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NR1D1 nuclear receptor subfamily 1 group D member 1 [ Homo sapiens (human) ]

Gene ID: 9572, updated on 13-Jan-2019

Summary

Official Symbol
NR1D1provided by HGNC
Official Full Name
nuclear receptor subfamily 1 group D member 1provided by HGNC
Primary source
HGNC:HGNC:7962
See related
Ensembl:ENSG00000126368 MIM:602408
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
EAR1; hRev; THRA1; THRAL; ear-1; REVERBA; REVERBalpha
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]
Expression
Ubiquitous expression in ovary (RPKM 21.5), brain (RPKM 21.4) and 24 other tissues See more
Orthologs

Genomic context

See NR1D1 in Genome Data Viewer
Location:
17q21.1
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (40092784..40100725, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (38249037..38256978, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene mediator complex subunit 24 Neighboring gene small nucleolar RNA, C/D box 124 Neighboring gene microRNA 6884 Neighboring gene thyroid hormone receptor alpha Neighboring gene MSL complex subunit 1 Neighboring gene CASC3 exon junction complex subunit Neighboring gene microRNA 6866

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • BMAL1:CLOCK,NPAS2 activates circadian gene expression, organism-specific biosystem (from REACTOME)
    BMAL1:CLOCK,NPAS2 activates circadian gene expression, organism-specific biosystemAs inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) and BMAL1:NPAS2 (ARNTL:NPAS2) heterodimers bind to sequence elements (E boxes) in the promoters of target genes and enhance transcription (Gekakis et...
  • Circadian Clock, organism-specific biosystem (from REACTOME)
    Circadian Clock, organism-specific biosystemAt the center of the mammalian circadian clock is a negative transcription/translation-based feedback loop: The BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) heterodimer transactivates CRY and PER genes by b...
  • Circadian rhythm, organism-specific biosystem (from KEGG)
    Circadian rhythm, organism-specific biosystemCircadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of ...
  • Circadian rhythm, conserved biosystem (from KEGG)
    Circadian rhythm, conserved biosystemCircadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of ...
  • Circadian rhythm pathway, organism-specific biosystem (from Pathway Interaction Database)
    Circadian rhythm pathway, organism-specific biosystem
    Circadian rhythm pathway
  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • Fatty acid, triacylglycerol, and ketone body metabolism, organism-specific biosystem (from REACTOME)
    Fatty acid, triacylglycerol, and ketone body metabolism, organism-specific biosystemThe reactions involved in the metabolism of fatty acids and of the triacylglycerols and ketone bodies derived from them form a closely interrelated, coordinately regulated module that plays a central...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • Mitochondrial biogenesis, organism-specific biosystem (from REACTOME)
    Mitochondrial biogenesis, organism-specific biosystemMitochondrial biogenesis and remodeling occur in response to exercise and redox state (reviewed in Scarpulla et al. 2012, Handy and Loscalzo 2012, Piantadosi and Suliman 2012, Scarpulla 2011, Wenz et...
  • NR1D1 (REV-ERBA) represses gene expression, organism-specific biosystem (from REACTOME)
    NR1D1 (REV-ERBA) represses gene expression, organism-specific biosystemREV-ERBA binds DNA elements very similar to those bound by the transcription activator RORA. RORAREV-ERBA bound to DNA and heme recruits the corepressors NCoR and HDAC3 to repress transcription. Thu...
  • Nuclear Receptor transcription pathway, organism-specific biosystem (from REACTOME)
    Nuclear Receptor transcription pathway, organism-specific biosystemA classic example of bifunctional transcription factors is the family of Nuclear Receptor (NR) proteins. These are DNA-binding transcription factors that bind certain hormones, vitamins, and other s...
  • Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
    Organelle biogenesis and maintenance, organism-specific biosystemThis module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reti...
  • PPARA activates gene expression, organism-specific biosystem (from REACTOME)
    PPARA activates gene expression, organism-specific biosystemThe set of genes regulated by PPAR-alpha is not fully known in humans, however many examples have been found in mice. Genes directly activated by PPAR-alpha contain peroxisome proliferator receptor e...
  • RORA activates gene expression, organism-specific biosystem (from REACTOME)
    RORA activates gene expression, organism-specific biosystemAs inferred from mouse, RORA binds ROR elements (ROREs) in DNA and recruits the coactivators PPARGC1A (PGC-1alpha) and p300 (EP300, a histone acetylase) to activate transcription.
  • Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha), organism-specific biosystem (from REACTOME)
    Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha), organism-specific biosystemPeroxisome proliferator-activated receptor alpha (PPAR-alpha) is the major regulator of fatty acid oxidation in the liver. PPARalpha is also the target of fibrate drugs used to treat abnormal plasma ...
  • Transcriptional activation of mitochondrial biogenesis, organism-specific biosystem (from REACTOME)
    Transcriptional activation of mitochondrial biogenesis, organism-specific biosystemPhosphorylated PPARGC1A (PGC-1alpha) does not bind DNA directly but instead interacts with other transcription factors, notably NRF1 and NRF2 (via HCF1). NRF1 and NRF2 together with PPARGC1A activate...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
E-box binding IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
heme binding IDA
Inferred from Direct Assay
more info
PubMed 
nuclear receptor activity TAS
Traceable Author Statement
more info
PubMed 
nuclear receptor transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
steroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
 
transcription corepressor activity TAS
Traceable Author Statement
more info
PubMed 
transcription corepressor binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to lipopolysaccharide IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT cholesterol homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
cholesterol homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
circadian rhythm TAS
Traceable Author Statement
more info
 
circadian temperature homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
glycogen biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
hormone-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
negative regulation of receptor biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of toll-like receptor 4 signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of bile acid biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
proteasomal protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of circadian rhythm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of fat cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of insulin secretion involved in cellular response to glucose stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of lipid metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of type B pancreatic cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
response to leptin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to leptin ISS
Inferred from Sequence or Structural Similarity
more info
 
response to lipid IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
steroid hormone mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
RNA polymerase II transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
dendrite ISS
Inferred from Sequence or Structural Similarity
more info
 
dendritic spine ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear body IDA
Inferred from Direct Assay
more info
 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
nuclear receptor subfamily 1 group D member 1
Names
Rev-ErbAalpha
V-erbA-related protein 1
nuclear receptor Rev-ErbA-alpha
rev-erbA-alpha

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033084.1 RefSeqGene

    Range
    5001..12942
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_021724.5NP_068370.1  nuclear receptor subfamily 1 group D member 1

    See identical proteins and their annotated locations for NP_068370.1

    Status: REVIEWED

    Source sequence(s)
    BC056148
    Consensus CDS
    CCDS11361.1
    UniProtKB/Swiss-Prot
    P20393
    UniProtKB/TrEMBL
    F1D8S3
    Related
    ENSP00000246672.3, ENST00000246672.3
    Conserved Domains (2) summary
    cd07166
    Location:127215
    NR_DBD_REV_ERB; DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers
    cl11397
    Location:418611
    NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p12 Primary Assembly

    Range
    40092784..40100725 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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