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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 ATR |
 Gene summary |
| Gene information | Gene symbol | ATR | Gene ID | 545 |
| Gene name | ATR serine/threonine kinase | |
| Synonyms | FCTCS|FRP1|MEC1|SCKL|SCKL1 | |
| Cytomap | 3q23 | |
| Type of gene | protein-coding | |
| Description | serine/threonine-protein kinase ATRFRAP-related protein-1MEC1, mitosis entry checkpoint 1, homologataxia telangiectasia and Rad3-related protein | |
| Modification date | 20200329 | |
| 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 |
| ATR | GO:0000077 | DNA damage checkpoint | 14657349 |
| ATR | GO:0006974 | cellular response to DNA damage stimulus | 27723717|27723720 |
| ATR | GO:0018105 | peptidyl-serine phosphorylation | 9733515 |
| ATR | GO:0046777 | protein autophosphorylation | 9733515 |
| ATR | GO:0071480 | cellular response to gamma radiation | 9925639 |
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Gene structures and expression levels for ATR |
| 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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ENSG00000175054
| 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 | ENST00000654170.1 | ATR-212:retained_intron:ATR | 1.521796e+02 | -1.149165e+00 | 1.738931e-14 | 5.504018e-12 |
| CB | DOWN | ENST00000515810.1 | ATR-208:nonsense_mediated_decay:ATR | 3.220613e+01 | -1.815423e+00 | 5.991756e-11 | 4.143000e-09 |
| CB | UP | ENST00000666447.1 | ATR-221:retained_intron:ATR | 4.310200e+01 | 8.320992e-01 | 5.712976e-06 | 6.558000e-05 |
| CB | DOWN | ENST00000658083.1 | ATR-217:retained_intron:ATR | 1.251728e+01 | -9.343178e-01 | 5.160952e-04 | 2.959733e-03 |
| TC | DOWN | ENST00000515810.1 | ATR-208:nonsense_mediated_decay:ATR | 2.371741e+01 | -1.182416e+00 | 2.031941e-05 | 4.534485e-04 |
| TC | DOWN | ENST00000658083.1 | ATR-217:retained_intron:ATR | 7.590193e+00 | -8.166630e-01 | 1.570582e-03 | 1.393506e-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 ATR |
| 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_100657 | chr3 | 142556070:142556139:142556383:142556575:142558624:142558776 | 142556383:142556575 |
| exon_skip_124309 | chr3 | 142513501:142513638:142515395:142515515:142519669:142519784 | 142515395:142515515 |
| exon_skip_127330 | chr3 | 142496397:142496520:142497134:142497192:142498597:142498774 | 142497134:142497192 |
| exon_skip_134679 | chr3 | 142449353:142449602:142450466:142450602:142453128:142453233 | 142450466:142450602 |
| exon_skip_136889 | chr3 | 142505139:142505303:142507931:142508109:142512260:142512470 | 142507931:142508109 |
| exon_skip_157390 | chr3 | 142566121:142566261:142568063:142568154:142578646:142578723 | 142568063:142568154 |
| exon_skip_157751 | chr3 | 142538532:142538625:142540904:142541034:142542665:142542757 | 142540904:142541034 |
| exon_skip_16604 | chr3 | 142559416:142559441:142560263:142560454:142561243:142561381 | 142560263:142560454 |
| exon_skip_170115 | chr3 | 142559251:142559441:142560263:142560454:142561243:142561381 | 142560263:142560454 |
| exon_skip_201691 | chr3 | 142540904:142541034:142542665:142542757:142547725:142547910 | 142542665:142542757 |
| exon_skip_232881 | chr3 | 142496397:142496520:142497013:142497192:142498597:142498774 | 142497013:142497192 |
| exon_skip_244296 | chr3 | 142449353:142449602:142450466:142450602:142453117:142453166 | 142450466:142450602 |
| exon_skip_245197 | chr3 | 142561243:142561421:142562232:142563109:142566121:142566261 | 142562232:142563109 |
| exon_skip_290101 | chr3 | 142459227:142459383:142461940:142462090:142465097:142465240 | 142461940:142462090 |
