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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 CLOCK |
 Gene summary |
| Gene information | Gene symbol | CLOCK | Gene ID | 9575 |
| Gene name | clock circadian regulator | |
| Synonyms | KAT13D|bHLHe8 | |
| Cytomap | 4q12 | |
| Type of gene | protein-coding | |
| Description | circadian locomoter output cycles protein kaputcircadian locomoter output cycles kaput proteinclass E basic helix-loop-helix protein 8clock homolog | |
| 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 |
| CLOCK | GO:0006473 | protein acetylation | 28985504 |
| CLOCK | GO:0032922 | circadian regulation of gene expression | 24005054 |
| CLOCK | GO:0045893 | positive regulation of transcription, DNA-templated | 23785138 |
| CLOCK | GO:0051775 | response to redox state | 11441146 |
| CLOCK | GO:0071479 | cellular response to ionizing radiation | 21659603 |
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Gene structures and expression levels for CLOCK |
| 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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ENSG00000134852
| 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 | UP | ENST00000511124.1 | CLOCK-209:retained_intron:CLOCK | 1.660973e+00 | 9.919912e-01 | 1.343799e-02 | 4.414229e-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 CLOCK |
| 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_102072 | chr4 | 55470744:55470806:55475963:55476054:55478815:55478963 | 55475963:55476054 |
| exon_skip_111512 | chr4 | 55438282:55438537:55442432:55442634:55443687:55443755 | 55442432:55442634 |
| exon_skip_125266 | chr4 | 55444633:55444785:55448779:55448868:55449396:55449426 | 55448779:55448868 |
| exon_skip_217389 | chr4 | 55459148:55459261:55463685:55463805:55470717:55470806 | 55463685:55463805 |
| exon_skip_249898 | chr4 | 55459148:55459261:55463685:55463805:55470717:55470784 | 55463685:55463805 |
| exon_skip_42660 | chr4 | 55482773:55482828:55486393:55486549:55489374:55489465 | 55486393:55486549 |
| exon_skip_47052 | chr4 | 55453054:55453129:55453677:55453824:55455897:55456003 | 55453677:55453824 |
| 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 CLOCK |
| 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 |
| ENST00000381322 | 55486393 | 55486549 | 3UTR-3UTR |
| ENST00000309964 | 55463685 | 55463805 | Frame-shift |
| ENST00000381322 | 55463685 | 55463805 | Frame-shift |
| ENST00000513440 | 55463685 | 55463805 | Frame-shift |
| ENST00000309964 | 55475963 | 55476054 | Frame-shift |
| ENST00000381322 | 55475963 | 55476054 | Frame-shift |
| ENST00000513440 | 55475963 | 55476054 | Frame-shift |
| ENST00000309964 | 55448779 | 55448868 | In-frame |
| ENST00000381322 | 55448779 | 55448868 | In-frame |
| ENST00000513440 | 55448779 | 55448868 | 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 |
| ENST00000381322 | 55486393 | 55486549 | 3UTR-3UTR |
| ENST00000309964 | 55463685 | 55463805 | Frame-shift |
| ENST00000381322 | 55463685 | 55463805 | Frame-shift |
| ENST00000513440 | 55463685 | 55463805 | Frame-shift |
| ENST00000309964 | 55475963 | 55476054 | Frame-shift |
| ENST00000381322 | 55475963 | 55476054 | Frame-shift |
| ENST00000513440 | 55475963 | 55476054 | 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 |
| ENST00000381322 | 55486393 | 55486549 | 3UTR-3UTR |
| ENST00000309964 | 55442432 | 55442634 | Frame-shift |
| ENST00000381322 | 55442432 | 55442634 | Frame-shift |
| ENST00000513440 | 55442432 | 55442634 | Frame-shift |
| ENST00000309964 | 55453677 | 55453824 | Frame-shift |
| ENST00000381322 | 55453677 | 55453824 | Frame-shift |
| ENST00000513440 | 55453677 | 55453824 | Frame-shift |
| ENST00000309964 | 55463685 | 55463805 | Frame-shift |
| ENST00000381322 | 55463685 | 55463805 | Frame-shift |
| ENST00000513440 | 55463685 | 55463805 | Frame-shift |
| ENST00000309964 | 55475963 | 55476054 | Frame-shift |
| ENST00000381322 | 55475963 | 55476054 | Frame-shift |
| ENST00000513440 | 55475963 | 55476054 | Frame-shift |
| ENST00000309964 | 55448779 | 55448868 | In-frame |
| ENST00000381322 | 55448779 | 55448868 | In-frame |
| ENST00000513440 | 55448779 | 55448868 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CLOCK |
p-ENSG00000134852_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 |
| ENST00000309964 | 10321 | 846 | 55448779 | 55448868 | 1701 | 1789 | 483 | 512 |
| ENST00000381322 | 4076 | 846 | 55448779 | 55448868 | 2376 | 2464 | 483 | 512 |
| ENST00000513440 | 3597 | 846 | 55448779 | 55448868 | 2096 | 2184 | 483 | 512 |
| 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 |
| ENST00000309964 | 10321 | 846 | 55448779 | 55448868 | 1701 | 1789 | 483 | 512 |
| ENST00000381322 | 4076 | 846 | 55448779 | 55448868 | 2376 | 2464 | 483 | 512 |
| ENST00000513440 | 3597 | 846 | 55448779 | 55448868 | 2096 | 2184 | 483 | 512 |
| 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 |
| O15516 | 483 | 512 | 1 | 846 | Chain | ID=PRO_0000127163;Note=Circadian locomoter output cycles protein kaput |
| O15516 | 483 | 512 | 1 | 846 | Chain | ID=PRO_0000127163;Note=Circadian locomoter output cycles protein kaput |
| O15516 | 483 | 512 | 1 | 846 | Chain | ID=PRO_0000127163;Note=Circadian locomoter output cycles protein kaput |
| O15516 | 483 | 512 | 371 | 845 | Region | Note=Interaction with NR3C1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:O08785 |
| O15516 | 483 | 512 | 371 | 845 | Region | Note=Interaction with NR3C1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:O08785 |
| O15516 | 483 | 512 | 371 | 845 | Region | Note=Interaction with NR3C1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:O08785 |
| O15516 | 483 | 512 | 450 | 570 | Region | Note=Interaction with SIRT1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:O08785 |
| O15516 | 483 | 512 | 450 | 570 | Region | Note=Interaction with SIRT1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:O08785 |
| O15516 | 483 | 512 | 450 | 570 | Region | Note=Interaction with SIRT1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:O08785 |
| 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 |
| O15516 | 483 | 512 | 1 | 846 | Chain | ID=PRO_0000127163;Note=Circadian locomoter output cycles protein kaput |
| O15516 | 483 | 512 | 1 | 846 | Chain | ID=PRO_0000127163;Note=Circadian locomoter output cycles protein kaput |
| O15516 | 483 | 512 | 1 | 846 | Chain | ID=PRO_0000127163;Note=Circadian locomoter output cycles protein kaput |
| O15516 | 483 | 512 | 371 | 845 | Region | Note=Interaction with NR3C1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:O08785 |
| O15516 | 483 | 512 | 371 | 845 | Region | Note=Interaction with NR3C1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:O08785 |
| O15516 | 483 | 512 | 371 | 845 | Region | Note=Interaction with NR3C1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:O08785 |
| O15516 | 483 | 512 | 450 | 570 | Region | Note=Interaction with SIRT1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:O08785 |
| O15516 | 483 | 512 | 450 | 570 | Region | Note=Interaction with SIRT1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:O08785 |
| O15516 | 483 | 512 | 450 | 570 | Region | Note=Interaction with SIRT1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:O08785 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CLOCK |
| 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 | ENST00000381322 | 55486393 | 55486549 | hsa-miR-605-3p | chr4:55486490-55486497 | 8mer-1a | chr4:55486477-55486497 | 151.00 | -13.44 |
| Mayo | ENST00000381322 | 55486393 | 55486549 | hsa-miR-708-3p | chr4:55486454-55486461 | 8mer-1a | chr4:55486448-55486471 | 158.00 | -10.83 |
| Mayo | ENST00000381322 | 55486393 | 55486549 | hsa-miR-4733-3p | chr4:55486435-55486442 | 8mer-1a | chr4:55486431-55486452 | 156.00 | -24.48 |
| Mayo | ENST00000381322 | 55486393 | 55486549 | hsa-miR-3065-5p | chr4:55486522-55486529 | 8mer-1a | chr4:55486510-55486530 | 162.00 | -18.33 |
| Mayo | ENST00000381322 | 55486393 | 55486549 | hsa-miR-766-5p | chr4:55486534-55486541 | 8mer-1a | chr4:55486520-55486541 | 153.00 | -15.21 |
| MSBB | ENST00000381322 | 55486393 | 55486549 | hsa-miR-605-3p | chr4:55486490-55486497 | 8mer-1a | chr4:55486477-55486497 | 151.00 | -13.44 |
| MSBB | ENST00000381322 | 55486393 | 55486549 | hsa-miR-708-3p | chr4:55486454-55486461 | 8mer-1a | chr4:55486448-55486471 | 158.00 | -10.83 |
| MSBB | ENST00000381322 | 55486393 | 55486549 | hsa-miR-4733-3p | chr4:55486435-55486442 | 8mer-1a | chr4:55486431-55486452 | 156.00 | -24.48 |
| MSBB | ENST00000381322 | 55486393 | 55486549 | hsa-miR-3065-5p | chr4:55486522-55486529 | 8mer-1a | chr4:55486510-55486530 | 162.00 | -18.33 |
| MSBB | ENST00000381322 | 55486393 | 55486549 | hsa-miR-766-5p | chr4:55486534-55486541 | 8mer-1a | chr4:55486520-55486541 | 153.00 | -15.21 |
| ROSMAP | ENST00000381322 | 55486393 | 55486549 | hsa-miR-605-3p | chr4:55486490-55486497 | 8mer-1a | chr4:55486477-55486497 | 151.00 | -13.44 |
| ROSMAP | ENST00000381322 | 55486393 | 55486549 | hsa-miR-708-3p | chr4:55486454-55486461 | 8mer-1a | chr4:55486448-55486471 | 158.00 | -10.83 |
| ROSMAP | ENST00000381322 | 55486393 | 55486549 | hsa-miR-4733-3p | chr4:55486435-55486442 | 8mer-1a | chr4:55486431-55486452 | 156.00 | -24.48 |
| ROSMAP | ENST00000381322 | 55486393 | 55486549 | hsa-miR-3065-5p | chr4:55486522-55486529 | 8mer-1a | chr4:55486510-55486530 | 162.00 | -18.33 |
| ROSMAP | ENST00000381322 | 55486393 | 55486549 | hsa-miR-766-5p | chr4:55486534-55486541 | 8mer-1a | chr4:55486520-55486541 | 153.00 | -15.21 |
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SNVs in the skipped exons for CLOCK |
| - 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 CLOCK |
| 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 CLOCK |
| 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 CLOCK |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM3 | exon_skip_42660 | 4.277410e-01 | 2.815862e-07 |
| CB | TRA2A | exon_skip_42660 | -4.063116e-01 | 1.218560e-06 |
| TC | KHDRBS2 | exon_skip_102072 | -5.367586e-01 | 4.424625e-10 |
| TC | NUP42 | exon_skip_102072 | -4.884803e-01 | 2.306605e-08 |
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RelatedDrugs for CLOCK |
| 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 CLOCK |
| 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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