|
||||||
|
 | |
| |
| |
| 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 RAD1 |
 Gene summary |
| Gene information | Gene symbol | RAD1 | Gene ID | 5810 |
| Gene name | RAD1 checkpoint DNA exonuclease | |
| Synonyms | HRAD1|REC1 | |
| Cytomap | 5p13.2 | |
| Type of gene | protein-coding | |
| Description | cell cycle checkpoint protein RAD1DNA repair exonuclease REC1DNA repair exonuclease rad1 homologRAD1 checkpoint clamp componentRAD1 homologcell cycle checkpoint protein Hrad1checkpoint control protein HRAD1exonuclease homolog RAD1rad1-like DNA dam | |
| Modification date | 20200313 | |
| 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 |
| RAD1 | GO:0071479 | cellular response to ionizing radiation | 21659603 |
Top |
Gene structures and expression levels for RAD1 |
| 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. |
 |
ENSG00000113456
| 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. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for RAD1 |
| 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_128415 | chr5 | 34911618:34911812:34913927:34914026:34914695:34914801 | 34913927:34914026 |
| exon_skip_12896 | chr5 | 34914695:34914961:34915416:34915626:34918052:34918136 | 34915416:34915626 |
| exon_skip_14890 | chr5 | 34911618:34911812:34913927:34914026:34914695:34914704 | 34913927:34914026 |
| exon_skip_153765 | chr5 | 34911618:34911812:34913470:34913578:34914695:34914704 | 34913470:34913578 |
| exon_skip_159549 | chr5 | 34909258:34909356:34911554:34911812:34914695:34914801 | 34911554:34911812 |
| exon_skip_192694 | chr5 | 34911618:34911812:34913470:34913578:34913927:34914026 | 34913470:34913578 |
| exon_skip_21224 | chr5 | 34913470:34913578:34913927:34914026:34914695:34914704 | 34913927:34914026 |
| exon_skip_222357 | chr5 | 34908655:34908948:34909258:34909356:34911554:34911812 | 34909258:34909356 |
| exon_skip_262339 | chr5 | 34911618:34911812:34914695:34914961:34915416:34915504 | 34914695:34914961 |
| exon_skip_275804 | chr5 | 34909258:34909356:34911554:34911812:34913470:34913578 | 34911554:34911812 |
| exon_skip_46092 | chr5 | 34914726:34914961:34915416:34915626:34918052:34918136 | 34915416:34915626 |
| exon_skip_86088 | chr5 | 34911618:34911812:34913470:34913578:34914695:34914801 | 34913470:34913578 |
| exon_skip_9207 | chr5 | 34911650:34911812:34913470:34913578:34913927:34914026 | 34913470:34913578 |
| exon_skip_9842 | chr5 | 34913470:34913578:34913927:34914026:34914695:34914801 | 34913927:34914026 |
| 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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for RAD1 |
| 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 |
| ENST00000341754 | 34915416 | 34915626 | 3UTR-3UTR |
| ENST00000341754 | 34913470 | 34913578 | Frame-shift |
| ENST00000382038 | 34913470 | 34913578 | Frame-shift |
| ENST00000341754 | 34909258 | 34909356 | In-frame |
| ENST00000382038 | 34909258 | 34909356 | In-frame |
| 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 |
| ENST00000341754 | 34915416 | 34915626 | 3UTR-3UTR |
| ENST00000341754 | 34913470 | 34913578 | Frame-shift |
| ENST00000382038 | 34913470 | 34913578 | 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 |
| ENST00000341754 | 34915416 | 34915626 | 3UTR-3UTR |
| ENST00000341754 | 34911554 | 34911812 | Frame-shift |
| ENST00000382038 | 34911554 | 34911812 | Frame-shift |
| ENST00000341754 | 34913470 | 34913578 | Frame-shift |
| ENST00000382038 | 34913470 | 34913578 | Frame-shift |
| ENST00000341754 | 34909258 | 34909356 | In-frame |
| ENST00000382038 | 34909258 | 34909356 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for RAD1 |
p-ENSG00000113456_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 |
| ENST00000341754 | 2358 | 282 | 34909258 | 34909356 | 1466 | 1563 | 189 | 221 |
| ENST00000382038 | 5787 | 282 | 34909258 | 34909356 | 1987 | 2084 | 189 | 221 |
| 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 |
| ENST00000341754 | 2358 | 282 | 34909258 | 34909356 | 1466 | 1563 | 189 | 221 |
| ENST00000382038 | 5787 | 282 | 34909258 | 34909356 | 1987 | 2084 | 189 | 221 |
| 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 |
| O60671 | 189 | 221 | 69 | 282 | Alternative sequence | ID=VSP_017336;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9878245;Dbxref=PMID:9878245 |
| O60671 | 189 | 221 | 69 | 282 | Alternative sequence | ID=VSP_017336;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9878245;Dbxref=PMID:9878245 |
| O60671 | 189 | 221 | 183 | 194 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 183 | 194 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 197 | 203 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 197 | 203 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 205 | 207 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3GGR |
| O60671 | 189 | 221 | 205 | 207 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3GGR |
| O60671 | 189 | 221 | 208 | 215 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 208 | 215 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 219 | 224 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 219 | 224 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 1 | 282 | Chain | ID=PRO_0000225005;Note=Cell cycle checkpoint protein RAD1 |
| O60671 | 189 | 221 | 1 | 282 | Chain | ID=PRO_0000225005;Note=Cell cycle checkpoint protein RAD1 |
| 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 |
| O60671 | 189 | 221 | 69 | 282 | Alternative sequence | ID=VSP_017336;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9878245;Dbxref=PMID:9878245 |
| O60671 | 189 | 221 | 69 | 282 | Alternative sequence | ID=VSP_017336;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9878245;Dbxref=PMID:9878245 |
| O60671 | 189 | 221 | 183 | 194 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 183 | 194 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 197 | 203 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 197 | 203 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 205 | 207 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3GGR |
| O60671 | 189 | 221 | 205 | 207 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3GGR |
| O60671 | 189 | 221 | 208 | 215 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 208 | 215 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 219 | 224 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 219 | 224 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3A1J |
| O60671 | 189 | 221 | 1 | 282 | Chain | ID=PRO_0000225005;Note=Cell cycle checkpoint protein RAD1 |
| O60671 | 189 | 221 | 1 | 282 | Chain | ID=PRO_0000225005;Note=Cell cycle checkpoint protein RAD1 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in RAD1 |
| 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 |
| Mayo | ENST00000341754 | 34915416 | 34915626 | hsa-miR-3059-3p | chr5:34915574-34915581 | 8mer-1a | chr5:34915565-34915586 | 156.00 | -24.70 |
| Mayo | ENST00000341754 | 34915416 | 34915626 | hsa-miR-211-3p | chr5:34915459-34915466 | 8mer-1a | chr5:34915443-34915467 | 161.00 | -26.33 |
| Mayo | ENST00000341754 | 34915416 | 34915626 | hsa-miR-6770-5p | chr5:34915446-34915453 | 8mer-1a | chr5:34915443-34915467 | 161.00 | -26.33 |
| Mayo | ENST00000341754 | 34915416 | 34915626 | hsa-miR-12128 | chr5:34915460-34915467 | 8mer-1a | chr5:34915443-34915467 | 161.00 | -26.33 |
| Mayo | ENST00000341754 | 34915416 | 34915626 | hsa-miR-6889-3p | chr5:34915618-34915625 | 8mer-1a | chr5:34915605-34915625 | 168.00 | -28.19 |
| Mayo | ENST00000341754 | 34915416 | 34915626 | hsa-miR-6529-3p | chr5:34915618-34915625 | 8mer-1a | chr5:34915605-34915625 | 168.00 | -28.19 |
| Mayo | ENST00000341754 | 34915416 | 34915626 | hsa-miR-877-3p | chr5:34915465-34915472 | 8mer-1a | chr5:34915461-34915484 | 154.00 | -24.39 |
| MSBB | ENST00000341754 | 34915416 | 34915626 | hsa-miR-3059-3p | chr5:34915574-34915581 | 8mer-1a | chr5:34915565-34915586 | 156.00 | -24.70 |
| MSBB | ENST00000341754 | 34915416 | 34915626 | hsa-miR-211-3p | chr5:34915459-34915466 | 8mer-1a | chr5:34915443-34915467 | 161.00 | -26.33 |
| MSBB | ENST00000341754 | 34915416 | 34915626 | hsa-miR-6770-5p | chr5:34915446-34915453 | 8mer-1a | chr5:34915443-34915467 | 161.00 | -26.33 |
| MSBB | ENST00000341754 | 34915416 | 34915626 | hsa-miR-12128 | chr5:34915460-34915467 | 8mer-1a | chr5:34915443-34915467 | 161.00 | -26.33 |
| MSBB | ENST00000341754 | 34915416 | 34915626 | hsa-miR-6889-3p | chr5:34915618-34915625 | 8mer-1a | chr5:34915605-34915625 | 168.00 | -28.19 |
| MSBB | ENST00000341754 | 34915416 | 34915626 | hsa-miR-6529-3p | chr5:34915618-34915625 | 8mer-1a | chr5:34915605-34915625 | 168.00 | -28.19 |
| MSBB | ENST00000341754 | 34915416 | 34915626 | hsa-miR-877-3p | chr5:34915465-34915472 | 8mer-1a | chr5:34915461-34915484 | 154.00 | -24.39 |
| ROSMAP | ENST00000341754 | 34915416 | 34915626 | hsa-miR-3059-3p | chr5:34915574-34915581 | 8mer-1a | chr5:34915565-34915586 | 156.00 | -24.70 |
| ROSMAP | ENST00000341754 | 34915416 | 34915626 | hsa-miR-211-3p | chr5:34915459-34915466 | 8mer-1a | chr5:34915443-34915467 | 161.00 | -26.33 |
| ROSMAP | ENST00000341754 | 34915416 | 34915626 | hsa-miR-6770-5p | chr5:34915446-34915453 | 8mer-1a | chr5:34915443-34915467 | 161.00 | -26.33 |
| ROSMAP | ENST00000341754 | 34915416 | 34915626 | hsa-miR-12128 | chr5:34915460-34915467 | 8mer-1a | chr5:34915443-34915467 | 161.00 | -26.33 |
| ROSMAP | ENST00000341754 | 34915416 | 34915626 | hsa-miR-6889-3p | chr5:34915618-34915625 | 8mer-1a | chr5:34915605-34915625 | 168.00 | -28.19 |
| ROSMAP | ENST00000341754 | 34915416 | 34915626 | hsa-miR-6529-3p | chr5:34915618-34915625 | 8mer-1a | chr5:34915605-34915625 | 168.00 | -28.19 |
| ROSMAP | ENST00000341754 | 34915416 | 34915626 | hsa-miR-877-3p | chr5:34915465-34915472 | 8mer-1a | chr5:34915461-34915484 | 154.00 | -24.39 |
Top |
SNVs in the skipped exons for RAD1 |
| - 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 |
Top |
AD stage-associated exon skippint events for RAD1 |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAD1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| PCC | exon_skip_86088 | rs37439 | chr5:34951045 | 1.037340e-04 | 1.773608e-02 |
Top |
Correlation with RNA binding proteins (RBPs) for RAD1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | DAZAP1 | exon_skip_86088 | -4.459715e-01 | 5.393421e-09 |
| CB | TRA2A | exon_skip_86088 | -4.967832e-01 | 4.222467e-11 |
| CB | FUBP1 | exon_skip_86088 | -5.160349e-01 | 5.404104e-12 |
| IFG | PTBP3 | exon_skip_86088 | -5.490083e-01 | 9.951531e-03 |
Top |
RelatedDrugs for RAD1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for RAD1 |
| 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)
|