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Nr1d1 nuclear receptor subfamily 1, group D, member 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 252917, updated on 2-Nov-2024

Summary

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Official Symbol: Nr1d1provided by RGD
Official Full Name: nuclear receptor subfamily 1, group D, member 1provided by RGD
Primary source: RGD:628827
See related: EnsemblRapid:ENSRNOG00000009329 AllianceGenome:RGD:628827
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: REV-ERBAALPHA
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, Feb 2014]
Expression: Biased expression in Muscle (RPKM 145.1), Lung (RPKM 142.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

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See Nr1d1 in Genome Data Viewer

Location:: 10q31

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (84224599..84231812, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (83728348..83735562, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (86683875..86690815, complement)

Chromosome 10 - NC_086028.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PTZ-kindled rat model; evaluation of seizure, hippocampal EGR-1, and Rev-erbalpha gene regulation, behavioral analysis, and antioxidant capacity of Gum Arabic.
Title: PTZ-kindled rat model; evaluation of seizure, hippocampal EGR-1, and Rev-erbα gene regulation, behavioral analysis, and antioxidant capacity of Gum Arabic.
Rev-erbalpha attenuates refractory periapical periodontitis via M1 polarization: An in vitro and in vivo study.
Title: Rev-erbα attenuates refractory periapical periodontitis via M1 polarization: An in vitro and in vivo study.
Regulation of Circadian Genes Nr1d1 and Nr1d2 in Sex-Different Manners during Liver Aging.
Title: Regulation of Circadian Genes Nr1d1 and Nr1d2 in Sex-Different Manners during Liver Aging.
Central administration of REV-ERBalpha agonist promotes opposite responses on energy balance in fasted and fed states.
Title: Central administration of REV-ERBα agonist promotes opposite responses on energy balance in fasted and fed states.
findings indicate that the attenuation of REV-ERBalpha leads to an upregulation of Gdf10 and Gdf15 in decidual cells
Title: The nuclear receptor REV-ERBα represses the transcription of growth/differentiation factor 10 and 15 genes in rat endometrium stromal cells.
REV-ERBalpha has a role in circadian oscillation in the expressions of Alas1, Ppargc1a, and Il6 genes in rat granulosa cells
Title: Integration of the nuclear receptor REV-ERBα linked with circadian oscillators in the expressions of Alas1, Ppargc1a, and Il6 genes in rat granulosa cells.
Bone morphogenetic protein gene expression is inhibited by REV-ERBalpha which acts as a transcriptional silencer.
Title: Inhibitory role of REV-ERBα in the expression of bone morphogenetic protein gene family in rat uterus endometrium stromal cells.
Data (including data from studies in transgenic rats) suggest attenuation of circadian clock system, especially Rev-erb-alpha, contributes to induction of prostaglandin G/H synthase 2 in endometrial stromal cells during decidualization/placentation.
Title: Removal of Rev-erbα inhibition contributes to the prostaglandin G/H synthase 2 expression in rat endometrial stromal cells.
REV-ERBalpha plays an important role in ventilation induced lung injury (VILI) and inflammation, and circadian rhythm disorder inflammation response may be a novel pathogenesis of VILI.
Title: A study on circadian rhythm disorder of rat lung tissue caused by mechanical ventilation induced lung injury.
Rev-erbalpha is a novel regulator of hepatic stellate cell transdifferentation
Title: Novel role of nuclear receptor Rev-erbα in hepatic stellate cell activation: potential therapeutic target for liver injury.

Submit: New GeneRIF Correction See all GeneRIFs (16)

