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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:ZNF844-CMSS1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ZNF844-CMSS1
FusionPDB ID: 103061
FusionGDB2.0 ID: 103061
HgeneTgene
Gene symbol

ZNF844

CMSS1

Gene ID

284391

84319

Gene namezinc finger protein 844cms1 ribosomal small subunit homolog
Synonyms-C3orf26
Cytomap

19p13.2

3q12.1

Type of geneprotein-codingprotein-coding
Descriptionzinc finger protein 844protein CMSS1
Modification date2020031320200313
UniProtAcc.

Q9BQ75

Main function of 5'-partner protein:
Ensembl transtripts involved in fusion geneENST idsENST00000439326, ENST00000441304, 
ENST00000489081, ENST00000496116, 
ENST00000421999, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 3 X 4=4811 X 9 X 9=891
# samples 413
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/891*10)=-2.77691380849347
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ZNF844 [Title/Abstract] AND CMSS1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ZNF844 [Title/Abstract] AND CMSS1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ZNF844(12184972)-CMSS1(99865817), # samples:2
Anticipated loss of major functional domain due to fusion event.ZNF844-CMSS1 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.
ZNF844-CMSS1 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/chr19:12184972/chr3:99865817)
- 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 ZNF844 (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 CMSS1 (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)
ENST00000439326ZNF844chr1912184972+ENST00000421999CMSS1chr399865817+12963051391080313
ENST00000441304ZNF844chr1912184972+ENST00000421999CMSS1chr399865817+118519428969313

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
ENST00000439326ENST00000421999ZNF844chr1912184972+CMSS1chr399865817+0.000681330.9993187
ENST00000441304ENST00000421999ZNF844chr1912184972+CMSS1chr399865817+0.0008763060.99912375

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 ZNF844-CMSS1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ZNF844chr1912184972CMSS1chr39986581719455EVMQETLRNLASIEASDGEGEGDTEV
ZNF844chr1912184972CMSS1chr39986581730555EVMQETLRNLASIEASDGEGEGDTEV

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Potential FusionNeoAntigen Information of ZNF844-CMSS1 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.
ZNF844-CMSS1_12184972_99865817.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)
ZNF844-CMSS1chr1912184972chr399865817305HLA-B39:06LRNLASIEA0.99260.7802615
ZNF844-CMSS1chr1912184972chr399865817305HLA-B73:01LRNLASIEA0.99630.7421615
ZNF844-CMSS1chr1912184972chr399865817305HLA-B73:01TLRNLASIEA0.87650.6667515
ZNF844-CMSS1chr1912184972chr399865817305HLA-B73:01ETLRNLASIEA0.93740.6351415

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Potential FusionNeoAntigen Information of ZNF844-CMSS1 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.
ZNF844-CMSS1_12184972_99865817.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)
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0101QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0101MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0102QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0102MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0102ETLRNLASIEASDGE419
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0102VMQETLRNLASIEAS116
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0105QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0105MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0107QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0107MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0109QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0111QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0111MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0113QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0115QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0117QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0119QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0119MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0121QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0121MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0123QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0123MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0123ETLRNLASIEASDGE419
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0125QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0125MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0127QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0127MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0129QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0131QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0131MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0403QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0403MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0413QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0413MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0415QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0415MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0419QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0419MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0427QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0427MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0431QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0436QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0436MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0437QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0437MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0439QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0439MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0440QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0440MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0440ETLRNLASIEASDGE419
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0441QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0441MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0442QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0442MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0443QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0443MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0444QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0444MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0444ETLRNLASIEASDGE419
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0446QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0446MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0447QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0449QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0449MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0450QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0450MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0451QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0451MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0452QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0452MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0453QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0453MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0454QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0455QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0455MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0456QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0456MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0456ETLRNLASIEASDGE419
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0458QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0458MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0459QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0459MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0460QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0460MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0461QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0461MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0465QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0465MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0468QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0468MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0468ETLRNLASIEASDGE419
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0470QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0470MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0471QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0471MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0473QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0473MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0475QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0478QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0478MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0479QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0479MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0479ETLRNLASIEASDGE419
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0479VMQETLRNLASIEAS116
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0482QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0482MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0485QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0485MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0488QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-0488MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1002QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1002MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1002ETLRNLASIEASDGE419
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1204QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1209QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1213QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1215QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1216QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1218QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1219QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1220QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1221QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1221MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1223QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1410QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1410MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1457QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1457MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1504QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1504MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1505QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1507QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1521QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1527QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1534QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1534MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1548QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1601QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1601MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1602QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1602MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1603QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1603MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1604QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1605QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1605MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1607QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1607MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1608QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1608MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1609QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1610QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1611QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1611MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1612QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1612MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1614QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1614MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1615QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1615MQETLRNLASIEASD217
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1615ETLRNLASIEASDGE419
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1615VMQETLRNLASIEAS116
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1616QETLRNLASIEASDG318
ZNF844-CMSS1chr1912184972chr399865817305DRB1-1616MQETLRNLASIEASD217

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Fusion breakpoint peptide structures of ZNF844-CMSS1

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
5542LRNLASIEASDGEGZNF844CMSS1chr1912184972chr399865817305

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ZNF844-CMSS1

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-B14:023BVN5542LRNLASIEASDGEG-7.15543-7.26883
HLA-B14:023BVN5542LRNLASIEASDGEG-4.77435-5.80965
HLA-B52:013W395542LRNLASIEASDGEG-6.80875-6.92215
HLA-B52:013W395542LRNLASIEASDGEG-4.20386-5.23916
HLA-A11:014UQ25542LRNLASIEASDGEG-7.5194-8.5547
HLA-A11:014UQ25542LRNLASIEASDGEG-6.9601-7.0735
HLA-A24:025HGA5542LRNLASIEASDGEG-7.52403-7.63743
HLA-A24:025HGA5542LRNLASIEASDGEG-5.82433-6.85963
HLA-B27:056PYJ5542LRNLASIEASDGEG-3.28285-4.31815
HLA-B44:053DX85542LRNLASIEASDGEG-5.91172-6.94702
HLA-B44:053DX85542LRNLASIEASDGEG-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of ZNF844-CMSS1

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
ZNF844-CMSS1chr1912184972chr399865817415ETLRNLASIEAAAACCTTGAGGAATCTGGCCTCCATAGAAGCAT
ZNF844-CMSS1chr1912184972chr399865817515TLRNLASIEACCTTGAGGAATCTGGCCTCCATAGAAGCAT
ZNF844-CMSS1chr1912184972chr399865817615LRNLASIEATGAGGAATCTGGCCTCCATAGAAGCAT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ZNF844-CMSS1chr1912184972chr399865817116VMQETLRNLASIEASTGATGCAGGAAACCTTGAGGAATCTGGCCTCCATAGAAGCATCAG
ZNF844-CMSS1chr1912184972chr399865817217MQETLRNLASIEASDTGCAGGAAACCTTGAGGAATCTGGCCTCCATAGAAGCATCAGATG
ZNF844-CMSS1chr1912184972chr399865817318QETLRNLASIEASDGAGGAAACCTTGAGGAATCTGGCCTCCATAGAAGCATCAGATGGTG
ZNF844-CMSS1chr1912184972chr399865817419ETLRNLASIEASDGEAAACCTTGAGGAATCTGGCCTCCATAGAAGCATCAGATGGTGAAG

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Information of the samples that have these potential fusion neoantigens of ZNF844-CMSS1

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
BLCAZNF844-CMSS1chr1912184972ENST00000439326chr399865817ENST00000421999TCGA-G2-A3VY-01A

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Potential target of CAR-T therapy development for ZNF844-CMSS1

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 ZNF844-CMSS1

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 ZNF844-CMSS1

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