NR1D2 nuclear receptor subfamily 1 group D member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NR1D2provided by HGNC
Official Full Name: nuclear receptor subfamily 1 group D member 2provided by HGNC
Primary source: HGNC:HGNC:7963
See related: Ensembl:ENSG00000174738 MIM:602304; AllianceGenome:HGNC:7963
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: RVR; BD73; EAR-1R; REVERBB; REVERBbeta
Summary: This gene encodes a member of the nuclear hormone receptor family, specifically the NR1 subfamily of receptors. The encoded protein functions as a transcriptional repressor and may play a role in circadian rhythms and carbohydrate and lipid metabolism. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]
Expression: Ubiquitous expression in thyroid (RPKM 35.4), ovary (RPKM 18.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p24.2

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (23945286..23980617)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (23950061..23985372)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (23986777..24022108)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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 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.
Novel CLOCK and NR1D2 variants in 64 sighted Japanese individuals with non-24-hour sleep-wake rhythm disorder.
Title: Novel CLOCK and NR1D2 variants in 64 sighted Japanese individuals with non-24-hour sleep-wake rhythm disorder.
Human nuclear hormone receptor activity contributes to malaria parasite liver stage development.
Title: Human nuclear hormone receptor activity contributes to malaria parasite liver stage development.
Role of Circadian Transcription Factor Rev-Erb in Metabolism and Tissue Fibrosis.
Title: Role of Circadian Transcription Factor Rev-Erb in Metabolism and Tissue Fibrosis.
RORalpha and REV-ERBalpha are Associated With Clinicopathological Parameters and are Independent Biomarkers of Prognosis in Gastric Cancer.
Title: RORα and REV-ERBα are Associated With Clinicopathological Parameters and are Independent Biomarkers of Prognosis in Gastric Cancer.
Burkholderia pseudomallei interferes with host lipid metabolism via NR1D2-mediated PNPLA2/ATGL suppression to block autophagy-dependent inhibition of infection.
Title: Burkholderia pseudomallei interferes with host lipid metabolism via NR1D2-mediated PNPLA2/ATGL suppression to block autophagy-dependent inhibition of infection.
Ferric heme as a CO/NO sensor in the nuclear receptor Rev-Erbss by coupling gas binding to electron transfer.
Title: Ferric heme as a CO/NO sensor in the nuclear receptor Rev-Erbß by coupling gas binding to electron transfer.
Determination of genetic changes of Rev-erb beta and Rev-erb alpha genes in Type 2 diabetes mellitus by next-generation sequencing.
Title: Determination of genetic changes of Rev-erb beta and Rev-erb alpha genes in Type 2 diabetes mellitus by next-generation sequencing.
REVIEW: Redox Regulation of Heme Oxygenase-2 and the Transcription Factor, Rev-Erb, Through Heme Regulatory Motifs
Title: Redox Regulation of Heme Oxygenase-2 and the Transcription Factor, Rev-Erb, Through Heme Regulatory Motifs.
A GBM-promoting role of NR1D2.
Title: Circadian regulator NR1D2 regulates glioblastoma cell proliferation and motility.

Submit: New GeneRIF Correction See all GeneRIFs (23)

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
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. 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

D11S2921 (e-PCR)
- UniSTS:152074

GDB:434012 (e-PCR)
- UniSTS:157204

Nr1d2 (e-PCR), detects polymorphism
- UniSTS:546583

SHGC-147591 (e-PCR)
- UniSTS:175896

STS-L31785 (e-PCR)
- UniSTS:62488

NR1D2_2031 (e-PCR)
- UniSTS:280872

L17705 (e-PCR)
- UniSTS:66091

GDB:314949 (e-PCR)
- UniSTS:156503

SHGC-76776 (e-PCR)
- UniSTS:69473

D3S3941 (e-PCR)
- UniSTS:5732

D10S16 (e-PCR)
- UniSTS:155756

D1S1423 (e-PCR)
- UniSTS:149619

L17877 (e-PCR)
- UniSTS:61334

L17809 (e-PCR)
- UniSTS:39087

D3S3477E (e-PCR)
- UniSTS:154042

SGC34561 (e-PCR)
- UniSTS:21444

RH47404 (e-PCR)
- UniSTS:21445

PMC115222P4 (e-PCR)
- UniSTS:270297

Nr1d2 (e-PCR), detects polymorphism
- UniSTS:507099

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	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 nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear 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 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 circadian behavior	ISS Inferred from Sequence or Structural Similarity more info
involved_in energy homeostasis	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 receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in lipid homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA-templated transcription	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 regulation of DNA-templated transcription	TAS Traceable Author Statement more info	PubMed
involved_in regulation of circadian rhythm	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of inflammatory response	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 skeletal muscle cell differentiation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	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	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: nuclear receptor subfamily 1 group D member 2

Names: V-erbA-related protein 1-related; orphan nuclear hormone receptor BD73; rev-erb alpha-related receptor; rev-erb-beta; rev-erba-alpha-related receptor

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_001145425.2 → NP_001138897.1 nuclear receptor subfamily 1 group D member 2 isoform 2

See identical proteins and their annotated locations for NP_001138897.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate first exon and initiates translation at a downstream start codon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

AC124914, AK301925, CA412377

UniProtKB/TrEMBL

B4DXD3, Q59GL8

Conserved Domains (2) summary

cd06940
Location:314 → 502

NR_LBD_REV_ERB; The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily

cd07166
Location:23 → 111

NR_DBD_REV_ERB; DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers
NM_005126.5 → NP_005117.3 nuclear receptor subfamily 1 group D member 2 isoform 1

See identical proteins and their annotated locations for NP_005117.3

Status: REVIEWED

Description

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

Source sequence(s)

AC124914, CA412377, D16815, DR004486

Consensus CDS

CCDS33718.1

UniProtKB/Swiss-Prot

B2R8Q3, O00402, Q14995, Q86XD4

UniProtKB/TrEMBL

B6ZGS3, F1D8P2, Q6I9S1

Related

ENSP00000310006.3, ENST00000312521.9

Conserved Domains (2) summary

cd06940
Location:389 → 577

NR_LBD_REV_ERB; The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily

cd07166
Location:98 → 186

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

RNA

NR_110524.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate exon compared to variant 1, that causes a frameshift. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC124914, BC015929, BC070035, CA312643, DR004486

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

23945286..23980617

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006713451.4 → XP_006713514.1 nuclear receptor subfamily 1 group D member 2 isoform X1

UniProtKB/TrEMBL

Q6NSM0

Related

ENSP00000373283.3, ENST00000383773.8

Conserved Domains (2) summary

cd07166
Location:98 → 186

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

cl11397
Location:389 → 445

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