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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:EDC3-SLC6A11

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: EDC3-SLC6A11
FusionPDB ID: 24947
FusionGDB2.0 ID: 24947
HgeneTgene
Gene symbol

EDC3

SLC6A11

Gene ID

80153

6538

Gene nameenhancer of mRNA decapping 3solute carrier family 6 member 11
SynonymsLSM16|MRT50|YJDC|YJEFN2|hYjeF_N2-15q23GAT-3|GAT3|GAT4
Cytomap

15q24.1

3p25.3

Type of geneprotein-codingprotein-coding
Descriptionenhancer of mRNA-decapping protein 3LSM16 homolog (EDC3, S. cerevisiae)enhancer of mRNA decapping 3 homologyjeF N-terminal domain-containing protein 2yjeF domain containingyjeF domain-containing protein 1sodium- and chloride-dependent GABA transporter 3GABA transporter 3solute carrier family 6 (neurotransmitter transporter), member 11solute carrier family 6 (neurotransmitter transporter, GABA), member 11
Modification date2020032720200313
UniProtAcc

Q96F86

.
Ensembl transtripts involved in fusion geneENST idsENST00000315127, ENST00000426797, 
ENST00000568176, ENST00000562047, 
ENST00000454147, ENST00000254488, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 9 X 6=5403 X 4 X 3=36
# samples 124
** MAII scorelog2(12/540*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: EDC3 [Title/Abstract] AND SLC6A11 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)EDC3(74948074)-SLC6A11(10967690), # samples:3
Anticipated loss of major functional domain due to fusion event.EDC3-SLC6A11 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.
EDC3-SLC6A11 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.
EDC3-SLC6A11 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.
EDC3-SLC6A11 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.
EDC3-SLC6A11 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
EDC3-SLC6A11 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted 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 EDC3 (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 SLC6A11 (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
ChimerDB4TGCTTCGA-2G-AAGA-01AEDC3chr15

74948074

-SLC6A11chr3

10967690

+
ChimerDB4TGCTTCGA-2G-AAGAEDC3chr15

74948073

-SLC6A11chr3

10967689

+
ChimerDB4TGCTTCGA-2G-AAGAEDC3chr15

74948074

-SLC6A11chr3

10967690

+


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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)
ENST00000426797EDC3chr1574948074-ENST00000254488SLC6A11chr310967690+439312834632061532
ENST00000426797EDC3chr1574948073-ENST00000254488SLC6A11chr310967689+439312834632061532

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
ENST00000426797ENST00000254488EDC3chr1574948074-SLC6A11chr310967690+0.0009409130.99905914
ENST00000426797ENST00000254488EDC3chr1574948073-SLC6A11chr310967689+0.0009409130.99905914

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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

>24947_24947_1_EDC3-SLC6A11_EDC3_chr15_74948073_ENST00000426797_SLC6A11_chr3_10967689_ENST00000254488_length(amino acids)=532AA_BP=273
MATDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPFHNGVKCLVPEVTFRAGDITELKILEIPGPGDNQHFGDLHQTELGPSGAG
CQVGINQNGTGKFVKKPASSSSAPQNIPKRTDVKSQDVAVSPQQQQCSKSYVDRHMESLSQSKSFRRRHNSWSSSSRHPNQATPKKSGLK
NGQMKNKDDECFGDDIEEIPDTDFDFEGNLALFDKAAVFEEIDTYERRSGTRSRGIPNERPTRYRHDENILESEPIVYRRIIVPHNVSKE
FCTGPGLAFIAYPKAVTMMPLSPLWATLFFMMLIFLGLDSQFVCVESLVTAVVDMYPKVFRRGYRRELLILALSVISYFLGLVMLTEGGM
YIFQLFDSYAASGMCLLFVAIFECICIGWVYGSNRFYDNIEDMIGYRPPSLIKWCWMIMTPGICAGIFIFFLIKYKPLKYNNIYTYPAWG

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

>24947_24947_2_EDC3-SLC6A11_EDC3_chr15_74948074_ENST00000426797_SLC6A11_chr3_10967690_ENST00000254488_length(amino acids)=532AA_BP=273
MATDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPFHNGVKCLVPEVTFRAGDITELKILEIPGPGDNQHFGDLHQTELGPSGAG
CQVGINQNGTGKFVKKPASSSSAPQNIPKRTDVKSQDVAVSPQQQQCSKSYVDRHMESLSQSKSFRRRHNSWSSSSRHPNQATPKKSGLK
NGQMKNKDDECFGDDIEEIPDTDFDFEGNLALFDKAAVFEEIDTYERRSGTRSRGIPNERPTRYRHDENILESEPIVYRRIIVPHNVSKE
FCTGPGLAFIAYPKAVTMMPLSPLWATLFFMMLIFLGLDSQFVCVESLVTAVVDMYPKVFRRGYRRELLILALSVISYFLGLVMLTEGGM
YIFQLFDSYAASGMCLLFVAIFECICIGWVYGSNRFYDNIEDMIGYRPPSLIKWCWMIMTPGICAGIFIFFLIKYKPLKYNNIYTYPAWG

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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/chr15:74948074/chr3:10967690)
- 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
EDC3

Q96F86

.
FUNCTION: Binds single-stranded RNA. Involved in the process of mRNA degradation and in the positive regulation of mRNA decapping. May play a role in spermiogenesis and oogenesis. {ECO:0000269|PubMed:16364915, ECO:0000269|PubMed:17533573, ECO:0000269|PubMed:18678652, ECO:0000269|PubMed:25701870}.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
HgeneEDC3chr15:74948073chr3:10967689ENST00000315127-47192_228273.3333333333333509.0DomainDFDF
HgeneEDC3chr15:74948073chr3:10967689ENST00000426797-710192_228273.3333333333333509.0DomainDFDF
HgeneEDC3chr15:74948073chr3:10967689ENST00000568176-58192_228273.3333333333333509.0DomainDFDF
HgeneEDC3chr15:74948074chr3:10967690ENST00000315127-47192_228273.3333333333333509.0DomainDFDF
HgeneEDC3chr15:74948074chr3:10967690ENST00000426797-710192_228273.3333333333333509.0DomainDFDF
HgeneEDC3chr15:74948074chr3:10967690ENST00000568176-58192_228273.3333333333333509.0DomainDFDF
TgeneSLC6A11chr15:74948073chr3:10967689ENST00000254488714572_632373.3333333333333633.0Topological domainCytoplasmic
TgeneSLC6A11chr15:74948074chr3:10967690ENST00000254488714572_632373.3333333333333633.0Topological domainCytoplasmic
TgeneSLC6A11chr15:74948073chr3:10967689ENST00000254488714389_408373.3333333333333633.0TransmembraneHelical%3B Name%3D8
TgeneSLC6A11chr15:74948073chr3:10967689ENST00000254488714438_456373.3333333333333633.0TransmembraneHelical%3B Name%3D9
TgeneSLC6A11chr15:74948073chr3:10967689ENST00000254488714473_493373.3333333333333633.0TransmembraneHelical%3B Name%3D10
TgeneSLC6A11chr15:74948073chr3:10967689ENST00000254488714514_533373.3333333333333633.0TransmembraneHelical%3B Name%3D11
TgeneSLC6A11chr15:74948073chr3:10967689ENST00000254488714553_571373.3333333333333633.0TransmembraneHelical%3B Name%3D12
TgeneSLC6A11chr15:74948074chr3:10967690ENST00000254488714389_408373.3333333333333633.0TransmembraneHelical%3B Name%3D8
TgeneSLC6A11chr15:74948074chr3:10967690ENST00000254488714438_456373.3333333333333633.0TransmembraneHelical%3B Name%3D9
TgeneSLC6A11chr15:74948074chr3:10967690ENST00000254488714473_493373.3333333333333633.0TransmembraneHelical%3B Name%3D10
TgeneSLC6A11chr15:74948074chr3:10967690ENST00000254488714514_533373.3333333333333633.0TransmembraneHelical%3B Name%3D11
TgeneSLC6A11chr15:74948074chr3:10967690ENST00000254488714553_571373.3333333333333633.0TransmembraneHelical%3B Name%3D12

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneEDC3chr15:74948073chr3:10967689ENST00000315127-47283_487273.3333333333333509.0DomainYjeF N-terminal
HgeneEDC3chr15:74948073chr3:10967689ENST00000426797-710283_487273.3333333333333509.0DomainYjeF N-terminal
HgeneEDC3chr15:74948073chr3:10967689ENST00000568176-58283_487273.3333333333333509.0DomainYjeF N-terminal
HgeneEDC3chr15:74948074chr3:10967690ENST00000315127-47283_487273.3333333333333509.0DomainYjeF N-terminal
HgeneEDC3chr15:74948074chr3:10967690ENST00000426797-710283_487273.3333333333333509.0DomainYjeF N-terminal
HgeneEDC3chr15:74948074chr3:10967690ENST00000568176-58283_487273.3333333333333509.0DomainYjeF N-terminal
TgeneSLC6A11chr15:74948073chr3:10967689ENST00000254488714152_225373.3333333333333633.0Topological domainExtracellular
TgeneSLC6A11chr15:74948073chr3:10967689ENST000002544887141_58373.3333333333333633.0Topological domainCytoplasmic
TgeneSLC6A11chr15:74948074chr3:10967690ENST00000254488714152_225373.3333333333333633.0Topological domainExtracellular
TgeneSLC6A11chr15:74948074chr3:10967690ENST000002544887141_58373.3333333333333633.0Topological domainCytoplasmic
TgeneSLC6A11chr15:74948073chr3:10967689ENST00000254488714131_151373.3333333333333633.0TransmembraneHelical%3B Name%3D3
TgeneSLC6A11chr15:74948073chr3:10967689ENST00000254488714226_244373.3333333333333633.0TransmembraneHelical%3B Name%3D4
TgeneSLC6A11chr15:74948073chr3:10967689ENST00000254488714253_270373.3333333333333633.0TransmembraneHelical%3B Name%3D5
TgeneSLC6A11chr15:74948073chr3:10967689ENST00000254488714306_323373.3333333333333633.0TransmembraneHelical%3B Name%3D6
TgeneSLC6A11chr15:74948073chr3:10967689ENST00000254488714335_356373.3333333333333633.0TransmembraneHelical%3B Name%3D7
TgeneSLC6A11chr15:74948073chr3:10967689ENST0000025448871459_79373.3333333333333633.0TransmembraneHelical%3B Name%3D1
TgeneSLC6A11chr15:74948073chr3:10967689ENST0000025448871487_106373.3333333333333633.0TransmembraneHelical%3B Name%3D2
TgeneSLC6A11chr15:74948074chr3:10967690ENST00000254488714131_151373.3333333333333633.0TransmembraneHelical%3B Name%3D3
TgeneSLC6A11chr15:74948074chr3:10967690ENST00000254488714226_244373.3333333333333633.0TransmembraneHelical%3B Name%3D4
TgeneSLC6A11chr15:74948074chr3:10967690ENST00000254488714253_270373.3333333333333633.0TransmembraneHelical%3B Name%3D5
TgeneSLC6A11chr15:74948074chr3:10967690ENST00000254488714306_323373.3333333333333633.0TransmembraneHelical%3B Name%3D6
TgeneSLC6A11chr15:74948074chr3:10967690ENST00000254488714335_356373.3333333333333633.0TransmembraneHelical%3B Name%3D7
TgeneSLC6A11chr15:74948074chr3:10967690ENST0000025448871459_79373.3333333333333633.0TransmembraneHelical%3B Name%3D1
TgeneSLC6A11chr15:74948074chr3:10967690ENST0000025448871487_106373.3333333333333633.0TransmembraneHelical%3B Name%3D2


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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)
PDB file >>>1139_EDC3_74948074_SLC6A11_10967690_1139_EDC3_74948074_SLC6A11_10967690_ranked_0.pdbEDC37494807374948074ENST00000254488SLC6A11chr310967690+
MATDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPFHNGVKCLVPEVTFRAGDITELKILEIPGPGDNQHFGDLHQTELGPSGAG
CQVGINQNGTGKFVKKPASSSSAPQNIPKRTDVKSQDVAVSPQQQQCSKSYVDRHMESLSQSKSFRRRHNSWSSSSRHPNQATPKKSGLK
NGQMKNKDDECFGDDIEEIPDTDFDFEGNLALFDKAAVFEEIDTYERRSGTRSRGIPNERPTRYRHDENILESEPIVYRRIIVPHNVSKE
FCTGPGLAFIAYPKAVTMMPLSPLWATLFFMMLIFLGLDSQFVCVESLVTAVVDMYPKVFRRGYRRELLILALSVISYFLGLVMLTEGGM
YIFQLFDSYAASGMCLLFVAIFECICIGWVYGSNRFYDNIEDMIGYRPPSLIKWCWMIMTPGICAGIFIFFLIKYKPLKYNNIYTYPAWG
532


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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.
EDC3_pLDDT.png
all structure
all structure
SLC6A11_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.
all structure


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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
EDC3
SLC6A11


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 EDC3-SLC6A11


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 EDC3-SLC6A11


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