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    NR1I2 nuclear receptor subfamily 1 group I member 2 [ Homo sapiens (human) ]

    Gene ID: 8856, updated on 10-Dec-2024

    Summary

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    Official Symbol
    NR1I2provided by HGNC
    Official Full Name
    nuclear receptor subfamily 1 group I member 2provided by HGNC
    Primary source
    HGNC:HGNC:7968
    See related
    Ensembl:ENSG00000144852 MIM:603065; AllianceGenome:HGNC:7968
    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
    BXR; PAR; PRR; PXR; SAR; SXR; ONR1; PAR1; PAR2; PARq
    Summary
    This gene product belongs to the nuclear receptor superfamily, members of which are transcription factors characterized by a ligand-binding domain and a DNA-binding domain. The encoded protein is a transcriptional regulator of the cytochrome P450 gene CYP3A4, binding to the response element of the CYP3A4 promoter as a heterodimer with the 9-cis retinoic acid receptor RXR. It is activated by a range of compounds that induce CYP3A4, including dexamethasone and rifampicin. Several alternatively spliced transcripts encoding different isoforms, some of which use non-AUG (CUG) translation initiation codon, have been described for this gene. Additional transcript variants exist, however, they have not been fully characterized. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in small intestine (RPKM 14.5), duodenum (RPKM 13.0) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NR1I2 in Genome Data Viewer
    Location:
    3q13.33
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (119782101..119818487)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (122501838..122538215)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (119500948..119537334)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20322 Neighboring gene uncharacterized LOC105374064 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:119419489-119420688 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:119421355-119422034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20325 Neighboring gene cytochrome c oxidase copper chaperone COX17 Neighboring gene cilia and flagella associated protein 91 Neighboring gene Sharpr-MPRA regulatory region 6912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:119528543-119529046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:119534511-119535011 Neighboring gene PHB1 pseudogene 8 Neighboring gene glycogen synthase kinase 3 beta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20328 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:119691277-119691494 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:119722393-119722919 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:119722920-119723445 Neighboring gene PARL pseudogene 1 Neighboring gene RFK pseudogene 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Investigation of associations between the pregnane-X receptor gene (NR1I2) and Crohn's disease in Canadian children using a gene-wide haplotype-based approach. Amre DK, et al. Inflamm Bowel Dis, 2008 Sep. PMID 18381611
    2. A pharmacogenetic study of pregnane X receptor (NR1I2) in Han Chinese. Wang XD, et al. Curr Drug Metab, 2007 Dec. PMID 18220558
    3. Regulation of hepatic energy metabolism by the nuclear receptor PXR. Hakkola J, et al. Biochim Biophys Acta, 2016 Sep. PMID 27041449
    4. Decreased Pregnane X Receptor Expression in Children with Active Crohn's Disease. Shakhnovich V, et al. Drug Metab Dispos, 2016 Jul. PMID 27013401, Free PMC Article
    5. Unique transcription start sites and distinct promoter regions differentiate the pregnane X receptor (PXR) isoforms PXR 1 and PXR 2. Tompkins LM, et al. Drug Metab Dispos, 2008 May. PMID 18276839

    See all (394) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DNA methylation determines the regulation of pregnane X receptor on CYP3A4 expression.
      Title: DNA methylation determines the regulation of pregnane X receptor on CYP3A4 expression.
    2. NEAT1_2 and DAZAP1, Paraspeckle Components, Interact with PXR to Negatively Regulate CYP3A4 Induction.
      Title: NEAT1_2 and DAZAP1, Paraspeckle Components, Interact with PXR to Negatively Regulate CYP3A4 Induction.
    3. Effect of pregnane X receptor and cytochrome P450 oxidoreductase gene polymorphisms on trough concentrations of rivaroxaban and edoxaban in patients with nonvalvular atrial fibrillation.
      Title: Effect of pregnane X receptor and cytochrome P450 oxidoreductase gene polymorphisms on trough concentrations of rivaroxaban and edoxaban in patients with nonvalvular atrial fibrillation.
    4. Pregnane X receptor gene variant rs7643645 and total mortality in subjects with nonalcoholic fatty liver disease.
      Title: Pregnane X receptor gene variant rs7643645 and total mortality in subjects with nonalcoholic fatty liver disease.
    5. Effects of NR1I2 and ABCB1 Genetic Polymorphisms on Everolimus Pharmacokinetics in Japanese Renal Transplant Patients.
      Title: Effects of NR1I2 and ABCB1 Genetic Polymorphisms on Everolimus Pharmacokinetics in Japanese Renal Transplant Patients.
    6. Relevance of gene polymorphisms of NAT2 and NR1I2 to anti-tuberculosis drug-induced hepatotoxicity.
      Title: Relevance of gene polymorphisms of NAT2 and NR1I2 to anti-tuberculosis drug-induced hepatotoxicity.
    7. Distinct Roles of the Sister Nuclear Receptors PXR and CAR in Liver Cancer Development.
      Title: Distinct Roles of the Sister Nuclear Receptors PXR and CAR in Liver Cancer Development.
    8. Protease-Activated Receptor 1 in Human Carotid Atheroma Is Significantly Related to Iron Metabolism, Plaque Vulnerability, and the Patient's Age.
      Title: Protease-Activated Receptor 1 in Human Carotid Atheroma Is Significantly Related to Iron Metabolism, Plaque Vulnerability, and the Patient's Age.
    9. No Effect of PXR (8055C>T) Polymorphism on the Pharmacokinetic Profiles of Piperaquine in Healthy Chinese Subjects.
      Title: No Effect of PXR (8055C>T) Polymorphism on the Pharmacokinetic Profiles of Piperaquine in Healthy Chinese Subjects.
    10. Molecular basis of crosstalk in nuclear receptors: heterodimerization between PXR and CAR and the implication in gene regulation.
      Title: Molecular basis of crosstalk in nuclear receptors: heterodimerization between PXR and CAR and the implication in gene regulation.
    Submit: New GeneRIF Correction See all GeneRIFs (337)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    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 transcription 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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nuclear receptor binding IDA
    Inferred from Direct Assay
    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 intracellular receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in steroid metabolic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in xenobiotic catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in xenobiotic metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in xenobiotic transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in intermediate filament cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear body IDA
    Inferred from Direct Assay
    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
    		  
