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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:GSE1-NOTCH3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: GSE1-NOTCH3
FusionPDB ID: 35011
FusionGDB2.0 ID: 42045
HgeneTgene
Gene symbol

GSE1

NOTCH3

Gene ID

23199

4854

Gene nameGse1 coiled-coil proteinnotch receptor 3
SynonymsCRHSP24|KIAA0182CADASIL|CADASIL1|CASIL|IMF2|LMNS
Cytomap

16q24.1

19p13.12

Type of geneprotein-codingprotein-coding
Descriptiongenetic suppressor element 1CTC-786C10.1Gse1 coiled-coil protein homologneurogenic locus notch homolog protein 3Notch homolog 3notch 3
Modification date2020032720200329
UniProtAcc

Q14687

Q9UM47

Ensembl transtripts involved in fusion geneENST idsENST00000253458, ENST00000393243, 
ENST00000405402, ENST00000471070, 
ENST00000263388, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score23 X 18 X 8=33124 X 5 X 5=100
# samples 236
** MAII scorelog2(23/3312*10)=-3.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/100*10)=-0.736965594166206
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: GSE1 [Title/Abstract] AND NOTCH3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)GSE1(85647004)-NOTCH3(15276902), # samples:2
Anticipated loss of major functional domain due to fusion event.GSE1-NOTCH3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
GSE1-NOTCH3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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

check buttonFusion gene breakpoints across GSE1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across NOTCH3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4LUADTCGA-05-4427-01AGSE1chr16

85647004

+NOTCH3chr19

15276902

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000253458GSE1chr1685647004+ENST00000263388NOTCH3chr1915276902-28161831611786541
ENST00000393243GSE1chr1685647004+ENST00000263388NOTCH3chr1915276902-268047251650541

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
ENST00000253458ENST00000263388GSE1chr1685647004+NOTCH3chr1915276902-0.0302209130.96977913
ENST00000393243ENST00000263388GSE1chr1685647004+NOTCH3chr1915276902-0.0288352850.9711647

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>35011_35011_1_GSE1-NOTCH3_GSE1_chr16_85647004_ENST00000253458_NOTCH3_chr19_15276902_ENST00000263388_length(amino acids)=541AA_BP=7
MRGPGMKDGFTPLMLASFCGGALEPMPTEEDEADDTSASIISDLICQGAQLGARTDRTGETALHLAARYARADAAKRLLDAGADTNAQDH
SGRTPLHTAVTADAQGVFQILIRNRSTDLDARMADGSTALILAARLAVEGMVEELIASHADVNAVDELGKSALHWAAAVNNVEATLALLK
NGANKDMQDSKEETPLFLAAREGSYEAAKLLLDHFANREITDHLDRLPRDVAQERLHQDIVRLLDQPSGPRSPPGPHGLGPLLCPPGAFL
PGLKAAQSGSKKSRRPPGKAGLGPQGPRGRGKKLTLACPGPLADSSVTLSPVDSLDSPRPFGGPPASPGGFPLEGPYAAATATAVSLAQL
GGPGRAGLGRQPPGGCVLSLGLLNPVAVPLDWARLPPPAPPGPSFLLPLAPGPQLLNPGTPVSPQERPPPYLAVPGHGEEYPAAGAHSSP
PKARFLRVPSEHPYLTPSPESPEHWASPSPPSLSDWSESTPSPATATGAMATTTGALPAQPLPLSVPSSLAQAQTQLGPQPEVTPKRQVL

--------------------------------------------------------------

>35011_35011_2_GSE1-NOTCH3_GSE1_chr16_85647004_ENST00000393243_NOTCH3_chr19_15276902_ENST00000263388_length(amino acids)=541AA_BP=7
MRGPGMKDGFTPLMLASFCGGALEPMPTEEDEADDTSASIISDLICQGAQLGARTDRTGETALHLAARYARADAAKRLLDAGADTNAQDH
SGRTPLHTAVTADAQGVFQILIRNRSTDLDARMADGSTALILAARLAVEGMVEELIASHADVNAVDELGKSALHWAAAVNNVEATLALLK
NGANKDMQDSKEETPLFLAAREGSYEAAKLLLDHFANREITDHLDRLPRDVAQERLHQDIVRLLDQPSGPRSPPGPHGLGPLLCPPGAFL
PGLKAAQSGSKKSRRPPGKAGLGPQGPRGRGKKLTLACPGPLADSSVTLSPVDSLDSPRPFGGPPASPGGFPLEGPYAAATATAVSLAQL
GGPGRAGLGRQPPGGCVLSLGLLNPVAVPLDWARLPPPAPPGPSFLLPLAPGPQLLNPGTPVSPQERPPPYLAVPGHGEEYPAAGAHSSP
PKARFLRVPSEHPYLTPSPESPEHWASPSPPSLSDWSESTPSPATATGAMATTTGALPAQPLPLSVPSSLAQAQTQLGPQPEVTPKRQVL

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Fusion Protein Functional Features


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/chr16:85647004/chr19:15276902)
- 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
GSE1

Q14687

NOTCH3

Q9UM47

FUNCTION: Functions as a receptor for membrane-bound ligands Jagged1, Jagged2 and Delta1 to regulate cell-fate determination (PubMed:15350543). Upon ligand activation through the released notch intracellular domain (NICD) it forms a transcriptional activator complex with RBPJ/RBPSUH and activates genes of the enhancer of split locus. Affects the implementation of differentiation, proliferation and apoptotic programs (By similarity). {ECO:0000250|UniProtKB:Q9R172, ECO:0000269|PubMed:15350543}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331838_18671787.33333333333332322.0RepeatNote=ANK 1
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331871_19011787.33333333333332322.0RepeatNote=ANK 2
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331905_19341787.33333333333332322.0RepeatNote=ANK 3
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331938_19671787.33333333333332322.0RepeatNote=ANK 4
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331971_20001787.33333333333332322.0RepeatNote=ANK 5

