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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-NUP93 (FusionGDB2 ID:HG11052TG9688)

Fusion Gene Summary for CPSF6-NUP93

check button Fusion gene summary
Fusion gene informationFusion gene name: CPSF6-NUP93
Fusion gene ID: hg11052tg9688
HgeneTgene
Gene symbol

CPSF6

NUP93

Gene ID

11052

9688

Gene namecleavage and polyadenylation specific factor 6nucleoporin 93
SynonymsCFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7NIC96
Cytomap('CPSF6')('NUP93')

12q15

16q13

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 nuclear pore complex protein Nup9393 kDa nucleoporinnucleoporin 93kDanucleoporin Nup93
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000266679, ENST00000435070, 
ENST00000456847, ENST00000551516, 
ENST00000550987, 
Fusion gene scores* DoF score69 X 12 X 19=1573213 X 15 X 8=1560
# samples 7117
** MAII scorelog2(71/15732*10)=-4.46973925655087
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(17/1560*10)=-3.19793937761191
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CPSF6 [Title/Abstract] AND NUP93 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCPSF6(69656342)-NUP93(56839415), # samples:2
Anticipated loss of major functional domain due to fusion event.CPSF6-NUP93 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CPSF6-NUP93 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
CPSF6-NUP93 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
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

TgeneNUP93

GO:0006998

nuclear envelope organization

26878725

TgeneNUP93

GO:0051292

nuclear pore complex assembly

26878725

TgeneNUP93

GO:0060391

positive regulation of SMAD protein signal transduction

26878725

TgeneNUP93

GO:0060395

SMAD protein signal transduction

26878725



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
ChimerDB4PRADTCGA-G9-6348CPSF6chr12

69656342

+NUP93chr16

56839415

+


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Fusion Gene ORF analysis for CPSF6-NUP93

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-3CDSENST00000266679ENST00000308159CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-3CDSENST00000266679ENST00000569842CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-3CDSENST00000435070ENST00000308159CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-3CDSENST00000435070ENST00000569842CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-3CDSENST00000456847ENST00000308159CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-3CDSENST00000456847ENST00000569842CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-3UTRENST00000266679ENST00000569595CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-3UTRENST00000435070ENST00000569595CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-3UTRENST00000456847ENST00000569595CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-5UTRENST00000266679ENST00000542526CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-5UTRENST00000266679ENST00000564887CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-5UTRENST00000435070ENST00000542526CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-5UTRENST00000435070ENST00000564887CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-5UTRENST00000456847ENST00000542526CPSF6chr12

69656342

+NUP93chr16

56839415

+
3UTR-5UTRENST00000456847ENST00000564887CPSF6chr12

69656342

+NUP93chr16

56839415

+
5CDS-3UTRENST00000551516ENST00000569595CPSF6chr12

69656342

+NUP93chr16

56839415

+
5CDS-5UTRENST00000551516ENST00000542526CPSF6chr12

69656342

+NUP93chr16

56839415

+
5CDS-5UTRENST00000551516ENST00000564887CPSF6chr12

69656342

+NUP93chr16

56839415

+
Frame-shiftENST00000551516ENST00000308159CPSF6chr12

69656342

+NUP93chr16

56839415

+
Frame-shiftENST00000551516ENST00000569842CPSF6chr12

69656342

+NUP93chr16

56839415

+
intron-3CDSENST00000550987ENST00000308159CPSF6chr12

69656342

+NUP93chr16

56839415

+
intron-3CDSENST00000550987ENST00000569842CPSF6chr12

69656342

+NUP93chr16

56839415

+
intron-3UTRENST00000550987ENST00000569595CPSF6chr12

69656342

+NUP93chr16

56839415

+
intron-5UTRENST00000550987ENST00000542526CPSF6chr12

69656342

+NUP93chr16

56839415

+
intron-5UTRENST00000550987ENST00000564887CPSF6chr12

69656342

+NUP93chr16

56839415

+

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 CPSF6-NUP93


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+NUP93chr1656839415+1.74E-101
CPSF6chr1269656342+NUP93chr1656839415+1.74E-101


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-NUP93


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/:69656342/:56839415)
- 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

- 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-NUP93


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 CPSF6-NUP93


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-NUP93


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-NUP93


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC1868672NEPHROTIC SYNDROME, STEROID-RESISTANT, AUTOSOMAL RECESSIVE1CTD_human;ORPHANET
TgeneC4225166NEPHROTIC SYNDROME, TYPE 121CTD_human;GENOMICS_ENGLAND;UNIPROT