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    RORA RAR related orphan receptor A [ Homo sapiens (human) ]

    Gene ID: 6095, updated on 28-Oct-2024

    Summary

    Official Symbol
    RORAprovided by HGNC
    Official Full Name
    RAR related orphan receptor Aprovided by HGNC
    Primary source
    HGNC:HGNC:10258
    See related
    Ensembl:ENSG00000069667 MIM:600825; AllianceGenome:HGNC:10258
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ROR1; ROR2; ROR3; RZRA; NR1F1; RORa1; IDDECA; RORalpha; RZR-ALPHA
    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. Four transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2014]
    Expression
    Broad expression in skin (RPKM 15.9), adrenal (RPKM 10.1) and 21 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RORA in Genome Data Viewer
    Location:
    15q22.2
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (60488284..61229302, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (58291519..59032551, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (60780483..61521501, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:60699237-60700436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9508 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:60770615-60771142 Neighboring gene ribosomal protein S10 pseudogene 22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6497 Neighboring gene RORA antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr15:60848032-60848533 Neighboring gene interactor of little elongation complex ELL subunit 2 Neighboring gene Sharpr-MPRA regulatory region 281 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:60868357-60868906 Neighboring gene NANOG hESC enhancer GRCh37_chr15:60872753-60873579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9510 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:60912500-60913000 Neighboring gene uncharacterized LOC105370846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:60927049-60927862 Neighboring gene CYCS pseudogene 38 Neighboring gene NANOG hESC enhancer GRCh37_chr15:60942340-60942841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9513 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9516 Neighboring gene Sharpr-MPRA regulatory region 10122 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:61043731-61043925 Neighboring gene RORA antisense RNA 2 Neighboring gene uncharacterized LOC105370844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:61080390-61080890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:61080891-61081391 Neighboring gene RNA, 5S ribosomal pseudogene 397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9517 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:61096911-61097892 Neighboring gene uncharacterized LOC124903500 Neighboring gene uncharacterized LOC102724802 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:61150768-61151321 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:61151721-61152920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9518 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:61199430-61199931 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:61200438-61201637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9519 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:61224144-61225343 Neighboring gene Sharpr-MPRA regulatory region 7352 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:61239167-61239924 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:61265032-61266231 Neighboring gene uncharacterized LOC107984805 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:61438991-61439492 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:61465732-61466232 Neighboring gene uncharacterized LOC105370841 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:61656438-61657212 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:61657213-61657987 Neighboring gene uncharacterized LOC105370847 Neighboring gene MPRA-validated peak2363 silencer Neighboring gene uncharacterized LOC107984782 Neighboring gene NANOG hESC enhancer GRCh37_chr15:61829371-61829872 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:61848165-61849364 Neighboring gene uncharacterized LOC101928850

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Intellectual developmental disorder with or without epilepsy or cerebellar ataxia
    MedGen: C4748041 OMIM: 618060 GeneReviews: Not available
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    EBI GWAS Catalog

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    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
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    Genome-wide association scan of trait depression.
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    Loci affecting gamma-glutamyl transferase in adults and adolescents show age × SNP interaction and cardiometabolic disease associations.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog
    Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC119326, MGC119329, DKFZp686M2414

    Gene Ontology Provided by GOA

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

    General protein information

    Preferred Names
    nuclear receptor ROR-alpha
    Names
    RAR-related orphan nuclear receptor alpha
    ROR-alpha
    nuclear receptor RZR-alpha
    nuclear receptor subfamily 1 group F member 1
    retinoic acid receptor-related orphan receptor alpha
    retinoid-related orphan receptor alpha
    transcription factor RZR-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.

    Genomic

    1. NG_029246.2 RefSeqGene

      Range
      5000..746018
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_002943.4NP_002934.1  nuclear receptor ROR-alpha isoform c

      See identical proteins and their annotated locations for NP_002934.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3), also called RORalpha3, contains a different 5' sequence as compared to variant 1. As a result, variant 3 encodes isoform c, whose 91 N-terminal aa differ from the 66 N-terminal aa of isoform a encoded by variant 1.
      Source sequence(s)
      AC009560, AC087385, KC877553
      Consensus CDS
      CCDS10178.1
      UniProtKB/TrEMBL
      A0A0C4DFP5, B6ZGS4
      Related
      ENSP00000309753.3, ENST00000309157.8
      Conserved Domains (2) summary
      cd06939
      Location:297536
      NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
      cd06968
      Location:91185
      NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
    2. NM_134260.3NP_599022.1  nuclear receptor ROR-alpha isoform b

      See identical proteins and their annotated locations for NP_599022.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), also called RORalpha2, contains a different 5' sequence as compared to variant 1. As a result, variant 2 encodes isoform b, whose 99 N-terminal aa differ from the 66 N-terminal aa of isoform a encoded by variant 1.
      Source sequence(s)
      AC009560, AC087385, AC107241, KC877553, KC877565
      Consensus CDS
      CCDS10179.1
      UniProtKB/TrEMBL
      B6ZGS4
      Related
      ENSP00000261523.5, ENST00000261523.9
      Conserved Domains (2) summary
      cd06939
      Location:305544
      NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
      cd06968
      Location:99193
      NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
    3. NM_134261.3NP_599023.1  nuclear receptor ROR-alpha isoform a

      See identical proteins and their annotated locations for NP_599023.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1), also called RORalpha1, utilizes a different 5' exon than the other variants and encodes isoform a.
      Source sequence(s)
      AC009560, AC087385, AC107905, KC877553
      Consensus CDS
      CCDS10177.1
      UniProtKB/Swiss-Prot
      P35397, P35398, P35399, P45445, Q495X4, Q96H83
      UniProtKB/TrEMBL
      B6ZGS4
      Related
      ENSP00000335087.6, ENST00000335670.11
      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
    4. NM_134262.3NP_599024.1  nuclear receptor ROR-alpha isoform d

      See identical proteins and their annotated locations for NP_599024.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4), also called RZR-alpha, contains a different 5' sequence as compared to variant 1. As a result, variant 4 encodes isoform d, whose 11 N-terminal aa differ from the 66 N-terminal aa of isoform a encoded by variant 1.
      Source sequence(s)
      AC087385, AC107241, KC877553
      Consensus CDS
      CCDS45271.1
      UniProtKB/TrEMBL
      A0A0C4DG53, B6ZGS4
      Related
      ENSP00000402971.2, ENST00000449337.6
      Conserved Domains (2) summary
      cd06939
      Location:217456
      NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
      cd06968
      Location:11105
      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_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      60488284..61229302 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047432928.1XP_047288884.1  nuclear receptor ROR-alpha isoform X4

    2. XM_011521875.3XP_011520177.1  nuclear receptor ROR-alpha isoform X2

      UniProtKB/TrEMBL
      B6ZGS4
      Conserved Domains (2) summary
      cd06939
      Location:253492
      NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
      cd06968
      Location:47141
      NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
    3. XM_011521877.4XP_011520179.1  nuclear receptor ROR-alpha isoform X3

      UniProtKB/TrEMBL
      B6ZGS4
      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
    4. XM_011521874.2XP_011520176.1  nuclear receptor ROR-alpha isoform X1

      UniProtKB/TrEMBL
      B6ZGS4
      Conserved Domains (2) summary
      cd06939
      Location:274513
      NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
      cd06968
      Location:68162
      NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
    5. XM_047432930.1XP_047288886.1  nuclear receptor ROR-alpha isoform X4

    6. XM_047432929.1XP_047288885.1  nuclear receptor ROR-alpha isoform X4

    7. XM_011521879.4XP_011520181.1  nuclear receptor ROR-alpha isoform X5

      Conserved Domains (1) summary
      cd06939
      Location:125364
      NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      58291519..59032551 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378582.1XP_054234557.1  nuclear receptor ROR-alpha isoform X4

    2. XM_054378580.1XP_054234555.1  nuclear receptor ROR-alpha isoform X2

    3. XM_054378581.1XP_054234556.1  nuclear receptor ROR-alpha isoform X3

    4. XM_054378579.1XP_054234554.1  nuclear receptor ROR-alpha isoform X1

    5. XM_054378584.1XP_054234559.1  nuclear receptor ROR-alpha isoform X4

    6. XM_054378583.1XP_054234558.1  nuclear receptor ROR-alpha isoform X4

    7. XM_054378585.1XP_054234560.1  nuclear receptor ROR-alpha isoform X5