Human Gene RXRB (ENST00000374680.4) from GENCODE V44
  Description: Homo sapiens retinoid X receptor beta (RXRB), transcript variant 2, mRNA. (from RefSeq NM_021976)
RefSeq Summary (NM_021976): 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].
Gencode Transcript: ENST00000374680.4
Gencode Gene: ENSG00000204231.11
Transcript (Including UTRs)
   Position: hg38 chr6:33,193,588-33,200,665 Size: 7,078 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg38 chr6:33,194,682-33,200,476 Size: 5,795 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:33,193,588-33,200,665)mRNA (may differ from genome)Protein (533 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: Q5STP9_HUMAN
DESCRIPTION: SubName: Full=Retinoid X nuclear receptor beta; SubName: Full=Retinoid X receptor, beta;
SIMILARITY: Belongs to the nuclear hormone receptor family.
SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: RXRB
Diseases sorted by gene-association score: wegener granulomatosis (10)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 42.12 RPKM in Thyroid
Total median expression: 1292.59 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -57.40189-0.304 Picture PostScript Text
3' UTR -446.001094-0.408 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)

ModBase Predicted Comparative 3D Structure on Q5STP9
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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 Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003707 steroid hormone receptor activity
GO:0008270 zinc ion binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0043401 steroid hormone mediated signaling pathway

Cellular Component:
GO:0005634 nucleus


-  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.
JD143222 - Sequence 124246 from Patent EP1572962.
JD066308 - Sequence 47332 from Patent EP1572962.
JD222767 - Sequence 203791 from Patent EP1572962.
JD437617 - Sequence 418641 from Patent EP1572962.
JD192874 - Sequence 173898 from Patent EP1572962.
JD563091 - Sequence 544115 from Patent EP1572962.
JD166344 - Sequence 147368 from Patent EP1572962.
JD394364 - Sequence 375388 from Patent EP1572962.
JD520110 - Sequence 501134 from Patent EP1572962.
JD470121 - Sequence 451145 from Patent EP1572962.
JD135072 - Sequence 116096 from Patent EP1572962.
JD545226 - Sequence 526250 from Patent EP1572962.
JD455780 - Sequence 436804 from Patent EP1572962.
JD168325 - Sequence 149349 from Patent EP1572962.
JD530504 - Sequence 511528 from Patent EP1572962.
JD080345 - Sequence 61369 from Patent EP1572962.
JD516917 - Sequence 497941 from Patent EP1572962.
JD318183 - Sequence 299207 from Patent EP1572962.
JD123571 - Sequence 104595 from Patent EP1572962.
JD530186 - Sequence 511210 from Patent EP1572962.
JD252767 - Sequence 233791 from Patent EP1572962.
JD261860 - Sequence 242884 from Patent EP1572962.
JD518358 - Sequence 499382 from Patent EP1572962.
JD431684 - Sequence 412708 from Patent EP1572962.
JD309559 - Sequence 290583 from Patent EP1572962.
JD450670 - Sequence 431694 from Patent EP1572962.
JD524458 - Sequence 505482 from Patent EP1572962.
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.
HQ692844 - Homo sapiens retinoid X nuclear receptor beta (NR2B2) mRNA, complete cds.
HQ709179 - Homo sapiens retinoid X nuclear receptor beta (NR2B2) mRNA, complete cds.
KJ897510 - Synthetic construct Homo sapiens clone ccsbBroadEn_06904 RXRB gene, encodes complete protein.
BT007280 - Homo sapiens retinoid X receptor, beta mRNA, complete cds.
KU178313 - Homo sapiens retinoid X receptor beta isoform 1 (RXRB) mRNA, partial cds, alternatively spliced.
KU178314 - Homo sapiens retinoid X receptor beta isoform 2 (RXRB) mRNA, partial cds, alternatively spliced.
KU178315 - Homo sapiens retinoid X receptor beta isoform 3 (RXRB) mRNA, partial cds, alternatively spliced.
KU178316 - Homo sapiens retinoid X receptor beta isoform 4 (RXRB) mRNA, complete cds, alternatively spliced.
AB384890 - Synthetic construct DNA, clone: pF1KB4058, Homo sapiens RXRB gene for retinoic acid receptor RXR-beta, complete cds, without stop codon, in Flexi system.
JD025404 - Sequence 6428 from Patent EP1572962.
JD033197 - Sequence 14221 from Patent EP1572962.
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.

-  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-100D22.1-001, DAMA-248N13.1-001, DAMC-269O2.1-001, DAQB-314F24.5-001, ENST00000374680.1, ENST00000374680.2, ENST00000374680.3, hCG_2042227, NM_021976, NR2B2, Q5STP9, Q5STP9_HUMAN, uc003odb.1, uc003odb.2, uc003odb.3, uc003odb.4, uc003odb.5, uc003odb.6
UCSC ID: ENST00000374680.4
RefSeq Accession: NM_021976
Protein: Q5STP9 CCDS: CCDS4768.1, CCDS59007.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.