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

    Gene ID: 19883, updated on 14-Jan-2025

    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
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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
    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_000075.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 4930502A04 gene Neighboring gene STARR-seq mESC enhancer starr_24506 Neighboring gene STARR-seq mESC enhancer starr_24507 Neighboring gene predicted gene, 31141 Neighboring gene STARR-seq mESC enhancer starr_24509 Neighboring gene predicted gene, 31325 Neighboring gene RIKEN cDNA 9530091C08 gene Neighboring gene STARR-seq mESC enhancer starr_24512 Neighboring gene predicted gene, 53536 Neighboring gene STARR-seq mESC enhancer starr_24514 Neighboring gene predicted gene, 53537 Neighboring gene STARR-seq mESC enhancer starr_24515 Neighboring gene predicted gene, 31262 Neighboring gene STARR-seq mESC enhancer starr_24516 Neighboring gene STARR-seq mESC enhancer starr_24517 Neighboring gene predicted gene, 46153 Neighboring gene predicted gene 15511 Neighboring gene STARR-seq mESC enhancer starr_24519 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)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Gene Ontology Provided by MGI

    Items 1 - 25 of 27
    Function Evidence Code Pubs
    enables DNA binding PubMed 
    enables DNA binding  
    enables DNA-binding transcription factor activity PubMed 
    enables DNA-binding transcription factor activity  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding PubMed 
    enables beta-catenin binding PubMed 
    enables ligand-activated transcription factor activity  
    enables ligand-activated transcription factor activity  
    enables nuclear receptor activity  
    enables nuclear receptor activity  
    enables oxysterol binding  
    enables oxysterol binding  
    enables oxysterol binding  
    enables protein binding PubMed 
    enables sequence-specific DNA binding PubMed 
    enables sequence-specific DNA binding  
    enables sequence-specific DNA binding PubMed 
    enables transcription coactivator binding PubMed 
    enables transcription coactivator binding  
    enables transcription coregulator binding  
    enables transcription corepressor binding  
    enables transcription corepressor binding  
    enables zinc ion binding  
    Items 1 - 25 of 27
    Items 1 - 25 of 47
    Process Evidence Code Pubs
    involved_in T-helper 17 cell differentiation PubMed 
    involved_in angiogenesis  
    involved_in angiogenesis  
    acts_upstream_of_or_within cGMP metabolic process PubMed 
    involved_in cellular response to hypoxia  
    involved_in cellular response to hypoxia  
    acts_upstream_of_or_within cellular response to interleukin-1 PubMed 
    involved_in cellular response to sterol  
    involved_in cellular response to sterol  
    acts_upstream_of_or_within cellular response to tumor necrosis factor PubMed 
    acts_upstream_of_or_within cerebellar Purkinje cell differentiation PubMed 
    involved_in cerebellar granule cell precursor proliferation PubMed 
    involved_in cholesterol homeostasis PubMed 
    involved_in circadian regulation of gene expression PubMed 
    involved_in intracellular receptor signaling pathway  
    involved_in intracellular receptor signaling pathway  
    involved_in muscle cell differentiation  
    involved_in muscle cell differentiation  
    involved_in negative regulation of canonical NF-kappaB signal transduction  
    involved_in negative regulation of canonical NF-kappaB signal transduction  
    involved_in negative regulation of fat cell differentiation PubMed 
    involved_in negative regulation of inflammatory response  
    involved_in negative regulation of inflammatory response  
    involved_in negative regulation of inflammatory response  
    acts_upstream_of_or_within nitric oxide biosynthetic process PubMed 
    involved_in positive regulation of DNA-templated transcription PubMed 
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of circadian rhythm PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of vascular endothelial growth factor production  
    involved_in positive regulation of vascular endothelial growth factor production  
    acts_upstream_of_or_within regulation of DNA-templated transcription PubMed 
    involved_in regulation of DNA-templated transcription PubMed 
    involved_in regulation of DNA-templated transcription  
    involved_in regulation of circadian rhythm PubMed 
    involved_in regulation of glucose metabolic process PubMed 
    acts_upstream_of_or_within regulation of macrophage activation PubMed 
    involved_in regulation of smoothened signaling pathway PubMed 
    involved_in regulation of steroid metabolic process PubMed 
    involved_in regulation of transcription by RNA polymerase II  
    involved_in regulation of transcription by RNA polymerase II PubMed 
    involved_in regulation of transcription by RNA polymerase II PubMed 
    involved_in triglyceride homeostasis PubMed 
    involved_in triglyceride homeostasis  
    involved_in xenobiotic metabolic process PubMed 
    Items 1 - 25 of 47
    Component Evidence Code Pubs
    located_in nucleolus  
    located_in nucleolus  
    located_in nucleoplasm  
    is_active_in nucleus  
    located_in nucleus PubMed 
    located_in nucleus  

    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_001289916.2NP_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: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_001289917.2NP_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
    3. NM_013646.3NP_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: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: 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

    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

      UniProtKB/TrEMBL
      Q8BRL5
      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

      UniProtKB/TrEMBL
      Q8BRL5
      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

      UniProtKB/TrEMBL
      Q8BRL5
      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

      UniProtKB/TrEMBL
      Q8BRL5
      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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