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in Kim Lab

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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:CPSF6-CDK13 (FusionGDB2 ID:HG11052TG8621)

Fusion Gene Summary for CPSF6-CDK13

check button Fusion gene summary
Fusion gene informationFusion gene name: CPSF6-CDK13
Fusion gene ID: hg11052tg8621
HgeneTgene
Gene symbol

CPSF6

CDK13

Gene ID

11052

8621

Gene namecleavage and polyadenylation specific factor 6cyclin dependent kinase 13
SynonymsCFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7CDC2L|CDC2L5|CHDFIDD|CHED|hCDK13
Cytomap('CPSF6')('CDK13')

12q15

7p14.1

Type of geneprotein-codingprotein-coding
Descriptioncleavage and polyadenylation specificity factor subunit 6CPSF 68 kDa subunitcleavage and polyadenylation specific factor 6, 68kDacleavage and polyadenylation specificity factor 68 kDa subunitcleavage factor Im complex 68 kDa subunitpre-mRNA cleavage cyclin-dependent kinase 13CDC2-related protein kinase 5cell division cycle 2-like protein kinase 5cell division protein kinase 13cholinesterase-related cell division controller
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000266679, ENST00000435070, 
ENST00000456847, ENST00000551516, 
ENST00000550987, 
Fusion gene scores* DoF score69 X 12 X 19=157325 X 6 X 2=60
# samples 716
** MAII scorelog2(71/15732*10)=-4.46973925655087
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/60*10)=0
Context

PubMed: CPSF6 [Title/Abstract] AND CDK13 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCPSF6(69656342)-CDK13(40027198), # samples:1
Anticipated loss of major functional domain due to fusion event.CPSF6-CDK13 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.
CPSF6-CDK13 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
HgeneCPSF6

GO:0006397

mRNA processing

14690600

HgeneCPSF6

GO:0051262

protein tetramerization

20695905

HgeneCPSF6

GO:0051290

protein heterotetramerization

23187700

HgeneCPSF6

GO:1990120

messenger ribonucleoprotein complex assembly

29276085

TgeneCDK13

GO:0070816

phosphorylation of RNA polymerase II C-terminal domain

20952539


check buttonFusion gene breakpoints across CPSF6 (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 CDK13 (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
ChimerDB4STADTCGA-D7-8574-01ACPSF6chr12

69656342

+CDK13chr7

40027198

+


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Fusion Gene ORF analysis for CPSF6-CDK13

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-3CDSENST00000266679ENST00000181839CPSF6chr12

69656342

+CDK13chr7

40027198

+
3UTR-3CDSENST00000266679ENST00000340829CPSF6chr12

69656342

+CDK13chr7

40027198

+
3UTR-3CDSENST00000435070ENST00000181839CPSF6chr12

69656342

+CDK13chr7

40027198

+
3UTR-3CDSENST00000435070ENST00000340829CPSF6chr12

69656342

+CDK13chr7

40027198

+
3UTR-3CDSENST00000456847ENST00000181839CPSF6chr12

69656342

+CDK13chr7

40027198

+
3UTR-3CDSENST00000456847ENST00000340829CPSF6chr12

69656342

+CDK13chr7

40027198

+
3UTR-intronENST00000266679ENST00000484589CPSF6chr12

69656342

+CDK13chr7

40027198

+
3UTR-intronENST00000435070ENST00000484589CPSF6chr12

69656342

+CDK13chr7

40027198

+
3UTR-intronENST00000456847ENST00000484589CPSF6chr12

69656342

+CDK13chr7

40027198

+
5CDS-intronENST00000551516ENST00000484589CPSF6chr12

69656342

+CDK13chr7

40027198

+
In-frameENST00000551516ENST00000181839CPSF6chr12

69656342

+CDK13chr7

40027198

+
In-frameENST00000551516ENST00000340829CPSF6chr12

69656342

+CDK13chr7

40027198

+
intron-3CDSENST00000550987ENST00000181839CPSF6chr12

69656342

+CDK13chr7

40027198

+
intron-3CDSENST00000550987ENST00000340829CPSF6chr12

69656342

+CDK13chr7

40027198

+
intron-intronENST00000550987ENST00000484589CPSF6chr12

69656342

+CDK13chr7

40027198

+

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)
ENST00000551516CPSF6chr1269656342+ENST00000181839CDK13chr740027198+5654172534991164
ENST00000551516CPSF6chr1269656342+ENST00000340829CDK13chr740027198+3895172533191104

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
ENST00000551516ENST00000181839CPSF6chr1269656342+CDK13chr740027198+0.0001807560.9998192
ENST00000551516ENST00000340829CPSF6chr1269656342+CDK13chr740027198+0.0005141250.99948585

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Fusion Genomic Features for CPSF6-CDK13


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)
CPSF6chr1269656342+CDK13chr740027197+5.37E-091
CPSF6chr1269656342+CDK13chr740027197+5.37E-091

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

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 CPSF6-CDK13


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/chr12:69656342/chr7:40027198)
- 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
HgeneCPSF6chr12:69656342chr7:40027198ENST00000266679+1011208_398590701.3333333333334Compositional biasNote=Pro-rich
HgeneCPSF6chr12:69656342chr7:40027198ENST00000266679+1011490_551590701.3333333333334Compositional biasNote=Arg-rich
HgeneCPSF6chr12:69656342chr7:40027198ENST00000435070+910208_3985532111.0Compositional biasNote=Pro-rich
HgeneCPSF6chr12:69656342chr7:40027198ENST00000435070+910490_5515532111.0Compositional biasNote=Arg-rich
HgeneCPSF6chr12:69656342chr7:40027198ENST00000266679+1011202_206590701.3333333333334MotifGAR
HgeneCPSF6chr12:69656342chr7:40027198ENST00000435070+910202_2065532111.0MotifGAR
HgeneCPSF6chr12:69656342chr7:40027198ENST00000266679+1011358_551590701.3333333333334Region(Microbial infection) Binds to HIV-1 capsid protein p24 (CA)
HgeneCPSF6chr12:69656342chr7:40027198ENST00000266679+1011404_551590701.3333333333334RegionSufficient for nuclear speckle localization
HgeneCPSF6chr12:69656342chr7:40027198ENST00000266679+1011405_551590701.3333333333334RegionNecessary for RNA-binding
HgeneCPSF6chr12:69656342chr7:40027198ENST00000266679+1011510_551590701.3333333333334RegionSufficient for nuclear targeting
HgeneCPSF6chr12:69656342chr7:40027198ENST00000266679+101181_161590701.3333333333334RegionNecessary for nuclear paraspeckles localization
HgeneCPSF6chr12:69656342chr7:40027198ENST00000435070+910358_5515532111.0Region(Microbial infection) Binds to HIV-1 capsid protein p24 (CA)
HgeneCPSF6chr12:69656342chr7:40027198ENST00000435070+910404_5515532111.0RegionSufficient for nuclear speckle localization
HgeneCPSF6chr12:69656342chr7:40027198ENST00000435070+910405_5515532111.0RegionNecessary for RNA-binding
HgeneCPSF6chr12:69656342chr7:40027198ENST00000435070+910510_5515532111.0RegionSufficient for nuclear targeting
HgeneCPSF6chr12:69656342chr7:40027198ENST00000435070+91081_1615532111.0RegionNecessary for nuclear paraspeckles localization
TgeneCDK13chr12:69656342chr7:40027198ENST00000181839014705_9984031513.0DomainProtein kinase
TgeneCDK13chr12:69656342chr7:40027198ENST00000340829014705_9984031453.0DomainProtein kinase
TgeneCDK13chr12:69656342chr7:40027198ENST00000181839014711_7194031513.0Nucleotide bindingATP
TgeneCDK13chr12:69656342chr7:40027198ENST00000340829014711_7194031453.0Nucleotide bindingATP

- 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 CPSF6-CDK13


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.
>19142_19142_1_CPSF6-CDK13_CPSF6_chr12_69656342_ENST00000551516_CDK13_chr7_40027198_ENST00000181839_length(transcript)=5654nt_BP=172nt
GGAAGATGGCGGACGGCGTGGACCACATAGACATTTACGCGGATGTCGGCGAAGAGTTCAACCAGGAAGCTGAATATGAGAGAGAAGCAG
AGAACGAGAGAGGCACCGGGATCGTGACCGAGACCGTGACCGAGAGCGTGACCGAGAGCGCGAATATCGTCATCGTTAGAAGACGGTCTG
GAAAATCCCGAAGCAGAAGCCCGTATTCATCTAGGCATTCAAGATCTCGTAGCAGGCACAGATTGTCTAGATCCAGAAGTCGTCATTCTA
GTATTTCTCCTAGCACACTAACTCTGAAGAGTAGCCTGGCAGCTGAATTGAACAAGAATAAAAAAGCACGAGCAGCAGAGGCAGCAAGAG
CCGCAGAAGCAGCGAAAGCTGCAGAAGCAACTAAGGCTGCTGAGGCTGCTGCCAAGGCTGCAAAAGCTTCAAACACTTCTACACCTACCA
AGGGGAACACGGAAACTAGTGCCAGTGCATCACAAACAAACCATGTGAAGGATGTGAAGAAAATTAAAATTGAACATGCACCTTCTCCCT
CAAGTGGTGGAACTTTAAAAAATGACAAAGCAAAAACAAAGCCACCTCTTCAGGTAACGAAGGTGGAAAATAATTTGATTGTAGATAAAG
CCACCAAGAAAGCAGTCATAGTTGGAAAGGAGAGTAAATCTGCTGCTACAAAGGAGGAATCAGTATCTCTTAAAGAGAAAACCAAACCAC
TTACACCAAGCATAGGAGCCAAGGAGAAGGAGCAACATGTAGCTTTAGTCACCTCTACATTACCACCGTTACCTTTGCCTCCCATGCTGC
CTGAAGATAAAGAAGCTGATAGCTTACGAGGAAATATTTCAGTAAAAGCAGTTAAAAAAGAAGTAGAAAAGAAACTCCGATGTCTTCTTG
CTGATTTACCGCTGCCCCCTGAGCTACCAGGAGGAGATGATCTTTCAAAGAGTCCAGAGGAAAAGAAAACAGCAACACAGTTACATAGTA
AAAGGAGGCCTAAAATATGTGGGCCTCGCTATGGTGAAACCAAAGAAAAAGATATTGACTGGGGAAAACGCTGCGTGGATAAATTTGATA
TCATCGGAATTATTGGAGAAGGTACTTACGGACAAGTTTACAAAGCCAGGGATAAAGACACTGGAGAAATGGTAGCCTTAAAAAAAGTAC
GTCTGGATAATGAAAAGGAAGGCTTTCCAATTACAGCAATTCGAGAAATTAAAATTCTCCGGCAGCTTACCCATCAGAGTATTATCAATA
TGAAGGAAATAGTGACTGATAAAGAAGATGCTTTGGATTTCAAGAAGGACAAAGGTGCATTTTATCTGGTGTTTGAATATATGGACCATG
ATCTGATGGGACTACTGGAATCAGGCTTGGTTCATTTTAATGAAAATCACATAAAGTCATTTATGAGACAGCTCATGGAGGGTCTGGATT
ATTGTCATAAGAAGAACTTTTTGCATAGAGATATTAAATGTTCCAATATCCTTCTAAATAATAGAGGGCAGATAAAACTTGCAGACTTTG
GACTTGCTCGATTGTATAGCTCAGAAGAAAGTCGGCCGTATACTAACAAGGTAATTACTTTATGGTACCGTCCACCTGAACTGCTACTGG
GAGAAGAACGATACACACCAGCCATTGATGTATGGAGCTGTGGCTGTATCCTTGGCGAACTCTTCACTAAAAAACCTATATTTCAAGCAA
ATCAGGAACTTGCACAACTAGAATTAATAAGCCGAATATGTGGGAGTCCATGTCCTGCAGTGTGGCCTGATGTAATCAAACTACCATATT
TCAACACCATGAAACCAAAGAAGCAATATCGTCGAAAGTTAAGAGAAGAATTTGTTTTTATTCCTGCAGCTGCGCTAGACTTATTTGATT
ACATGCTTGCCTTGGATCCTAGTAAGCGCTGCACTGCTGAACAGGCTCTTCAGTGCGAGTTCCTCCGAGATGTGGAACCCTCAAAAATGC
CTCCACCAGATCTCCCTTTATGGCAAGATTGTCATGAGTTATGGAGTAAAAAGCGAAGAAGACAGAAGCAGATGGGCATGACTGATGATG
TTTCCACAATTAAAGCCCCCAGGAAGGACTTGTCTCTGGGCTTGGATGACAGCAGAACCAACACACCCCAGGGTGTGCTGCCATCTTCAC
AGCTGAAATCTCAGGGCAGCTCAAATGTGGCACCTGTAAAAACAGGCCCTGGACAGCACTTAAACCACAGTGAATTGGCAATTCTACTAA
ACCTACTACAATCTAAAACAAGTGTTAATATGGCTGATTTTGTCCAAGTGTTGAACATTAAGGTAAACTCTGAGACTCAACAGCAGCTAA
ATAAAATAAACCTTCCTGCTGGAATTTTGGCAACAGGTGAAAAACAGACAGATCCATCAACACCACAACAGGAGTCTTCGAAACCGTTGG
GAGGAATTCAGCCTTCTTCTCAGACCATCCAGCCTAAAGTGGAGACTGATGCTGCCCAGGCGGCTGTGCAGAGTGCATTTGCAGTTCTGT
TGACTCAGTTAATAAAGGCTCAGCAGTCAAAGCAGAAAGATGTGCTACTAGAAGAGAGGGAAAATGGATCGGGACATGAAGCGTCATTAC
AACTCAGGCCACCTCCAGAACCTAGCACTCCGGTGTCGGGACAAGATGACCTCATCCAGCATCAAGATATGAGGATCTTGGAGCTAACGC
CAGAACCAGACCGGCCTCGAATTCTGCCTCCTGACCAACGACCTCCCGAGCCTCCTGAACCACCACCAGTCACTGAGGAAGATCTAGATT
ATCGGACAGAAAACCAGCATGTACCCACCACCAGTTCTTCATTAACTGACCCTCATGCCGGAGTGAAGGCAGCCCTGTTACAGCTGCTTG
CTCAGCATCAGCCCCAGGATGACCCCAAAAGAGAAGGTGGGATTGATTATCAAGCAGGAGACACTTACGTGTCCACTTCAGACTACAAGG
ACAACTTTGGATCCTCTTCTTTCTCTTCTGCTCCTTATGTTAGCAATGATGGTCTAGGAAGCAGTTCTGCTCCACCACTAGAACGACGTA
GTTTCATTGGAAATTCAGATATTCAGTCTTTGGATAACTACAGTACTGCTTCATCTCATTCTGGTGGTCCACCTCAGCCTTCTGCCTTTT
CTGAGTCATTTCCCAGTTCAGTAGCTGGATATGGAGACATTTACCTCAATGCTGGTCCCATGTTGTTTAGTGGAGACAAGGACCATAGAT
TTGAATATAGCCATGGTCCTATTGCAGTCCTGGCAAACAGCAGTGACCCTTCCACGGGGCCAGAGAGTACTCATCCTTTGCCAGCAAAGA
TGCACAACTATAACTATGGTGGTAACTTACAGGAAAATCCGAGTGGCCCCAGCCTCATGCATGGACAGACCTGGACTTCTCCTGCCCAAG
GACCTGGATATTCACAAGGATACAGGGGACATATTAGCACATCAACTGGCAGAGGCAGAGGCAGAGGGTTACCATACTGAGTATCTGTTT
TTCCTCAGGCACATCATTTTTATCTGGAAAGACTTTTCTAGCTGCAATTTAAGGCAGCAATCCAAGAGACTTGAATAATAATAATTCAAC
AACAGCTTTATTTTTATGTGGAGAAGGGTCTTGCATACAATAGTTTAAAAAAGACAAAAAAAACCTTTGCTTAAATTCATGCTGTTCTAA
AAACTAGATCGATTGTACATCTTCACAAATTCTAGTTAACAATTTTATTTTGTATTCTTGCAGTTTTAAGTGGATGCTAATTTTAGGGGC
ATAAGCCTTTTATGGCCCTCTTGCAGATCTTCTGAACTATGCACATTTGTGCTTTTTTTGTAAGTTTGGACCAACTTTTATGTAACAAAC
AGCCCCTCCCCACCTCCAGTTTTACAACAATCAGAAAGGGCACTGATTTATTTGGTATTTTTCTTTTTACAAAGCTACCTTTAGTCAAAG
GTCACTGTCAGTCTTTGCACCTGCTTTCAGTGTTATTGTGAAAGGTGTACTTTGTGCTCATTTCAGAAAATAAAACACAACCTTTCTCTT
GATGCAACAGTTTTATAAAAAAAAAAATGGTCAACGTTATTTTTGTTTTGTTTTGCAGATTATCAAAGCCTAGCAAAATGCATTTAAATG
AAATAGTGGGTTTTATATGAAAACTATGGGTGGGGTGGGGAGGGAAAGTAAGTGCCTTAACAGGTAAGCTTAAGGTCTGAAAAAAATAGT
TAACTTTTACCCCCATTTGTCTTTTAAAGGGAATCAATGCATTAAAAAGGCAAGAAACTCTGAAGTTTCAGGGGCTGCCTGTTCAGTTCC
TGTTAGGTCCATTCCCTCTGCTTGTCACACTTTCTCCTTTTCTGCCTGTCTTTGGGCTGTGTTGCCTTTCACTACCACCTTCTCTTGATA
GGGGAGTGAGAGCAAAGAAAGGGAGTAGAACTGCAATCAGTACATATTGTTTGAGAAGTTCTACAAAGTTTTGTCATTTAAATGGTTGAA
AGTAATAGCTCCAGGAGAATTTTAGAGTACCATTTTCTTTCAGGCTGCCATATTATCCCTGTTTCCATTTGCCATGGATAATTGGAGGGT
CATGGTATAGAAGCAAGAGTTAATAACAGAACTTGCCTAAATGTGTTAAAGTTCATGGGGGAGGGGTGGCAAATACCGTATTTTAAGTTA
TGCAATTGCCCTTTTAAGAAAGTCAATTCTATTCACTTGTTAACTAGAAACATTGCTTAGATTGAATTTATTGAAGCAAAAAGAAAAGGC
AATGAGAGAGAACTTTTATCTTCCTTCCTGTCACATTCTGTAAAGTTGATTATGACTTCTGCCAGACTTAGAGCAACAACTTTAGTTCAT
TTTAACATTTTTTTTTAATGAAGAGCATCAAAGAATGGAGTAGTCCTTATTTAAACTGTAATGGTGTCAAGTCTCACTGTGTGCACACTC
TCACACATACACACACAATTATACTAATTCTAGAAAGGAACCAAAGGTAAATAACCAGTGTTTCCATTATCACTAAATGGAAAAATTGAC
TGGAAGTTAGAGTTGTGCCAATTAATCATTTTGTTCATCAACTGTTCTGGTAACTTATTTTTTTTTATTGGAATCTTAAATTGGAACAAC
TGTTACAGAATGTATATTGCTCCAGTTCTAAAGCCAGTTAACCCTGTGCCCTCTAACTTATGAACCTTCATTTCAAAACAGTATGTGGGA
AGTCCTGTAGTTTGATAAGAGTAAAATTATTTTAAAGAGGATAATTTACCATTTTACTACTATAAAATAAGTTGATATCAGTTGACCATT
TTATTTTTTGATGGACTCTTTTTGTTGGGAGAAAGAAATGAATGGAAGAAAAAAATATGTTGCTTTTATTTGAATATTGATTACTAACAA
CTTATAAACTACATTGCAGGAAATGAAGAAATATTTTGAAATTAGCAAAATAGCAACAGTATTCAAGTATCTGAAATTTTAATATGGTGA
GTCTTAGAGCTTTAGACTTTCCTATAAGTGACAGTATCTAAGTTATTCTTAATAGTCACACTTGATAATTCTGCTGACCATAAGCAGCTA

>19142_19142_1_CPSF6-CDK13_CPSF6_chr12_69656342_ENST00000551516_CDK13_chr7_40027198_ENST00000181839_length(amino acids)=1164AA_BP=71
MADGVDHIDIYADVGEEFNQEAEYEREAENERGTGIVTETVTESVTESANIVIVRRRSGKSRSRSPYSSRHSRSRSRHRLSRSRSRHSSI
SPSTLTLKSSLAAELNKNKKARAAEAARAAEAAKAAEATKAAEAAAKAAKASNTSTPTKGNTETSASASQTNHVKDVKKIKIEHAPSPSS
GGTLKNDKAKTKPPLQVTKVENNLIVDKATKKAVIVGKESKSAATKEESVSLKEKTKPLTPSIGAKEKEQHVALVTSTLPPLPLPPMLPE
DKEADSLRGNISVKAVKKEVEKKLRCLLADLPLPPELPGGDDLSKSPEEKKTATQLHSKRRPKICGPRYGETKEKDIDWGKRCVDKFDII
GIIGEGTYGQVYKARDKDTGEMVALKKVRLDNEKEGFPITAIREIKILRQLTHQSIINMKEIVTDKEDALDFKKDKGAFYLVFEYMDHDL
MGLLESGLVHFNENHIKSFMRQLMEGLDYCHKKNFLHRDIKCSNILLNNRGQIKLADFGLARLYSSEESRPYTNKVITLWYRPPELLLGE
ERYTPAIDVWSCGCILGELFTKKPIFQANQELAQLELISRICGSPCPAVWPDVIKLPYFNTMKPKKQYRRKLREEFVFIPAAALDLFDYM
LALDPSKRCTAEQALQCEFLRDVEPSKMPPPDLPLWQDCHELWSKKRRRQKQMGMTDDVSTIKAPRKDLSLGLDDSRTNTPQGVLPSSQL
KSQGSSNVAPVKTGPGQHLNHSELAILLNLLQSKTSVNMADFVQVLNIKVNSETQQQLNKINLPAGILATGEKQTDPSTPQQESSKPLGG
IQPSSQTIQPKVETDAAQAAVQSAFAVLLTQLIKAQQSKQKDVLLEERENGSGHEASLQLRPPPEPSTPVSGQDDLIQHQDMRILELTPE
PDRPRILPPDQRPPEPPEPPPVTEEDLDYRTENQHVPTTSSSLTDPHAGVKAALLQLLAQHQPQDDPKREGGIDYQAGDTYVSTSDYKDN
FGSSSFSSAPYVSNDGLGSSSAPPLERRSFIGNSDIQSLDNYSTASSHSGGPPQPSAFSESFPSSVAGYGDIYLNAGPMLFSGDKDHRFE

