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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:CDK13-POU6F2

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CDK13-POU6F2
FusionPDB ID: 15164
FusionGDB2.0 ID: 15164
HgeneTgene
Gene symbol

CDK13

POU6F2

Gene ID

8621

11281

Gene namecyclin dependent kinase 13POU class 6 homeobox 2
SynonymsCDC2L|CDC2L5|CHDFIDD|CHED|hCDK13RPF-1|WT5|WTSL
Cytomap

7p14.1

7p14.1

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 controllerPOU domain, class 6, transcription factor 2Wilms tumor suppressor locusretina-derived POU-domain factor-1
Modification date2020031320200313
UniProtAcc

Q14004

.
Ensembl transtripts involved in fusion geneENST idsENST00000484589, ENST00000181839, 
ENST00000340829, 
ENST00000403058, 
ENST00000518318, ENST00000464276, 
ENST00000517348, ENST00000559001, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score16 X 14 X 13=29127 X 9 X 9=567
# samples 3112
** MAII scorelog2(31/2912*10)=-3.23167023492446
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/567*10)=-2.24031432933371
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: CDK13 [Title/Abstract] AND POU6F2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CDK13(40041630)-POU6F2(39500146), # samples:2
CDK13(40118450)-POU6F2(39379241), # samples:2
Anticipated loss of major functional domain due to fusion event.CDK13-POU6F2 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.
CDK13-POU6F2 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.
CDK13-POU6F2 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.
CDK13-POU6F2 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.
CDK13-POU6F2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CDK13-POU6F2 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CDK13-POU6F2 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
CDK13-POU6F2 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
CDK13-POU6F2 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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


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.
all structure

check buttonFusion gene breakpoints across POU6F2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4ESCATCGA-LN-A8I0-01ACDK13chr7

40041630

+POU6F2chr7

39472676

+
ChimerDB4OVTCGA-13-0890-01ACDK13chr7

39991451

+POU6F2chr7

39472676

+
ChimerDB4OVTCGA-13-0890CDK13chr7

39991451

+POU6F2chr7

39446198

+
ChimerDB4OVTCGA-13-0890CDK13chr7

39991451

+POU6F2chr7

39472675

+
ChimerDB4OVTCGA-61-1724-01ACDK13chr7

40041630

+POU6F2chr7

39500146

+
ChimerDB4STADTCGA-BR-7716-01ACDK13chr7

40118450

+POU6F2chr7

39379241

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000181839CDK13chr740041630+ENST00000403058POU6F2chr739500146+3737295860536311008
ENST00000181839CDK13chr740041630+ENST00000518318POU6F2chr739500146+743929586053523972
ENST00000340829CDK13chr740041630+ENST00000403058POU6F2chr739500146+3264248513231581008
ENST00000340829CDK13chr740041630+ENST00000518318POU6F2chr739500146+696624851323050972

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
ENST00000181839ENST00000403058CDK13chr740041630+POU6F2chr739500146+0.0077863770.99221367
ENST00000181839ENST00000518318CDK13chr740041630+POU6F2chr739500146+0.0010303660.9989697
ENST00000340829ENST00000403058CDK13chr740041630+POU6F2chr739500146+0.0057209520.994279
ENST00000340829ENST00000518318CDK13chr740041630+POU6F2chr739500146+0.0006484470.99935156

