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RXRA Gene

protein-coding   GIFtS: 73
GCID: GC09P137208

Retinoid X Receptor, Alpha

  See RXRA-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Retinoid X Receptor, Alpha1 2
Nuclear Receptor Subfamily 2 Group B Member 11 2 3
NR2B12 3
Retinoic Acid Receptor RXR-Alpha2
Retinoid X Nuclear Receptor Alpha2
Retinoid X Receptor Alpha3

External Ids:    HGNC: 104771   Entrez Gene: 62562   Ensembl: ENSG000001863507   OMIM: 1802455   UniProtKB: P197933   
ORGUL members:         

Export aliases for RXRA gene to outside databases

Previous GC identifers: GC09P128442 GC09P129062 GC09P130816 GC09P132732 GC09P132661 GC09P134519 GC09P136358 GC09P106757


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RXRA Gene:
Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological
effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their
action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and
regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone
receptor superfamily of transcriptional regulators. (provided by RefSeq, Jul 2008)

GeneCards Summary for RXRA Gene:
RXRA (retinoid X receptor, alpha) is a protein-coding gene. Diseases associated with RXRA include x-linked adrenal hypoplasia congenita, and recessive dystrophic epidermolysis bullosa. GO annotations related to this gene include protein heterodimerization activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is RXRG.

UniProtKB/Swiss-Prot: RXRA_HUMAN, P19793
Function: 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 RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of
tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves
as a common heterodimeric partner for a number of nuclear receptors. 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. The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation
genes such as ACOX1 and the P450 system genes

summary for RXRA Gene:
Retinoid X receptors (RXR) are members of the NR2B family of nuclear receptors and are common binding
partners to many other nuclear receptors, including PPARs, liver X receptors (LXRs) and vitamin D receptors
(VDR). RXR heterodimers act as ligand-dependent transcriptional regulators and increase the DNA-binding
efficiency of its partner. Despite numerous studies, the physiological role of RXRs have yet to been fully
elucidated and, as they can also exist as homodimers, there is the possibility that an independent RXR
signaling pathway exists. There are three RXR subtypes; RXRalpha, RXRbeta and RXRgamma, each with two major
isoforms (1 and 2). RXRalpha is expressed in the liver, kidney, epidermis and intestine, RXRbeta is widely
distributed and RXRgamma is restricted to muscle, pituitary gland and certain parts of the brain.

Gene Wiki entry for RXRA (Retinoid X receptor alpha) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000009.11  NT_008470.20  NC_018920.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the RXRA gene promoter:
         c-Fos   AhR   AP-1   p300   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 3): RXRA promoter sequence
   Search Chromatin IP Primers for RXRA

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RXRA


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 9q34.3   Ensembl cytogenetic band:  9q34.2   HGNC cytogenetic band: 9q34

RXRA Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RXRA gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P137208:  view genomic region     (about GC identifiers)

Start:
137,208,944 bp from pter      End:
137,332,431 bp from pter
Size:
123,488 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: RXRA_HUMAN, P19793 (See protein sequence)
Recommended Name: Retinoic acid receptor RXR-alpha  
Size: 462 amino acids; 50811 Da
Subunit: Homodimer. Heterodimer with RARA; required for ligand-dependent retinoic acid receptor transcriptional
activity. Heterodimer with PPARA (via the leucine-like zipper in the LBD); the interaction is required for PPARA
transcriptional activity. Also heterodimerizes with PPARG. Interacts with NCOA3 and NCOA6 coactivators. Interacts
with FAM120B (By similarity). Interacts with PELP1, SENP6, SFPQ, DNTTIP2 and RNF8. Interacts (via the DNA binding
domain) with HCV core protein; the interaction enhances the transcriptional activities of the RXRA/RARA and the
RXRA/PPARA heterodimers. Interacts with PRMT2. Interacts with ASXL1 and NCOA1 (By similarity)
Selected PDB 3D structures from and Proteopedia for RXRA (see all 50):
1BY4 (3D)        1DSZ (3D)        1FBY (3D)        1FM6 (3D)        1FM9 (3D)        1G1U (3D)    
Secondary accessions: Q2NL52 Q2V504

Explore the universe of human proteins at neXtProt for RXRA: NX_P19793

Explore proteomics data for RXRA at MOPED

Post-translational modifications: 

  • Phosphorylated on serine and threonine residues mainly in the N-terminal modulating domain. Constiutively
    phosphorylated on Ser-21 in the presence or absence of ligand. Under stress conditions, hyperphosphorylated by
    activated JNK on Ser-56, Ser-70, Thr-82 and Ser-260 (By similarity). Phosphorylated on Ser-27, in vitro, by PKA.
    This phosphorylation is required for repression of cAMP-mediated transcriptional activity of RARA1
  • Sumoylation negatively regulates transcriptional activity. Desumoylated specifically by SENP61
  • Ubiquitination2 at Lys417
  • Modification sites at PhosphoSitePlus

  • See RXRA Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_002948.1  
    ENSEMBL proteins: 
     ENSP00000419692   ENSP00000442123  
    Reactome Protein details: P19793

    RXRA Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
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    OriGene Purified Protein for RXRA
    Browse OriGene Protein Over-expression Lysates
    OriGene MassSpec for RXRA
    OriGene Custom Protein Services for RXRA
    GenScript Custom Purified and Recombinant Proteins Services for RXRA
    Novus Biologicals RXRA Proteins
    Novus Biologicals RXRA Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    ProSpec Recombinant Protein for RXRA
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for RXRA 

    RXRA Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of RXRA
    R&D Systems Antibodies for RXRA (RXR alpha/NR2B1)
    Cell Signaling Technology (CST) Antibodies for RXRA 
    OriGene Antibodies for RXRA
    OriGene Custom Antibody Services for RXRA
    Novus Biologicals RXRA Antibodies
    Abcam antibodies for RXRA
    Browse Antibodies at Cloud-Clone Corp.
    ThermoFisher Antibodies for RXRA
    LSBio Antibodies in human, mouse, rat for RXRA

    RXRA Assay Products:

    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for RXRA
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for RXRA
    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for RXRA 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    NR: Nuclear hormone receptors

    IUPHAR Guide to PHARMACOLOGY protein family classification: Retinoid X receptor-alpha
    2B. Retinoid X receptors

    Selected InterPro protein domains (see all 7):
     IPR013088 Znf_NHR/GATA
     IPR008946 Nucl_hormone_rcpt_ligand-bd
     IPR000536 Nucl_hrmn_rcpt_lig-bd_core
     IPR001628 Znf_hrmn_rcpt
     IPR021780 Nuc_recep-AF1

    Graphical View of Domain Structure for InterPro Entry P19793

    ProtoNet protein and cluster: P19793

    2 Blocks protein domains:
    IPB000003 Retinoic acid receptor signature
    IPB001723 Steroid hormone receptor signature


    UniProtKB/Swiss-Prot: RXRA_HUMAN, P19793
    Domain: Composed of three domains: a modulating N-terminal domain (AF1 domain), a DNA-binding domain and a
    C-terminal ligand-binding domain (AF2 domain)
    Similarity: Belongs to the nuclear hormone receptor family. NR2 subfamily
    Similarity: Contains 1 nuclear receptor DNA-binding domain


    Find genes that share domains with RXRA           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RXRA_HUMAN, P19793
    Function: 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 RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of
    tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves
    as a common heterodimeric partner for a number of nuclear receptors. 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. The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation
    genes such as ACOX1 and the P450 system genes

         Genatlas biochemistry entry for RXRA:
    retinoic acid X receptor binding and activated by 9-cis-retinoic acid,only (9-cis-RA),alpha subunit,regulating
    cardiac morphogenesis,obligate member of heterodimeric nuclear receptors,steroid/thyroid/retinoic receptor
    superfamily

         Gene Ontology (GO): Selected molecular function terms (see all 18):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IDA12037571
    GO:0003700contributes to sequence-specific DNA binding transcription factor activity IDA17426122
    GO:0003707steroid hormone receptor activity IEA--
    GO:0003708retinoic acid receptor activity TAS--
    GO:0003713transcription coactivator activity TAS1651173
         
    Find genes that share ontologies with RXRA           About GenesLikeMe


    Phenotypes:
         Selected MGI mutant phenotypes (inferred from 10 alleles(MGI details for Rxra) (see all 26):
     behavior/neurological  cardiovascular system  cellular  craniofacial  digestive/alimentary 
     embryogenesis  endocrine/exocrine gland  growth/size/body  hearing/vestibular/ear  hematopoietic system 
     homeostasis/metabolism  immune system  integument  limbs/digits/tail  liver/biliary system 

    Find genes that share phenotypes with RXRA           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for RXRA: Rxratm1.1Pcn Rxratm1Ipc Rxratm4.1Ipc Rxratm1.1Krc Rxratm3Ipc Rxratm1Rev
                                                         Rxratm2Ipc

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RXRA
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for RXRA

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for RXRA
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for RXRA

    Transcription Factor Targeting: 
    Targeting motifs: HOMER Transcription Factor Regulatory Elements motif viewer 
                                          Consensus sequence:  TAGGGCAAAGGTCA 

    miRNA
    Products:
        
    miRTarBase miRNAs that target RXRA:
    hsa-mir-423-3p (MIRT042547)

    Block miRNA regulation of human, mouse, rat RXRA using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate RXRA (see all 58):
    hsa-miR-520f hsa-miR-513a-5p hsa-miR-1224-3p hsa-miR-574-3p hsa-miR-128 hsa-miR-1260b hsa-let-7a-2* hsa-miR-219-5p
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for RXRA
    Predesigned siRNA for gene silencing in human, mouse, rat RXRA

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for RXRA

    Clone
    Products:
         
    OriGene clones in human, mouse for RXRA (see all 7)
    OriGene ORF clones in mouse, rat for RXRA
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: RXRA (NM_002957)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for RXRA
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RXRA
    Addgene plasmids for RXRA 

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for RXRA
    Browse ESI BIO Cell Lines and PureStem Progenitors for RXRA 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RXRA


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    RXRA_HUMAN, P19793: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    golgi apparatus3
    peroxisome3
    extracellular1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000790nuclear chromatin IDA18511497
    GO:0005634nucleus IDA19917671
    GO:0005654nucleoplasm TAS--

    Find genes that share ontologies with RXRA           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for RXRA About   (see all 36)  
    See pathways by source

    SuperPathContained pathways About
    1Nuclear Receptor transcription pathway
    Nuclear Receptor transcription pathway0.67
    Nuclear Receptors0.67
    2Fatty acid, triacylglycerol, and ketone body metabolism
    Fatty acid, triacylglycerol, and ketone body metabolism0.65
    PPARA Activates Gene Expression0.63
    Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)0.65
    Transcriptional Regulation of White Adipocyte Differentiation0.38
    3Circadian Repression of Expression by REV-ERBA
    Circadian Repression of Expression by REV-ERBA0.88
    YAP1- and WWTR1 (TAZ)-stimulated gene expression0.40
    RORA Activates Circadian Expression0.88
    4Regulation of Cholesterol Biosynthesis by SREBP (SREBF)
    Regulation of Cholesterol Biosynthesis by SREBP (SREBF)0.75
    Activation of Gene Expression by SREBP (SREBF)0.75
    5Apoptotic Pathways in Synovial Fibroblasts
    PPAR Pathway0.66
    Nuclear Receptor Activation by Vitamin-A0.57


    Find genes that share SuperPaths with RXRA           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    4 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for RXRA
        Nuclear Receptor Activation by Vitamin-A
    Nur77 Signaling in T-Cell
    PPAR Pathway
    RAR-Gamma-RXR-Alpha Degradation

    5 GeneGo (Thomson Reuters) Pathways for RXRA
        Development Beta-adrenergic receptors signaling via cAMP
    Transcription Sin3 and NuRD in transcription regulation
    Transcription Ligand-Dependent Transcription of Retinoid-Target genes
    Transcription PPAR Pathway
    Transcription Role of VDR in regulation of genes involved in osteoporosis

