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 function as transcription factors by binding as homodimers or heterodimers to specific sequences in the promoters of target genes. The protein encoded by this gene is... See more...

Aliases for RXRA Gene

Aliases for RXRA Gene

  • Retinoid X Receptor Alpha 2 3 4 5
  • Nuclear Receptor Subfamily 2 Group B Member 1 2 3 4
  • NR2B1 2 3 4
  • Retinoic Acid Receptor RXR-Alpha 3 4
  • Retinoid X Nuclear Receptor Alpha 3
  • Retinoid X Receptor, Alpha 2
  • RXRA 5

External Ids for RXRA Gene

Previous GeneCards Identifiers for RXRA Gene

  • GC09P128442
  • GC09P129062
  • GC09P130816
  • GC09P132732
  • GC09P132661
  • GC09P134519
  • GC09P136358
  • GC09P137208
  • GC09P106757

Summaries for RXRA Gene

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 function as transcription factors by binding as homodimers or heterodimers to specific sequences in the promoters of target genes. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]

GeneCards Summary for RXRA Gene

RXRA (Retinoid X Receptor Alpha) is a Protein Coding gene. Diseases associated with RXRA include Pancreatic Adenocarcinoma and Bladder Urothelial Carcinoma. Among its related pathways are Signaling by Retinoic Acid and Farnesoid X Receptor Pathway. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and protein heterodimerization activity. An important paralog of this gene is RXRG.

UniProtKB/Swiss-Prot Summary for RXRA Gene

  • Receptor for retinoic acid that acts as a transcription factor (PubMed:11162439, PubMed:11915042). Forms homo- or heterodimers with retinoic acid receptors (RARs) and binds to target response elements in response to their ligands, all-trans or 9-cis retinoic acid, to regulate gene expression in various biological processes (PubMed:10195690, PubMed:11162439, PubMed:11915042, PubMed:28167758, PubMed:17761950, PubMed:16107141, PubMed:18800767, PubMed:19167885). The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5 to regulate transcription (PubMed:10195690, PubMed:11162439, PubMed:11915042, PubMed:17761950, PubMed:28167758). The high affinity ligand for retinoid X receptors (RXRs) is 9-cis retinoic acid (PubMed:1310260). In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone deacetylation, chromatin condensation and transcriptional suppression (PubMed:20215566). On ligand binding, the corepressors dissociate from the receptors and coactivators are recruited leading to transcriptional activation (PubMed:20215566, PubMed:9267036). Serves as a common heterodimeric partner for a number of nuclear receptors, such as RARA, RARB and PPARA (PubMed:10195690, PubMed:11915042, PubMed:28167758, PubMed:29021580). The RXRA/RARB heterodimer can act as a transcriptional repressor or transcriptional activator, depending on the RARE DNA element context (PubMed:29021580). The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes (PubMed:10195690). Together with RARA, positively regulates microRNA-10a expression, thereby inhibiting the GATA6/VCAM1 signaling response to pulsatile shear stress in vascular endothelial cells (PubMed:28167758). Acts as an enhancer of RARA binding to RARE DNA element (PubMed:28167758). May facilitate the nuclear import of heterodimerization partners such as VDR and NR4A1 (PubMed:12145331, PubMed:15509776). Promotes myelin debris phagocytosis and remyelination by macrophages (PubMed:26463675). Plays a role in the attenuation of the innate immune system in response to viral infections, possibly by negatively regulating the transcription of antiviral genes such as type I IFN genes (PubMed:25417649). Involved in the regulation of calcium signaling by repressing ITPR2 gene expression, thereby controlling cellular senescence (PubMed:30216632).

Tocris Summary for RXRA Gene

  • Retinoid X receptors (RXR) are members of the NR2B nuclear receptor family and are common binding partners to many other nuclear receptors, including PPARs, liver X receptors (LXRs) and vitamin D receptors (VDRs). There are three RXR subtypes; alpha, beta and gamma.

Gene Wiki entry for RXRA Gene

No data available for CIViC Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RXRA Gene

Genomics for RXRA Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RXRA Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J134323 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 262.3 +10.3 10288 7.6 ZNF600 IKZF1 ZMYM3 CEBPA ZNF223 ZNF10 ATF3 POLR2A ZIC2 CHD4 RXRA HSALNG0075068 HSALNG0075069 COL5A1
GH09J134315 Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 261.6 +1.6 1579 7.4 NCOR1 ZMYM3 ATF3 NFIC ZIC2 YY1 MXD4 THAP11 KDM6A SMAD4 RXRA COL5A1-AS1 BRD3 COL5A1 HSALNG0075068
GH09J134353 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 21.1 +40.7 40700 7.7 MYC NCOR1 ZNF600 JUND ZNF10 ZIC2 ZNF217 CEBPB BHLHE40 MBD2 RXRA HSALNG0075069 lnc-BRD3-7 HSALNG0075068 COL5A1
GH09J134369 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 16.5 +61.6 61636 18.8 ZNF600 ZMYM3 KLF9 CEBPA ZIC2 YY1 CTCF CEBPB DEK ELK1 MIR4669 lnc-BRD3-7 RXRA LOC100130548 WDR5 HSALNG0075070 lnc-BRD3-8 COL5A1
GH09J134363 Promoter/Enhancer 2 VISTA FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.4 +49.1 49141 5.4 ZNF600 ZNF10 ZIC2 ZBTB10 YY1 CEBPB FOXA1 BHLHE40 ZNF341 KLF7 HSALNG0075069 RXRA WDR5 HSALNG0075070 lnc-BRD3-7 COL5A1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RXRA on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RXRA

Top Transcription factor binding sites by QIAGEN in the RXRA gene promoter:
  • AhR
  • AP-1
  • c-Fos
  • c-Jun
  • p300

Genomic Locations for RXRA Gene

Latest Assembly
chr9:134,317,098-134,440,585
(GRCh38/hg38)
Size:
123,488 bases
Orientation:
Plus strand

Previous Assembly
chr9:137,218,301-137,332,431
(GRCh37/hg19 by Entrez Gene)
Size:
114,131 bases
Orientation:
Plus strand

chr9:137,208,944-137,332,431
(GRCh37/hg19 by Ensembl)
Size:
123,488 bases
Orientation:
Plus strand

Genomic View for RXRA Gene

Genes around RXRA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RXRA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RXRA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RXRA Gene

Proteins for RXRA Gene

  • Protein details for RXRA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P19793-RXRA_HUMAN
    Recommended name:
    Retinoic acid receptor RXR-alpha
    Protein Accession:
    P19793
    Secondary Accessions:
    • B3KY83
    • Q2NL52
    • Q2V504

    Protein attributes for RXRA Gene

    Size:
    462 amino acids
    Molecular mass:
    50811 Da
    Quaternary structure:
    • Homodimer (PubMed:10669605, PubMed:17761950). Heterodimer (via C-terminus) with RARA; required for ligand-dependent retinoic acid receptor transcriptional activity; association with RARA is enhanced by pulsatile shear stress (PubMed:28167758, PubMed:10698945, PubMed:15509776). Heterodimer with PPARA (via the leucine-like zipper in the LBD); the interaction is required for PPARA transcriptional activity (PubMed:10195690, PubMed:11915042, PubMed:11698662). Heterodimerizes with PPARG (PubMed:10882139, PubMed:11698662). Heterodimerizes (via NR LBD) with RARB (PubMed:29021580). Heterodimerizes with NR1H4; the heterodimerization enhances the binding affinity for LXXLL motifs from coactivators (PubMed:30275017). Interacts with NCOA3 and NCOA6 coactivators (PubMed:9267036, PubMed:10567404). Interacts with coactivator FAM120B (By similarity). Interacts with coactivator PELP1, SENP6, SFPQ, DNTTIP2 and RNF8 (PubMed:16574651, PubMed:16912044, PubMed:11259580, PubMed:15047147, PubMed:14981089). Interacts with PRMT2 (PubMed:12039952). Interacts with ASXL1 (By similarity). Interacts with BHLHE40/DEC1, BHLHE41/DEC2, NCOR1 and NCOR2 (PubMed:19786558). Interacts in a ligand-dependent fashion with MED1 and NCOA1 (PubMed:19786558, PubMed:10882139, PubMed:11698662). Interacts with VDR (PubMed:28698609). Interacts with EP300; the interaction is decreased by 9-cis retinoic acid (PubMed:17761950). Heterodimer (via C-terminus) with NR4A1 (via DNA-binding domain); DNA-binding of the heterodimer is enhanced by 9-cis retinoic acid (PubMed:17761950, PubMed:15509776). NR4A1 competes with EP300 for interaction with RXRA and thereby attenuates EP300 mediated acetylation of RXRA (PubMed:17761950). In the absence of hormonal ligand, interacts with TACC1 (PubMed:20078863).
    • (Microbial infection) 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.

    Three dimensional structures from OCA and Proteopedia for RXRA Gene

    Alternative splice isoforms for RXRA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RXRA Gene

Post-translational modifications for RXRA Gene

  • Acetylated by EP300; acetylation enhances DNA binding and transcriptional activity.
  • Phosphorylated on serine and threonine residues mainly in the N-terminal modulating domain (By similarity). Constitutively phosphorylated on Ser-21 in the presence or absence of ligand (By similarity). 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 (PubMed:11162439). This phosphorylation is required for repression of cAMP-mediated transcriptional activity of RARA (PubMed:11162439).
  • Sumoylation negatively regulates transcriptional activity. Desumoylated specifically by SENP6.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RXRA Gene

No data available for DME Specific Peptides for RXRA Gene

Domains & Families for RXRA Gene

Gene Families for RXRA Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Cancer-related genes
  • FDA approved drug targets
  • Nuclear receptors
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for RXRA Gene

InterPro:
Blocks:
  • Steroid hormone receptor signature
  • Retinoic acid receptor signature

Suggested Antigen Peptide Sequences for RXRA Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ16020 fis, clone BRAMY2003287, highly similar to RETINOIC ACID RECEPTOR RXR-ALPHA (B3KY83_HUMAN)
  • Retinoid X nuclear receptor alpha (F1D8Q5_HUMAN)
  • RXRA protein (Q6P3U7_HUMAN)
  • Retinoid X receptor alpha (RXRA_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P19793

UniProtKB/Swiss-Prot:

RXRA_HUMAN :
  • Composed of three domains: a modulating N-terminal domain (AF1 domain), a DNA-binding domain and a C-terminal ligand-binding domain (AF2 domain).
  • Belongs to the nuclear hormone receptor family. NR2 subfamily.
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).
Family:
  • Belongs to the nuclear hormone receptor family. NR2 subfamily.
genes like me logo Genes that share domains with RXRA: view

Function for RXRA Gene

Molecular function for RXRA Gene

UniProtKB/Swiss-Prot Function:
Receptor for retinoic acid that acts as a transcription factor (PubMed:11162439, PubMed:11915042). Forms homo- or heterodimers with retinoic acid receptors (RARs) and binds to target response elements in response to their ligands, all-trans or 9-cis retinoic acid, to regulate gene expression in various biological processes (PubMed:10195690, PubMed:11162439, PubMed:11915042, PubMed:28167758, PubMed:17761950, PubMed:16107141, PubMed:18800767, PubMed:19167885). The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5 to regulate transcription (PubMed:10195690, PubMed:11162439, PubMed:11915042, PubMed:17761950, PubMed:28167758). The high affinity ligand for retinoid X receptors (RXRs) is 9-cis retinoic acid (PubMed:1310260). In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone deacetylation, chromatin condensation and transcriptional suppression (PubMed:20215566). On ligand binding, the corepressors dissociate from the receptors and coactivators are recruited leading to transcriptional activation (PubMed:20215566, PubMed:9267036). Serves as a common heterodimeric partner for a number of nuclear receptors, such as RARA, RARB and PPARA (PubMed:10195690, PubMed:11915042, PubMed:28167758, PubMed:29021580). The RXRA/RARB heterodimer can act as a transcriptional repressor or transcriptional activator, depending on the RARE DNA element context (PubMed:29021580). The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes (PubMed:10195690). Together with RARA, positively regulates microRNA-10a expression, thereby inhibiting the GATA6/VCAM1 signaling response to pulsatile shear stress in vascular endothelial cells (PubMed:28167758). Acts as an enhancer of RARA binding to RARE DNA element (PubMed:28167758). May facilitate the nuclear import of heterodimerization partners such as VDR and NR4A1 (PubMed:12145331, PubMed:15509776). Promotes myelin debris phagocytosis and remyelination by macrophages (PubMed:26463675). Plays a role in the attenuation of the innate immune system in response to viral infections, possibly by negatively regulating the transcription of antiviral genes such as type I IFN genes (PubMed:25417649). Involved in the regulation of calcium signaling by repressing ITPR2 gene expression, thereby controlling cellular senescence (PubMed:30216632).
UniProtKB/Swiss-Prot Induction:
Down-regulated by aging (PubMed:26463675). Induced by pulsatile shear stress (PubMed:28167758).
GENATLAS Biochemistry:
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

Phenotypes From GWAS Catalog for RXRA Gene

Gene Ontology (GO) - Molecular Function for RXRA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IDA 18511497
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 7831303
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 12037571
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001972 retinoic acid binding IDA 19043829
genes like me logo Genes that share ontologies with RXRA: view
genes like me logo Genes that share phenotypes with RXRA: view

Animal Models for RXRA Gene

MGI Knock Outs for RXRA:

Animal Models for research

  • Taconic Biosciences Mouse Models for RXRA
Targeted motifs for RXRA Gene
HOMER Transcription Factor Regulatory Elements motif RXRA
  • Consensus sequence: TAGGGCAAAGGTCA Submotif: DR1 Cell Type: 3T3L1 GEO ID: GSE13511

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RXRA

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for RXRA Gene

Localization for RXRA Gene

Subcellular locations from UniProtKB/Swiss-Prot for RXRA Gene

Nucleus. Cytoplasm. Mitochondrion. Note=Localization to the nucleus is enhanced by vitamin D3 (PubMed:15509776). Nuclear localization may be enhanced by the interaction with heterodimerization partner VDR (PubMed:12145331). Translocation to the mitochondrion upon interaction with NR4A1 (PubMed:17761950, PubMed:15509776). Increased nuclear localization upon pulsatile shear stress (PubMed:28167758). {ECO:0000269 PubMed:12145331, ECO:0000269 PubMed:15509776, ECO:0000269 PubMed:17761950, ECO:0000269 PubMed:28167758}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RXRA gene
Compartment Confidence
nucleus 5
mitochondrion 4
plasma membrane 2
extracellular 2
cytoskeleton 2
peroxisome 2
cytosol 2
golgi apparatus 2
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RXRA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IDA,ISA --
GO:0005634 nucleus IEA,IDA 7990953
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IEA --
genes like me logo Genes that share ontologies with RXRA: view

Pathways & Interactions for RXRA Gene

genes like me logo Genes that share pathways with RXRA: view

Pathways by source for RXRA Gene

5 GeneGo (Thomson Reuters) pathways for RXRA Gene
  • Development Beta-adrenergic receptors signaling via cAMP
  • Transcription Ligand-Dependent Transcription of Retinoid-Target genes
  • Transcription PPAR Pathway
  • Transcription Sin3 and NuRD in transcription regulation
  • Transcription_Role of VDR in regulation of genes involved in osteoporosis
4 Qiagen pathways for RXRA Gene
  • Nuclear Receptor Activation by Vitamin-A
  • Nur77 Signaling in T-Cell
  • PPAR Pathway
  • RAR-Gamma-RXR-Alpha Degradation

SIGNOR curated interactions for RXRA Gene

Activates:
Inactivates:
Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for RXRA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 17426122
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0006367 transcription initiation from RNA polymerase II promoter TAS --
GO:0008203 cholesterol metabolic process TAS 19374686
genes like me logo Genes that share ontologies with RXRA: view

Drugs & Compounds for RXRA Gene

(57) Drugs for RXRA Gene - From: DrugBank, PharmGKB, ApexBio, DGIdb, IUPHAR, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Bexarotene Approved, Investigational Pharma Agonist, Target Potent and selective RXR agonist, Others 45
Adapalene Approved Pharma Target, agonist, binder RAR尾 and RAR纬 agonist 92
Alitretinoin Approved, Investigational Pharma Agonist, Target 18
Acitretin Approved Pharma Target, agonist Metabolite of etretinate 33
Tretinoin Approved, Investigational Nutra Target 288

(15) Additional Compounds for RXRA Gene - From: IUPHAR and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
SR11237
Agonist

(4) Tocris Compounds for RXRA Gene

Compound Action Cas Number
Bexarotene Potent and selective RXR agonist 153559-49-0
CD 3254 Potent and selective RXRalpha agonist. 196961-43-0
HX 531 Potent RXR antagonist 188844-34-0
LG 100754 RXR:PPAR agonist 180713-37-5

(12) ApexBio Compounds for RXRA Gene

Compound Action Cas Number
Acitretin Metabolite of etretinate 55079-83-9
Adapalene RAR尾 and RAR纬 agonist 106685-40-9
Bexarotene 153559-49-0
CD 3254 RXRα agonist,potent and selective 196961-43-0
Fluorobexarotene 1190848-23-7
HX 531 188844-34-0
HX 630 188844-52-2
LG 100754 180713-37-5
LG 101506 331248-11-4
PA 452 457657-34-0
SR 11237 146670-40-8
UVI 3003 847239-17-2
genes like me logo Genes that share compounds with RXRA: view

Drug products for research

Transcripts for RXRA Gene

mRNA/cDNA for RXRA Gene

3 REFSEQ mRNAs :
20 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RXRA

Alternative Splicing Database (ASD) splice patterns (SP) for RXRA Gene

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

Relevant External Links for RXRA Gene

GeneLoc Exon Structure for
RXRA

Expression for RXRA Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RXRA Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RXRA Gene

This gene is overexpressed in Whole Blood (x4.6).

Protein differential expression in normal tissues from HIPED for RXRA Gene

This gene is overexpressed in Liver (41.9) and Fetal gut (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RXRA Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RXRA

SOURCE GeneReport for Unigene cluster for RXRA Gene:

Hs.590886

mRNA Expression by UniProt/SwissProt for RXRA Gene:

P19793-RXRA_HUMAN
Tissue specificity: Expressed in lung fibroblasts (at protein level) (PubMed:30216632). Expressed in monocytes (PubMed:26463675). Highly expressed in liver, also found in kidney and brain (PubMed:24275569, PubMed:2159111, PubMed:14702039).

Evidence on tissue expression from TISSUES for RXRA Gene

  • Nervous system(4.7)
  • Liver(4.7)
  • Kidney(4.5)
  • Muscle(3.1)
  • Skin(2.9)
  • Blood(2.9)
  • Lung(2.7)
  • Thyroid gland(2.6)
  • Intestine(2.4)
  • Heart(2.4)
  • Spleen(2.2)
  • Pancreas(2.2)
  • Adrenal gland(2.1)
  • Stomach(2)
  • Bone marrow(2)
genes like me logo Genes that share expression patterns with RXRA: view

Primer products for research

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for RXRA Gene

Orthologs for RXRA Gene

This gene was present in the common ancestor of animals.

Orthologs for RXRA Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RXRA 29 30
  • 99.54 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RXRA 30
  • 97 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RXRA 30
  • 92 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia RXRALPHA 30
  • 92 (a)
OneToOne
RXRA 29
  • 91.89 (n)
Cow
(Bos Taurus)
Mammalia RXRA 29 30
  • 91.96 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rxra 29
  • 89.39 (n)
Mouse
(Mus musculus)
Mammalia Rxra 29 16 30
  • 88.96 (n)
OneToOne
Chicken
(Gallus gallus)
Aves RXRA 29 30
  • 86.08 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RXRA 30
  • 92 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rxra 29
  • 79.81 (n)
Str.60 29
African clawed frog
(Xenopus laevis)
Amphibia rxra-A 29
Zebrafish
(Danio rerio)
Actinopterygii rxrab 30
  • 89 (a)
OneToMany
rxraa 29 30
  • 77.11 (n)
OneToMany
rxrg 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9980 29
Fruit Fly
(Drosophila melanogaster)
Insecta usp 29 30 31
  • 62.59 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002095 29
  • 61.68 (n)
Worm
(Caenorhabditis elegans)
Secernentea nhr-14 31
  • 31 (a)
nhr-17 31
  • 30 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.10537 30
  • 54 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.304 29
Species where no ortholog for RXRA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for RXRA Gene

ENSEMBL:
Gene Tree for RXRA (if available)
TreeFam:
Gene Tree for RXRA (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RXRA: view image
Alliance of Genome Resources:
Additional Orthologs for RXRA

Paralogs for RXRA Gene

Paralogs for RXRA Gene

genes like me logo Genes that share paralogs with RXRA: view

Variants for RXRA Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RXRA Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
992288 Uncertain Significance: not provided 134,326,660(+) G/A
NM_002957.6(RXRA):c.28+1G>A
SPLICE_DONOR
rs1057519958 Likely Pathogenic: Hepatocellular carcinoma; Pancreatic adenocarcinoma; Transitional cell carcinoma of the bladder. Likely Pathogenic: Hepatocellular carcinoma; Pancreatic adenocarcinoma; Transitional cell carcinoma of the bladder 134,436,505(+) C/AC/T
NM_002957.6(RXRA):c.1280C>A (p.Ser427Tyr)
MISSENSE
rs1588299621 Likely Pathogenic: Multiple myeloma 134,417,218(+) G/A
NM_002957.6(RXRA):c.671G>A (p.Ser224Asn)
MISSENSE
rs1805337 Likely Benign: not provided 134,401,726(+) C/T
NM_002957.6(RXRA):c.123C>T (p.Ile41=)
SYNONYMOUS
rs200082299 Likely Benign: not provided 134,401,735(+) G/A
NM_002957.6(RXRA):c.132G>A (p.Pro44=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RXRA Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RXRA Gene

