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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:SRCAP-IL11RA

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SRCAP-IL11RA
FusionPDB ID: 86237
FusionGDB2.0 ID: 86237
HgeneTgene
Gene symbol

SRCAP

IL11RA

Gene ID

10847

3590

Gene nameSnf2 related CREBBP activator proteininterleukin 11 receptor subunit alpha
SynonymsDOMO1|EAF1|FLHS|SWR1CRSDA
Cytomap

16p11.2

9p13.3

Type of geneprotein-codingprotein-coding
Descriptionhelicase SRCAPSnf2-related CBP activator proteinSwi2/Snf2-related ATPase homolog, domino homolog 1domino homolog 2interleukin-11 receptor subunit alphaIL-11 receptor subunit alphaIL-11R subunit alphainterleukin 11 receptor, alphainterleukin-11 receptor alpha chain
Modification date2020031320200313
UniProtAcc.

Q14626

Main function of 5'-partner protein: FUNCTION: Receptor for interleukin-11 (IL11). The receptor systems for IL6, LIF, OSM, CNTF, IL11 and CT1 can utilize IL6ST for initiating signal transmission. The IL11/IL11RA/IL6ST complex may be involved in the control of proliferation and/or differentiation of skeletogenic progenitor or other mesenchymal cells (Probable). Essential for the normal development of craniofacial bones and teeth. Restricts suture fusion and tooth number. {ECO:0000269|PubMed:21741611, ECO:0000305}.; FUNCTION: [Soluble interleukin-11 receptor subunit alpha]: Soluble form of IL11 receptor (sIL11RA) that acts as an agonist of IL11 activity (PubMed:30279168, PubMed:26876177). The IL11:sIL11RA complex binds to IL6ST/gp130 on cell surfaces and induces signaling also on cells that do not express membrane-bound IL11RA in a process called IL11 trans-signaling (PubMed:30279168, PubMed:26876177). {ECO:0000269|PubMed:26876177, ECO:0000269|PubMed:30279168}.; FUNCTION: [Isoform HCR2]: Soluble form of IL11 receptor (sIL11RA) that acts as an agonist of IL11 activity (PubMed:30279168, PubMed:26876177). The IL11:sIL11RA complex binds to IL6ST/gp130 on cell surfaces and induces signaling also on cells that do not express membrane-bound IL11RA in a process called IL11 trans-signaling (PubMed:30279168, PubMed:26876177). {ECO:0000269|PubMed:26876177, ECO:0000269|PubMed:30279168}.
Ensembl transtripts involved in fusion geneENST idsENST00000262518, ENST00000344771, 
ENST00000395059, 		ENST00000478802, 
ENST00000318041, ENST00000378817, 
ENST00000441545, ENST00000555003, 
ENST00000602473, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 10 X 6=6001 X 2 X 1=2
# samples 132
** MAII scorelog2(13/600*10)=-2.20645087746743
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/2*10)=3.32192809488736
Fusion gene context

PubMed: SRCAP [Title/Abstract] AND IL11RA [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SRCAP [Title/Abstract] AND IL11RA [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SRCAP(30725032)-IL11RA(34655215), # samples:1
SRCAP(30725032)-IL11RA(34655214), # samples:1
Anticipated loss of major functional domain due to fusion event.SRCAP-IL11RA 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.
SRCAP-IL11RA 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.
SRCAP-IL11RA 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.
SRCAP-IL11RA 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.
SRCAP-IL11RA seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
SRCAP-IL11RA seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
SRCAP-IL11RA seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
SRCAP-IL11RA seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
SRCAP-IL11RA 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 button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr16:30725032/chr9:34655215)
- 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 SRCAP (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 IL11RA (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)
ENST00000344771SRCAPchr1630725032+ENST00000555003IL11RAchr934655215+4530287820841461312
ENST00000344771SRCAPchr1630725032+ENST00000441545IL11RAchr934655215+4536287820841461312
ENST00000344771SRCAPchr1630725032+ENST00000378817IL11RAchr934655215+4263287820840501280
ENST00000344771SRCAPchr1630725032+ENST00000318041IL11RAchr934655215+4541287820841461312
ENST00000344771SRCAPchr1630725032+ENST00000602473IL11RAchr934655215+4266287820840501280
ENST00000395059SRCAPchr1630725032+ENST00000555003IL11RAchr934655215+4530287820841461312
ENST00000395059SRCAPchr1630725032+ENST00000441545IL11RAchr934655215+4536287820841461312
ENST00000395059SRCAPchr1630725032+ENST00000378817IL11RAchr934655215+4263287820840501280
ENST00000395059SRCAPchr1630725032+ENST00000318041IL11RAchr934655215+4541287820841461312
ENST00000395059SRCAPchr1630725032+ENST00000602473IL11RAchr934655215+4266287820840501280
ENST00000262518SRCAPchr1630725032+ENST00000555003IL11RAchr934655215+4530287820841461312
ENST00000262518SRCAPchr1630725032+ENST00000441545IL11RAchr934655215+4536287820841461312
ENST00000262518SRCAPchr1630725032+ENST00000378817IL11RAchr934655215+4263287820840501280
ENST00000262518SRCAPchr1630725032+ENST00000318041IL11RAchr934655215+4541287820841461312
ENST00000262518SRCAPchr1630725032+ENST00000602473IL11RAchr934655215+4266287820840501280
ENST00000344771SRCAPchr1630725032+ENST00000555003IL11RAchr934655214+4530287820841461312
ENST00000344771SRCAPchr1630725032+ENST00000441545IL11RAchr934655214+4536287820841461312
ENST00000344771SRCAPchr1630725032+ENST00000378817IL11RAchr934655214+4263287820840501280
ENST00000344771SRCAPchr1630725032+ENST00000318041IL11RAchr934655214+4541287820841461312
ENST00000344771SRCAPchr1630725032+ENST00000602473IL11RAchr934655214+4266287820840501280
ENST00000395059SRCAPchr1630725032+ENST00000555003IL11RAchr934655214+4530287820841461312
ENST00000395059SRCAPchr1630725032+ENST00000441545IL11RAchr934655214+4536287820841461312
ENST00000395059SRCAPchr1630725032+ENST00000378817IL11RAchr934655214+4263287820840501280
ENST00000395059SRCAPchr1630725032+ENST00000318041IL11RAchr934655214+4541287820841461312
ENST00000395059SRCAPchr1630725032+ENST00000602473IL11RAchr934655214+4266287820840501280
ENST00000262518SRCAPchr1630725032+ENST00000555003IL11RAchr934655214+4530287820841461312
ENST00000262518SRCAPchr1630725032+ENST00000441545IL11RAchr934655214+4536287820841461312
ENST00000262518SRCAPchr1630725032+ENST00000378817IL11RAchr934655214+4263287820840501280
ENST00000262518SRCAPchr1630725032+ENST00000318041IL11RAchr934655214+4541287820841461312
ENST00000262518SRCAPchr1630725032+ENST00000602473IL11RAchr934655214+4266287820840501280

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
ENST00000344771ENST00000555003SRCAPchr1630725032+IL11RAchr934655215+0.0044776440.9955224
ENST00000344771ENST00000441545SRCAPchr1630725032+IL11RAchr934655215+0.0044117670.9955882
ENST00000344771ENST00000378817SRCAPchr1630725032+IL11RAchr934655215+0.007058410.9929416
ENST00000344771ENST00000318041SRCAPchr1630725032+IL11RAchr934655215+0.0043576360.9956424
ENST00000344771ENST00000602473SRCAPchr1630725032+IL11RAchr934655215+0.0069645240.9930355
ENST00000395059ENST00000555003SRCAPchr1630725032+IL11RAchr934655215+0.0044776440.9955224
ENST00000395059ENST00000441545SRCAPchr1630725032+IL11RAchr934655215+0.0044117670.9955882
ENST00000395059ENST00000378817SRCAPchr1630725032+IL11RAchr934655215+0.007058410.9929416
ENST00000395059ENST00000318041SRCAPchr1630725032+IL11RAchr934655215+0.0043576360.9956424
ENST00000395059ENST00000602473SRCAPchr1630725032+IL11RAchr934655215+0.0069645240.9930355
ENST00000262518ENST00000555003SRCAPchr1630725032+IL11RAchr934655215+0.0044776440.9955224
ENST00000262518ENST00000441545SRCAPchr1630725032+IL11RAchr934655215+0.0044117670.9955882
ENST00000262518ENST00000378817SRCAPchr1630725032+IL11RAchr934655215+0.007058410.9929416
ENST00000262518ENST00000318041SRCAPchr1630725032+IL11RAchr934655215+0.0043576360.9956424
ENST00000262518ENST00000602473SRCAPchr1630725032+IL11RAchr934655215+0.0069645240.9930355
ENST00000344771ENST00000555003SRCAPchr1630725032+IL11RAchr934655214+0.0044776440.9955224
ENST00000344771ENST00000441545SRCAPchr1630725032+IL11RAchr934655214+0.0044117670.9955882
ENST00000344771ENST00000378817SRCAPchr1630725032+IL11RAchr934655214+0.007058410.9929416
ENST00000344771ENST00000318041SRCAPchr1630725032+IL11RAchr934655214+0.0043576360.9956424
ENST00000344771ENST00000602473SRCAPchr1630725032+IL11RAchr934655214+0.0069645240.9930355
ENST00000395059ENST00000555003SRCAPchr1630725032+IL11RAchr934655214+0.0044776440.9955224
ENST00000395059ENST00000441545SRCAPchr1630725032+IL11RAchr934655214+0.0044117670.9955882
ENST00000395059ENST00000378817SRCAPchr1630725032+IL11RAchr934655214+0.007058410.9929416
ENST00000395059ENST00000318041SRCAPchr1630725032+IL11RAchr934655214+0.0043576360.9956424
ENST00000395059ENST00000602473SRCAPchr1630725032+IL11RAchr934655214+0.0069645240.9930355
ENST00000262518ENST00000555003SRCAPchr1630725032+IL11RAchr934655214+0.0044776440.9955224
ENST00000262518ENST00000441545SRCAPchr1630725032+IL11RAchr934655214+0.0044117670.9955882
ENST00000262518ENST00000378817SRCAPchr1630725032+IL11RAchr934655214+0.007058410.9929416
ENST00000262518ENST00000318041SRCAPchr1630725032+IL11RAchr934655214+0.0043576360.9956424
ENST00000262518ENST00000602473SRCAPchr1630725032+IL11RAchr934655214+0.0069645240.9930355

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 SRCAP-IL11RA

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SRCAPchr1630725032IL11RAchr9346552142878890QEYNEGLVKRLHKMSSSCSGLSRVLV
SRCAPchr1630725032IL11RAchr9346552152878890QEYNEGLVKRLHKMSSSCSGLSRVLV

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Potential FusionNeoAntigen Information of SRCAP-IL11RA 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.
SRCAP-IL11RA_30725032_34655214.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)
SRCAP-IL11RAchr1630725032chr9346552142878HLA-A02:13GLVKRLHKM0.44610.6754514
SRCAP-IL11RAchr1630725032chr9346552142878HLA-A74:09KMSSSCSGLSR0.98520.61391223
SRCAP-IL11RAchr1630725032chr9346552142878HLA-A74:11KMSSSCSGLSR0.98520.61391223
SRCAP-IL11RAchr1630725032chr9346552142878HLA-A74:03KMSSSCSGLSR0.98520.61391223
SRCAP-IL11RAchr1630725032chr9346552142878HLA-A02:03GLVKRLHKM0.70790.6112514
SRCAP-IL11RAchr1630725032chr9346552142878HLA-A74:01KMSSSCSGLSR0.98520.61391223

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Potential FusionNeoAntigen Information of SRCAP-IL11RA 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 SRCAP-IL11RA

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
5781LVKRLHKMSSSCSGSRCAPIL11RAchr1630725032chr9346552142878

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SRCAP-IL11RA

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-B14:023BVN5781LVKRLHKMSSSCSG-7.15543-7.26883
HLA-B14:023BVN5781LVKRLHKMSSSCSG-4.77435-5.80965
HLA-B52:013W395781LVKRLHKMSSSCSG-6.80875-6.92215
HLA-B52:013W395781LVKRLHKMSSSCSG-4.20386-5.23916
HLA-A11:014UQ25781LVKRLHKMSSSCSG-7.5194-8.5547
HLA-A11:014UQ25781LVKRLHKMSSSCSG-6.9601-7.0735
HLA-A24:025HGA5781LVKRLHKMSSSCSG-7.52403-7.63743
HLA-A24:025HGA5781LVKRLHKMSSSCSG-5.82433-6.85963
HLA-B27:056PYJ5781LVKRLHKMSSSCSG-3.28285-4.31815
HLA-B44:053DX85781LVKRLHKMSSSCSG-5.91172-6.94702
HLA-B44:053DX85781LVKRLHKMSSSCSG-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of SRCAP-IL11RA

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
SRCAP-IL11RAchr1630725032chr9346552141223KMSSSCSGLSRAAGATGAGCAGCAGCTGCTCAGGGCTGAGCAGG
SRCAP-IL11RAchr1630725032chr934655214514GLVKRLHKMGGTCTAGTCAAACGCCTCCACAAGATG

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 SRCAP-IL11RA

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
LUSCSRCAP-IL11RAchr1630725032ENST00000262518chr934655214ENST00000318041TCGA-43-7658

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Potential target of CAR-T therapy development for SRCAP-IL11RA

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
TgeneIL11RAchr16:30725032chr9:34655214ENST00000318041013371_3910423.0TransmembraneHelical
TgeneIL11RAchr16:30725032chr9:34655214ENST00000378817011371_3910391.0TransmembraneHelical
TgeneIL11RAchr16:30725032chr9:34655214ENST00000441545013371_3910423.0TransmembraneHelical
TgeneIL11RAchr16:30725032chr9:34655214ENST00000555003013371_3910423.0TransmembraneHelical
TgeneIL11RAchr16:30725032chr9:34655214ENST00000602473-110371_3910391.0TransmembraneHelical
TgeneIL11RAchr16:30725032chr9:34655215ENST00000318041013371_3910423.0TransmembraneHelical
TgeneIL11RAchr16:30725032chr9:34655215ENST00000378817011371_3910391.0TransmembraneHelical
TgeneIL11RAchr16:30725032chr9:34655215ENST00000441545013371_3910423.0TransmembraneHelical
TgeneIL11RAchr16:30725032chr9:34655215ENST00000555003013371_3910423.0TransmembraneHelical
TgeneIL11RAchr16:30725032chr9:34655215ENST00000602473-110371_3910391.0TransmembraneHelical

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 SRCAP-IL11RA

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 SRCAP-IL11RA

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