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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:MEIS1-SUPT3H

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: MEIS1-SUPT3H
FusionPDB ID: 52889
FusionGDB2.0 ID: 52889
HgeneTgene
Gene symbol

MEIS1

SUPT3H

Gene ID

4211

8464

Gene nameMeis homeobox 1SPT3 homolog, SAGA and STAGA complex component
Synonyms-SPT3|SPT3L
Cytomap

2p14

6p21.1

Type of geneprotein-codingprotein-coding
Descriptionhomeobox protein Meis1Meis1, myeloid ecotropic viral integration site 1 homologWUGSC:H_NH0444B04.1leukemogenic homolog proteintranscription initiation protein SPT3 homologSPT3-like proteinsuppressor of Ty 3 homolog
Modification date2020031320200313
UniProtAcc

O00470

Main function of 5'-partner protein: FUNCTION: Acts as a transcriptional regulator of PAX6. Acts as a transcriptional activator of PF4 in complex with PBX1 or PBX2. Required for hematopoiesis, megakaryocyte lineage development and vascular patterning. May function as a cofactor for HOXA7 and HOXA9 in the induction of myeloid leukemias. {ECO:0000269|PubMed:12609849}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000272369, ENST00000398506, 
ENST00000407092, ENST00000488550, 
ENST00000495021, ENST00000560281, 
ENST00000409517, ENST00000444274, 
ENST00000459689, ENST00000306867, 
ENST00000371458, ENST00000371459, 
ENST00000371460, ENST00000371461, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score3 X 2 X 3=1819 X 9 X 9=1539
# samples 322
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
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: MEIS1 [Title/Abstract] AND SUPT3H [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: MEIS1 [Title/Abstract] AND SUPT3H [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)MEIS1(66739426)-SUPT3H(44900500), # samples:1
Anticipated loss of major functional domain due to fusion event.MEIS1-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.
MEIS1-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.
MEIS1-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.
MEIS1-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.
* 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
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/chr2:66739426/chr6:44900500)
- 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 MEIS1 (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)
ENST00000560281MEIS1chr266739426+ENST00000371460SUPT3Hchr644900500-284916127241764346
ENST00000560281MEIS1chr266739426+ENST00000371459SUPT3Hchr644900500-273616127241764346
ENST00000560281MEIS1chr266739426+ENST00000371461SUPT3Hchr644900500-176516127241764347
ENST00000560281MEIS1chr266739426+ENST00000306867SUPT3Hchr644900500-176516127241764347
ENST00000560281MEIS1chr266739426+ENST00000371458SUPT3Hchr644900500-183316127241788354
ENST00000407092MEIS1chr266739426+ENST00000371460SUPT3Hchr644900500-258213454571497346
ENST00000407092MEIS1chr266739426+ENST00000371459SUPT3Hchr644900500-246913454571497346
ENST00000407092MEIS1chr266739426+ENST00000371461SUPT3Hchr644900500-149813454571497347
ENST00000407092MEIS1chr266739426+ENST00000306867SUPT3Hchr644900500-149813454571497347
ENST00000407092MEIS1chr266739426+ENST00000371458SUPT3Hchr644900500-156613454571521354
ENST00000272369MEIS1chr266739426+ENST00000371460SUPT3Hchr644900500-258213454571497346
ENST00000272369MEIS1chr266739426+ENST00000371459SUPT3Hchr644900500-246913454571497346
ENST00000272369MEIS1chr266739426+ENST00000371461SUPT3Hchr644900500-149813454571497347
ENST00000272369MEIS1chr266739426+ENST00000306867SUPT3Hchr644900500-149813454571497347
ENST00000272369MEIS1chr266739426+ENST00000371458SUPT3Hchr644900500-156613454571521354
ENST00000488550MEIS1chr266739426+ENST00000371460SUPT3Hchr644900500-242411872991339346
ENST00000488550MEIS1chr266739426+ENST00000371459SUPT3Hchr644900500-231111872991339346
ENST00000488550MEIS1chr266739426+ENST00000371461SUPT3Hchr644900500-134011872991339347
ENST00000488550MEIS1chr266739426+ENST00000306867SUPT3Hchr644900500-134011872991339347
ENST00000488550MEIS1chr266739426+ENST00000371458SUPT3Hchr644900500-140811872991363354
ENST00000398506MEIS1chr266739426+ENST00000371460SUPT3Hchr644900500-245712203111372353
ENST00000398506MEIS1chr266739426+ENST00000371459SUPT3Hchr644900500-234412203111372353
ENST00000398506MEIS1chr266739426+ENST00000371461SUPT3Hchr644900500-137312203111372354
ENST00000398506MEIS1chr266739426+ENST00000306867SUPT3Hchr644900500-137312203111372354
ENST00000398506MEIS1chr266739426+ENST00000371458SUPT3Hchr644900500-144112203111396361
ENST00000495021MEIS1chr266739426+ENST00000371460SUPT3Hchr644900500-223710003071152281
ENST00000495021MEIS1chr266739426+ENST00000371459SUPT3Hchr644900500-212410003071152281
ENST00000495021MEIS1chr266739426+ENST00000371461SUPT3Hchr644900500-115310003071152282
ENST00000495021MEIS1chr266739426+ENST00000306867SUPT3Hchr644900500-115310003071152282
ENST00000495021MEIS1chr266739426+ENST00000371458SUPT3Hchr644900500-122110003071176289

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
ENST00000560281ENST00000371460MEIS1chr266739426+SUPT3Hchr644900500-0.0016860790.9983139
ENST00000560281ENST00000371459MEIS1chr266739426+SUPT3Hchr644900500-0.0022863420.9977137
ENST00000560281ENST00000371461MEIS1chr266739426+SUPT3Hchr644900500-0.0062127580.9937873
ENST00000560281ENST00000306867MEIS1chr266739426+SUPT3Hchr644900500-0.0062127580.9937873
ENST00000560281ENST00000371458MEIS1chr266739426+SUPT3Hchr644900500-0.0058305640.9941695
ENST00000407092ENST00000371460MEIS1chr266739426+SUPT3Hchr644900500-0.0010862360.99891376
ENST00000407092ENST00000371459MEIS1chr266739426+SUPT3Hchr644900500-0.0015469570.998453
ENST00000407092ENST00000371461MEIS1chr266739426+SUPT3Hchr644900500-0.0047058780.99529415
ENST00000407092ENST00000306867MEIS1chr266739426+SUPT3Hchr644900500-0.0047058780.99529415
ENST00000407092ENST00000371458MEIS1chr266739426+SUPT3Hchr644900500-0.0040747540.9959253
ENST00000272369ENST00000371460MEIS1chr266739426+SUPT3Hchr644900500-0.0010862360.99891376
ENST00000272369ENST00000371459MEIS1chr266739426+SUPT3Hchr644900500-0.0015469570.998453
ENST00000272369ENST00000371461MEIS1chr266739426+SUPT3Hchr644900500-0.0047058780.99529415
ENST00000272369ENST00000306867MEIS1chr266739426+SUPT3Hchr644900500-0.0047058780.99529415
ENST00000272369ENST00000371458MEIS1chr266739426+SUPT3Hchr644900500-0.0040747540.9959253
ENST00000488550ENST00000371460MEIS1chr266739426+SUPT3Hchr644900500-0.0011190970.9988809
ENST00000488550ENST00000371459MEIS1chr266739426+SUPT3Hchr644900500-0.0015984910.99840146
ENST00000488550ENST00000371461MEIS1chr266739426+SUPT3Hchr644900500-0.0058177030.9941823
ENST00000488550ENST00000306867MEIS1chr266739426+SUPT3Hchr644900500-0.0058177030.9941823
ENST00000488550ENST00000371458MEIS1chr266739426+SUPT3Hchr644900500-0.0049989490.995001
ENST00000398506ENST00000371460MEIS1chr266739426+SUPT3Hchr644900500-0.0026242130.99737585
ENST00000398506ENST00000371459MEIS1chr266739426+SUPT3Hchr644900500-0.0033963140.9966037
ENST00000398506ENST00000371461MEIS1chr266739426+SUPT3Hchr644900500-0.0110697070.9889303
ENST00000398506ENST00000306867MEIS1chr266739426+SUPT3Hchr644900500-0.0110697070.9889303
ENST00000398506ENST00000371458MEIS1chr266739426+SUPT3Hchr644900500-0.0108302110.9891698
ENST00000495021ENST00000371460MEIS1chr266739426+SUPT3Hchr644900500-0.0019946840.99800533
ENST00000495021ENST00000371459MEIS1chr266739426+SUPT3Hchr644900500-0.0025473020.9974527
ENST00000495021ENST00000371461MEIS1chr266739426+SUPT3Hchr644900500-0.0085883840.99141157
ENST00000495021ENST00000306867MEIS1chr266739426+SUPT3Hchr644900500-0.0085883840.99141157
ENST00000495021ENST00000371458MEIS1chr266739426+SUPT3Hchr644900500-0.0097592980.9902407

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 MEIS1-SUPT3H

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
MEIS1chr266739426SUPT3Hchr6449005001000231TNIMRAWLFQHLTSTAACGVEAHSDA
MEIS1chr266739426SUPT3Hchr6449005001187296TNIMRAWLFQHLTSTAACGVEAHSDA
MEIS1chr266739426SUPT3Hchr6449005001220303TNIMRAWLFQHLTSTAACGVEAHSDA
MEIS1chr266739426SUPT3Hchr6449005001345296TNIMRAWLFQHLTSTAACGVEAHSDA
MEIS1chr266739426SUPT3Hchr6449005001612296TNIMRAWLFQHLTSTAACGVEAHSDA

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Potential FusionNeoAntigen Information of MEIS1-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.
MEIS1-SUPT3H_66739426_44900500.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)
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-B39:06QHLTSTAA0.99940.786917
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-B39:06FQHLTSTAA0.98580.8243817
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-B39:06QHLTSTAAC0.98520.7769918
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-B39:24QHLTSTAAC0.98480.5745918
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-A02:22WLFQHLTST0.97140.7149615
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-B39:01QHLTSTAAC0.96540.8702918
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-A02:13WLFQHLTST0.96010.8005615
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-B50:01FQHLTSTAA0.89360.8408817
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-A02:38WLFQHLTST0.86620.6913615
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-B15:04FQHLTSTAA0.94760.9507817
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-B39:05QHLTSTAAC0.94290.866918
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-A02:03WLFQHLTST0.97670.8273615
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-B50:05FQHLTSTAA0.89360.8408817
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-B50:04FQHLTSTAA0.89360.8408817
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-B15:09QHLTSTAAC0.88380.8187918
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-B15:09FQHLTSTAA0.36510.9187817
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-A02:03WLFQHLTSTA0.99410.7078616
MEIS1-SUPT3Hchr266739426chr6449005001345HLA-A02:03AWLFQHLTST0.24540.8427515

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Potential FusionNeoAntigen Information of MEIS1-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 MEIS1-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
10498WLFQHLTSTAACGVMEIS1SUPT3Hchr266739426chr6449005001345

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of MEIS1-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-B14:023BVN10498WLFQHLTSTAACGV-7.15543-7.26883
HLA-B14:023BVN10498WLFQHLTSTAACGV-4.77435-5.80965
HLA-B52:013W3910498WLFQHLTSTAACGV-6.80875-6.92215
HLA-B52:013W3910498WLFQHLTSTAACGV-4.20386-5.23916
HLA-A11:014UQ210498WLFQHLTSTAACGV-7.5194-8.5547
HLA-A11:014UQ210498WLFQHLTSTAACGV-6.9601-7.0735
HLA-A24:025HGA10498WLFQHLTSTAACGV-7.52403-7.63743
HLA-A24:025HGA10498WLFQHLTSTAACGV-5.82433-6.85963
HLA-B27:056PYJ10498WLFQHLTSTAACGV-3.28285-4.31815
HLA-B44:053DX810498WLFQHLTSTAACGV-5.91172-6.94702
HLA-B44:053DX810498WLFQHLTSTAACGV-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of MEIS1-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
MEIS1-SUPT3Hchr266739426chr644900500515AWLFQHLTSTGCGTGGCTGTTCCAGCATCTAACAAGCACT
MEIS1-SUPT3Hchr266739426chr644900500615WLFQHLTSTTGGCTGTTCCAGCATCTAACAAGCACT
MEIS1-SUPT3Hchr266739426chr644900500616WLFQHLTSTATGGCTGTTCCAGCATCTAACAAGCACTGCA
MEIS1-SUPT3Hchr266739426chr644900500817FQHLTSTAATTCCAGCATCTAACAAGCACTGCAGCC
MEIS1-SUPT3Hchr266739426chr644900500917QHLTSTAACAGCATCTAACAAGCACTGCAGCC
MEIS1-SUPT3Hchr266739426chr644900500918QHLTSTAACCAGCATCTAACAAGCACTGCAGCCTGT

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 MEIS1-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
OVMEIS1-SUPT3Hchr266739426ENST00000272369chr644900500ENST00000306867TCGA-24-1546

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Potential target of CAR-T therapy development for MEIS1-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 MEIS1-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 MEIS1-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