Human Gene RXRB (uc011hgo.3) Description and Page Index
  Description: Homo sapiens retinoid X receptor, beta (RXRB), transcript variant 1, mRNA.
RefSeq Summary (NM_001270401): This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the effects of retinoic acid (RA). The encoded protein forms homodimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene lies within the major histocompatibility complex (MHC) class II region on chromosome 6. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012].
Transcript (Including UTRs)
   Position: chr6_mann_hap4:4,618,677-4,625,789 Size: 7,113 Total Exon Count: 10 Strand: -
Coding Region
   Position: chr6_mann_hap4:4,619,775-4,625,569 Size: 5,795 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDMicroarray
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated: 2013-06-14

+  Sequence and Links to Tools and Databases
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-  Comments and Description Text from UniProtKB
  ID: RXRB_HUMAN
DESCRIPTION: RecName: Full=Retinoic acid receptor RXR-beta; AltName: Full=Nuclear receptor subfamily 2 group B member 2; AltName: Full=Retinoid X receptor beta;
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 (By similarity). Specifically binds 9-cis retinoic acid (9C-RA).
SUBUNIT: Homodimer (By similarity). Heterodimer with a RAR molecule. Binds DNA preferentially as a RAR/RXR heterodimer.
INTERACTION: Q00975:CACNA1B; NbExp=3; IntAct=EBI-748576, EBI-1055161;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in a variety of tumor cell lines.
DOMAIN: Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
SIMILARITY: Belongs to the nuclear hormone receptor family. NR2 subfamily.
SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.
SEQUENCE CAUTION: Sequence=BAD92481.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database: RXRB
CDC HuGE Published Literature: RXRB
Positive Disease Associations: Cholesterol, LDL , Creatinine , schizophrenia
Related Studies:
  1. Cholesterol, LDL
    Cristen J Willer et al. Nature genetics 2008, Newly identified loci that influence lipid concentrations and risk of coronary artery disease., Nature genetics. [PubMed 18193043]
  2. Creatinine
    , , . [PubMed 0]
  3. Creatinine
    , , . [PubMed 0]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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GNF Expression Atlas 1 Human Data on Affy U95 Chips

      
    
     
      
    
    
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -77.63220-0.353 Picture PostScript Text
3' UTR -466.721098-0.425 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008946 - Nucl_hormone_rcpt_ligand-bd
IPR000536 - Nucl_hrmn_rcpt_lig-bd_core
IPR000003 - Retinoid-X_rcpt/HNF4
IPR001723 - Str_hrmn_rcpt
IPR001628 - Znf_hrmn_rcpt
IPR013088 - Znf_NHR/GATA

Pfam Domains:
PF00104 - Ligand-binding domain of nuclear hormone receptor
PF00105 - Zinc finger, C4 type (two domains)

SCOP Domains:
48508 - Nuclear receptor ligand-binding domain
57716 - Glucocorticoid receptor-like (DNA-binding domain)

Protein Data Bank (PDB) 3-D Structure

1H9U
- X-ray Chimera LS-SNP

1UHL
- X-ray Chimera LS-SNP
Chimera help

ModBase Predicted Comparative 3D Structure on P28702
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
Jackson LabRGD    
Protein Sequence     
Alignment     

-  Descriptions from all associated GenBank mRNAs
  X63523 - H.sapiens mRNA DAUDI6 3'-region.
BC001167 - Homo sapiens retinoid X receptor, beta, mRNA (cDNA clone MGC:1831 IMAGE:3502936), complete cds.
X65463 - H.sapiens mRNA for MHC class I promoter binding protein.
X63522 - H.sapiens mRNA DAUDI6 for retinoic acid X receptor b.
AK225842 - Homo sapiens mRNA for retinoid X receptor, beta variant, clone: FCC126E12.
AK302125 - Homo sapiens cDNA FLJ61673 complete cds, highly similar to Retinoic acid receptor RXR-beta.
AB209244 - Homo sapiens mRNA for retinoid X receptor, beta variant protein.
M84820 - Human retinoid X receptor beta (RXR-beta) mRNA, complete cds.
BT007280 - Homo sapiens retinoid X receptor, beta mRNA, complete cds.
AB384890 - Synthetic construct DNA, clone: pF1KB4058, Homo sapiens RXRB gene for retinoic acid receptor RXR-beta, complete cds, without stop codon, in Flexi system.
AK301096 - Homo sapiens cDNA FLJ50703 complete cds, highly similar to Retinoic acid receptor RXR-beta.
X66424 - H.sapiens mRNA for retinoid X receptor b, exons a and b.
AK295759 - Homo sapiens cDNA FLJ50538 complete cds, highly similar to Retinoic acid receptor RXR-beta.
AK300402 - Homo sapiens cDNA FLJ61401 complete cds, highly similar to Retinoic acid receptor RXR-beta.
HQ692844 - Homo sapiens retinoid X nuclear receptor beta (NR2B2) mRNA, complete cds.
HQ709179 - Homo sapiens retinoid X nuclear receptor beta (NR2B2) mRNA, complete cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03320 - PPAR signaling pathway
hsa04920 - Adipocytokine signaling pathway
hsa05200 - Pathways in cancer
hsa05216 - Thyroid cancer
hsa05222 - Small cell lung cancer
hsa05223 - Non-small cell lung cancer

-  Other Names for This Gene
  Alternate Gene Symbols: DADB-100D22.1-002, DAMA-248N13.1-002, DAMC-269O2.1-002, DAQB-314F24.5-002, NM_001270401, NP_001257330, NR2B2, Q5JP92, Q5STQ1, Q5STQ1_HUMAN, uc011hgo.2
UCSC ID: uc011hgo.3
RefSeq Accession: NM_001270401
Protein: P28702 (aka RXRB_HUMAN