|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
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 | 20180522 | |
| UniProtAcc | P19793 | |
| Context | PubMed: RXRA [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| 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 |
| RXRA | GO:0051289 | protein homotetramerization | 7831303 |
Top |
Exon skipping events across known transcript of Ensembl for RXRA from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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. |
 |
Top |
Gene isoform structures and expression levels for RXRA |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for RXRA |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_500886 | 9 | 137218425:137218505:137293477:137293728:137299994:137300145 | 137293477:137293728 | ENSG00000186350.8 | ENST00000481739.1 |
| exon_skip_500887 | 9 | 137263816:137263985:137265852:137265976:137293241:137293386 | 137265852:137265976 | ENSG00000186350.8 | ENST00000356384.4 |
| exon_skip_500894 | 9 | 137265852:137265976:137293241:137293386:137293477:137293728 | 137293241:137293386 | ENSG00000186350.8 | ENST00000356384.4 |
| exon_skip_500896 | 9 | 137313521:137313651:137320953:137321086:137323750:137323842 | 137320953:137321086 | ENSG00000186350.8 | ENST00000540193.1,ENST00000356384.4,ENST00000481739.1 |
| exon_skip_500899 | 9 | 137320953:137321086:137323750:137323842:137325947:137326053 | 137323750:137323842 | ENSG00000186350.8 | ENST00000540193.1,ENST00000356384.4,ENST00000481739.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for RXRA |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_500886 | 9 | 137218425:137218505:137293477:137293728:137299994:137300145 | 137293477:137293728 | ENSG00000186350.8 | ENST00000481739.1 |
| exon_skip_500894 | 9 | 137265852:137265976:137293241:137293386:137293477:137293728 | 137293241:137293386 | ENSG00000186350.8 | ENST00000356384.4 |
| exon_skip_500896 | 9 | 137313521:137313651:137320953:137321086:137323750:137323842 | 137320953:137321086 | ENSG00000186350.8 | ENST00000481739.1,ENST00000356384.4,ENST00000540193.1 |
| exon_skip_500899 | 9 | 137320953:137321086:137323750:137323842:137325947:137326053 | 137323750:137323842 | ENSG00000186350.8 | ENST00000481739.1,ENST00000356384.4,ENST00000540193.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for RXRA |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000481739 | 137293477 | 137293728 | Frame-shift |
| ENST00000481739 | 137320953 | 137321086 | Frame-shift |
| ENST00000481739 | 137323750 | 137323842 | Frame-shift |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000481739 | 137293477 | 137293728 | Frame-shift |
| ENST00000481739 | 137320953 | 137321086 | Frame-shift |
| ENST00000481739 | 137323750 | 137323842 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for RXRA |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| Loci of skipped exons in TCGA 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 GTEx 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 TCGA. |
| 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 GTEx. |
| 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 |
Top |
SNVs in the skipped exons for RXRA |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_500886 | 137293478 | 137293728 | 137293616 | 137293616 | Frame_Shift_Del | C | - | p.S56fs |
| COAD | TCGA-D5-6928-01 | exon_skip_500886 | 137293478 | 137293728 | 137293658 | 137293658 | Frame_Shift_Del | C | - | p.S70fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_500886 | 137293478 | 137293728 | 137293658 | 137293658 | Frame_Shift_Del | C | - | p.S70fs |
| BLCA | TCGA-4Z-AA82-01 | exon_skip_500886 | 137293478 | 137293728 | 137293678 | 137293679 | Frame_Shift_Ins | - | T | p.M77fs |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| UMUC5_URINARY_TRACT | 137293478 | 137293728 | 137293523 | 137293523 | Missense_Mutation | G | A | p.R25Q |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 137293478 | 137293728 | 137293537 | 137293537 | Missense_Mutation | G | A | p.A30T |
| NUGC3_STOMACH | 137293478 | 137293728 | 137293597 | 137293597 | Missense_Mutation | C | T | p.P50S |
| NCIH1930_LUNG | 137293478 | 137293728 | 137293604 | 137293604 | Missense_Mutation | G | T | p.S52I |
| WM2664_SKIN | 137293478 | 137293728 | 137293646 | 137293646 | Missense_Mutation | C | T | p.S66L |
| WM115_SKIN | 137293478 | 137293728 | 137293646 | 137293646 | Missense_Mutation | C | T | p.S66L |
| R262_CENTRAL_NERVOUS_SYSTEM | 137293478 | 137293728 | 137293680 | 137293680 | Missense_Mutation | G | T | p.M77I |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 137320954 | 137321086 | 137320990 | 137320990 | Missense_Mutation | G | A | p.R316H |
| MN60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 137320954 | 137321086 | 137320990 | 137320990 | Missense_Mutation | G | A | p.R316H |
| CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 137320954 | 137321086 | 137321028 | 137321028 | Missense_Mutation | G | A | p.G329R |
| OVCAR4_OVARY | 137320954 | 137321086 | 137321028 | 137321028 | Missense_Mutation | G | A | p.G329R |
| LS180_LARGE_INTESTINE | 137293478 | 137293728 | 137293522 | 137293522 | Nonsense_Mutation | C | T | p.R25* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RXRA |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RXRA |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RXRA |
Top |
RelatedDrugs for RXRA |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P19793 | DB00210 | Adapalene | Retinoic acid receptor RXR-alpha | small molecule | approved | |
| P19793 | DB00459 | Acitretin | Retinoic acid receptor RXR-alpha | small molecule | approved | |
| P19793 | DB00307 | Bexarotene | Retinoic acid receptor RXR-alpha | small molecule | approved|investigational | |
| P19793 | DB00412 | Rosiglitazone | Retinoic acid receptor RXR-alpha | small molecule | approved|investigational | |
| P19793 | DB00523 | Alitretinoin | Retinoic acid receptor RXR-alpha | small molecule | approved|investigational | |
| P19793 | DB01393 | Bezafibrate | Retinoic acid receptor RXR-alpha | small molecule | approved|investigational | |
| P19793 | DB00755 | Tretinoin | Retinoic acid receptor RXR-alpha | small molecule | approved|investigational|nutraceutical | |
| P19793 | DB00749 | Etodolac | Retinoic acid receptor RXR-alpha | small molecule | approved|investigational|vet_approved | |
| P19793 | DB01436 | Alfacalcidol | Retinoic acid receptor RXR-alpha | small molecule | approved|nutraceutical |
Top |
RelatedDiseases for RXRA |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| RXRA | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
| RXRA | C0040136 | Thyroid Neoplasm | 1 | CTD_human |
| RXRA | C0149940 | Sciatic Neuropathy | 1 | CTD_human |
| RXRA | C0345967 | Malignant mesothelioma | 1 | CTD_human |
| RXRA | C1862939 | AMYOTROPHIC LATERAL SCLEROSIS 1 | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|