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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 33992

FusionGeneSummary for SKI_CLK3

check button Fusion gene summary
Fusion gene informationFusion gene name: SKI_CLK3
Fusion gene ID: 33992
HgeneTgene
Gene symbol

SKI

CLK3

Gene ID

6497

1198

Gene nameSKI proto-oncogeneCDC like kinase 3
SynonymsSGS|SKVPHCLK3|PHCLK3/152
Cytomap

1p36.33-p36.32

15q24.1

Type of geneprotein-codingprotein-coding
Descriptionski oncogeneproto-oncogene c-Skiski oncoproteinv-ski avian sarcoma viral oncogene homologdual specificity protein kinase CLK3
Modification date2018052320180522
UniProtAcc

P12755

P49761

Ensembl transtripts involved in fusion geneENST00000378536, ENST00000478223, 
ENST00000564353, ENST00000345005, 
ENST00000395066, ENST00000348245, 
ENST00000352989, 
Fusion gene scores* DoF score11 X 5 X 8=4404 X 4 X 2=32
# samples 134
** MAII scorelog2(13/440*10)=-1.7589919004962
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

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

Functional or gene categories assigned by FusionGDB annotation
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneSKI

GO:0000122

negative regulation of transcription by RNA polymerase II

17469184

HgeneSKI

GO:0008285

negative regulation of cell proliferation

11430826

HgeneSKI

GO:0014902

myotube differentiation

19008232

HgeneSKI

GO:0030512

negative regulation of transforming growth factor beta receptor signaling pathway

17469184

HgeneSKI

GO:0030514

negative regulation of BMP signaling pathway

14699069

HgeneSKI

GO:0032926

negative regulation of activin receptor signaling pathway

14699069

HgeneSKI

GO:0043388

positive regulation of DNA binding

15107821

HgeneSKI

GO:0045668

negative regulation of osteoblast differentiation

14699069

HgeneSKI

GO:0060395

SMAD protein signal transduction

12874272

HgeneSKI

GO:0070207

protein homotrimerization

8514802

TgeneCLK3

GO:0006468

protein phosphorylation

9637771

TgeneCLK3

GO:0043484

regulation of RNA splicing

9637771


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1BE770177SKIchr1

2233981

-CLK3chr15

74919979

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-intronENST00000378536ENST00000564353SKIchr1

2233981

-CLK3chr15

74919979

+
intron-intronENST00000378536ENST00000345005SKIchr1

2233981

-CLK3chr15

74919979

+
intron-intronENST00000378536ENST00000395066SKIchr1

2233981

-CLK3chr15

74919979

+
intron-3UTRENST00000378536ENST00000348245SKIchr1

2233981

-CLK3chr15

74919979

+
intron-3UTRENST00000378536ENST00000352989SKIchr1

2233981

-CLK3chr15

74919979

+
intron-intronENST00000478223ENST00000564353SKIchr1

2233981

-CLK3chr15

74919979

+
intron-intronENST00000478223ENST00000345005SKIchr1

2233981

-CLK3chr15

74919979

+
intron-intronENST00000478223ENST00000395066SKIchr1

2233981

-CLK3chr15

74919979

+
intron-3UTRENST00000478223ENST00000348245SKIchr1

2233981

-CLK3chr15

74919979

+
intron-3UTRENST00000478223ENST00000352989SKIchr1

2233981

-CLK3chr15

74919979

+

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FusionProtFeatures for SKI_CLK3


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

P12755

CLK3

P49761

May play a role in terminal differentiation of skeletalmuscle cells but not in the determination of cells to the myogeniclineage. Functions as a repressor of TGF-beta signaling.{ECO:0000269|PubMed:19049980}. Dual specificity kinase acting on both serine/threonineand tyrosine-containing substrates. Phosphorylates serine- andarginine-rich (SR) proteins of the spliceosomal complex. May be aconstituent of a network of regulatory mechanisms that enable SRproteins to control RNA splicing and can cause redistribution ofSR proteins from speckles to a diffuse nucleoplasmic distribution.Phosphorylates SRSF1 and SRSF3. Regulates the alternative splicingof tissue factor (F3) pre-mRNA in endothelial cells.{ECO:0000269|PubMed:19168442, ECO:0000269|PubMed:9637771}.

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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for SKI_CLK3


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for SKI_CLK3


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for SKI_CLK3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for SKI_CLK3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSKIC1321551Shprintzen-Goldberg syndrome4CTD_human;ORPHANET;UNIPROT
HgeneSKIC0003486Aortic Aneurysm1CTD_human
HgeneSKIC0027794Neural Tube Defects1CTD_human
HgeneSKIC0151491Congenital musculoskeletal anomalies1CTD_human
HgeneSKIC0376634Craniofacial Abnormalities1CTD_human