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

Gene ID: 19885, updated on 10-Jan-2023

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 AllianceGenome:MGI:104856
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
Summary
Enables DNA-binding transcription factor activity, RNA polymerase II-specific and transcription coactivator binding activity. Involved in several processes, including hematopoietic or lymphoid organ development; negative regulation of thymocyte apoptotic process; and regulation of gene expression. Acts upstream of or within hematopoietic or lymphoid organ development; protein phosphorylation; and regulation of gamma-delta T cell differentiation. Located in external side of plasma membrane and nucleus. Is expressed in several structures, including central nervous system; genitourinary system; hemolymphoid system; sensory organ; and thyroid gland. Used to study Sjogren's syndrome. Human ortholog(s) of this gene implicated in immunodeficiency 42. Orthologous to human RORC (RAR related orphan receptor C). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in thymus adult (RPKM 78.6), colon adult (RPKM 8.4) and 9 other tissues See more
Orthologs
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Genomic context

See Rorc in Genome Data Viewer
Location:
3; 3 F2.1
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (94280101..94305583)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (94372794..94398276)

Chromosome 3 - NC_000069.7Genomic 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)

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 IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
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 ISO
Inferred from Sequence Orthology
more info
 
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 IEA
Inferred from Electronic Annotation
more info
 
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription coactivator 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 Peyer's patch development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within T cell differentiation in thymus IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within T-helper 17 cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in T-helper 17 cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in T-helper cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in adipose tissue development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within alpha-beta T cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cellular response to sterol ISO
Inferred from Sequence Orthology
more info
 
involved_in circadian regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within lymph node development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within mucosa-associated lymphoid tissue development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of thymocyte apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
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 IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of fat cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within regulation of gamma-delta T cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of glucose metabolic process 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 
acts_upstream_of_or_within rhythmic process IEA
Inferred from Electronic Annotation
more info
 
involved_in xenobiotic metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in external side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear body ISO
Inferred from Sequence Orthology
more info
 
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-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)

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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
    ENSMUSP00000143763.2, ENSMUST00000197040.5
    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
    ENSMUSP00000029795.4, ENSMUST00000029795.10
    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 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_000069.7 Reference GRCm39 C57BL/6J

    Range
    94280101..94305583
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006501163.4XP_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_006501162.5XP_006501225.3  nuclear receptor ROR-gamma isoform X1

    Conserved Domains (2) summary
    cd06939
    Location:213451
    NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
    cl02596
    Location:4765
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers