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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:CDK13-SON (FusionGDB2 ID:15167)

Fusion Gene Summary for CDK13-SON

check button Fusion gene summary
Fusion gene informationFusion gene name: CDK13-SON
Fusion gene ID: 15167
HgeneTgene
Gene symbol

CDK13

SON

Gene ID

8621

6651

Gene namecyclin dependent kinase 13SON DNA and RNA binding protein
SynonymsCDC2L|CDC2L5|CHDFIDD|CHED|hCDK13BASS1|C21orf50|DBP-5|NREBP|SON3|TOKIMS
Cytomap

7p14.1

21q22.11

Type of geneprotein-codingprotein-coding
Descriptioncyclin-dependent kinase 13CDC2-related protein kinase 5cell division cycle 2-like protein kinase 5cell division protein kinase 13cholinesterase-related cell division controllerprotein SONBax antagonist selected in Saccharomyces 1NRE-binding proteinSON DNA binding proteinnegative regulatory element-binding protein
Modification date2020031320200313
UniProtAcc

Q14004

SHH

Ensembl transtripts involved in fusion geneENST00000484589, ENST00000181839, 
ENST00000340829, 		ENST00000290239, 
ENST00000356577, ENST00000300278, 
ENST00000381679, ENST00000381692, 
ENST00000470533, 
Fusion gene scores* DoF score16 X 14 X 13=291216 X 15 X 5=1200
# samples 3116
** MAII scorelog2(31/2912*10)=-3.23167023492446
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1200*10)=-2.90689059560852
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CDK13 [Title/Abstract] AND SON [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCDK13(40037263)-SON(34921781), # samples:1
Anticipated loss of major functional domain due to fusion event.CDK13-SON seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CDK13-SON seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CDK13-SON seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
CDK13-SON seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
CDK13-SON seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted 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
HgeneCDK13

GO:0070816

phosphorylation of RNA polymerase II C-terminal domain

20952539

TgeneSON

GO:0006397

mRNA processing

21504830

TgeneSON

GO:0043066

negative regulation of apoptotic process

10509013

TgeneSON

GO:0048024

regulation of mRNA splicing, via spliceosome

21504830


check buttonFusion gene breakpoints across CDK13 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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

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
ChimerDB4STADTCGA-FP-A4BFCDK13chr7

40037263

+SONchr21

34921781

+


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Fusion Gene ORF analysis for CDK13-SON

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
3UTR-3CDSENST00000484589ENST00000290239CDK13chr7

40037263

+SONchr21

34921781

+
3UTR-3CDSENST00000484589ENST00000356577CDK13chr7

40037263

+SONchr21

34921781

+
3UTR-intronENST00000484589ENST00000300278CDK13chr7

40037263

+SONchr21

34921781

+
3UTR-intronENST00000484589ENST00000381679CDK13chr7

40037263

+SONchr21

34921781

+
3UTR-intronENST00000484589ENST00000381692CDK13chr7

40037263

+SONchr21

34921781

+
3UTR-intronENST00000484589ENST00000470533CDK13chr7

40037263

+SONchr21

34921781

+
5CDS-intronENST00000181839ENST00000300278CDK13chr7

40037263

+SONchr21

34921781

+
5CDS-intronENST00000181839ENST00000381679CDK13chr7

40037263

+SONchr21

34921781

+
5CDS-intronENST00000181839ENST00000381692CDK13chr7

40037263

+SONchr21

34921781

+
5CDS-intronENST00000181839ENST00000470533CDK13chr7

40037263

+SONchr21

34921781

+
5CDS-intronENST00000340829ENST00000300278CDK13chr7

40037263

+SONchr21

34921781

+
5CDS-intronENST00000340829ENST00000381679CDK13chr7

40037263

+SONchr21

34921781

+
5CDS-intronENST00000340829ENST00000381692CDK13chr7

40037263

+SONchr21

34921781

+
5CDS-intronENST00000340829ENST00000470533CDK13chr7

40037263

+SONchr21

34921781

+
Frame-shiftENST00000181839ENST00000290239CDK13chr7

40037263

+SONchr21

34921781

+
Frame-shiftENST00000181839ENST00000356577CDK13chr7

40037263

+SONchr21

34921781

+
Frame-shiftENST00000340829ENST00000290239CDK13chr7

40037263

+SONchr21

34921781

+
Frame-shiftENST00000340829ENST00000356577CDK13chr7

40037263

+SONchr21

34921781

+

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 CDK13-SON


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)
CDK13chr740037263+SONchr2134921781+1.65E-050.99998355
CDK13chr740037263+SONchr2134921781+1.65E-050.99998355

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.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for CDK13-SON


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/:40037263/:34921781)
- 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
CDK13

Q14004

SON

SHH

FUNCTION: Cyclin-dependent kinase which displays CTD kinase activity and is required for RNA splicing. Has CTD kinase activity by hyperphosphorylating the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit RPB1, thereby acting as a key regulator of transcription elongation. Required for RNA splicing, probably by phosphorylating SRSF1/SF2. Required during hematopoiesis. In case of infection by HIV-1 virus, interacts with HIV-1 Tat protein acetylated at 'Lys-50' and 'Lys-51', thereby increasing HIV-1 mRNA splicing and promoting the production of the doubly spliced HIV-1 protein Nef. {ECO:0000269|PubMed:16721827, ECO:0000269|PubMed:1731328, ECO:0000269|PubMed:18480452, ECO:0000269|PubMed:20952539}.462

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 CDK13-SON


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 CDK13-SON


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 CDK13-SON


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 CDK13-SON


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