U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Rara retinoic acid receptor, alpha [ Mus musculus (house mouse) ]

Gene ID: 19401, updated on 11-Jan-2023

Summary

Official Symbol
Raraprovided by MGI
Official Full Name
retinoic acid receptor, alphaprovided by MGI
Primary source
MGI:MGI:97856
See related
Ensembl:ENSMUSG00000037992 AllianceGenome:MGI:97856
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
RAR; Nr1b1; RARalpha1
Summary
Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity and nuclear receptor activity. Involved in several processes, including Sertoli cell fate commitment; cellular response to lipopolysaccharide; and germ cell development. Acts upstream of or within several processes, including animal organ development; negative regulation of cartilage development; and regulation of cellular macromolecule biosynthetic process. Located in several cellular components, including dendrite; neuronal cell body; and nucleus. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; limb; and sensory organ. 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, Apr 2022]
Expression
Ubiquitous expression in lung adult (RPKM 17.4), stomach adult (RPKM 16.8) and 27 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See Rara in Genome Data Viewer
Location:
11 D; 11 62.76 cM
Exon count:
16
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (98818626..98865768)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (98927800..98974942)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene WAS/WASL interacting protein family, member 2 Neighboring gene VISTA enhancer mm1323 Neighboring gene cell division cycle 6 Neighboring gene predicted gene, 46294 Neighboring gene predicted gene, 22061 Neighboring gene gap junction protein, delta 3 Neighboring gene topoisomerase (DNA) II alpha Neighboring gene predicted gene, 23451

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 (7)  1 citation
  • Endonuclease-mediated (2) 

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 IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
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
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
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 ISO
Inferred from Sequence Orthology
more info
 
enables histone deacetylase binding ISO
Inferred from Sequence Orthology
more info
 
enables mRNA 5'-UTR binding ISO
Inferred from Sequence Orthology
more info
 
enables mRNA regulatory element binding translation repressor 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 nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables nuclear receptor activity ISO
Inferred from Sequence Orthology
more info
 
enables phosphatidylinositol 3-kinase regulator activity ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
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 IDA
Inferred from Direct Assay
more info
PubMed 
enables sequence-specific DNA binding IGI
Inferred from Genetic Interaction
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription cis-regulatory region binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables transcription coactivator binding IPI
Inferred from Physical Interaction
more info
PubMed 
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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in apoptotic cell clearance ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within bone development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cellular response to estrogen stimulus ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to lipopolysaccharide IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to retinoic acid ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within chondroblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within embryonic camera-type eye development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within face development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in germ cell development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within glandular epithelial cell development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within growth plate cartilage development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in hormone-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within limb development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in mRNA transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in mRNA transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
involved_in male gonad development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within multicellular organism growth IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of cartilage development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of gene expression IGI
Inferred from Genetic Interaction
more info
PubMed 
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
PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of translation ISO
Inferred from Sequence Orthology
more info
 
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 IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of ERK1 and ERK2 cascade 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 binding 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 IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of phosphatidylinositol 3-kinase signaling ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of protein kinase B signaling ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in protein phosphorylation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of apoptotic process ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of granulocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within regulation of hematopoietic progenitor cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of myelination ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of synaptic plasticity ISO
Inferred from Sequence Orthology
more info
 
involved_in response to ethanol ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within response to retinoic acid IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in response to retinoic acid ISO
Inferred from Sequence Orthology
more info
 
involved_in retinoic acid receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in retinoic acid receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within trachea cartilage development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ureteric bud development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ventricular cardiac muscle cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex ISO
Inferred from Sequence Orthology
more info
 
part_of RNA polymerase II transcription regulator complex NAS
Non-traceable Author Statement
more info
PubMed 
located_in actin cytoskeleton ISO
Inferred from Sequence Orthology
more info
 
located_in chromatin ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in dendrite ISO
Inferred from Sequence Orthology
more info
 
located_in neuron projection ISO
Inferred from Sequence Orthology
more info
 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in perinuclear region of cytoplasm ISO
Inferred from Sequence Orthology
more info
 
