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

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; AllianceGenome:HGNC:7962
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: mouse all
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Genomic context

Location:: 17q21.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (40092793..40100589, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (40956678..40964476, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (38249046..38256842, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Functional inversion of circadian regulator REV-ERBalpha leads to tumorigenic gene reprogramming.
Title: Functional inversion of circadian regulator REV-ERBα leads to tumorigenic gene reprogramming.
REVERBA couples the circadian clock to Leydig cell steroidogenesis.
Title: REVERBA couples the circadian clock to Leydig cell steroidogenesis.
Nuclear receptor Rev-erbalpha role in fine-tuning erythropoietin gene expression.
Title: Nuclear receptor Rev-erbα role in fine-tuning erythropoietin gene expression.
NR1D1-rearranged soft tissue tumour: A clinicopathological and molecular analysis of four additional cases.
Title: NR1D1-rearranged soft tissue tumour: A clinicopathological and molecular analysis of four additional cases.
Functional Characterization of Circadian Nuclear Receptors REV-ERBalpha and REV-ERBbeta in Human Osteosarcoma Cell Cultures.
Title: Functional Characterization of Circadian Nuclear Receptors REV-ERBα and REV-ERBβ in Human Osteosarcoma Cell Cultures.
Sex-dependent relationship of polymorphisms in CLOCK and REV-ERBalpha genes with body mass index and lipid levels in children.
Title: Sex-dependent relationship of polymorphisms in CLOCK and REV-ERBα genes with body mass index and lipid levels in children.
Uncovering the Novel Role of NR1D1 in Regulating BNIP3-Mediated Mitophagy in Ulcerative Colitis.
Title: Uncovering the Novel Role of NR1D1 in Regulating BNIP3-Mediated Mitophagy in Ulcerative Colitis.
Clock gene NR1D1 might be a novel target for the treatment of bladder cancer.
Title: Clock gene NR1D1 might be a novel target for the treatment of bladder cancer.
Nuclear Receptor NR1D1 Regulates Abdominal Aortic Aneurysm Development by Targeting the Mitochondrial Tricarboxylic Acid Cycle Enzyme Aconitase-2.
Title: Nuclear Receptor NR1D1 Regulates Abdominal Aortic Aneurysm Development by Targeting the Mitochondrial Tricarboxylic Acid Cycle Enzyme Aconitase-2.
Helicobacter pylori-Induced Rev-erbalpha Fosters Gastric Bacteria Colonization by Impairing Host Innate and Adaptive Defense.
Title: Helicobacter pylori-Induced Rev-erbα Fosters Gastric Bacteria Colonization by Impairing Host Innate and Adaptive Defense.

Submit: New GeneRIF Correction See all GeneRIFs (66)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Multiple loci are associated with white blood cell phenotypes. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D17S1644E (e-PCR)
- UniSTS:147478

NR1D1_2626 (e-PCR)
- UniSTS:280871

AW259572 (e-PCR)
- UniSTS:180310

D10S2160 (e-PCR)
- UniSTS:66466

SHGC-146999 (e-PCR)
- UniSTS:175551

RH125185 (e-PCR)
- UniSTS:162007

MARC_5497-5498:996690469:1 (e-PCR)
- UniSTS:269530

THRA_2263 (e-PCR)
- UniSTS:281056

RH110 (e-PCR)
- UniSTS:25599

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables E-box binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables heme binding	IDA Inferred from Direct Assay more info	PubMed
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear steroid receptor activity	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to interleukin-1	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to lipopolysaccharide	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to tumor necrosis factor	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in cholesterol homeostasis	IDA Inferred from Direct Assay more info	PubMed
involved_in cholesterol homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in circadian regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in circadian temperature homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in glycogen biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in hormone-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular glucose homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of astrocyte activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in negative regulation of inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of microglial cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of neuroinflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of toll-like receptor 4 signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of bile acid biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteasomal protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein destabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of circadian rhythm	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of circadian sleep/wake cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of fat cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of insulin secretion involved in cellular response to glucose stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of lipid metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of type B pancreatic cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to leptin	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to leptin	ISS Inferred from Sequence or Structural Similarity more info
involved_in steroid hormone receptor signaling pathway	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic spine	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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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)

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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

NG_033084.1 RefSeqGene

Range

5137..12933

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_021724.5 → NP_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, Q0P5Z4, Q15304

UniProtKB/TrEMBL

F1D8S3

Related

ENSP00000246672.3, ENST00000246672.4

Conserved Domains (2) summary

cd07166
Location:127 → 215

NR_DBD_REV_ERB; DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers

cl11397
Location:418 → 611

NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators