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Fusion Protein:SPECC1L-CDH4

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SPECC1L-CDH4
	FusionPDB ID: 85675
	FusionGDB2.0 ID: 85675
		Hgene	Tgene
	Gene symbol	SPECC1L	CDH4
	Gene ID	23384	1002
	Gene name	sperm antigen with calponin homology and coiled-coil domains 1 like	cadherin 4
	Synonyms	CYTSA\|GBBB2\|OBLFC1\|TBHS	CAD4\|R-CAD\|RCAD
	Cytomap	22q11.23	20q13.33
	Type of gene	protein-coding	protein-coding
	Description	cytospin-ASPECC1-like proteincytokinesis and spindle organization Arenal carcinoma antigen NY-REN-22	cadherin-4R-cadherincadherin 4, type 1, R-cadherin (retinal)cadherin 4, type 1, preproproteinretinal cadherin
	Modification date	20200313	20200313
	UniProtAcc	.	P55283 Main function of 5'-partner protein: FUNCTION: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. May play an important role in retinal development.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000314328, ENST00000437398, ENST00000541492, ENST00000416735,	ENST00000360469, ENST00000543233,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	24 X 9 X 16=3456	16 X 14 X 7=1568
	# samples	37	21
	** MAII score	log2(37/3456*10)=-3.22350604164716 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(21/1568*10)=-2.90046432644909 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SPECC1L [Title/Abstract] AND CDH4 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SPECC1L [Title/Abstract] AND CDH4 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SPECC1L(24765288)-CDH4(60427810), # samples:2
Anticipated loss of major functional domain due to fusion event.	SPECC1L-CDH4 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. SPECC1L-CDH4 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. SPECC1L-CDH4 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. SPECC1L-CDH4 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	SPECC1L	GO:0007155	cell adhesion	21703590

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr22:24765288/chr20:60427810)
- 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 SPECC1L (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 CDH4 (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)
ENST00000437398	SPECC1L	chr22	24765288	+	ENST00000360469	CDH4	chr20	60427810	+	8981	3290	95	5308	1737
ENST00000437398	SPECC1L	chr22	24765288	+	ENST00000543233	CDH4	chr20	60427810	+	5615	3290	95	5308	1737
ENST00000314328	SPECC1L	chr22	24765288	+	ENST00000360469	CDH4	chr20	60427810	+	9063	3372	285	5390	1701
ENST00000314328	SPECC1L	chr22	24765288	+	ENST00000543233	CDH4	chr20	60427810	+	5697	3372	285	5390	1701
ENST00000541492	SPECC1L	chr22	24765288	+	ENST00000360469	CDH4	chr20	60427810	+	8916	3225	30	5243	1737
ENST00000541492	SPECC1L	chr22	24765288	+	ENST00000543233	CDH4	chr20	60427810	+	5550	3225	30	5243	1737
ENST00000437398	SPECC1L	chr22	24765288	+	ENST00000360469	CDH4	chr20	60427809	+	8981	3290	95	5308	1737
ENST00000437398	SPECC1L	chr22	24765288	+	ENST00000543233	CDH4	chr20	60427809	+	5615	3290	95	5308	1737
ENST00000314328	SPECC1L	chr22	24765288	+	ENST00000360469	CDH4	chr20	60427809	+	9063	3372	285	5390	1701
ENST00000314328	SPECC1L	chr22	24765288	+	ENST00000543233	CDH4	chr20	60427809	+	5697	3372	285	5390	1701
ENST00000541492	SPECC1L	chr22	24765288	+	ENST00000360469	CDH4	chr20	60427809	+	8916	3225	30	5243	1737
ENST00000541492	SPECC1L	chr22	24765288	+	ENST00000543233	CDH4	chr20	60427809	+	5550	3225	30	5243	1737

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
ENST00000437398	ENST00000360469	SPECC1L	chr22	24765288	+	CDH4	chr20	60427810	+	0.00258222	0.9974178
ENST00000437398	ENST00000543233	SPECC1L	chr22	24765288	+	CDH4	chr20	60427810	+	0.005278153	0.9947219
ENST00000314328	ENST00000360469	SPECC1L	chr22	24765288	+	CDH4	chr20	60427810	+	0.002796703	0.99720335
ENST00000314328	ENST00000543233	SPECC1L	chr22	24765288	+	CDH4	chr20	60427810	+	0.005588424	0.9944115
ENST00000541492	ENST00000360469	SPECC1L	chr22	24765288	+	CDH4	chr20	60427810	+	0.002400003	0.9976
ENST00000541492	ENST00000543233	SPECC1L	chr22	24765288	+	CDH4	chr20	60427810	+	0.004989411	0.9950106
ENST00000437398	ENST00000360469	SPECC1L	chr22	24765288	+	CDH4	chr20	60427809	+	0.00258222	0.9974178
ENST00000437398	ENST00000543233	SPECC1L	chr22	24765288	+	CDH4	chr20	60427809	+	0.005278153	0.9947219
ENST00000314328	ENST00000360469	SPECC1L	chr22	24765288	+	CDH4	chr20	60427809	+	0.002796703	0.99720335
ENST00000314328	ENST00000543233	SPECC1L	chr22	24765288	+	CDH4	chr20	60427809	+	0.005588424	0.9944115
ENST00000541492	ENST00000360469	SPECC1L	chr22	24765288	+	CDH4	chr20	60427809	+	0.002400003	0.9976
ENST00000541492	ENST00000543233	SPECC1L	chr22	24765288	+	CDH4	chr20	60427809	+	0.004989411	0.9950106

