U.S. flag

An official website of the United States government

NR1H3 nuclear receptor subfamily 1 group H member 3 [ Homo sapiens (human) ]

Gene ID: 10062, updated on 4-Jan-2025

Summary

Official Symbol
NR1H3provided by HGNC
Official Full Name
nuclear receptor subfamily 1 group H member 3provided by HGNC
Primary source
HGNC:HGNC:7966
See related
Ensembl:ENSG00000025434 MIM:602423; AllianceGenome:HGNC:7966
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
LXRA; LXR-a; RLD-1
Summary
The protein encoded by this gene belongs to the NR1 subfamily of the nuclear receptor superfamily. The NR1 family members are key regulators of macrophage function, controlling transcriptional programs involved in lipid homeostasis and inflammation. This protein is highly expressed in visceral organs, including liver, kidney and intestine. It forms a heterodimer with retinoid X receptor (RXR), and regulates expression of target genes containing retinoid response elements. Studies in mice lacking this gene suggest that it may play an important role in the regulation of cholesterol homeostasis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
Expression
Ubiquitous expression in fat (RPKM 25.1), spleen (RPKM 16.7) and 23 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See NR1H3 in Genome Data Viewer
Location:
11p11.2
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (47248300..47269033)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (47405058..47425803)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (47269851..47290584)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein S20 pseudogene 26 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:47231264-47231443 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47235129-47235965 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:47236089-47237288 Neighboring gene damage specific DNA binding protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4694 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:47270641-47270808 Neighboring gene acid phosphatase 2, lysosomal Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47280987-47281555 Neighboring gene Sharpr-MPRA regulatory region 2100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3325 Neighboring gene Sharpr-MPRA regulatory region 9889 Neighboring gene MADD antisense RNA 1 Neighboring gene MAP kinase activating death domain Neighboring gene myosin binding protein C3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47371915-47372896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47372897-47373877

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

EBI GWAS Catalog

Description
Biological, clinical and population relevance of 95 loci for blood lipids.
EBI GWAS Catalog
Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.
EBI GWAS Catalog
Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits.
EBI GWAS Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
matrix gag HIV-1 MA activates NR1H3 signaling in primary hepatocytes PubMed
gag HIV-1 MA upregulates NR1H3 mRNA expression in HepG2 cells and primary hepatocytes PubMed
gag HIV-1 MA upregulates NR1H3 (LXR-alpha) gene expresssion in HepG2 cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

General gene information

Gene Ontology Provided by GOA

Items 1 - 25 of 49
Process Evidence Code Pubs
involved_in apoptotic cell clearance PubMed 
involved_in cell differentiation  
involved_in cellular response to lipopolysaccharide PubMed 
involved_in cholesterol homeostasis PubMed 
involved_in cholesterol homeostasis  
involved_in hormone-mediated signaling pathway PubMed 
involved_in hormone-mediated signaling pathway  
involved_in intracellular receptor signaling pathway  
involved_in lipid homeostasis  
involved_in mRNA transcription by RNA polymerase II PubMed 
involved_in mRNA transcription by RNA polymerase II  
involved_in negative regulation of cholesterol storage PubMed 
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 lipid transport PubMed 
involved_in negative regulation of macrophage activation  
involved_in negative regulation of macrophage derived foam cell differentiation PubMed 
involved_in negative regulation of pancreatic juice secretion  
involved_in negative regulation of pinocytosis PubMed 
involved_in negative regulation of proteolysis  
involved_in negative regulation of response to endoplasmic reticulum stress  
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 type II interferon-mediated signaling pathway PubMed 
involved_in phosphatidylcholine acyl-chain remodeling  
involved_in positive regulation of DNA-templated transcription PubMed 
involved_in positive regulation of DNA-templated transcription PubMed 
involved_in positive regulation of cholesterol efflux PubMed 
involved_in positive regulation of cholesterol efflux PubMed 
involved_in positive regulation of cholesterol efflux PubMed 
involved_in positive regulation of cholesterol transport PubMed 
involved_in positive regulation of fatty acid biosynthetic process PubMed 
involved_in positive regulation of lipid biosynthetic process PubMed 
involved_in positive regulation of lipoprotein lipase activity PubMed 
involved_in positive regulation of protein metabolic process PubMed 
involved_in positive regulation of toll-like receptor 4 signaling pathway PubMed 
involved_in positive regulation of transcription by RNA polymerase II  
involved_in positive regulation of transcription by RNA polymerase II PubMed 
involved_in positive regulation of transcription by RNA polymerase II PubMed 
involved_in positive regulation of transcription by RNA polymerase II  
involved_in positive regulation of transcription by RNA polymerase II PubMed 
involved_in positive regulation of transporter activity PubMed 
involved_in positive regulation of triglyceride biosynthetic process PubMed 
involved_in regulation of circadian rhythm PubMed 
involved_in response to progesterone PubMed 
involved_in sterol homeostasis  
involved_in triglyceride homeostasis  
Items 1 - 25 of 49
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex PubMed 
part_of RNA polymerase II transcription regulator complex  
part_of RNA polymerase II transcription regulator complex PubMed 
part_of RNA polymerase II transcription regulator complex PubMed 
located_in chromatin PubMed 
located_in chromatin  
located_in cytoplasm  
located_in cytosol  
located_in nucleoplasm  
located_in nucleoplasm  
is_active_in nucleus  
located_in nucleus PubMed 
part_of receptor complex PubMed 

General protein information

Preferred Names
oxysterols receptor LXR-alpha
NP_001123573.1
NP_001123574.1
NP_001238863.1
NP_001238864.1
NP_001350524.1
NP_005684.2
XP_005252763.1
XP_011518107.1
XP_011518108.1
XP_011518109.1
XP_011518110.1
XP_016872545.1
XP_024304066.1
XP_047282149.1
XP_047282150.1
XP_047282151.1
XP_047282153.1
XP_047282154.1
XP_047282155.1
XP_047282156.1
XP_047282157.1
XP_047282158.1
XP_054223344.1
XP_054223345.1
XP_054223346.1
XP_054223347.1
XP_054223348.1
XP_054223349.1
XP_054223350.1
XP_054223351.1
XP_054223352.1
XP_054223353.1
XP_054223354.1
XP_054223355.1
XP_054223356.1
XP_054223357.1
XP_054223358.1
XP_054223359.1

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.

Genomic

  1. NG_030392.1 RefSeqGene

    Range
    14697..25734
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001130101.3NP_001123573.1  oxysterols receptor LXR-alpha isoform 2

    See identical proteins and their annotated locations for NP_001123573.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an internal in-frame coding exon compared to variant 1. This results in a shorter isoform (2) missing an internal protein segment compared to isoform 1.
    Source sequence(s)
    AA644385, AI097478, AU133574, BC008819
    Consensus CDS
    CCDS44584.1
    UniProtKB/TrEMBL
    B2R8B9, B3KV37
    Related
    ENSP00000384745.3, ENST00000405853.7
    Conserved Domains (2) summary
    cd07160
    Location:78178
    NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
    cl11397
    Location:210385
    NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
  2. NM_001130102.3NP_001123574.1  oxysterols receptor LXR-alpha isoform 3

    See identical proteins and their annotated locations for NP_001123574.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' terminal exon and lacks another exon compared to variant 1. This results in translation initiation from an in-frame downstream AUG, and an isoform (3) with a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AA644385, AC018410, AI097478, AU135617, BC041172
    Consensus CDS
    CCDS44585.1
    UniProtKB/TrEMBL
    B2R8B9, B3KV37
    Related
    ENSP00000378793.3, ENST00000395397.7
    Conserved Domains (2) summary
    cd06954
    Location:165400
    NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
    cd07160
    Location:33133
    NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
  3. NM_001251934.2NP_001238863.1  oxysterols receptor LXR-alpha isoform 4

    See identical proteins and their annotated locations for NP_001238863.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains 2 alternate exons at the 5' end compared to variant 1. This results in translation initiation from an in-frame upstream AUG, and an isoform (4) with a longer and distinct N-terminus compared to isoform 1. Variants 4 and 5 (which differ in the 5'UTR) encode the same isoform.
    Source sequence(s)
    AA644385, AI097478, AK302132, AK311590
    Consensus CDS
    CCDS73285.1
    UniProtKB/TrEMBL
    B2R8B9, B3KV37, B4DXU5
    Related
    ENST00000529540.5
    Conserved Domains (2) summary
    cd06954
    Location:216451
    NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
    cd07160
    Location:84184
    NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
  4. NM_001251935.2NP_001238864.1  oxysterols receptor LXR-alpha isoform 4

    See identical proteins and their annotated locations for NP_001238864.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains 2 alternate exons at the 5' end compared to variant 1. This results in translation initiation from an in-frame upstream AUG, and an isoform (4) with a longer and distinct N-terminus compared to isoform 1. Variants 4 and 5 (which differ in the 5'UTR) encode the same isoform (4).
    Source sequence(s)
    AA644385, AI097478, AK302132, AK311590
    Consensus CDS
    CCDS73285.1
    UniProtKB/TrEMBL
    B2R8B9, B3KV37, B4DXU5
    Related
    ENSP00000477707.1, ENST00000616973.4
    Conserved Domains (2) summary
    cd06954
    Location:216451
    NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
    cd07160
    Location:84184
    NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
  5. NM_001363595.2NP_001350524.1  oxysterols receptor LXR-alpha isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC018410
    Consensus CDS
    CCDS86200.1
    UniProtKB/TrEMBL
    B5MBY7, E9PID2
    Related
    ENSP00000385073.1, ENST00000405576.5
    Conserved Domains (2) summary
    cd07160
    Location:33133
    NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
    cl11397
    Location:165340
    NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
  6. NM_005693.4NP_005684.2  oxysterols receptor LXR-alpha isoform 1

    See identical proteins and their annotated locations for NP_005684.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript, and encodes isoform 1.
    Source sequence(s)
    AA644385, AI097478, AK290614, AK302132
    Consensus CDS
    CCDS7929.1
    UniProtKB/Swiss-Prot
    A8K3J9, D3DQR1, Q13133, Q8IW13, Q96H87
    UniProtKB/TrEMBL
    B2R8B9, B3KV37, F1D8N1
    Related
    ENSP00000387946.2, ENST00000441012.7
    Conserved Domains (2) summary
    cd06954
    Location:210445
    NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
    cd07160
    Location:78178
    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_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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    47248300..47269033
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426201.1XP_047282157.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
  2. XM_011519805.3XP_011518107.1  oxysterols receptor LXR-alpha isoform X2

    See identical proteins and their annotated locations for XP_011518107.1

    UniProtKB/Swiss-Prot
    A8K3J9, D3DQR1, Q13133, Q8IW13, Q96H87
    UniProtKB/TrEMBL
    B2R8B9, B3KV37, F1D8N1
    Conserved Domains (2) summary
    cd06954
    Location:210445
    NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
    cd07160
    Location:78178
    NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
  3. XM_047426198.1XP_047282154.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
  4. XM_011519808.3XP_011518110.1  oxysterols receptor LXR-alpha isoform X8

    Conserved Domains (1) summary
    cd06954
    Location:1233
    NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
  5. XM_024448298.2XP_024304066.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
    Conserved Domains (2) summary
    cd06954
    Location:165400
    NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
    cd07160
    Location:33133
    NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
  6. XM_047426197.1XP_047282153.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
  7. XM_047426193.1XP_047282149.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
  8. XM_047426202.1XP_047282158.1  oxysterols receptor LXR-alpha isoform X7

  9. XM_047426194.1XP_047282150.1  oxysterols receptor LXR-alpha isoform X2

    UniProtKB/Swiss-Prot
    A8K3J9, D3DQR1, Q13133, Q8IW13, Q96H87
    UniProtKB/TrEMBL
    B2R8B9, B3KV37, F1D8N1
    Related
    ENSP00000420656.1, ENST00000467728.5
  10. XM_047426200.1XP_047282156.1  oxysterols receptor LXR-alpha isoform X6

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
  11. XM_005252706.2XP_005252763.1  oxysterols receptor LXR-alpha isoform X2

    See identical proteins and their annotated locations for XP_005252763.1

    UniProtKB/Swiss-Prot
    A8K3J9, D3DQR1, Q13133, Q8IW13, Q96H87
    UniProtKB/TrEMBL
    B2R8B9, B3KV37, F1D8N1
    Conserved Domains (2) summary
    cd06954
    Location:210445
    NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
    cd07160
    Location:78178
    NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
  12. XM_047426195.1XP_047282151.1  oxysterols receptor LXR-alpha isoform X2

    UniProtKB/Swiss-Prot
    A8K3J9, D3DQR1, Q13133, Q8IW13, Q96H87
    UniProtKB/TrEMBL
    B2R8B9, B3KV37, F1D8N1
  13. XM_011519806.2XP_011518108.1  oxysterols receptor LXR-alpha isoform X3

    UniProtKB/TrEMBL
    B5MBY7, E9PID2
    Conserved Domains (2) summary
    cd07160
    Location:33133
    NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
    cl11397
    Location:165340
    NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
  14. XM_011519807.2XP_011518109.1  oxysterols receptor LXR-alpha isoform X5

    See identical proteins and their annotated locations for XP_011518109.1

    Conserved Domains (1) summary
    cd06954
    Location:76311
    NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors
  15. XM_017017056.2XP_016872545.1  oxysterols receptor LXR-alpha isoform X4

  16. XM_047426199.1XP_047282155.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    47405058..47425803
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054367381.1XP_054223356.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
  2. XM_054367372.1XP_054223347.1  oxysterols receptor LXR-alpha isoform X2

    UniProtKB/Swiss-Prot
    A8K3J9, D3DQR1, Q13133, Q8IW13, Q96H87
    UniProtKB/TrEMBL
    B2R8B9, B3KV37, F1D8N1
  3. XM_054367376.1XP_054223351.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
  4. XM_054367384.1XP_054223359.1  oxysterols receptor LXR-alpha isoform X8

  5. XM_054367382.1XP_054223357.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
  6. XM_054367378.1XP_054223353.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
  7. XM_054367375.1XP_054223350.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
  8. XM_054367369.1XP_054223344.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
  9. XM_054367383.1XP_054223358.1  oxysterols receptor LXR-alpha isoform X7

  10. XM_054367370.1XP_054223345.1  oxysterols receptor LXR-alpha isoform X2

    UniProtKB/Swiss-Prot
    A8K3J9, D3DQR1, Q13133, Q8IW13, Q96H87
    UniProtKB/TrEMBL
    B2R8B9, B3KV37, F1D8N1
  11. XM_054367380.1XP_054223355.1  oxysterols receptor LXR-alpha isoform X6

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
  12. XM_054367371.1XP_054223346.1  oxysterols receptor LXR-alpha isoform X2

    UniProtKB/Swiss-Prot
    A8K3J9, D3DQR1, Q13133, Q8IW13, Q96H87
    UniProtKB/TrEMBL
    B2R8B9, B3KV37, F1D8N1
  13. XM_054367373.1XP_054223348.1  oxysterols receptor LXR-alpha isoform X3

    UniProtKB/TrEMBL
    B5MBY7, E9PID2
  14. XM_054367379.1XP_054223354.1  oxysterols receptor LXR-alpha isoform X5

  15. XM_054367374.1XP_054223349.1  oxysterols receptor LXR-alpha isoform X4

  16. XM_054367377.1XP_054223352.1  oxysterols receptor LXR-alpha isoform X1

    UniProtKB/TrEMBL
    B2R8B9, B3KV37
External link. Please review our privacy policy.