Free for academic non-profit institutions. Other users need a Commercial license

Aliases for RARA Gene

Aliases for RARA Gene

  • Retinoic Acid Receptor, Alpha 2 3
  • Nuclear Receptor Subfamily 1 Group B Member 1 3 4
  • RAR-Alpha 3 4
  • NR1B1 3 4
  • Nucleophosmin-Retinoic Acid Receptor Alpha Fusion Protein NPM-RAR Long Form 3
  • Retinoic Acid Nuclear Receptor Alpha Variant 1 3
  • Retinoic Acid Nuclear Receptor Alpha Variant 2 3
  • Retinoic Acid Receptor, Alpha Polypeptide 3
  • Retinoic Acid Receptor Alpha 3
  • RAR 3

External Ids for RARA Gene

Previous GeneCards Identifiers for RARA Gene

  • GC17P037961
  • GC17P040640
  • GC17P038374
  • GC17P038838
  • GC17P038860
  • GC17P035718
  • GC17P038465
  • GC17P034259

Summaries for RARA Gene

Entrez Gene Summary for RARA Gene

  • This gene represents a nuclear retinoic acid receptor. The encoded protein, retinoic acid receptor alpha, regulates transcription in a ligand-dependent manner. This gene has been implicated in regulation of development, differentiation, apoptosis, granulopoeisis, and transcription of clock genes. Translocations between this locus and several other loci have been associated with acute promyelocytic leukemia. Alternatively spliced transcript variants have been found for this locus.[provided by RefSeq, Sep 2010]

GeneCards Summary for RARA Gene

RARA (Retinoic Acid Receptor, Alpha) is a Protein Coding gene. Diseases associated with RARA include aleukemic leukemia cutis and leukemia, acute promyelocytic. Among its related pathways are Pathways in cancer and ERK Signaling. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and protein heterodimerization activity. An important paralog of this gene is NR1I2.

UniProtKB/Swiss-Prot for RARA Gene

  • Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5-AGGTCA-3 sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. RARA plays an essential role in the regulation of retinoic acid-induced germ cell development during spermatogenesis. Has a role in the survival of early spermatocytes at the beginning prophase of meiosis. In Sertoli cells, may promote the survival and development of early meiotic prophase spermatocytes. In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function (By similarity). Regulates expression of target genes in a ligand-dependent manner by recruiting chromatin complexes containing KMT2E/MLL5. Mediates retinoic acid-induced granulopoiesis.

Tocris Summary for RARA Gene

  • Retinoic acid receptors (RARs) are nuclear hormone receptors of the NRB1 class, which function as heterodimers with retinoid X receptors (RXRs). There are three distinct RAR subtypes; RARalpha, RARbeta and RARgamma. RARalpha is present in most tissue types, whereas RARbeta and RARgamma expression is more selective. RXR-RAR heterodimers act as ligand-dependent transcriptional regulators by binding to the specific retinoic acid response element (RARE) found in the promoter regions of target genes. In the absence of an RAR agonist, RXR-RAR recruits co-repressor proteins such as NCoR and associated factors such as histone deacetylase to maintain a condensed chromatin structure. RAR agonist binding stimulates co-repressor release and co-activator complexes, such as histone acetyltransferase, are recruited to activate transcription. RARs transduce retinoid signals in vivo, which mediates proper embryogenesis, differentiation and growth arrest. Specifically, RXRalpha-RARgamma heterodimers are necessary for growth arrest and viseral and primitive endodermal differentiation, whereas RXRalpha-RARalpha is required for cAMP-dependent parietal endodermal differentiation. In vitro it has been difficult to elucidate the roles of individual subtypes as functional RAR knockouts generate artificial redundancies that are thought not to exist under normal conditions.

Gene Wiki entry for RARA Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RARA Gene

Genomics for RARA Gene

Regulatory Elements for RARA Gene

Genomic Location for RARA Gene

Start:
40,309,171 bp from pter
End:
40,357,643 bp from pter
Size:
48,473 bases
Orientation:
Plus strand

Genomic View for RARA Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for RARA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RARA Gene

Proteins for RARA Gene

  • Protein details for RARA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P10276-RARA_HUMAN
    Recommended name:
    Retinoic acid receptor alpha
    Protein Accession:
    P10276
    Secondary Accessions:
    • B8Y636
    • P78456
    • Q13440
    • Q13441
    • Q96S41
    • Q9NQS0

    Protein attributes for RARA Gene

    Size:
    462 amino acids
    Molecular mass:
    50771 Da
    Quaternary structure:
    • Heterodimer; with RXRA. Binds DNA preferentially as a heterodimer. Interacts with CDK7 (By similarity). Interacts with coactivators NCOA3 and NCOA6. Interacts with NCOA7; the interaction requires ligand-binding. Interacts with KMT2E/MLL5. Interacts (via the ligand-binding domain) with PRAME; the interaction is ligand (retinoic acid)-dependent. Interacts with AKT1; the interaction phosphorylates RARA and represses transactivation. Interacts with PRKAR1A; the interaction negatively regulates RARA transcriptional activity. Interacts with NCOR1 and NCOR2. Interacts with PRMT2. Interacts with LRIF1. Interacts with ASXL1 and NCOA1. Interacts with ACTN4.
    SequenceCaution:
    • Sequence=AAB00112.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAB00113.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB62809.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RARA Gene

    Alternative splice isoforms for RARA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RARA Gene

Proteomics data for RARA Gene at MOPED

Post-translational modifications for RARA Gene

  • Phosphorylated on serine and threonine residues. Phosphorylation does not change during cell cycle. Phosphorylation on Ser-77 is crucial for transcriptional activity (By similarity). Phosphorylation by AKT1 is required for the repressor activity but has no effect on DNA binding, protein stability nor subcellular localization. Phosphorylated by PKA in vitro. This phosphorylation on Ser-219 and Ser-369 is critical for ligand binding, nuclear localization and transcriptional activity in response to FSH signaling.
  • Sumoylated with SUMO2, mainly on Lys-399 which is also required for SENP6 binding. On all-trans retinoic acid (ATRA) binding, a confromational change may occur that allows sumoylation on two additional site, Lys-166 and Lys-171. Probably desumoylated by SENP6. Sumoylation levels determine nuclear localization and regulate ATRA-mediated transcriptional activity.
  • Trimethylation enhances heterodimerization with RXRA and positively modulates the transcriptional activation
  • Ubiquitinated
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RARA Gene

Domains for RARA Gene

Gene Families for RARA Gene

HGNC:
  • NR :Nuclear hormone receptors
IUPHAR :

Graphical View of Domain Structure for InterPro Entry

P10276

UniProtKB/Swiss-Prot:

RARA_HUMAN :
  • P10276
Domain:
  • Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain
  • Contains 1 nuclear receptor DNA-binding domain.
Family:
  • Belongs to the nuclear hormone receptor family. NR1 subfamily.
genes like me logo Genes that share domains with RARA: view

Function for RARA Gene

Molecular function for RARA Gene

GENATLAS Biochemistry: retinoic acid receptor binding and activated by both all-trans (T-RA) and its 9-cis isomer (9-cis-RA) retinoic acids,alpha subunit,steroid/thyroid hormone receptor superfamily
UniProtKB/Swiss-Prot Function: Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5-AGGTCA-3 sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. RARA plays an essential role in the regulation of retinoic acid-induced germ cell development during spermatogenesis. Has a role in the survival of early spermatocytes at the beginning prophase of meiosis. In Sertoli cells, may promote the survival and development of early meiotic prophase spermatocytes. In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function (By similarity). Regulates expression of target genes in a ligand-dependent manner by recruiting chromatin complexes containing KMT2E/MLL5. Mediates retinoic acid-induced granulopoiesis.

Gene Ontology (GO) - Molecular Function for RARA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000900 translation repressor activity, nucleic acid binding IEA --
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA --
GO:0001012 RNA polymerase II regulatory region DNA binding --
GO:0001972 retinoic acid binding IDA 2825025
GO:0003677 DNA binding --
genes like me logo Genes that share ontologies with RARA: view
genes like me logo Genes that share phenotypes with RARA: view

Animal Models for RARA Gene

MGI Knock Outs for RARA:

miRNA for RARA Gene

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for RARA Gene

Localization for RARA Gene

Subcellular locations from UniProtKB/Swiss-Prot for RARA Gene

Nucleus. Cytoplasm. Note=Nuclear localization depends on ligand binding, phosphorylation and sumoylation. Transloaction to the nucleus in the absence of ligand is dependent on activation of PKC and the downstream MAPK phosphorylation.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RARA Gene COMPARTMENTS Subcellular localization image for RARA gene
Compartment Confidence
nucleus 5
extracellular 3
cytoskeleton 1
mitochondrion 1
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for RARA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IDA 17363140
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IDA --
GO:0009986 cell surface IC 2825025
genes like me logo Genes that share ontologies with RARA: view

