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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:GLT8D2-YY1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: GLT8D2-YY1
FusionPDB ID: 33369
FusionGDB2.0 ID: 33369
HgeneTgene
Gene symbol

GLT8D2

YY1

Gene ID

83468

7528

Gene nameglycosyltransferase 8 domain containing 2YY1 transcription factor
Synonyms-DELTA|GADEVS|INO80S|NF-E1|UCRBP|YIN-YANG-1
Cytomap

12q23.3

14q32.2

Type of geneprotein-codingprotein-coding
Descriptionglycosyltransferase 8 domain-containing protein 2transcriptional repressor protein YY1INO80 complex subunit SYY-1Yin and Yang 1 proteindelta transcription factor
Modification date2020031320200313
UniProtAcc

Q9H1C3

Main function of 5'-partner protein:

YY1AP1

Main function of 5'-partner protein: 796
Ensembl transtripts involved in fusion geneENST idsENST00000360814, ENST00000546436, 
ENST00000548660, ENST00000547583, 
ENST00000262238, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score3 X 3 X 2=1812 X 7 X 7=588
# samples 313
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(13/588*10)=-2.17730453180791
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: GLT8D2 [Title/Abstract] AND YY1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: GLT8D2 [Title/Abstract] AND YY1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)GLT8D2(104396913)-YY1(100741035), # samples:3
Anticipated loss of major functional domain due to fusion event.GLT8D2-YY1 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.
GLT8D2-YY1 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.
GLT8D2-YY1 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.
GLT8D2-YY1 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.
GLT8D2-YY1 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
GLT8D2-YY1 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
TgeneYY1

GO:0000122

negative regulation of transcription by RNA polymerase II

9857059|16260628

TgeneYY1

GO:0032688

negative regulation of interferon-beta production

16260628



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/chr12:104396913/chr14:100741035)
- 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 GLT8D2 (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 YY1 (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)
ENST00000548660GLT8D2chr12104396913-ENST00000262238YY1chr14100741035+65369416571343228

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
ENST00000548660ENST00000262238GLT8D2chr12104396913-YY1chr14100741035+0.0007203680.9992797

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 GLT8D2-YY1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
GLT8D2chr12104396913YY1chr1410074103594193LFYVVGLRNTLTRIRMKPRKIKEDDA

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Potential FusionNeoAntigen Information of GLT8D2-YY1 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.
GLT8D2-YY1_104396913_100741035.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)
GLT8D2-YY1chr12104396913chr14100741035941HLA-B27:05TRIRMKPRK0.99730.73581120
GLT8D2-YY1chr12104396913chr14100741035941HLA-A30:08RIRMKPRKI0.97210.7581221
GLT8D2-YY1chr12104396913chr14100741035941HLA-A02:13GLRNTLTRI0.91680.7334514
GLT8D2-YY1chr12104396913chr14100741035941HLA-A30:08RIRMKPRKIK0.9940.72041222
GLT8D2-YY1chr12104396913chr14100741035941HLA-A30:08RNTLTRIRMK0.98510.7709717
GLT8D2-YY1chr12104396913chr14100741035941HLA-B27:14TRIRMKPRK0.98880.6711120
GLT8D2-YY1chr12104396913chr14100741035941HLA-B27:10TRIRMKPRK0.99630.78081120
GLT8D2-YY1chr12104396913chr14100741035941HLA-A02:03GLRNTLTRI0.98810.7823514
GLT8D2-YY1chr12104396913chr14100741035941HLA-A30:01RIRMKPRKI0.97730.8451221
GLT8D2-YY1chr12104396913chr14100741035941HLA-A30:01RIRMKPRKIK0.99460.82221222
GLT8D2-YY1chr12104396913chr14100741035941HLA-A30:01RNTLTRIRMK0.98520.8479717
GLT8D2-YY1chr12104396913chr14100741035941HLA-B27:10RIRMKPRKIK0.78840.76011222

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Potential FusionNeoAntigen Information of GLT8D2-YY1 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.
GLT8D2-YY1_104396913_100741035.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)
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1102LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1102TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1102TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1103LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1103TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1103TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1111LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1114LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1116LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1116TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1116TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1120LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1121LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1121TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1121TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1136LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1136TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1136TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1141LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1148LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1155LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1155TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1155TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1159LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1159TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1163LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1163TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1163TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1165LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1165TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1165TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1168LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1170LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1170TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1170TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1176LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1176TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1176TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1185LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1185TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1185TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1186LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1186TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1186TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1301LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1301TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1301TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1302LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1308LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1315LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1315TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1315TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1315NTLTRIRMKPRKIKE823
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1316LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1316TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1316TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1317LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1317TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1319LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1319TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1319TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1320LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1320TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1320TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1322LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1322TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1322TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1323LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1324LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1324TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1324TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1327LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1327TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1329LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1334LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1335LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1335TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1335TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1339LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1351LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1351TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1351TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1352LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1352TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1352TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1353LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1353TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1353TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1357LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1357TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1357TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1357NTLTRIRMKPRKIKE823
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1359LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1359TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1359TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1361LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1361TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1361TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1363LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1364LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1364TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1364TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1368LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1368TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1368TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1369LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1369TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1369TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1370LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1371LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1371TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1372LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1373LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1374LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1375LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1376LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1378LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1378TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1378TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1379LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1379TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1379TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1380LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1380TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1380TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1383LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1383TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1383TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1384LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1387LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1387TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1387TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1391LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1391TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1391TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1392LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1392TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1392TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1397LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1398LTRIRMKPRKIKEDD1025
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1398TLTRIRMKPRKIKED924
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1398TRIRMKPRKIKEDDA1126
GLT8D2-YY1chr12104396913chr14100741035941DRB1-1399LTRIRMKPRKIKEDD1025

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Fusion breakpoint peptide structures of GLT8D2-YY1

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
5545LRNTLTRIRMKPRKGLT8D2YY1chr12104396913chr14100741035941

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of GLT8D2-YY1

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-B14:023BVN5545LRNTLTRIRMKPRK-7.15543-7.26883
HLA-B14:023BVN5545LRNTLTRIRMKPRK-4.77435-5.80965
HLA-B52:013W395545LRNTLTRIRMKPRK-6.80875-6.92215
HLA-B52:013W395545LRNTLTRIRMKPRK-4.20386-5.23916
HLA-A11:014UQ25545LRNTLTRIRMKPRK-7.5194-8.5547
HLA-A11:014UQ25545LRNTLTRIRMKPRK-6.9601-7.0735
HLA-A24:025HGA5545LRNTLTRIRMKPRK-7.52403-7.63743
HLA-A24:025HGA5545LRNTLTRIRMKPRK-5.82433-6.85963
HLA-B27:056PYJ5545LRNTLTRIRMKPRK-3.28285-4.31815
HLA-B44:053DX85545LRNTLTRIRMKPRK-5.91172-6.94702
HLA-B44:053DX85545LRNTLTRIRMKPRK-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of GLT8D2-YY1

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
GLT8D2-YY1chr12104396913chr141007410351120TRIRMKPRKAATACGAATGAAGCCAAGAAAAATTAA
GLT8D2-YY1chr12104396913chr141007410351221RIRMKPRKIACGAATGAAGCCAAGAAAAATTAAAGA
GLT8D2-YY1chr12104396913chr141007410351222RIRMKPRKIKACGAATGAAGCCAAGAAAAATTAAAGAAGA
GLT8D2-YY1chr12104396913chr14100741035514GLRNTLTRICCGGAATACTCTGACTCGAATACGAAT
GLT8D2-YY1chr12104396913chr14100741035717RNTLTRIRMKTACTCTGACTCGAATACGAATGAAGCCAAG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
GLT8D2-YY1chr12104396913chr141007410351025LTRIRMKPRKIKEDDTCGAATACGAATGAAGCCAAGAAAAATTAAAGAAGATGATGCTCC
GLT8D2-YY1chr12104396913chr141007410351126TRIRMKPRKIKEDDAAATACGAATGAAGCCAAGAAAAATTAAAGAAGATGATGCTCCAAG
GLT8D2-YY1chr12104396913chr14100741035823NTLTRIRMKPRKIKETCTGACTCGAATACGAATGAAGCCAAGAAAAATTAAAGAAGATGA
GLT8D2-YY1chr12104396913chr14100741035924TLTRIRMKPRKIKEDGACTCGAATACGAATGAAGCCAAGAAAAATTAAAGAAGATGATGC

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Information of the samples that have these potential fusion neoantigens of GLT8D2-YY1

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
SARCGLT8D2-YY1chr12104396913ENST00000548660chr14100741035ENST00000262238TCGA-DX-A2IZ-01A

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Potential target of CAR-T therapy development for GLT8D2-YY1

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
HgeneGLT8D2chr12:104396913chr14:100741035ENST00000360814-5117_2494350.0TransmembraneHelical%3B Signal-anchor for type II membrane protein
HgeneGLT8D2chr12:104396913chr14:100741035ENST00000546436-4107_2494350.0TransmembraneHelical%3B Signal-anchor for type II membrane protein
HgeneGLT8D2chr12:104396913chr14:100741035ENST00000548660-5117_2494350.0TransmembraneHelical%3B Signal-anchor for type II membrane protein

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 GLT8D2-YY1

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 GLT8D2-YY1

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
TgeneYY1C4479652GABRIELE-DE VRIES SYNDROME2GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneYY1C0006826Malignant Neoplasms1CTD_human
TgeneYY1C0007873Uterine Cervical Neoplasm1CTD_human
TgeneYY1C0019693HIV Infections1CTD_human
TgeneYY1C0020796Profound Mental Retardation1CTD_human
TgeneYY1C0025363Mental Retardation, Psychosocial1CTD_human
TgeneYY1C0027651Neoplasms1CTD_human
TgeneYY1C0086692Benign Neoplasm1CTD_human
TgeneYY1C0235874Disease Exacerbation1CTD_human
TgeneYY1C0917816Mental deficiency1CTD_human
TgeneYY1C3714756Intellectual Disability1CTD_human;GENOMICS_ENGLAND
TgeneYY1C4048328cervical cancer1CTD_human
TgeneYY1C4505456HIV Coinfection1CTD_human