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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:HPCAL1-CPSF3 (FusionGDB2 ID:HG3241TG51692)

Fusion Gene Summary for HPCAL1-CPSF3

check button Fusion gene summary
Fusion gene informationFusion gene name: HPCAL1-CPSF3
Fusion gene ID: hg3241tg51692
HgeneTgene
Gene symbol

HPCAL1

CPSF3

Gene ID

3241

51692

Gene namehippocalcin like 1cleavage and polyadenylation specific factor 3
SynonymsBDR1|HLP2|VILIP-3CPSF-73|CPSF73
Cytomap('HPCAL1')('CPSF3')

2p25.1

2p25.1

Type of geneprotein-codingprotein-coding
Descriptionhippocalcin-like protein 1calcium-binding protein BDR-1visinin-like protein 3cleavage and polyadenylation specificity factor subunit 3cleavage and polyadenylation specific factor 3, 73kDamRNA 3'-end-processing endonuclease CPSF-73
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000307845, ENST00000381765, 
Fusion gene scores* DoF score7 X 5 X 3=1056 X 13 X 7=546
# samples 812
** MAII scorelog2(8/105*10)=-0.39231742277876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/546*10)=-2.18586654531133
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HPCAL1 [Title/Abstract] AND CPSF3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHPCAL1(10537046)-CPSF3(9607836), # 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
TgeneCPSF3

GO:0006398

mRNA 3'-end processing by stem-loop binding and cleavage

18688255



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
ChimerDB4BRCATCGA-A1-A0SO-01AHPCAL1chr2

10537046

-CPSF3chr2

9607836

+
ChimerDB4BRCATCGA-A1-A0SO-01AHPCAL1chr2

10537046

+CPSF3chr2

9607836

+
ChimerDB4BRCATCGA-A1-A0SOHPCAL1chr2

10537046

+CPSF3chr2

9607835

+


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Fusion Gene ORF analysis for HPCAL1-CPSF3

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-3CDSENST00000307845ENST00000238112HPCAL1chr2

10537046

+CPSF3chr2

9607836

+
5UTR-3CDSENST00000307845ENST00000238112HPCAL1chr2

10537046

+CPSF3chr2

9607835

+
5UTR-3CDSENST00000307845ENST00000460593HPCAL1chr2

10537046

+CPSF3chr2

9607836

+
5UTR-3CDSENST00000307845ENST00000460593HPCAL1chr2

10537046

+CPSF3chr2

9607835

+
5UTR-3CDSENST00000381765ENST00000238112HPCAL1chr2

10537046

+CPSF3chr2

9607836

+
5UTR-3CDSENST00000381765ENST00000238112HPCAL1chr2

10537046

+CPSF3chr2

9607835

+
5UTR-3CDSENST00000381765ENST00000460593HPCAL1chr2

10537046

+CPSF3chr2

9607836

+
5UTR-3CDSENST00000381765ENST00000460593HPCAL1chr2

10537046

+CPSF3chr2

9607835

+
5UTR-3UTRENST00000307845ENST00000489403HPCAL1chr2

10537046

+CPSF3chr2

9607836

+
5UTR-3UTRENST00000307845ENST00000489403HPCAL1chr2

10537046

+CPSF3chr2

9607835

+
5UTR-3UTRENST00000381765ENST00000489403HPCAL1chr2

10537046

+CPSF3chr2

9607836

+
5UTR-3UTRENST00000381765ENST00000489403HPCAL1chr2

10537046

+CPSF3chr2

9607835

+

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 HPCAL1-CPSF3


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)
HPCAL1chr210537046+CPSF3chr29607835+0.0021682030.99783176
HPCAL1chr210537046+CPSF3chr29607835+0.0021682030.99783176
HPCAL1chr210537046+CPSF3chr29607835+0.0021682030.99783176
HPCAL1chr210537046+CPSF3chr29607835+0.0021682030.99783176


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 HPCAL1-CPSF3


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/:10537046/:9607836)
- 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 HPCAL1-CPSF3


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 HPCAL1-CPSF3


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 HPCAL1-CPSF3


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 HPCAL1-CPSF3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHPCAL1C0023893Liver Cirrhosis, Experimental1CTD_human