Atlas of Genetics and Cytogenetics in Oncology and Haematology


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RXRA (retinoid X receptor alpha)

Identity

Alias_namesretinoid X receptor
Alias_symbol (synonym)NR2B1
Other alias
HGNC (Hugo) RXRA
LocusID (NCBI) 6256
Atlas_Id 42186
Location 9q34.2  [Link to chromosome band 9q34]
Location_base_pair Starts at 134379295 and ends at 134440586 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
RXRA (9q34.2) / LRBA (4q31.3)RXRA (9q34.2) / RXRA (9q34.2)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  M3/M3v acute myeloid leukemia (AML M3/M3v)
::Acute promyelocytic leukemia (APL)
::Acute promyelocytic leukemia (APL) PML/RARA

t(12;12)(p13;q13) ETV6/BAZ2A


External links

Nomenclature
HGNC (Hugo)RXRA   10477
Cards
Entrez_Gene (NCBI)RXRA  6256  retinoid X receptor alpha
AliasesNR2B1
GeneCards (Weizmann)RXRA
Ensembl hg19 (Hinxton)ENSG00000186350 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000186350 [Gene_View]  chr9:134379295-134440586 [Contig_View]  RXRA [Vega]
ICGC DataPortalENSG00000186350
TCGA cBioPortalRXRA
AceView (NCBI)RXRA
Genatlas (Paris)RXRA
WikiGenes6256
SOURCE (Princeton)RXRA
Genetics Home Reference (NIH)RXRA
Genomic and cartography
GoldenPath hg38 (UCSC)RXRA  -     chr9:134379295-134440586 +  9q34.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)RXRA  -     9q34.2   [Description]    (hg19-Feb_2009)
EnsemblRXRA - 9q34.2 [CytoView hg19]  RXRA - 9q34.2 [CytoView hg38]
Mapping of homologs : NCBIRXRA [Mapview hg19]  RXRA [Mapview hg38]
OMIM180245   
Gene and transcription
Genbank (Entrez)AB307705 AF052092 AK090416 AK131081 AK131192
RefSeq transcript (Entrez)NM_001291920 NM_001291921 NM_002957
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)RXRA
Cluster EST : UnigeneHs.590886 [ NCBI ]
CGAP (NCI)Hs.590886
Alternative Splicing GalleryENSG00000186350
Gene ExpressionRXRA [ NCBI-GEO ]   RXRA [ EBI - ARRAY_EXPRESS ]   RXRA [ SEEK ]   RXRA [ MEM ]
Gene Expression Viewer (FireBrowse)RXRA [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6256
GTEX Portal (Tissue expression)RXRA
Human Protein AtlasENSG00000186350-RXRA [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP19793   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP19793  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP19793
Splice isoforms : SwissVarP19793
PhosPhoSitePlusP19793
Domaine pattern : Prosite (Expaxy)NUCLEAR_REC_DBD_1 (PS00031)    NUCLEAR_REC_DBD_2 (PS51030)   
Domains : Interpro (EBI)Nuc_recep-AF1    Nucl_hrmn_rcpt_lig-bd    Nuclear_hrmn_rcpt    Retinoid-X_rcpt/HNF4    Znf_hrmn_rcpt    Znf_NHR/GATA   
Domain families : Pfam (Sanger)Hormone_recep (PF00104)    Nuc_recep-AF1 (PF11825)    zf-C4 (PF00105)   
Domain families : Pfam (NCBI)pfam00104    pfam11825    pfam00105   
Domain families : Smart (EMBL)HOLI (SM00430)  ZnF_C4 (SM00399)  
Conserved Domain (NCBI)RXRA
DMDM Disease mutations6256
Blocks (Seattle)RXRA
PDB (SRS)###############################################################################################################################################################################################################################################################   
PDB (PDBSum)###############################################################################################################################################################################################################################################################   
PDB (IMB)###############################################################################################################################################################################################################################################################   
PDB (RSDB)###############################################################################################################################################################################################################################################################   
Structural Biology KnowledgeBase###############################################################################################################################################################################################################################################################   
SCOP (Structural Classification of Proteins)###############################################################################################################################################################################################################################################################   
CATH (Classification of proteins structures)###############################################################################################################################################################################################################################################################   
SuperfamilyP19793
Human Protein Atlas [tissue]ENSG00000186350-RXRA [tissue]
Peptide AtlasP19793
HPRD01577
IPIIPI00418394   IPI01011260   IPI00431177   IPI00442358   IPI00386192   IPI00979550   
Protein Interaction databases
DIP (DOE-UCLA)P19793
IntAct (EBI)P19793
FunCoupENSG00000186350
BioGRIDRXRA
STRING (EMBL)RXRA
ZODIACRXRA
Ontologies - Pathways
QuickGOP19793
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  nuclear chromatin  RNA polymerase II regulatory region sequence-specific DNA binding  in utero embryonic development  maternal placenta development  retinoic acid binding  DNA binding  double-stranded DNA binding  transcription factor activity, sequence-specific DNA binding  transcription factor activity, sequence-specific DNA binding  steroid hormone receptor activity  retinoic acid receptor activity  transcription coactivator activity  RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding  9-cis retinoic acid receptor activity  protein binding  nucleus  nucleoplasm  transcription initiation from RNA polymerase II promoter  vitamin metabolic process  embryo implantation  cholesterol metabolic process  zinc ion binding  bile acid and bile salt transport  ligand-dependent nuclear receptor binding  modulation by virus of host morphology or physiology  enzyme binding  chromatin DNA binding  response to retinoic acid  peroxisome proliferator activated receptor signaling pathway  peptide binding  vitamin D receptor binding  camera-type eye development  protein complex  receptor complex  steroid hormone mediated signaling pathway  sequence-specific DNA binding  transcription regulatory region DNA binding  cellular lipid metabolic process  retinoic acid-responsive element binding  positive regulation of transcription from RNA polymerase II promoter  positive regulation of translational initiation by iron  protein heterodimerization activity  retinoic acid receptor signaling pathway  DBD domain binding  LBD domain binding  protein homotetramerization  ventricular cardiac muscle tissue morphogenesis  ventricular cardiac muscle cell differentiation  cardiac muscle cell proliferation  secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development  regulation of branching involved in prostate gland morphogenesis  vitamin D response element binding  RNA polymerase II transcription factor complex  positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  nuclear chromatin  RNA polymerase II regulatory region sequence-specific DNA binding  in utero embryonic development  maternal placenta development  retinoic acid binding  DNA binding  double-stranded DNA binding  transcription factor activity, sequence-specific DNA binding  transcription factor activity, sequence-specific DNA binding  steroid hormone receptor activity  retinoic acid receptor activity  transcription coactivator activity  RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding  9-cis retinoic acid receptor activity  protein binding  nucleus  nucleoplasm  transcription initiation from RNA polymerase II promoter  vitamin metabolic process  embryo implantation  cholesterol metabolic process  zinc ion binding  bile acid and bile salt transport  ligand-dependent nuclear receptor binding  modulation by virus of host morphology or physiology  enzyme binding  chromatin DNA binding  response to retinoic acid  peroxisome proliferator activated receptor signaling pathway  peptide binding  vitamin D receptor binding  camera-type eye development  protein complex  receptor complex  steroid hormone mediated signaling pathway  sequence-specific DNA binding  transcription regulatory region DNA binding  cellular lipid metabolic process  retinoic acid-responsive element binding  positive regulation of transcription from RNA polymerase II promoter  positive regulation of translational initiation by iron  protein heterodimerization activity  retinoic acid receptor signaling pathway  DBD domain binding  LBD domain binding  protein homotetramerization  ventricular cardiac muscle tissue morphogenesis  ventricular cardiac muscle cell differentiation  cardiac muscle cell proliferation  secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development  regulation of branching involved in prostate gland morphogenesis  vitamin D response element binding  RNA polymerase II transcription factor complex  positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus  
Pathways : BIOCARTA [Genes]   
Pathways : KEGG   
NDEx NetworkRXRA
Atlas of Cancer Signalling NetworkRXRA
Wikipedia pathwaysRXRA
Orthology - Evolution
OrthoDB6256
GeneTree (enSembl)ENSG00000186350
Phylogenetic Trees/Animal Genes : TreeFamRXRA
HOVERGENP19793
HOGENOMP19793
Homologs : HomoloGeneRXRA
Homology/Alignments : Family Browser (UCSC)RXRA
Gene fusions - Rearrangements
Fusion: Tumor Portal RXRA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerRXRA [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RXRA
dbVarRXRA
ClinVarRXRA
1000_GenomesRXRA 
Exome Variant ServerRXRA
ExAC (Exome Aggregation Consortium)ENSG00000186350
GNOMAD BrowserENSG00000186350
Genetic variants : HAPMAP6256
Genomic Variants (DGV)RXRA [DGVbeta]
DECIPHERRXRA [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisRXRA 
Mutations
ICGC Data PortalRXRA 
TCGA Data PortalRXRA 
Broad Tumor PortalRXRA
OASIS PortalRXRA [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRXRA  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDRXRA
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)Pharmacogenomics of Infectious Diseases (PGx_IfD )
BioMutasearch RXRA
DgiDB (Drug Gene Interaction Database)RXRA
DoCM (Curated mutations)RXRA (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RXRA (select a term)
intoGenRXRA
Cancer3DRXRA(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM180245   
Orphanet
MedgenRXRA
Genetic Testing Registry RXRA
NextProtP19793 [Medical]
TSGene6256
GENETestsRXRA
Target ValidationRXRA
Huge Navigator RXRA [HugePedia]
snp3D : Map Gene to Disease6256
BioCentury BCIQRXRA
ClinGenRXRA
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6256
Chemical/Pharm GKB GenePA34890
Clinical trialRXRA
Miscellaneous
canSAR (ICR)RXRA (select the gene name)
Probes
Litterature
PubMed410 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineRXRA
EVEXRXRA
GoPubMedRXRA
iHOPRXRA
Genes in titleautomatic search in PubMed
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 Nov 9 13:09:34 CET 2017

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