CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-003923
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Retinoic acid receptor alpha 
Protein Synonyms/Alias
 RAR-alpha; Nuclear receptor subfamily 1 group B member 1 
Gene Name
 Rara 
Gene Synonyms/Alias
 Nr1b1 
Created Date
 July 27, 2013 
Organism
 Mus musculus (Mouse) 
NCBI Taxa ID
 10090 
Lysine Modification
Position
Peptide
Type
References
109VSACEGCKGFFRRSImethylation[1]
171KKKKEAPKPECSESYmethylation[1]
347QDLEQPDKVDMLQEPmethylation[2, 3]
Reference
 [1] Modulation of retinoic acid receptor alpha activity by lysine methylation in the DNA binding domain.
 Huq MD, Ha SG, Wei LN.
 J Proteome Res. 2008 Oct;7(10):4538-45. [PMID: 18781795]
 [2] Lysine trimethylation of retinoic acid receptor-alpha: a novel means to regulate receptor function.
 Huq MD, Tsai NP, Khan SA, Wei LN.
 Mol Cell Proteomics. 2007 Apr;6(4):677-88. [PMID: 17205979]
 [3] Update on activities at the Universal Protein Resource (UniProt) in 2013.
 e="String">UniProt Consortium.
 Nucleic Acids Res. 2013 Jan;41(Database issue):D43-7. [PMID: 23161681] 
Functional Description
 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. Regulates expression of target genes in a ligand-dependent manner by recruiting chromatin complexes containing KMT2E/MLL5. Mediates retinoic acid-induced granulopoiesis. 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. 
Sequence Annotation
 DNA_BIND 88 153 Nuclear receptor.
 ZN_FING 88 108 NR C4-type.
 ZN_FING 124 148 NR C4-type.
 REGION 1 87 Modulating.
 REGION 154 199 Hinge.
 REGION 200 419 Ligand-binding.
 REGION 404 419 Required for binding corepressor NCOR1.
 MOD_RES 77 77 Phosphoserine; by CDK7.
 MOD_RES 96 96 Phosphoserine; by PKB/AKT1 (By
 MOD_RES 219 219 Phosphoserine; by PKA (By similarity).
 MOD_RES 347 347 N6,N6,N6-trimethyllysine.
 MOD_RES 369 369 Phosphoserine; by PKA and RPS6KA5.
 CROSSLNK 166 166 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 171 171 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 399 399 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 Alternative splicing; Complete proteome; Cytoplasm; Direct protein sequencing; DNA-binding; Isopeptide bond; Metal-binding; Methylation; Nucleus; Phosphoprotein; Polymorphism; Receptor; Reference proteome; Transcription; Transcription regulation; Ubl conjugation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 462 AA 
Protein Sequence
MASNSSSCPT PGGGHLNGYP VPPYAFFFPP MLGGLSPPGA LTSLQHQLPV SGYSTPSPAT 60
IETQSSSSEE IVPSPPSPPP LPRIYKPCFV CQDKSSGYHY GVSACEGCKG FFRRSIQKNM 120
VYTCHRDKNC IINKVTRNRC QYCRLQKCFD VGMSKESVRN DRNKKKKEAP KPECSESYTL 180
TPEVGELIEK VRKAHQETFP ALCQLGKYTT NNSSEQRVSL DIDLWDKFSE LSTKCIIKTV 240
EFAKQLPGFT TLTIADQITL LKAACLDILI LRICTRYTPE QDTMTFSDGL TLNRTQMHNA 300
GFGPLTDLVF AFANQLLPLE MDDAETGLLS AICLICGDRQ DLEQPDKVDM LQEPLLEALK 360
VYVRKRRPSR PHMFPKMLMK ITDLRSISAK GAERVITLKM EIPGSMPPLI QEMLENSEGL 420
DTLSGQSGGG TRDGGGLAPP PGSCSPSLSP SSHRSSPATQ SP 462 
Gene Ontology
 GO:0005737; C:cytoplasm; IDA:MGI.
 GO:0030425; C:dendrite; IDA:MGI.
 GO:0043025; C:neuronal cell body; IDA:MGI.
 GO:0000790; C:nuclear chromatin; IEA:Compara.
 GO:0005634; C:nucleus; IDA:UniProtKB.
 GO:0031490; F:chromatin DNA binding; IEA:Compara.
 GO:0035014; F:phosphatidylinositol 3-kinase regulator activity; IEA:Compara.
 GO:0001972; F:retinoic acid binding; IEA:Compara.
 GO:0003708; F:retinoic acid receptor activity; IDA:MGI.
 GO:0044323; F:retinoic acid-responsive element binding; IEA:Compara.
 GO:0043565; F:sequence-specific DNA binding; IDA:MGI.
 GO:0003707; F:steroid hormone receptor activity; IEA:InterPro.
 GO:0003713; F:transcription coactivator activity; IEA:Compara.
 GO:0003714; F:transcription corepressor activity; IEA:Compara.
 GO:0044212; F:transcription regulatory region DNA binding; IMP:UniProtKB.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0043277; P:apoptotic cell clearance; IEA:Compara.
 GO:0071391; P:cellular response to estrogen stimulus; IEA:Compara.
 GO:0071222; P:cellular response to lipopolysaccharide; IDA:UniProtKB.
 GO:0071300; P:cellular response to retinoic acid; IEA:Compara.
 GO:0060591; P:chondroblast differentiation; IMP:MGI.
 GO:0007281; P:germ cell development; IMP:UniProtKB.
 GO:0003417; P:growth plate cartilage development; IGI:MGI.
 GO:0030520; P:intracellular estrogen receptor signaling pathway; IEA:Compara.
 GO:0035264; P:multicellular organism growth; IGI:MGI.
 GO:0061037; P:negative regulation of cartilage development; IMP:MGI.
 GO:0045596; P:negative regulation of cell differentiation; IMP:MGI.
 GO:0030853; P:negative regulation of granulocyte differentiation; IEA:Compara.
 GO:0032689; P:negative regulation of interferon-gamma production; IEA:Compara.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IDA:MGI.
 GO:0045892; P:negative regulation of transcription, DNA-dependent; IDA:MGI.
 GO:0045947; P:negative regulation of translational initiation; IDA:MGI.
 GO:0032720; P:negative regulation of tumor necrosis factor production; IEA:Compara.
 GO:0051099; P:positive regulation of binding; IEA:Compara.
 GO:0045787; P:positive regulation of cell cycle; IEA:Compara.
 GO:0008284; P:positive regulation of cell proliferation; IGI:MGI.
 GO:0070374; P:positive regulation of ERK1 and ERK2 cascade; IEA:Compara.
 GO:0010628; P:positive regulation of gene expression; IMP:UniProtKB.
 GO:0032736; P:positive regulation of interleukin-13 production; IEA:Compara.
 GO:0032753; P:positive regulation of interleukin-4 production; IEA:Compara.
 GO:0032754; P:positive regulation of interleukin-5 production; IEA:Compara.
 GO:0014068; P:positive regulation of phosphatidylinositol 3-kinase cascade; IEA:Compara.
 GO:0051897; P:positive regulation of protein kinase B signaling cascade; IEA:Compara.
 GO:0045630; P:positive regulation of T-helper 2 cell differentiation; IEA:Compara.
 GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IEA:Compara.
 GO:0006468; P:protein phosphorylation; IEA:Compara.
 GO:0030852; P:regulation of granulocyte differentiation; IMP:MGI.
 GO:0032355; P:response to estradiol stimulus; IEA:Compara.
 GO:0032526; P:response to retinoic acid; IMP:MGI.
 GO:0060010; P:Sertoli cell fate commitment; IMP:UniProtKB.
 GO:0007283; P:spermatogenesis; IMP:MGI.
 GO:0001657; P:ureteric bud development; IMP:MGI.
 GO:0055012; P:ventricular cardiac muscle cell differentiation; IMP:MGI. 
Interpro
 IPR008946; Nucl_hormone_rcpt_ligand-bd.
 IPR000536; Nucl_hrmn_rcpt_lig-bd_core.
 IPR003078; Retinoic_acid_rcpt.
 IPR001723; Str_hrmn_rcpt.
 IPR001628; Znf_hrmn_rcpt.
 IPR013088; Znf_NHR/GATA. 
Pfam
 PF00104; Hormone_recep
 PF00105; zf-C4 
SMART
 SM00430; HOLI
 SM00399; ZnF_C4 
PROSITE
 PS00031; NUCLEAR_REC_DBD_1
 PS51030; NUCLEAR_REC_DBD_2 
PRINTS
 PR01292; RETNOICACIDR.
 PR00398; STRDHORMONER.
 PR00047; STROIDFINGER.