Rora RAR-related orphan receptor alpha [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Roraprovided by MGI
Official Full Name: RAR-related orphan receptor alphaprovided by MGI
Primary source: MGI:MGI:104661
See related: Ensembl:ENSMUSG00000032238 AllianceGenome:MGI:104661
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: sg; ROR1; ROR2; ROR3; Nr1f1; nmf267; tmgc26; staggerer; 9530021D13Rik
Summary: The protein encoded by this gene is a member of the NR1 subfamily of nuclear hormone receptors. It can bind as a monomer or as a homodimer to hormone response elements upstream of several genes to enhance the expression of those genes. The encoded protein has been shown to interact with NM23-2, a nucleoside diphosphate kinase involved in organogenesis and differentiation, as well as with NM23-1, the product of a tumor metastasis suppressor candidate gene. Also, it has been shown to aid in the transcriptional regulation of some genes involved in circadian rhythm. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2014]
Expression: Broad expression in cerebellum adult (RPKM 8.5), cortex adult (RPKM 3.0) and 19 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9 C; 9 37.45 cM

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (68560627..69295528)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (68653404..69388246)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Epidermal RORalpha Maintains Barrier Integrity and Prevents Allergic Inflammation by Regulating Late Differentiation and Lipid Metabolism.
Title: Epidermal RORα Maintains Barrier Integrity and Prevents Allergic Inflammation by Regulating Late Differentiation and Lipid Metabolism.
RORalpha-GABP-TFAM axis alleviates myosteatosis with fatty atrophy through reinforcement of mitochondrial capacity.
Title: RORα-GABP-TFAM axis alleviates myosteatosis with fatty atrophy through reinforcement of mitochondrial capacity.
RORalpha is required for expansion and memory maintenance of ILC1s via a lymph node-liver axis.
Title: RORα is required for expansion and memory maintenance of ILC1s via a lymph node-liver axis.
Mechanism of lncRNA HOTAIR in attenuating cardiomyocyte pyroptosis in mice with heart failure via the miR-17-5p/RORA axis.
Title: Mechanism of lncRNA HOTAIR in attenuating cardiomyocyte pyroptosis in mice with heart failure via the miR-17-5p/RORA axis.
RORalpha overexpression reduced interleukin-33 expression and prevented mast cell degranulation and inflammation by inducing autophagy in allergic rhinitis.
Title: RORα overexpression reduced interleukin-33 expression and prevented mast cell degranulation and inflammation by inducing autophagy in allergic rhinitis.
MicroRNA-155 suppressed cholesterol-induced matrix degradation, pyroptosis and apoptosis by targeting RORalpha in nucleus pulposus cells.
Title: MicroRNA-155 suppressed cholesterol-induced matrix degradation, pyroptosis and apoptosis by targeting RORα in nucleus pulposus cells.
Maternal diabetes-mediated RORA suppression contributes to gastrointestinal symptoms in autism-like mouse offspring.
Title: Maternal diabetes-mediated RORA suppression contributes to gastrointestinal symptoms in autism-like mouse offspring.
RORalpha is critical for mTORC1 activity in T cell-mediated colitis.
Title: RORα is critical for mTORC1 activity in T cell-mediated colitis.
The nuclear receptor RORalpha preserves cardiomyocyte mitochondrial function by regulating caveolin-3-mediated mitophagy.
Title: The nuclear receptor RORα preserves cardiomyocyte mitochondrial function by regulating caveolin-3-mediated mitophagy.
RORalpha contributes to the maintenance of genome ploidy in the liver of mice with diet-induced nonalcoholic steatohepatitis.
Title: RORα contributes to the maintenance of genome ploidy in the liver of mice with diet-induced nonalcoholic steatohepatitis.

Submit: New GeneRIF Correction See all GeneRIFs (107)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (2)
Endonuclease-mediated (8) 1 citation
Spontaneous (1) 1 citation
Targeted (11) 1 citation
Transgenic (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D9Mit289 (e-PCR), detects polymorphism
- UniSTS:131858

D9Dcr8 (e-PCR), detects polymorphism
- UniSTS:498962

MTH864 (e-PCR)
- UniSTS:125497

Rora (e-PCR), detects polymorphism
- UniSTS:507195

G64932 (e-PCR)
- UniSTS:164933

D9Mit158 (e-PCR), detects polymorphism
- UniSTS:131713

D9Mit165 (e-PCR), detects polymorphism
- UniSTS:131721

NoName (e-PCR)
- UniSTS:236179

AW743275 (e-PCR)
- UniSTS:208839

D45910 (e-PCR)
- UniSTS:179925

Rora (e-PCR), detects polymorphism
- UniSTS:144355

D9Mit260 (e-PCR), detects polymorphism
- UniSTS:131830

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology 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 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info	PubMed
enables beta-catenin binding	IPI Inferred from Physical Interaction more info	PubMed
enables ligand-activated transcription factor activity	ISO Inferred from Sequence Orthology more info
enables ligand-activated transcription factor activity	ISS Inferred from Sequence or Structural Similarity 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 oxysterol binding	IBA Inferred from Biological aspect of Ancestor more info
enables oxysterol binding	ISO Inferred from Sequence Orthology more info
enables oxysterol binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables transcription coactivator binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator binding	ISO Inferred from Sequence Orthology more info
enables transcription coregulator binding	ISO Inferred from Sequence Orthology more info
enables transcription corepressor binding	IEA Inferred from Electronic Annotation more info
enables transcription corepressor 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 T-helper 17 cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in angiogenesis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within cGMP metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to hypoxia	ISO Inferred from Sequence Orthology more info
involved_in cellular response to hypoxia	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within cellular response to interleukin-1	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to sterol	ISO Inferred from Sequence Orthology more info
involved_in cellular response to sterol	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within cellular response to tumor necrosis factor	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cerebellar Purkinje cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cerebellar granule cell precursor proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cholesterol homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in circadian regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in intracellular receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in intracellular receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in muscle cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in muscle cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of fat cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within nitric oxide biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of circadian rhythm	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info	PubMed
involved_in positive regulation of vascular endothelial growth factor production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of vascular endothelial growth factor production	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of glucose metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of macrophage activation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of smoothened signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of steroid metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in triglyceride homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in triglyceride homeostasis	ISO Inferred from Sequence Orthology more info
involved_in xenobiotic metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: nuclear receptor ROR-alpha

Names: RAR-related orphan receptor A; nuclear receptor RZR-alpha; nuclear receptor subfamily 1 group F member 1; retinoid-related orphan receptor-alpha

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_001289916.2 → NP_001276845.1 nuclear receptor ROR-alpha isoform 2

See identical proteins and their annotated locations for NP_001276845.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) has an alternate exon in place of the first two exons compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

CT009708, CT030683

Consensus CDS

CCDS72268.1

UniProtKB/TrEMBL

Q3U1P4

Related

ENSMUSP00000109254.3, ENSMUST00000113624.3

Conserved Domains (2) summary

cd06939
Location:216 → 455

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cd06968
Location:10 → 104

NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
NM_001289917.2 → NP_001276846.1 nuclear receptor ROR-alpha isoform 3

See identical proteins and their annotated locations for NP_001276846.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence and shares only the first exon compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AC155931

UniProtKB/TrEMBL

Q8C3F5

Related

ENSMUST00000140351.8
NM_013646.3 → NP_038674.1 nuclear receptor ROR-alpha isoform 1

See identical proteins and their annotated locations for NP_038674.1

Status: VALIDATED

Description

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

Source sequence(s)

AC155931, AC160977, CT009708

Consensus CDS

CCDS23314.1

UniProtKB/Swiss-Prot

P51448, P70283, P97741, P97773, Q923G1

Related

ENSMUSP00000034766.7, ENSMUST00000034766.14

Conserved Domains (2) summary

cd06939
Location:272 → 511

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cd06968
Location:66 → 160

NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000075.7 Reference GRCm39 C57BL/6J

Range

68560627..69295528

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036154733.1 → XP_036010626.1 nuclear receptor ROR-alpha isoform X1

Conserved Domains (2) summary

cd06939
Location:272 → 510

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cd06968
Location:66 → 160

NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
XM_030244146.2 → XP_030100006.1 nuclear receptor ROR-alpha isoform X6

UniProtKB/TrEMBL

Q8BRL5

Conserved Domains (2) summary

cd06939
Location:135 → 374

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cl02596
Location:1 → 23

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
XM_011242682.4 → XP_011240984.1 nuclear receptor ROR-alpha isoform X8
XM_006510880.2 → XP_006510943.1 nuclear receptor ROR-alpha isoform X5

Conserved Domains (2) summary

cd06939
Location:208 → 447

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cd06968
Location:2 → 96

NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
XM_006510878.4 → XP_006510941.1 nuclear receptor ROR-alpha isoform X3

Conserved Domains (2) summary

cd06939
Location:224 → 463

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cd06968
Location:18 → 112

NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
XM_036154734.1 → XP_036010627.1 nuclear receptor ROR-alpha isoform X4

Conserved Domains (2) summary

cd06939
Location:216 → 454

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cd06968
Location:10 → 104

NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
XM_030244147.2 → XP_030100007.1 nuclear receptor ROR-alpha isoform X6

UniProtKB/TrEMBL

Q8BRL5

Conserved Domains (2) summary

cd06939
Location:135 → 374

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cl02596
Location:1 → 23

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
XM_036154737.1 → XP_036010630.1 nuclear receptor ROR-alpha isoform X7

UniProtKB/TrEMBL

Q8BRL5

Conserved Domains (2) summary

cd06939
Location:135 → 373

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cl02596
Location:1 → 23

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
XM_036154736.1 → XP_036010629.1 nuclear receptor ROR-alpha isoform X6

UniProtKB/TrEMBL

Q8BRL5

Conserved Domains (2) summary

cd06939
Location:135 → 374

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cl02596
Location:1 → 23

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
XM_006510877.5 → XP_006510940.1 nuclear receptor ROR-alpha isoform X2

Conserved Domains (2) summary

cd06939
Location:269 → 508

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cd06968
Location:63 → 157

NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers