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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:ZC3H3-YY1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ZC3H3-YY1
FusionPDB ID: 100565
FusionGDB2.0 ID: 100565
HgeneTgene
Gene symbol

ZC3H3

YY1

Gene ID

23144

7528

Gene namezinc finger CCCH-type containing 3YY1 transcription factor
SynonymsSMICL|ZC3HDC3DELTA|GADEVS|INO80S|NF-E1|UCRBP|YIN-YANG-1
Cytomap

8q24.3

14q32.2

Type of geneprotein-codingprotein-coding
Descriptionzinc finger CCCH domain-containing protein 3smad-interacting CPSF-like factorzinc finger CCCH-type domain containing 3transcriptional repressor protein YY1INO80 complex subunit SYY-1Yin and Yang 1 proteindelta transcription factor
Modification date2020031320200313
UniProtAcc.

YY1AP1

Main function of 5'-partner protein: 796
Ensembl transtripts involved in fusion geneENST idsENST00000262577, ENST00000262238, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 8 X 9=100812 X 7 X 7=588
# samples 1713
** MAII scorelog2(17/1008*10)=-2.56788898736222
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
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: ZC3H3 [Title/Abstract] AND YY1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ZC3H3 [Title/Abstract] AND YY1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ZC3H3(144557568)-YY1(100728641), # samples:3
Anticipated loss of major functional domain due to fusion event.ZC3H3-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.
ZC3H3-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.
ZC3H3-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.
ZC3H3-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.
* 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/chr8:144557568/chr14:100728641)
- 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 ZC3H3 (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)
ENST00000262577ZC3H3chr8144557568-ENST00000262238YY1chr14100728641+76931935322500822
ENST00000262577ZC3H3chr8144557567-ENST00000262238YY1chr14100728640+76931935322500822

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
ENST00000262577ENST00000262238ZC3H3chr8144557568-YY1chr14100728641+0.001380850.9986192
ENST00000262577ENST00000262238ZC3H3chr8144557567-YY1chr14100728640+0.001380850.9986192

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 ZC3H3-YY1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ZC3H3chr8144557567YY1chr141007286401935634QPSDAGSRPLLRTDEKKDIDHETVVE
ZC3H3chr8144557568YY1chr141007286411935634QPSDAGSRPLLRTDEKKDIDHETVVE

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Potential FusionNeoAntigen Information of ZC3H3-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.
ZC3H3-YY1_144557567_100728640.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)
ZC3H3-YY1chr8144557567chr141007286401935HLA-A30:01GSRPLLRTDEK0.99810.8449516

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Potential FusionNeoAntigen Information of ZC3H3-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.
ZC3H3-YY1_144557567_100728640.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)
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0301RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0301SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0301GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0303RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0303SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0305RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0307RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0307SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0310RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0310SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0310GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0310PLLRTDEKKDIDHET823
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0313RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0313SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0313GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0315RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0315SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0318RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0318SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0318GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0320RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0320SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0320GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0322RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0322SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0322GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0324RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0324SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0326RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0326SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0328RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0328SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0328GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0330RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0330SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0330GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0332RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0332SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0332GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0334RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0334SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0334GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0336RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0336SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0336GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0338RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0340RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0342RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0342SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0344RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0344SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0344GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0346RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0346SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0346GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0348RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0348SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0348GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0350RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0350SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0350GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0352RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0352SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0352GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0354RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0354SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-0354GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-1107RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-1107SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-1394RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-1438RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-1476RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-1476SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-1476GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-1479RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-1479SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB1-1479GSRPLLRTDEKKDID520
ZC3H3-YY1chr8144557567chr141007286401935DRB1-1482RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB1-1482SRPLLRTDEKKDIDH621
ZC3H3-YY1chr8144557567chr141007286401935DRB3-0114RPLLRTDEKKDIDHE722
ZC3H3-YY1chr8144557567chr141007286401935DRB3-0114SRPLLRTDEKKDIDH621

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Fusion breakpoint peptide structures of ZC3H3-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
8971SRPLLRTDEKKDIDZC3H3YY1chr8144557567chr141007286401935

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ZC3H3-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-B14:023BVN8971SRPLLRTDEKKDID-7.15543-7.26883
HLA-B14:023BVN8971SRPLLRTDEKKDID-4.77435-5.80965
HLA-B52:013W398971SRPLLRTDEKKDID-6.80875-6.92215
HLA-B52:013W398971SRPLLRTDEKKDID-4.20386-5.23916
HLA-A11:014UQ28971SRPLLRTDEKKDID-7.5194-8.5547
HLA-A11:014UQ28971SRPLLRTDEKKDID-6.9601-7.0735
HLA-A24:025HGA8971SRPLLRTDEKKDID-7.52403-7.63743
HLA-A24:025HGA8971SRPLLRTDEKKDID-5.82433-6.85963
HLA-B27:056PYJ8971SRPLLRTDEKKDID-3.28285-4.31815
HLA-B44:053DX88971SRPLLRTDEKKDID-5.91172-6.94702
HLA-B44:053DX88971SRPLLRTDEKKDID-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of ZC3H3-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
ZC3H3-YY1chr8144557567chr14100728640516GSRPLLRTDEKGCAGCAGGCCCCTCCTGCGCACAGATGAAAAAA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ZC3H3-YY1chr8144557567chr14100728640520GSRPLLRTDEKKDIDGCAGCAGGCCCCTCCTGCGCACAGATGAAAAAAAAGATATTGACC
ZC3H3-YY1chr8144557567chr14100728640621SRPLLRTDEKKDIDHGCAGGCCCCTCCTGCGCACAGATGAAAAAAAAGATATTGACCATG
ZC3H3-YY1chr8144557567chr14100728640722RPLLRTDEKKDIDHEGGCCCCTCCTGCGCACAGATGAAAAAAAAGATATTGACCATGAGA
ZC3H3-YY1chr8144557567chr14100728640823PLLRTDEKKDIDHETCCCTCCTGCGCACAGATGAAAAAAAAGATATTGACCATGAGACAG

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Information of the samples that have these potential fusion neoantigens of ZC3H3-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
BRCAZC3H3-YY1chr8144557567ENST00000262577chr14100728640ENST00000262238TCGA-A8-A09N

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Potential target of CAR-T therapy development for ZC3H3-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

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 ZC3H3-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 ZC3H3-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