Rora RAR-related orphan receptor A [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Roraprovided by RGD
Full Name: RAR-related orphan receptor Aprovided by RGD
Primary source: RGD:1308419
See related: EnsemblRapid:ENSRNOG00000077683 AllianceGenome:RGD:1308419
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
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. [provided by RefSeq, Feb 2014]
Expression: Biased expression in Adrenal (RPKM 181.6), Muscle (RPKM 180.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q24

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (78182710..78915730)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (69301635..70034741)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (75515886..75616477)

Chromosome 8 - NC_086026.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Vitamin A supplementation ameliorates motor incoordination via modulating RORalpha in the cerebellum in a valproic acid-treated rat autism model with vitamin A deficiency.
Title: Vitamin A supplementation ameliorates motor incoordination via modulating RORα in the cerebellum in a valproic acid-treated rat autism model with vitamin A deficiency.
RORalpha Regulates Odontoblastic Differentiation and Mediates the Pro-Odontogenic Effect of Melatonin on Dental Papilla Cells.
Title: RORα Regulates Odontoblastic Differentiation and Mediates the Pro-Odontogenic Effect of Melatonin on Dental Papilla Cells.
This is the first report describing the Sertoli cell specific role of ROR-alpha in maintaining quantitatively normal sperm output.
Title: Sertoli cell specific knockdown of RAR-related orphan receptor (ROR) alpha at puberty reduces sperm count in rats.
Vitamin A deficiency resulted in decreased mRNA levels of RARalpha, RARbeta and NR1 (P<.05). The protein level of RARalpha and NR1 in the MVAD group was lower than that of the control group
Title: Effect of marginal vitamin A deficiency during pregnancy on retinoic acid receptors and N-methyl-D-aspartate receptor expression in the offspring of rats.
This form of RA signaling operates via a translation-dependent but transcription-independent mechanism, causes an upregulation of postsynaptic glutamate receptor levels, and requires RARalpha receptors.
Title: Synaptic signaling by all-trans retinoic acid in homeostatic synaptic plasticity.
These results indicate that rat HSCs become retinoid responsive after activation in vitro, through post-transcriptional up-regulation of RARalpha gene expression.
Title: Rat hepatic stellate cells acquire retinoid responsiveness after activation in vitro by post-transcriptional regulation of retinoic acid receptor alpha gene expression.

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General gene information

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Markers

RH138861 (e-PCR)
- UniSTS:220948

d8mgh17 (e-PCR)
- UniSTS:122390

BF400829 (e-PCR)
- UniSTS:245039

D8Got108 (e-PCR)
- UniSTS:113465

Rora (e-PCR), detects polymorphism
- UniSTS:507195

D8Rat33 (e-PCR)
- UniSTS:119100

AU025961 (e-PCR)
- UniSTS:114750

G64932 (e-PCR)
- UniSTS:164933

RH138143 (e-PCR)
- UniSTS:220230

BE101994 (e-PCR)
- UniSTS:243793

AU026180 (e-PCR)
- UniSTS:114534

D8Rat146 (e-PCR), detects polymorphism
- UniSTS:228231

RH137194 (e-PCR)
- UniSTS:219282

RH142618 (e-PCR)
- UniSTS:231865

SGC33753 (e-PCR)
- UniSTS:74171

RH138260 (e-PCR)
- UniSTS:220347

RH144170 (e-PCR)
- UniSTS:233416

D8Rat234 (e-PCR), detects polymorphism
- UniSTS:228298

AU049942 (e-PCR)
- UniSTS:146384

Rora (e-PCR), detects polymorphism
- UniSTS:144355

AI406875 (e-PCR)
- UniSTS:250083

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor 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 RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables beta-catenin 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 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	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in angiogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cGMP metabolic process	ISO Inferred from Sequence Orthology more info
involved_in cellular response to hypoxia	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to interleukin-1	ISO Inferred from Sequence Orthology more info
involved_in cellular response to sterol	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to tumor necrosis factor	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellar Purkinje cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in cerebellar granule cell precursor proliferation	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	ISO Inferred from Sequence Orthology more info
involved_in circadian regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in circadian rhythm	IEP Inferred from Expression Pattern more info	PubMed
involved_in intracellular receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in muscle cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of fat cell differentiation	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nitric oxide biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of vascular endothelial growth factor production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in regulation of glucose metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of macrophage activation	ISO Inferred from Sequence Orthology more info
involved_in regulation of smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in regulation of steroid metabolic process	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in triglyceride homeostasis	ISO Inferred from Sequence Orthology more info
involved_in xenobiotic metabolic process	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: nuclear receptor ROR-alpha

Names: RAR-related orphan receptor alpha; nuclear receptor ROR-alpha-like

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)

NM_001427366.2 → NP_001414295.1 nuclear receptor ROR-alpha isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008

UniProtKB/TrEMBL

F1LZZ3

Related

ENSRNOP00000101210.1, ENSRNOT00000142307.1
NM_001427367.2 → NP_001414296.1 nuclear receptor ROR-alpha isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008

UniProtKB/TrEMBL

A0A8I6A803

Related

ENSRNOP00000112617.1, ENSRNOT00000148602.1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086026.1 Reference GRCr8

Range

78182710..78915730

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039082824.2 → XP_038938752.1 nuclear receptor ROR-alpha isoform X1

Conserved Domains (2) summary

cd06939
Location:272 → 510

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

cd06968
Location:66 → 160

NR_DBD_ROR; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers
XM_063265167.1 → XP_063121237.1 nuclear receptor ROR-alpha isoform X3
XM_063265166.1 → XP_063121236.1 nuclear receptor ROR-alpha isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001106834.1: Suppressed sequence

Description

NM_001106834.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.