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

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 several processes, including T cell differentiation; mucosa-associated lymphoid tissue development; 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; gut; hemolymphoid system; and sensory organ. 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, Nov 2024]
Expression: Biased expression in thymus adult (RPKM 78.6), colon adult (RPKM 8.4) and 9 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 3 F2.1; 3 40.56 cM

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (94280106..94305583)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (94372794..94398276)

Chromosome 3 - NC_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: Mouse ENCODE transcriptome data 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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RORgammat up-regulates RAG gene expression in DP thymocytes to expand the Tcra repertoire.
Title: RORγt up-regulates RAG gene expression in DP thymocytes to expand the Tcra repertoire.
Retinoid orphan receptor gamma t (rorgammat) promotes inflammatory eosinophilia but is dispensable for innate immune-mediated colitis.
Title: Retinoid orphan receptor gamma t (rorγt) promotes inflammatory eosinophilia but is dispensable for innate immune-mediated colitis.
Downregulation of Mirlet7 miRNA family promotes Tc17 differentiation and emphysema via de-repression of RORgammat.
Title: Downregulation of Mirlet7 miRNA family promotes Tc17 differentiation and emphysema via de-repression of RORγt.
RORgammat[+] c-Maf[+] Vgamma4[+] gammadelta T cells are generated in the adult thymus but do not reach the periphery.
Title: RORγt(+) c-Maf(+) Vγ4(+) γδ T cells are generated in the adult thymus but do not reach the periphery.
A cis-element at the Rorc locus regulates the development of type 3 innate lymphoid cells.
Title: A cis-element at the Rorc locus regulates the development of type 3 innate lymphoid cells.
Mesenchymal stem cells protect against sepsis-associated acute kidney injury by inducing Gal-9/Tim-3 to remodel immune homeostasis.
Title: Mesenchymal stem cells protect against sepsis-associated acute kidney injury by inducing Gal-9/Tim-3 to remodel immune homeostasis.
Nsun2 coupling with RoRgammat shapes the fate of Th17 cells and promotes colitis.
Title: Nsun2 coupling with RoRγt shapes the fate of Th17 cells and promotes colitis.
RORgammat-Expressing Pathogenic CD4(+) T Cells Cause Brain Inflammation during Chronic Colitis.
Title: RORγt-Expressing Pathogenic CD4(+) T Cells Cause Brain Inflammation during Chronic Colitis.
RORgammat phosphorylation protects against T cell-mediated inflammation.
Title: RORγt phosphorylation protects against T cell-mediated inflammation.
T-bet represses collagen-induced arthritis by suppressing Th17 lineage commitment through inhibition of RORgammat expression and function.
Title: T-bet represses collagen-induced arthritis by suppressing Th17 lineage commitment through inhibition of RORγt expression and function.

Submit: New GeneRIF Correction See all GeneRIFs (138)

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (3)
Endonuclease-mediated (13) 1 citation
Targeted (8) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

U39071 (e-PCR)
- UniSTS:125741

Rorc (e-PCR), detects polymorphism
- UniSTS:536546

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
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
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 nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear receptor activity	IEA Inferred from Electronic Annotation more info
enables oxysterol binding	IBA Inferred from Biological aspect of Ancestor more info
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
involved_in intracellular receptor signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lymph node development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in 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
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 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
involved_in regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
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
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

Go to the top of the page Help

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)

Go to the top of the page Help

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)

NM_001293734.1 → NP_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

E9Q8I1, P51450, Q3U513, Q61027, Q91YT5, Q9QXD9, Q9R177

UniProtKB/TrEMBL

A0A0G2JGZ6, Q3TVH3

Related

ENSMUSP00000143763.2, ENSMUST00000197040.5

Conserved Domains (2) summary

cd06939
Location:245 → 483

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cd06968
Location:4 → 97

NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
NM_011281.4 → NP_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) encodes the longer isoform (1).

Source sequence(s)

AC164562

Consensus CDS

CCDS17591.1

UniProtKB/Swiss-Prot

E9Q8I1, P51450, Q3U513, Q61027, Q91YT5, Q9QXD9, Q9R177

UniProtKB/TrEMBL

A0A0R4J096, Q3TVH3

Related

ENSMUSP00000029795.4, ENSMUST00000029795.10

Conserved Domains (2) summary

cd06939
Location:266 → 504

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cd06968
Location:24 → 118

NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers

RNA

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: 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

NC_000069.7 Reference GRCm39 C57BL/6J

Range

94280106..94305583

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006501163.4 → XP_006501226.1 nuclear receptor ROR-gamma isoform X2

UniProtKB/TrEMBL

Q3UUW3

Conserved Domains (2) summary

cd06968
Location:24 → 118

NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers

cl11397
Location:266 → 311

NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
XM_006501164.4 → XP_006501227.1 nuclear receptor ROR-gamma isoform X3

UniProtKB/TrEMBL

Q3UUW3

Conserved Domains (2) summary

cd06968
Location:24 → 118

NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers

cl11397
Location:266 → 311

NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
XM_006501162.5 → XP_006501225.3 nuclear receptor ROR-gamma isoform X1

UniProtKB/Swiss-Prot

E9Q8I1, P51450, Q3U513, Q61027, Q91YT5, Q9QXD9, Q9R177

UniProtKB/TrEMBL

Q3TVH3

Conserved Domains (2) summary

cd06939
Location:213 → 451

NR_LBD_ROR_like; The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

cl02596
Location:47 → 65

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers