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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret jlhuret@AtlasGeneticsOncology.org
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RARA (Retinoic acid receptor, alpha)

Identity

HGNC (Hugo) RARA
LocusID (NCBI) 5914
Location 17q21.2
Location_base_pair Starts at 38465423 and ends at 38513895 bp from pter ( according to hg19-Feb_2009)  [Mapping]
 
  c-RARA (17q21) in normal cells: PAC 833D9 - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics.

DNA/RNA

Description 9 exons; total gene sequence: 7450 bp
Transcription 2.8 and 3.6 kb transcripts

Protein

 
Description 462 amino acids - 5 functional domains A/B (transcriptional regulation), C (DNA binding domain, contains 2 zinc fingers), D (cellular localization signal), E (ligand-binding domain) and F (function?)
Expression in hematopoietic cells
Localisation nuclear
Function
  • ligand-dependent transcription factor specifically involved in hematopoietic cells differentiation and maturation = receptor for all-trans retinoic acid (ATRA) and 9-cis RA which are intracellular metabolites of vitamine A, active in cellular differentiation and morphogenesis
  • after linking with ATRA, RARA binds with a high affinity as a heterodimer with RXR (retinoid X receptor protein) to the RARE domain (retinoic acid response elements), a DNA sequence common to a number of genes and located in their promoter
  • the gene response to RARA binding is modulated by a series of co-repressors and co-activators
    • Homology with RARB and RARG (retinoic acid receptors ? and ?), 9-cis RA receptors (RXRs) and receptors for thyroid and steroid hormones and for vitamine D3

    Implicated in

    Entity t(15;17)(q24;q21) / acute promyelocytic leukemia (APL) -->PML - RARA
    Disease typical APL (or M3 ANLL, FAB classification), approximately 98% of APL cases; abnormal promyelocytes with Auer rods and bundles (faggots); disruption of the PODs with a microspeckeled pattern; maturation response to all-trans retinoic acid (ATRA) therapy
    Prognosis immediate prognosis impaired by intravascular disseminated coagulopathy; long term prognosis is favorable with treatment combining ATRA plus chemotherapy
    Cytogenetics variant or complex t(15;17) translocation in 5% of cases, no known prognosis implication; secondary chromosomal abnormalities in 30 to 35% of APL at diagnosis; association with +8 in 17 to 28% of cases; other associations are rare but recurrent: del(7q), del(9q), ider(17)t(15;17), +21
    Hybrid/Mutated Gene
  • the crucial fusion transcript is 5'PML-3'RARA, encoded by der(15) chromosome; the counterpart 5'RARA-3'PML encoded by der(17) is inconstant
  • breakpoint in RARA gene is always located in intron between A and B domains
  • three breakpoint clusters in PML gene: bcr1 (70% of patients), bcr2 (10%) and bcr3 (20%), giving rise respectively to the long (L), intermediate (V) and short (S) length hybrid PML-RARAtranscripts; V form would be linked to ATRA decreased sensitivity and S form to association with an excess of secondary chromosome changes.
    • Abnormal Protein 106 Kda fusion protein; role in the leukemogenic process by probable interference with the signalling pathway leading to differentiation and maturation of myeloid precursors (mainly dysregulation of retinoid-inducible genes involved in myeloid differentiation)
      
    Entity t(11;17)(q23;q12) / acute promyelocytic leukemia -->PLZF-RARA
    Disease variant acute promyelocytic leukemia (APL) form with atypical cytologic aspects (intermediate morphology between M2 and M3, no Auer rods) and no response to ATRA therapy; less than 1% of APL cases.
      
    Entity t(5;17)(q35;q12) / acute promyelocytic leukemia --> NPM-RARA
    Disease exceptional; probable response to ATRA
      
    Entity t(11;17)(q13;q12) / acute promyelocytic leukemia --> NuMA-RARA
    Disease exceptional: probable response to ATRA
      
    Entity t(11;17)(q23;q12) / M5 acute non lymphocytic leukemia --> MLL-RARA
    Disease 1 case to date; not to be confused with the t(11;17)(q23;q12) mentioned above; not found in APL; belongs to the MLL/11q23 leukemias
      

    Breakpoints

     

    Other Leukemias implicated (Data extracted from papers in the Atlas)

    Leukemias 11q23ChildAMLID1615 11q23ID1030 11q23secondLeukID1131 t1119ELLID1029 t0812q24q22ID2057
    t0814ID1050 8p11inMPDID1091 inv8p11q13ID1189 PrimarCutanALCLID2118 t0708q34p11ID1409
    t0809p12q33ID1129 t0811p11p15ID1200 t0811p12p15ID1521 t0812p12p11ID1330 t0812p12q15ID1201