--------------------------------------------------------------
>19142_19142_2_CPSF6-CDK13_CPSF6_chr12_69656342_ENST00000551516_CDK13_chr7_40027198_ENST00000340829_length(transcript)=3895nt_BP=172nt
GGAAGATGGCGGACGGCGTGGACCACATAGACATTTACGCGGATGTCGGCGAAGAGTTCAACCAGGAAGCTGAATATGAGAGAGAAGCAG
AGAACGAGAGAGGCACCGGGATCGTGACCGAGACCGTGACCGAGAGCGTGACCGAGAGCGCGAATATCGTCATCGTTAGAAGACGGTCTG
GAAAATCCCGAAGCAGAAGCCCGTATTCATCTAGGCATTCAAGATCTCGTAGCAGGCACAGATTGTCTAGATCCAGAAGTCGTCATTCTA
GTATTTCTCCTAGCACACTAACTCTGAAGAGTAGCCTGGCAGCTGAATTGAACAAGAATAAAAAAGCACGAGCAGCAGAGGCAGCAAGAG
CCGCAGAAGCAGCGAAAGCTGCAGAAGCAACTAAGGCTGCTGAGGCTGCTGCCAAGGCTGCAAAAGCTTCAAACACTTCTACACCTACCA
AGGGGAACACGGAAACTAGTGCCAGTGCATCACAAACAAACCATGTGAAGGATGTGAAGAAAATTAAAATTGAACATGCACCTTCTCCCT
CAAGTGGTGGAACTTTAAAAAATGACAAAGCAAAAACAAAGCCACCTCTTCAGGTAACGAAGGTGGAAAATAATTTGATTGTAGATAAAG
CCACCAAGAAAGCAGTCATAGTTGGAAAGGAGAGTAAATCTGCTGCTACAAAGGAGGAATCAGTATCTCTTAAAGAGAAAACCAAACCAC
TTACACCAAGCATAGGAGCCAAGGAGAAGGAGCAACATGTAGCTTTAGTCACCTCTACATTACCACCGTTACCTTTGCCTCCCATGCTGC
CTGAAGATAAAGAAGCTGATAGCTTACGAGGAAATATTTCAGTAAAAGCAGTTAAAAAAGAAGTAGAAAAGAAACTCCGATGTCTTCTTG
CTGATTTACCGCTGCCCCCTGAGCTACCAGGAGGAGATGATCTTTCAAAGAGTCCAGAGGAAAAGAAAACAGCAACACAGTTACATAGTA
AAAGGAGGCCTAAAATATGTGGGCCTCGCTATGGTGAAACCAAAGAAAAAGATATTGACTGGGGAAAACGCTGCGTGGATAAATTTGATA
TCATCGGAATTATTGGAGAAGGTACTTACGGACAAGTTTACAAAGCCAGGGATAAAGACACTGGAGAAATGGTAGCCTTAAAAAAAGTAC
GTCTGGATAATGAAAAGGAAGGCTTTCCAATTACAGCAATTCGAGAAATTAAAATTCTCCGGCAGCTTACCCATCAGAGTATTATCAATA
TGAAGGAAATAGTGACTGATAAAGAAGATGCTTTGGATTTCAAGAAGGACAAAGGTGCATTTTATCTGGTGTTTGAATATATGGACCATG
ATCTGATGGGACTACTGGAATCAGGCTTGGTTCATTTTAATGAAAATCACATAAAGTCATTTATGAGACAGCTCATGGAGGGTCTGGATT
ATTGTCATAAGAAGAACTTTTTGCATAGAGATATTAAATGTTCCAATATCCTTCTAAATAATAGAGGGCAGATAAAACTTGCAGACTTTG
GACTTGCTCGATTGTATAGCTCAGAAGAAAGTCGGCCGTATACTAACAAGGTAATTACTTTATGGTACCGTCCACCTGAACTGCTACTGG
GAGAAGAACGATACACACCAGCCATTGATGTATGGAGCTGTGGCTGTATCCTTGGCGAACTCTTCACTAAAAAACCTATATTTCAAGCAA
ATCAGGAACTTGCACAACTAGAATTAATAAGCCGAATATGTGGGAGTCCATGTCCTGCAGTGTGGCCTGATGTAATCAAACTACCATATT
TCAACACCATGAAACCAAAGAAGCAATATCGTCGAAAGTTAAGAGAAGAATTTGTTTTTATTCCTGCAGCTGCGCTAGACTTATTTGATT
ACATGCTTGCCTTGGATCCTAGTAAGCGCTGCACTGCTGAACAGGCTCTTCAGTGCGAGTTCCTCCGAGATGTGGAACCCTCAAAAATGC
CTCCACCAGATCTCCCTTTATGGCAAGATTGTCATGAGTTATGGAGTAAAAAGCGAAGAAGACAGAAGCAGATGGGCATGACTGATGATG
TTTCCACAATTAAAGCCCCCAGGAAGGACTTGTCTCTGGGCTTGGATGACAGCAGAACCAACACACCCCAGGGTGTGCTGCCATCTTCAC
AGCTGAAATCTCAGGGCAGCTCAAATGTGGCACCTGGTGAAAAACAGACAGATCCATCAACACCACAACAGGAGTCTTCGAAACCGTTGG
GAGGAATTCAGCCTTCTTCTCAGACCATCCAGCCTAAAGTGGAGACTGATGCTGCCCAGGCGGCTGTGCAGAGTGCATTTGCAGTTCTGT
TGACTCAGTTAATAAAGGCTCAGCAGTCAAAGCAGAAAGATGTGCTACTAGAAGAGAGGGAAAATGGATCGGGACATGAAGCGTCATTAC
AACTCAGGCCACCTCCAGAACCTAGCACTCCGGTGTCGGGACAAGATGACCTCATCCAGCATCAAGATATGAGGATCTTGGAGCTAACGC
CAGAACCAGACCGGCCTCGAATTCTGCCTCCTGACCAACGACCTCCCGAGCCTCCTGAACCACCACCAGTCACTGAGGAAGATCTAGATT
ATCGGACAGAAAACCAGCATGTACCCACCACCAGTTCTTCATTAACTGACCCTCATGCCGGAGTGAAGGCAGCCCTGTTACAGCTGCTTG
CTCAGCATCAGCCCCAGGATGACCCCAAAAGAGAAGGTGGGATTGATTATCAAGCAGGAGACACTTACGTGTCCACTTCAGACTACAAGG
ACAACTTTGGATCCTCTTCTTTCTCTTCTGCTCCTTATGTTAGCAATGATGGTCTAGGAAGCAGTTCTGCTCCACCACTAGAACGACGTA
GTTTCATTGGAAATTCAGATATTCAGTCTTTGGATAACTACAGTACTGCTTCATCTCATTCTGGTGGTCCACCTCAGCCTTCTGCCTTTT
CTGAGTCATTTCCCAGTTCAGTAGCTGGATATGGAGACATTTACCTCAATGCTGGTCCCATGTTGTTTAGTGGAGACAAGGACCATAGAT
TTGAATATAGCCATGGTCCTATTGCAGTCCTGGCAAACAGCAGTGACCCTTCCACGGGGCCAGAGAGTACTCATCCTTTGCCAGCAAAGA
TGCACAACTATAACTATGGTGGTAACTTACAGGAAAATCCGAGTGGCCCCAGCCTCATGCATGGACAGACCTGGACTTCTCCTGCCCAAG
GACCTGGATATTCACAAGGATACAGGGGACATATTAGCACATCAACTGGCAGAGGCAGAGGCAGAGGGTTACCATACTGAGTATCTGTTT
TTCCTCAGGCACATCATTTTTATCTGGAAAGACTTTTCTAGCTGCAATTTAAGGCAGCAATCCAAGAGACTTGAATAATAATAATTCAAC
AACAGCTTTATTTTTATGTGGAGAAGGGTCTTGCATACAATAGTTTAAAAAAGACAAAAAAAACCTTTGCTTAAATTCATGCTGTTCTAA
AAACTAGATCGATTGTACATCTTCACAAATTCTAGTTAACAATTTTATTTTGTATTCTTGCAGTTTTAAGTGGATGCTAATTTTAGGGGC
ATAAGCCTTTTATGGCCCTCTTGCAGATCTTCTGAACTATGCACATTTGTGCTTTTTTTGTAAGTTTGGACCAACTTTTATGTAACAAAC
AGCCCCTCCCCACCTCCAGTTTTACAACAATCAGAAAGGGCACTGATTTATTTGGTATTTTTCTTTTTACAAAGCTACCTTTAGTCAAAG
GTCACTGTCAGTCTTTGCACCTGCTTTCAGTGTTATTGTGAAAGGTGTACTTTGTGCTCATTTCAGAAAATAAAACACAACCTTTCTCTT

>19142_19142_2_CPSF6-CDK13_CPSF6_chr12_69656342_ENST00000551516_CDK13_chr7_40027198_ENST00000340829_length(amino acids)=1104AA_BP=71
MADGVDHIDIYADVGEEFNQEAEYEREAENERGTGIVTETVTESVTESANIVIVRRRSGKSRSRSPYSSRHSRSRSRHRLSRSRSRHSSI
SPSTLTLKSSLAAELNKNKKARAAEAARAAEAAKAAEATKAAEAAAKAAKASNTSTPTKGNTETSASASQTNHVKDVKKIKIEHAPSPSS
GGTLKNDKAKTKPPLQVTKVENNLIVDKATKKAVIVGKESKSAATKEESVSLKEKTKPLTPSIGAKEKEQHVALVTSTLPPLPLPPMLPE
DKEADSLRGNISVKAVKKEVEKKLRCLLADLPLPPELPGGDDLSKSPEEKKTATQLHSKRRPKICGPRYGETKEKDIDWGKRCVDKFDII
GIIGEGTYGQVYKARDKDTGEMVALKKVRLDNEKEGFPITAIREIKILRQLTHQSIINMKEIVTDKEDALDFKKDKGAFYLVFEYMDHDL
MGLLESGLVHFNENHIKSFMRQLMEGLDYCHKKNFLHRDIKCSNILLNNRGQIKLADFGLARLYSSEESRPYTNKVITLWYRPPELLLGE
ERYTPAIDVWSCGCILGELFTKKPIFQANQELAQLELISRICGSPCPAVWPDVIKLPYFNTMKPKKQYRRKLREEFVFIPAAALDLFDYM
LALDPSKRCTAEQALQCEFLRDVEPSKMPPPDLPLWQDCHELWSKKRRRQKQMGMTDDVSTIKAPRKDLSLGLDDSRTNTPQGVLPSSQL
KSQGSSNVAPGEKQTDPSTPQQESSKPLGGIQPSSQTIQPKVETDAAQAAVQSAFAVLLTQLIKAQQSKQKDVLLEERENGSGHEASLQL
RPPPEPSTPVSGQDDLIQHQDMRILELTPEPDRPRILPPDQRPPEPPEPPPVTEEDLDYRTENQHVPTTSSSLTDPHAGVKAALLQLLAQ
HQPQDDPKREGGIDYQAGDTYVSTSDYKDNFGSSSFSSAPYVSNDGLGSSSAPPLERRSFIGNSDIQSLDNYSTASSHSGGPPQPSAFSE
SFPSSVAGYGDIYLNAGPMLFSGDKDHRFEYSHGPIAVLANSSDPSTGPESTHPLPAKMHNYNYGGNLQENPSGPSLMHGQTWTSPAQGP

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Fusion Gene PPI Analysis for CPSF6-CDK13


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 CPSF6-CDK13


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 CPSF6-CDK13


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC4479246CONGENITAL HEART DEFECTS, DYSMORPHIC FACIAL FEATURES, AND INTELLECTUAL DEVELOPMENTAL DISORDER3CTD_human;GENOMICS_ENGLAND;UNIPROT