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Center for Computational Systems Medicine level2
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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 Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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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:NOTCH3-DEFB132

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NOTCH3-DEFB132
FusionPDB ID: 59781
FusionGDB2.0 ID: 59781
HgeneTgene
Gene symbol

NOTCH3

DEFB132

Gene ID

4854

400830

Gene namenotch receptor 3defensin beta 132
SynonymsCADASIL|CADASIL1|CASIL|IMF2|LMNSBD-32|DEFB-32|DEFB32|HEL-75|KFLL827|UNQ827
Cytomap

19p13.12

20p13

Type of geneprotein-codingprotein-coding
Descriptionneurogenic locus notch homolog protein 3Notch homolog 3notch 3beta-defensin 132RP5-1103G7.6beta-defensin 32defensin HEL-75defensin, beta 32
Modification date2020032920200313
UniProtAcc

Q9UM47

.
Ensembl transtripts involved in fusion geneENST idsENST00000263388, ENST00000382376, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 17 X 11=28051 X 1 X 1=1
# samples 181
** MAII scorelog2(18/2805*10)=-3.96193195916648
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context (manual curation of fusion genes in FusionPDB)

PubMed: NOTCH3 [Title/Abstract] AND DEFB132 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NOTCH3(15278060)-DEFB132(239718), # samples:2
Anticipated loss of major functional domain due to fusion event.NOTCH3-DEFB132 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.
NOTCH3-DEFB132 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
TgeneDEFB132

GO:0031640

killing of cells of other organism

18343807


check buttonFusion gene breakpoints across NOTCH3 (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 DEFB132 (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
ChimerDB4LUSCTCGA-34-5236-01ANOTCH3chr19

15278060

-DEFB132chr20

239718

+
ChimerDB4LUSCTCGA-34-5236NOTCH3chr19

15278060

-DEFB132chr20

239718

+


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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)
ENST00000263388NOTCH3chr1915278060-ENST00000382376DEFB132chr20239718+745854387656671863

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
ENST00000263388ENST00000382376NOTCH3chr1915278060-DEFB132chr20239718+0.0018978810.9981021

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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

>59781_59781_1_NOTCH3-DEFB132_NOTCH3_chr19_15278060_ENST00000263388_DEFB132_chr20_239718_ENST00000382376_length(amino acids)=1863AA_BP=1787
MGPGARGRRRRRRPMSPPPPPPPVRALPLLLLLAGPGAAAPPCLDGSPCANGGRCTQLPSREAACLCPPGWVGERCQLEDPCHSGPCAGR
GVCQSSVVAGTARFSCRCPRGFRGPDCSLPDPCLSSPCAHGARCSVGPDGRFLCSCPPGYQGRSCRSDVDECRVGEPCRHGGTCLNTPGS
FRCQCPAGYTGPLCENPAVPCAPSPCRNGGTCRQSGDLTYDCACLPGFEGQNCEVNVDDCPGHRCLNGGTCVDGVNTYNCQCPPEWTGQF
CTEDVDECQLQPNACHNGGTCFNTLGGHSCVCVNGWTGESCSQNIDDCATAVCFHGATCHDRVASFYCACPMGKTGLLCHLDDACVSNPC
HEDAICDTNPVNGRAICTCPPGFTGGACDQDVDECSIGANPCEHLGRCVNTQGSFLCQCGRGYTGPRCETDVNECLSGPCRNQATCLDRI
GQFTCICMAGFTGTYCEVDIDECQSSPCVNGGVCKDRVNGFSCTCPSGFSGSTCQLDVDECASTPCRNGAKCVDQPDGYECRCAEGFEGT
LCDRNVDDCSPDPCHHGRCVDGIASFSCACAPGYTGTRCESQVDECRSQPCRHGGKCLDLVDKYLCRCPSGTTGVNCEVNIDDCASNPCT
FGVCRDGINRYDCVCQPGFTGPLCNVEINECASSPCGEGGSCVDGENGFRCLCPPGSLPPLCLPPSHPCAHEPCSHGICYDAPGGFRCVC
EPGWSGPRCSQSLARDACESQPCRAGGTCSSDGMGFHCTCPPGVQGRQCELLSPCTPNPCEHGGRCESAPGQLPVCSCPQGWQGPRCQQD
VDECAGPAPCGPHGICTNLAGSFSCTCHGGYTGPSCDQDINDCDPNPCLNGGSCQDGVGSFSCSCLPGFAGPRCARDVDECLSNPCGPGT
CTDHVASFTCTCPPGYGGFHCEQDLPDCSPSSCFNGGTCVDGVNSFSCLCRPGYTGAHCQHEADPCLSRPCLHGGVCSAAHPGFRCTCLE
SFTGPQCQTLVDWCSRQPCQNGGRCVQTGAYCLCPPGWSGRLCDIRSLPCREAAAQIGVRLEQLCQAGGQCVDEDSSHYCVCPEGRTGSH
CEQEVDPCLAQPCQHGGTCRGYMGGYMCECLPGYNGDNCEDDVDECASQPCQHGGSCIDLVARYLCSCPPGTLGVLCEINEDDCGPGPPL
DSGPRCLHNGTCVDLVGGFRCTCPPGYTGLRCEADINECRSGACHAAHTRDCLQDPGGGFRCLCHAGFSGPRCQTVLSPCESQPCQHGGQ
CRPSPGPGGGLTFTCHCAQPFWGPRCERVARSCRELQCPVGVPCQQTPRGPRCACPPGLSGPSCRSFPGSPPGASNASCAAAPCLHGGSC
RPAPLAPFFRCACAQGWTGPRCEAPAAAPEVSEEPRCPRAACQAKRGDQRCDRECNSPGCGWDGGDCSLSVGDPWRQCEALQCWRLFNNS
RCDPACSSPACLYDNFDCHAGGRERTCNPVYEKYCADHFADGRCDQGCNTEECGWDGLDCASEVPALLARGVLVLTVLLPPEELLRSSAD
FLQRLSAILRTSLRFRLDAHGQAMVFPYHRPSPGSEPRARRELAPEVIGSVVMLEIDNRLCLQSPENDHCFPDAQSAADYLGALSAVERL
DFPYPLRDVRGEPLEPPEPSVPLLPLLVAGAVLLLVILVLGVMVARRKREHSTLWFPEGFSLHKDVASGHKGRREPVGQDALGMKNMAKG
ESLMGEVATDWMDTECPEAKRLKVEEPGMGAEEAVDCRQWTQHHLVAADIRVAPAMALTPPQGDADADGMDVNVRGPASAGGSKCVSNTP

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

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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/chr19:15278060/chr20:239718)
- 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
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}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331000_10341787.33333333333332322.0DomainEGF-like 26
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331036_10821787.33333333333332322.0DomainEGF-like 27
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331084_11201787.33333333333332322.0DomainEGF-like 28
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331122_11581787.33333333333332322.0DomainEGF-like 29%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331160_12031787.33333333333332322.0DomainEGF-like 30%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933119_1561787.33333333333332322.0DomainEGF-like 3
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331205_12441787.33333333333332322.0DomainEGF-like 31
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331246_12871787.33333333333332322.0DomainEGF-like 32
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331289_13251787.33333333333332322.0DomainEGF-like 33
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331335_13731787.33333333333332322.0DomainEGF-like 34
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933158_1951787.33333333333332322.0DomainEGF-like 4%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933197_2341787.33333333333332322.0DomainEGF-like 5
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933236_2721787.33333333333332322.0DomainEGF-like 6%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933274_3121787.33333333333332322.0DomainEGF-like 7
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933314_3501787.33333333333332322.0DomainEGF-like 8%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933351_3891787.33333333333332322.0DomainEGF-like 9
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933391_4291787.33333333333332322.0DomainEGF-like 10%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-293340_771787.33333333333332322.0DomainEGF-like 1
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933431_4671787.33333333333332322.0DomainEGF-like 11%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933469_5051787.33333333333332322.0DomainEGF-like 12%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933507_5431787.33333333333332322.0DomainEGF-like 13%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933545_5801787.33333333333332322.0DomainEGF-like 14%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933582_6181787.33333333333332322.0DomainEGF-like 15%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933620_6551787.33333333333332322.0DomainEGF-like 16%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933657_6931787.33333333333332322.0DomainEGF-like 17%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933695_7301787.33333333333332322.0DomainEGF-like 18
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933734_7701787.33333333333332322.0DomainEGF-like 19
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933771_8081787.33333333333332322.0DomainEGF-like 20
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-293378_1181787.33333333333332322.0DomainEGF-like 2
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933810_8471787.33333333333332322.0DomainEGF-like 21%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933849_8851787.33333333333332322.0DomainEGF-like 22%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933887_9221787.33333333333332322.0DomainEGF-like 23%3B calcium-binding
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933924_9601787.33333333333332322.0DomainEGF-like 24
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-2933962_9981787.33333333333332322.0DomainEGF-like 25
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331387_14271787.33333333333332322.0RepeatNote=LNR 1
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331428_14581787.33333333333332322.0RepeatNote=LNR 2
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331467_15051787.33333333333332322.0RepeatNote=LNR 3
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-293340_16431787.33333333333332322.0Topological domainExtracellular
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331644_16641787.33333333333332322.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331838_18671787.33333333333332322.0RepeatNote=ANK 1
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331871_19011787.33333333333332322.0RepeatNote=ANK 2
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331905_19341787.33333333333332322.0RepeatNote=ANK 3
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331938_19671787.33333333333332322.0RepeatNote=ANK 4
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331971_20001787.33333333333332322.0RepeatNote=ANK 5
HgeneNOTCH3chr19:15278060chr20:239718ENST00000263388-29331665_23211787.33333333333332322.0Topological domainCytoplasmic


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
NOTCH3_pLDDT.png
all structure
all structure
DEFB132_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
NOTCH3
DEFB132


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 NOTCH3-DEFB132


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 NOTCH3-DEFB132


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