Atlas of Genetics and Cytogenetics in Oncology and Haematology

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   
X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

RARA (Retinoic acid receptor, alpha)

Written2000-10Franck Vigué
Laboratoire de Cytogenetique - Service d'Hematologie Biologique, Hopital Hotel-Dieu - 75181 Paris Cedex 04, France

(Note : for Links provided by Atlas : click)

Identity

Alias_namesretinoic acid receptor
Alias_symbol (synonym)RAR
NR1B1
Other alias
HGNC (Hugo) RARA
LocusID (NCBI) 5914
Atlas_Id 46
Location 17q21.2  [Link to chromosome band 17q21]
Location_base_pair Starts at 40318221 and ends at 40357643 bp from pter ( according to hg19-Feb_2009)  [Mapping RARA.png]
 
  c-RARA (17q21) in normal cells: PAC 833D9 - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics.
 
  RARA (Retinoic acid receptor, alpha) Hybridization with LSI RARA Dual Color, Break Apart Rearrangement Probe (Abbott Molecular, US), showing the RARA gene on 17q21.2 (red-green or a fused yellow signal - Courtesy Adriana Zamecnikova.
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
- () / RARA (17q21.2)BCOR (Xp11.4) / RARA (17q21.2)CELF2 (10p14) / RARA (17q21.2)
ETV6 (12p13.2) / RARA (17q21.2)FIP1L1 (4q12) / RARA (17q21.2)GTF2I (7q11.23) / RARA (17q21.2)
H2AFV (7p13) / RARA (17q21.2)IRF2BP2 (1q42.3) / RARA (17q21.2)KMT2A (11q23.3) / RARA (17q21.2)
NABP1 (2q32.3) / RARA (17q21.2)NPM1 (5q35.1) / RARA (17q21.2)NUMA1 (11q13.4) / RARA (17q21.2)
PML (15q24.1) / RARA (17q21.2)PRKAR1A (17q24.2) / RARA (17q21.2)RARA (17q21.2) / BRD4 (19p13.12)
RARA (17q21.2) / CA10 (17q21.33)RARA (17q21.2) / CDC6 (17q21.2)RARA (17q21.2) / CDK12 (17q12)
RARA (17q21.2) / COL10A1 (6q22.1)RARA (17q21.2) / HOXB3 (17q21.32)RARA (17q21.2) / KMT2A (11q23.3)
RARA (17q21.2) / MSL1 (17q21.1)RARA (17q21.2) / MYO1D (17q11.2)RARA (17q21.2) / NARS2 (11q14.1)
RARA (17q21.2) / NPM1 (5q35.1)RARA (17q21.2) / NUMA1 (11q13.4)RARA (17q21.2) / PCTP (17q22)
RARA (17q21.2) / PGAP3 (17q12)RARA (17q21.2) / PKIA (8q21.12)RARA (17q21.2) / PML (15q24.1)
RARA (17q21.2) / POLDIP2 (17q11.2)RARA (17q21.2) / PRKAR1A (17q24.2)RARA (17q21.2) / PRR11 (17q22)
RARA (17q21.2) / PSMD3 (17q21.1)RARA (17q21.2) / RARA (17q21.2)RARA (17q21.2) / RP11-1407O15.2 ()
RARA (17q21.2) / SKAP1 (17q21.32)RARA (17q21.2) / STAC2 (17q12)RARA (17q21.2) / STAT3 (17q21.2)
RARA (17q21.2) / STAT5B (17q21.2)RARA (17q21.2) / TIF1 ()RARA (17q21.2) / TMEM94 (17q25.1)
RARA (17q21.2) / TRIM24 (7q33)RARA (17q21.2) / WIPF2 (17q21.1)RARA (17q21.2) / ZBTB16 (11q23.2)
RARA (17q21.2) / ZNF145 ()RARA (17q21.2) / ZNF595 (4p16.3)SNU13 (22q13.2) / RARA (17q21.2)
STAT5A (17q21.2) / RARA (17q21.2)STAT5B (17q21.2) / RARA (17q21.2)TAOK1 (17q11.2) / RARA (17q21.2)
TBL1XR1 (3q26.32) / RARA (17q21.2)TMEM11 (17p11.2) / RARA (17q21.2)TPCN2 (11q13.3) / RARA (17q21.2)
TRIM24 (7q33) / RARA (17q21.2)ZBTB16 (11q23.2) / RARA (17q21.2)

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

    Note
      
    Entity t(15;17)(q24;q21) / acute promyelocytic leukemia (APL) -->PML - -RARA
    Disease typical APL (or M3 AML, 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 --> KMT2A -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

     

    Bibliography

    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
     
    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
     
    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
     
    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
     
    The t(15;17) translocation of acute promyelocytic leukaemia fuses the retinoic acid receptor alpha gene to a novel transcribed locus.
    de Thé H, Chomienne C, Lanotte M, Degos L, Dejean A
    Nature. 1990 ; 347 (6293) : 558-561.
    PMID 2170850
     

    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 ]
    On line version : http://AtlasGeneticsOncology.org/Genes/RARAID46.html

    Other Leukemias implicated (Data extracted from papers in the Atlas) [ 33 ]
      11q23 rearrangements (KMT2A) in leukaemia
    Classification of acute myeloid leukemias
    del(18)(p11)
    del(4)(q12q12) FIP1L1/PDGFRA
    M3/M3v acute myeloid leukemia (AML M3/M3v)
    ::Acute promyelocytic leukemia (APL)
    ::Acute promyelocytic leukemia (APL) PML/RARA
    t(1;17)(p34;q21) IRF2BP2/RARA
    t(2;17)(q32;q21) NABP1/RARA
    t(3;17)(q26;q12-21) TBL1XR1/RARA
    t(4;17)(q12;q21) FIP1L1/RARA
    t(5;11)(q33;q13) NUMA1/PDGFRB a novel fusion
    t(5;17)(q35;q21) without RARA involvement in non-M3 AML
    t(7;17)(q11;q21) GTF2I/RARA in APL
    t(X;17)(p11;q21) BCOR/RARA
    t(11;17)(q23;q21) ZBTB16/RARA
    t(11;17)(q13;q21) NUMA1/RARA
    t(11;17)(q23;q12) KMT2A/RARA
    t(11;17)(q23;q12-21) KMT2A/MMLT6
    t(11;17)(q23;q12-21) KMT2A/LASP1
    t(12;12)(p13;q13) ETV6/BAZ2A
    t(12;13)(p13;q14) LIN00598/ETV6
    t(15;17)(q24;q21) PML/RARA
    t(15;17)(q22;q21) in treatment related leukemia
    der(17)t(17;17)(p13;q12-21)
    t(17;17)(q21;q21) STAT5B/RARA::dup(17)(q12q21) STAT5B/RARA
    t(17;17)(q21;q24) PRKAR1A/RARA::del(17)(q21q24) PRKAR1A/RARA
    t(17;20)(q21;q11)
    t(5;17)(q35;q21) NPM1/RARA
    ins(15;17)(q22;q21q21) PML/CDC6/RARA
    ins(15;17)(q22;q21q26) PML/ADAMTS17/RARA
    t(1;17)(q42;q21) IRF2BP2/RARA
    t(12;17)(p13;q21) ETV6/RARA
    t(15;17)(q22;q21) RARA/PML
    t(15;17)(q22;q21)|t(15;17)(q24;q21) PML/RARA

    Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 21 ]
      t(4;17)(p16;q21) RARA/ZNF595
    t(6;17)(q22;q21) RARA/COL10A1
    t(8;17)(q21;q21) RARA/PKIA
    t(11;17)(q13;q21) TPCN2/RARA
    t(11;17)(q14;q21) RARA/NARS2
    t(17;17)(q11;q21) RARA/MYO1D
    t(17;17)(q11;q21) RARA/POLDIP2
    t(17;17)(q11;q21) TAOK1/RARA
    t(17;17)(q12;q21) RARA/CDK12
    t(17;17)(q12;q21) RARA/PGAP3
    t(17;17)(q12;q21) RARA/STAC2
    RARA/CDC6 (17q21)
    RARA/HOXB3 (17q21)
    RARA/MSL1 (17q21)
    RARA/PSMD3 (17q21)
    RARA/SKAP1 (17q21)
    RARA/STAT3 (17q21)
    RARA/WIPF2 (17q21)
    t(17;17)(q21;q22) RARA/CA10
    t(17;17)(q21;q22) RARA/PCTP
    t(17;17)(q21;q22) RARA/PRR11

