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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:ELK3-CDK17 (FusionGDB2 ID:HG2004TG5128)

Fusion Gene Summary for ELK3-CDK17

check button Fusion gene summary
Fusion gene informationFusion gene name: ELK3-CDK17
Fusion gene ID: hg2004tg5128
HgeneTgene
Gene symbol

ELK3

CDK17

Gene ID

2004

5128

Gene nameETS transcription factor ELK3cyclin dependent kinase 17
SynonymsERP|NET|SAP-2|SAP2PCTAIRE2|PCTK2
Cytomap('ELK3')('CDK17')

12q23.1

12q23.1

Type of geneprotein-codingprotein-coding
DescriptionETS domain-containing protein Elk-3ELK3, ETS transcription factorELK3, ETS-domain protein (SRF accessory protein 2)ETS-related protein ERPETS-related protein NETSRF accessory protein 2serum response factor accessory protein 2cyclin-dependent kinase 17PCTAIRE-motif protein kinase 2cell division protein kinase 17protein kinase cdc2-related PCTAIRE-2serine/threonine-protein kinase PCTAIRE-2
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000228741, ENST00000552142, 
ENST00000549529, 
ENST00000228741, 
ENST00000552142, ENST00000549529, 
Fusion gene scores* DoF score13 X 5 X 6=3909 X 6 X 4=216
# samples 139
** MAII scorelog2(13/390*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/216*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ELK3 [Title/Abstract] AND CDK17 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointELK3(96617551)-CDK17(96694138), # samples:4
Anticipated loss of major functional domain due to fusion event.ELK3-CDK17 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
ELK3-CDK17 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
ELK3-CDK17 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
ELK3-CDK17 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
* 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
HgeneELK3

GO:0045892

negative regulation of transcription, DNA-templated

12933792

HgeneELK3

GO:0045944

positive regulation of transcription by RNA polymerase II

12788937


check buttonFusion gene breakpoints across ELK3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across CDK17 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button Fusion gene information
* 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
ChimerDB4SARCTCGA-DX-A2J0-01AELK3chr12

96617551

-CDK17chr12

96694138

-
ChimerDB4SARCTCGA-DX-A2J0-01AELK3chr12

96617551

+CDK17chr12

96694138

-
ChimerDB4SARCTCGA-DX-A2J0ELK3chr12

96617551

+CDK17chr12

96694138

-


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Fusion Gene ORF analysis for ELK3-CDK17

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-5UTRENST00000228741ENST00000553042ELK3chr12

96617551

+CDK17chr12

96694138

-
5CDS-5UTRENST00000552142ENST00000553042ELK3chr12

96617551

+CDK17chr12

96694138

-
In-frameENST00000228741ENST00000261211ELK3chr12

96617551

+CDK17chr12

96694138

-
In-frameENST00000228741ENST00000542666ELK3chr12

96617551

+CDK17chr12

96694138

-
In-frameENST00000228741ENST00000543119ELK3chr12

96617551

+CDK17chr12

96694138

-
In-frameENST00000552142ENST00000261211ELK3chr12

96617551

+CDK17chr12

96694138

-
In-frameENST00000552142ENST00000542666ELK3chr12

96617551

+CDK17chr12

96694138

-
In-frameENST00000552142ENST00000543119ELK3chr12

96617551

+CDK17chr12

96694138

-
intron-3CDSENST00000549529ENST00000261211ELK3chr12

96617551

+CDK17chr12

96694138

-
intron-3CDSENST00000549529ENST00000542666ELK3chr12

96617551

+CDK17chr12

96694138

-
intron-3CDSENST00000549529ENST00000543119ELK3chr12

96617551

+CDK17chr12

96694138

-
intron-5UTRENST00000549529ENST00000553042ELK3chr12

96617551

+CDK17chr12

96694138

-

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 ELK3-CDK17


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.
genomic feature

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Fusion Protein Features for ELK3-CDK17


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/chr12:96617551/chr12:96694138)
- 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
..
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}.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
TgeneCDK17chr12:96617551chr12:96694138ENST00000261211417192_473181524.0DomainProtein kinase
TgeneCDK17chr12:96617551chr12:96694138ENST00000543119416192_473181524.0DomainProtein kinase
TgeneCDK17chr12:96617551chr12:96694138ENST00000261211417198_206181524.0Nucleotide bindingATP
TgeneCDK17chr12:96617551chr12:96694138ENST00000543119416198_206181524.0Nucleotide bindingATP

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneELK3chr12:96617551chr12:96694138ENST00000228741+25207_21269408.0Compositional biasNote=Poly-Ala
HgeneELK3chr12:96617551chr12:96694138ENST00000228741+255_8569408.0DNA bindingETS
HgeneELK3chr12:96617551chr12:96694138ENST00000228741+25273_27769408.0MotifNote=CTBP-binding motif


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Fusion Gene Sequence for ELK3-CDK17


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 ELK3-CDK17


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 ELK3-CDK17


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 ELK3-CDK17


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneELK3C0006142Malignant neoplasm of breast1CTD_human
HgeneELK3C0678222Breast Carcinoma1CTD_human
HgeneELK3C1135196Heart Failure, Diastolic1CTD_human
HgeneELK3C1257931Mammary Neoplasms, Human1CTD_human
HgeneELK3C1458155Mammary Neoplasms1CTD_human
HgeneELK3C4704874Mammary Carcinoma, Human1CTD_human