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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for RARA |
 Gene summary |
| Gene information | Gene symbol | RARA | Gene ID | 5914 |
| Gene name | retinoic acid receptor alpha | |
| Synonyms | NR1B1|RAR | |
| Cytomap | 17q21.2 | |
| Type of gene | protein-coding | |
| Description | retinoic acid receptor alphaRAR-alphanuclear receptor subfamily 1 group B member 1nucleophosmin-retinoic acid receptor alpha fusion protein NPM-RAR long formretinoic acid nuclear receptor alpha variant 1retinoic acid nuclear receptor alpha variant 2 | |
| Modification date | 20200327 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| RARA | GO:0007165 | signal transduction | 2825025 |
| RARA | GO:0030853 | negative regulation of granulocyte differentiation | 19917671 |
| RARA | GO:0032689 | negative regulation of interferon-gamma production | 18416830 |
| RARA | GO:0032720 | negative regulation of tumor necrosis factor production | 18416830 |
| RARA | GO:0032736 | positive regulation of interleukin-13 production | 18416830 |
| RARA | GO:0032753 | positive regulation of interleukin-4 production | 18416830 |
| RARA | GO:0032754 | positive regulation of interleukin-5 production | 18416830 |
| RARA | GO:0045630 | positive regulation of T-helper 2 cell differentiation | 18416830 |
| RARA | GO:0045892 | negative regulation of transcription, DNA-templated | 20080953 |
| RARA | GO:0045893 | positive regulation of transcription, DNA-templated | 18845237|19850744|20080953 |
| RARA | GO:0045944 | positive regulation of transcription by RNA polymerase II | 19850744|21131358 |
| RARA | GO:0071300 | cellular response to retinoic acid | 19917671 |
| RARA | GO:0071391 | cellular response to estrogen stimulus | 20080953 |
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Gene structures and expression levels for RARA |
| Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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ENSG00000131759
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | DOWN | ENST00000425707.7 | RARA-206:protein_coding:RARA | 3.734195e+01 | -2.696531e+00 | 3.027131e-05 | 2.686101e-04 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for RARA |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_226080 | chr17 | 40309192:40309286:40326475:40326551:40330857:40331168 | 40326475:40326551 |
| exon_skip_237777 | chr17 | 40330857:40331396:40348316:40348464:40349784:40349818 | 40348316:40348464 |
| exon_skip_27489 | chr17 | 40318285:40318448:40330857:40331396:40348316:40348336 | 40330857:40331396 |
| exon_skip_292742 | chr17 | 40342796:40342867:40348316:40348464:40349784:40349818 | 40348316:40348464 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for RARA |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000394089 | 40330857 | 40331396 | 5CDS-5UTR |
| ENST00000254066 | 40348316 | 40348464 | Frame-shift |
| ENST00000394089 | 40348316 | 40348464 | Frame-shift |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000254066 | 40348316 | 40348464 | Frame-shift |
| ENST00000394089 | 40348316 | 40348464 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for RARA |
p-ENSG00000131759_img4.png |
| Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Lost protein functional features of individual exon skipping events in MSBB. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Lost protein functional features of individual exon skipping events in Mayo. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
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3'-UTR located exon skipping events that lost miRNA binding sites in RARA |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for RARA |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for RARA |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RARA |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for RARA |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for RARA |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P10276 | approved | DB00210 | Adapalene | small molecule | P10276 |
| P10276 | approved | DB00459 | Acitretin | small molecule | P10276 |
| P10276 | approved|investigational | DB00523 | Alitretinoin | small molecule | P10276 |
| P10276 | approved|investigational|nutraceutical | DB00755 | Tretinoin | small molecule | P10276 |
| P10276 | approved|investigational | DB00799 | Tazarotene | small molecule | P10276 |
| P10276 | approved | DB00982 | Isotretinoin | small molecule | P10276 |
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RelatedDiseases for RARA |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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