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

Gene ID: 9975, updated on 9-Jan-2019

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
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

Genomic context

See NR1D2 in Genome Data Viewer
Location:
3p24.2
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (23945260..23980618)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (23986751..24022109)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ubiquitin conjugating enzyme E2 E1 Neighboring gene ADP ribosylation factor like GTPase 4A pseudogene 4 Neighboring gene NFKB inhibitor interacting Ras like 1 Neighboring gene ribosomal protein L15 Neighboring gene long intergenic non-protein coding RNA 691 Neighboring gene nucleophosmin 1 pseudogene 23

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?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
NHGRI GWA Catalog

Pathways from BioSystems

  • 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...
  • Diurnally Regulated Genes with Circadian Orthologs, organism-specific biosystem (from WikiPathways)
    Diurnally Regulated Genes with Circadian Orthologs, organism-specific biosystemHuman genes regulated in the diurnal comparison with orthologues that display circadian regulation in mouse heart and liver (Panda 2002, Storch 2002), and SCN (Panda 2002). The 608 significantly regu...
  • 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...
  • 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...
  • Nuclear Receptors, organism-specific biosystem (from WikiPathways)
    Nuclear Receptors, organism-specific biosystemNuclear receptors are a class of proteins found within the interior of cells that are responsible for sensing the presence of steroid and thyroid hormones and certain other molecules. In response, th...

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 
RNA polymerase II distal enhancer sequence-specific DNA 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 regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
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 factor binding IBA
Inferred from Biological aspect of Ancestor
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 
energy homeostasis 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
 
lipid homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
multicellular organism development IBA
Inferred from Biological aspect of Ancestor
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, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
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
 
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 inflammatory response 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 skeletal muscle cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of transcription, DNA-templated TAS
Traceable Author Statement
more info
PubMed 
response to lipid IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
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 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
nuclear receptor subfamily 1 group D member 2
Names
V-erbA-related protein 1-related
nuclear receptor Rev-ErbA beta variant 1
nuclear receptor Rev-ErbA beta variant 2
orphan nuclear hormone receptor BD73
rev-erb alpha-related receptor
rev-erb-beta
rev-erba-alpha-related receptor

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.

mRNA and Protein(s)

  1. NM_001145425.1NP_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
    Conserved Domains (2) summary
    cd06940
    Location:314502
    NR_LBD_REV_ERB; The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily
    cd07166
    Location:23111
    NR_DBD_REV_ERB; DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers
  2. NM_005126.5NP_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
    Q14995
    UniProtKB/TrEMBL
    F1D8P2
    Related
    ENSP00000310006.3, ENST00000312521.8
    Conserved Domains (2) summary
    cd06940
    Location:389577
    NR_LBD_REV_ERB; The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily
    cd07166
    Location:98186
    NR_DBD_REV_ERB; DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers

RNA

  1. NR_110524.1 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: 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_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    23945260..23980618
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006713451.3XP_006713514.1  nuclear receptor subfamily 1 group D member 2 isoform X1

    Related
    ENSP00000373283.3, ENST00000383773.8
    Conserved Domains (2) summary
    cd07166
    Location:98186
    NR_DBD_REV_ERB; DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers
    cl11397
    Location:389445
    NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
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