    part_of transcription regulator complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    nuclear receptor subfamily 1 group I member 2
    Names
    orphan nuclear receptor PAR1
    orphan nuclear receptor PXR
    pregnane X receptor
    steroid and xenobiotic receptor

    NCBI Reference Sequences (RefSeq)

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    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_011856.2 RefSeqGene

      Range
      5002..41388
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_003889.4 → NP_003880.3  nuclear receptor subfamily 1 group I member 2 isoform 1

      See identical proteins and their annotated locations for NP_003880.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) contains an alternate 5' terminal exon compared to transcript variant 2, and initiates translation from an in-frame, downstream non-AUG (CUG) codon, resulting in a shorter isoform (1) with a different N-terminus compared to isoform 2.
      Source sequence(s)
      AC069444, KF457674
      Consensus CDS
      CCDS43136.1
      UniProtKB/Swiss-Prot
      O75469, Q006P5, Q008C8, Q96AC7, Q9UJ22, Q9UJ23, Q9UJ24, Q9UJ25, Q9UJ26, Q9UJ27, Q9UNW4
      UniProtKB/TrEMBL
      J3KPQ3
      Related
      ENSP00000377319.3, ENST00000393716.8
      Conserved Domains (2) summary
      cd06934
      Location:143 → 428
      NR_LBD_PXR_like; The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor
      cl02596
      Location:40 → 127
      NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers

    2. NM_022002.3 → NP_071285.1  nuclear receptor subfamily 1 group I member 2 isoform 2

      See identical proteins and their annotated locations for NP_071285.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) encodes the longest isoform (2) and initiates translation from the standard AUG codon present in its 5' terminal exon.
      Source sequence(s)
      AC069444, KF457674
      Consensus CDS
      CCDS2995.1
      UniProtKB/TrEMBL
      F1D8P9, F1DAL3
      Related
      ENSP00000336528.4, ENST00000337940.4
      Conserved Domains (2) summary
      cd06934
      Location:182 → 467
      NR_LBD_PXR_like; The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor
      cd07162
      Location:79 → 166
      NR_DBD_PXR; DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers

    3. NM_033013.3 → NP_148934.1  nuclear receptor subfamily 1 group I member 2 isoform 3

      See identical proteins and their annotated locations for NP_148934.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' terminal exon, and uses a different acceptor splice site at one of the internal coding exons, compared to transcript variant 2. It initiates translation from an in-frame, downstream non-AUG (CUG) codon, resulting in a shorter isoform (3) with a different N-terminus and missing an internal segment, compared to isoform 2.
      Source sequence(s)
      AC069444, KF457674
      Consensus CDS
      CCDS54627.1
      UniProtKB/TrEMBL
      H0Y8E2
      Related
      ENSP00000420297.2, ENST00000466380.6
      Conserved Domains (2) summary
      cd06934
      Location:143 → 391
      NR_LBD_PXR_like; The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor
      cl02596
      Location:40 → 127
      NR_DBD_like; DNA-binding domain of nuclear receptors 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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      119782101..119818487
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      122501838..122538215
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75469.1 GenPept UniProtKB/Swiss-Prot:O75469

    Gene LinkOut

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

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