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>15164_15164_1_CDK13-POU6F2_CDK13_chr7_40041630_ENST00000181839_POU6F2_chr7_39500146_ENST00000403058_length(amino acids)=1008AA_BP=29
MPSSSDTALGGGGGLSWAEKKLEERRKRRRFLSPQQPPLLLPLLQPQLLQPPPPPPPLLFLAAPGTAAAAAAAAAASSSCFSPGPPLEVK
RLARGKRRAGGRQKRRRGPRAGQEAEKRRVFSLPQPQQDGGGGASSGGGVTPLVEYEDVSSQSEQGLLLGGASAATAATAAGGTGGSGGS
PASSSGTQRRGEGSERRPRRDRRSSSGRSKERHREHRRRDGQRGGSEASKSRSRHSHSGEERAEVAKSGSSSSSGGRRKSASATSSSSSS
RKDRDSKAHRSRTKSSKEPPSAYKEPPKAYREDKTEPKAYRRRRSLSPLGGRDDSPVSHRASQSLRSRKSPSPAGGGSSPYSRRLPRSPS
PYSRRRSPSYSRHSSYERGGDVSPSPYSSSSWRRSRSPYSPVLRRSGKSRSRSPYSSRHSRSRSRHRLSRSRSRHSSISPSTLTLKSSLA
AELNKNKKARAAEAARAAEAAKAAEATKAAEAAAKAAKASNTSTPTKGNTETSASASQTNHVKDVKKIKIEHAPSPSSGGTLKNDKAKTK
PPLQVTKVENNLIVDKATKKAVIVGKESKSAATKEESVSLKEKTKPLTPSIGAKEKEQHVALVTSTLPPLPLPPMLPEDKEADSLRGNIS
VKAVKKEVEKKLRCLLADLPLPPELPGGDDLSKSPEEKKTATQLHSKRRPKICGPRYGETKEKDIDWGKRCVDKFDIIGIIGEGTYGQVY
KARDKDTGEMVALKKVRLDNEKEGFPITAIREIKILRQLTHQSIINMKEIVTDKEDALDFKKDKDPQTAAGEVDGVNLEEIREFAKAFKI
RRLSLGLTQTQVGQALSATEGPAYSQSAICRHTILRSHFFLPQEAQENTIASSLTAKLNPGLLYPARFEKLDITPKSAQKIKPVLERWMA
EAEARHRAGMQNLTEFIGSEPSKKRKRRTSFTPQALEILNAHFEKNTHPSGQEMTEIAEKLNYDREVVRVWFCNKRQALKNTIKRLKQHE

--------------------------------------------------------------

>15164_15164_2_CDK13-POU6F2_CDK13_chr7_40041630_ENST00000181839_POU6F2_chr7_39500146_ENST00000518318_length(amino acids)=972AA_BP=29
MPSSSDTALGGGGGLSWAEKKLEERRKRRRFLSPQQPPLLLPLLQPQLLQPPPPPPPLLFLAAPGTAAAAAAAAAASSSCFSPGPPLEVK
RLARGKRRAGGRQKRRRGPRAGQEAEKRRVFSLPQPQQDGGGGASSGGGVTPLVEYEDVSSQSEQGLLLGGASAATAATAAGGTGGSGGS
PASSSGTQRRGEGSERRPRRDRRSSSGRSKERHREHRRRDGQRGGSEASKSRSRHSHSGEERAEVAKSGSSSSSGGRRKSASATSSSSSS
RKDRDSKAHRSRTKSSKEPPSAYKEPPKAYREDKTEPKAYRRRRSLSPLGGRDDSPVSHRASQSLRSRKSPSPAGGGSSPYSRRLPRSPS
PYSRRRSPSYSRHSSYERGGDVSPSPYSSSSWRRSRSPYSPVLRRSGKSRSRSPYSSRHSRSRSRHRLSRSRSRHSSISPSTLTLKSSLA
AELNKNKKARAAEAARAAEAAKAAEATKAAEAAAKAAKASNTSTPTKGNTETSASASQTNHVKDVKKIKIEHAPSPSSGGTLKNDKAKTK
PPLQVTKVENNLIVDKATKKAVIVGKESKSAATKEESVSLKEKTKPLTPSIGAKEKEQHVALVTSTLPPLPLPPMLPEDKEADSLRGNIS
VKAVKKEVEKKLRCLLADLPLPPELPGGDDLSKSPEEKKTATQLHSKRRPKICGPRYGETKEKDIDWGKRCVDKFDIIGIIGEGTYGQVY
KARDKDTGEMVALKKVRLDNEKEGFPITAIREIKILRQLTHQSIINMKEIVTDKEDALDFKKDKDPQTAAGEVDGVNLEEIREFAKAFKI
RRLSLGLTQTQVGQALSATEGPAYSQSAICRFEKLDITPKSAQKIKPVLERWMAEAEARHRAGMQNLTEFIGSEPSKKRKRRTSFTPQAL

--------------------------------------------------------------

>15164_15164_3_CDK13-POU6F2_CDK13_chr7_40041630_ENST00000340829_POU6F2_chr7_39500146_ENST00000403058_length(amino acids)=1008AA_BP=29
MPSSSDTALGGGGGLSWAEKKLEERRKRRRFLSPQQPPLLLPLLQPQLLQPPPPPPPLLFLAAPGTAAAAAAAAAASSSCFSPGPPLEVK
RLARGKRRAGGRQKRRRGPRAGQEAEKRRVFSLPQPQQDGGGGASSGGGVTPLVEYEDVSSQSEQGLLLGGASAATAATAAGGTGGSGGS
PASSSGTQRRGEGSERRPRRDRRSSSGRSKERHREHRRRDGQRGGSEASKSRSRHSHSGEERAEVAKSGSSSSSGGRRKSASATSSSSSS
RKDRDSKAHRSRTKSSKEPPSAYKEPPKAYREDKTEPKAYRRRRSLSPLGGRDDSPVSHRASQSLRSRKSPSPAGGGSSPYSRRLPRSPS
PYSRRRSPSYSRHSSYERGGDVSPSPYSSSSWRRSRSPYSPVLRRSGKSRSRSPYSSRHSRSRSRHRLSRSRSRHSSISPSTLTLKSSLA
AELNKNKKARAAEAARAAEAAKAAEATKAAEAAAKAAKASNTSTPTKGNTETSASASQTNHVKDVKKIKIEHAPSPSSGGTLKNDKAKTK
PPLQVTKVENNLIVDKATKKAVIVGKESKSAATKEESVSLKEKTKPLTPSIGAKEKEQHVALVTSTLPPLPLPPMLPEDKEADSLRGNIS
VKAVKKEVEKKLRCLLADLPLPPELPGGDDLSKSPEEKKTATQLHSKRRPKICGPRYGETKEKDIDWGKRCVDKFDIIGIIGEGTYGQVY
KARDKDTGEMVALKKVRLDNEKEGFPITAIREIKILRQLTHQSIINMKEIVTDKEDALDFKKDKDPQTAAGEVDGVNLEEIREFAKAFKI
RRLSLGLTQTQVGQALSATEGPAYSQSAICRHTILRSHFFLPQEAQENTIASSLTAKLNPGLLYPARFEKLDITPKSAQKIKPVLERWMA
EAEARHRAGMQNLTEFIGSEPSKKRKRRTSFTPQALEILNAHFEKNTHPSGQEMTEIAEKLNYDREVVRVWFCNKRQALKNTIKRLKQHE

--------------------------------------------------------------

>15164_15164_4_CDK13-POU6F2_CDK13_chr7_40041630_ENST00000340829_POU6F2_chr7_39500146_ENST00000518318_length(amino acids)=972AA_BP=29
MPSSSDTALGGGGGLSWAEKKLEERRKRRRFLSPQQPPLLLPLLQPQLLQPPPPPPPLLFLAAPGTAAAAAAAAAASSSCFSPGPPLEVK
RLARGKRRAGGRQKRRRGPRAGQEAEKRRVFSLPQPQQDGGGGASSGGGVTPLVEYEDVSSQSEQGLLLGGASAATAATAAGGTGGSGGS
PASSSGTQRRGEGSERRPRRDRRSSSGRSKERHREHRRRDGQRGGSEASKSRSRHSHSGEERAEVAKSGSSSSSGGRRKSASATSSSSSS
RKDRDSKAHRSRTKSSKEPPSAYKEPPKAYREDKTEPKAYRRRRSLSPLGGRDDSPVSHRASQSLRSRKSPSPAGGGSSPYSRRLPRSPS
PYSRRRSPSYSRHSSYERGGDVSPSPYSSSSWRRSRSPYSPVLRRSGKSRSRSPYSSRHSRSRSRHRLSRSRSRHSSISPSTLTLKSSLA
AELNKNKKARAAEAARAAEAAKAAEATKAAEAAAKAAKASNTSTPTKGNTETSASASQTNHVKDVKKIKIEHAPSPSSGGTLKNDKAKTK
PPLQVTKVENNLIVDKATKKAVIVGKESKSAATKEESVSLKEKTKPLTPSIGAKEKEQHVALVTSTLPPLPLPPMLPEDKEADSLRGNIS
VKAVKKEVEKKLRCLLADLPLPPELPGGDDLSKSPEEKKTATQLHSKRRPKICGPRYGETKEKDIDWGKRCVDKFDIIGIIGEGTYGQVY
KARDKDTGEMVALKKVRLDNEKEGFPITAIREIKILRQLTHQSIINMKEIVTDKEDALDFKKDKDPQTAAGEVDGVNLEEIREFAKAFKI
RRLSLGLTQTQVGQALSATEGPAYSQSAICRFEKLDITPKSAQKIKPVLERWMAEAEARHRAGMQNLTEFIGSEPSKKRKRRTSFTPQAL

--------------------------------------------------------------

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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/chr7:40041630/chr7:39500146)
- 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

.
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}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCDK13chr7:40041630chr7:39500146ENST00000181839+514711_719784.33333333333341513.0Nucleotide bindingATP
HgeneCDK13chr7:40041630chr7:39500146ENST00000340829+514711_719784.33333333333341453.0Nucleotide bindingATP
TgenePOU6F2chr7:40041630chr7:39500146ENST00000403058811607_666467.3333333333333692.0DNA bindingHomeobox
TgenePOU6F2chr7:40041630chr7:39500146ENST00000518318710607_666467.3333333333333656.0DNA bindingHomeobox
TgenePOU6F2chr7:40041630chr7:39500146ENST00000403058811476_586467.3333333333333692.0DomainPOU-specific
TgenePOU6F2chr7:40041630chr7:39500146ENST00000518318710476_586467.3333333333333656.0DomainPOU-specific

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCDK13chr7:40041630chr7:39500146ENST00000181839+514705_998784.33333333333341513.0DomainProtein kinase
HgeneCDK13chr7:40041630chr7:39500146ENST00000340829+514705_998784.33333333333341453.0DomainProtein kinase
TgenePOU6F2chr7:40041630chr7:39500146ENST00000403058811167_446467.3333333333333692.0Compositional biasNote=Gln-rich
TgenePOU6F2chr7:40041630chr7:39500146ENST00000403058811197_293467.3333333333333692.0Compositional biasNote=Pro-rich
TgenePOU6F2chr7:40041630chr7:39500146ENST00000403058811435_461467.3333333333333692.0Compositional biasNote=Ser-rich
TgenePOU6F2chr7:40041630chr7:39500146ENST00000518318710167_446467.3333333333333656.0Compositional biasNote=Gln-rich
TgenePOU6F2chr7:40041630chr7:39500146ENST00000518318710197_293467.3333333333333656.0Compositional biasNote=Pro-rich
TgenePOU6F2chr7:40041630chr7:39500146ENST00000518318710435_461467.3333333333333656.0Compositional biasNote=Ser-rich


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
CDK13
POU6F2


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to CDK13-POU6F2


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

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Related Diseases to CDK13-POU6F2


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

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