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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
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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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