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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:CAP1-NFYC (FusionGDB2 ID:HG10487TG4802)

Fusion Gene Summary for CAP1-NFYC

check button Fusion gene summary
Fusion gene informationFusion gene name: CAP1-NFYC
Fusion gene ID: hg10487tg4802
HgeneTgene
Gene symbol

CAP1

NFYC

Gene ID

10487

4802

Gene namecyclase associated actin cytoskeleton regulatory protein 1nuclear transcription factor Y subunit gamma
SynonymsCAP|CAP1-PENCBF-C|CBFC|H1TF2A|HAP5|HSM|NF-YC
Cytomap('CAP1')('NFYC')

1p34.2

1p34.2

Type of geneprotein-codingprotein-coding
Descriptionadenylyl cyclase-associated protein 1CAP, adenylate cyclase-associated protein 1adenylate cyclase associated protein 1testis secretory sperm-binding protein Li 218pnuclear transcription factor Y subunit gammaCAAT box DNA-binding protein subunit CCCAAT binding factor subunit CCCAAT transcription binding factor subunit gammahistone H1 transcription factor large subunit 2Anuclear transcription factor Y subunit Cn
Modification date2020031320200313
UniProtAcc.

Q13952

Ensembl transtripts involved in fusion geneENST00000340450, ENST00000372792, 
ENST00000372798, ENST00000372805, 
ENST00000372797, ENST00000372802, 
ENST00000479759, 
ENST00000340450, 
ENST00000372792, ENST00000372797, 
ENST00000372798, ENST00000372802, 
ENST00000372805, ENST00000479759, 
Fusion gene scores* DoF score16 X 13 X 7=145616 X 10 X 7=1120
# samples 1918
** MAII scorelog2(19/1456*10)=-2.93793903186775
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(18/1120*10)=-2.63742992061529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CAP1 [Title/Abstract] AND NFYC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCAP1(40506473)-NFYC(41204508), # samples:2
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
TgeneNFYC

GO:0006355

regulation of transcription, DNA-templated

15243141



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-KQ-A41P-01ACAP1chr1

40506473

+NFYCchr1

41204508

+


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Fusion Gene ORF analysis for CAP1-NFYC

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
5UTR-5UTRENST00000340450ENST00000308733CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000340450ENST00000372651CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000340450ENST00000372652CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000340450ENST00000372653CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000340450ENST00000372654CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000340450ENST00000425457CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000340450ENST00000427410CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000340450ENST00000440226CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000340450ENST00000447388CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000340450ENST00000456393CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372792ENST00000308733CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372792ENST00000372651CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372792ENST00000372652CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372792ENST00000372653CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372792ENST00000372654CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372792ENST00000425457CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372792ENST00000427410CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372792ENST00000440226CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372792ENST00000447388CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372792ENST00000456393CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372798ENST00000308733CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372798ENST00000372651CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372798ENST00000372652CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372798ENST00000372653CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372798ENST00000372654CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372798ENST00000425457CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372798ENST00000427410CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372798ENST00000440226CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372798ENST00000447388CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372798ENST00000456393CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372805ENST00000308733CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372805ENST00000372651CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372805ENST00000372652CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372805ENST00000372653CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372805ENST00000372654CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372805ENST00000425457CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372805ENST00000427410CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372805ENST00000440226CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372805ENST00000447388CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-5UTRENST00000372805ENST00000456393CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-intronENST00000340450ENST00000483091CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-intronENST00000372792ENST00000483091CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-intronENST00000372798ENST00000483091CAP1chr1

40506473

+NFYCchr1

41204508

+
5UTR-intronENST00000372805ENST00000483091CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372797ENST00000308733CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372797ENST00000372651CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372797ENST00000372652CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372797ENST00000372653CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372797ENST00000372654CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372797ENST00000425457CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372797ENST00000427410CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372797ENST00000440226CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372797ENST00000447388CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372797ENST00000456393CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372802ENST00000308733CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372802ENST00000372651CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372802ENST00000372652CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372802ENST00000372653CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372802ENST00000372654CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372802ENST00000425457CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372802ENST00000427410CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372802ENST00000440226CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372802ENST00000447388CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000372802ENST00000456393CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000479759ENST00000308733CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000479759ENST00000372651CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000479759ENST00000372652CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000479759ENST00000372653CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000479759ENST00000372654CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000479759ENST00000425457CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000479759ENST00000427410CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000479759ENST00000440226CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000479759ENST00000447388CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-5UTRENST00000479759ENST00000456393CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-intronENST00000372797ENST00000483091CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-intronENST00000372802ENST00000483091CAP1chr1

40506473

+NFYCchr1

41204508

+
intron-intronENST00000479759ENST00000483091CAP1chr1

40506473

+NFYCchr1

41204508

+

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 CAP1-NFYC


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)
CAP1chr140506473+NFYCchr141204509+1.88E-060.9999981
CAP1chr140506473+NFYCchr141204509+1.88E-060.9999981


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 CAP1-NFYC


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/:40506473/:41204508)
- 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
.NFYC

Q13952

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: Component of the sequence-specific heterotrimeric transcription factor (NF-Y) which specifically recognizes a 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors.

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 CAP1-NFYC


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 CAP1-NFYC


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 CAP1-NFYC


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 CAP1-NFYC


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCAP1C0001787Osteoporosis, Age-Related1CTD_human
HgeneCAP1C0019193Hepatitis, Toxic1CTD_human
HgeneCAP1C0029456Osteoporosis1CTD_human
HgeneCAP1C0029459Osteoporosis, Senile1CTD_human
HgeneCAP1C0751406Post-Traumatic Osteoporosis1CTD_human
HgeneCAP1C0860207Drug-Induced Liver Disease1CTD_human
HgeneCAP1C1262760Hepatitis, Drug-Induced1CTD_human
HgeneCAP1C3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneCAP1C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneCAP1C4279912Chemically-Induced Liver Toxicity1CTD_human