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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:PREP-AIM1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PREP-AIM1
FusionPDB ID: 68512
FusionGDB2.0 ID: 68512
HgeneTgene
Gene symbol

PREP

AIM1

Gene ID

5550

51151

Gene nameprolyl endopeptidasesolute carrier family 45 member 2
SynonymsPE|PEP1A1|AIM1|MATP|OCA4|SHEP5
Cytomap

6q21

5p13.2

Type of geneprotein-codingprotein-coding
Descriptionprolyl endopeptidasedJ355L5.1 (prolyl endopeptidase)post-proline cleaving enzymeprolyl oligopeptidasemembrane-associated transporter proteinmelanoma antigen AIM1protein AIM-1underwhite
Modification date2020031320200313
UniProtAcc

PNOC

Main function of 5'-partner protein: 176
.
Ensembl transtripts involved in fusion geneENST idsENST00000369110, ENST00000487681, 
ENST00000369066, ENST00000535438, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 10 X 6=8408 X 8 X 4=256
# samples 168
** MAII scorelog2(16/840*10)=-2.39231742277876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/256*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PREP [Title/Abstract] AND AIM1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PREP [Title/Abstract] AND AIM1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PREP(105729621)-AIM1(107003643), # samples:3
Anticipated loss of major functional domain due to fusion event.PREP-AIM1 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.
PREP-AIM1 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.
PREP-AIM1 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.
PREP-AIM1 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/chr6:105729621/chr6:107003643)
- 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 PREP (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 AIM1 (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)
ENST00000369110PREPchr6105729621-ENST00000369066AIM1chr6107003643+47272031732841922
ENST00000369110PREPchr6105729621-ENST00000535438AIM1chr6107003643+35042031732841922

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
ENST00000369110ENST00000369066PREPchr6105729621-AIM1chr6107003643+0.0004061540.9995939
ENST00000369110ENST00000535438PREPchr6105729621-AIM1chr6107003643+0.0003388930.9996611

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 PREP-AIM1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PREPchr6105729621AIM1chr61070036432031653CSDSKQHFEWLVNWVVYDGENFTGNQ

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Potential FusionNeoAntigen Information of PREP-AIM1 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.
PREP-AIM1_105729621_107003643.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)
PREP-AIM1chr6105729621chr61070036432031HLA-B38:02QHFEWLVNW0.93190.9952514
PREP-AIM1chr6105729621chr61070036432031HLA-B38:01QHFEWLVNW0.92850.9958514
PREP-AIM1chr6105729621chr61070036432031HLA-A24:15QHFEWLVNW0.84070.5702514
PREP-AIM1chr6105729621chr61070036432031HLA-A31:08QHFEWLVNW0.83310.8005514
PREP-AIM1chr6105729621chr61070036432031HLA-A24:17QHFEWLVNW0.78820.6716514
PREP-AIM1chr6105729621chr61070036432031HLA-A32:13QHFEWLVNW0.68850.9826514
PREP-AIM1chr6105729621chr61070036432031HLA-B15:18QHFEWLVNW0.66190.9088514
PREP-AIM1chr6105729621chr61070036432031HLA-A24:14QHFEWLVNW0.3680.5191514
PREP-AIM1chr6105729621chr61070036432031HLA-B15:37QHFEWLVNW0.28560.7541514
PREP-AIM1chr6105729621chr61070036432031HLA-B27:02QHFEWLVNW0.02070.6515514
PREP-AIM1chr6105729621chr61070036432031HLA-A31:08KQHFEWLVNW0.99460.6373414
PREP-AIM1chr6105729621chr61070036432031HLA-B18:01FEWLVNWVVY0.98050.923717
PREP-AIM1chr6105729621chr61070036432031HLA-A32:13KQHFEWLVNW0.940.9919414
PREP-AIM1chr6105729621chr61070036432031HLA-B38:05QHFEWLVNW0.92850.9958514
PREP-AIM1chr6105729621chr61070036432031HLA-B18:06FEWLVNWVV0.77420.9656716
PREP-AIM1chr6105729621chr61070036432031HLA-B18:03FEWLVNWVV0.72590.9409716
PREP-AIM1chr6105729621chr61070036432031HLA-B15:24KQHFEWLVNW0.99950.9412414
PREP-AIM1chr6105729621chr61070036432031HLA-A32:01KQHFEWLVNW0.99360.9879414
PREP-AIM1chr6105729621chr61070036432031HLA-B18:04FEWLVNWVVY0.99050.9325717
PREP-AIM1chr6105729621chr61070036432031HLA-B18:05FEWLVNWVVY0.98050.923717
PREP-AIM1chr6105729621chr61070036432031HLA-B18:08FEWLVNWVVY0.97990.8284717
PREP-AIM1chr6105729621chr61070036432031HLA-B18:06FEWLVNWVVY0.97920.9267717
PREP-AIM1chr6105729621chr61070036432031HLA-B18:03FEWLVNWVVY0.96920.9133717
PREP-AIM1chr6105729621chr61070036432031HLA-B18:11FEWLVNWVVY0.93290.9035717

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Potential FusionNeoAntigen Information of PREP-AIM1 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.
PREP-AIM1_105729621_107003643.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)
PREP-AIM1chr6105729621chr61070036432031DRB1-0129KQHFEWLVNWVVYDG419
PREP-AIM1chr6105729621chr61070036432031DRB1-1527KQHFEWLVNWVVYDG419
PREP-AIM1chr6105729621chr61070036432031DRB1-1529LVNWVVYDGENFTGN1025
PREP-AIM1chr6105729621chr61070036432031DRB1-1534KQHFEWLVNWVVYDG419
PREP-AIM1chr6105729621chr61070036432031DRB1-1602KQHFEWLVNWVVYDG419
PREP-AIM1chr6105729621chr61070036432031DRB1-1605KQHFEWLVNWVVYDG419
PREP-AIM1chr6105729621chr61070036432031DRB1-1605SKQHFEWLVNWVVYD318
PREP-AIM1chr6105729621chr61070036432031DRB1-1607KQHFEWLVNWVVYDG419
PREP-AIM1chr6105729621chr61070036432031DRB1-1607SKQHFEWLVNWVVYD318
PREP-AIM1chr6105729621chr61070036432031DRB1-1609KQHFEWLVNWVVYDG419
PREP-AIM1chr6105729621chr61070036432031DRB1-1610KQHFEWLVNWVVYDG419
PREP-AIM1chr6105729621chr61070036432031DRB1-1611KQHFEWLVNWVVYDG419
PREP-AIM1chr6105729621chr61070036432031DRB1-1614KQHFEWLVNWVVYDG419
PREP-AIM1chr6105729621chr61070036432031DRB1-1616KQHFEWLVNWVVYDG419

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Fusion breakpoint peptide structures of PREP-AIM1

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
3308HFEWLVNWVVYDGEPREPAIM1chr6105729621chr61070036432031

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PREP-AIM1

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-B14:023BVN3308HFEWLVNWVVYDGE-7.9962-8.1096
HLA-B14:023BVN3308HFEWLVNWVVYDGE-5.70842-6.74372
HLA-B52:013W393308HFEWLVNWVVYDGE-6.83737-6.95077
HLA-B52:013W393308HFEWLVNWVVYDGE-4.4836-5.5189
HLA-A11:014UQ23308HFEWLVNWVVYDGE-10.0067-10.1201
HLA-A11:014UQ23308HFEWLVNWVVYDGE-9.03915-10.0745
HLA-A24:025HGA3308HFEWLVNWVVYDGE-6.56204-6.67544
HLA-A24:025HGA3308HFEWLVNWVVYDGE-5.42271-6.45801
HLA-B44:053DX83308HFEWLVNWVVYDGE-7.85648-8.89178
HLA-B44:053DX83308HFEWLVNWVVYDGE-5.3978-5.5112
HLA-A02:016TDR3308HFEWLVNWVVYDGE-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of PREP-AIM1

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
PREP-AIM1chr6105729621chr6107003643414KQHFEWLVNWCAAACAACACTTTGAATGGCTTGTCAACTG
PREP-AIM1chr6105729621chr6107003643514QHFEWLVNWACAACACTTTGAATGGCTTGTCAACTG
PREP-AIM1chr6105729621chr6107003643716FEWLVNWVVCTTTGAATGGCTTGTCAACTGGGTTGT
PREP-AIM1chr6105729621chr6107003643717FEWLVNWVVYCTTTGAATGGCTTGTCAACTGGGTTGTATA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
PREP-AIM1chr6105729621chr61070036431025LVNWVVYDGENFTGNGCTTGTCAACTGGGTTGTATATGATGGAGAAAATTTCACTGGTAA
PREP-AIM1chr6105729621chr6107003643318SKQHFEWLVNWVVYDCAGCAAACAACACTTTGAATGGCTTGTCAACTGGGTTGTATATGA
PREP-AIM1chr6105729621chr6107003643419KQHFEWLVNWVVYDGCAAACAACACTTTGAATGGCTTGTCAACTGGGTTGTATATGATGG

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Information of the samples that have these potential fusion neoantigens of PREP-AIM1

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
BRCAPREP-AIM1chr6105729621ENST00000369110chr6107003643ENST00000369066TCGA-C8-A137-01A

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Potential target of CAR-T therapy development for PREP-AIM1

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 PREP-AIM1

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 PREP-AIM1

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