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UniProtKB - P11416 (RARA_MOUSE)

Entry version 215 (13 Nov 2019)
Sequence version 1 (01 Oct 1989)
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Protein

Retinoic acid receptor alpha

Gene

Rara

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Receptor for retinoic acid (PubMed:17205979). 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 (PubMed:17205979). The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5 (PubMed:17205979). In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone deacetylation, chromatin condensation and transcriptional suppression (By similarity). On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation (PubMed:17205979, PubMed:9230306, PubMed:19078967). Formation of heterocomplex with histone deacetylases might lead to inhibition of RARE DNA element binding and to transcriptional repression (By similarity). Transcriptional activation and RARE DNA element binding might be supported by the transcription factor KLF2 (By similarity). RARA plays an essential role in the regulation of retinoic acid-induced germ cell development during spermatogenesis (PubMed:15901285). Has a role in the survival of early spermatocytes at the beginning prophase of meiosis (PubMed:15901285, PubMed:17905941). In Sertoli cells, may promote the survival and development of early meiotic prophase spermatocytes (PubMed:10660575, PubMed:17905941). In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function (PubMed:19389355). Together with RXRA, positively regulates microRNA-10a expression, thereby inhibiting the GATA6/VCAM1 signaling response to pulsatile shear stress in vascular endothelial cells (By similarity). In association with HDAC3, HDAC5 and HDAC7 corepressors, plays a role in the repression of microRNA-10a and thereby promotes the inflammatory response (By similarity).By similarity7 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section specifies the position and type of each DNA-binding domain present within the protein.<p><a href='/help/dna_bind' target='_top'>More...</a></p>DNA bindingi88 – 153Nuclear receptorPROSITE-ProRule annotationAdd BLAST66
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri88 – 108NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri124 – 148NR C4-typePROSITE-ProRule annotationAdd BLAST25

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionDNA-binding, Receptor
Biological processTranscription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...Reactomei		R-MMU-383280 Nuclear Receptor transcription pathway
R-MMU-4090294 SUMOylation of intracellular receptors
R-MMU-5362517 Signaling by Retinoic Acid
R-MMU-9616222 Transcriptional regulation of granulopoiesis

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Retinoic acid receptor alpha
Short name:
RAR-alpha
Alternative name(s):
Nuclear receptor subfamily 1 group B member 1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:Rara
Synonyms:Nr1b1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiMus musculus (Mouse)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri10090 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Mus › Mus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000589 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 11

Organism-specific databases

Mouse genome database (MGD) from Mouse Genome Informatics (MGI)

More...MGIi		MGI:97856 Rara

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Seminiferous tubules of 6 month-old animals display varying degrees of testicular degeneration, with moderate to severe levels of germ-cell degeneration. Epithelial cells in the epididymis show general disorganization. Sperm count is reduced to about 1.7% of wild-type and sperm mobility reduced by half. Rara and Rarg, but not Rara and Rarb, double knockout mice exhibit growth retardation after 3 weeks. Defects are found in the growth plates with deficiency in cartilage. Growth retardation was noticable in limb sketal elements such as femurs. Early lethality and male sterility due to squamous metaplasia of the seminal vesicles and prostate are also observed.3 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi74S → A: No effect on phosphorylation, no effect on transcriptional activity. 1 Publication1
Mutagenesisi77S → A: Decreases phosphorylation and no effect on interaction with CDK7. Strongly reduces transcriptional activity. 2 Publications1
Mutagenesisi347K → A or Q: Greatly reduced interaction with RXRA and NCOR1 and transcriptional activation. 1 Publication1
Mutagenesisi347K → F: Reduced methylation levels. Little effect on interaction with RXRA or NCOR1. Small loss in transcriptional activation. 1 Publication1
Mutagenesisi369S → A: Abolishes phosphorylation and prevents phosphorylation of S-77. 1 Publication1
Mutagenesisi449S → A: No change in phosphorylation levels and no effect on transcriptional activity. 1 Publication1
Mutagenesisi456S → A: No change in phosphorylation levels and no effect on transcriptional activity. 1 Publication1
Mutagenesisi461S → A: No change in phosphorylation levels and no effect on transcriptional activity. 1 Publication1

Chemistry databases

ChEMBL database of bioactive drug-like small molecules

More...ChEMBLi		CHEMBL2792

DrugCentral

More...DrugCentrali		P11416

IUPHAR/BPS Guide to PHARMACOLOGY

More...GuidetoPHARMACOLOGYi		590

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000534621 – 462Retinoic acid receptor alphaAdd BLAST462

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei77Phosphoserine; by CDK72 Publications1
Modified residuei96Phosphoserine; by PKB/AKT1By similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section describes <strong>covalent linkages</strong> of various types formed <strong>between two proteins (interchain cross-links)</strong> or <strong>between two parts of the same protein (intrachain cross-links)</strong>, except the disulfide bonds that are annotated in the <a href="http://www.uniprot.org/manual/disulfid">'Disulfide bond'</a> subsection.<p><a href='/help/crosslnk' target='_top'>More...</a></p>Cross-linki166Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
Cross-linki171Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
Modified residuei219Phosphoserine; by PKABy similarity1
Modified residuei347N6,N6,N6-trimethyllysine1 Publication1
Modified residuei369Phosphoserine; by PKA and RPS6KA51 Publication1
Cross-linki399Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Phosphorylated on serine and threonine residues. Phosphorylation does not change during cell cycle. Phosphorylation on Ser-77 is crucial for the N-terminal AF1 transcriptional activity. Under stress conditions, MAPK8 enhances phosphorylation on Thr-181, Ser-445 and Ser-461 leading to RARA ubiquitination and degradation. Phosphorylation by AKT1 inhibits the transactivation activity. On retinoic acid stimulation, phosphorylation on Ser-369 by RPS6KA5 promotes interaction with GTF2H3 and the CDK7-mediated phosphorylation of Ser-77.3 Publications
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 (By similarity).By similarity
Acetylated; acetylation is increased upon pulsatile shear stress and decreased upon oscillatory shear stress.By similarity

Keywords - PTMi

Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P11416

PRoteomics IDEntifications database

More...PRIDEi		P11416

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		P11416

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

More...PhosphoSitePlusi		P11416

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms. By default, the information is derived from experiments at the mRNA level, unless specified ‘at protein level’. <br></br>Examples: <a href="http://www.uniprot.org/uniprot/P92958#expression">P92958</a>, <a href="http://www.uniprot.org/uniprot/Q8TDN4#expression">Q8TDN4</a>, <a href="http://www.uniprot.org/uniprot/O14734#expression">O14734</a><p><a href='/help/tissue_specificity' target='_top'>More...</a></p>Tissue specificityi

Expressed in Sertoli cells and germ cells.1 Publication

<p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

By retinoic acid.1 Publication

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...Bgeei		ENSMUSG00000037992 Expressed in 214 organ(s), highest expression level in head

ExpressionAtlas, Differential and Baseline Expression

More...ExpressionAtlasi		P11416 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...Genevisiblei		P11416 MM

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Heterodimer; with RXRA (PubMed:17205979). Binds DNA preferentially as a heterodimer (By similarity). RXRA serves as enhancer to induce RARA binding to RARE (By similarity).

Interacts with RXRG (By similarity).

Interacts with NCOA3 and NCOA6 coactivators, leading to a strong increase of transcription of target genes (PubMed:10788465, PubMed:9192892).

Interacts with NCOA7; the interaction requires ligand-binding (By similarity).

Interacts (via the ligand-binding domain) with PRAME; interaction is direct and ligand (retinoic acid)-dependent (By similarity).

Interacts with PRKAR1A; the interaction negatively regulates RARA transcriptional activity (By similarity).

Interacts with NCOR1; the interaction occurs in the absence of ligand and represses transcriptional activity (PubMed:17205979).

Interacts with NCOR2 (By similarity).

Interacts with PRMT2 (By similarity).

Interacts with LRIF1 (By similarity).

Interacts with ASXL1 and NCOA1 (By similarity).

Interacts with ACTN4 (By similarity).

Interacts with CDK7; the interaction is enhanced by interaction with GTF2H3 (PubMed:9230306).

Interacts with GTF2H3; the interaction requires prior phosphorylation on Ser-369 which then enhances interaction with CDK7 (PubMed:19078967). In a complex with HDAC3, HDAC5 and HDAC7; the HDACs serve as corepressors of RARA, causing its deacetylation and inhibition of RARE DNA element binding; association with HDAC3, HDAC5 and HDAC7 is increased upon oscillatory shear stress (By similarity). In the absence of hormonal ligand, interacts with TACC1 (PubMed:20078863).

By similarity6 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

GO - Molecular functioni

Complete GO annotation on QuickGO ...

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		202586, 74 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...ComplexPortali		CPX-584 RXRalpha-RARalpha retinoic acid receptor complex
CPX-818 RXRalpha-RARalpha-NCOA2 retinoic acid receptor complex

Database of interacting proteins

More...DIPi		DIP-31480N

Protein interaction database and analysis system

More...IntActi		P11416, 15 interactors

Molecular INTeraction database

More...MINTi		P11416

STRING: functional protein association networks

More...STRINGi		10090.ENSMUSP00000069744

Chemistry databases

BindingDB database of measured binding affinities

More...BindingDBi		P11416

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P11416

Database of comparative protein structure models

More...ModBasei		Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini183 – 417NR LBDPROSITE-ProRule annotationAdd BLAST235

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 87ModulatingAdd BLAST87
Regioni154 – 182HingeAdd BLAST29
Regioni404 – 419Required for binding corepressor NCOR1Add BLAST16

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a short (usually not more than 20 amino acids) conserved sequence motif of biological significance.<p><a href='/help/motif' target='_top'>More...</a></p>Motifi408 – 4169aaTADBy similarity9

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
The 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.By similarity

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the nuclear hormone receptor family. NR1 subfamily.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri88 – 108NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri124 – 148NR C4-typePROSITE-ProRule annotationAdd BLAST25

Keywords - Domaini

Zinc-finger

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG3575 Eukaryota
ENOG410XRZC LUCA

Ensembl GeneTree

More...GeneTreei		ENSGT00940000159997

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000010312

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P11416

KEGG Orthology (KO)

More...KOi		K08527

Identification of Orthologs from Complete Genome Data

More...OMAi		AECSESY

Database of Orthologous Groups

More...OrthoDBi		1165737at2759

Database for complete collections of gene phylogenies

More...PhylomeDBi		P11416

TreeFam database of animal gene trees

More...TreeFami		TF328382

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		1.10.565.10, 1 hit
3.30.50.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR035500 NHR-like_dom_sf
IPR000536 Nucl_hrmn_rcpt_lig-bd
IPR001723 Nuclear_hrmn_rcpt
IPR003078 Retinoic_acid_rcpt
IPR001628 Znf_hrmn_rcpt
IPR013088 Znf_NHR/GATA

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00104 Hormone_recep, 1 hit
PF00105 zf-C4, 1 hit

Protein Motif fingerprint database; a protein domain database

More...PRINTSi		PR01292 RETNOICACIDR
PR00398 STRDHORMONER
PR00047 STROIDFINGER

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00430 HOLI, 1 hit
SM00399 ZnF_C4, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF48508 SSF48508, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS51843 NR_LBD, 1 hit
PS00031 NUCLEAR_REC_DBD_1, 1 hit
PS51030 NUCLEAR_REC_DBD_2, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequences (2)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

This entry describes 2 <p>This subsection of the ‘Sequence’ section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by alternative splicing. AlignAdd to basket
Isoform Alpha-1 (identifier: P11416-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MASNSSSCPT PGGGHLNGYP VPPYAFFFPP MLGGLSPPGA LTSLQHQLPV 
        60         70         80         90        100
SGYSTPSPAT IETQSSSSEE IVPSPPSPPP LPRIYKPCFV CQDKSSGYHY 
       110        120        130        140        150
GVSACEGCKG FFRRSIQKNM VYTCHRDKNC IINKVTRNRC QYCRLQKCFD 
       160        170        180        190        200
VGMSKESVRN DRNKKKKEAP KPECSESYTL TPEVGELIEK VRKAHQETFP 
       210        220        230        240        250
ALCQLGKYTT NNSSEQRVSL DIDLWDKFSE LSTKCIIKTV EFAKQLPGFT 
       260        270        280        290        300
TLTIADQITL LKAACLDILI LRICTRYTPE QDTMTFSDGL TLNRTQMHNA 
       310        320        330        340        350
GFGPLTDLVF AFANQLLPLE MDDAETGLLS AICLICGDRQ DLEQPDKVDM 
       360        370        380        390        400
LQEPLLEALK VYVRKRRPSR PHMFPKMLMK ITDLRSISAK GAERVITLKM 
       410        420        430        440        450
EIPGSMPPLI QEMLENSEGL DTLSGQSGGG TRDGGGLAPP PGSCSPSLSP 
       460 
SSHRSSPATQ SP
Length:462
Mass (Da):50,735
Last modified:October 1, 1989 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i726F7799633A85AD
GO
Isoform Alpha-2 (identifier: P11416-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-60: MASNSSSCPT...SGYSTPSPAT → MYESVEVGGL...TPLWNGSNHS

Show »
Length:459
Mass (Da):50,935
Checksum:i15096242FF09896E
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti163N → K in AAA40031 (PubMed:2174108).Curated1
Sequence conflicti179T → S in AAA40031 (PubMed:2174108).Curated1
Sequence conflicti284M → L in AAA40031 (PubMed:2174108).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes natural variant(s) of the protein sequence.<p><a href='/help/variant' target='_top'>More...</a></p>Natural varianti391G → A in embryonal carcinoma cell line RAC65. 1
Natural varianti392 – 462Missing in embryonal carcinoma cell line RAC65. Add BLAST71

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes the sequence of naturally occurring alternative protein isoform(s). The changes in the amino acid sequence may be due to alternative splicing, alternative promoter usage, alternative initiation, or ribosomal frameshifting.<p><a href='/help/var_seq' target='_top'>More...</a></p>Alternative sequenceiVSP_0036301 – 60MASNS…PSPAT → MYESVEVGGLTPAPNPFLVV DFYNQNRACLLQEKGLPAPG PYSTPLRTPLWNGSNHS in isoform Alpha-2. 1 PublicationAdd BLAST60

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
X56572 mRNA Translation: CAA39919.1
X56565 mRNA Translation: CAA39917.1
S56656 mRNA Translation: AAB25783.1
X57528 mRNA Translation: CAA40749.1
M60909 mRNA Translation: AAA40031.1
BC010216 mRNA Translation: AAH10216.1

The Consensus CDS (CCDS) project

More...CCDSi		CCDS36304.1 [P11416-1]
CCDS48905.1 [P11416-2]

Protein sequence database of the Protein Information Resource

More...PIRi		S05050

NCBI Reference Sequences

More...RefSeqi		NP_001169999.1, NM_001176528.1 [P11416-2]
NP_001170773.1, NM_001177302.1 [P11416-1]
NP_001170774.1, NM_001177303.1 [P11416-1]
NP_033050.2, NM_009024.2 [P11416-1]
XP_006532655.1, XM_006532592.3 [P11416-1]
XP_006532656.1, XM_006532593.2 [P11416-1]
XP_017169842.1, XM_017314353.1

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...Ensembli		ENSMUST00000068133; ENSMUSP00000069744; ENSMUSG00000037992 [P11416-1]
ENSMUST00000107473; ENSMUSP00000103097; ENSMUSG00000037992 [P11416-2]
ENSMUST00000107474; ENSMUSP00000103098; ENSMUSG00000037992 [P11416-1]
ENSMUST00000107475; ENSMUSP00000103099; ENSMUSG00000037992 [P11416-1]
ENSMUST00000164748; ENSMUSP00000129791; ENSMUSG00000037992 [P11416-1]

Database of genes from NCBI RefSeq genomes

More...GeneIDi		19401

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		mmu:19401

UCSC genome browser

More...UCSCi		uc007lhx.1 mouse [P11416-1]
uc007lhz.2 mouse [P11416-2]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56572 mRNA Translation: CAA39919.1
X56565 mRNA Translation: CAA39917.1
S56656 mRNA Translation: AAB25783.1
X57528 mRNA Translation: CAA40749.1
M60909 mRNA Translation: AAA40031.1
BC010216 mRNA Translation: AAH10216.1
CCDSiCCDS36304.1 [P11416-1]
CCDS48905.1 [P11416-2]
PIRiS05050
RefSeqiNP_001169999.1, NM_001176528.1 [P11416-2]
NP_001170773.1, NM_001177302.1 [P11416-1]
NP_001170774.1, NM_001177303.1 [P11416-1]
NP_033050.2, NM_009024.2 [P11416-1]
XP_006532655.1, XM_006532592.3 [P11416-1]
XP_006532656.1, XM_006532593.2 [P11416-1]
XP_017169842.1, XM_017314353.1

3D structure databases

SMRiP11416
ModBaseiSearch...

Protein-protein interaction databases

BioGridi202586, 74 interactors
ComplexPortaliCPX-584 RXRalpha-RARalpha retinoic acid receptor complex
CPX-818 RXRalpha-RARalpha-NCOA2 retinoic acid receptor complex
DIPiDIP-31480N
IntActiP11416, 15 interactors
MINTiP11416
STRINGi10090.ENSMUSP00000069744

Chemistry databases

BindingDBiP11416
ChEMBLiCHEMBL2792
DrugCentraliP11416
GuidetoPHARMACOLOGYi590

PTM databases

iPTMnetiP11416
PhosphoSitePlusiP11416

Proteomic databases

PaxDbiP11416
PRIDEiP11416

Genome annotation databases

EnsembliENSMUST00000068133; ENSMUSP00000069744; ENSMUSG00000037992 [P11416-1]
ENSMUST00000107473; ENSMUSP00000103097; ENSMUSG00000037992 [P11416-2]
ENSMUST00000107474; ENSMUSP00000103098; ENSMUSG00000037992 [P11416-1]
ENSMUST00000107475; ENSMUSP00000103099; ENSMUSG00000037992 [P11416-1]
ENSMUST00000164748; ENSMUSP00000129791; ENSMUSG00000037992 [P11416-1]
GeneIDi19401
KEGGimmu:19401
UCSCiuc007lhx.1 mouse [P11416-1]
uc007lhz.2 mouse [P11416-2]

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		5914
MGIiMGI:97856 Rara

Phylogenomic databases

eggNOGiKOG3575 Eukaryota
ENOG410XRZC LUCA
GeneTreeiENSGT00940000159997
HOGENOMiHOG000010312
InParanoidiP11416
KOiK08527
OMAiAECSESY
OrthoDBi1165737at2759
PhylomeDBiP11416
TreeFamiTF328382

Enzyme and pathway databases

ReactomeiR-MMU-383280 Nuclear Receptor transcription pathway
R-MMU-4090294 SUMOylation of intracellular receptors
R-MMU-5362517 Signaling by Retinoic Acid
R-MMU-9616222 Transcriptional regulation of granulopoiesis

Miscellaneous databases

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

More...ChiTaRSi		Rara mouse

Protein Ontology

More...PROi		PR:P11416

The Stanford Online Universal Resource for Clones and ESTs

More...SOURCEi		Search...

Gene expression databases

BgeeiENSMUSG00000037992 Expressed in 214 organ(s), highest expression level in head
ExpressionAtlasiP11416 baseline and differential
GenevisibleiP11416 MM

Family and domain databases

Gene3Di1.10.565.10, 1 hit
3.30.50.10, 1 hit
InterProiView protein in InterPro
IPR035500 NHR-like_dom_sf
IPR000536 Nucl_hrmn_rcpt_lig-bd
IPR001723 Nuclear_hrmn_rcpt
IPR003078 Retinoic_acid_rcpt
IPR001628 Znf_hrmn_rcpt
IPR013088 Znf_NHR/GATA
PfamiView protein in Pfam
PF00104 Hormone_recep, 1 hit
PF00105 zf-C4, 1 hit
PRINTSiPR01292 RETNOICACIDR
PR00398 STRDHORMONER
PR00047 STROIDFINGER
SMARTiView protein in SMART
SM00430 HOLI, 1 hit
SM00399 ZnF_C4, 1 hit
SUPFAMiSSF48508 SSF48508, 1 hit
PROSITEiView protein in PROSITE
PS51843 NR_LBD, 1 hit
PS00031 NUCLEAR_REC_DBD_1, 1 hit
PS51030 NUCLEAR_REC_DBD_2, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRARA_MOUSE
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P11416
Secondary accession number(s): P22603
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: November 13, 2019
This is version 215 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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