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

Gene ID: 19883, updated on 2-Sep-2018

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 Vega:OTTMUSG00000023055
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

Genomic context

See Rora in Genome Data Viewer
Location:
9 C; 9 37.45 cM
Exon count:
19
Annotation release Status Assembly Chr Location
106 current GRCm38.p4 (GCF_000001635.24) 9 NC_000075.6 (68653407..69388246)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (68501609..69226838)

Chromosome 9 - NC_000075.6Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 4930502A04 gene Neighboring gene predicted gene, 31141 Neighboring gene predicted gene, 31325 Neighboring gene RIKEN cDNA 9530091C08 gene Neighboring gene predicted gene, 31262 Neighboring gene predicted gene, 46153 Neighboring gene predicted gene 15511 Neighboring gene dynein light chain 1, cytoplasmic-like Neighboring gene interactor of little elongation complex ELL subunit 2

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Variation

Alleles

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

Pathways from BioSystems

  • Adipogenesis genes, organism-specific biosystem (from WikiPathways)
    Adipogenesis genes, organism-specific biosystemThe different classes of factors involved in adipogenesis are shown. Adipogenesis is the process by which fat cells differentiate from predadipocytes to adipocytes (fat cells). Adipose tissue, compos...
  • BMAL1:CLOCK,NPAS2 activates circadian gene expression, organism-specific biosystem (from REACTOME)
    BMAL1:CLOCK,NPAS2 activates circadian gene expression, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Bmal1:Clock,Npas2 activates circadian gene expression, organism-specific biosystem (from REACTOME)
    Bmal1:Clock,Npas2 activates circadian gene expression, organism-specific biosystemBmal1:Clock (Arntl:Clock) and Bmal1:Npas2 (Arntl:Npas2) heterodimers bind to sequence elements (E boxes) in the promoters of target genes and enhance transcription (Gekakis et al. 1998, reviewed in M...
  • Circadian Clock, organism-specific biosystem (from REACTOME)
    Circadian Clock, organism-specific biosystemAt the center of the mouse circadian clock is a negative transcription/translation-based feedback loop: The Bmal1:Clock/Npas2 (Arntl:Clock/Npas2) heterodimer transactivates Cryptochrome (Cry) and Per...
  • Circadian Clock, organism-specific biosystem (from REACTOME)
    Circadian Clock, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Circadian rhythm, organism-specific biosystem (from KEGG)
    Circadian rhythm, organism-specific biosystemCircadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of ...
  • Circadian rhythm, conserved biosystem (from KEGG)
    Circadian rhythm, conserved biosystemCircadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of ...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Inflammatory bowel disease (IBD), organism-specific biosystem (from KEGG)
    Inflammatory bowel disease (IBD), organism-specific biosystemInflammatory bowel disease (IBD), which includes Crohn disease (CD) and ulcerative colitis (UC), is characterized by chronic inflammation of the gastrointestinal tract due to environmental and geneti...
  • Inflammatory bowel disease (IBD), conserved biosystem (from KEGG)
    Inflammatory bowel disease (IBD), conserved biosystemInflammatory bowel disease (IBD), which includes Crohn disease (CD) and ulcerative colitis (UC), is characterized by chronic inflammation of the gastrointestinal tract due to environmental and geneti...
  • Mus musculus biological processes, organism-specific biosystem (from REACTOME)
    Mus musculus biological processes, organism-specific biosystemCertain mouse pathways have been fully manually curated in Reactome in order to support the manual inference of well-conserved but less well-studied human pathways. These pathways include Circadian...
  • Nuclear Receptor transcription pathway, organism-specific biosystem (from REACTOME)
    Nuclear Receptor transcription pathway, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Nuclear Receptors, organism-specific biosystem (from WikiPathways)
    Nuclear Receptors, organism-specific biosystemNuclear receptors are a class of proteins found within the interior of cells that are responsible for sensing the presence of steroid and thyroid hormones and certain other molecules. In response, th...
  • RORA activates gene expression, organism-specific biosystem (from REACTOME)
    RORA activates gene expression, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Rora activates gene expression, organism-specific biosystem (from REACTOME)
    Rora activates gene expression, organism-specific biosystemRora binds ROR elements (ROREs) in DNA and recruits the coactivators Ppargc1a (Pgc-1alpha) and p300 (Ep300, a histone acetylase) to activate transcription.
  • SIDS Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
    SIDS Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...
  • Th17 cell differentiation, organism-specific biosystem (from KEGG)
    Th17 cell differentiation, organism-specific biosystemInterleukin (IL)-17-producing helper T (Th17) cells serve as a subset of CD4+ T cells involved in epithelial cell- and neutrophil mediated immune responses against extracellular microbes and in the p...
  • Th17 cell differentiation, conserved biosystem (from KEGG)
    Th17 cell differentiation, conserved biosystemInterleukin (IL)-17-producing helper T (Th17) cells serve as a subset of CD4+ T cells involved in epithelial cell- and neutrophil mediated immune responses against extracellular microbes and in the p...
  • White fat cell differentiation, organism-specific biosystem (from WikiPathways)
    White fat cell differentiation, organism-specific biosystemThe transcription factors involved in white fat cell differentiation are shown, specifically their pattern of activity from the preadipocyte to the adipocyte (fat cells) stage. Adipose tissue, compos...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA binding ISO
Inferred from Sequence Orthology
more info
 
DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
PubMed 
beta-catenin binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
nuclear receptor activity IEA
Inferred from Electronic Annotation
more info
 
oxysterol binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
oxysterol binding ISO
Inferred from Sequence Orthology
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
steroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
 
transcription coactivator binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription coactivator binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription coactivator binding ISO
Inferred from Sequence Orthology
more info
 
transcription corepressor binding ISO
Inferred from Sequence Orthology
more info
 
transcription factor activity, direct ligand regulated sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
T-helper 17 cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
angiogenesis ISO
Inferred from Sequence Orthology
more info
 
cGMP metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to hypoxia ISO
Inferred from Sequence Orthology
more info
 
cellular response to interleukin-1 IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to sterol ISO
Inferred from Sequence Orthology
more info
 
cellular response to tumor necrosis factor IDA
Inferred from Direct Assay
more info
PubMed 
cerebellar Purkinje cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cerebellar granule cell precursor proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cholesterol homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
circadian regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
intracellular receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
muscle cell differentiation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of I-kappaB kinase/NF-kappaB signaling ISO
Inferred from Sequence Orthology
more info
 
negative regulation of fat cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of inflammatory response ISO
Inferred from Sequence Orthology
more info
 
nitric oxide biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of circadian rhythm IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
positive regulation of vascular endothelial growth factor production ISO
Inferred from Sequence Orthology
more info
 
regulation of circadian rhythm IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of glucose metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of macrophage activation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of smoothened signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of steroid metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription involved in cell fate commitment IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription involved in cell fate commitment IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
triglyceride homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
triglyceride homeostasis ISO
Inferred from Sequence Orthology
more info
 
xenobiotic metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

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)

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)

  1. NM_001289916.1NP_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)
    AK155827, CT009708, Y08640
    Consensus CDS
    CCDS72268.1
    UniProtKB/Swiss-Prot
    P51448
    UniProtKB/TrEMBL
    Q3U1P4
    Related
    ENSMUSP00000109254.2, OTTMUSP00000026560, ENSMUST00000113624.2, OTTMUST00000055461
    Conserved Domains (2) summary
    cd06939
    Location:216455
    NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
    cd06968
    Location:10104
    NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
  2. NM_001289917.1NP_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, AK086033
    UniProtKB/TrEMBL
    Q8C3F5
  3. NM_013646.2NP_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)
    AK086033, CT009708, U53228
    Consensus CDS
    CCDS23314.1
    UniProtKB/Swiss-Prot
    P51448
    UniProtKB/TrEMBL
    Q8C3F5
    Related
    ENSMUSP00000034766.6, OTTMUSP00000026559, ENSMUST00000034766.13, OTTMUST00000055460
    Conserved Domains (2) summary
    cd06939
    Location:272511
    NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
    cd06968
    Location:66160
    NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

Reference GRCm38.p4 C57BL/6J

Genomic

  1. NC_000075.6 Reference GRCm38.p4 C57BL/6J

    Range
    68653407..69388246
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011242682.2XP_011240984.1  nuclear receptor ROR-alpha isoform X5

  2. XM_017313219.1XP_017168708.1  nuclear receptor ROR-alpha isoform X4

    Conserved Domains (2) summary
    cd06939
    Location:135374
    NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
    cl02596
    Location:123
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  3. XM_006510880.1XP_006510943.1  nuclear receptor ROR-alpha isoform X3

    Conserved Domains (2) summary
    cd06939
    Location:208447
    NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
    cd06968
    Location:296
    NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
  4. XM_006510878.2XP_006510941.1  nuclear receptor ROR-alpha isoform X2

    Conserved Domains (2) summary
    cd06939
    Location:224463
    NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
    cd06968
    Location:18112
    NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
  5. XM_006510877.3XP_006510940.1  nuclear receptor ROR-alpha isoform X1

    Conserved Domains (2) summary
    cd06939
    Location:269508
    NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
    cd06968
    Location:63157
    NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers

RNA

  1. XR_001778824.1 RNA Sequence

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