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Rorc RAR-related orphan receptor gamma [ Mus musculus (house mouse) ]

Gene ID: 19885, updated on 11-Nov-2019

Summary

Official Symbol
Rorcprovided by MGI
Official Full Name
RAR-related orphan receptor gammaprovided by MGI
Primary source
MGI:MGI:104856
See related
Ensembl:ENSMUSG00000028150
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
TOR; Thor; Nr1f3; RORgamma
Expression
Biased expression in thymus adult (RPKM 78.6), colon adult (RPKM 8.4) and 9 other tissues See more
Orthologs

Genomic context

See Rorc in Genome Data Viewer
Location:
3; 3 F2.1
Exon count:
13
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (94372794..94398276)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (94176748..94202161)

Chromosome 3 - NC_000069.6Genomic Context describing neighboring genes Neighboring gene C2 calcium-dependent domain containing 4D Neighboring gene predicted gene, 38411 Neighboring gene leucine rich repeat and Ig domain containing 4 Neighboring gene RIKEN cDNA 1700040D17 gene

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)
  • Targeted (5)  1 citation
  • Chemically induced (ENU) (3) 
  • Endonuclease-mediated (1) 

Pathways from BioSystems

  • 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...
  • 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...
  • 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...

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 transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
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 
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 factor activity, direct ligand regulated sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
Peyer's patch development IMP
Inferred from Mutant Phenotype
more info
PubMed 
T cell differentiation in thymus IMP
Inferred from Mutant Phenotype
more info
PubMed 
T-helper 17 cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
T-helper 17 cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
T-helper cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
adipose tissue development IMP
Inferred from Mutant Phenotype
more info
PubMed 
alpha-beta T cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to sterol ISO
Inferred from Sequence Orthology
more info
 
circadian regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
interleukin-17 production IDA
Inferred from Direct Assay
more info
PubMed 
interleukin-17 secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
lymph node development IMP
Inferred from Mutant Phenotype
more info
PubMed 
mucosal-associated lymphoid tissue development IMP
Inferred from Mutant Phenotype
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of thymocyte apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
positive regulation of circadian rhythm IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of fat cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of gamma-delta T cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of glucose metabolic process 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, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
xenobiotic metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
external side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
nuclear body ISO
Inferred from Sequence Orthology
more info
 
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-gamma
Names
RAR-related orphan receptor C
nuclear receptor RZR-gamma
nuclear receptor subfamily 1 group F member 3
retinoid-related orphan receptor-gamma
thymus orphan receptor

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_001293734.1NP_001280663.1  nuclear receptor ROR-gamma isoform 2

    See identical proteins and their annotated locations for NP_001280663.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has a different 5' structure, lacks a portion of the 5' coding region, and initiates translation from an alternate start codon compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC164562, AF163668
    Consensus CDS
    CCDS79971.1
    UniProtKB/Swiss-Prot
    P51450
    UniProtKB/TrEMBL
    A0A0G2JGZ6
    Related
    ENSMUSP00000143763.1, ENSMUST00000197040.4
    Conserved Domains (2) summary
    cd06939
    Location:245483
    NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
    cd06968
    Location:497
    NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
  2. NM_011281.3NP_035411.2  nuclear receptor ROR-gamma isoform 1

    See identical proteins and their annotated locations for NP_035411.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the shortest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC164562
    Consensus CDS
    CCDS17591.1
    UniProtKB/Swiss-Prot
    P51450
    UniProtKB/TrEMBL
    A0A0R4J096
    Related
    ENSMUSP00000029795.3, ENSMUST00000029795.9
    Conserved Domains (2) summary
    cd06939
    Location:266504
    NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
    cd06968
    Location:24118
    NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers

RNA

  1. NR_121656.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has a different 5' structure and uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC164562, AK137866

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 108 details...Open this link in a new tab

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

Reference GRCm38.p6 C57BL/6J

Genomic

  1. NC_000069.6 Reference GRCm38.p6 C57BL/6J

    Range
    94372794..94398276
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006501163.3XP_006501226.1  nuclear receptor ROR-gamma isoform X2

    Conserved Domains (2) summary
    cd06968
    Location:24118
    NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
    cl11397
    Location:266311
    NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
  2. XM_006501164.4XP_006501227.1  nuclear receptor ROR-gamma isoform X3

    Conserved Domains (2) summary
    cd06968
    Location:24118
    NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
    cl11397
    Location:266311
    NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
  3. XM_006501162.4XP_006501225.3  nuclear receptor ROR-gamma isoform X1

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