General gene information

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Markers

D17S1644E (e-PCR)
- UniSTS:147478

NR1D1_2626 (e-PCR)
- UniSTS:280871

AW259572 (e-PCR)
- UniSTS:180310

RH133144 (e-PCR)
- UniSTS:216427

BF387429 (e-PCR)
- UniSTS:244356

RH125185 (e-PCR)
- UniSTS:162007

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

THRA_2263 (e-PCR)
- UniSTS:281056

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables E-box binding	IEA Inferred from Electronic Annotation more info
enables E-box binding	ISO Inferred from Sequence Orthology more info
enables E-box binding	ISS Inferred from Sequence or Structural Similarity 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	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables heme binding	IEA Inferred from Electronic Annotation more info
enables heme binding	ISO Inferred from Sequence Orthology more info
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription corepressor binding	IEA Inferred from Electronic Annotation more info
enables transcription corepressor binding	ISO Inferred from Sequence Orthology more info
enables transcription corepressor binding	ISS Inferred from Sequence or Structural Similarity more info
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 cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to interleukin-1	IEA Inferred from Electronic Annotation more info
involved_in cellular response to interleukin-1	ISO Inferred from Sequence Orthology more info
involved_in cellular response to interleukin-1	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in cellular response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in cellular response to tumor necrosis factor	IEA Inferred from Electronic Annotation more info
involved_in cellular response to tumor necrosis factor	ISO Inferred from Sequence Orthology more info
involved_in cellular response to tumor necrosis factor	ISS Inferred from Sequence or Structural Similarity more info
involved_in cholesterol homeostasis	IEA Inferred from Electronic Annotation more info
NOT involved_in cholesterol homeostasis	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in circadian regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in circadian regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in circadian regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in circadian rhythm	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in circadian temperature homeostasis	IEA Inferred from Electronic Annotation more info
involved_in circadian temperature homeostasis	ISO Inferred from Sequence Orthology more info
involved_in circadian temperature homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in glycogen biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in glycogen biosynthetic process	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation more info
involved_in intracellular glucose homeostasis	ISO Inferred from Sequence Orthology more info
involved_in intracellular glucose homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of astrocyte activation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of astrocyte activation	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of microglial cell activation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of microglial cell activation	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of toll-like receptor 4 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in photoperiodism	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of bile acid biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of bile acid biosynthetic process	ISO Inferred from Sequence Orthology 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 circadian rhythm	IDA Inferred from Direct Assay more info	PubMed
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	IEA Inferred from Electronic Annotation more info
involved_in proteasomal protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in proteasomal protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein destabilization	IEA Inferred from Electronic Annotation more info
involved_in protein destabilization	ISO Inferred from Sequence Orthology more info
involved_in protein destabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of circadian rhythm	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in regulation of circadian sleep/wake cycle	IEA Inferred from Electronic Annotation more info
involved_in regulation of circadian sleep/wake cycle	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation more info
involved_in regulation of fat cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of fat cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of hepatic stellate cell activation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of insulin secretion involved in cellular response to glucose stimulus	IEA Inferred from Electronic Annotation more info
involved_in regulation of insulin secretion involved in cellular response to glucose stimulus	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation more info
involved_in regulation of type B pancreatic cell proliferation	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation more info
involved_in response to leptin	ISO Inferred from Sequence Orthology more info
involved_in response to leptin	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in chromatin	IEA Inferred from Electronic Annotation more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in dendrite	ISO Inferred from Sequence Orthology more info
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic spine	IEA Inferred from Electronic Annotation more info
located_in dendritic spine	ISO Inferred from Sequence Orthology more info
located_in dendritic spine	ISS Inferred from Sequence or Structural Similarity more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear body	IEA Inferred from Electronic Annotation more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology 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: EAR-1; V-erbA-related protein 1; V-erbA-related protein EAR-1; rev-erb 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.

mRNA and Protein(s)

NM_001113422.2 → NP_001106893.2 nuclear receptor subfamily 1 group D member 1 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

Q63503, Q6P6S7

UniProtKB/TrEMBL

A6HIU8, G3V770

Related

ENSRNOP00000012537.5, ENSRNOT00000012537.9

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
NM_145775.3 → NP_665718.2 nuclear receptor subfamily 1 group D member 1 isoform 2

See identical proteins and their annotated locations for NP_665718.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) has an alternate 5' exon and uses a downstream AUG start codon, as compared to variant 1. The resulting isoform (2) is shorter at the N-temrinus, as compared to isoform 1.

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A6HIU9, G3V9L8

Related

ENSRNOP00000052200.3, ENSRNOT00000055333.4

Conserved Domains (2) summary

cd07166
Location:21 → 109

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

cl11397
Location:312 → 505

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