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    Nr1h3 nuclear receptor subfamily 1, group H, member 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 58852, updated on 4-Jan-2025

    Summary

    Official Symbol
    Nr1h3provided by RGD
    Official Full Name
    nuclear receptor subfamily 1, group H, member 3provided by RGD
    Primary source
    RGD:61909
    See related
    EnsemblRapid:ENSRNOG00000013172 AllianceGenome:RGD:61909
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    LXRalpha
    Summary
    Enables nuclear retinoid X receptor binding activity and sequence-specific DNA binding activity. Involved in several processes, including hematopoietic or lymphoid organ development; insulin receptor signaling pathway; and response to cholesterol. Located in nucleolus. Used to study metabolic dysfunction and alcohol associated liver disease. Biomarker of metabolic dysfunction and alcohol associated liver disease and obesity. Human ortholog(s) of this gene implicated in cerebral infarction; cerebrovascular disease; myocardial infarction; and obesity. Orthologous to human NR1H3 (nuclear receptor subfamily 1 group H member 3). [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Biased expression in Liver (RPKM 481.1), Spleen (RPKM 343.8) and 7 other tissues See more
    Orthologs
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    Genomic context

    See Nr1h3 in Genome Data Viewer
    Location:
    3q24
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (97614616..97632053, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (77158808..77168907, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (80004130..80014197, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene myosin binding protein C3 Neighboring gene MAP-kinase activating death domain Neighboring gene transfer RNA alanine (anticodon AGC) 34 Neighboring gene U6 spliceosomal RNA Neighboring gene acid phosphatase 2, lysosomal Neighboring gene damage specific DNA binding protein 2 Neighboring gene protein kinase C and casein kinase substrate in neurons 3

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific  
    enables DNA-binding transcription factor activity  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables chromatin DNA binding  
    enables chromatin DNA binding  
    enables nuclear receptor activity  
    enables nuclear receptor activity  
    contributes_to nuclear receptor activity  
    enables nuclear receptor activity  
    enables nuclear receptor activity  
    enables nuclear retinoid X receptor binding PubMed 
    enables nuclear steroid receptor activity PubMed 
    enables protein-containing complex binding PubMed 
    enables sequence-specific DNA binding PubMed 
    enables sequence-specific DNA binding  
    enables sterol response element binding  
    enables sterol response element binding  
    contributes_to transcription cis-regulatory region binding  
    enables transcription cis-regulatory region binding  
    enables zinc ion binding  
    Items 1 - 25 of 83
    Process Evidence Code Pubs
    involved_in apoptotic cell clearance  
    involved_in apoptotic cell clearance  
    involved_in cell differentiation  
    involved_in cellular response to lipopolysaccharide  
    involved_in cellular response to lipopolysaccharide  
    involved_in cellular response to starvation PubMed 
    involved_in cholesterol homeostasis  
    involved_in cholesterol homeostasis  
    involved_in cholesterol homeostasis  
    involved_in digestive tract development PubMed 
    involved_in hormone-mediated signaling pathway  
    involved_in hormone-mediated signaling pathway  
    involved_in insulin receptor signaling pathway PubMed 
    involved_in intracellular receptor signaling pathway  
    involved_in lipid homeostasis  
    involved_in lipid metabolic process  
    involved_in liver development PubMed 
    involved_in mRNA transcription by RNA polymerase II  
    involved_in mRNA transcription by RNA polymerase II  
    acts_upstream_of_or_within negative regulation of DNA-templated transcription  
    involved_in negative regulation of cholesterol storage  
    involved_in negative regulation of cholesterol storage  
    involved_in negative regulation of cold-induced thermogenesis  
    involved_in negative regulation of cold-induced thermogenesis  
    involved_in negative regulation of cold-induced thermogenesis PubMed 
    involved_in negative regulation of inflammatory response  
    involved_in negative regulation of inflammatory response  
    involved_in negative regulation of inflammatory response  
    involved_in negative regulation of lipid transport  
    involved_in negative regulation of lipid transport  
    involved_in negative regulation of macrophage activation  
    involved_in negative regulation of macrophage activation  
    involved_in negative regulation of pancreatic juice secretion  
    involved_in negative regulation of pancreatic juice secretion  
    involved_in negative regulation of pinocytosis  
    involved_in negative regulation of pinocytosis  
    involved_in negative regulation of proteolysis  
    involved_in negative regulation of proteolysis  
    involved_in negative regulation of response to endoplasmic reticulum stress  
    involved_in negative regulation of response to endoplasmic reticulum stress  
    involved_in negative regulation of response to endoplasmic reticulum stress  
    involved_in negative regulation of secretion of lysosomal enzymes  
    involved_in negative regulation of secretion of lysosomal enzymes  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in phosphatidylcholine acyl-chain remodeling  
    involved_in phosphatidylcholine acyl-chain remodeling  
    involved_in phosphatidylcholine acyl-chain remodeling  
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of cholesterol efflux  
    involved_in positive regulation of cholesterol efflux  
    involved_in positive regulation of cholesterol efflux  
    involved_in positive regulation of cholesterol transport  
    involved_in positive regulation of fatty acid biosynthetic process  
    involved_in positive regulation of fatty acid biosynthetic process  
    involved_in positive regulation of lipid biosynthetic process  
    involved_in positive regulation of lipoprotein lipase activity  
    involved_in positive regulation of protein metabolic process  
    involved_in positive regulation of protein metabolic process  
    involved_in positive regulation of toll-like receptor 4 signaling pathway  
    involved_in positive regulation of toll-like receptor 4 signaling pathway  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of triglyceride biosynthetic process  
    involved_in positive regulation of triglyceride biosynthetic process  
    acts_upstream_of_or_within regulation of DNA-templated transcription  
    involved_in regulation of fatty acid metabolic process PubMed 
    involved_in regulation of transcription by RNA polymerase II  
    involved_in response to cholesterol PubMed 
    involved_in response to nutrient levels PubMed 
    involved_in response to organic cyclic compound PubMed 
    involved_in response to progesterone  
    involved_in response to progesterone  
    involved_in spleen development PubMed 
    involved_in steroid hormone receptor signaling pathway  
    involved_in sterol homeostasis  
    involved_in thymus development PubMed 
    involved_in triglyceride homeostasis  
    involved_in triglyceride homeostasis  
    Items 1 - 25 of 83
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex  
    part_of RNA polymerase II transcription regulator complex  
    part_of RNA polymerase II transcription regulator complex  
    located_in chromatin  
    located_in chromatin  
    located_in cytoplasm  
    located_in cytosol  
    located_in cytosol  
    located_in nucleolus PubMed 
    located_in nucleoplasm  
    located_in nucleoplasm  
    is_active_in nucleus  
    located_in nucleus  
    located_in nucleus  
    part_of receptor complex  
    part_of receptor complex  

    General protein information

    Preferred Names
    oxysterols receptor LXR-alpha
    Names
    RLD-1
    liver X receptor alpha
    nuclear orphan receptor LXR-alpha
    NP_113815.2
    XP_006234595.1
    XP_006234596.1
    XP_006234597.1
    XP_006234599.1
    XP_038961679.1
    XP_038961680.1
    XP_038961681.1
    XP_063140496.1
    XP_063140498.1
    XP_063140499.1

    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_031627.2NP_113815.2  oxysterols receptor LXR-alpha

      See identical proteins and their annotated locations for NP_113815.2

      Status: PROVISIONAL

      Source sequence(s)
      BC088750
      UniProtKB/Swiss-Prot
      Q62685
      UniProtKB/TrEMBL
      A6HNB3, A6HNB4, Q5I035
      Related
      ENSRNOP00000018154.5, ENSRNOT00000018154.7
      Conserved Domains (2) summary
      cd06954
      Location:208443
      NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
      cd07160
      Location:76176
      NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      97614616..97632053 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063284426.1XP_063140496.1  oxysterols receptor LXR-alpha isoform X1

      UniProtKB/Swiss-Prot
      Q62685
      UniProtKB/TrEMBL
      A6HNB3, A6HNB4, Q5I035
    2. XM_006234535.5XP_006234597.1  oxysterols receptor LXR-alpha isoform X1

      See identical proteins and their annotated locations for XP_006234597.1

      UniProtKB/Swiss-Prot
      Q62685
      UniProtKB/TrEMBL
      A6HNB3, A6HNB4, Q5I035
      Conserved Domains (2) summary
      cd06954
      Location:208443
      NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
      cd07160
      Location:76176
      NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
    3. XM_039105751.2XP_038961679.1  oxysterols receptor LXR-alpha isoform X1

      UniProtKB/Swiss-Prot
      Q62685
      UniProtKB/TrEMBL
      A6HNB3, A6HNB4, Q5I035
      Conserved Domains (2) summary
      cd06954
      Location:208443
      NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
      cd07160
      Location:76176
      NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
    4. XM_006234537.3XP_006234599.1  oxysterols receptor LXR-alpha isoform X2

      See identical proteins and their annotated locations for XP_006234599.1

      UniProtKB/Swiss-Prot
      Q62685
      Conserved Domains (1) summary
      cd06954
      Location:119354
      NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
    5. XM_063284428.1XP_063140498.1  oxysterols receptor LXR-alpha isoform X2

      UniProtKB/Swiss-Prot
      Q62685
    6. XM_006234534.4XP_006234596.1  oxysterols receptor LXR-alpha isoform X1

      See identical proteins and their annotated locations for XP_006234596.1

      UniProtKB/Swiss-Prot
      Q62685
      UniProtKB/TrEMBL
      A6HNB3, A6HNB4, Q5I035
      Conserved Domains (2) summary
      cd06954
      Location:208443
      NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
      cd07160
      Location:76176
      NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
    7. XM_063284429.1XP_063140499.1  oxysterols receptor LXR-alpha isoform X2

      UniProtKB/Swiss-Prot
      Q62685
    8. XM_039105752.2XP_038961680.1  oxysterols receptor LXR-alpha isoform X1

      UniProtKB/Swiss-Prot
      Q62685
      UniProtKB/TrEMBL
      A6HNB3, A6HNB4, Q5I035
      Conserved Domains (2) summary
      cd06954
      Location:208443
      NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
      cd07160
      Location:76176
      NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
    9. XM_006234533.5XP_006234595.1  oxysterols receptor LXR-alpha isoform X1

      See identical proteins and their annotated locations for XP_006234595.1

      UniProtKB/Swiss-Prot
      Q62685
      UniProtKB/TrEMBL
      A6HNB3, A6HNB4, Q5I035
      Related
      ENSRNOP00000088605.1, ENSRNOT00000103975.2
      Conserved Domains (2) summary
      cd06954
      Location:208443
      NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
      cd07160
      Location:76176
      NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
    10. XM_039105753.2XP_038961681.1  oxysterols receptor LXR-alpha isoform X2

      UniProtKB/Swiss-Prot
      Q62685
      Conserved Domains (1) summary
      cd06954
      Location:119354
      NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
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