor Regulatory Elements motif NR1D1
  • Consensus sequence: GTAGGTCACTGGGTCA Submotif: DR2 Cell Type: RAW GEO ID: GSE45914

Clone Products

  • Addgene plasmids for NR1D1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for NR1D1 Gene

Localization for NR1D1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NR1D1 Gene

Nucleus. Cytoplasm. Cell projection, dendrite. Cell projection, dendritic spine. Note=Localizes to the cytoplasm, dendrites and dendritic spine in the presence of OPHN1. Localizes predominantly to the nucleus at ZT8 whereas it is cytoplasmic at ZT20. Phosphorylation by CSNK1E enhances its cytoplasmic localization. {ECO:0000250 UniProtKB:Q3UV55}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NR1D1 gene
Compartment Confidence
nucleus 5
extracellular 2
mitochondrion 2
peroxisome 2
cytosol 2
plasma membrane 1
cytoskeleton 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NR1D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IDA,ISA --
GO:0005634 nucleus ISS,TAS --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm ISS --
GO:0016604 nuclear body IDA --
genes like me logo Genes that share ontologies with NR1D1: view

Pathways & Interactions for NR1D1 Gene

genes like me logo Genes that share pathways with NR1D1: view

Pathways by source for NR1D1 Gene

1 Qiagen pathway for NR1D1 Gene
  • Circadian Clock in Mammals
3 Cell Signaling Technology pathways for NR1D1 Gene

SIGNOR curated interactions for NR1D1 Gene

Activates:
Inactivates:
Is activated by:

Gene Ontology (GO) - Biological Process for NR1D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IMP 18511497
GO:0005978 glycogen biosynthetic process ISS --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006367 transcription initiation from RNA polymerase II promoter TAS --
GO:0007275 multicellular organism development IBA 21873635
genes like me logo Genes that share ontologies with NR1D1: view

Drugs & Compounds for NR1D1 Gene

(8) Drugs for NR1D1 Gene - From: DrugBank, PharmGKB, ApexBio, DGIdb, and IUPHAR

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
SR-9009 Experimental Pharma Target, agonist 0
SR-9011 Experimental Pharma Target, agonist 0
lithium Experimental Pharma 0
GSK4112 Pharma Agonist 0
heme Pharma Agonist 0

(2) ApexBio Compounds for NR1D1 Gene

Compound Action Cas Number
GSK 4112 antagonist of the Nuclear Heme Receptor REV-ERB 1216744-19-2
SR 8278 1254944-66-5
genes like me logo Genes that share compounds with NR1D1: view

Drug Products

Transcripts for NR1D1 Gene

mRNA/cDNA for NR1D1 Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

  • Addgene plasmids for NR1D1

Alternative Splicing Database (ASD) splice patterns (SP) for NR1D1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9
SP1:
SP2: -
SP3:
SP4: - - -
SP5:
SP6:

Relevant External Links for NR1D1 Gene

GeneLoc Exon Structure for
NR1D1

Expression for NR1D1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NR1D1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NR1D1 Gene

This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x6.2) and Skin - Not Sun Exposed (Suprapubic) (x6.1).

Protein differential expression in normal tissues from HIPED for NR1D1 Gene

This gene is overexpressed in Heart (49.6), Urine (9.7), and Stomach (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for NR1D1 Gene



Protein tissue co-expression partners for NR1D1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NR1D1

SOURCE GeneReport for Unigene cluster for NR1D1 Gene:

Hs.592130

mRNA Expression by UniProt/SwissProt for NR1D1 Gene:

P20393-NR1D1_HUMAN
Tissue specificity: Widely expressed. Expressed at high levels in the liver, adipose tissue, skeletal muscle and brain. Also expressed in endothelial cells (ECs), vascular smooth muscle cells (VSMCs) and macrophages. Expression oscillates diurnally in the suprachiasmatic nucleus (SCN) of the hypothalamus as well as in peripheral tissues. Expression increases during the differentiation of pre-adipocytes into mature adipocytes. Expressed at high levels in some squamous carcinoma cell lines.

Evidence on tissue expression from TISSUES for NR1D1 Gene

  • Nervous system(4.7)
  • Muscle(4.6)
  • Liver(4.4)
  • Eye(2.2)
  • Thyroid gland(2.2)
genes like me logo Genes that share expression patterns with NR1D1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for NR1D1 Gene

Orthologs for NR1D1 Gene

This gene was present in the common ancestor of animals.

