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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:TNIK-STXBP5L

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TNIK-STXBP5L
FusionPDB ID: 92702
FusionGDB2.0 ID: 92702
HgeneTgene
Gene symbol

TNIK

STXBP5L

Gene ID

23043

9515

Gene nameTRAF2 and NCK interacting kinasesyntaxin binding protein 5 like
SynonymsMRT54LLGL4
Cytomap

3q26.2-q26.31

3q13.33

Type of geneprotein-codingprotein-coding
DescriptionTRAF2 and NCK-interacting protein kinasesyntaxin-binding protein 5-likelethal(2) giant larvae protein homolog 4tomosyn-2tomosyn-like
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000284483, ENST00000341852, 
ENST00000357327, ENST00000369326, 
ENST00000436636, ENST00000460047, 
ENST00000470834, ENST00000475336, 
ENST00000488470, ENST00000538048, 
ENST00000464785, ENST00000465393, 
ENST00000492541, ENST00000497029, 
ENST00000273666, ENST00000471454, 
ENST00000472879, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 13 X 6=10924 X 4 X 3=48
# samples 134
** MAII scorelog2(13/1092*10)=-3.0703893278914
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
Fusion gene context

PubMed: TNIK [Title/Abstract] AND STXBP5L [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: TNIK [Title/Abstract] AND STXBP5L [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TNIK(170801944)-STXBP5L(121097563), # samples:2
Anticipated loss of major functional domain due to fusion event.TNIK-STXBP5L 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.
TNIK-STXBP5L 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.
TNIK-STXBP5L 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.
TNIK-STXBP5L 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
HgeneTNIK

GO:0006468

protein phosphorylation

10521462|15342639|22797597

HgeneTNIK

GO:0007256

activation of JNKK activity

15342639

HgeneTNIK

GO:0031532

actin cytoskeleton reorganization

15342639

HgeneTNIK

GO:0035556

intracellular signal transduction

10521462

HgeneTNIK

GO:0046777

protein autophosphorylation

10521462|15342639

HgeneTNIK

GO:0048814

regulation of dendrite morphogenesis

20159449



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/chr3:170801944/chr3:121097563)
- 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 buttonRetention analysis results 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, are available here.

check buttonFusion gene breakpoints across TNIK (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 STXBP5L (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 Amino Acid Sequences


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)
ENST00000436636TNIKchr3170801944-ENST00000273666STXBP5Lchr3121097563+10491351431548261503
ENST00000436636TNIKchr3170801944-ENST00000471454STXBP5Lchr3121097563+5013351431548261503
ENST00000436636TNIKchr3170801944-ENST00000472879STXBP5Lchr3121097563+4351351431543461343
ENST00000538048TNIKchr3170801944-ENST00000273666STXBP5Lchr3121097563+10347337031546821455
ENST00000538048TNIKchr3170801944-ENST00000471454STXBP5Lchr3121097563+4869337031546821455
ENST00000538048TNIKchr3170801944-ENST00000472879STXBP5Lchr3121097563+4207337031542021295
ENST00000369326TNIKchr3170801944-ENST00000273666STXBP5Lchr3121097563+10425344831547601481
ENST00000369326TNIKchr3170801944-ENST00000471454STXBP5Lchr3121097563+4947344831547601481
ENST00000369326TNIKchr3170801944-ENST00000472879STXBP5Lchr3121097563+4285344831542801321
ENST00000341852TNIKchr3170801944-ENST00000273666STXBP5Lchr3121097563+10239326231545741419
ENST00000341852TNIKchr3170801944-ENST00000471454STXBP5Lchr3121097563+4761326231545741419
ENST00000341852TNIKchr3170801944-ENST00000472879STXBP5Lchr3121097563+4099326231540941259
ENST00000284483TNIKchr3170801944-ENST00000273666STXBP5Lchr3121097563+101223145044571485
ENST00000284483TNIKchr3170801944-ENST00000471454STXBP5Lchr3121097563+46443145044571485
ENST00000284483TNIKchr3170801944-ENST00000472879STXBP5Lchr3121097563+39823145039771325
ENST00000470834TNIKchr3170801944-ENST00000273666STXBP5Lchr3121097563+100353058043701456
ENST00000470834TNIKchr3170801944-ENST00000471454STXBP5Lchr3121097563+45573058043701456
ENST00000470834TNIKchr3170801944-ENST00000472879STXBP5Lchr3121097563+38953058038901296
ENST00000460047TNIKchr3170801944-ENST00000273666STXBP5Lchr3121097563+99572980042921430
ENST00000460047TNIKchr3170801944-ENST00000471454STXBP5Lchr3121097563+44792980042921430
ENST00000460047TNIKchr3170801944-ENST00000472879STXBP5Lchr3121097563+38172980038121270
ENST00000475336TNIKchr3170801944-ENST00000273666STXBP5Lchr3121097563+98702893042051401
ENST00000475336TNIKchr3170801944-ENST00000471454STXBP5Lchr3121097563+43922893042051401
ENST00000475336TNIKchr3170801944-ENST00000472879STXBP5Lchr3121097563+37302893037251241
ENST00000488470TNIKchr3170801944-ENST00000273666STXBP5Lchr3121097563+99813004043161438
ENST00000488470TNIKchr3170801944-ENST00000471454STXBP5Lchr3121097563+45033004043161438
ENST00000488470TNIKchr3170801944-ENST00000472879STXBP5Lchr3121097563+38413004038361278
ENST00000357327TNIKchr3170801944-ENST00000273666STXBP5Lchr3121097563+100593082043941464
ENST00000357327TNIKchr3170801944-ENST00000471454STXBP5Lchr3121097563+45813082043941464
ENST00000357327TNIKchr3170801944-ENST00000472879STXBP5Lchr3121097563+39193082039141304

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
ENST00000436636ENST00000273666TNIKchr3170801944-STXBP5Lchr3121097563+0.000339950.99966
ENST00000436636ENST00000471454TNIKchr3170801944-STXBP5Lchr3121097563+0.0049162790.99508375
ENST00000436636ENST00000472879TNIKchr3170801944-STXBP5Lchr3121097563+0.0059125090.99408746
ENST00000538048ENST00000273666TNIKchr3170801944-STXBP5Lchr3121097563+0.0002950960.9997049
ENST00000538048ENST00000471454TNIKchr3170801944-STXBP5Lchr3121097563+0.0039118050.99608827
ENST00000538048ENST00000472879TNIKchr3170801944-STXBP5Lchr3121097563+0.0036085170.9963915
ENST00000369326ENST00000273666TNIKchr3170801944-STXBP5Lchr3121097563+0.0002753530.9997247
ENST00000369326ENST00000471454TNIKchr3170801944-STXBP5Lchr3121097563+0.0036300890.99636996
ENST00000369326ENST00000472879TNIKchr3170801944-STXBP5Lchr3121097563+0.0035240080.996476
ENST00000341852ENST00000273666TNIKchr3170801944-STXBP5Lchr3121097563+0.0002189540.9997811
ENST00000341852ENST00000471454TNIKchr3170801944-STXBP5Lchr3121097563+0.0030585710.9969414
ENST00000341852ENST00000472879TNIKchr3170801944-STXBP5Lchr3121097563+0.0031906780.9968093
ENST00000284483ENST00000273666TNIKchr3170801944-STXBP5Lchr3121097563+0.0002486340.9997514
ENST00000284483ENST00000471454TNIKchr3170801944-STXBP5Lchr3121097563+0.004123530.99587643
ENST00000284483ENST00000472879TNIKchr3170801944-STXBP5Lchr3121097563+0.0043599530.99564004
ENST00000470834ENST00000273666TNIKchr3170801944-STXBP5Lchr3121097563+0.0002247090.99977535
ENST00000470834ENST00000471454TNIKchr3170801944-STXBP5Lchr3121097563+0.0035422560.99645776
ENST00000470834ENST00000472879TNIKchr3170801944-STXBP5Lchr3121097563+0.0037889420.99621105
ENST00000460047ENST00000273666TNIKchr3170801944-STXBP5Lchr3121097563+0.0002162530.9997838
ENST00000460047ENST00000471454TNIKchr3170801944-STXBP5Lchr3121097563+0.0035343790.99646556
ENST00000460047ENST00000472879TNIKchr3170801944-STXBP5Lchr3121097563+0.0042391830.99576086
ENST00000475336ENST00000273666TNIKchr3170801944-STXBP5Lchr3121097563+0.0002570010.99974304
ENST00000475336ENST00000471454TNIKchr3170801944-STXBP5Lchr3121097563+0.0036808260.9963192
ENST00000475336ENST00000472879TNIKchr3170801944-STXBP5Lchr3121097563+0.0025952590.99740475
ENST00000488470ENST00000273666TNIKchr3170801944-STXBP5Lchr3121097563+0.0002248710.9997751
ENST00000488470ENST00000471454TNIKchr3170801944-STXBP5Lchr3121097563+0.0039398230.9960602
ENST00000488470ENST00000472879TNIKchr3170801944-STXBP5Lchr3121097563+0.0039130130.99608696
ENST00000357327ENST00000273666TNIKchr3170801944-STXBP5Lchr3121097563+0.0002180060.999782
ENST00000357327ENST00000471454TNIKchr3170801944-STXBP5Lchr3121097563+0.0037207930.9962792
ENST00000357327ENST00000472879TNIKchr3170801944-STXBP5Lchr3121097563+0.0043765810.9956234

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for TNIK-STXBP5L

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
TNIKchr3170801944STXBP5Lchr31210975632893964KRFNSEILCAALWDHVNGHCTSPTSQ
TNIKchr3170801944STXBP5Lchr31210975632980993KRFNSEILCAALWDHVNGHCTSPTSQ
TNIKchr3170801944STXBP5Lchr312109756330041001KRFNSEILCAALWDHVNGHCTSPTSQ
TNIKchr3170801944STXBP5Lchr312109756330581019KRFNSEILCAALWDHVNGHCTSPTSQ
TNIKchr3170801944STXBP5Lchr312109756330821027KRFNSEILCAALWDHVNGHCTSPTSQ
TNIKchr3170801944STXBP5Lchr312109756331451048KRFNSEILCAALWDHVNGHCTSPTSQ
TNIKchr3170801944STXBP5Lchr31210975633262982KRFNSEILCAALWDHVNGHCTSPTSQ
TNIKchr3170801944STXBP5Lchr312109756333701018KRFNSEILCAALWDHVNGHCTSPTSQ
TNIKchr3170801944STXBP5Lchr312109756334481044KRFNSEILCAALWDHVNGHCTSPTSQ
TNIKchr3170801944STXBP5Lchr312109756335141066KRFNSEILCAALWDHVNGHCTSPTSQ

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Potential FusionNeoAntigen Information of TNIK-STXBP5L in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)

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Potential FusionNeoAntigen Information of TNIK-STXBP5L in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of TNIK-STXBP5L

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TNIK-STXBP5L

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score

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Vaccine Design for the FusionNeoAntigens of TNIK-STXBP5L

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of TNIK-STXBP5L

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample

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Potential target of CAR-T therapy development for TNIK-STXBP5L

check button Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to TNIK-STXBP5L

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 TNIK-STXBP5L

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