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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:TRERF1-SUPT3H

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TRERF1-SUPT3H
FusionPDB ID: 93946
FusionGDB2.0 ID: 93946
HgeneTgene
Gene symbol

TRERF1

SUPT3H

Gene ID

55809

8464

Gene nametranscriptional regulating factor 1SPT3 homolog, SAGA and STAGA complex component
SynonymsBCAR2|HSA277276|RAPA|TREP132|TReP-132|dJ139D8.5SPT3|SPT3L
Cytomap

6p21.1

6p21.1

Type of geneprotein-codingprotein-coding
Descriptiontranscriptional-regulating factor 1breast cancer anti-estrogen resistance 2rapa-1rapa-2transcriptional regulating protein 132zinc finger protein rapazinc finger transcription factor TReP-132transcription initiation protein SPT3 homologSPT3-like proteinsuppressor of Ty 3 homolog
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000340840, ENST00000354325, 
ENST00000372917, ENST00000372922, 
ENST00000541110, 
ENST00000371458, 
ENST00000459689, ENST00000306867, 
ENST00000371459, ENST00000371460, 
ENST00000371461, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 11 X 7=115519 X 9 X 9=1539
# samples 1622
** MAII scorelog2(16/1155*10)=-2.85174904141606
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(22/1539*10)=-2.80641780280355
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: TRERF1 [Title/Abstract] AND SUPT3H [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: TRERF1 [Title/Abstract] AND SUPT3H [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TRERF1(42210986)-SUPT3H(44988369), # samples:2
Anticipated loss of major functional domain due to fusion event.TRERF1-SUPT3H 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.
TRERF1-SUPT3H 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.
TRERF1-SUPT3H 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.
TRERF1-SUPT3H 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.
TRERF1-SUPT3H seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
TRERF1-SUPT3H seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
TRERF1-SUPT3H seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
TRERF1-SUPT3H seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneTRERF1

GO:0045893

positive regulation of transcription, DNA-templated

11349124

TgeneSUPT3H

GO:0016578

histone deubiquitination

18206972

TgeneSUPT3H

GO:0043966

histone H3 acetylation

11564863



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/chr6:42210986/chr6:44988369)
- 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 TRERF1 (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 SUPT3H (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)
ENST00000340840TRERF1chr642210986-ENST00000371460SUPT3Hchr644988369-5050319848339651160
ENST00000340840TRERF1chr642210986-ENST00000371459SUPT3Hchr644988369-4937319848339651160
ENST00000340840TRERF1chr642210986-ENST00000371461SUPT3Hchr644988369-3966319848339651160
ENST00000340840TRERF1chr642210986-ENST00000306867SUPT3Hchr644988369-3966319848339651160
ENST00000354325TRERF1chr642210986-ENST00000371460SUPT3Hchr644988369-5050319848339651160
ENST00000354325TRERF1chr642210986-ENST00000371459SUPT3Hchr644988369-4937319848339651160
ENST00000354325TRERF1chr642210986-ENST00000371461SUPT3Hchr644988369-3966319848339651160
ENST00000354325TRERF1chr642210986-ENST00000306867SUPT3Hchr644988369-3966319848339651160

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
ENST00000340840ENST00000371460TRERF1chr642210986-SUPT3Hchr644988369-0.0025320020.997468
ENST00000340840ENST00000371459TRERF1chr642210986-SUPT3Hchr644988369-0.0032634650.99673647
ENST00000340840ENST00000371461TRERF1chr642210986-SUPT3Hchr644988369-0.0080553250.9919446
ENST00000340840ENST00000306867TRERF1chr642210986-SUPT3Hchr644988369-0.0080553250.9919446
ENST00000354325ENST00000371460TRERF1chr642210986-SUPT3Hchr644988369-0.0025320020.997468
ENST00000354325ENST00000371459TRERF1chr642210986-SUPT3Hchr644988369-0.0032634650.99673647
ENST00000354325ENST00000371461TRERF1chr642210986-SUPT3Hchr644988369-0.0080553250.9919446
ENST00000354325ENST00000306867TRERF1chr642210986-SUPT3Hchr644988369-0.0080553250.9919446

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 TRERF1-SUPT3H

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
TRERF1chr642210986SUPT3Hchr6449883693198903RKHRTRLAEIIDDCVLQQAAEVSQLR

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Potential FusionNeoAntigen Information of TRERF1-SUPT3H 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.
TRERF1-SUPT3H_42210986_44988369.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)
TRERF1-SUPT3Hchr642210986chr6449883693198HLA-B39:13AEIIDDCVL0.35580.9423716
TRERF1-SUPT3Hchr642210986chr6449883693198HLA-B39:08AEIIDDCVL0.47040.848716
TRERF1-SUPT3Hchr642210986chr6449883693198HLA-B40:04AEIIDDCVL0.99480.6491716
TRERF1-SUPT3Hchr642210986chr6449883693198HLA-B41:03AEIIDDCVL0.48070.5923716
TRERF1-SUPT3Hchr642210986chr6449883693198HLA-A68:02EIIDDCVLQQA0.99420.8177819

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Potential FusionNeoAntigen Information of TRERF1-SUPT3H 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 TRERF1-SUPT3H

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
4731LAEIIDDCVLQQAATRERF1SUPT3Hchr642210986chr6449883693198

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TRERF1-SUPT3H

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-B14:023BVN4731LAEIIDDCVLQQAA-7.9962-8.1096
HLA-B14:023BVN4731LAEIIDDCVLQQAA-5.70842-6.74372
HLA-B52:013W394731LAEIIDDCVLQQAA-6.83737-6.95077
HLA-B52:013W394731LAEIIDDCVLQQAA-4.4836-5.5189
HLA-A11:014UQ24731LAEIIDDCVLQQAA-10.0067-10.1201
HLA-A11:014UQ24731LAEIIDDCVLQQAA-9.03915-10.0745
HLA-A24:025HGA4731LAEIIDDCVLQQAA-6.56204-6.67544
HLA-A24:025HGA4731LAEIIDDCVLQQAA-5.42271-6.45801
HLA-B44:053DX84731LAEIIDDCVLQQAA-7.85648-8.89178
HLA-B44:053DX84731LAEIIDDCVLQQAA-5.3978-5.5112
HLA-A02:016TDR4731LAEIIDDCVLQQAA-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of TRERF1-SUPT3H

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
TRERF1-SUPT3Hchr642210986chr644988369716AEIIDDCVLATCATCGACGATTGTGTGTTACAGCAA
TRERF1-SUPT3Hchr642210986chr644988369819EIIDDCVLQQAATCGACGATTGTGTGTTACAGCAAGCTGCTGAA

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 TRERF1-SUPT3H

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
SARCTRERF1-SUPT3Hchr642210986ENST00000340840chr644988369ENST00000306867TCGA-QQ-A5VC-01A

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Potential target of CAR-T therapy development for TRERF1-SUPT3H

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 TRERF1-SUPT3H

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 TRERF1-SUPT3H

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