Nr1i3 nuclear receptor subfamily 1, group I, member 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nr1i3provided by RGD
Official Full Name: nuclear receptor subfamily 1, group I, member 3provided by RGD
Primary source: RGD:621400
See related: Ensembl:ENSRNOG00000003260 AllianceGenome:RGD:621400
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: CAR
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and nuclear receptor activity. Involved in osteoblast differentiation. Located in cytoplasm and nucleus. Biomarker of cholestasis. Orthologous to human NR1I3 (nuclear receptor subfamily 1 group I member 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Liver (RPKM 146.4), Heart (RPKM 114.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q24

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (86165327..86170362)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (83632940..83638193)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (89585072..89591278)

Chromosome 13 - NC_086031.1 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Critical evaluation of the human relevance of the mode of action for rodent liver tumor formation by activators of the constitutive androstane receptor (CAR).
Title: Critical evaluation of the human relevance of the mode of action for rodent liver tumor formation by activators of the constitutive androstane receptor (CAR).
nuclear expression virtually disappeared in the late stage of cholestatic injury, after an initial increase
Title: Pregnane X receptor and constitutive androstane receptor modulate differently CYP3A-mediated metabolism in early- and late-stage cholestasis.
Metabolism of methiocarb and carbaryl does not alter CAR activity.
Title: Metabolism of methiocarb and carbaryl by rat and human livers and plasma, and effect on their PXR, CAR and PPARα activities.
results are the first report that CaR plays an important role in Ca(2+) signaling involved in cardiac fibrosis through the phospholipase C- inositol 3,4,5 phosphate (PLC-IP3) pathway.
Title: Calcium sensing receptor promotes cardiac fibroblast proliferation and extracellular matrix secretion.
Report a CAR-responsive enhancer element locating approximately 31 kb upstream in the 5'-flanking region of rat CYP3A1 gene.
Title: A CAR-responsive enhancer element locating approximately 31 kb upstream in the 5'-flanking region of rat cytochrome P450 (CYP) 3A1 gene.
Serum 5-HT regulates the expression of Mrp2 and P-gp, and the underlying mechanism may be related to the altered expression of the nuclear receptor constitutive androstane receptor.
Title: Serum serotonin reduced the expression of hepatic transporter Mrp2 and P-gp via regulating nuclear receptor CAR in PI-IBS rats.
CAR ligands might augment the endocrine disrupting potential of AhR activators by an induction of the hepatic AhR.
Title: Enhanced thyroid hormone breakdown in hepatocytes by mutual induction of the constitutive androstane receptor (CAR, NR1I3) and arylhydrocarbon receptor by benzo[a]pyrene and phenobarbital.
Dissociation of CAR nuclear receptor from thyroid hormone receptors results in down-regulation of hepatic cytochrome P450-PB2 (CYP2B)1.
Title: Reduction of thyroid hormones triggers down-regulation of hepatic CYP2B through nuclear receptors CAR and TR in a rat model of acute stroke.
CAR nuclear receptors are activated following ethyl tertiary-butyl ether administration leading to tumorigenesis.
Title: Mode of action of ethyl tertiary-butyl ether hepatotumorigenicity in the rat: evidence for a role of oxidative stress via activation of CAR, PXR and PPAR signaling pathways.
FXR, PXR and CAR expression levels are decreased in the liver after intestinal ischemia-reperfusion; interleukin-6 is one of main causes the decreases in expressions of these receptors.
Title: The decrease in farnesoid X receptor, pregnane X receptor and constitutive androstane receptor in the liver after intestinal ischemia-reperfusion.

Submit: New GeneRIF Correction See all GeneRIFs (18)

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear receptor activity	IEA Inferred from Electronic Annotation more info
enables nuclear receptor activity	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in osteoblast differentiation	IEP Inferred from Expression Pattern more info	PubMed
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	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: nuclear receptor subfamily 1 group I member 3

Names: constitutive androstane receptor; nuclear receptor constitutive active receptor; strain Fischer nuclear receptor (CAR)

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_001270838.1 → NP_001257767.1 nuclear receptor subfamily 1 group I member 3 isoform 3

See identical proteins and their annotated locations for NP_001257767.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice junction at the 3' end of an exon that extends the exon to an in-frame stop codon compared to variant 1. The resulting isoform (3) is shorter at the C-terminus compared to isoform 1.

Source sequence(s)

BC089763, JAXUCZ010000013

UniProtKB/TrEMBL

A0A8I6AVD8, A6JFV0, Q402C1

Related

ENSRNOP00000072813.1, ENSRNOT00000079355.2

Conserved Domains (2) summary

cd07156
Location:21 → 92

NR_DBD_VDR_like; The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers

cl11397
Location:116 → 316

NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
NM_001270839.1 → NP_001257768.1 nuclear receptor subfamily 1 group I member 3 isoform 4

See identical proteins and their annotated locations for NP_001257768.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses an alternate splice site at the 5' end of an exon compared to variant 1, that causes a frameshift. The resulting isoform (4) has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

BC089763, JAXUCZ010000013

UniProtKB/TrEMBL

A0A8I6AVD8, A6JFV0, Q402C0

Related

ENSRNOP00000096651.1, ENSRNOT00000104224.1

Conserved Domains (2) summary

cd07156
Location:21 → 92

NR_DBD_VDR_like; The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers

cl11397
Location:116 → 281

NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
NM_001270840.1 → NP_001257769.1 nuclear receptor subfamily 1 group I member 3 isoform 2

See identical proteins and their annotated locations for NP_001257769.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice site at the 5' end of an exon and uses an alternate splice junction at the 3' end of an exon that extends the exon to an in-frame stop codon compared to variant 1. The resulting isoform (2) is shorter at the C-terminus and lacks a single internal aa compared to isoform 1.

Source sequence(s)

BC089763

UniProtKB/TrEMBL

A0A8I6AVD8, A6JFV0, Q5FVU7

Conserved Domains (2) summary

cd07156
Location:21 → 92

NR_DBD_VDR_like; The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers

cl11397
Location:116 → 315

NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
NM_001429503.1 → NP_001416432.1 nuclear receptor subfamily 1 group I member 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013
NM_022941.4 → NP_075230.1 nuclear receptor subfamily 1 group I member 3 isoform 1

See identical proteins and their annotated locations for NP_075230.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

BC089763, JAXUCZ010000013

UniProtKB/Swiss-Prot

Q9QUS1

UniProtKB/TrEMBL

A6JFU9

Related

ENSRNOP00000048836.3, ENSRNOT00000049873.3

Conserved Domains (2) summary

cd07156
Location:21 → 92

NR_DBD_VDR_like; The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers

cl11397
Location:116 → 356

NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators

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

NC_086031.1 Reference GRCr8

Range

86165327..86170362

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063272586.1 → XP_063128656.1 nuclear receptor subfamily 1 group I member 3 isoform X5
XM_063272587.1 → XP_063128657.1 nuclear receptor subfamily 1 group I member 3 isoform X6
XM_063272588.1 → XP_063128658.1 nuclear receptor subfamily 1 group I member 3 isoform X8
XM_063272589.1 → XP_063128659.1 nuclear receptor subfamily 1 group I member 3 isoform X9
XM_063272583.1 → XP_063128653.1 nuclear receptor subfamily 1 group I member 3 isoform X1
XM_063272591.1 → XP_063128661.1 nuclear receptor subfamily 1 group I member 3 isoform X10
XM_063272584.1 → XP_063128654.1 nuclear receptor subfamily 1 group I member 3 isoform X2
XM_063272585.1 → XP_063128655.1 nuclear receptor subfamily 1 group I member 3 isoform X3
XM_039091080.2 → XP_038947008.1 nuclear receptor subfamily 1 group I member 3 isoform X4

UniProtKB/TrEMBL

A0A8I6A462

Conserved Domains (2) summary

cd07156
Location:21 → 92

NR_DBD_VDR_like; The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers

cl11397
Location:116 → 385

NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
XM_039091081.2 → XP_038947009.1 nuclear receptor subfamily 1 group I member 3 isoform X7

Conserved Domains (2) summary

cd07156
Location:21 → 92

NR_DBD_VDR_like; The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers

cl11397
Location:116 → 355

NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators