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Fusion Protein:CDYL-ZNF277

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CDYL-ZNF277
	FusionPDB ID: 15502
	FusionGDB2.0 ID: 15502
		Hgene	Tgene
	Gene symbol	CDYL	ZNF277
	Gene ID	9425	11179
	Gene name	chromodomain Y like	zinc finger protein 277
	Synonyms	CDYL1	NRIF4\|ZNF277P
	Cytomap	6p25.1	7q31.1
	Type of gene	protein-coding	protein-coding
	Description	chromodomain Y-like proteinCDY-like, autosomalchromodomain protein, Y-likecrotonyl-CoA hydratasetestis-specific chromodomain Y-like protein	zinc finger protein 277nuclear receptor-interacting factor 4zinc finger protein (C2H2 type) 277zinc finger protein 277 pseudogene
	Modification date	20200313	20200313
	UniProtAcc	Q8N8U2 Main function of 5'-partner protein:	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000328908, ENST00000343762, ENST00000397588, ENST00000449732, ENST00000472453,	ENST00000361822, ENST00000421043, ENST00000450657,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	10 X 8 X 6=480	6 X 4 X 4=96
	# samples	12	6
	** MAII score	log2(12/480*10)=-2 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(6/96*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: CDYL [Title/Abstract] AND ZNF277 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CDYL [Title/Abstract] AND ZNF277 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CDYL(4892613)-ZNF277(111926927), # samples:1
Anticipated loss of major functional domain due to fusion event.	CDYL-ZNF277 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. CDYL-ZNF277 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. CDYL-ZNF277 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. CDYL-ZNF277 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	CDYL	GO:0120094	negative regulation of peptidyl-lysine crotonylation	28803779

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr6:4892613/chr7:111926927)
- 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.

Retention 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.

Fusion gene breakpoints across CDYL (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across ZNF277 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000328908	CDYL	chr6	4892613	+	ENST00000361822	ZNF277	chr7	111926927	+	2613	984	131	2245	704
ENST00000328908	CDYL	chr6	4892613	+	ENST00000450657	ZNF277	chr7	111926927	+	1952	984	131	1765	544
ENST00000328908	CDYL	chr6	4892613	+	ENST00000421043	ZNF277	chr7	111926927	+	3091	984	131	1189	352
ENST00000397588	CDYL	chr6	4892613	+	ENST00000361822	ZNF277	chr7	111926927	+	2669	1040	148	2301	717
ENST00000397588	CDYL	chr6	4892613	+	ENST00000450657	ZNF277	chr7	111926927	+	2008	1040	148	1821	557
ENST00000397588	CDYL	chr6	4892613	+	ENST00000421043	ZNF277	chr7	111926927	+	3147	1040	148	1245	365
ENST00000449732	CDYL	chr6	4892613	+	ENST00000361822	ZNF277	chr7	111926927	+	2507	878	262	2139	625
ENST00000449732	CDYL	chr6	4892613	+	ENST00000450657	ZNF277	chr7	111926927	+	1846	878	262	1659	465
ENST00000449732	CDYL	chr6	4892613	+	ENST00000421043	ZNF277	chr7	111926927	+	2985	878	262	1083	273
ENST00000343762	CDYL	chr6	4892613	+	ENST00000361822	ZNF277	chr7	111926927	+	2431	802	186	2063	625
ENST00000343762	CDYL	chr6	4892613	+	ENST00000450657	ZNF277	chr7	111926927	+	1770	802	186	1583	465
ENST00000343762	CDYL	chr6	4892613	+	ENST00000421043	ZNF277	chr7	111926927	+	2909	802	186	1007	273

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000328908	ENST00000361822	CDYL	chr6	4892613	+	ZNF277	chr7	111926927	+	0.002553266	0.9974468
ENST00000328908	ENST00000450657	CDYL	chr6	4892613	+	ZNF277	chr7	111926927	+	0.00120192	0.998798
ENST00000328908	ENST00000421043	CDYL	chr6	4892613	+	ZNF277	chr7	111926927	+	0.000801177	0.99919885
ENST00000397588	ENST00000361822	CDYL	chr6	4892613	+	ZNF277	chr7	111926927	+	0.001727623	0.9982724
ENST00000397588	ENST00000450657	CDYL	chr6	4892613	+	ZNF277	chr7	111926927	+	0.00118974	0.9988103
ENST00000397588	ENST00000421043	CDYL	chr6	4892613	+	ZNF277	chr7	111926927	+	0.000717881	0.9992822
ENST00000449732	ENST00000361822	CDYL	chr6	4892613	+	ZNF277	chr7	111926927	+	0.002857031	0.997143
ENST00000449732	ENST00000450657	CDYL	chr6	4892613	+	ZNF277	chr7	111926927	+	0.001262192	0.9987379
ENST00000449732	ENST00000421043	CDYL	chr6	4892613	+	ZNF277	chr7	111926927	+	0.002778374	0.9972216
ENST00000343762	ENST00000361822	CDYL	chr6	4892613	+	ZNF277	chr7	111926927	+	0.002321339	0.9976787
ENST00000343762	ENST00000450657	CDYL	chr6	4892613	+	ZNF277	chr7	111926927	+	0.000805484	0.99919456
ENST00000343762	ENST00000421043	CDYL	chr6	4892613	+	ZNF277	chr7	111926927	+	0.003342134	0.99665785

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 CDYL-ZNF277

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
CDYL	chr6	4892613	ZNF277	chr7	111926927	1040	297	TAAMATGLAVNGKDSKDCILEPLSLP
CDYL	chr6	4892613	ZNF277	chr7	111926927	802	205	TAAMATGLAVNGKDSKDCILEPLSLP
CDYL	chr6	4892613	ZNF277	chr7	111926927	878	205	TAAMATGLAVNGKDSKDCILEPLSLP
CDYL	chr6	4892613	ZNF277	chr7	111926927	984	284	TAAMATGLAVNGKDSKDCILEPLSLP

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Potential FusionNeoAntigen Information of CDYL-ZNF277 in HLA I

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.

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA I

FusionNeoAntigen peptide

Binding score

Immunogenic score

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

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Potential FusionNeoAntigen Information of CDYL-ZNF277 in HLA II

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA II

FusionNeoAntigen peptide

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of CDYL-ZNF277

3D 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.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CDYL-ZNF277

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele

PDB ID

File name

BPseq

Docking score

Glide score

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Vaccine Design for the FusionNeoAntigens of CDYL-ZNF277

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide sequence

FusionNeoAntigen RNA sequence

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide

FusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of CDYL-ZNF277

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 type

Fusion gene

Hchr

Hbp

Henst

Tchr

Tbp

Tenst

Sample

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Potential target of CAR-T therapy development for CDYL-ZNF277

Predicted 3D structure. We used RoseTTAFold.

Retention 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'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to CDYL-ZNF277

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to CDYL-ZNF277

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)