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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:CCDC9-NUP62 (FusionGDB2 ID:HG26093TG23636)

Fusion Gene Summary for CCDC9-NUP62

check button Fusion gene summary
Fusion gene informationFusion gene name: CCDC9-NUP62
Fusion gene ID: hg26093tg23636
HgeneTgene
Gene symbol

CCDC9

NUP62

Gene ID

26093

23636

Gene namecoiled-coil domain containing 9nucleoporin 62
Synonyms-IBSN|SNDI|p62
Cytomap('CCDC9')('NUP62')

19q13.32

19q13.33

Type of geneprotein-codingprotein-coding
Descriptioncoiled-coil domain-containing protein 9nuclear pore glycoprotein p6262 kDa nucleoporinnucleoporin 62kDnucleoporin 62kDanucleoporin Nup62
Modification date2020031320200327
UniProtAcc

Q9Y3X0

.
Ensembl transtripts involved in fusion geneENST00000221922, ENST00000601154, 
Fusion gene scores* DoF score3 X 3 X 4=363 X 1 X 3=9
# samples 63
** MAII scorelog2(6/36*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CCDC9 [Title/Abstract] AND NUP62 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCCDC9(47770049)-NUP62(50413141), # samples:3
Anticipated loss of major functional domain due to fusion event.
* 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
TgeneNUP62

GO:0006351

transcription, DNA-templated

10373430

TgeneNUP62

GO:0007166

cell surface receptor signaling pathway

10799545

TgeneNUP62

GO:0008285

negative regulation of cell proliferation

11013214

TgeneNUP62

GO:0043066

negative regulation of apoptotic process

11755531

TgeneNUP62

GO:0043069

negative regulation of programmed cell death

11244088

TgeneNUP62

GO:0043123

positive regulation of I-kappaB kinase/NF-kappaB signaling

10356400

TgeneNUP62

GO:0045893

positive regulation of transcription, DNA-templated

15625236



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
ChimerDB4BLCATCGA-FD-A6TC-01ACCDC9chr19

47770049

-NUP62chr19

50413141

-
ChimerDB4BLCATCGA-FD-A6TC-01ACCDC9chr19

47770049

+NUP62chr19

50413141

-


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Fusion Gene ORF analysis for CCDC9-NUP62

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-5UTRENST00000221922ENST00000352066CCDC9chr19

47770049

+NUP62chr19

50413141

-
5CDS-5UTRENST00000221922ENST00000413454CCDC9chr19

47770049

+NUP62chr19

50413141

-
5CDS-5UTRENST00000221922ENST00000422090CCDC9chr19

47770049

+NUP62chr19

50413141

-
5CDS-5UTRENST00000221922ENST00000596217CCDC9chr19

47770049

+NUP62chr19

50413141

-
5CDS-5UTRENST00000221922ENST00000597029CCDC9chr19

47770049

+NUP62chr19

50413141

-
5CDS-5UTRENST00000221922ENST00000597723CCDC9chr19

47770049

+NUP62chr19

50413141

-
5CDS-5UTRENST00000221922ENST00000600583CCDC9chr19

47770049

+NUP62chr19

50413141

-
intron-5UTRENST00000601154ENST00000352066CCDC9chr19

47770049

+NUP62chr19

50413141

-
intron-5UTRENST00000601154ENST00000413454CCDC9chr19

47770049

+NUP62chr19

50413141

-
intron-5UTRENST00000601154ENST00000422090CCDC9chr19

47770049

+NUP62chr19

50413141

-
intron-5UTRENST00000601154ENST00000596217CCDC9chr19

47770049

+NUP62chr19

50413141

-
intron-5UTRENST00000601154ENST00000597029CCDC9chr19

47770049

+NUP62chr19

50413141

-
intron-5UTRENST00000601154ENST00000597723CCDC9chr19

47770049

+NUP62chr19

50413141

-
intron-5UTRENST00000601154ENST00000600583CCDC9chr19

47770049

+NUP62chr19

50413141

-

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 CCDC9-NUP62


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)


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Fusion Protein Features for CCDC9-NUP62


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/:47770049/:50413141)
- 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
CCDC9

Q9Y3X0

.
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 CCDC9-NUP62


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 CCDC9-NUP62


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 CCDC9-NUP62


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 CCDC9-NUP62


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0795996STRIATONIGRAL DEGENERATION, INFANTILE (disorder)4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND