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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:RABEP2-SRCAP

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RABEP2-SRCAP
FusionPDB ID: 71533
FusionGDB2.0 ID: 71533
HgeneTgene
Gene symbol

RABEP2

SRCAP

Gene ID

79874

10847

Gene namerabaptin, RAB GTPase binding effector protein 2Snf2 related CREBBP activator protein
SynonymsFRADOMO1|EAF1|FLHS|SWR1
Cytomap

16p11.2

16p11.2

Type of geneprotein-codingprotein-coding
Descriptionrab GTPase-binding effector protein 2Rabaptin-5 betarabaptin-5betahelicase SRCAPSnf2-related CBP activator proteinSwi2/Snf2-related ATPase homolog, domino homolog 1domino homolog 2
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000561803, ENST00000357573, 
ENST00000358201, ENST00000544477, 
ENST00000262518, ENST00000344771, 
ENST00000395059, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 3 X 3=366 X 7 X 4=168
# samples 48
** MAII scorelog2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(8/168*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: RABEP2 [Title/Abstract] AND SRCAP [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: RABEP2 [Title/Abstract] AND SRCAP [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RABEP2(28931107)-SRCAP(30740287), # samples:1
Anticipated loss of major functional domain due to fusion event.RABEP2-SRCAP 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.
RABEP2-SRCAP 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.
RABEP2-SRCAP 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.
RABEP2-SRCAP 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


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/chr16:28931107/chr16:30740287)
- 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 RABEP2 (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 SRCAP (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)
ENST00000357573RABEP2chr1628931107-ENST00000344771SRCAPchr1630740287+49134835145171488
ENST00000357573RABEP2chr1628931107-ENST00000395059SRCAPchr1630740287+49134835145171488
ENST00000357573RABEP2chr1628931107-ENST00000262518SRCAPchr1630740287+49144835145171488
ENST00000358201RABEP2chr1628931107-ENST00000344771SRCAPchr1630740287+5451102158950551488
ENST00000358201RABEP2chr1628931107-ENST00000395059SRCAPchr1630740287+5451102158950551488
ENST00000358201RABEP2chr1628931107-ENST00000262518SRCAPchr1630740287+5452102158950551488
ENST00000544477RABEP2chr1628931107-ENST00000344771SRCAPchr1630740287+46822523342861417
ENST00000544477RABEP2chr1628931107-ENST00000395059SRCAPchr1630740287+46822523342861417
ENST00000544477RABEP2chr1628931107-ENST00000262518SRCAPchr1630740287+46832523342861417

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
ENST00000357573ENST00000344771RABEP2chr1628931107-SRCAPchr1630740287+0.0022777030.9977223
ENST00000357573ENST00000395059RABEP2chr1628931107-SRCAPchr1630740287+0.0022777030.9977223
ENST00000357573ENST00000262518RABEP2chr1628931107-SRCAPchr1630740287+0.0023074950.9976926
ENST00000358201ENST00000344771RABEP2chr1628931107-SRCAPchr1630740287+0.004343380.9956566
ENST00000358201ENST00000395059RABEP2chr1628931107-SRCAPchr1630740287+0.004343380.9956566
ENST00000358201ENST00000262518RABEP2chr1628931107-SRCAPchr1630740287+0.0043946170.9956054
ENST00000544477ENST00000344771RABEP2chr1628931107-SRCAPchr1630740287+0.0021019840.997898
ENST00000544477ENST00000395059RABEP2chr1628931107-SRCAPchr1630740287+0.0021019840.997898
ENST00000544477ENST00000262518RABEP2chr1628931107-SRCAPchr1630740287+0.0021309010.99786913

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 RABEP2-SRCAP

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
RABEP2chr1628931107SRCAPchr16307402871021144AYPLDSLEKQMEKDSLEEKRKRQRSE
RABEP2chr1628931107SRCAPchr16307402871021694TTPPRCSPARERVPRPAPRPRPTPAS
RABEP2chr1628931107SRCAPchr1630740287252623TTPPRCSPARERVPRPAPRPRPTPAS
RABEP2chr1628931107SRCAPchr163074028725273AYPLDSLEKQMEKDSLEEKRKRQRSE
RABEP2chr1628931107SRCAPchr1630740287483144AYPLDSLEKQMEKDSLEEKRKRQRSE
RABEP2chr1628931107SRCAPchr1630740287483694TTPPRCSPARERVPRPAPRPRPTPAS

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Potential FusionNeoAntigen Information of RABEP2-SRCAP 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.
RABEP2-SRCAP_28931107_30740287.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)
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B50:01RERVPRPA0.84230.8733917
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B45:01RERVPRPAP0.98030.8413918
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B50:02RERVPRPAP0.82580.6691918
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B41:01RERVPRPAP0.54170.8566918
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B50:01RERVPRPAP0.17840.8899918
RABEP2-SRCAPchr1628931107chr1630740287483HLA-A74:11RVPRPAPRPR0.97210.76021121
RABEP2-SRCAPchr1628931107chr1630740287483HLA-A74:09RVPRPAPRPR0.97210.76021121
RABEP2-SRCAPchr1628931107chr1630740287483HLA-A74:03RVPRPAPRPR0.97210.76021121
RABEP2-SRCAPchr1628931107chr1630740287483HLA-A30:08RVPRPAPRPR0.97040.74021121
RABEP2-SRCAPchr1628931107chr1630740287483HLA-A31:02RVPRPAPRPR0.96290.73781121
RABEP2-SRCAPchr1628931107chr1630740287483HLA-A31:06RVPRPAPRPR0.87170.58411121
RABEP2-SRCAPchr1628931107chr1630740287483HLA-A03:12RVPRPAPRPR0.7710.50011121
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B40:06RERVPRPA0.99990.7374917
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B40:06RERVPRPAP0.99220.8272918
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B73:01ARERVPRPA0.96470.8774817
RABEP2-SRCAPchr1628931107chr1630740287483HLA-A31:01RVPRPAPRPR0.97490.70851121
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B73:01ERVPRPAPRP0.96550.90241020
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B50:04RERVPRPA0.84230.8733917
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B50:05RERVPRPA0.84230.8733917
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B07:09VPRPAPRPR0.98460.79551221
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B50:04RERVPRPAP0.17840.8899918
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B50:05RERVPRPAP0.17840.8899918
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B27:10RERVPRPAPR0.98690.6456919
RABEP2-SRCAPchr1628931107chr1630740287483HLA-A30:01RVPRPAPRPR0.97750.85581121
RABEP2-SRCAPchr1628931107chr1630740287483HLA-A74:01RVPRPAPRPR0.97210.76021121
RABEP2-SRCAPchr1628931107chr1630740287483HLA-B55:02SPARERVPRPA0.97560.5063617

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Potential FusionNeoAntigen Information of RABEP2-SRCAP 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 RABEP2-SRCAP

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
8872SPARERVPRPAPRPRABEP2SRCAPchr1628931107chr1630740287483

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RABEP2-SRCAP

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-B14:023BVN8872SPARERVPRPAPRP-7.9962-8.1096
HLA-B14:023BVN8872SPARERVPRPAPRP-5.70842-6.74372
HLA-B52:013W398872SPARERVPRPAPRP-6.83737-6.95077
HLA-B52:013W398872SPARERVPRPAPRP-4.4836-5.5189
HLA-A11:014UQ28872SPARERVPRPAPRP-10.0067-10.1201
HLA-A11:014UQ28872SPARERVPRPAPRP-9.03915-10.0745
HLA-A24:025HGA8872SPARERVPRPAPRP-6.56204-6.67544
HLA-A24:025HGA8872SPARERVPRPAPRP-5.42271-6.45801
HLA-B44:053DX88872SPARERVPRPAPRP-7.85648-8.89178
HLA-B44:053DX88872SPARERVPRPAPRP-5.3978-5.5112
HLA-A02:016TDR8872SPARERVPRPAPRP-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of RABEP2-SRCAP

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
RABEP2-SRCAPchr1628931107chr16307402871020ERVPRPAPRPATGGAAAAGGACTCCCTGGAGGAAAAGCGG
RABEP2-SRCAPchr1628931107chr16307402871121RVPRPAPRPRGAAAAGGACTCCCTGGAGGAAAAGCGGAAG
RABEP2-SRCAPchr1628931107chr16307402871221VPRPAPRPRAAGGACTCCCTGGAGGAAAAGCGGAAG
RABEP2-SRCAPchr1628931107chr1630740287617SPARERVPRPACTGGAGAAGCAGATGGAAAAGGACTCCCTGGAG
RABEP2-SRCAPchr1628931107chr1630740287817ARERVPRPAAAGCAGATGGAAAAGGACTCCCTGGAG
RABEP2-SRCAPchr1628931107chr1630740287917RERVPRPACAGATGGAAAAGGACTCCCTGGAG
RABEP2-SRCAPchr1628931107chr1630740287918RERVPRPAPCAGATGGAAAAGGACTCCCTGGAGGAA
RABEP2-SRCAPchr1628931107chr1630740287919RERVPRPAPRCAGATGGAAAAGGACTCCCTGGAGGAAAAG

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 RABEP2-SRCAP

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
PRADRABEP2-SRCAPchr1628931107ENST00000357573chr1630740287ENST00000262518TCGA-EJ-7794-01A

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Potential target of CAR-T therapy development for RABEP2-SRCAP

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 RABEP2-SRCAP

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 RABEP2-SRCAP

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