Orthologs for NR1D1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NR1D1 31 30
  • 99.84 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NR1D1 31 30
  • 92.59 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NR1D1 31 30
  • 91.72 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nr1d1 30
  • 90.07 (n)
mouse
(Mus musculus)
Mammalia Nr1d1 17 31 30
  • 90.01 (n)
oppossum
(Monodelphis domestica)
Mammalia NR1D1 31
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves -- 31
  • 30 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia NR1D1 31
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nr1d1 30
  • 69.79 (n)
Str.16697 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.9778 30
zebrafish
(Danio rerio)
Actinopterygii nr1d1 31 30
  • 62.27 (n)
OneToOne
Dr.27124 30
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8023 30
fruit fly
(Drosophila melanogaster)
Insecta Eip78C 32
  • 71 (a)
Eip75B 31 32
  • 14 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sex-1 31
  • 24 (a)
ManyToMany
nhr-85 31
  • 24 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 19 (a)
OneToMany
Species where no ortholog for NR1D1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NR1D1 Gene

ENSEMBL:
Gene Tree for NR1D1 (if available)
TreeFam:
Gene Tree for NR1D1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NR1D1: view image

Paralogs for NR1D1 Gene

(2) SIMAP similar genes for NR1D1 Gene using alignment to 2 proteins:

  • NR1D1_HUMAN
  • F1D8S3_HUMAN

Pseudogenes.org Pseudogenes for NR1D1 Gene

genes like me logo Genes that share paralogs with NR1D1: view

Variants for NR1D1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NR1D1 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
738966 Likely Benign: not provided 40,095,127(-) G/A INTRON_VARIANT
780425 Benign: not provided 40,095,630(-) G/A SYNONYMOUS_VARIANT
781299 Benign: not provided 40,097,216(-) G/A SYNONYMOUS_VARIANT
rs201037953 Uncertain Significance: Hypothyroidism, congenital, nongoitrous, 6 40,093,275(-) C/T NONSENSE,SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for NR1D1 Gene

Structural Variations from Database of Genomic Variants (DGV) for NR1D1 Gene

Variant ID Type Subtype PubMed ID
nsv1146669 OTHER inversion 26484159
nsv520636 CNV loss 19592680
nsv528369 CNV loss 19592680
nsv833444 CNV loss 17160897

Variation tolerance for NR1D1 Gene

Residual Variation Intolerance Score: 10.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.87; 35.04% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NR1D1 Gene

Human Gene Mutation Database (HGMD)
NR1D1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NR1D1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NR1D1 Gene

Disorders for NR1D1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for NR1D1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
hypothyroidism, congenital, nongoitrous, 6
  • chng6
rem sleep behavior disorder
  • rapid eye movement sleep behavior disorder
major depressive disorder
  • mdd
enhanced s-cone syndrome
  • escs
delayed sleep phase disorder
  • delayed sleep phase disorder, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search NR1D1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NR1D1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NR1D1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NR1D1 Gene

Publications for NR1D1 Gene

  1. Association study in a Sardinian sample between bipolar disorder and the nuclear receptor REV-ERBalpha gene, a critical component of the circadian clock system. (PMID: 19267705) Severino G … Del Zompo M (Bipolar disorders 2009) 3 23 41 54
  2. Association analysis of nuclear receptor Rev-erb alpha gene (NR1D1) with mood disorders in the Japanese population. (PMID: 18804497) Kishi T … Iwata N (Neuroscience research 2008) 3 23 41 54
  3. Isolation of a cDNA encoding human Rev-ErbA alpha: transcription from the noncoding DNA strand of a thyroid hormone receptor gene results in a related protein that does not bind thyroid hormone. (PMID: 1971514) Lazar MA … Chin WW (DNA and cell biology 1990) 2 3 4 54
  4. Circadian Amplitude Regulation via FBXW7-Targeted REV-ERBα Degradation. (PMID: 27238018) Zhao X … Evans RM (Cell 2016) 3 4 54
  5. Ubiquitin ligase Siah2 regulates RevErbα degradation and the mammalian circadian clock. (PMID: 26392558) DeBruyne JP … Hogenesch JB (Proceedings of the National Academy of Sciences of the United States of America 2015) 3 4 54

Products for NR1D1 Gene