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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:TRIO-KDSR

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TRIO-KDSR
FusionPDB ID: 94207
FusionGDB2.0 ID: 94207
HgeneTgene
Gene symbol

TRIO

KDSR

Gene ID

7204

2531

Gene nametrio Rho guanine nucleotide exchange factor3-ketodihydrosphingosine reductase
SynonymsARHGEF23|MEBAS|MRD44|tgatDHSR|EKVP4|FVT1|SDR35C1
Cytomap

5p15.2

18q21.33

Type of geneprotein-codingprotein-coding
Descriptiontriple functional domain proteinPTPRF-interacting proteintriple functional domain (PTPRF interacting)3-ketodihydrosphingosine reductase3-dehydrosphinganine reductaseFVT-1KDS reductasefollicular lymphoma variant translocation 1follicular variant translocation protein 1short chain dehydrogenase/reductase family 35C member 1
Modification date2020031320200313
UniProtAcc

TPI1

Q06136

Ensembl transtripts involved in fusion geneENST idsENST00000344204, ENST00000509967, 
ENST00000537187, ENST00000344135, 
ENST00000515710, 		ENST00000326575, 
ENST00000589592, ENST00000406396, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score34 X 28 X 12=114244 X 4 X 3=48
# samples 354
** MAII scorelog2(35/11424*10)=-5.02856915219677
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: TRIO [Title/Abstract] AND KDSR [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TRIO(14297372)-KDSR(61006116), # samples:1
Anticipated loss of major functional domain due to fusion event.TRIO-KDSR 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.
TRIO-KDSR 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.
TRIO-KDSR 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.
TRIO-KDSR 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
TgeneKDSR

GO:0006666

3-keto-sphinganine metabolic process

15364918


check buttonFusion gene breakpoints across TRIO (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 KDSR (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
ChimerDB4COADTCGA-AY-6196-01ATRIOchr5

14297372

-KDSRchr18

61006116

-


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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)
ENST00000344204TRIOchr514297372-ENST00000406396KDSRchr1861006116-57541392241697557
ENST00000537187TRIOchr514297372-ENST00000406396KDSRchr1861006116-5736137461679557
ENST00000509967TRIOchr514297372-ENST00000406396KDSRchr1861006116-573513731521678508

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
ENST00000344204ENST00000406396TRIOchr514297372-KDSRchr1861006116-0.0004665230.99953353
ENST00000537187ENST00000406396TRIOchr514297372-KDSRchr1861006116-0.000469310.9995307
ENST00000509967ENST00000406396TRIOchr514297372-KDSRchr1861006116-0.0005179760.9994821

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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

>94207_94207_1_TRIO-KDSR_TRIO_chr5_14297372_ENST00000344204_KDSR_chr18_61006116_ENST00000406396_length(amino acids)=557AA_BP=456
MSGSSGGAAAPAASSGPAAAASAAGSGCGGGAGEGAEEAAKDLADIAAFFRSGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTF
PARSNHDRIRQEDLRRLISYLACIPSEEVCKRGFTVIVDMRGSKWDSIKPLLKILQESFPCCIHVALIIKPDNFWQKQRTNFGSSKFEFE
TNMVSLEGLTKVVDPSQLTPEFDGCLEYNHEEWIEIRVAFEDYISNATHMLSRLEELQDILAKKELPQDLEGARNMIEEHSQLKKKVIKA
PIEDLDLEGQKLLQRIQSSESFPKKNSGSGNADLQNLLPKVSTMLDRLHSTRQHLHQMWHVRKLKLDQCFQLRLFEQDAEKMFDWITHNK
GLFLNSYTEIGTSHPHAMELQTQHNHFAMNCMNVYVNINRIMSVANRLVESGHYASQQIRQIASQLEQEWKAFAAALDERSTLLDMSSIF
HQKAEKPLETRLISETTSVCKPEQVAKQIVKDAIQGNFNSSLGSDGYMLSALTCGMAPVTSITEGLQQVVTMGLFRTIALFYLGSFDSIV

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

>94207_94207_2_TRIO-KDSR_TRIO_chr5_14297372_ENST00000509967_KDSR_chr18_61006116_ENST00000406396_length(amino acids)=508AA_BP=407
MAEGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTFPARSNHDRIRQEDLRRLISYLACIPSEEVCKRGFTVIVDMRGSKWDSIK
PLLKILQESFPCCIHVALIIKPDNFWQKQRTNFGSSKFEFETNMVSLEGLTKVVDPSQLTPEFDGCLEYNHEEWIEIRVAFEDYISNATH
MLSRLEELQDILAKKELPQDLEGARNMIEEHSQLKKKVIKAPIEDLDLEGQKLLQRIQSSESFPKKNSGSGNADLQNLLPKVSTMLDRLH
STRQHLHQMWHVRKLKLDQCFQLRLFEQDAEKMFDWITHNKGLFLNSYTEIGTSHPHAMELQTQHNHFAMNCMNVYVNINRIMSVANRLV
ESGHYASQQIRQIASQLEQEWKAFAAALDERSTLLDMSSIFHQKAEKPLETRLISETTSVCKPEQVAKQIVKDAIQGNFNSSLGSDGYML

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>94207_94207_3_TRIO-KDSR_TRIO_chr5_14297372_ENST00000537187_KDSR_chr18_61006116_ENST00000406396_length(amino acids)=557AA_BP=456
MSGSSGGAAAPAASSGPAAAASAAGSGCGGGAGEGAEEAAKDLADIAAFFRSGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTF
PARSNHDRIRQEDLRRLISYLACIPSEEVCKRGFTVIVDMRGSKWDSIKPLLKILQESFPCCIHVALIIKPDNFWQKQRTNFGSSKFEFE
TNMVSLEGLTKVVDPSQLTPEFDGCLEYNHEEWIEIRVAFEDYISNATHMLSRLEELQDILAKKELPQDLEGARNMIEEHSQLKKKVIKA
PIEDLDLEGQKLLQRIQSSESFPKKNSGSGNADLQNLLPKVSTMLDRLHSTRQHLHQMWHVRKLKLDQCFQLRLFEQDAEKMFDWITHNK
GLFLNSYTEIGTSHPHAMELQTQHNHFAMNCMNVYVNINRIMSVANRLVESGHYASQQIRQIASQLEQEWKAFAAALDERSTLLDMSSIF
HQKAEKPLETRLISETTSVCKPEQVAKQIVKDAIQGNFNSSLGSDGYMLSALTCGMAPVTSITEGLQQVVTMGLFRTIALFYLGSFDSIV

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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/chr5:14297372/chr18:61006116)
- 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
TRIO

TPI1

KDSR

Q06136

249FUNCTION: Catalyzes the reduction of 3-ketodihydrosphingosine (KDS) to dihydrosphingosine (DHS). {ECO:0000269|PubMed:28575652}.

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
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-75765_210456.03098.0DomainCRAL-TRIO
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-75865_210456.02922.0DomainCRAL-TRIO
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-757311_418456.03098.0RepeatNote=Spectrin 1
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-758311_418456.02922.0RepeatNote=Spectrin 1
TgeneKDSRchr5:14297372chr18:61006116ENST00000406396610292_293231.0333.0Topological domainLumenal
TgeneKDSRchr5:14297372chr18:61006116ENST00000406396610315_332231.0333.0Topological domainCytoplasmic
TgeneKDSRchr5:14297372chr18:61006116ENST00000406396610271_291231.0333.0TransmembraneHelical
TgeneKDSRchr5:14297372chr18:61006116ENST00000406396610294_314231.0333.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1101845_18500597.0Compositional biasNote=Poly-Ser
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1102292_23120597.0Compositional biasNote=Poly-Gly
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1102545_25510597.0Compositional biasNote=Poly-Ser
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-110715_7180597.0Compositional biasNote=Poly-Gln
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7571845_1850456.03098.0Compositional biasNote=Poly-Ser
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7572292_2312456.03098.0Compositional biasNote=Poly-Gly
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7572545_2551456.03098.0Compositional biasNote=Poly-Ser
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-757715_718456.03098.0Compositional biasNote=Poly-Gln
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7581845_1850456.02922.0Compositional biasNote=Poly-Ser
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7582292_2312456.02922.0Compositional biasNote=Poly-Gly
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7582545_2551456.02922.0Compositional biasNote=Poly-Ser
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-758715_718456.02922.0Compositional biasNote=Poly-Gln
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1101292_14670597.0DomainDH 1
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1101480_15910597.0DomainPH 1
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1101656_17210597.0DomainSH3 1
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1101969_21450597.0DomainDH 2
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1102157_22710597.0DomainPH 2
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1102551_26160597.0DomainSH3 2
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1102685_27750597.0DomainNote=Ig-like C2-type
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1102796_30520597.0DomainProtein kinase
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-11065_2100597.0DomainCRAL-TRIO
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7571292_1467456.03098.0DomainDH 1
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7571480_1591456.03098.0DomainPH 1
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7571656_1721456.03098.0DomainSH3 1
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7571969_2145456.03098.0DomainDH 2
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7572157_2271456.03098.0DomainPH 2
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7572551_2616456.03098.0DomainSH3 2
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7572685_2775456.03098.0DomainNote=Ig-like C2-type
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7572796_3052456.03098.0DomainProtein kinase
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7581292_1467456.02922.0DomainDH 1
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7581480_1591456.02922.0DomainPH 1
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7581656_1721456.02922.0DomainSH3 1
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7581969_2145456.02922.0DomainDH 2
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7582157_2271456.02922.0DomainPH 2
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7582551_2616456.02922.0DomainSH3 2
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7582685_2775456.02922.0DomainNote=Ig-like C2-type
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7582796_3052456.02922.0DomainProtein kinase
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1102802_28100597.0Nucleotide bindingATP
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7572802_2810456.03098.0Nucleotide bindingATP
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7582802_2810456.02922.0Nucleotide bindingATP
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-1101109_12160597.0RepeatNote=Spectrin 4
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-110311_4180597.0RepeatNote=Spectrin 1
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-110538_6440597.0RepeatNote=Spectrin 2
HgeneTRIOchr5:14297372chr18:61006116ENST00000344135-110878_9840597.0RepeatNote=Spectrin 3
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-7571109_1216456.03098.0RepeatNote=Spectrin 4
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-757538_644456.03098.0RepeatNote=Spectrin 2
HgeneTRIOchr5:14297372chr18:61006116ENST00000344204-757878_984456.03098.0RepeatNote=Spectrin 3
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-7581109_1216456.02922.0RepeatNote=Spectrin 4
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-758538_644456.02922.0RepeatNote=Spectrin 2
HgeneTRIOchr5:14297372chr18:61006116ENST00000537187-758878_984456.02922.0RepeatNote=Spectrin 3
TgeneKDSRchr5:14297372chr18:61006116ENST0000040639661036_60231.0333.0Nucleotide bindingNADP
TgeneKDSRchr5:14297372chr18:61006116ENST0000040639661026_270231.0333.0Topological domainCytoplasmic


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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
TRIO
KDSR


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 TRIO-KDSR


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 TRIO-KDSR


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