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 EXP
Inferred from Experiment
more info
PubMed 
part_of transcription regulator complex IPI
Inferred from Physical Interaction
more info
PubMed 
part_of transcription regulator complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
retinoic acid receptor alpha
Names
RAR alpha 1
RAR-alpha
nuclear receptor subfamily 1 group B member 1

NCBI Reference Sequences (RefSeq)

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)

  1. NM_001176528.1NP_001169999.1  retinoic acid receptor alpha isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has an alternate 5' sequence including the 5' CDS, as compared to variant 1. The resulting isoform (2) has a shorter and different N-terminus, as compared to isoform 1.
    Source sequence(s)
    AL591067
    Consensus CDS
    CCDS48905.1
    UniProtKB/Swiss-Prot
    P11416
    Related
    ENSMUSP00000103097.3, ENSMUST00000107473.3
    Conserved Domains (2) summary
    cd06937
    Location:183413
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:79163
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  2. NM_001177302.1NP_001170773.1  retinoic acid receptor alpha isoform 1

    See identical proteins and their annotated locations for NP_001170773.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an additional exon in the 5' UTR, as compared to variant 1. Variants 1-3 encode the same isoform 1.
    Source sequence(s)
    AL591067
    Consensus CDS
    CCDS36304.1
    UniProtKB/Swiss-Prot
    P11416, P22603
    UniProtKB/TrEMBL
    Q3U3R3
    Related
    ENSMUSP00000069744.4, ENSMUST00000068133.10
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)
  3. NM_001177303.1NP_001170774.1  retinoic acid receptor alpha isoform 1

    See identical proteins and their annotated locations for NP_001170774.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate 5' UTR exon, as compared to variant 1. Variants 1-3 encode the same isoform 1.
    Source sequence(s)
    AK042163, AL591067
    Consensus CDS
    CCDS36304.1
    UniProtKB/Swiss-Prot
    P11416, P22603
    UniProtKB/TrEMBL
    Q3U3R3
    Related
    ENSMUSP00000129791.2, ENSMUST00000164748.8
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)
  4. NM_001361954.1NP_001348883.1  retinoic acid receptor alpha isoform 3

    Status: VALIDATED

    Source sequence(s)
    AI465528, AK153644, AL591067
    UniProtKB/TrEMBL
    Q3U5E7
    Conserved Domains (2) summary
    cd06937
    Location:67297
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cl02596
    Location:144
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  5. NM_009024.2NP_033050.2  retinoic acid receptor alpha isoform 1

    See identical proteins and their annotated locations for NP_033050.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK042163, AL591067
    Consensus CDS
    CCDS36304.1
    UniProtKB/Swiss-Prot
    P11416, P22603
    UniProtKB/TrEMBL
    Q3U3R3
    Related
    ENSMUSP00000103099.3, ENSMUST00000107475.9
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)

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_000077.7 Reference GRCm39 C57BL/6J

    Range
    98818626..98865768
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006532592.4XP_006532655.1  retinoic acid receptor alpha isoform X1

    See identical proteins and their annotated locations for XP_006532655.1

    UniProtKB/Swiss-Prot
    P11416, P22603
    UniProtKB/TrEMBL
    Q3U3R3
    Related
    ENSMUSP00000103098.2, ENSMUST00000107474.8
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)
  2. XM_006532593.2XP_006532656.1  retinoic acid receptor alpha isoform X1

    See identical proteins and their annotated locations for XP_006532656.1

    UniProtKB/Swiss-Prot
    P11416, P22603
    UniProtKB/TrEMBL
    Q3U3R3
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)
  3. XM_030245701.2XP_030101561.1  retinoic acid receptor alpha isoform X1

    UniProtKB/Swiss-Prot
    P22603
    UniProtKB/TrEMBL
    Q3U3R3
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)
  4. XM_006532597.2XP_006532660.1  retinoic acid receptor alpha isoform X2

    See identical proteins and their annotated locations for XP_006532660.1

    UniProtKB/TrEMBL
    Q3U5E7
    Conserved Domains (2) summary
    cd06937
    Location:67297
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cl02596
    Location:144
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  5. XM_030245702.1XP_030101562.1  retinoic acid receptor alpha isoform X2

    UniProtKB/TrEMBL
    Q3U5E7
    Conserved Domains (2) summary
    cd06937
    Location:67297
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cl02596
    Location:144
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers