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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 XPA |
Gene summary |
Gene information | Gene symbol | XPA | Gene ID | 7507 |
Gene name | XPA, DNA damage recognition and repair factor | |
Synonyms | XP1|XPAC | |
Cytomap | 9q22.33 | |
Type of gene | protein-coding | |
Description | DNA repair protein complementing XP-A cellsxeroderma pigmentosum group A-complementing proteinxeroderma pigmentosum, complementation group A | |
Modification date | 20200322 | |
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 |
XPA | GO:0006281 | DNA repair | 1601884 |
XPA | GO:0009650 | UV protection | 1601884 |
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Gene structures and expression levels for XPA |
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 |
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 XPA |
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 |
exon_skip_102939 | chr9 | 97687096:97687261:97689534:97689639:97693649:97693759 | 97689534:97689639 |
exon_skip_103505 | chr9 | 97684961:97685040:97687096:97687261:97693649:97693759 | 97687096:97687261 |
exon_skip_23008 | chr9 | 97687103:97687261:97689534:97689639:97693649:97693759 | 97689534:97689639 |
exon_skip_264676 | chr9 | 97684961:97685040:97687096:97687261:97689534:97689639 | 97687096:97687261 |
exon_skip_277065 | chr9 | 97675067:97675587:97682200:97682430:97684923:97685040 | 97682200:97682430 |
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 |
exon_skip_242015 | Mayo_CB | 5.417073e-01 | 6.980519e-01 | -1.563446e-01 | 7.494160e-06 |
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Open reading frame (ORF) annotation in the exon skipping event for XPA |
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 |
ENST00000375128 | 97687096 | 97687261 | Frame-shift |
ENST00000375128 | 97689534 | 97689639 | 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 |
ENST00000375128 | 97689534 | 97689639 | Frame-shift |
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 |
ENST00000375128 | 97687096 | 97687261 | Frame-shift |
ENST00000375128 | 97689534 | 97689639 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for XPA |
p-ENSG00000136936_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 XPA |
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 XPA |
- 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 XPA |
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 XPA |
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 XPA |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | RBM6 | exon_skip_89310 | 5.179010e-01 | 3.492625e-11 |
CB | TRA2A | exon_skip_89310 | 4.254028e-01 | 1.182170e-07 |
CB | RBM45 | exon_skip_89310 | -5.553136e-01 | 6.115312e-13 |
CB | NUP42 | exon_skip_103505 | 4.904438e-01 | 3.303948e-10 |
CB | RBM6 | exon_skip_242015 | -5.859376e-01 | 4.925970e-16 |
CB | TRA2A | exon_skip_242015 | -6.000061e-01 | 6.384836e-17 |
CB | FUBP1 | exon_skip_242015 | -4.513786e-01 | 2.351593e-09 |
CB | HNRNPDL | exon_skip_242015 | 4.178063e-01 | 4.265451e-08 |
CB | NUP42 | exon_skip_242015 | 5.392818e-01 | 2.234627e-13 |
CB | PABPC4 | exon_skip_242015 | 4.001095e-01 | 1.738487e-07 |
TC | RBM3 | exon_skip_277065 | -4.182115e-01 | 3.737049e-08 |
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RelatedDrugs for XPA |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for XPA |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |