Rara retinoic acid receptor, alpha [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Raraprovided by RGD
Official Full Name: retinoic acid receptor, alphaprovided by RGD
Primary source: RGD:3534
See related: EnsemblRapid:ENSRNOG00000009972 AllianceGenome:RGD:3534
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: Enables heterocyclic compound binding activity; histone deacetylase binding activity; and nucleic acid binding activity. Involved in several processes, including reproductive structure development; response to estradiol; and response to vitamin A. Located in dendrite and perinuclear region of cytoplasm. Biomarker of amyotrophic lateral sclerosis. Human ortholog(s) of this gene implicated in acute promyelocytic leukemia. Orthologous to human RARA (retinoic acid receptor alpha). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Lung (RPKM 102.3), Kidney (RPKM 75.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q31

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (84379780..84424371)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (83883490..83928932)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (86838819..86884224)

Chromosome 10 - NC_086028.1 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?

Activation of the RARalpha Attenuated CSF Hypersecretion to Inhibit Hydrocephalus Development via Regulating the MAFB/MSR1 Pathway.
Title: Activation of the RARα Attenuated CSF Hypersecretion to Inhibit Hydrocephalus Development via Regulating the MAFB/MSR1 Pathway.
Retinoic acid receptor alpha activation is necessary and sufficient for plasticity induced by recurrent central apnea.
Title: Retinoic acid receptor alpha activation is necessary and sufficient for plasticity induced by recurrent central apnea.
Vitamin A regulates neural stem cell proliferation in rats after hypoxic-ischemic brain damage via RARa-mediated modulation of the beta-catenin pathway.
Title: Vitamin A regulates neural stem cell proliferation in rats after hypoxic-ischemic brain damage via RARɑ-mediated modulation of the β-catenin pathway.
Data suggest that marginal vitamin A deficiency in pregnant rats down-regulates expression of Rara in hippocampal neurons of offspring leading to decreases in Src and Nr1 expression and causing learning and memory deficits in offspring. (Rara = retinoic acid receptor alpha; Src = proto-oncogene protein src; Nr1 = N-methyl-D-asparate receptor Nr1a)
Title: The change in retinoic acid receptor signaling induced by prenatal marginal vitamin A deficiency and its effects on learning and memory.
Data show that retinoic acid receptor alpha (RARalpha) improved the renal function and attenuated the progression of glomerulosclerosis (GS) that was associated with the over-expression of matrix metalloproteinases MMP2 and MMP9.
Title: The potential role of retinoic acid receptor α on glomerulosclerosis in rats and podocytes injury is associated with the induction of MMP2 and MMP9.
upregulated in blood, spleen, and bone marrow in IgA nephropathy
Title: Regulation of IgA Class Switch Recombination in Immunoglobulin A Nephropathy: Retinoic Acid Signaling and BATF.
Renal interstitial fibrosis (RIF) is a common denominator of chronic kidney disease. This study investigated whether a potential signaling pathway existed between PPARgamma and RARalpha in RIF.
Title: The potential signaling pathway between peroxisome proliferator-activated receptor gamma and retinoic acid receptor alpha in renal interstitial fibrosis disease.
Neonatal maternal separation attenuates the capacity of adult hippocampal neural precursor cells to differentiate into neurons by decreasing expression of RARalpha through DNMT1-mediated methylation of its promoter.
Title: Neonatal maternal separation alters the capacity of adult neural precursor cells to differentiate into neurons via methylation of retinoic acid receptor gene promoter.
RARalpha mediates CREB-binding protein histone acetylation which impairs memory and learning in Vitamin A deficiency.
Title: Vitamin A deficiency impairs spatial learning and memory: the mechanism of abnormal CBP-dependent histone acetylation regulated by retinoic acid receptor alpha.
We showed that the embryo hearts from vitamin A insufficient groups exhibited ultrastructural changes and significantly lowe expression of GATA-4, RARalpha and gamma, and higher expression of RXRalpha and beta.
Title: Ectopic expression of retinoic acid receptors and change of myocardial structure in the offspring heart with vitamin A deficiency.

Submit: New GeneRIF Correction See all GeneRIFs (25)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH141071 (e-PCR)
- UniSTS:223071

Rara (e-PCR), detects polymorphism
- UniSTS:462692

Rara (e-PCR), detects polymorphism
- UniSTS:462695

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 repressor activity	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 alpha-actinin binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables heterocyclic compound binding	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase binding	IPI Inferred from Physical Interaction more info	PubMed
enables mRNA 5'-UTR binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA regulatory element binding translation repressor activity	IDA Inferred from Direct Assay more info	PubMed
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear receptor activity	ISO Inferred from Sequence Orthology more info
enables nuclear receptor activity	TAS Traceable Author Statement more info	PubMed
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables protein kinase A binding	ISO Inferred from Sequence Orthology more info
enables protein kinase B binding	ISO Inferred from Sequence Orthology more info
enables retinoic acid binding	ISO Inferred from Sequence Orthology more info
enables retinoic acid-responsive element binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables signaling receptor binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator 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 Sertoli cell fate commitment	ISO Inferred from Sequence Orthology more info
involved_in apoptotic cell clearance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within bone development	ISO Inferred from Sequence Orthology more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to estrogen stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in cellular response to retinoic acid	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chondroblast differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic camera-type eye development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within face development	ISO Inferred from Sequence Orthology more info
involved_in female pregnancy	IEP Inferred from Expression Pattern more info	PubMed
involved_in germ cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within glandular epithelial cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within growth plate cartilage development	ISO Inferred from Sequence Orthology more info
involved_in hippocampus development	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within intracellular receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within limb development	ISO Inferred from Sequence Orthology more info
involved_in liver development	IEP Inferred from Expression Pattern more info	PubMed
involved_in mRNA transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in male gonad development	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within multicellular organism growth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of cartilage development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell population proliferation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of granulocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of miRNA transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of translation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of type II interferon production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural tube closure	ISO Inferred from Sequence Orthology more info
involved_in outflow tract septum morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T-helper 2 cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell cycle	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-13 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-4 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-5 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor 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 transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in prostate gland development	IEP Inferred from Expression Pattern more info	PubMed
involved_in protein phosphorylation	IEA Inferred from Electronic Annotation more info
involved_in protein phosphorylation	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 apoptotic process	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of granulocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of hematopoietic progenitor cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of myelination	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synaptic plasticity	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in response to cytokine	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to estradiol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to ethanol	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to retinoic acid	ISO Inferred from Sequence Orthology more info
involved_in response to retinoic acid	ISO Inferred from Sequence Orthology more info
involved_in response to vitamin A	IEP Inferred from Expression Pattern more info	PubMed
involved_in retinoic acid receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in retinoic acid receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within trachea cartilage development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ureteric bud development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ventricular cardiac muscle cell differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
located_in actin cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in actin cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	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
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: retinoic acid receptor alpha

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_001429976.1 → NP_001416905.1 retinoic acid receptor alpha isoform a

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A0A0G2JW78, A6HIV8
NM_001429977.1 → NP_001416906.1 retinoic acid receptor alpha isoform a

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A0A0G2JW78, A6HIV8
NM_001429978.1 → NP_001416907.1 retinoic acid receptor alpha isoform a

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A0A0G2JW78, A6HIV8
NM_031528.3 → NP_113716.2 retinoic acid receptor alpha isoform b

See identical proteins and their annotated locations for NP_113716.2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A6HIV9, F7EXR0, Q499N1, Q9QWJ1

Related

ENSRNOP00000008659.4, ENSRNOT00000008659.6

Conserved Domains (2) summary

cd06937
Location:183 → 413

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cd06964
Location:79 → 163

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

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_086028.1 Reference GRCr8

Range

84379780..84424371

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063268421.1 → XP_063124491.1 retinoic acid receptor alpha isoform X1

UniProtKB/TrEMBL

A0A0G2JW78, A6HIV8
XM_017597011.3 → XP_017452500.1 retinoic acid receptor alpha isoform X1

Related

ENSRNOP00000069776.1, ENSRNOT00000084644.3

Conserved Domains (2) summary

cd06937
Location:186 → 416

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cd06964
Location:82 → 166

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
XM_063268422.1 → XP_063124492.1 retinoic acid receptor alpha isoform X1

UniProtKB/TrEMBL

A0A0G2JW78, A6HIV8
XM_063268423.1 → XP_063124493.1 retinoic acid receptor alpha isoform X1

UniProtKB/TrEMBL

A0A0G2JW78, A6HIV8
XM_039085214.2 → XP_038941142.1 retinoic acid receptor alpha isoform X1

Conserved Domains (2) summary

cd06937
Location:186 → 416

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cd06964
Location:82 → 166

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
XM_063268424.1 → XP_063124494.1 retinoic acid receptor alpha isoform X1

UniProtKB/TrEMBL

A0A0G2JW78, A6HIV8
XM_039085219.2 → XP_038941147.1 retinoic acid receptor alpha isoform X1

UniProtKB/TrEMBL

A0A0G2JW78, A6HIV8, Q9QWJ1

Conserved Domains (2) summary

cd06937
Location:186 → 416

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cd06964
Location:82 → 166

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers