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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:SEL1L3-CCKAR

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SEL1L3-CCKAR
FusionPDB ID: 80204
FusionGDB2.0 ID: 80204
HgeneTgene
Gene symbol

SEL1L3

CCKAR

Gene ID

23231

886

Gene nameSEL1L family member 3cholecystokinin A receptor
SynonymsSel-1L3CCK-A|CCK1-R|CCK1R|CCKRA
Cytomap

4p15.2

4p15.2

Type of geneprotein-codingprotein-coding
Descriptionprotein sel-1 homolog 3sel-1 suppressor of lin-12-like 3suppressor of lin-12-like protein 3cholecystokinin receptor type ACCK-A receptorCCK-ARcholecystokinin type-A receptorcholecystokinin-1 receptor
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000264868, ENST00000399878, 
ENST00000502949, ENST00000513364, 
ENST00000295589, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score11 X 12 X 7=9241 X 1 X 1=1
# samples 122
** MAII scorelog2(12/924*10)=-2.94485844580754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/1*10)=4.32192809488736
Fusion gene context

PubMed: SEL1L3 [Title/Abstract] AND CCKAR [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SEL1L3 [Title/Abstract] AND CCKAR [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SEL1L3(25759156)-CCKAR(26484905), # samples:3
Anticipated loss of major functional domain due to fusion event.SEL1L3-CCKAR 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
TgeneCCKAR

GO:0038188

cholecystokinin signaling pathway

8503909



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/chr4:25759156/chr4:26484905)
- 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 SEL1L3 (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 CCKAR (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)
ENST00000502949SEL1L3chr425759156-ENST00000295589CCKARchr426484905-410032011732471076
ENST00000502949SEL1L3chr425759155-ENST00000295589CCKARchr426484905-410032011732471076

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
ENST00000502949ENST00000295589SEL1L3chr425759156-CCKARchr426484905-0.0013016960.99869823
ENST00000502949ENST00000295589SEL1L3chr425759155-CCKARchr426484905-0.0013016960.99869823

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 SEL1L3-CCKAR

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SEL1L3chr425759155CCKARchr42648490532011061LIAWTVQYFQSVSGTHSCYSSSFLFL
SEL1L3chr425759156CCKARchr42648490532011061LIAWTVQYFQSVSGTHSCYSSSFLFL

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Potential FusionNeoAntigen Information of SEL1L3-CCKAR 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.
SEL1L3-CCKAR_25759155_26484905.msa

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)
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:01SVSGTHSCY0.99010.80851019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:25SVSGTHSCY0.98950.77841019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:02SVSGTHSCY0.97550.78971019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B35:08SVSGTHSCY0.9470.76651019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B35:01SVSGTHSCY0.8490.72061019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:17QSVSGTHSCY0.98020.8361919
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:01FQSVSGTHSCY0.99990.8951819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:25FQSVSGTHSCY0.99540.9133819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:21SVSGTHSCY0.97660.74561019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:05SVSGTHSCY0.88930.70721019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:31SVSGTHSCY0.83530.71451019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:04SVSGTHSCY0.62940.82631019
SEL1L3-CCKARchr425759155chr4264849053201HLA-C15:04SVSGTHSCY0.30540.85111019
SEL1L3-CCKARchr425759155chr4264849053201HLA-C03:14SVSGTHSCY0.10850.95861019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:07FQSVSGTHSCY0.99940.7382819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:05FQSVSGTHSCY0.97890.919819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:27SVSGTHSCY0.99040.7151019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:33SVSGTHSCY0.99010.80851019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:34SVSGTHSCY0.99010.80851019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:125SVSGTHSCY0.99010.80851019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:135SVSGTHSCY0.98870.81681019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:39SVSGTHSCY0.9880.65821019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:50SVSGTHSCY0.98610.83081019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:11SVSGTHSCY0.98110.741019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:08SVSGTHSCY0.97970.73461019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B35:43SVSGTHSCY0.97660.7361019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B35:11SVSGTHSCY0.96730.70861019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:12SVSGTHSCY0.95630.85311019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:35SVSGTHSCY0.91270.74781019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:20SVSGTHSCY0.90340.78231019
SEL1L3-CCKARchr425759155chr4264849053201HLA-A25:01SVSGTHSCY0.89340.73581019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B35:77SVSGTHSCY0.8490.72061019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B35:28SVSGTHSCY0.84760.77821019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B35:23SVSGTHSCY0.83840.62371019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B35:20SVSGTHSCY0.83660.79021019
SEL1L3-CCKARchr425759155chr4264849053201HLA-C03:02SVSGTHSCY0.51060.93171019
SEL1L3-CCKARchr425759155chr4264849053201HLA-C15:09SVSGTHSCY0.30540.85111019
SEL1L3-CCKARchr425759155chr4264849053201HLA-C12:02SVSGTHSCY0.19740.93831019
SEL1L3-CCKARchr425759155chr4264849053201HLA-C02:10SVSGTHSCY0.00260.97151019
SEL1L3-CCKARchr425759155chr4264849053201HLA-C02:02SVSGTHSCY0.00260.97151019
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:33FQSVSGTHSCY0.99990.8951819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:27FQSVSGTHSCY0.99990.8985819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:50FQSVSGTHSCY0.99990.91819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:34FQSVSGTHSCY0.99990.8951819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:125FQSVSGTHSCY0.99990.8951819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:135FQSVSGTHSCY0.99990.9262819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:53FQSVSGTHSCY0.99960.8892819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:12FQSVSGTHSCY0.99950.8822819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:35FQSVSGTHSCY0.99930.9065819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:54FQSVSGTHSCY0.99630.8565819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:39FQSVSGTHSCY0.99590.8325819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B15:20FQSVSGTHSCY0.97880.9507819
SEL1L3-CCKARchr425759155chr4264849053201HLA-B35:28FQSVSGTHSCY0.96290.9529819

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Potential FusionNeoAntigen Information of SEL1L3-CCKAR 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.
SEL1L3-CCKAR_25759155_26484905.msa

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)
SEL1L3-CCKARchr425759155chr4264849053201DRB1-0473AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1501AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1505AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1506AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1507AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1509AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1513AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1516AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1518AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1520AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1521AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1521IAWTVQYFQSVSGTH116
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1522AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1524AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1528AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1532AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1533AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1535AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1536AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1540AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1541AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1542AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1543AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1545AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1546AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1548AWTVQYFQSVSGTHS217
SEL1L3-CCKARchr425759155chr4264849053201DRB1-1549AWTVQYFQSVSGTHS217

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Fusion breakpoint peptide structures of SEL1L3-CCKAR

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.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
7649QYFQSVSGTHSCYSSEL1L3CCKARchr425759155chr4264849053201

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SEL1L3-CCKAR

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
HLA-B14:023BVN7649QYFQSVSGTHSCYS-7.15543-7.26883
HLA-B14:023BVN7649QYFQSVSGTHSCYS-4.77435-5.80965
HLA-B52:013W397649QYFQSVSGTHSCYS-6.80875-6.92215
HLA-B52:013W397649QYFQSVSGTHSCYS-4.20386-5.23916
HLA-A11:014UQ27649QYFQSVSGTHSCYS-7.5194-8.5547
HLA-A11:014UQ27649QYFQSVSGTHSCYS-6.9601-7.0735
HLA-A24:025HGA7649QYFQSVSGTHSCYS-7.52403-7.63743
HLA-A24:025HGA7649QYFQSVSGTHSCYS-5.82433-6.85963
HLA-B27:056PYJ7649QYFQSVSGTHSCYS-3.28285-4.31815
HLA-B44:053DX87649QYFQSVSGTHSCYS-5.91172-6.94702
HLA-B44:053DX87649QYFQSVSGTHSCYS-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of SEL1L3-CCKAR

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
SEL1L3-CCKARchr425759155chr4264849051019SVSGTHSCYCTGTCTCAGGCACACATTCCTGTTACT
SEL1L3-CCKARchr425759155chr426484905819FQSVSGTHSCYTCCAGTCTGTCTCAGGCACACATTCCTGTTACT
SEL1L3-CCKARchr425759155chr426484905919QSVSGTHSCYAGTCTGTCTCAGGCACACATTCCTGTTACT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
SEL1L3-CCKARchr425759155chr426484905116IAWTVQYFQSVSGTHTCGCCTGGACTGTGCAGTATTTCCAGTCTGTCTCAGGCACACATT
SEL1L3-CCKARchr425759155chr426484905217AWTVQYFQSVSGTHSCCTGGACTGTGCAGTATTTCCAGTCTGTCTCAGGCACACATTCCT

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Information of the samples that have these potential fusion neoantigens of SEL1L3-CCKAR

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
STADSEL1L3-CCKARchr425759155ENST00000502949chr426484905ENST00000295589TCGA-VQ-A925

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Potential target of CAR-T therapy development for SEL1L3-CCKAR

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
HgeneSEL1L3chr4:25759155chr4:26484905ENST00000399878-23241057_107710861133.0TransmembraneHelical
HgeneSEL1L3chr4:25759156chr4:26484905ENST00000399878-23241057_107710861133.0TransmembraneHelical
TgeneCCKARchr4:25759155chr4:26484905ENST0000029558925211_2340429.0TransmembraneHelical%3B Name%3D5
TgeneCCKARchr4:25759155chr4:26484905ENST0000029558925314_3340429.0TransmembraneHelical%3B Name%3D6
TgeneCCKARchr4:25759155chr4:26484905ENST0000029558925350_3730429.0TransmembraneHelical%3B Name%3D7
TgeneCCKARchr4:25759156chr4:26484905ENST0000029558925211_2340429.0TransmembraneHelical%3B Name%3D5
TgeneCCKARchr4:25759156chr4:26484905ENST0000029558925314_3340429.0TransmembraneHelical%3B Name%3D6
TgeneCCKARchr4:25759156chr4:26484905ENST0000029558925350_3730429.0TransmembraneHelical%3B Name%3D7

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 SEL1L3-CCKAR

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 SEL1L3-CCKAR

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