    External links

    Nomenclature
    HGNC (Hugo)RARA   9864
    Cards
    AtlasRARAID46
    Entrez_Gene (NCBI)RARA  5914  retinoic acid receptor, alpha
    GeneCards (Weizmann)RARA
    Ensembl hg19 (Hinxton) [Gene_View]  chr17:38465423-38513895 [Contig_View]  RARA [Vega]
    Ensembl hg38 (Hinxton) [Gene_View]  chr17:38465423-38513895 [Contig_View]  RARA [Vega]
    cBioPortalRARA
    AceView (NCBI)RARA
    Genatlas (Paris)RARA
    WikiGenes5914
    SOURCE (Princeton)RARA
    Genomic and cartography
    GoldenPath hg19 (UCSC)RARA  -     chr17:38465423-38513895 +  17q21   [Description]    (hg19-Feb_2009)
    GoldenPath hg38 (UCSC)RARA  -     17q21   [Description]    (hg38-Dec_2013)
    EnsemblRARA - 17q21 [CytoView hg19]  RARA - 17q21 [CytoView hg38]
    Mapping of homologs : NCBIRARA [Mapview hg19]  RARA [Mapview hg38]
    OMIM180240   612376   
    Gene and transcription
    Genbank (Entrez)AK098172 AK130192 AK292205 AK303868 AK312564
    RefSeq transcript (Entrez)NM_000964 NM_001024809 NM_001033603 NM_001145301 NM_001145302
    RefSeq genomic (Entrez)AC_000149 NC_000017 NC_018928 NG_027701 NT_010783 NW_001838435 NW_004929407
    Consensus coding sequences : CCDS (NCBI)RARA
    Cluster EST : UnigeneHs.654583 [ NCBI ]
    CGAP (NCI)Hs.654583
    Alternative Splicing : Fast-db (Paris)GSHG0012478
    Gene ExpressionRARA [ NCBI-GEO ]     RARA [ SEEK ]   RARA [ MEM ]
    SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
    Protein : pattern, domain, 3D structure
    UniProt/SwissProtP10276 (Uniprot)
    NextProtP10276  [Medical]
    With graphics : InterProP10276
    Splice isoforms : SwissVarP10276 (Swissvar)
    Domaine pattern : Prosite (Expaxy)NUCLEAR_REC_DBD_1 (PS00031)    NUCLEAR_REC_DBD_2 (PS51030)   
    Domains : Interpro (EBI)Nucl_hormone_rcpt_ligand-bd    Nucl_hrmn_rcpt_lig-bd_core    Retinoic_acid_rcpt    Str_hrmn_rcpt    Znf_hrmn_rcpt    Znf_NHR/GATA   
    Related proteins : CluSTrP10276
    Domain families : Pfam (Sanger)Hormone_recep (PF00104)    zf-C4 (PF00105)   
    Domain families : Pfam (NCBI)pfam00104    pfam00105   
    Domain families : Smart (EMBL)HOLI (SM00430)  ZnF_C4 (SM00399)  
    DMDM Disease mutations5914
    Blocks (Seattle)P10276
    PDB (SRS)1DKF    1DSZ    3A9E    3KMR    3KMZ    4DQM   
    PDB (PDBSum)1DKF    1DSZ    3A9E    3KMR    3KMZ    4DQM   
    PDB (IMB)1DKF    1DSZ    3A9E    3KMR    3KMZ    4DQM   
    PDB (RSDB)1DKF    1DSZ    3A9E    3KMR    3KMZ    4DQM   
    Peptide AtlasP10276
    HPRD06769
    IPIIPI00020071   IPI00218375   IPI00908598   IPI00470378   IPI00922641   IPI00014923   IPI00791851   
    Protein Interaction databases
    DIP (DOE-UCLA)P10276
    IntAct (EBI)P10276
    BioGRIDRARA
    IntegromeDBRARA
    STRING (EMBL)RARA
    Ontologies - Pathways
    QuickGOP10276
    Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  nuclear chromatin  translation repressor activity, nucleic acid binding  ureteric bud development  liver development  retinoic acid binding  growth plate cartilage development  sequence-specific DNA binding transcription factor activity  steroid hormone receptor activity  retinoic acid receptor activity  transcription coactivator activity  transcription coactivator activity  transcription corepressor activity  receptor binding  protein binding  nucleus  nucleoplasm  cytoplasm  transcription initiation from RNA polymerase II promoter  protein phosphorylation  signal transduction  germ cell development  spermatogenesis  female pregnancy  transcription factor binding  drug binding  zinc ion binding  positive regulation of cell proliferation  negative regulation of cell proliferation  cell surface  gene expression  positive regulation of phosphatidylinositol 3-kinase signaling  enzyme binding  protein domain specific binding  dendrite  intracellular estrogen receptor signaling pathway  prostate gland development  negative regulation of granulocyte differentiation  chromatin DNA binding  regulation of myelination  response to estradiol  response to retinoic acid  negative regulation of interferon-gamma production  negative regulation of tumor necrosis factor production  positive regulation of interleukin-13 production  positive regulation of interleukin-4 production  positive regulation of interleukin-5 production  response to vitamin A  response to cytokine  phosphatidylinositol 3-kinase regulator activity  multicellular organism growth  regulation of apoptotic process  neuronal cell body  apoptotic cell clearance  steroid hormone mediated signaling pathway  protein kinase B binding  regulation of phosphatidylinositol 3-kinase activity  sequence-specific DNA binding  retinoic acid-responsive element binding  response to ethanol  positive regulation of T-helper 2 cell differentiation  positive regulation of neuron differentiation  positive regulation of cell cycle  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  negative regulation of translational initiation  protein heterodimerization activity  mRNA 5'-UTR binding  regulation of synaptic plasticity  retinoic acid receptor signaling pathway  perinuclear region of cytoplasm  protein kinase A binding  positive regulation of binding  positive regulation of protein kinase B signaling  ventricular cardiac muscle cell differentiation  Sertoli cell fate commitment  chondroblast differentiation  negative regulation of cartilage development  positive regulation of ERK1 and ERK2 cascade  cellular response to lipopolysaccharide  cellular response to retinoic acid  cellular response to estrogen stimulus  
    Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  nuclear chromatin  translation repressor activity, nucleic acid binding  ureteric bud development  liver development  retinoic acid binding  growth plate cartilage development  sequence-specific DNA binding transcription factor activity  steroid hormone receptor activity  retinoic acid receptor activity  transcription coactivator activity  transcription coactivator activity  transcription corepressor activity  receptor binding  protein binding  nucleus  nucleoplasm  cytoplasm  transcription initiation from RNA polymerase II promoter  protein phosphorylation  signal transduction  germ cell development  spermatogenesis  female pregnancy  transcription factor binding  drug binding  zinc ion binding  positive regulation of cell proliferation  negative regulation of cell proliferation  cell surface  gene expression  positive regulation of phosphatidylinositol 3-kinase signaling  enzyme binding  protein domain specific binding  dendrite  intracellular estrogen receptor signaling pathway  prostate gland development  negative regulation of granulocyte differentiation  chromatin DNA binding  regulation of myelination  response to estradiol  response to retinoic acid  negative regulation of interferon-gamma production  negative regulation of tumor necrosis factor production  positive regulation of interleukin-13 production  positive regulation of interleukin-4 production  positive regulation of interleukin-5 production  response to vitamin A  response to cytokine  phosphatidylinositol 3-kinase regulator activity  multicellular organism growth  regulation of apoptotic process  neuronal cell body  apoptotic cell clearance  steroid hormone mediated signaling pathway  protein kinase B binding  regulation of phosphatidylinositol 3-kinase activity  sequence-specific DNA binding  retinoic acid-responsive element binding  response to ethanol  positive regulation of T-helper 2 cell differentiation  positive regulation of neuron differentiation  positive regulation of cell cycle  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  negative regulation of translational initiation  protein heterodimerization activity  mRNA 5'-UTR binding  regulation of synaptic plasticity  retinoic acid receptor signaling pathway  perinuclear region of cytoplasm  protein kinase A binding  positive regulation of binding  positive regulation of protein kinase B signaling  ventricular cardiac muscle cell differentiation  Sertoli cell fate commitment  chondroblast differentiation  negative regulation of cartilage development  positive regulation of ERK1 and ERK2 cascade  cellular response to lipopolysaccharide  cellular response to retinoic acid  cellular response to estrogen stimulus  
    Pathways : BIOCARTAMap Kinase Inactivation of SMRT Corepressor [Genes]    Nuclear Receptors in Lipid Metabolism and Toxicity [Genes]    Transcription Regulation by Methyltransferase of CARM1 [Genes]    Degradation of the RAR and RXR by the proteasome [Genes]    Regulation of transcriptional activity by PML [Genes]    Nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells [Genes]   
    Pathways : KEGGPathways in cancer    Transcriptional misregulation in cancer    Acute myeloid leukemia   
    REACTOMEP10276 [protein]
    REACTOME PathwaysREACT_71 Gene Expression [pathway]
    Protein Interaction DatabaseRARA
    DoCM (Curated mutations)RARA
    Wikipedia pathwaysRARA
    Gene fusion - rearrangements
    Rearrangement : TICdbBCOR [Xp11.4]  -  RARA [5q32]
    Rearrangement : TICdbFIP1L1 [4q12]  -  RARA [8q22.2]
    Rearrangement : TICdbNABP1 [2q32.3]  -  RARA [7p15.2]
    Rearrangement : TICdbNPM1 [5q35.1]  -  RARA [3q12.2]
    Rearrangement : TICdbNUMA1 [11q13.4]  -  RARA [1q24.2]
    Rearrangement : TICdbPML [15q24.1]  -  RARA [8q21.3]
    Rearrangement : TICdbPRKAR1A [17q24.2]  -  RARA [1p35.3]
    Rearrangement : TICdbSTAT5B [17q21.2]  -  RARA [-]
    Rearrangement : TICdbZBTB16 [11q23.2]  -  RARA []
    Polymorphisms : SNP, variants
    NCBI Variation ViewerRARA [hg38]
    dbSNP Single Nucleotide Polymorphism (NCBI)RARA
    dbVarRARA
    ClinVarRARA
    1000_GenomesRARA 
    Exome Variant ServerRARA
    SNP (GeneSNP Utah)RARA
    SNP : HGBaseRARA
    Genetic variants : HAPMAPRARA
    Genomic Variants (DGV)RARA [DGVbeta]
    Mutations
    Cancer Gene: CensusRARA 
    Somatic Mutations in Cancer : COSMICRARA 
    CONAN: Copy Number AnalysisRARA 
    LOVD (Leiden Open Variation Database)Whole genome datasets
    LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
    Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
    Diseases
    DECIPHER (Syndromes)17:38465423-38513895
    Mutations and Diseases : HGMDRARA
    OMIM180240    612376   
    MedgenRARA
    NextProtP10276 [Medical]
    GENETestsRARA
    Disease Genetic AssociationRARA
    Huge Navigator RARA [HugePedia]  RARA [HugeCancerGEM]
    snp3D : Map Gene to Disease5914
    DGIdb (Drug Gene Interaction db)RARA
    General knowledge
    Homologs : HomoloGeneRARA
    Homology/Alignments : Family Browser (UCSC)RARA
    Phylogenetic Trees/Animal Genes : TreeFamRARA
    Chemical/Protein Interactions : CTD5914
    Chemical/Pharm GKB GenePA34225
    Clinical trialRARA
    Other databases
    Probes
    ProbeRARA (17q21) in normal cells (Bari)
    Litterature
    PubMed332 Pubmed reference(s) in Entrez
    CoreMineRARA
    GoPubMedRARA
    iHOPRARA