| exon_skip_32471 | chr3 | 142499627:142499718:142503362:142503453:142505139:142505303 | 142503362:142503453 |
| exon_skip_61391 | chr3 | 142449353:142449602:142453128:142453233:142457604:142457755 | 142453128:142453233 |
| exon_skip_65791 | chr3 | 142556448:142556575:142558624:142558776:142559251:142559441 | 142558624:142558776 |
| exon_skip_9572 | chr3 | 142522728:142522841:142523993:142524199:142535080:142535205 | 142523993:142524199 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_290101 | Mayo_CB | 6.457317e-01 | 8.623377e-01 | -2.166060e-01 | 7.443368e-07 |
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Open reading frame (ORF) annotation in the exon skipping event for ATR |
| 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 |
| ENST00000350721 | 142461940 | 142462090 | Frame-shift |
| ENST00000350721 | 142503362 | 142503453 | Frame-shift |
| ENST00000350721 | 142507931 | 142508109 | Frame-shift |
| ENST00000350721 | 142515395 | 142515515 | Frame-shift |
| ENST00000350721 | 142540904 | 142541034 | Frame-shift |
| ENST00000350721 | 142556383 | 142556575 | Frame-shift |
| ENST00000350721 | 142562232 | 142563109 | Frame-shift |
| ENST00000350721 | 142568063 | 142568154 | Frame-shift |
| ENST00000350721 | 142497013 | 142497192 | In-frame |
| ENST00000350721 | 142542665 | 142542757 | In-frame |
| ENST00000350721 | 142560263 | 142560454 | 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 |
| ENST00000350721 | 142461940 | 142462090 | Frame-shift |
| ENST00000350721 | 142503362 | 142503453 | Frame-shift |
| ENST00000350721 | 142507931 | 142508109 | Frame-shift |
| ENST00000350721 | 142540904 | 142541034 | Frame-shift |
| ENST00000350721 | 142556383 | 142556575 | Frame-shift |
| ENST00000350721 | 142568063 | 142568154 | Frame-shift |
| ENST00000350721 | 142523993 | 142524199 | In-frame |
| ENST00000350721 | 142560263 | 142560454 | In-frame |
| 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 |
| ENST00000350721 | 142453128 | 142453233 | Frame-shift |
| ENST00000350721 | 142461940 | 142462090 | Frame-shift |
| ENST00000350721 | 142503362 | 142503453 | Frame-shift |
| ENST00000350721 | 142507931 | 142508109 | Frame-shift |
| ENST00000350721 | 142515395 | 142515515 | Frame-shift |
| ENST00000350721 | 142540904 | 142541034 | Frame-shift |
| ENST00000350721 | 142497013 | 142497192 | In-frame |
| ENST00000350721 | 142523993 | 142524199 | In-frame |
| ENST00000350721 | 142558624 | 142558776 | In-frame |
| ENST00000350721 | 142560263 | 142560454 | In-frame |
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Infer the effects of exon skipping event on protein functional features for ATR |
p-ENSG00000175054_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 |
| ENST00000350721 | 8266 | 2644 | 142560263 | 142560454 | 1472 | 1662 | 450 | 513 |
| ENST00000350721 | 8266 | 2644 | 142542665 | 142542757 | 3480 | 3571 | 1119 | 1149 |
| ENST00000350721 | 8266 | 2644 | 142497013 | 142497192 | 5681 | 5859 | 1853 | 1912 |
| 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 |
| ENST00000350721 | 8266 | 2644 | 142560263 | 142560454 | 1472 | 1662 | 450 | 513 |
| ENST00000350721 | 8266 | 2644 | 142523993 | 142524199 | 4068 | 4273 | 1315 | 1383 |
| 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 |
| ENST00000350721 | 8266 | 2644 | 142560263 | 142560454 | 1472 | 1662 | 450 | 513 |
| ENST00000350721 | 8266 | 2644 | 142558624 | 142558776 | 1855 | 2006 | 577 | 628 |
| ENST00000350721 | 8266 | 2644 | 142523993 | 142524199 | 4068 | 4273 | 1315 | 1383 |
| ENST00000350721 | 8266 | 2644 | 142497013 | 142497192 | 5681 | 5859 | 1853 | 1912 |
| 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 |
| Q13535 | 450 | 513 | 450 | 450 | Alternative sequence | ID=VSP_013305;Note=In isoform 2. E->D;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11470508;Dbxref=PMID:11470508 |
| Q13535 | 450 | 513 | 451 | 514 | Alternative sequence | ID=VSP_013304;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11470508;Dbxref=PMID:11470508 |
| Q13535 | 450 | 513 | 1 | 2644 | Chain | ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR |
| Q13535 | 1119 | 1149 | 1 | 2644 | Chain | ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR |
| Q13535 | 1853 | 1912 | 1 | 2644 | Chain | ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR |
| Q13535 | 1853 | 1912 | 1640 | 2185 | Domain | Note=FAT;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00534 |
| 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 |
| Q13535 | 450 | 513 | 450 | 450 | Alternative sequence | ID=VSP_013305;Note=In isoform 2. E->D;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11470508;Dbxref=PMID:11470508 |
| Q13535 | 450 | 513 | 451 | 514 | Alternative sequence | ID=VSP_013304;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11470508;Dbxref=PMID:11470508 |
| Q13535 | 450 | 513 | 1 | 2644 | Chain | ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR |
| Q13535 | 1315 | 1383 | 1 | 2644 | Chain | ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR |
| Q13535 | 1315 | 1383 | 1329 | 1365 | Repeat | Note=HEAT 2 |
| 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 |
| Q13535 | 450 | 513 | 450 | 450 | Alternative sequence | ID=VSP_013305;Note=In isoform 2. E->D;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11470508;Dbxref=PMID:11470508 |
| Q13535 | 450 | 513 | 451 | 514 | Alternative sequence | ID=VSP_013304;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11470508;Dbxref=PMID:11470508 |
| Q13535 | 450 | 513 | 1 | 2644 | Chain | ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR |
| Q13535 | 577 | 628 | 1 | 2644 | Chain | ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR |
| Q13535 | 1315 | 1383 | 1 | 2644 | Chain | ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR |
| Q13535 | 1315 | 1383 | 1329 | 1365 | Repeat | Note=HEAT 2 |
| Q13535 | 1853 | 1912 | 1 | 2644 | Chain | ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR |
| Q13535 | 1853 | 1912 | 1640 | 2185 | Domain | Note=FAT;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00534 |
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3'-UTR located exon skipping events that lost miRNA binding sites in ATR |
| 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 ATR |
| - 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 ATR |
| 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 ATR |
| 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 ATR |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM3 | exon_skip_134679 | 5.384577e-01 | 2.468977e-13 |
| CB | PCBP4 | exon_skip_134679 | 5.085000e-01 | 7.760710e-12 |
| CB | TRA2A | exon_skip_134679 | -5.108414e-01 | 5.998896e-12 |
| CB | HNRNPA2B1 | exon_skip_134679 | -4.409557e-01 | 5.981884e-09 |
| CB | NUP42 | exon_skip_134679 | 4.386097e-01 | 7.349155e-09 |
| CB | TARDBP | exon_skip_290101 | -4.767513e-01 | 2.115354e-10 |
| CB | RBM3 | exon_skip_290101 | 4.341134e-01 | 1.085665e-08 |
| CB | TRA2A | exon_skip_290101 | -6.381346e-01 | 1.468529e-19 |
| CB | NUP42 | exon_skip_290101 | 4.248434e-01 | 2.384347e-08 |
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RelatedDrugs for ATR |
| 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 ATR |
| 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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