    External links

    Nomenclature
    HGNC (Hugo)RARA   9864
    LRG (Locus Reference Genomic)LRG_1070
    Cards
    AtlasRARAID46
    Entrez_Gene (NCBI)RARA  5914  retinoic acid receptor alpha
    AliasesNR1B1; RAR
    GeneCards (Weizmann)RARA
    Ensembl hg19 (Hinxton)ENSG00000131759 [Gene_View]
    Ensembl hg38 (Hinxton)ENSG00000131759 [Gene_View]  ENSG00000131759 [Sequence]  chr17:40318221-40357643 [Contig_View]  RARA [Vega]
    ICGC DataPortalENSG00000131759
    TCGA cBioPortalRARA
    AceView (NCBI)RARA
    Genatlas (Paris)RARA
    WikiGenes5914
    SOURCE (Princeton)RARA
    Genetics Home Reference (NIH)RARA
    Genomic and cartography
    GoldenPath hg38 (UCSC)RARA  -     chr17:40318221-40357643 +  17q21.2   [Description]    (hg38-Dec_2013)
    GoldenPath hg19 (UCSC)RARA  -     17q21.2   [Description]    (hg19-Feb_2009)
    EnsemblRARA - 17q21.2 [CytoView hg19]  RARA - 17q21.2 [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)
    Consensus coding sequences : CCDS (NCBI)RARA
    Cluster EST : UnigeneHs.654583 [ NCBI ]
    CGAP (NCI)Hs.654583
    Alternative Splicing GalleryENSG00000131759
    Gene ExpressionRARA [ NCBI-GEO ]   RARA [ EBI - ARRAY_EXPRESS ]   RARA [ SEEK ]   RARA [ MEM ]
    Gene Expression Viewer (FireBrowse)RARA [ Firebrowse - Broad ]
    SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
    GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
    BioGPS (Tissue expression)5914
    GTEX Portal (Tissue expression)RARA
    Human Protein AtlasENSG00000131759-RARA [pathology]   [cell]   [tissue]
    Protein : pattern, domain, 3D structure
    UniProt/SwissProtP10276   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
    NextProtP10276  [Sequence]  [Exons]  [Medical]  [Publications]
    With graphics : InterProP10276
    Splice isoforms : SwissVarP10276
    PhosPhoSitePlusP10276
    Domaine pattern : Prosite (Expaxy)NR_LBD (PS51843)    NUCLEAR_REC_DBD_1 (PS00031)    NUCLEAR_REC_DBD_2 (PS51030)   
    Domains : Interpro (EBI)NHR_like_dom_sf    Nucl_hrmn_rcpt_lig-bd    Nuclear_hrmn_rcpt    Retinoic_acid_rcpt    Znf_hrmn_rcpt    Znf_NHR/GATA   
    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)  
    Conserved Domain (NCBI)RARA
    DMDM Disease mutations5914
    Blocks (Seattle)RARA
    PDB (SRS)1DKF    1DSZ    3A9E    3KMR    3KMZ    4DQM    5K13   
    PDB (PDBSum)1DKF    1DSZ    3A9E    3KMR    3KMZ    4DQM    5K13   
    PDB (IMB)1DKF    1DSZ    3A9E    3KMR    3KMZ    4DQM    5K13   
    PDB (RSDB)1DKF    1DSZ    3A9E    3KMR    3KMZ    4DQM    5K13   
    Structural Biology KnowledgeBase1DKF    1DSZ    3A9E    3KMR    3KMZ    4DQM    5K13   
    SCOP (Structural Classification of Proteins)1DKF    1DSZ    3A9E    3KMR    3KMZ    4DQM    5K13   
    CATH (Classification of proteins structures)1DKF    1DSZ    3A9E    3KMR    3KMZ    4DQM    5K13   
    SuperfamilyP10276
    Human Protein Atlas [tissue]ENSG00000131759-RARA [tissue]
    Peptide AtlasP10276
    HPRD06769
    IPIIPI00020071   IPI00218375   IPI00908598   IPI00470378   IPI00922641   IPI00014923   IPI00791851   
    Protein Interaction databases
    DIP (DOE-UCLA)P10276
    IntAct (EBI)P10276
    FunCoupENSG00000131759
    BioGRIDRARA
    STRING (EMBL)RARA
    ZODIACRARA
    Ontologies - Pathways
    QuickGOP10276
    Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  negative regulation of transcription by RNA polymerase II  nuclear chromatin  translation repressor activity, mRNA regulatory element binding  transcription regulatory region sequence-specific DNA binding  RNA polymerase II regulatory region sequence-specific DNA binding  RNA polymerase II transcription factor activity, sequence-specific DNA binding  RNA polymerase II transcription factor activity, sequence-specific DNA binding  RNA polymerase II transcription factor activity, sequence-specific DNA binding  transcription factor activity, RNA polymerase II transcription factor binding  ureteric bud development  neural tube closure  liver development  liver development  retinoic acid binding  glandular epithelial cell development  outflow tract septum morphogenesis  growth plate cartilage development  DNA-binding transcription factor activity  DNA-binding transcription factor activity  steroid hormone receptor activity  retinoic acid receptor activity  retinoic acid receptor activity  transcription coactivator activity  transcription coactivator activity  transcription corepressor activity  nuclear receptor activity  signaling receptor binding  protein binding  nucleus  nucleus  nucleoplasm  cytoplasm  cytosol  transcription initiation from RNA polymerase II promoter  protein phosphorylation  signal transduction  multicellular organism development  germ cell development  spermatogenesis  brain development  heart development  female pregnancy  transcription factor binding  transcription factor binding  drug binding  zinc ion binding  positive regulation of cell proliferation  negative regulation of cell proliferation  hormone-mediated signaling pathway  cell surface  actin cytoskeleton  enzyme binding  protein domain specific binding  hippocampus development  cell differentiation  nuclear receptor transcription coactivator activity  dendrite  prostate gland development  negative regulation of granulocyte differentiation  epithelial cell differentiation  embryonic camera-type eye development  chromatin DNA binding  regulation of myelination  response to estradiol  response to retinoic acid  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 lipid  response to cytokine  multicellular organism growth  histone deacetylase binding  neuronal cell body  negative regulation of apoptotic process  apoptotic cell clearance  steroid hormone mediated signaling pathway  protein kinase B 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 by RNA polymerase II  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  negative regulation of translational initiation  protein heterodimerization activity  mRNA 5'-UTR binding  regulation of synaptic plasticity  retinoic acid receptor signaling pathway  retinoic acid receptor signaling pathway  perinuclear region of cytoplasm  embryonic organ development  gland development  protein kinase A binding  positive regulation of binding  alpha-actinin binding  ventricular cardiac muscle cell differentiation  Sertoli cell fate commitment  limb development  face development  bone morphogenesis  epithelium development  trachea cartilage development  chondroblast differentiation  negative regulation of cartilage development  cellular response to lipopolysaccharide  cellular response to retinoic acid  cellular response to retinoic acid  cellular response to estrogen stimulus  RNA polymerase II transcription factor complex  transcription factor activity, direct ligand regulated sequence-specific DNA binding  
    Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  negative regulation of transcription by RNA polymerase II  nuclear chromatin  translation repressor activity, mRNA regulatory element binding  transcription regulatory region sequence-specific DNA binding  RNA polymerase II regulatory region sequence-specific DNA binding  RNA polymerase II transcription factor activity, sequence-specific DNA binding  RNA polymerase II transcription factor activity, sequence-specific DNA binding  RNA polymerase II transcription factor activity, sequence-specific DNA binding  transcription factor activity, RNA polymerase II transcription factor binding  ureteric bud development  neural tube closure  liver development  liver development  retinoic acid binding  glandular epithelial cell development  outflow tract septum morphogenesis  growth plate cartilage development  DNA-binding transcription factor activity  DNA-binding transcription factor activity  steroid hormone receptor activity  retinoic acid receptor activity  retinoic acid receptor activity  transcription coactivator activity  transcription coactivator activity  transcription corepressor activity  nuclear receptor activity  signaling receptor binding  protein binding  nucleus  nucleus  nucleoplasm  cytoplasm  cytosol  transcription initiation from RNA polymerase II promoter  protein phosphorylation  signal transduction  multicellular organism development  germ cell development  spermatogenesis  brain development  heart development  female pregnancy  transcription factor binding  transcription factor binding  drug binding  zinc ion binding  positive regulation of cell proliferation  negative regulation of cell proliferation  hormone-mediated signaling pathway  cell surface  actin cytoskeleton  enzyme binding  protein domain specific binding  hippocampus development  cell differentiation  nuclear receptor transcription coactivator activity  dendrite  prostate gland development  negative regulation of granulocyte differentiation  epithelial cell differentiation  embryonic camera-type eye development  chromatin DNA binding  regulation of myelination  response to estradiol  response to retinoic acid  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 lipid  response to cytokine  multicellular organism growth  histone deacetylase binding  neuronal cell body  negative regulation of apoptotic process  apoptotic cell clearance  steroid hormone mediated signaling pathway  protein kinase B 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 by RNA polymerase II  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  negative regulation of translational initiation  protein heterodimerization activity  mRNA 5'-UTR binding  regulation of synaptic plasticity  retinoic acid receptor signaling pathway  retinoic acid receptor signaling pathway  perinuclear region of cytoplasm  embryonic organ development  gland development  protein kinase A binding  positive regulation of binding  alpha-actinin binding  ventricular cardiac muscle cell differentiation  Sertoli cell fate commitment  limb development  face development  bone morphogenesis  epithelium development  trachea cartilage development  chondroblast differentiation  negative regulation of cartilage development  cellular response to lipopolysaccharide  cellular response to retinoic acid  cellular response to retinoic acid  cellular response to estrogen stimulus  RNA polymerase II transcription factor complex  transcription factor activity, direct ligand regulated sequence-specific DNA binding  
    Pathways : KEGGPathways in cancer    Transcriptional misregulation in cancer    Acute myeloid leukemia   
    REACTOMEP10276 [protein]
    REACTOME PathwaysR-HSA-5617472 [pathway]   
    NDEx NetworkRARA
    Atlas of Cancer Signalling NetworkRARA
    Wikipedia pathwaysRARA
    Orthology - Evolution
    OrthoDB5914
    GeneTree (enSembl)ENSG00000131759
    Phylogenetic Trees/Animal Genes : TreeFamRARA
    HOVERGENP10276
    HOGENOMP10276
    Homologs : HomoloGeneRARA
    Homology/Alignments : Family Browser (UCSC)RARA
    Gene fusions - Rearrangements
    Fusion : Mitelman-/17q21.2 [RARA/ins(15;17)(q22;q21q21)|ins(15;17)(q22;q21q26)]  
    Fusion : MitelmanBCOR/RARA [Xp11.4/17q21.2]  [t(X;17)(p11;q21)]  
    Fusion : MitelmanFIP1L1/RARA [4q12/17q21.2]  [t(4;17)(q12;q21)]  
    Fusion : MitelmanGTF2I/RARA [7q11.23/17q21.2]  [t(7;17)(q11;q21)]  
    Fusion : MitelmanNABP1/RARA [2q32.3/17q21.2]  [t(2;17)(q32;q21)]  
    Fusion : MitelmanNPM1/RARA [5q35.1/17q21.2]  [t(11;17)(q23;q21)]  [t(15;17)(q22;q21)]  
    [t(5;17)(q35;q21)]  
    Fusion : MitelmanNUMA1/RARA [11q13.4/17q21.2]  [t(11;17)(q13;q21)]  
    Fusion : MitelmanPML/RARA [15q24.1/17q21.2]  [ins(15;17)(q22;q21q21)]  [ins(17;15)(q21;q22q22)]  
    [ins(4;15)(q21;q?q22)t(15;17)(q22;q21)]  [t(11;17)(q23;q21)]  [t(11;17;15)(q13;q21;q22)]  
    [t(13;17;15)(p13;q21;q22)]  [t(15;17)(q22;q21)]  [t(15;17;16)(q22;q21;q13)]  [t(15;17;18)(q22;q21;q12)]  
    [t(15;17;19)(q22;q21;q13)]  [t(1;17;15)(p32;q21;q22)]  [t(3;17;15)(p21;q21;q22)]  [t(3;17;15)(q27;q21;q22)]  
    [t(5;17)(q35;q21)]  [t(5;17;15)(q11;q21;q22)]  [t(5;17;15)(q14;q21;q22)]  [t(5;17;15)(q35;q21;q22)]  
    [t(6;17;15)(p21;q21;q22)]  [t(7;17;15)(q22;q21;q22)]  [t(8;17;15)(q22;q21;q22)]  [t(8;17;15)(q24;q21;q22)]  
    [t(9;17;15)(q31;q21;q22)]  
    Fusion : MitelmanPRKAR1A/RARA [17q24.2/17q21.2]  [t(17;17)(q21;q24)]  
    Fusion : MitelmanRARA/CA10 [17q21.2/17q21.33]  [t(17;17)(q21;q22)]  
    Fusion : MitelmanRARA/CDC6 [17q21.2/17q21.2]  [t(17;17)(q21;q21)]  
    Fusion : MitelmanRARA/CDK12 [17q21.2/17q12]  [t(17;17)(q12;q21)]  
    Fusion : MitelmanRARA/COL10A1 [17q21.2/6q22.1]  [t(6;17)(q22;q21)]  
    Fusion : MitelmanRARA/HOXB3 [17q21.2/17q21.32]  [t(17;17)(q21;q21)]  
    Fusion : MitelmanRARA/MSL1 [17q21.2/17q21.1]  [t(17;17)(q21;q21)]  
    Fusion : MitelmanRARA/MYO1D [17q21.2/17q11.2]  [t(17;17)(q11;q21)]  
    Fusion : MitelmanRARA/NARS2 [17q21.2/11q14.1]  [t(11;17)(q14;q21)]  
    Fusion : MitelmanRARA/PCTP [17q21.2/17q22]  [t(17;17)(q21;q22)]  
    Fusion : MitelmanRARA/PGAP3 [17q21.2/17q12]  [t(17;17)(q12;q21)]  
    Fusion : MitelmanRARA/PKIA [17q21.2/8q21.12]  [t(8;17)(q21;q21)]  
    Fusion : MitelmanRARA/PML [17q21.2/15q24.1]  [t(15;17)(q22;q21)]  
    Fusion : MitelmanRARA/POLDIP2 [17q21.2/17q11.2]  [t(17;17)(q11;q21)]  
    Fusion : MitelmanRARA/PRR11 [17q21.2/17q22]  [t(17;17)(q21;q22)]  
    Fusion : MitelmanRARA/PSMD3 [17q21.2/17q21.1]  [t(17;17)(q21;q21)]  
    Fusion : MitelmanRARA/SKAP1 [17q21.2/17q21.32]  [t(17;17)(q21;q21)]  
    Fusion : MitelmanRARA/STAC2 [17q21.2/17q12]  [t(17;17)(q12;q21)]  
    Fusion : MitelmanRARA/STAT3 [17q21.2/17q21.2]  [t(17;17)(q21;q21)]  
    Fusion : MitelmanRARA/WIPF2 [17q21.2/17q21.1]  [t(17;17)(q21;q21)]  
    Fusion : MitelmanRARA/ZNF595 [17q21.2/4p16.3]  [t(4;17)(p16;q21)]  
    Fusion : MitelmanSTAT5B/RARA [17q21.2/17q21.2]  [t(17;17)(q21;q21)]  
    Fusion : MitelmanTAOK1/RARA [17q11.2/17q21.2]  [t(17;17)(q11;q21)]  
    Fusion : MitelmanTBL1XR1/RARA [3q26.32/17q21.2]  [t(3;17)(q26;q21)]  
    Fusion : MitelmanTPCN2/RARA [11q13.3/17q21.2]  [t(11;17)(q13;q21)]  
    Fusion : MitelmanZBTB16/RARA [11q23.2/17q21.2]  [ins(11;17)(q23;q21q21)]  [t(11;17)(q23;q21)]  
    [t(15;17)(q22;q21)]  [t(5;17)(q35;q21)]  
    Fusion : COSMICPML [RARA]  -  2299 [2300]  [fusion_2301]  [fusion_2302]  [fusion_2304]  [fusion_2305]  [fusion_2307]  [fusion_2310]  [fusion_2311]  
    [fusion_2312]  [fusion_2313]  [fusion_2316]  [fusion_2317]  [fusion_2318]  [fusion_2320]  [fusion_2322]  
    Fusion PortalPML 15q24.1 RARA 17q21.2 LAML
    Fusion PortalRARA 17q21.2 CA10 17q21.33 BRCA
    Fusion PortalRARA 17q21.2 CDC6 17q21.2 LUAD
    Fusion PortalRARA 17q21.2 CDK12 17q12 BRCA
    Fusion PortalRARA 17q21.2 COL10A1 6q22.1 BRCA
    Fusion PortalRARA 17q21.2 HOXB3 17q21.32 BRCA
    Fusion PortalRARA 17q21.2 MSL1 17q21.1 BRCA
    Fusion PortalRARA 17q21.2 MYO1D 17q11.2 BRCA
    Fusion PortalRARA 17q21.2 PCTP 17q22 BRCA
    Fusion PortalRARA 17q21.2 PGAP3 17q12 BRCA
    Fusion PortalRARA 17q21.2 PML 15q24.1 LAML
    Fusion PortalRARA 17q21.2 PRR11 17q22 BRCA
    Fusion PortalRARA 17q21.2 PSMD3 17q21.1 BRCA
    Fusion PortalRARA 17q21.2 RP11-1407O15.2 BRCA
    Fusion PortalRARA 17q21.2 SKAP1 17q21.32 BRCA
    Fusion PortalRARA 17q21.2 STAC2 17q12 LUAD
    Fusion PortalRARA 17q21.2 STAT3 17q21.2 BRCA
    Fusion PortalRARA 17q21.2 WIPF2 17q21.1 BRCA
    Fusion PortalRARA 17q21.2 ZNF595 4p16.3 BRCA
    Fusion PortalTAOK1 17q11.2 RARA 17q21.2 GBM
    Fusion PortalTPCN2 11q13.3 RARA 17q21.2 BRCA
    Fusion : TICdbBCOR [Xp11.4]  -  RARA [17q21.2]
    Fusion : TICdbFIP1L1 [4q12]  -  RARA [17q21.2]
    Fusion : TICdbNABP1 [2q32.3]  -  RARA [17q21.2]
    Fusion : TICdbNPM1 [5q35.1]  -  RARA [17q21.2]
    Fusion : TICdbNUMA1 [11q13.4]  -  RARA [17q21.2]
    Fusion : TICdbPML [15q24.1]  -  RARA [17q21.2]
    Fusion : TICdbPRKAR1A [17q24.2]  -  RARA [17q21.2]
    Fusion : TICdbSTAT5B [17q21.2]  -  RARA [17q21.2]
    Fusion : TICdbZBTB16 [11q23.2]  -  RARA [17q21.2]
    Fusion : QuiverRARA
    Polymorphisms : SNP and Copy number variants
    NCBI Variation ViewerRARA [hg38]
    dbSNP Single Nucleotide Polymorphism (NCBI)RARA
    dbVarRARA
    ClinVarRARA
    1000_GenomesRARA 
    Exome Variant ServerRARA
    ExAC (Exome Aggregation Consortium)ENSG00000131759
    GNOMAD BrowserENSG00000131759
    Varsome BrowserRARA
    Genetic variants : HAPMAP5914
    Genomic Variants (DGV)RARA [DGVbeta]
    DECIPHERRARA [patients]   [syndromes]   [variants]   [genes]  
    CONAN: Copy Number AnalysisRARA 
    Mutations
    ICGC Data PortalRARA 
    TCGA Data PortalRARA 
    Broad Tumor PortalRARA
    OASIS PortalRARA [ Somatic mutations - Copy number]
    Cancer Gene: CensusRARA 
    Somatic Mutations in Cancer : COSMICRARA  [overview]  [genome browser]  [tissue]  [distribution]  
    Mutations and Diseases : HGMDRARA
    LOVD (Leiden Open Variation Database)Whole genome datasets
    LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
    BioMutasearch RARA
    DgiDB (Drug Gene Interaction Database)RARA
    DoCM (Curated mutations)RARA (select the gene name)
    CIViC (Clinical Interpretations of Variants in Cancer)RARA (select a term)
    intoGenRARA
    NCG5 (London)RARA
    Cancer3DRARA(select the gene name)
    Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
    Diseases
    OMIM180240    612376   
    Orphanet8559   
    DisGeNETRARA
    MedgenRARA
    Genetic Testing Registry RARA
    NextProtP10276 [Medical]
    TSGene5914
    GENETestsRARA
    Target ValidationRARA
    Huge Navigator RARA [HugePedia]
    snp3D : Map Gene to Disease5914
    BioCentury BCIQRARA
    ClinGenRARA
    Clinical trials, drugs, therapy
    Chemical/Protein Interactions : CTD5914
    Chemical/Pharm GKB GenePA34225
    Clinical trialRARA
    Miscellaneous
    canSAR (ICR)RARA (select the gene name)
    Probes
    Litterature
    PubMed398 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    CoreMineRARA
    EVEXRARA
    GoPubMedRARA
    iHOPRARA
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

    Search in all EBI   NCBI

    © Atlas of Genetics and Cytogenetics in Oncology and Haematology
    indexed on : Thu Aug 16 12:06:02 CEST 2018
    Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

    For comments and suggestions or contributions, please contact us

    jlhuret@AtlasGeneticsOncology.org.