Human Gene RARA (ENST00000254066.10_8) from GENCODE V47lift37
  Description: retinoic acid receptor alpha, transcript variant 1 (from RefSeq NM_000964.4)
Gencode Transcript: ENST00000254066.10_8
Gencode Gene: ENSG00000131759.18_16
Transcript (Including UTRs)
   Position: hg19 chr17:38,465,432-38,513,895 Size: 48,464 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr17:38,487,471-38,512,478 Size: 25,008 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:38,465,432-38,513,895)mRNA (may differ from genome)Protein (462 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: Q6I9R7_HUMAN
DESCRIPTION: SubName: Full=RARA protein; SubName: Full=Retinoic acid nuclear receptor alpha variant 1; SubName: Full=Retinoic acid receptor, alpha, isoform CRA_c; SubName: Full=cDNA, FLJ92939, Homo sapiens retinoic acid receptor, alpha (RARA), mRNA;
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: RARA
Diseases sorted by gene-association score: leukemia, acute promyelocytic, somatic* (307), myeloid leukemia (10), leukemia (10), teratocarcinoma (6), embryonal carcinoma (6), cleft lip (4), cleft palate, isolated (3), caudal regression syndrome (3), keratomalacia (2), breast cancer (2), peach allergy (2), aleukemic leukemia cutis (1), leukemia, acute myeloid (1), infant botulism (1)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 43.88 RPKM in Whole Blood
Total median expression: 616.67 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 -204.60469-0.436 Picture PostScript Text
3' UTR -588.201417-0.415 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
IPR003078 - Retinoic_acid_rcpt
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)

ModBase Predicted Comparative 3D Structure on Q6I9R7
FrontTopSide
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000900 translation repressor activity, nucleic acid binding
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0001012 RNA polymerase II regulatory region DNA binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003707 steroid hormone receptor activity
GO:0003708 retinoic acid receptor activity
GO:0004879 RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
GO:0008134 transcription factor binding
GO:0008144 drug binding
GO:0008270 zinc ion binding
GO:0042826 histone deacetylase binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding
GO:0046872 metal ion binding
GO:0048027 mRNA 5'-UTR binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001657 ureteric bud development
GO:0001843 neural tube closure
GO:0001889 liver development
GO:0002068 glandular epithelial cell development
GO:0003148 outflow tract septum morphogenesis
GO:0003417 growth plate cartilage development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007281 germ cell development
GO:0007283 spermatogenesis
GO:0007565 female pregnancy
GO:0008284 positive regulation of cell proliferation
GO:0008285 negative regulation of cell proliferation
GO:0008584 male gonad development
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0017148 negative regulation of translation
GO:0021766 hippocampus development
GO:0030850 prostate gland development
GO:0030852 regulation of granulocyte differentiation
GO:0031076 embryonic camera-type eye development
GO:0031641 regulation of myelination
GO:0032355 response to estradiol
GO:0032526 response to retinoic acid
GO:0033189 response to vitamin A
GO:0034097 response to cytokine
GO:0035264 multicellular organism growth
GO:0042981 regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0043401 steroid hormone mediated signaling pathway
GO:0045471 response to ethanol
GO:0045596 negative regulation of cell differentiation
GO:0045666 positive regulation of neuron differentiation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0045947 negative regulation of translational initiation
GO:0048167 regulation of synaptic plasticity
GO:0048384 retinoic acid receptor signaling pathway
GO:0055012 ventricular cardiac muscle cell differentiation
GO:0060010 Sertoli cell fate commitment
GO:0060173 limb development
GO:0060324 face development
GO:0060348 bone development
GO:0060534 trachea cartilage development
GO:0060591 chondroblast differentiation
GO:0061037 negative regulation of cartilage development
GO:0071222 cellular response to lipopolysaccharide

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0015629 actin cytoskeleton
GO:0030425 dendrite
GO:0043005 neuron projection
GO:0043025 neuronal cell body
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  DQ893531 - Synthetic construct clone IMAGE:100006161; FLH164152.01X; RZPDo839D03162D retinoic acid receptor, alpha (RARA) gene, encodes complete protein.
BC008727 - Homo sapiens retinoic acid receptor, alpha, mRNA (cDNA clone MGC:1651 IMAGE:3163891), complete cds.
AK312564 - Homo sapiens cDNA, FLJ92939, Homo sapiens retinoic acid receptor, alpha (RARA), mRNA.
AK292205 - Homo sapiens cDNA FLJ78006 complete cds, highly similar to Homo sapiens retinoic acid receptor, alpha, mRNA.
FJ487576 - Homo sapiens retinoic acid receptor alpha isoform 1 deltaBC (RARA) mRNA, complete cds, alternatively spliced.
AK130192 - Homo sapiens cDNA FLJ26682 fis, clone MPG04930, highly similar to Retinoic acid receptor alpha (RAR-alpha).
DL491558 - Novel nucleic acids.
DL490160 - Novel nucleic acids.
X06614 - Human mRNA for receptor of retinoic acid.
JD190848 - Sequence 171872 from Patent EP1572962.
JD530318 - Sequence 511342 from Patent EP1572962.
JD115521 - Sequence 96545 from Patent EP1572962.
CU679063 - Synthetic construct Homo sapiens gateway clone IMAGE:100019512 5' read RARA mRNA.
KJ891981 - Synthetic construct Homo sapiens clone ccsbBroadEn_01375 RARA gene, encodes complete protein.
AB590379 - Synthetic construct DNA, clone: pFN21AE1591, Homo sapiens RARA gene for retinoic acid receptor, alpha, without stop codon, in Flexi system.
DQ893744 - Synthetic construct Homo sapiens clone IMAGE:100008204; FLH164148.01L; RZPDo839D03161D retinoic acid receptor, alpha (RARA) gene, encodes complete protein.
CR457438 - Homo sapiens full open reading frame cDNA clone RZPDo834D086D for gene RARA, retinoic acid receptor, alpha; complete cds, incl. stopcodon.
HQ692826 - Homo sapiens retinoic acid nuclear receptor alpha variant 1 (NR1B1) mRNA, complete cds.
AF242867 - Synthetic construct ECFP-retinoic acid receptor alpha fusion protein mRNA, complete cds.
X06538 - Human mRNA for retinoic acid receptor.
AK098172 - Homo sapiens cDNA FLJ40853 fis, clone TRACH2015486, highly similar to RETINOIC ACID RECEPTOR ALPHA.
AK303868 - Homo sapiens cDNA FLJ61038 complete cds, highly similar to Homo sapiens retinoic acid receptor, alpha (RARA), transcript variant 2, mRNA.
AL834159 - Homo sapiens mRNA; cDNA DKFZp761C0417 (from clone DKFZp761C0417).
BC071733 - Homo sapiens retinoic acid receptor, alpha, mRNA (cDNA clone MGC:88071 IMAGE:5217484), complete cds.
CU687150 - Synthetic construct Homo sapiens gateway clone IMAGE:100022820 5' read RARA mRNA.
HQ692827 - Homo sapiens retinoic acid nuclear receptor alpha variant 2 (NR1B1) mRNA, complete cds.
KJ905891 - Synthetic construct Homo sapiens clone ccsbBroadEn_15561 RARA gene, encodes complete protein.
AJ417079 - Homo sapiens partial mRNA for PML/RARA fusion protein (PML/RARA gene).
AF012304 - Homo sapiens nuclear mitotic apparatus protein-retinoic acid receptor alpha fusion protein (NuMA-RARA fusion) mRNA, partial cds.
KP100665 - Homo sapiens GTF2I-RARA fusion protein (GTF2I-RARA) mRNA, complete cds.
U41743 - Human nucleophosmin-retinoic acid receptor alpha fusion protein NPM-RAR short form mRNA, complete cds.
S50916 - PML-RAR fusion gene {fusion transcript} [human, mRNA Partial, 1284 nt].
U41742 - Human nucleophosmin-retinoic acid receptor alpha fusion protein NPM-RAR long form mRNA, complete cds.
M73779 - Human PML-RAR protein (PML-RAR) mRNA, complete cds.
X63645 - H.sapiens PML-RAR alpha-bcr1-2 gene.
EF535849 - Homo sapiens PML/RARA fusion mRNA, partial sequence.
X58685 - Human mRNA for retinoic acid receptor-alpha, exon 3.
KF589333 - Homo sapiens TBLR1-RARA fusion protein (TBLR1-RARA fusion) mRNA, complete cds.
AF242868 - Synthetic construct ECFP-retinoic acid receptor ligand binding domain fusion protein mRNA, complete cds.
JD098295 - Sequence 79319 from Patent EP1572962.
JD202419 - Sequence 183443 from Patent EP1572962.
JD261105 - Sequence 242129 from Patent EP1572962.
JD190924 - Sequence 171948 from Patent EP1572962.
JD071572 - Sequence 52596 from Patent EP1572962.
JD368863 - Sequence 349887 from Patent EP1572962.
JD477489 - Sequence 458513 from Patent EP1572962.
JD210822 - Sequence 191846 from Patent EP1572962.
JD346858 - Sequence 327882 from Patent EP1572962.
JD227278 - Sequence 208302 from Patent EP1572962.
JD233566 - Sequence 214590 from Patent EP1572962.
JD528691 - Sequence 509715 from Patent EP1572962.
JD413988 - Sequence 395012 from Patent EP1572962.
JD541030 - Sequence 522054 from Patent EP1572962.
JD485394 - Sequence 466418 from Patent EP1572962.
JD122404 - Sequence 103428 from Patent EP1572962.
JD385427 - Sequence 366451 from Patent EP1572962.
JD076083 - Sequence 57107 from Patent EP1572962.
JD415442 - Sequence 396466 from Patent EP1572962.
JD062457 - Sequence 43481 from Patent EP1572962.
JD458297 - Sequence 439321 from Patent EP1572962.
JD383555 - Sequence 364579 from Patent EP1572962.
JD341660 - Sequence 322684 from Patent EP1572962.
JD431701 - Sequence 412725 from Patent EP1572962.
JD216613 - Sequence 197637 from Patent EP1572962.
JD103324 - Sequence 84348 from Patent EP1572962.
JD115531 - Sequence 96555 from Patent EP1572962.
JD110495 - Sequence 91519 from Patent EP1572962.
JD052784 - Sequence 33808 from Patent EP1572962.
JD157694 - Sequence 138718 from Patent EP1572962.
JD253907 - Sequence 234931 from Patent EP1572962.
JD120760 - Sequence 101784 from Patent EP1572962.
JD219738 - Sequence 200762 from Patent EP1572962.
JD054897 - Sequence 35921 from Patent EP1572962.
JD322063 - Sequence 303087 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_egfr_smrtePathway - Map Kinase Inactivation of SMRT Corepressor
h_nuclearRsPathway - Nuclear Receptors in Lipid Metabolism and Toxicity
h_carm1Pathway - Transcription Regulation by Methyltransferase of CARM1
h_rarPathway - Degradation of the RAR and RXR by the proteasome
h_pmlPathway - Regulation of transcriptional activity by PML
h_rarrxrPathway - Nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000254066.1, ENST00000254066.2, ENST00000254066.3, ENST00000254066.4, ENST00000254066.5, ENST00000254066.6, ENST00000254066.7, ENST00000254066.8, ENST00000254066.9, hCG_2007196 , NM_000964, NR1B1 , Q6I9R7, Q6I9R7_HUMAN, RARA , uc317fnb.1, uc317fnb.2
UCSC ID: ENST00000254066.10_8
RefSeq Accession: NM_000964.4
Protein: Q6I9R7

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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