U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 9975, updated on 11-Apr-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See NR1D2 in Genome Data Viewer
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_000003.12Genomic Context describing neighboring genes Neighboring gene NFKB inhibitor interacting Ras like 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:23958136-23959335 Neighboring gene ribosomal protein L15 Neighboring gene uncharacterized LOC124909354 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:23987327-23987868 Neighboring gene Sharpr-MPRA regulatory region 12700 Neighboring gene MPRA-validated peak4577 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:24023426-24023962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:24023963-24024497 Neighboring gene Sharpr-MPRA regulatory region 5785 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:24136149-24136737 Neighboring gene long intergenic non-protein coding RNA 691 Neighboring gene nucleophosmin 1 pseudogene 23

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Human nuclear hormone receptor activity contributes to malaria parasite liver stage development. Mittal N, et al. Cell Chem Biol, 2023 May 18. PMID 37172592, Free PMC Article
  2. Role of Circadian Transcription Factor Rev-Erb in Metabolism and Tissue Fibrosis. Raza GS, et al. Int J Mol Sci, 2022 Oct 26. PMID 36361737, Free PMC Article
  3. Ferric heme as a CO/NO sensor in the nuclear receptor Rev-Erbß by coupling gas binding to electron transfer. Sarkar A, et al. Proc Natl Acad Sci U S A, 2021 Jan 19. PMID 33436410, Free PMC Article
  4. Circadian regulator NR1D2 regulates glioblastoma cell proliferation and motility. Yu M, et al. Oncogene, 2018 Aug. PMID 29773903
  5. The heme-regulatory motif of nuclear receptor Rev-erbβ is a key mediator of heme and redox signaling in circadian rhythm maintenance and metabolism. Carter EL, et al. J Biol Chem, 2017 Jul 7. PMID 28500133, Free PMC Article

See all (56) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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

Go to the top of the page Help

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

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

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

Go to the top of the page Help
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)

Go to the top of the page Help

NEW Try the new Transcript table

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)

  1. 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

  2. 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

  1. 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

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    23945286..23980617
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    23950061..23985372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348681.1 → XP_054204656.1  nuclear receptor subfamily 1 group D member 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q14995.4 GenPept UniProtKB/Swiss-Prot:Q14995

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous