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PsychedeliaDokholyan Laboratory
TargetNuclear receptors

Retinoic acid receptor beta

Steroid and other ligand-activated transcription factors.

Measurements
2
Compounds
1
Binding constants
0
Median pX
—

I · Identity

What this target is

Its function as UniProt states it, where in a cell the protein is found, and which cell types and tissues transcribe its gene.

Protein

RARB_HUMANRARBHomo sapiens

Retinoic acid receptor beta

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 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 or presence of hormone ligand, acts mainly as an activator of gene expression due to weak binding to corepressors12554770. The RXRA/RARB heterodimer can act as a repressor on the DR1 element and as an activator on the DR5 element29021580. In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function (By similarity)

Quoted from UniProt’s FUNCTION annotation for P10826 (reviewed). The superscript numbers are UniProt’s own PubMed citations, kept in the sentence and in order, each linking to the paper it names.

What it acts with

STRING’s highest-confidence human functional partners. The combined score mixes several kinds of evidence, so each channel is shown separately — a partner supported by experiment is a different claim from one supported only by text mining, and for a receptor this is where its coupling appears as evidence rather than as assertion.

PartnerCombinedExperimentDatabaseText mining
RXRA0.9960.9710.8000.470
RXRB0.9920.7160.9000.754
RARA0.9840.9210.5000.638
NCOA10.9840.9640.0000.573
RXRG0.9730.6420.8000.630
CRABP20.9670.0500.5000.937
RARS10.9580.0000.0000.958
MED10.9370.7970.5000.432
RARG0.9110.0000.5000.824
RASSF10.7890.0000.0000.789

Where it sits in the cell

  • Nucleoplasm

Human Protein Atlas, by antibody immunofluorescence in cell lines — a different assay from the expression figures below, which are RNA.

UniProt, curated Nucleus · Cytoplasm

Expression by cell type

Single cell type RNA, the 9 highest of those the Human Protein Atlas reports for this gene. Transcript, not protein, and a cell type rather than a tissue.

  • Müller glia680.2 nCPM
  • Conjunctival goblet cells338.8 nCPM
  • Cone photoreceptor cells302.2 nCPM
  • Brain inhibitory neurons292.7 nCPM
  • Pituicytes/FSCs291.2 nCPM
  • Salivary duct cells285.9 nCPM
  • Prostatic glandular cells273.4 nCPM
  • Renal collecting duct intercalated cells268.1 nCPM
  • Thymic myoid cells224.3 nCPM

II · Anatomy

Where the gene is transcribed

The same two atlases the compound plates use, asked about this gene alone. Brain on the left, peripheral and autonomic tissues on the right.

Brain

cerebral cortex — 4.4 nTPM, from RARBcerebellum — 0.1 nTPM, from RARBhippocampal formation — 0.9 nTPM, from RARBamygdala — 0.8 nTPM, from RARBhypothalamus — 0.9 nTPM, from RARBthalamus — no resolved target expressed herebasal ganglia — 8.8 nTPM, from RARBmedulla oblongata — no resolved target expressed here

basal ganglia: drawn as the caudate nucleus, putamen and globus pallidus.

Measured but not drawn — this anatomogram has no outline for them: retina 9.6, pituitary gland 5.0, spinal cord 1.3, midbrain 0.8.

Body

heart — 12.1 nTPM, from RARBsmooth muscle — 5.1 nTPM, from RARBlung — 4.0 nTPM, from RARBliver — 5.6 nTPM, from RARBkidney — 12.8 nTPM, from RARBstomach — 2.1 nTPM, from RARBduodenum — 1.5 nTPM, from RARBsmall intestine — 1.1 nTPM, from RARBcolon — 3.9 nTPM, from RARBadrenal gland — 6.3 nTPM, from RARBthyroid gland — 7.4 nTPM, from RARBpancreas — 1.0 nTPM, from RARBurinary bladder — 5.9 nTPM, from RARBskeletal muscle — 1.4 nTPM, from RARBspleen — 3.8 nTPM, from RARBsalivary gland — 10.4 nTPM, from RARB
013 nTPM

Square-root ramp · shared scale across both plates

Shading is transcript level — not affinity, and not affinity combined with expression. Outlined but unshaded organs hold none of RARB transcript above the atlas’s detection threshold. Anatomy from EMBL-EBI Anatomogram (Apache License 2.0); regions identified by Uberon (uberon.org), CC BY 3.0.

Brain · 10

  • retina9.6 nTPM
  • basal ganglia8.8 nTPM
  • pituitary gland5.0 nTPM
  • cerebral cortex4.4 nTPM
  • spinal cord1.3 nTPM
  • hippocampal formation0.9 nTPM
  • hypothalamus0.9 nTPM
  • amygdala0.8 nTPM
  • midbrain0.8 nTPM
  • cerebellum0.1 nTPM

Peripheral and autonomic · 16

  • kidney12.8 nTPM
  • heart muscle12.1 nTPM
  • salivary gland10.4 nTPM
  • thyroid gland7.4 nTPM
  • adrenal gland6.3 nTPM
  • urinary bladder5.9 nTPM
  • liver5.6 nTPM
  • smooth muscle5.1 nTPM
  • lung4.0 nTPM
  • colon3.9 nTPM
  • spleen3.8 nTPM
  • stomach 12.1 nTPM
  • duodenum1.5 nTPM
  • skeletal muscle1.4 nTPM
  • small intestine1.1 nTPM
  • pancreas1.0 nTPM

Transcript is not protein. These are RNA levels for RARB, shaded on √nTPM so that a three-order range stays legible — on a linear ramp every region but the strongest would read as blank, which looks like absence rather than less. A region carrying no shading is one the atlas reports no consensus value for, not one where the gene is silent. And a gene being transcribed somewhere is not evidence that any compound reaches it. Human Protein Atlas, RNA expression, nTPM (normalized transcripts per million), consensus tissue dataset.

IV · Evidence

Every measurement at this target

Each row links to the ChEMBL assay it came from.

Functional readouts 2

IC₅₀, EC₅₀, AC₅₀ and potency. Assay-dependent, and not interchangeable with a binding constant.

TargetClassTypeValue (nM)pXOrganismAssay
Retinoic acid receptor betaNuclear receptorsAC50— no normalized value— value does not convert to pXHomo sapiensCHEMBL5291874
Retinoic acid receptor betaNuclear receptorsAC50— no normalized value— value does not convert to pXHomo sapiensCHEMBL5291875
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