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

    Gene ID: 19883, updated on 25-Nov-2021

    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
    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
    NEW
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    Genomic context

    See Rora in Genome Data Viewer
    Location:
    9 C; 9 37.45 cM
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    109 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)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (68501609..69226838)

    Chromosome 9 - NC_000075.7Genomic 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, 53536 Neighboring gene predicted gene, 53537 Neighboring gene predicted gene, 31262 Neighboring gene predicted gene, 46153 Neighboring gene predicted gene 15511 Neighboring gene predicted gene 7802 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 Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Spontaneous (1)  1 citation
    • Targeted (9)  1 citation
    • Chemically induced (ENU) (2) 
    • Endonuclease-mediated (1) 

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    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
    PubMed 
    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables nuclear receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables oxysterol binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables oxysterol binding ISO
    Inferred from Sequence Orthology
    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 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
     
    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
     
    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
     
    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
     
    acts_upstream_of_or_within multicellular organism development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in muscle cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of I-kappaB kinase/NF-kappaB signaling ISO
    Inferred from Sequence Orthology
    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
    PubMed 
    involved_in negative regulation of inflammatory response ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within nitric oxide biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of vascular endothelial growth factor production 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
    PubMed 
    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 
    acts_upstream_of_or_within regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within rhythmic process IEA
    Inferred from Electronic Annotation
    more info
     
    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 nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in 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)

    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.

    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
      ENSMUSP00000109254.3, ENSMUST00000113624.3
      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
      Related
      ENSMUST00000140351.8
    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
      ENSMUSP00000034766.7, ENSMUST00000034766.14
      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 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000075.7 Reference GRCm39 C57BL/6J

      Range
      68560627..69295528
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      Conserved Domains (2) summary
      cd06939
      Location:272510
      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
    2. XM_030244146.2XP_030100006.1  nuclear receptor ROR-alpha isoform X6

      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_011242682.4XP_011240984.1  nuclear receptor ROR-alpha isoform X8

    4. XM_006510880.2XP_006510943.1  nuclear receptor ROR-alpha isoform X5

      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
    5. XM_006510878.4XP_006510941.1  nuclear receptor ROR-alpha isoform X3

      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
    6. XM_036154734.1XP_036010627.1  nuclear receptor ROR-alpha isoform X4

      Conserved Domains (2) summary
      cd06939
      Location:216454
      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
    7. XM_030244147.2XP_030100007.1  nuclear receptor ROR-alpha isoform X6

      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
    8. XM_036154737.1XP_036010630.1  nuclear receptor ROR-alpha isoform X7

      Conserved Domains (2) summary
      cd06939
      Location:135373
      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
    9. XM_036154736.1XP_036010629.1  nuclear receptor ROR-alpha isoform X6

      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
    10. XM_006510877.5XP_006510940.1  nuclear receptor ROR-alpha isoform X2

      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_004935350.1 RNA Sequence

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