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Center for Computational Systems Medicine
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Kinase Fusion Gene Summary

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Kinase Fusion Gene Sample Information

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Kinase Fusion ORF Analysis

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Kinase Fusion Amino Acid Sequences

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Multiple Sequence Alignment of All Fusion Protein Isoforms

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Kinase Fusion Protein Functional Features

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Kinase Fusion Protein Structures

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Comparison of Fusion Protein Isoforms

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Comparison of Fusion Protein Sequences/Structures with Known Sequences/Structures from PDB

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pLDDT Scores and Difference Analysis of pLDDT Scores Between the Active Sites (Best) and Non-Active Sites.

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Ramachandran Plot of Kinase Fusion Protein Structure

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Potential Active Site Information

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Virtual Screening Results

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Kinase-Substrate Information

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Related Drugs with This Kinase Fusion Protein

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Related Disease with This Kinase Fusion Protein

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Clinical Trials of the Found Drugs/Small Molecules

Kinase Fusion Gene:CLK3_EDC3

Kinase Fusion Protein Summary

check button Kinase Fusion gene summary
Kinase Fusion partner gene informationKinase Fusion gene name: CLK3_EDC3
KinaseFusionDB ID: KFG1339
FusionGDB2.0 ID: KFG1339
HgeneTgene
Gene symbol

CLK3

EDC3

Gene ID

1198

80153

Gene nameCDC like kinase 3enhancer of mRNA decapping 3
SynonymsPHCLK3|PHCLK3/152LSM16|MRT50|YJDC|YJEFN2|hYjeF_N2-15q23
Cytomap

15q24.1

15q24.1

Type of geneprotein-codingprotein-coding
Descriptiondual specificity protein kinase CLK3enhancer of mRNA-decapping protein 3LSM16 homolog (EDC3, S. cerevisiae)enhancer of mRNA decapping 3 homologyjeF N-terminal domain-containing protein 2yjeF domain containingyjeF domain-containing protein 1
Modification date2024030520240305
UniProtAcc

P49761

Q96F86

Ensembl transtripts involved in fusion geneENST idsENST00000345005, ENST00000348245, 
ENST00000352989, ENST00000395066, 
ENST00000564353, 
ENST00000315127, 
ENST00000426797, ENST00000562047, 
ENST00000568176, 
Context (manual curation of fusion genes in KinaseFusionDB)

PubMed: CLK3 [Title/Abstract] AND EDC3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)EDC3(74927439)-CLK3(74927557), # samples:1
CLK3(74925601)-EDC3(74925665), # samples:1
check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCLK3

GO:0006468

protein phosphorylation

9637771

HgeneCLK3

GO:0043484

regulation of RNA splicing

9637771


check buttonKinase Fusion gene breakpoints across CLK3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonKinase Fusion gene breakpoints across EDC3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.


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Kinase Fusion Gene Sample Information

check buttonKinase Fusion gene information.
check button Kinase Fusion gene information from four resources (ChiTars 5.0, ChimerDB 4.0, COSMIC, and CCLE)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceSampleHgeneHchrHbpTgeneTchrTbp
ChiTaRS5.0BE095213CLK3chr15

74925601

EDC3chr15

74925665



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Kinase Fusion ORF Analysis


check buttonKinase Fusion information from ORFfinder translation from full-length transcript sequence from KinaseFusionDB.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)
Seq length
(amino acids)

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Kinase Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from KinaseFusionDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>Henst_Tenst_Hgene_Hchr_Hbp_Tgene_Tchr_Tbp_length(fusion AA)_AAseq

Multiple Sequence Alignment of All Fusion Protein Isoforms



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Kinase Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:74927439/:74927557)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CLK3

P49761

EDC3

Q96F86

FUNCTION: Dual specificity kinase acting on both serine/threonine and tyrosine-containing substrates. Phosphorylates serine- and arginine-rich (SR) proteins of the spliceosomal complex. May be a constituent of a network of regulatory mechanisms that enable SR proteins to control RNA splicing and can cause redistribution of SR proteins from speckles to a diffuse nucleoplasmic distribution. Phosphorylates SRSF1 and SRSF3. Regulates the alternative splicing of tissue factor (F3) pre-mRNA in endothelial cells. {ECO:0000269|PubMed:19168442, ECO:0000269|PubMed:9637771}.FUNCTION: Binds single-stranded RNA. Involved in the process of mRNA degradation and in the positive regulation of mRNA decapping. May play a role in spermiogenesis and oogenesis. {ECO:0000269|PubMed:16364915, ECO:0000269|PubMed:17533573, ECO:0000269|PubMed:18678652, ECO:0000269|PubMed:25701870}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

* Minus value of BPloci means that the break pointn is located before the CDS.

check button - Retained domain in the 5'-partner of fusion protein (protein functional feature from UniProt).
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote


check button - Retained domain in the 3'-partner of fusion protein (protein functional feature from UniProt).
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote


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Kinase-Substrate Information of CLK3_EDC3


check button Phosphorylation target of the kinase
(phosphosite, 03-17-2024)
KinaseKinase UniProt AccKinase speciesSubstrateSubstrate UniProt AccSubstrate phosphorylated residuesSubstrate phosphorylated sites (+/-7AA)Domain
CLK3P49761humanUSP13Q92995Y708EPLTMPGyGGAASAGUCH


check button Biological Network Integration of This Kinase and Substrates
(GeneMANIA website)

check button Enriched GO biological processes of the phosphorylation target genes of the kinase
KinaseGOIDGO termP.adjust
CLK3IDDescription0.00e+00
CLK3GO:1904294positive regulation of ERAD pathway7.31e-03
CLK3GO:1904292regulation of ERAD pathway7.31e-03
CLK3GO:0030318melanocyte differentiation7.31e-03
CLK3GO:0070536protein K63-linked deubiquitination7.31e-03
CLK3GO:0050931pigment cell differentiation7.31e-03
CLK3GO:1905898positive regulation of response to endoplasmic reticulum stress7.31e-03
CLK3GO:0048066developmental pigmentation8.71e-03
CLK3GO:1905897regulation of response to endoplasmic reticulum stress1.19e-02
CLK3GO:0036503ERAD pathway1.19e-02
CLK3GO:0016579protein deubiquitination1.19e-02
CLK3GO:0043473pigmentation1.19e-02
CLK3GO:1901800positive regulation of proteasomal protein catabolic process1.19e-02
CLK3GO:0070646protein modification by small protein removal1.21e-02
CLK3GO:1903052positive regulation of proteolysis involved in protein catabolic process1.21e-02
CLK3GO:0061136regulation of proteasomal protein catabolic process1.56e-02
CLK3GO:0045732positive regulation of protein catabolic process1.56e-02
CLK3GO:0050821protein stabilization1.56e-02
CLK3GO:1903050regulation of proteolysis involved in protein catabolic process1.59e-02
CLK3GO:0034976response to endoplasmic reticulum stress1.71e-02
CLK3GO:0031647regulation of protein stability1.93e-02
CLK3GO:0045862positive regulation of proteolysis1.93e-02
CLK3GO:0010506regulation of autophagy1.93e-02
CLK3GO:0042176regulation of protein catabolic process1.93e-02

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Related Drugs to CLK3_EDC3


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

check button Distribution of the number of studies mentioning CLK3-EDC3 and kinase inhibitors the PubMed Abstract (04-01-2024)

Fusion gene - drug pair 1Fusion gene - drug pair 2PMIDPublication dateDOIStudy title

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Related Diseases to CLK3_EDC3


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Related diseases from the literature mentioned this fusion gene and drug.
(PubMed, 04-01-2024)
MeSH IDMeSH term

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource


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Clinical Trials of the Found Drugs/Small Molecules


check button Statistics of the Clinical Trials of the Found Kinase Inibitors from clinicaltrials.gov (06-17-2024)

check button Clinical Trials from clinicaltrials.gov (06-17-2024)

Fusion GeneKinase InhibitorNCT IDStudy StatusPhasesDisease# EnrolmentDate