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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 CLK4 |
 Gene summary |
| Gene information | Gene symbol | CLK4 | Gene ID | 57396 |
| Gene name | CDC like kinase 4 | |
| Synonyms | - | |
| Cytomap | 5q35.3 | |
| Type of gene | protein-coding | |
| Description | dual specificity protein kinase CLK4protein serine threonine kinase Clk4 | |
| Modification date | 20200313 | |
| UniProtAcc | A0A087WX74, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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Gene structures and expression levels for CLK4 |
| 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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ENSG00000113240
| 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 |
| PG | DOWN | ENST00000523013.1 | CLK4-213:retained_intron:CLK4 | 9.276594e+00 | -8.613187e-01 | 1.562283e-04 | 3.805185e-03 |
| CB | UP | ENST00000520199.5 | CLK4-205:retained_intron:CLK4 | 1.647028e+01 | 1.427571e+00 | 1.303579e-09 | 5.419182e-08 |
| 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 CLK4 |
| 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_122922 | chr5 | 178605303:178605382:178608376:178608458:178612416:178612545 | 178608376:178608458 |
| exon_skip_140230 | chr5 | 178618653:178618778:178619838:178620673:178623256:178623416 | 178619838:178620673 |
| exon_skip_152326 | chr5 | 178616882:178616948:178617344:178617434:178618556:178618778 | 178617344:178617434 |
| exon_skip_163462 | chr5 | 178605303:178605382:178605825:178605865:178608376:178608452 | 178605825:178605865 |
| exon_skip_165659 | chr5 | 178603930:178603934:178605303:178605382:178608376:178608458 | 178605303:178605382 |
| exon_skip_168676 | chr5 | 178605303:178605382:178605825:178605865:178608376:178608458 | 178605825:178605865 |
| exon_skip_169992 | chr5 | 178618556:178618778:178619838:178620673:178623256:178623416 | 178619838:178620673 |
| exon_skip_189831 | chr5 | 178613727:178613843:178616882:178616948:178618556:178618778 | 178616882:178616948 |
| exon_skip_191131 | chr5 | 178613473:178613639:178613727:178613843:178616882:178616948 | 178613727:178613843 |
| exon_skip_19651 | chr5 | 178617344:178618778:178619838:178619896:178623256:178623416 | 178619838:178619896 |
| exon_skip_226667 | chr5 | 178608376:178608458:178612416:178612545:178612796:178612890 | 178612416:178612545 |
| exon_skip_229394 | chr5 | 178605303:178605382:178612416:178612545:178612796:178612890 | 178612416:178612545 |
| exon_skip_237575 | chr5 | 178619838:178620673:178622393:178622459:178623256:178623416 | 178622393:178622459 |
| exon_skip_247426 | chr5 | 178605318:178605382:178605825:178605865:178608376:178608458 | 178605825:178605865 |
| exon_skip_262635 | chr5 | 178616886:178616948:178617344:178617434:178618556:178618778 | 178617344:178617434 |
| exon_skip_293906 | chr5 | 178605303:178605382:178608376:178608458:178612416:178612514 | 178608376:178608458 |
| exon_skip_59464 | chr5 | 178619838:178620673:178622393:178622459:178623256:178623339 | 178622393:178622459 |
| 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_190556 | Mayo_CB | 1.003659e-01 | 2.209459e-01 | -1.205801e-01 | 1.559555e-07 |
| exon_skip_140230 | Mayo_CB | 4.560976e-01 | 6.532468e-01 | -1.971492e-01 | 4.230621e-08 |
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Open reading frame (ORF) annotation in the exon skipping event for CLK4 |
| 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 |
| ENST00000316308 | 178605303 | 178605382 | Frame-shift |
| ENST00000316308 | 178608376 | 178608458 | Frame-shift |
| ENST00000316308 | 178617344 | 178617434 | Frame-shift |
| ENST00000316308 | 178613727 | 178613843 | 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 |
| ENST00000316308 | 178608376 | 178608458 | Frame-shift |
| ENST00000316308 | 178617344 | 178617434 | Frame-shift |
| ENST00000316308 | 178613727 | 178613843 | 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 |
| ENST00000316308 | 178605303 | 178605382 | Frame-shift |
| ENST00000316308 | 178608376 | 178608458 | Frame-shift |
| ENST00000316308 | 178612416 | 178612545 | Frame-shift |
| ENST00000316308 | 178617344 | 178617434 | Frame-shift |
| ENST00000316308 | 178613727 | 178613843 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CLK4 |
p-ENSG00000113240_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 |
| ENST00000316308 | 2585 | 481 | 178613727 | 178613843 | 712 | 827 | 181 | 219 |
| 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 |
| ENST00000316308 | 2585 | 481 | 178613727 | 178613843 | 712 | 827 | 181 | 219 |
| 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 |
| ENST00000316308 | 2585 | 481 | 178613727 | 178613843 | 712 | 827 | 181 | 219 |
| 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 |
| Q9HAZ1 | 181 | 219 | 189 | 189 | Binding site | Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q9HAZ1 | 181 | 219 | 1 | 481 | Chain | ID=PRO_0000085873;Note=Dual specificity protein kinase CLK4 |
| Q9HAZ1 | 181 | 219 | 159 | 475 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q9HAZ1 | 181 | 219 | 189 | 189 | Mutagenesis | Note=Loss of function. K->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11170754;Dbxref=PMID:11170754 |
| 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 |
| Q9HAZ1 | 181 | 219 | 189 | 189 | Binding site | Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q9HAZ1 | 181 | 219 | 1 | 481 | Chain | ID=PRO_0000085873;Note=Dual specificity protein kinase CLK4 |
| Q9HAZ1 | 181 | 219 | 159 | 475 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q9HAZ1 | 181 | 219 | 189 | 189 | Mutagenesis | Note=Loss of function. K->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11170754;Dbxref=PMID:11170754 |
| 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 |
| Q9HAZ1 | 181 | 219 | 189 | 189 | Binding site | Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q9HAZ1 | 181 | 219 | 1 | 481 | Chain | ID=PRO_0000085873;Note=Dual specificity protein kinase CLK4 |
| Q9HAZ1 | 181 | 219 | 159 | 475 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q9HAZ1 | 181 | 219 | 189 | 189 | Mutagenesis | Note=Loss of function. K->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11170754;Dbxref=PMID:11170754 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CLK4 |
| 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 CLK4 |
| - 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 CLK4 |
| 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 CLK4 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| CB | exon_skip_59464 | rs1023916 | chr5:178656798 | 3.377510e-04 | 4.445192e-02 |
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Correlation with RNA binding proteins (RBPs) for CLK4 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | ZNF638 | exon_skip_293906 | -5.622360e-01 | 1.241970e-14 |
| CB | RBM6 | exon_skip_191131 | -5.188622e-01 | 2.446051e-12 |
| CB | NUP42 | exon_skip_191131 | 4.173497e-01 | 4.427490e-08 |
| CB | SRSF4 | exon_skip_191131 | -5.202535e-01 | 2.088540e-12 |
| CB | RBM6 | exon_skip_110082 | -4.092927e-01 | 1.360243e-07 |
| CB | TIA1 | exon_skip_110082 | 4.070666e-01 | 1.613603e-07 |
| CB | PCBP4 | exon_skip_110082 | 6.125173e-01 | 3.134138e-17 |
| CB | FUBP1 | exon_skip_110082 | -4.137464e-01 | 9.628868e-08 |
| CB | TARDBP | exon_skip_190556 | -4.969076e-01 | 4.168463e-11 |
| CB | ZNF638 | exon_skip_190556 | -4.887554e-01 | 9.588110e-11 |
| CB | U2AF2 | exon_skip_190556 | -5.545307e-01 | 5.883057e-14 |
| CB | RBM3 | exon_skip_190556 | 4.843189e-01 | 1.494983e-10 |
| CB | PCBP1 | exon_skip_190556 | -4.318720e-01 | 1.810089e-08 |
| CB | PCBP4 | exon_skip_190556 | 6.612769e-01 | 5.697273e-21 |
| CB | FUBP1 | exon_skip_190556 | -4.638792e-01 | 1.068003e-09 |
| CB | HNRNPA2B1 | exon_skip_190556 | -5.053111e-01 | 1.725597e-11 |
| CB | HNRNPC | exon_skip_190556 | -5.350006e-01 | 6.260758e-13 |
| CB | NUP42 | exon_skip_190556 | 4.922621e-01 | 6.718736e-11 |
| CB | HNRNPF | exon_skip_190556 | -4.174772e-01 | 5.893224e-08 |
| CB | DAZAP1 | exon_skip_140230 | -4.452676e-01 | 4.080816e-09 |
| CB | TARDBP | exon_skip_140230 | -5.150078e-01 | 3.775403e-12 |
| CB | ELAVL1 | exon_skip_140230 | -4.083318e-01 | 9.142041e-08 |
| CB | ZNF638 | exon_skip_140230 | -5.463362e-01 | 9.410749e-14 |
| CB | U2AF2 | exon_skip_140230 | -6.127371e-01 | 9.200164e-18 |
| CB | PCBP1 | exon_skip_140230 | -5.010284e-01 | 1.742278e-11 |
| CB | PCBP4 | exon_skip_140230 | 6.473192e-01 | 2.985368e-20 |
| CB | FUBP1 | exon_skip_140230 | -4.801764e-01 | 1.504932e-10 |
| CB | KHSRP | exon_skip_140230 | -4.042836e-01 | 1.257213e-07 |
| CB | HNRNPA2B1 | exon_skip_140230 | -5.706509e-01 | 4.067470e-15 |
| CB | HNRNPC | exon_skip_140230 | -5.769352e-01 | 1.730561e-15 |
| CB | NUP42 | exon_skip_140230 | 4.344221e-01 | 1.057157e-08 |
| CB | PTBP1 | exon_skip_140230 | -4.706036e-01 | 3.861261e-10 |
| CB | RBM23 | exon_skip_140230 | -4.264417e-01 | 2.085398e-08 |
| CB | HNRNPF | exon_skip_140230 | -4.744367e-01 | 2.656990e-10 |
| CB | HNRNPDL | exon_skip_59464 | 4.157754e-01 | 6.751390e-08 |
| CB | NUP42 | exon_skip_59464 | 5.414043e-01 | 2.931978e-13 |
| CB | PABPC4 | exon_skip_59464 | 4.721922e-01 | 4.875745e-10 |
| FL | SRSF2 | exon_skip_156685 | 5.189496e-01 | 8.452768e-14 |
| FL | RBM3 | exon_skip_156685 | 7.541038e-01 | 2.481509e-34 |
| FL | ILF2 | exon_skip_156685 | 4.739409e-01 | 1.816466e-11 |
| FL | HNRNPK | exon_skip_156685 | 4.679150e-01 | 3.519042e-11 |
| FL | G3BP2 | exon_skip_156685 | 5.280996e-01 | 2.567728e-14 |
| FL | RBM24 | exon_skip_156685 | 4.533339e-01 | 1.654306e-10 |
| FL | HNRNPA0 | exon_skip_156685 | 5.063801e-01 | 4.102304e-13 |
| FL | HNRNPDL | exon_skip_156685 | 4.140656e-01 | 7.558399e-09 |
| FL | PUF60 | exon_skip_156685 | 4.224347e-01 | 3.485418e-09 |
| FL | NUP42 | exon_skip_156685 | 4.361244e-01 | 9.379649e-10 |
| FL | HNRNPL | exon_skip_156685 | 4.736120e-01 | 1.883868e-11 |
| FL | HNRNPH2 | exon_skip_156685 | 4.782540e-01 | 1.122536e-11 |
| FL | EIF4B | exon_skip_156685 | 4.621122e-01 | 6.572606e-11 |
| FL | ZCRB1 | exon_skip_156685 | 4.017781e-01 | 2.267724e-08 |
| IFG | EWSR1 | exon_skip_152326 | -5.999158e-01 | 4.042427e-03 |
| IFG | SRSF1 | exon_skip_152326 | -4.443085e-01 | 4.360340e-02 |
| IFG | SRSF5 | exon_skip_152326 | -5.383350e-01 | 1.181679e-02 |
| PG | RBM3 | exon_skip_156685 | 6.819884e-01 | 2.096775e-22 |
| PG | KHDRBS2 | exon_skip_156685 | 4.630231e-01 | 1.481255e-09 |
| PG | ZFP36 | exon_skip_156685 | -5.228830e-01 | 3.490171e-12 |
| PG | HNRNPA0 | exon_skip_156685 | 4.063213e-01 | 1.708104e-07 |
| PG | PUF60 | exon_skip_156685 | 5.528095e-01 | 1.056709e-13 |
| PG | CPEB1 | exon_skip_156685 | 4.714007e-01 | 6.803257e-10 |
| PG | EIF4B | exon_skip_156685 | 4.375156e-01 | 1.396578e-08 |
| TC | RBM3 | exon_skip_262635 | -4.281809e-01 | 1.801099e-08 |
| TC | RBMS2 | exon_skip_156685 | -4.274544e-01 | 1.914997e-08 |
| TC | SRSF2 | exon_skip_156685 | 5.040190e-01 | 1.263447e-11 |
| TC | RBM25 | exon_skip_156685 | 4.218281e-01 | 3.064156e-08 |
| TC | RBM3 | exon_skip_156685 | 7.232851e-01 | 4.955958e-27 |
| TC | G3BP2 | exon_skip_156685 | 4.146400e-01 | 5.517593e-08 |
| TC | KHDRBS2 | exon_skip_156685 | 4.600459e-01 | 1.055930e-09 |
| TC | HNRNPA0 | exon_skip_156685 | 4.399414e-01 | 6.539944e-09 |
| TC | HNRNPDL | exon_skip_156685 | 4.480567e-01 | 3.177414e-09 |
| TC | HNRNPD | exon_skip_156685 | 4.738320e-01 | 2.819243e-10 |
| TC | NUP42 | exon_skip_156685 | 4.886307e-01 | 6.389224e-11 |
| TC | RALYL | exon_skip_156685 | 4.192592e-01 | 3.786917e-08 |
| TC | SRSF5 | exon_skip_156685 | 4.907861e-01 | 5.116328e-11 |
| TC | HNRNPH2 | exon_skip_156685 | 4.469580e-01 | 3.507540e-09 |
| TC | NOVA1 | exon_skip_156685 | 5.365182e-01 | 3.118698e-13 |
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RelatedDrugs for CLK4 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Q9HAZ1 | approved|investigational | DB12010 | Fostamatinib | small molecule | Q9HAZ1 |
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RelatedDiseases for CLK4 |
| 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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