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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for CLK3 |
 Gene summary |
| Gene information | Gene symbol | CLK3 | Gene ID | 1198 |
| Gene name | CDC like kinase 3 | |
| Synonyms | PHCLK3|PHCLK3/152 | |
| Cytomap | 15q24.1 | |
| Type of gene | protein-coding | |
| Description | dual specificity protein kinase CLK3 | |
| Modification date | 20180522 | |
| UniProtAcc | P49761 | |
| Context | PubMed: CLK3 [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 |
| CLK3 | GO:0006468 | protein phosphorylation | 9637771 |
| CLK3 | GO:0043484 | regulation of RNA splicing | 9637771 |
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Exon skipping events across known transcript of Ensembl for CLK3 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. |
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Gene isoform structures and expression levels for CLK3 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for CLK3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_123502 | 15 | 74893932:74894236:74895507:74895587:74897273:74898074 | 74895507:74895587 | ENSG00000179335.14 | ENST00000564353.1 |
| exon_skip_123510 | 15 | 74897940:74898074:74898583:74898756:74900617:74901068 | 74898583:74898756 | ENSG00000179335.14 | ENST00000564353.1 |
| exon_skip_123514 | 15 | 74908214:74908239:74911537:74911689:74912349:74912548 | 74911537:74911689 | ENSG00000179335.14 | ENST00000568605.1,ENST00000352989.5,ENST00000395066.3,ENST00000454830.2,ENST00000569063.1,ENST00000348245.3,ENST00000568488.1 |
| exon_skip_123518 | 15 | 74912349:74912566:74914460:74914557:74914834:74914850 | 74914460:74914557 | ENSG00000179335.14 | ENST00000568139.1,ENST00000566126.1,ENST00000395066.3,ENST00000564096.1,ENST00000345005.4 |
| exon_skip_123519 | 15 | 74912349:74912566:74914460:74914901:74917242:74917310 | 74914460:74914901 | ENSG00000179335.14 | ENST00000568605.1 |
| exon_skip_123522 | 15 | 74912349:74912566:74914834:74914901:74917242:74917310 | 74914834:74914901 | ENSG00000179335.14 | ENST00000563297.1,ENST00000569063.1,ENST00000348245.3,ENST00000483723.1 |
| exon_skip_123523 | 15 | 74917310:74917359:74918142:74918309:74919692:74919742 | 74918142:74918309 | ENSG00000179335.14 | ENST00000569406.1,ENST00000352989.5,ENST00000562078.1,ENST00000395066.3,ENST00000454830.2,ENST00000569063.1,ENST00000348245.3,ENST00000483723.1,ENST00000563842.1,ENST00000345005.4 |
| exon_skip_123526 | 15 | 74918193:74918309:74919329:74919407:74919692:74919742 | 74919329:74919407 | ENSG00000179335.14 | ENST00000564468.1 |
| exon_skip_123527 | 15 | 74918193:74918309:74919692:74919787:74919879:74920009 | 74919692:74919787 | ENSG00000179335.14 | ENST00000569406.1,ENST00000352989.5,ENST00000562078.1,ENST00000395066.3,ENST00000454830.2,ENST00000348245.3,ENST00000483723.1,ENST00000563842.1,ENST00000345005.4 |
| exon_skip_123528 | 15 | 74919957:74920009:74920310:74920393:74920944:74921024 | 74920310:74920393 | ENSG00000179335.14 | ENST00000569406.1,ENST00000352989.5,ENST00000562078.1,ENST00000395066.3,ENST00000454830.2,ENST00000348245.3,ENST00000483723.1,ENST00000566926.1,ENST00000563842.1,ENST00000345005.4,ENST00000564468.1 |
| exon_skip_123531 | 15 | 74920944:74921024:74921282:74921373:74922047:74922303 | 74921282:74921373 | ENSG00000179335.14 | ENST00000569406.1,ENST00000352989.5,ENST00000562078.1,ENST00000395066.3,ENST00000454830.2,ENST00000348245.3,ENST00000483723.1,ENST00000345005.4,ENST00000564468.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CLK3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_123502 | 15 | 74893932:74894236:74895507:74895587:74897273:74898074 | 74895507:74895587 | ENSG00000179335.14 | ENST00000564353.1 |
| exon_skip_123510 | 15 | 74897940:74898074:74898583:74898756:74900617:74901068 | 74898583:74898756 | ENSG00000179335.14 | ENST00000564353.1 |
| exon_skip_123514 | 15 | 74908214:74908239:74911537:74911689:74912349:74912548 | 74911537:74911689 | ENSG00000179335.14 | ENST00000395066.3,ENST00000454830.2,ENST00000569063.1,ENST00000568488.1,ENST00000568605.1,ENST00000352989.5,ENST00000348245.3 |
| exon_skip_123516 | 15 | 74908214:74908239:74912349:74912566:74914834:74914850 | 74912349:74912566 | ENSG00000179335.14 | ENST00000563297.1 |
| exon_skip_123518 | 15 | 74912349:74912566:74914460:74914557:74914834:74914850 | 74914460:74914557 | ENSG00000179335.14 | ENST00000345005.4,ENST00000395066.3,ENST00000568139.1,ENST00000566126.1,ENST00000564096.1 |
| exon_skip_123519 | 15 | 74912349:74912566:74914460:74914901:74917242:74917310 | 74914460:74914901 | ENSG00000179335.14 | ENST00000568605.1 |
| exon_skip_123522 | 15 | 74912349:74912566:74914834:74914901:74917242:74917310 | 74914834:74914901 | ENSG00000179335.14 | ENST00000483723.1,ENST00000569063.1,ENST00000563297.1,ENST00000348245.3 |
| exon_skip_123523 | 15 | 74917310:74917359:74918142:74918309:74919692:74919742 | 74918142:74918309 | ENSG00000179335.14 | ENST00000345005.4,ENST00000483723.1,ENST00000395066.3,ENST00000454830.2,ENST00000569063.1,ENST00000352989.5,ENST00000348245.3,ENST00000569406.1,ENST00000562078.1,ENST00000563842.1 |
| exon_skip_123526 | 15 | 74918193:74918309:74919329:74919407:74919692:74919742 | 74919329:74919407 | ENSG00000179335.14 | ENST00000564468.1 |
| exon_skip_123527 | 15 | 74918193:74918309:74919692:74919787:74919879:74920009 | 74919692:74919787 | ENSG00000179335.14 | ENST00000345005.4,ENST00000483723.1,ENST00000395066.3,ENST00000454830.2,ENST00000352989.5,ENST00000348245.3,ENST00000569406.1,ENST00000562078.1,ENST00000563842.1 |
| exon_skip_123528 | 15 | 74919957:74920009:74920310:74920393:74920944:74921024 | 74920310:74920393 | ENSG00000179335.14 | ENST00000345005.4,ENST00000483723.1,ENST00000395066.3,ENST00000454830.2,ENST00000352989.5,ENST00000348245.3,ENST00000569406.1,ENST00000562078.1,ENST00000563842.1,ENST00000564468.1,ENST00000566926.1 |
| exon_skip_123531 | 15 | 74920944:74921024:74921282:74921373:74922047:74922303 | 74921282:74921373 | ENSG00000179335.14 | ENST00000345005.4,ENST00000483723.1,ENST00000395066.3,ENST00000454830.2,ENST00000352989.5,ENST00000348245.3,ENST00000569406.1,ENST00000562078.1,ENST00000564468.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for CLK3 |
| 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 |
| ENST00000345005 | 74914460 | 74914557 | Frame-shift |
| ENST00000345005 | 74918142 | 74918309 | Frame-shift |
| ENST00000345005 | 74919692 | 74919787 | Frame-shift |
| ENST00000345005 | 74920310 | 74920393 | Frame-shift |
| ENST00000345005 | 74921282 | 74921373 | 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 |
| ENST00000345005 | 74914460 | 74914557 | Frame-shift |
| ENST00000345005 | 74918142 | 74918309 | Frame-shift |
| ENST00000345005 | 74919692 | 74919787 | Frame-shift |
| ENST00000345005 | 74920310 | 74920393 | Frame-shift |
| ENST00000345005 | 74921282 | 74921373 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for CLK3 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| 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 |
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SNVs in the skipped exons for CLK3 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
CLK3_LIHC_exon_skip_123519_psi_boxplot.png |
CLK3_PRAD_exon_skip_123519_psi_boxplot.png |
| - 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-G3-A3CJ-01 | exon_skip_123514 | 74911538 | 74911689 | 74911650 | 74911650 | Frame_Shift_Del | C | - | p.S186fs |
| LIHC | TCGA-BC-A3KG-01 | exon_skip_123518 | 74914461 | 74914557 | 74914531 | 74914531 | Frame_Shift_Del | G | - | p.R295fs |
| LIHC | TCGA-BC-A3KG-01 | exon_skip_123519 | 74914461 | 74914901 | 74914531 | 74914531 | Frame_Shift_Del | G | - | p.R295fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_123531 | 74921283 | 74921373 | 74921350 | 74921350 | Frame_Shift_Del | A | - | p.K573fs |
| STAD | TCGA-BR-A4QL-01 | exon_skip_123514 | 74911538 | 74911689 | 74911553 | 74911553 | Nonsense_Mutation | C | T | p.R154* |
| STAD | TCGA-BR-A4QL-01 | exon_skip_123514 | 74911538 | 74911689 | 74911553 | 74911553 | Nonsense_Mutation | C | T | p.R154X |
| BLCA | TCGA-DK-AA71-01 | exon_skip_123514 | 74911538 | 74911689 | 74911640 | 74911640 | Nonsense_Mutation | C | T | p.R183* |
| COAD | TCGA-AD-5900-01 | exon_skip_123514 | 74911538 | 74911689 | 74911640 | 74911640 | Nonsense_Mutation | C | T | p.R183X |
| PAAD | TCGA-IB-7651-01 | exon_skip_123514 | 74911538 | 74911689 | 74911640 | 74911640 | Nonsense_Mutation | C | T | p.R183* |
| PAAD | TCGA-IB-7651-01 | exon_skip_123514 | 74911538 | 74911689 | 74911640 | 74911640 | Nonsense_Mutation | C | T | p.R183X |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_123514 | 74911538 | 74911689 | 74911640 | 74911640 | Nonsense_Mutation | C | T | p.R183* |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_123514 | 74911538 | 74911689 | 74911640 | 74911640 | Nonsense_Mutation | C | T | p.R183X |
| PRAD | TCGA-XK-AAIW-01 | exon_skip_123518 | 74914461 | 74914557 | 74914554 | 74914554 | Nonsense_Mutation | C | T | p.R303* |
| PRAD | TCGA-XK-AAIW-01 | exon_skip_123519 | 74914461 | 74914901 | 74914554 | 74914554 | Nonsense_Mutation | C | T | p.R303* |
| STAD | TCGA-BR-8284-01 | exon_skip_123523 | 74918143 | 74918309 | 74918310 | 74918311 | Splice_Site | - | T | . |
| STAD | TCGA-BR-8284-01 | exon_skip_123523 | 74918143 | 74918309 | 74918311 | 74918312 | Splice_Site | - | T | p.F421_splice |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_123531 | 74921283 | 74921373 | 74921281 | 74921281 | Splice_Site | A | G | . |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-XK-AAIW-01 |
| Cancer type: PRAD | |
| ESID: exon_skip_123519 | |
| Skipped exon start: 74914461 | |
| Skipped exon end: 74914901 | |
| Mutation start: 74914554 | |
| Mutation end: 74914554 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: C | |
| Mutation seq: T | |
| AAchange: p.R303* | |
| Sample: TCGA-XK-AAIW-01 |
| Cancer type: PRAD | |
| ESID: exon_skip_123518 | |
| Skipped exon start: 74914461 | |
| Skipped exon end: 74914557 | |
| Mutation start: 74914554 | |
| Mutation end: 74914554 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: C | |
| Mutation seq: T | |
| AAchange: p.R303* | |
exon_skip_101989_PRAD_TCGA-XK-AAIW-01.png | |
exon_skip_123519_PRAD_TCGA-XK-AAIW-01.png | |
exon_skip_141370_PRAD_TCGA-XK-AAIW-01.png | |
exon_skip_307491_PRAD_TCGA-XK-AAIW-01.png | |
exon_skip_312596_PRAD_TCGA-XK-AAIW-01.png | |
exon_skip_312597_PRAD_TCGA-XK-AAIW-01.png | |
exon_skip_312599_PRAD_TCGA-XK-AAIW-01.png | |
exon_skip_382100_PRAD_TCGA-XK-AAIW-01.png | |
exon_skip_500520_PRAD_TCGA-XK-AAIW-01.png | |
exon_skip_66767_PRAD_TCGA-XK-AAIW-01.png | |
exon_skip_74728_PRAD_TCGA-XK-AAIW-01.png | |
 | Sample: TCGA-BC-A3KG-01 |
| Cancer type: LIHC | |
| ESID: exon_skip_123519 | |
| Skipped exon start: 74914461 | |
| Skipped exon end: 74914901 | |
| Mutation start: 74914531 | |
| Mutation end: 74914531 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: G | |
| Mutation seq: - | |
| AAchange: p.R295fs | |
| Sample: TCGA-BC-A3KG-01 |
| Cancer type: LIHC | |
| ESID: exon_skip_123518 | |
| Skipped exon start: 74914461 | |
| Skipped exon end: 74914557 | |
| Mutation start: 74914531 | |
| Mutation end: 74914531 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: G | |
| Mutation seq: - | |
| AAchange: p.R295fs | |
exon_skip_107008_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_107009_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_107010_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_10760_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_11532_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_123519_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_17069_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_300924_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_346623_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_374970_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_387350_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_423555_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_441299_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_441300_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_444819_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_450818_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_456987_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_459274_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_494352_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_64409_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_64412_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_69788_LIHC_TCGA-BC-A3KG-01.png | |
exon_skip_98384_LIHC_TCGA-BC-A3KG-01.png | |
| - 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 |
| HCC202_BREAST | 74914461 | 74914901 | 74914551 | 74914551 | Missense_Mutation | G | C | p.E302Q |
| HCC202_BREAST | 74914461 | 74914557 | 74914551 | 74914551 | Missense_Mutation | G | C | p.E302Q |
| DKMG_CENTRAL_NERVOUS_SYSTEM | 74914461 | 74914901 | 74914555 | 74914555 | Missense_Mutation | G | A | p.R303Q |
| DKMG_CENTRAL_NERVOUS_SYSTEM | 74914461 | 74914557 | 74914555 | 74914555 | Missense_Mutation | G | A | p.R303Q |
| SNU1040_LARGE_INTESTINE | 74918143 | 74918309 | 74918195 | 74918195 | Missense_Mutation | G | A | p.A383T |
| CCK81_LARGE_INTESTINE | 74918143 | 74918309 | 74918219 | 74918219 | Missense_Mutation | A | G | p.T391A |
| COLO684_ENDOMETRIUM | 74918143 | 74918309 | 74918300 | 74918300 | Missense_Mutation | G | A | p.A418T |
| COLO704_OVARY | 74918143 | 74918309 | 74918300 | 74918300 | Missense_Mutation | G | A | p.A418T |
| CAL51_BREAST | 74919693 | 74919787 | 74919695 | 74919695 | Missense_Mutation | C | G | p.L422V |
| DJM1_SKIN | 74919693 | 74919787 | 74919780 | 74919780 | Missense_Mutation | A | C | p.E450A |
| HCC2998_LARGE_INTESTINE | 74920311 | 74920393 | 74920358 | 74920358 | Missense_Mutation | C | A | p.L512I |
| LN443_CENTRAL_NERVOUS_SYSTEM | 74920311 | 74920393 | 74920374 | 74920374 | Missense_Mutation | G | A | p.R517Q |
| SNU81_LARGE_INTESTINE | 74921283 | 74921373 | 74921289 | 74921289 | Missense_Mutation | G | T | p.Q552H |
| KARPAS1106P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 74921283 | 74921373 | 74921291 | 74921291 | Missense_Mutation | A | G | p.K553R |
| IM95_STOMACH | 74921283 | 74921373 | 74921338 | 74921338 | Missense_Mutation | G | A | p.G569S |
| SNU175_LARGE_INTESTINE | 74911538 | 74911689 | 74911553 | 74911553 | Nonsense_Mutation | C | T | p.R154* |
| SNU175_LARGE_INTESTINE | 74911538 | 74911689 | 74911640 | 74911640 | Nonsense_Mutation | C | T | p.R183* |
| TE9_OESOPHAGUS | 74920311 | 74920393 | 74920320 | 74920320 | Nonsense_Mutation | G | A | p.W499* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CLK3 |
| 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 |
| exon_skip_123519 | 15 | 74912349:74912566:74914460:74914901:74917242:74917310 | 74914460:74914901 | ENST00000568605.1 | GBM | rs56298217 | chr15:74914649 | G/A | 5.52e-04 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CLK3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CLK3 |
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RelatedDrugs for CLK3 |
| 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 |
| P49761 | DB12010 | Fostamatinib | Dual specificity protein kinase CLK3 | small molecule | approved|investigational |
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RelatedDiseases for CLK3 |
| 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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