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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:CCNT2-YSK4 (FusionGDB2 ID:HG905TG80122)

Fusion Gene Summary for CCNT2-YSK4

check button Fusion gene summary
Fusion gene informationFusion gene name: CCNT2-YSK4
Fusion gene ID: hg905tg80122
HgeneTgene
Gene symbol

CCNT2

YSK4

Gene ID

905

80122

Gene namecyclin T2mitogen-activated protein kinase kinase kinase 19
SynonymsCYCT2RCK|YSK4
Cytomap('CCNT2','CCNT2')('MAP3K19','YSK4')

2q21.3

2q21.3

Type of geneprotein-codingprotein-coding
Descriptioncyclin-T2SDS-stable vimentin-bound DNA fragment HEF42VIM22cyclin T2acyclin T2bsubunit of positive elongation transcription factor bmitogen-activated protein kinase kinase kinase 19SPS1/STE20-related protein kinase YSK4YSK4 Sps1/Ste20-related kinase homologregulated in COPD kinaseregulated in COPD, protein kinaseyeast Sps1/Ste20-related kinase 4
Modification date2020031320200320
UniProtAcc

O60583

.
Ensembl transtripts involved in fusion geneENST00000264157, ENST00000295238, 
ENST00000537343, 
Fusion gene scores* DoF score5 X 4 X 6=1201 X 1 X 1=1
# samples 71
** MAII scorelog2(7/120*10)=-0.777607578663552
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(1/1*10)=3.32192809488736
Context

PubMed: CCNT2 [Title/Abstract] AND YSK4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCCNT2(135705469)-MAP3K19(135722486), # samples:2
CCNT2(135705469)-YSK4(135722486), # samples:2
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneCCNT2

GO:0019085

early viral transcription

21509660

HgeneCCNT2

GO:0019086

late viral transcription

21509660

HgeneCCNT2

GO:0045944

positive regulation of transcription by RNA polymerase II

15563843



check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4KIRCTCGA-B0-4815-01ACCNT2chr2

135705469

+MAP3K19chr2

135722486

-
ChimerDB4STADTCGA-D7-6822-01ACCNT2chr2

135705469

+MAP3K19chr2

135722486

-
ChimerDB4KIRCTCGA-B0-4815-01ACCNT2chr2

135705469

-YSK4chr2

135722486

-
ChimerDB4STADTCGA-D7-6822CCNT2chr2

135705469

+YSK4chr2

135722486

-


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Fusion Gene ORF analysis for CCNT2-YSK4

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
5CDS-intronENST00000264157ENST00000315513CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000264157ENST00000358371CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000264157ENST00000375844CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000264157ENST00000375845CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000264157ENST00000392915CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000264157ENST00000392917CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000264157ENST00000392918CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000264157ENST00000486077CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000295238ENST00000315513CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000295238ENST00000358371CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000295238ENST00000375844CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000295238ENST00000375845CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000295238ENST00000392915CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000295238ENST00000392917CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000295238ENST00000392918CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000295238ENST00000486077CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000537343ENST00000315513CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000537343ENST00000358371CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000537343ENST00000375844CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000537343ENST00000375845CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000537343ENST00000392915CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000537343ENST00000392917CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000537343ENST00000392918CCNT2chr2

135705469

+MAP3K19chr2

135722486

-
5CDS-intronENST00000537343ENST00000486077CCNT2chr2

135705469

+MAP3K19chr2

135722486

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for CCNT2-YSK4


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for CCNT2-YSK4


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/:135705469/:135722486)
- 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
CCNT2

O60583

.
FUNCTION: Regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFB), which is proposed to facilitate the transition from abortive to production elongation by phosphorylating the CTD (carboxy-terminal domain) of the large subunit of RNA polymerase II (RNAP II) (PubMed:9499409, PubMed:15563843). The activity of this complex is regulated by binding with 7SK snRNA (PubMed:11713533). Plays a role during muscle differentiation; P-TEFB complex interacts with MYOD1; this tripartite complex promotes the transcriptional activity of MYOD1 through its CDK9-mediated phosphorylation and binds the chromatin of promoters and enhancers of muscle-specific genes; this event correlates with hyperphosphorylation of the CTD domain of RNA pol II (By similarity). In addition, enhances MYOD1-dependent transcription through interaction with PKN1 (PubMed:16331689). Involved in early embryo development (By similarity). {ECO:0000250|UniProtKB:Q7TQK0, ECO:0000269|PubMed:11713533, ECO:0000269|PubMed:15563843, ECO:0000269|PubMed:16331689, ECO:0000269|PubMed:9499409}.; FUNCTION: (Microbial infection) Promotes transcriptional activation of early and late herpes simplex virus 1/HHV-1 promoters. {ECO:0000269|PubMed:21509660}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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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Fusion Gene Sequence for CCNT2-YSK4


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for CCNT2-YSK4


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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Related Drugs for CCNT2-YSK4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for CCNT2-YSK4


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