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PsychedeliaDokholyan Laboratory
TargetNuclear receptors

Retinoic acid receptor alpha

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

RARA_HUMANRARAHomo sapiens

Retinoic acid receptor alpha

Receptor for retinoic acid16417524,19850744,20215566,21152046,37478846. 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 processes21152046,28167758,37478846. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR519398580,28167758. 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 suppression16417524. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation19850744,20215566,37478846,9267036. Formation of a complex with histone deacetylases might lead to inhibition of RARE DNA element binding and to transcriptional repression28167758. Transcriptional activation and RARE DNA element binding might be supported by the transcription factor KLF228167758. RARA plays an essential role in the regulation of retinoic acid-induced germ cell development during spermatogenesis (By similarity). Has a role in the survival of early spermatocytes at the beginning prophase of meiosis (By similarity). In Sertoli cells, may promote the survival and development of early meiotic prophase spermatocytes (By similarity). In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function (By similarity). Together with RXRA, positively regulates microRNA-10a expression, thereby inhibiting the GATA6/VCAM1 signaling response to pulsatile shear stress in vascular endothelial cells28167758. In association with HDAC3, HDAC5 and HDAC7 corepressors, plays a role in the repression of microRNA-10a and thereby promotes the inflammatory response28167758

Quoted from UniProt’s FUNCTION annotation for P10276 (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
NCOR10.9990.9880.5000.989
NCOR20.9990.8560.5000.987
RXRA0.9990.9910.9000.983
PML0.9980.8370.9000.904
ZBTB160.9970.3110.9000.960
NCOA10.9960.9890.0000.631
RXRB0.9930.8620.8000.756
NCOA20.9920.9800.0000.632
RARB0.9840.9210.5000.638
RXRG0.9830.8480.8000.476

Where it sits in the cell

  • Nucleoplasm
  • Nucleoliadditional
  • Actin filamentsadditional
  • Cytosoladditional

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

  • Late spermatids303.7 nCPM
  • Neutrophils281 nCPM
  • Early spermatids170.1 nCPM
  • monocytes112.6 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 — 11.6 nTPM, from RARAcerebellum — 13.3 nTPM, from RARAhippocampal formation — 8.7 nTPM, from RARAamygdala — 6.0 nTPM, from RARAhypothalamus — 8.9 nTPM, from RARAthalamus — no resolved target expressed herebasal ganglia — 5.4 nTPM, from RARAmedulla 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: pituitary gland 27.2, retina 17.0, midbrain 5.7, spinal cord 4.9.

Body

heart — 37.4 nTPM, from RARAsmooth muscle — 26.7 nTPM, from RARAlung — 52.3 nTPM, from RARAliver — 37.9 nTPM, from RARAkidney — 21.0 nTPM, from RARAstomach — 20.5 nTPM, from RARAduodenum — 26.8 nTPM, from RARAsmall intestine — 28.8 nTPM, from RARAcolon — 28.3 nTPM, from RARAadrenal gland — 19.1 nTPM, from RARAthyroid gland — 24.4 nTPM, from RARApancreas — 13.9 nTPM, from RARAurinary bladder — 26.3 nTPM, from RARAskeletal muscle — 53.7 nTPM, from RARAspleen — 37.5 nTPM, from RARAsalivary gland — 18.4 nTPM, from RARA
054 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 RARA 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

  • pituitary gland27.2 nTPM
  • retina17.0 nTPM
  • cerebellum13.3 nTPM
  • cerebral cortex11.6 nTPM
  • hypothalamus8.9 nTPM
  • hippocampal formation8.7 nTPM
  • amygdala6.0 nTPM
  • midbrain5.7 nTPM
  • basal ganglia5.4 nTPM
  • spinal cord4.9 nTPM

Peripheral and autonomic · 16

  • skeletal muscle53.7 nTPM
  • lung52.3 nTPM
  • liver37.9 nTPM
  • spleen37.5 nTPM
  • heart muscle37.4 nTPM
  • small intestine28.8 nTPM
  • colon28.3 nTPM
  • duodenum26.8 nTPM
  • smooth muscle26.7 nTPM
  • urinary bladder26.3 nTPM
  • thyroid gland24.4 nTPM
  • kidney21.0 nTPM
  • stomach 120.5 nTPM
  • adrenal gland19.1 nTPM
  • salivary gland18.4 nTPM
  • pancreas13.9 nTPM

Transcript is not protein. These are RNA levels for RARA, 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 alphaNuclear receptorsAC50— no normalized value— value does not convert to pXHomo sapiensCHEMBL5291872
Retinoic acid receptor alphaNuclear receptorsAC50— no normalized value— value does not convert to pXHomo sapiensCHEMBL5291873
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