nr1i2 nuclear receptor subfamily 1, group I, member 2 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: nr1i2provided by ZNC
Official Full Name: nuclear receptor subfamily 1, group I, member 2provided by ZNC
Primary source: ZFIN:ZDB-GENE-030903-3
See related: Ensembl:ENSDARG00000029766 AllianceGenome:ZFIN:ZDB-GENE-030903-3
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: PXR
Summary: Enables nuclear steroid receptor activity. Acts upstream of or within regulation of DNA-templated transcription; response to toxic substance; and transcription by RNA polymerase II. Predicted to be active in nucleus. Is expressed in several structures, including adenohypophyseal placode; brain; heart; liver; and pleuroperitoneal region. Orthologous to human NR1I2 (nuclear receptor subfamily 1 group I member 2). [provided by Alliance of Genome Resources, Oct 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 9

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	9	NC_007120.7 (9502610..9567880)
105	previous assembly	GRCz10 (GCF_000002035.5)	9	NC_007120.6 (9524480..9584819)

Chromosome 9 - NC_007120.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Pxr variants differed in both their ability to bind these structurally different ligands and to regulate reporter gene expression in vitro. We infer that the observed sequence variations in zebrafish Pxrs likely affect the response to putative Pxr agonists in vivo and potentially cause strain-specific biotransformation of xenobiotics in zebrafish.
Title: Sequence Variations in pxr (nr1i2) From Zebrafish (Danio rerio) Strains Affect Nuclear Receptor Function.
Selected zebrafish CYP1, CYP2 and CYP3 genes appear to be under the regulation of both pregnane X receptor and aryl hydrocarbon receptor 2.
Title: Role of pregnane X receptor and aryl hydrocarbon receptor in transcriptional regulation of pxr, CYP2, and CYP3 genes in developing zebrafish.
CYP3A65 and PXR may be involved in the metabolization and detoxification of microcystins in zebrafish, which may be regulated by dre-miR-27b.
Title: Transcription alterations of microRNAs, cytochrome P4501A1 and 3A65, and AhR and PXR in the liver of zebrafish exposed to crude microcystins.
similar pattern of mRNA expression of PXR, cytochrome P4503A and multiple drug resistance 1 genes found in fish treated with different PXR inducers suggests that the intrinsic association between these three genes is conserved in zebrafish
Title: Expression of PXR, CYP3A and MDR1 genes in liver of zebrafish.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
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 steroid receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative 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	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within response to toxic substance	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: nuclear receptor subfamily 1 group I member 2

Names: pregnane X receptor

NCBI Reference Sequences (RefSeq)

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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)

NM_001098617.2 → NP_001092087.2 nuclear receptor subfamily 1 group I member 2

Status: VALIDATED

Source sequence(s)

CR848676

UniProtKB/TrEMBL

A0A8M2BET5, A5WYG8, B0V1H8

Related

ENSDARP00000106185.2, ENSDART00000125174.4

Conserved Domains (2) summary

cd06934
Location:141 → 425

NR_LBD_PXR_like; The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor

cd07162
Location:45 → 131

NR_DBD_PXR; DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007120.7 Reference GRCz11 Primary Assembly

Range

9502610..9567880

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021478724.2 → XP_021334399.1 nuclear receptor subfamily 1 group I member 2 isoform X1

UniProtKB/TrEMBL

A0A8M9QAV5, A5WYG8

Conserved Domains (2) summary

cd06934
Location:128 → 412

NR_LBD_PXR_like; The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor

cd07162
Location:32 → 118

NR_DBD_PXR; DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers