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

    Gene ID: 9975, updated on 10-Dec-2024

    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
    NEW
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    Try the new Transcript table

    Genomic context

    See NR1D2 in Genome Data Viewer
    Location:
    3p24.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (23945286..23980617)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (23950061..23985372)
    RS_2024_09 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

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (15 hits/1291 screens)

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cell differentiation  
    involved_in circadian behavior  
    involved_in energy homeostasis  
    involved_in hormone-mediated signaling pathway  
    involved_in intracellular receptor signaling pathway  
    involved_in lipid homeostasis  
    involved_in negative regulation of DNA-templated transcription PubMed 
    involved_in negative regulation of inflammatory response  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in regulation of DNA-templated transcription PubMed 
    involved_in regulation of circadian rhythm  
    involved_in regulation of inflammatory response  
    involved_in regulation of lipid metabolic process  
    involved_in regulation of skeletal muscle cell differentiation  
    Component Evidence Code Pubs
    located_in chromatin  
    located_in cytoplasm  
    located_in nucleoplasm  
    located_in nucleoplasm  
    is_active_in nucleus  
    located_in nucleus PubMed 
    located_in nucleus PubMed 

    General protein information

    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)

    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
      Related
      ENSP00000520893.1, ENST00000492552.6
      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_2024_08

    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

      UniProtKB/TrEMBL
      Q6NSM0
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