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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for RXRA |
Gene summary |
Gene information | Gene symbol | RXRA | Gene ID | 6256 |
Gene name | retinoid X receptor alpha | |
Synonyms | NR2B1 | |
Cytomap | 9q34.2 | |
Type of gene | protein-coding | |
Description | retinoic acid receptor RXR-alphanuclear receptor subfamily 2 group B member 1retinoid X nuclear receptor alpha | |
Modification date | 20200320 | |
UniProtAcc | ||
Context | - 19374686(RXRA gene variations influence Alzheimer's disease risk and cholesterol metabolism) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
RXRA | GO:0000122 | negative regulation of transcription by RNA polymerase II | 17426122 |
RXRA | GO:0019048 | modulation by virus of host morphology or physiology | 11915042 |
RXRA | GO:0035357 | peroxisome proliferator activated receptor signaling pathway | 10195690 |
RXRA | GO:0045944 | positive regulation of transcription by RNA polymerase II | 12037571|20219900 |
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Gene structures and expression levels for RXRA |
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. |
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. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
STG | UP | ENST00000672570.1 | RXRA-205:protein_coding:RXRA | 1.022837e+01 | 9.767094e-01 | 6.448744e-04 | 3.078570e-02 |
PG | UP | ENST00000484822.1 | RXRA-203:retained_intron:RXRA | 1.005872e+02 | 8.176504e-01 | 3.572719e-05 | 1.280447e-03 |
PG | UP | ENST00000672570.1 | RXRA-205:protein_coding:RXRA | 1.134982e+01 | 9.538838e-01 | 1.162511e-04 | 3.069024e-03 |
PG | UP | ENST00000649020.1 | RXRA-204:protein_coding:RXRA | 1.208440e+00 | 1.059017e+00 | 5.199259e-03 | 4.691914e-02 |
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 RXRA |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
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 RXRA |
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 |
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 |
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Infer the effects of exon skipping event on protein functional features for RXRA |
p-ENSG00000186350_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 RXRA |
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 RXRA |
- 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 RXRA |
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 RXRA |
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 RXRA |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for RXRA |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
P19793 | approved | DB00210 | Adapalene | small molecule | P19793 |
P19793 | approved|investigational | DB00307 | Bexarotene | small molecule | P19793 |
P19793 | approved|investigational | DB00412 | Rosiglitazone | small molecule | P19793 |
P19793 | approved | DB00459 | Acitretin | small molecule | P19793 |
P19793 | approved|investigational | DB00523 | Alitretinoin | small molecule | P19793 |
P19793 | approved|investigational|vet_approved | DB00749 | Etodolac | small molecule | P19793 |
P19793 | approved|investigational|nutraceutical | DB00755 | Tretinoin | small molecule | P19793 |
P19793 | approved|investigational | DB01393 | Bezafibrate | small molecule | P19793 |
P19793 | approved|nutraceutical | DB01436 | Alfacalcidol | small molecule | P19793 |
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RelatedDiseases for RXRA |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |