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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:KIDINS220-SOX7

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: KIDINS220-SOX7
FusionPDB ID: 42514
FusionGDB2.0 ID: 42514
HgeneTgene
Gene symbol

KIDINS220

SOX7

Gene ID

57498

83595

Gene namekinase D interacting substrate 220SRY-box transcription factor 7
SynonymsARMS|SINO-
Cytomap

2p25.1

8p23.1

Type of geneprotein-codingprotein-coding
Descriptionkinase D-interacting substrate of 220 kDaankyrin repeat-rich membrane-spanning proteinkinase D-interacting substrate 220kDatranscription factor SOX-7SRY (sex determining region Y)-box 7SRY-box 7
Modification date2020031320200313
UniProtAcc

Q9ULH0

Main function of 5'-partner protein: FUNCTION: Promotes a prolonged MAP-kinase signaling by neurotrophins through activation of a Rap1-dependent mechanism. Provides a docking site for the CRKL-C3G complex, resulting in Rap1-dependent sustained ERK activation. May play an important role in regulating postsynaptic signal transduction through the syntrophin-mediated localization of receptor tyrosine kinases such as EPHA4. In cooperation with SNTA1 can enhance EPHA4-induced JAK/STAT activation. Plays a role in nerve growth factor (NGF)-induced recruitment of RAPGEF2 to late endosomes and neurite outgrowth. May play a role in neurotrophin- and ephrin-mediated neuronal outgrowth and in axon guidance during neural development and in neuronal regeneration (By similarity). Modulates stress-induced apoptosis of melanoma cells via regulation of the MEK/ERK signaling pathway. {ECO:0000250, ECO:0000269|PubMed:18089783}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000256707, ENST00000418530, 
ENST00000427284, ENST00000473731, 
ENST00000319688, ENST00000436566, 
ENST00000304501, ENST00000553390, 
ENST00000554914, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 11 X 9=12875 X 5 X 3=75
# samples 115
** MAII scorelog2(11/1287*10)=-3.54843662469604
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: KIDINS220 [Title/Abstract] AND SOX7 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: KIDINS220 [Title/Abstract] AND SOX7 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KIDINS220(8890242)-SOX7(10692285), # samples:1
Anticipated loss of major functional domain due to fusion event.KIDINS220-SOX7 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.
KIDINS220-SOX7 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.
KIDINS220-SOX7 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.
KIDINS220-SOX7 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.
KIDINS220-SOX7 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
KIDINS220-SOX7 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
KIDINS220-SOX7 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgeneSOX7

GO:0001706

endoderm formation

18682240

TgeneSOX7

GO:0008285

negative regulation of cell proliferation

19108950

TgeneSOX7

GO:0043280

positive regulation of cysteine-type endopeptidase activity involved in apoptotic process

19108950

TgeneSOX7

GO:0045892

negative regulation of transcription, DNA-templated

19108950

TgeneSOX7

GO:0060828

regulation of canonical Wnt signaling pathway

19108950



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/chr2:8890242/chr8:10692285)
- 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 KIDINS220 (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 SOX7 (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)
ENST00000418530KIDINS220chr28890242-ENST00000554914SOX7chr810692285-5239359616436791171
ENST00000418530KIDINS220chr28890242-ENST00000553390SOX7chr810692285-5239359616436791171

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
ENST00000418530ENST00000554914KIDINS220chr28890242-SOX7chr810692285-0.0002798870.99972004
ENST00000418530ENST00000553390KIDINS220chr28890242-SOX7chr810692285-0.0002798870.99972004

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 KIDINS220-SOX7

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
KIDINS220chr28890242SOX7chr81069228535961144SGMTGPQHPFYNRVGGSRSGLWILRT

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Potential FusionNeoAntigen Information of KIDINS220-SOX7 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 KIDINS220-SOX7 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 KIDINS220-SOX7

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 KIDINS220-SOX7

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 KIDINS220-SOX7

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 KIDINS220-SOX7

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 KIDINS220-SOX7

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
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000256707-2430500_52011381772.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000256707-2430525_54511381772.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000256707-2430660_68011381772.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000256707-2430686_70611381772.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000418530-2428500_52010961673.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000418530-2428525_54510961673.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000418530-2428660_68010961673.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000418530-2428686_70610961673.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000427284-2429500_52011381753.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000427284-2429525_54511381753.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000427284-2429660_68011381753.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000427284-2429686_70611381753.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000473731-2429500_52011381753.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000473731-2429525_54511381753.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000473731-2429660_68011381753.0TransmembraneHelical
HgeneKIDINS220chr2:8890242chr8:10692285ENST00000473731-2429686_70611381753.0TransmembraneHelical

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 KIDINS220-SOX7

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 KIDINS220-SOX7

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