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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:INTS6-SERPINE3 (FusionGDB2 ID:39980)

Fusion Gene Summary for INTS6-SERPINE3

check button Fusion gene summary
Fusion gene informationFusion gene name: INTS6-SERPINE3
Fusion gene ID: 39980
HgeneTgene
Gene symbol

INTS6

SERPINE3

Gene ID

26512

647174

Gene nameintegrator complex subunit 6serpin family E member 3
SynonymsDBI-1|DDX26|DDX26A|DICE1|HDB|INT6|Notchl2-
Cytomap

13q14.3

13q14.3

Type of geneprotein-codingprotein-coding
Descriptionintegrator complex subunit 6DEAD box proteinDEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26RNA helicase HDBprotein deleted in cancer 1serpin E3nexin-related serine protease inhibitorserpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 3
Modification date2020031320200313
UniProtAcc

Q9UL03

.
Ensembl transtripts involved in fusion geneENST00000311234, ENST00000398119, 
ENST00000420668, ENST00000425000, 
ENST00000442263, ENST00000463928, 
ENST00000490542, ENST00000491723, 
ENST00000497989, 		ENST00000400389, 
ENST00000521255, ENST00000524365, 
Fusion gene scores* DoF score6 X 5 X 5=1502 X 3 X 2=12
# samples 83
** MAII scorelog2(8/150*10)=-0.906890595608519
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: INTS6 [Title/Abstract] AND SERPINE3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointINTS6(51936827)-SERPINE3(51936878), # samples:1
INTS6(51936878)-SERPINE3(51936827), # samples:1
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
HgeneINTS6

GO:0016180

snRNA processing

16239144


check buttonFusion gene breakpoints across INTS6 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across SERPINE3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChiTaRS5.0N/ACD240438INTS6chr13

51936827

-SERPINE3chr13

51936878

+
ChiTaRS5.0N/ACD240450INTS6chr13

51936878

-SERPINE3chr13

51936827

+


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Fusion Gene ORF analysis for INTS6-SERPINE3

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
intron-intronENST00000311234ENST00000400389INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000311234ENST00000400389INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000311234ENST00000521255INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000311234ENST00000521255INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000311234ENST00000524365INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000311234ENST00000524365INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000398119ENST00000400389INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000398119ENST00000400389INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000398119ENST00000521255INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000398119ENST00000521255INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000398119ENST00000524365INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000398119ENST00000524365INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000420668ENST00000400389INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000420668ENST00000400389INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000420668ENST00000521255INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000420668ENST00000521255INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000420668ENST00000524365INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000420668ENST00000524365INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000425000ENST00000400389INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000425000ENST00000400389INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000425000ENST00000521255INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000425000ENST00000521255INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000425000ENST00000524365INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000425000ENST00000524365INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000442263ENST00000400389INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000442263ENST00000400389INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000442263ENST00000521255INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000442263ENST00000521255INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000442263ENST00000524365INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000442263ENST00000524365INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000463928ENST00000400389INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000463928ENST00000400389INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000463928ENST00000521255INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000463928ENST00000521255INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000463928ENST00000524365INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000463928ENST00000524365INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000490542ENST00000400389INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000490542ENST00000400389INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000490542ENST00000521255INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000490542ENST00000521255INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000490542ENST00000524365INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000490542ENST00000524365INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000491723ENST00000400389INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000491723ENST00000400389INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000491723ENST00000521255INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000491723ENST00000521255INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000491723ENST00000524365INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000491723ENST00000524365INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000497989ENST00000400389INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000497989ENST00000400389INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000497989ENST00000521255INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000497989ENST00000521255INTS6chr13

51936878

-SERPINE3chr13

51936827

+
intron-intronENST00000497989ENST00000524365INTS6chr13

51936827

-SERPINE3chr13

51936878

+
intron-intronENST00000497989ENST00000524365INTS6chr13

51936878

-SERPINE3chr13

51936827

+

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 INTS6-SERPINE3


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)

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.

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.

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Fusion Protein Features for INTS6-SERPINE3


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/:51936827/:51936878)
- 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
INTS6

Q9UL03

.
FUNCTION: Component of the Integrator (INT) complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (Probable). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). May have a tumor suppressor role; an ectopic expression suppressing tumor cell growth (PubMed:15254679, PubMed:16239144). {ECO:0000269|PubMed:15254679, ECO:0000269|PubMed:16239144, ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:16239144}.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 INTS6-SERPINE3


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 INTS6-SERPINE3


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 INTS6-SERPINE3


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 INTS6-SERPINE3


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