    Selected BioSystems Pathways for RXRA (see all 9)
        Vitamin D synthesis
    Adipogenesis
    Nuclear Receptors
    Vitamin A and carotenoid metabolism
    IL-3 Signaling Pathway

    Selected Reactome Pathways for RXRA (see all 11)
        Transcriptional regulation of white adipocyte differentiation
    Circadian Clock
    Nuclear Receptor transcription pathway
    Transcriptional activation of mitochondrial biogenesis
    YAP1- and WWTR1 (TAZ)-stimulated gene expression


    Selected Kegg Pathways  (Kegg details for RXRA) (see all 12):
        PPAR signaling pathway
    PI3K-Akt signaling pathway
    Thyroid hormone signaling pathway
    Adipocytokine signaling pathway
    Non-alcoholic fatty liver disease (NAFLD)

        Pathway & Disease-focused RT2 Profiler PCR Arrays including RXRA (see all 6): 
              Atherosclerosis in human mouse rat
              Nuclear Receptors & Coregulators in human mouse rat
              Cancer Drug Resistance in human mouse rat
              Fatty Liver in human mouse rat
              PPAR Targets in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for RXRA

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for RXRA (P197931, 2, 3 ENSP000004196924) via UniProtKB, MINT, STRING, and/or I2D (see all 293)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NCOA1Q157881, 2, 3, ENSP000003209404EBI-78598,EBI-455189 MINT-7986700 MINT-7986678 MINT-7986848 MINT-7986760 MINT-5224970 MINT-7986720 MINT-7986865 MINT-7986787 MINT-7986736 MINT-7986639 MINT-7986822 I2D: score=5 STRING: ENSP00000320940
    RARAP102761, 2, 3, ENSP000002540664EBI-78598,EBI-413374 MINT-24895 I2D: score=7 STRING: ENSP00000254066
    NR1H3Q131332, 3MINT-7986720 MINT-7986700 MINT-7986678 MINT-7986736 MINT-7986787 MINT-7986760 MINT-7986639 I2D: score=5 
    CSNK2BP678702, 3MINT-8253627 I2D: score=2 
    ENSG00000206406P678702, 3MINT-8253627 I2D: score=2 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 26):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IDA17426122
    GO:0001701in utero embryonic development IEA--
    GO:0001890placenta development ----
    GO:0001893maternal placenta development IEA--
    GO:0006355regulation of transcription, DNA-templated ----

    Find genes that share ontologies with RXRA           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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      Browse compounds at ApexBio 

    Compounds for RXRA available from Tocris Bioscience    About this table
    CompoundAction CAS #
    FluorobexaroteneRXR agonist[1190848-23-7]
    SR 11237Pan RXR agonist[146670-40-8]
    HX 531RXR antagonist[188844-34-0]
    UVI 3003RXR antagonist[847239-17-2]
    CD 3254Potent and selective RXRalpha agonist.[196961-43-0]

    2 HMDB Compounds for RXRA    About this table
    CompoundSynonyms CAS #PubMed Ids
    9-cis-Retinoic acidTretinoin [usan:ban:inn] (see all 69)----
    Retinoic acidRetinoate (see all 21)302-79-4--

    Selected DrugBank Compounds for RXRA (see all 11)    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Bexarotene-- 153559-49-0targetagonist15632250 17483357 18765556 11702369 16495926 17008586 15897247 14700480 15056048
    Alitretinoin9-cis-Retinoic acid (see all 4)5300-03-8targetagonist18321241 19678713 16819260 16428452 16946489 16782282 16751185
    Etretinate-- 54350-48-0targetagonist9298126 8301142 9074840
    Acitretin-- 55079-83-9targetagonist9153406 9074840
    AdapaleneAdapaleno [INN-Spanish] (see all 2)106685-40-9targetother/unknown10651997 8142113
    (5BETA)-PREGNANE-3,20-DIONE-- --target--10592235
    1-BENZYL-3-(4-METHOXYPHENYLAMINO)-4-PHENYLPYRROLE-2,5-DIONE-- --target--10592235
    2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID-- --target--10592235
    2-chloro-5-nitro-N-phenylbenzamide-- --target--10592235
    Etodolac-- 41340-25-4targetother15699354

    8 IUPHAR Ligands for RXRA (Retinoid X receptor-alpha)    About this table
    LigandTypeActionAffinityPubmed IDs
    AGN194204
    AgonistAgonist9.411428923
    LG100268
    AgonistAgonist8.510637371 8837780 8308867
    LG100754
    AntagonistAntagonist8.4711463859
    9-cis-retinoic acid
    AgonistAgonist7.14 - 8.28380496 1309942 8837780 1312497 7791761 1310260
    bexarotene
    AgonistAgonist7.4410052980 10637371 8071941
    methoprene acid
    AgonistAgonist5.77597096
    SR11237
    AgonistAgonist5.71335166
    PA451
    AntagonistAntagonist5.712139443

    Selected Novoseek inferred chemical compound relationships for RXRA gene (see all 34)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    retinoic acid 86.7 136 10346893 (3), 8264664 (2), 8584029 (2), 12006543 (2) (see all 83)
    acyclic retinoid 83.9 3 19520494 (1), 11779708 (1)
    retinoid 83.1 18 12365798 (2), 15082790 (2), 9823320 (1), 11779708 (1) (see all 13)
    androstane 72.3 5 16099843 (1), 15610735 (1), 17276571 (1), 19480556 (1) (see all 5)
    vitamin d 67.6 39 10692108 (4), 17707062 (3), 20049159 (3), 8552086 (2) (see all 24)
    bexarotene 65.6 2 12006543 (2)
    etya 61.2 1 10231366 (1)
    clofibric acid 55.8 2 1324435 (1)
    calcitriol 50.1 3 10585721 (1), 19255064 (1), 17707062 (1)
    steroid 47.2 7 9111344 (1), 10551830 (1), 7567979 (1), 17224343 (1) (see all 7)



    Find genes that share compounds with RXRA           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for RXRA gene: 
    NM_002957.4  

    Unigene Cluster for RXRA:

    Retinoid X receptor, alpha
    Hs.590886  [show with all ESTs]
    Unigene Representative Sequence: AK131081
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000484822(uc004cfa.1) ENST00000481739(uc004cfd.1) ENST00000356384(uc004cfb.2 uc004cfc.1)
    ENST00000540193
    miRNA
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    hsa-miR-520f hsa-miR-513a-5p hsa-miR-1224-3p hsa-miR-574-3p hsa-miR-128 hsa-miR-1260b hsa-let-7a-2* hsa-miR-219-5p
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    Additional mRNA sequence: 

    AB307705.1 AF052092.1 AK131081.1 AK131513.1 BC007925.1 BC009882.2 BC031356.1 BC063827.1 
    BC096246.2 BC110998.1 HQ692843.1 U66306.1 X52773.1 

    9 DOTS entries:

    DT.116413  DT.102827176  DT.100785446  DT.91709154  DT.100785440  DT.121164622  DT.75120807  DT.95338039 
    DT.121164592 

    Selected AceView cDNA sequences (see all 320):

    CA393592 AW137188 AA682398 BM930927 BM994884 BM674588 AA865269 F26256 
    CA433814 AA236526 W86756 CB160375 BU192986 BM980455 BU686739 AA492475 
    CF136885 BQ575740 AI375273 BU738433 F31386 BU684863 BQ637881 BM975617 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for RXRA    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b
    SP1:                                      -                                 
    SP2:                    -     -     -     -     -     -                     
    SP3:                                                                        


    ECgene alternative splicing isoforms for RXRA

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    RXRA expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TATGTGCTGT
    RXRA Expression
    About this image


    RXRA expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Tooth (Integumentary System)    fully expand to see all 10 entries
             Odontoblasts Dentin
             Dentin
     
     Epithelial Cells
             Early Ameloblasts Dental Enamel
     
     Adipose (Muscoskeletal System)
             Adipocyte-like cells
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
     
     Blood (Cardiovascular System)
             Conventional Dendritic Cells I Spleen
    RXRA Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RXRA Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.590886

    UniProtKB/Swiss-Prot: RXRA_HUMAN, P19793
    Tissue specificity: Highly expressed in liver, also found in lung, kidney and heart

        Pathway & Disease-focused RT2 Profiler PCR Arrays including RXRA (see all 6): 
              Atherosclerosis in human mouse rat
              Nuclear Receptors & Coregulators in human mouse rat
              Cancer Drug Resistance in human mouse rat
              Fatty Liver in human mouse rat
              PPAR Targets in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for RXRA gene from Selected species (see all 18)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rxra1 , 5 retinoid X receptor alpha1, 5 88.96(n)1
    98.48(a)1
      2 (19.38 cM)5
    201811  NM_011305.31  NP_035435.11 
     276764405 
    chicken
    (Gallus gallus)
    Aves RXRA1 retinoid X receptor, alpha 86.08(n)
    96.32(a)
      417143  XM_003642291.2  XP_003642339.1 
    lizard
    (Anolis carolinensis)
    Reptilia RXRA6
    retinoid X receptor, alpha
    92(a)
    1 ↔ 1
    LGg(292780-338860)
    African clawed frog
    (Xenopus laevis)
    Amphibia rxra-A2 retinoid X receptor, alpha 83.66(n)    L11446.1 
    zebrafish
    (Danio rerio)
    Actinopterygii rxrg2 retinoid x receptor, gamma 79.65(n)   30389  NM_131153.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta usp1 , 3 metamorphosis ecdysteroid hormone
    receptor3
    ultraspiracle1
    47(a)3
    62.59(n)1
    57.61(a)1
      2C73
    311651  NM_001272239.11  NP_001259168.11 


    ENSEMBL Gene Tree for RXRA (if available)
    TreeFam Gene Tree for RXRA (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RXRA gene
    RXRG2  NR2F12  NR2F22  HNF4G2  NR2C12  NR2F62  NR2E12  HNF4A2  
    RXRB2  NR2C22  
    Selected SIMAP similar genes for RXRA using alignment to 3 protein entries:     RXRA_HUMAN (see all proteins) (see all similar genes):
    NR2B1    FLJ00318    NR2B3    RXRG    RXRB    NR2B2
    DKFZp779O0162    NR3C2    RORA    HNF4G    VDR    HNF4alpha
    NR2A2    NR2A3    PPARG    ESR1    NR2F2    NR2F1

    Find genes that share paralogs with RXRA           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for RXRA (see all 2664)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1148506231,2
    F--137216471(+) CCCCCC/GCAACC 1 -- us2k11Minor allele frequency- G:0.05WA 118
    rs1388448951,2
    --137216533(+) TGGAAC/TGCGGC 1 -- us2k10--------
    rs1896270561,2
    --137216535(+) GAACGC/TGGCGG 1 -- us2k10--------
    rs1420352531,2
    --137216611(+) TTGCCA/GCCCCC 1 -- us2k10--------
    rs1811075431,2
    --137216616(+) GCCCCC/TCTCCC 1 -- us2k10--------
    rs625762881,2
    C--137216737(+) CAACAG/ATGGCC 1 -- us2k14Minor allele frequency- A:0.16NA WA EA 360
    rs1859530401,2
    --137217140(+) AATGGG/TCAGTC 1 -- us2k10--------
    rs1903641201,2
    C--137217516(+) GAGTGC/TGGGTC 1 -- us2k10--------
    rs1178467901,2
    F--137217556(+) CGTTCC/TCGGTG 1 -- us2k11Minor allele frequency- T:0.07EA 120
    rs1833843441,2
    --137217648(+) CGGACA/GAGGAG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for RXRA (137208944 - 137332431 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for RXRA (see all 34):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2673192CNV Deletion23128226
    esv2739209CNV Deletion23290073
    esv2105964CNV Deletion18987734
    esv2739138CNV Deletion23290073
    esv1103609CNV Insertion17803354
    esv1003062CNV Insertion20482838
    esv2561499CNV Insertion19546169
    nsv512999CNV Insertion21212237
    nsv894178CNV Loss21882294
    dgv8346n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 180245    OMIM disorders: --

    2 diseases for RXRA:    
    About MalaCards
    x-linked adrenal hypoplasia congenita    recessive dystrophic epidermolysis bullosa


    Find genes that share disorders with RXRA           About GenesLikeMe

    Selected Novoseek inferred disease relationships for RXRA gene (see all 17)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    carcinoma embryonal 33.2 2 9892176 (1), 7624356 (1)
    choriocarcinoma 29.8 1 19133314 (1)
    hepatocellular carcinoma 27.1 9 11826406 (1), 19520494 (1), 11606411 (1), 19068086 (1) (see all 5)
    cancer 23.2 4 15140235 (1), 17909831 (1), 20428830 (1), 16621885 (1)
    colon cancer 3.54 2 14670614 (1), 18202021 (1)
    necrosis 2.36 1 17224343 (1)
    breast carcinoma 0 1 15082790 (1)
    inflammation 0 1 19700678 (1), 20463294 (1)
    breast cancer 0 5 15082790 (2), 12365798 (1), 15171703 (1)
    gastric cancer 0 2 9342842 (1), 12970875 (1)

    Genetic Association Database (GAD): RXRA
    Human Genome Epidemiology (HuGE) Navigator: RXRA (37 documents)

    Export disorders for RXRA gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for RXRA gene, integrated from 10 sources (see all 612):
    (articles sorted by number of sources associating them with RXRA)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Nuclear receptor that identifies a novel retinoic acid response pathway. (PubMed id 2159111)1, 2, 3 Mangelsdorf D.J.... Evans R.M. (Nature 1990)
    2. RXRA gene variations influence Alzheimer's disease risk and cholesterol metabolism. (PubMed id 19374686)1, 4, 9 KAPlsch H....Heun R. (J. Cell. Mol. Med. 2009)
    3. Analysis of SNPs and haplotypes in vitamin D pathway genes and renal cancer risk. (PubMed id 19753122)1, 4, 9 Karami S....Moore L.E. (PLoS ONE 2009)
    4. 9-cis-retinoic acid up-regulates expression of transcriptional coregulator PELP1, a novel coactivator of the retinoid X receptor alpha pathway. (PubMed id 16574651)1, 2, 9 Singh R.R.... Kumar R. (J. Biol. Chem. 2006)
    5. Vitamin D-related genes, serum vitamin D concentrations and prostate cancer risk. (PubMed id 19255064)1, 4, 9 Ahn J....Hayes R.B. (Carcinogenesis 2009)
    6. MicroRNA-related genetic variations as predictors for risk of second primary tumor and/or recurrence in patients with early-stage head and neck cancer. (PubMed id 20819778)1, 4 Zhang X....Wu X. (Carcinogenesis 2010)
    7. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    8. Physiogenomic analysis of statin-treated patients: domain-specific counter effects within the ACACB gene on low-density lipoprotein cholesterol? (PubMed id 20602615)1, 4 RuaA+o G....Wu A.H. (Pharmacogenomics 2010)
    9. Genetic variation in the retinoid X receptor and calcium-sensing receptor and risk of colorectal cancer in the Colon Cancer Family Registry. (PubMed id 20558521)1, 4 Jacobs E.T....Baron J.A. (Carcinogenesis 2010)
    10. Common genetic variation in multiple metabolic pathways influences susceptibility to low HDL-cholesterol and coronary heart disease. (PubMed id 20855565)1, 4 Peloso G.M....Brousseau M.E. (J. Lipid Res. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6256 HGNC: 10477 AceView: RXRA Ensembl:ENSG00000186350 euGenes: HUgn6256
    ECgene: RXRA Kegg: 6256 H-InvDB: RXRA

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for RXRA Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for RXRA Genetics and Cytogenetics in Oncology and Haematology
    NIEHS-SNPshttp://egp.gs.washington.edu/data/rxra/
    Wikipedia http://en.wikipedia.org/wiki/Retinoid_X_receptor

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RXRA gene:
    Search GeneIP for patents involving RXRA

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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