Variant ID Type Subtype PubMed ID
dgv12970n54 CNV loss 21841781
dgv12971n54 CNV loss 21841781
dgv12972n54 CNV gain+loss 21841781
dgv12973n54 CNV loss 21841781
dgv12974n54 CNV gain 21841781
dgv7722n100 CNV gain 25217958
dgv7723n100 CNV gain 25217958
esv1003062 CNV insertion 20482838
esv1103609 CNV insertion 17803354
esv2105964 CNV deletion 18987734
esv2561499 CNV insertion 19546169
esv2673192 CNV deletion 23128226
esv2739138 CNV deletion 23290073
esv2739209 CNV deletion 23290073
esv27796 CNV loss 19812545
esv3360601 CNV insertion 20981092
nsv1053733 CNV gain 25217958
nsv1075687 CNV deletion 25765185
nsv1111377 CNV tandem duplication 24896259
nsv1125319 OTHER inversion 24896259
nsv1126927 CNV deletion 24896259
nsv1133747 CNV deletion 24896259
nsv1142559 CNV tandem duplication 24896259
nsv428227 CNV gain 18775914
nsv466633 CNV loss 19166990
nsv466634 CNV loss 19166990
nsv466635 CNV loss 19166990
nsv466636 CNV loss 19166990
nsv469908 CNV loss 18288195
nsv472234 CNV novel sequence insertion 20440878
nsv473477 CNV novel sequence insertion 20440878
nsv473482 CNV novel sequence insertion 20440878
nsv473849 CNV novel sequence insertion 20440878
nsv473892 CNV novel sequence insertion 20440878
nsv473991 CNV novel sequence insertion 20440878
nsv474419 CNV novel sequence insertion 20440878
nsv475454 CNV novel sequence insertion 20440878
nsv477697 CNV novel sequence insertion 20440878
nsv479201 CNV novel sequence insertion 20440878
nsv479221 CNV novel sequence insertion 20440878
nsv479878 CNV novel sequence insertion 20440878
nsv511426 CNV gain 21212237
nsv512999 CNV insertion 21212237
nsv615804 CNV loss 21841781
nsv615805 CNV loss 21841781
nsv615823 CNV loss 21841781
nsv615824 CNV gain 21841781
nsv615825 CNV loss 21841781
nsv615826 CNV loss 21841781
nsv825150 CNV gain 20364138
nsv825151 CNV gain 20364138
nsv825152 CNV gain 20364138
nsv825153 CNV loss 20364138
nsv831750 CNV gain+loss 17160897
nsv831751 CNV loss 17160897
nsv831752 CNV loss 17160897
nsv951809 CNV deletion 24416366

Variation tolerance for RXRA Gene

Residual Variation Intolerance Score: 9.11% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.48; 28.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RXRA Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RXRA
Leiden Open Variation Database (LOVD)
RXRA

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RXRA Gene

Disorders for RXRA Gene

MalaCards: The human disease database

(16) MalaCards diseases for RXRA Gene - From: CVR, COP, and GCD

Disorder Aliases PubMed IDs
pancreatic adenocarcinoma
  • adenocarcinoma of the pancreas
bladder urothelial carcinoma
  • bladder transitional cell carcinoma
adult hepatocellular carcinoma
  • adult hepatoma
hepatocellular carcinoma
  • hcc
plasma cell neoplasm
  • plasma cell dyscrasia
- elite association - COSMIC cancer census association via MalaCards
Search RXRA in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RXRA

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with RXRA: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RXRA Gene

Publications for RXRA Gene

  1. RXRA gene variations influence Alzheimer's disease risk and cholesterol metabolism. (PMID: 19374686) Kölsch H … Heun R (Journal of cellular and molecular medicine 2009) 3 22 40
  2. Analysis of SNPs and haplotypes in vitamin D pathway genes and renal cancer risk. (PMID: 19753122) Karami S … Moore LE (PloS one 2009) 3 22 40
  3. Vitamin D-related genes, serum vitamin D concentrations and prostate cancer risk. (PMID: 19255064) Ahn J … Prostate, Lung, Colorectal and Ovarian Trial Project Team (Carcinogenesis 2009) 3 22 40
  4. Orphan receptor TR3 attenuates the p300-induced acetylation of retinoid X receptor-alpha. (PMID: 17761950) Zhao WX … Wu Q (Molecular endocrinology (Baltimore, Md.) 2007) 3 4 22
  5. 9-cis-retinoic acid up-regulates expression of transcriptional coregulator PELP1, a novel coactivator of the retinoid X receptor alpha pathway. (PMID: 16574651) Singh RR … Kumar R (The Journal of biological chemistry 2006) 3 4 22

Products for RXRA Gene

  • Addgene plasmids for RXRA

Sources for RXRA Gene