Pathways for RARA Gene

genes like me logo Genes that share pathways with RARA: view

Gene Ontology (GO) - Biological Process for RARA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0001657 ureteric bud development IEA --
GO:0001843 neural tube closure IEA --
GO:0001889 liver development IEA --
GO:0002068 glandular epithelial cell development IEA --
genes like me logo Genes that share ontologies with RARA: view

Compounds for RARA Gene

(5) Tocris Compounds for RARA Gene

Compound Action Cas Number
AM 580 Retinoic acid analog; RARalpha agonist [102121-60-8]
BMS 493 Pan-RAR inverse agonist [215030-90-3]
CD 2665 Selective RARbeta/gamma antagonist [170355-78-9]
Liarozole hydrochloride Blocks retinoic acid metabolism [145858-50-0]
Retinoic acid Endogenous retinoic acid receptor agonist [302-79-4]

(1) HMDB Compounds for RARA Gene

Compound Synonyms Cas Number PubMed IDs
Retinoic acid
  • Retinoate
302-79-4

(7) Drugbank Compounds for RARA Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Acitretin
55079-83-9 target agonist
Adapalene
  • Adapaleno [INN-Spanish]
106685-40-9 target agonist
Alitretinoin
  • 9-cis-Retinoic acid
5300-03-8 target agonist
Etretinate
54350-48-0 target agonist
Isotretinoin
4759-48-2 target other/unknown

(12) IUPHAR Ligand for RARA Gene

Ligand Type Action Affinity Pubmed IDs
9-cis-retinoic acid Agonist Agonist 9.7
all-trans-retinoic acid Agonist Agonist 9.4
BMS614 Antagonist Antagonist 8.7
AGN193109 Antagonist Inverse agonist 8.7
BMS753 Agonist Agonist 8.7
BMS493 Antagonist Inverse agonist 8.54
AGN193836 Agonist Agonist 8.4
TTNPB Agonist Agonist 8
Ro 40-6055 Agonist Agonist 7.44
Ro 41-5253 Antagonist Antagonist 7.22
tamibarotene Agonist Agonist 6.9
CD666 Agonist Agonist 5.64

(94) Novoseek inferred chemical compound relationships for RARA Gene

Compound -log(P) Hits PubMed IDs
retinoic acid 97.7 374
retinoid 95.8 141
ttnpb 91.2 29
am 580 89.5 29
alpha-retinoic acid 86.2 9

(2) PharmGKB related drug/compound annotations for RARA Gene

Drug/compound Annotation
arsenic trioxide
tretinoin
genes like me logo Genes that share compounds with RARA: view

Transcripts for RARA Gene

Unigene Clusters for RARA Gene

Retinoic acid receptor, alpha:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for RARA Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15
SP1: - - - - - - - -
SP2: - - - - - - - - -
SP3: - - - - -
SP4: -
SP5: - - - -
SP6:
SP7: -
SP8: -

Relevant External Links for RARA Gene

GeneLoc Exon Structure for
RARA
ECgene alternative splicing isoforms for
RARA

Expression for RARA Gene

mRNA expression in normal human tissues for RARA Gene

mRNA differential expression in normal tissues according to GTEx for RARA Gene

This gene is overexpressed in Whole Blood (9.5).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for RARA Gene

SOURCE GeneReport for Unigene cluster for RARA Gene Hs.654583

genes like me logo Genes that share expressions with RARA: view

No data available for mRNA Expression by UniProt/SwissProt for RARA Gene

Orthologs for RARA Gene

This gene was present in the common ancestor of animals.

Orthologs for RARA Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RARA 36
  • 91 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RARA 35
  • 94.59 (n)
  • 99.57 (a)
RARA 36
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RARA 35
  • 94.66 (n)
  • 99.35 (a)
RARA 36
  • 95 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rara 35
  • 91.56 (n)
  • 98.27 (a)
Rara 16
Rara 36
  • 98 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RARA 36
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RARA 36
  • 74 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rara 35
  • 90.27 (n)
  • 98.14 (a)
chicken
(Gallus gallus)
Aves RARA 35
  • 87 (n)
  • 95.27 (a)
RARA 36
  • 97 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RARA 36
  • 93 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia rara2a 35
tropical clawed frog
(Silurana tropicalis)
Amphibia rara 35
  • 79.13 (n)
  • 90.65 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4014 35
zebrafish
(Danio rerio)
Actinopterygii rara2a 35
raraa 35
  • 79.37 (n)
  • 88.62 (a)
raraa 36
  • 80 (a)
OneToMany
rarab 36
  • 84 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Eip75B 37
  • 30 (a)
worm
(Caenorhabditis elegans)
Secernentea sex-1 37
  • 29 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8261 36
  • 40 (a)
OneToMany
Species with no ortholog for RARA:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RARA Gene

ENSEMBL:
Gene Tree for RARA (if available)
TreeFam:
Gene Tree for RARA (if available)

Paralogs for RARA Gene

genes like me logo Genes that share paralogs with RARA: view

Variants for RARA Gene

Sequence variations from dbSNP and Humsavar for RARA Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type MAF
rs482284 -- 40,347,989(+) GGGCA(A/G)GAGCT intron-variant
rs1348379 -- 40,323,864(+) CCTGC(A/T)GCGTG intron-variant
rs1348380 -- 40,323,865(+) CTGCA(G/T)CGTGG intron-variant
rs2229771 -- 40,348,368(+) CCCTC(A/G)CCACC synonymous-codon, reference, intron-variant
rs2229772 -- 40,356,317(+) CTGCC(C/G)CCACC utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for RARA Gene

Variant ID Type Subtype PubMed ID
nsv833445 CNV Loss 17160897
nsv908222 CNV Loss 21882294
esv2671593 CNV Deletion 23128226

Relevant External Links for RARA Gene

HapMap Linkage Disequilibrium report
RARA

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RARA Gene

Disorders for RARA Gene

(1) OMIM Diseases for RARA Gene (180240)

UniProtKB/Swiss-Prot

RARA_HUMAN
  • Note=Chromosomal aberrations involving RARA are commonly found in acute promyelocytic leukemia. Translocation t(11;17)(q32;q21) with ZBTB16/PLZF; translocation t(15;17)(q21;q21) with PML; translocation t(5;17)(q32;q11) with NPM. The PML-RARA oncoprotein requires both the PML ring structure and coiled-coil domain for both interaction with UBE2I, nuclear microspeckle location and sumoylation. In addition, the coiled-coil domain functions in blocking RA-mediated transactivation and cell differentiation.

(5) University of Copenhagen DISEASES for RARA Gene

(89) Novoseek inferred disease relationships for RARA Gene

Disease -log(P) Hits PubMed IDs
leukemia promyelocytic acute 95.9 114
promyelocytic leukemia 87.9 92
leukemogenesis 76.1 14
leukemia 69 85
carcinoma embryonal 68.5 10

Genatlas disease for RARA Gene

acute promyelocytic leukemia or myeloid leukemia (APL),common breakpoints in translocation t (15;17) clustered in RARA second intron (see PML),in translocation t(11;17) (see ZNF145),in translocation t(5;17),and others

Relevant External Links for RARA

Genetic Association Database (GAD)
RARA
Human Genome Epidemiology (HuGE) Navigator
RARA
Tumor Gene Database (TGDB):
RARA
genes like me logo Genes that share disorders with RARA: view

Publications for RARA Gene

  1. The t(5;17) variant of acute promyelocytic leukemia expresses a nucleophosmin-retinoic acid receptor fusion. (PMID: 8562957) Redner R.L. … Corey S.J. (Blood 1996) 3 4 23
  2. PLZF-RAR alpha fusion proteins generated from the variant t(11;17)(q23;q21) translocation in acute promyelocytic leukemia inhibit ligand-dependent transactivation of wild-type retinoic acid receptors. (PMID: 8302850) Chen Z. … Chomienne C. (Proc. Natl. Acad. Sci. U.S.A. 1994) 3 4 23
  3. Retinoic acid receptor alpha gene variants, multivitamin use, and liver intake as risk factors for oral clefts: a population-based case-control study in Denmark, 1991-1994. (PMID: 12835288) Mitchell L.E. … Christensen K. (Am. J. Epidemiol. 2003) 3 23 48
  4. Structural variants in the retinoid receptor genes in patients with schizophrenia and other psychiatric diseases. (PMID: 15635645) Feng J. … Sommer S.S. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2005) 3 23 48
  5. The human tumor antigen PRAME is a dominant repressor of retinoic acid receptor signaling. (PMID: 16179254) Epping M.T. … Bernards R. (Cell 2005) 3 4 23

Products for RARA Gene

  • Addgene plasmids for RARA

Sources for RARA Gene

Back to Top

Content