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneGSE1chr16:85647004chr19:15276902ENST00000253458+1161127_12012.33333333333333351218.0Coiled coilOntology_term=ECO:0000255
HgeneGSE1chr16:85647004chr19:15276902ENST00000253458+116321_4032.33333333333333351218.0Coiled coilOntology_term=ECO:0000255
HgeneGSE1chr16:85647004chr19:15276902ENST00000393243+1151127_12012.33333333333333351145.0Coiled coilOntology_term=ECO:0000255
HgeneGSE1chr16:85647004chr19:15276902ENST00000393243+115321_4032.33333333333333351145.0Coiled coilOntology_term=ECO:0000255
HgeneGSE1chr16:85647004chr19:15276902ENST00000405402+1151127_120101114.0Coiled coilOntology_term=ECO:0000255
HgeneGSE1chr16:85647004chr19:15276902ENST00000405402+115321_40301114.0Coiled coilOntology_term=ECO:0000255
HgeneGSE1chr16:85647004chr19:15276902ENST00000253458+1161102_11072.33333333333333351218.0Compositional biasNote=Poly-Glu
HgeneGSE1chr16:85647004chr19:15276902ENST00000253458+116532_7222.33333333333333351218.0Compositional biasNote=Pro-rich
HgeneGSE1chr16:85647004chr19:15276902ENST00000253458+116745_7482.33333333333333351218.0Compositional biasNote=Poly-Arg
HgeneGSE1chr16:85647004chr19:15276902ENST00000393243+1151102_11072.33333333333333351145.0Compositional biasNote=Poly-Glu
HgeneGSE1chr16:85647004chr19:15276902ENST00000393243+115532_7222.33333333333333351145.0Compositional biasNote=Pro-rich
HgeneGSE1chr16:85647004chr19:15276902ENST00000393243+115745_7482.33333333333333351145.0Compositional biasNote=Poly-Arg
HgeneGSE1chr16:85647004chr19:15276902ENST00000405402+1151102_110701114.0Compositional biasNote=Poly-Glu
HgeneGSE1chr16:85647004chr19:15276902ENST00000405402+115532_72201114.0Compositional biasNote=Pro-rich
HgeneGSE1chr16:85647004chr19:15276902ENST00000405402+115745_74801114.0Compositional biasNote=Poly-Arg
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331000_10341787.33333333333332322.0DomainEGF-like 26
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331036_10821787.33333333333332322.0DomainEGF-like 27
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331084_11201787.33333333333332322.0DomainEGF-like 28
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331122_11581787.33333333333332322.0DomainEGF-like 29%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331160_12031787.33333333333332322.0DomainEGF-like 30%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833119_1561787.33333333333332322.0DomainEGF-like 3
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331205_12441787.33333333333332322.0DomainEGF-like 31
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331246_12871787.33333333333332322.0DomainEGF-like 32
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331289_13251787.33333333333332322.0DomainEGF-like 33
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331335_13731787.33333333333332322.0DomainEGF-like 34
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833158_1951787.33333333333332322.0DomainEGF-like 4%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833197_2341787.33333333333332322.0DomainEGF-like 5
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833236_2721787.33333333333332322.0DomainEGF-like 6%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833274_3121787.33333333333332322.0DomainEGF-like 7
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833314_3501787.33333333333332322.0DomainEGF-like 8%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833351_3891787.33333333333332322.0DomainEGF-like 9
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833391_4291787.33333333333332322.0DomainEGF-like 10%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST00000263388283340_771787.33333333333332322.0DomainEGF-like 1
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833431_4671787.33333333333332322.0DomainEGF-like 11%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833469_5051787.33333333333332322.0DomainEGF-like 12%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833507_5431787.33333333333332322.0DomainEGF-like 13%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833545_5801787.33333333333332322.0DomainEGF-like 14%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833582_6181787.33333333333332322.0DomainEGF-like 15%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833620_6551787.33333333333332322.0DomainEGF-like 16%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833657_6931787.33333333333332322.0DomainEGF-like 17%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833695_7301787.33333333333332322.0DomainEGF-like 18
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833734_7701787.33333333333332322.0DomainEGF-like 19
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833771_8081787.33333333333332322.0DomainEGF-like 20
TgeneNOTCH3chr16:85647004chr19:15276902ENST00000263388283378_1181787.33333333333332322.0DomainEGF-like 2
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833810_8471787.33333333333332322.0DomainEGF-like 21%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833849_8851787.33333333333332322.0DomainEGF-like 22%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833887_9221787.33333333333332322.0DomainEGF-like 23%3B calcium-binding
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833924_9601787.33333333333332322.0DomainEGF-like 24
TgeneNOTCH3chr16:85647004chr19:15276902ENST000002633882833962_9981787.33333333333332322.0DomainEGF-like 25
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331387_14271787.33333333333332322.0RepeatNote=LNR 1
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331428_14581787.33333333333332322.0RepeatNote=LNR 2
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331467_15051787.33333333333332322.0RepeatNote=LNR 3
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331665_23211787.33333333333332322.0Topological domainCytoplasmic
TgeneNOTCH3chr16:85647004chr19:15276902ENST00000263388283340_16431787.33333333333332322.0Topological domainExtracellular
TgeneNOTCH3chr16:85647004chr19:15276902ENST0000026338828331644_16641787.33333333333332322.0TransmembraneHelical


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
GSE1
NOTCH3


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to GSE1-NOTCH3


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to GSE1-NOTCH3


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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