    Bibliography

    The t(15;17) translocation of acute promyelocytic leukaemia fuses the retinoic acid receptor alpha gene to a novel transcribed locus.
    de Thˆ© H, Chomienne C, Lanotte M, Degos L, Dejean A
    Nature. 1990 ; 347 (6293) : 558-561.
    PMID 2170850
     
    Chromosomal translocation t(15;17) in human acute promyelocytic leukemia fuses RAR alpha with a novel putative transcription factor, PML.
    Kakizuka A, Miller WH Jr, Umesono K, Warrell RP Jr, Frankel SR, Murty VV, Dmitrovsky E, Evans RM
    Cell. 1991 ; 66 (4) : 663-674.
    PMID 1652368
     
    Characterization of the PML-RAR alpha chimeric product of the acute promyelocytic leukemia-specific t(15;17) translocation.
    Nervi C, Poindexter EC, Grignani F, Pandolfi PP, Lo Coco F, Avvisati G, Pelicci PG, Jetten AM
    Cancer research. 1992 ; 52 (13) : 3687-3692.
    PMID 1319828
     
    Genetics of APL and the molecular basis of retinoic acid treatment.
    Casini T, Grignani F, Pelicci PG
    International journal of cancer. Journal international du cancer. 1997 ; 70 (4) : 473-474.
    PMID 9033658
     
    The pathogenesis of acute promyelocytic leukaemia: evaluation of the role of molecular diagnosis and monitoring in the management of the disease.
    Grimwade D
    British journal of haematology. 1999 ; 106 (3) : 591-613.
    PMID 10468848
     
    Deconstructing a disease: RARalpha, its fusion partners, and their roles in the pathogenesis of acute promyelocytic leukemia.
    Melnick A, Licht JD
    Blood. 1999 ; 93 (10) : 3167-3215.
    PMID 10233871
     
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

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    Contributor(s)

    Written10-2000Franck Viguié

    Citation

    This paper should be referenced as such :
    Viguié, F
    RARA (retinoic acid receptor, alpha)
    Atlas Genet Cytogenet Oncol Haematol. 2000;4(4):195-196.
    Free journal version : [ pdf ]   [ DOI ]
    URL : http://AtlasGeneticsOncology.org/Genes/RARAID46.html

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    indexed on : Tue Feb 17 20:33:06 CET 2015
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