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 SPECC1L-CDH4

+/-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
SPECC1L	chr22	24765288	CDH4	chr20	60427809	3225	1064	ALLKWCQKKTEGYQLRAHAVDMNGNK
SPECC1L	chr22	24765288	CDH4	chr20	60427809	3290	1064	ALLKWCQKKTEGYQLRAHAVDMNGNK
SPECC1L	chr22	24765288	CDH4	chr20	60427809	3372	1028	ALLKWCQKKTEGYQLRAHAVDMNGNK
SPECC1L	chr22	24765288	CDH4	chr20	60427810	3225	1064	ALLKWCQKKTEGYQLRAHAVDMNGNK
SPECC1L	chr22	24765288	CDH4	chr20	60427810	3290	1064	ALLKWCQKKTEGYQLRAHAVDMNGNK
SPECC1L	chr22	24765288	CDH4	chr20	60427810	3372	1028	ALLKWCQKKTEGYQLRAHAVDMNGNK

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Potential FusionNeoAntigen Information of SPECC1L-CDH4 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.

SPECC1L-CDH4_24765288_60427809.msa

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)
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	HLA-B08:09	YQLRAHAV	0.9958	0.7805	12	20
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	HLA-B13:02	YQLRAHAV	0.989	0.8815	12	20
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	HLA-B52:01	YQLRAHAV	0.8237	0.9903	12	20
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	HLA-B50:02	TEGYQLRAHA	0.914	0.7313	9	19
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	HLA-B51:07	YQLRAHAV	0.7292	0.973	12	20

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Potential FusionNeoAntigen Information of SPECC1L-CDH4 in HLA II

SPECC1L-CDH4_24765288_60427809.msa

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)
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0801	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0801	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0801	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0801	EGYQLRAHAVDMNGN	10	25
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0803	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0803	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0803	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0805	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0808	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0808	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0811	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0811	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0814	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0814	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0814	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0816	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0816	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0816	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0816	EGYQLRAHAVDMNGN	10	25
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0823	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0823	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0823	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0826	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0826	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0826	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0826	EGYQLRAHAVDMNGN	10	25
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0827	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0827	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0827	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0833	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0833	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0833	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0835	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0835	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0835	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0836	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0836	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0836	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0837	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0837	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0838	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0838	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0838	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0839	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0839	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0839	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-0839	EGYQLRAHAVDMNGN	10	25
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-1313	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-1313	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-1338	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-1355	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-1355	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-1355	KKTEGYQLRAHAVDM	7	22
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-1355	EGYQLRAHAVDMNGN	10	25
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-1365	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-1463	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-1463	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-1485	TEGYQLRAHAVDMNG	9	24
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB1-1485	KTEGYQLRAHAVDMN	8	23
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB4-0101	GYQLRAHAVDMNGNK	11	26
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB4-0101	EGYQLRAHAVDMNGN	10	25
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB4-0103	GYQLRAHAVDMNGNK	11	26
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB4-0103	EGYQLRAHAVDMNGN	10	25
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB4-0104	GYQLRAHAVDMNGNK	11	26
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB4-0104	EGYQLRAHAVDMNGN	10	25
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB4-0106	GYQLRAHAVDMNGNK	11	26
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB4-0106	EGYQLRAHAVDMNGN	10	25
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB4-0107	GYQLRAHAVDMNGNK	11	26
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB4-0107	EGYQLRAHAVDMNGN	10	25
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB4-0108	GYQLRAHAVDMNGNK	11	26
SPECC1L-CDH4	chr22	24765288	chr20	60427809	3372	DRB4-0108	EGYQLRAHAVDMNGN	10	25

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Fusion breakpoint peptide structures of SPECC1L-CDH4

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.

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
7346	QKKTEGYQLRAHAV	SPECC1L	CDH4	chr22	24765288	chr20	60427809	3372

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SPECC1L-CDH4

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
HLA-B14:02	3BVN	7346	QKKTEGYQLRAHAV	-6.35143	-7.38673
HLA-B14:02	3BVN	7346	QKKTEGYQLRAHAV	-5.20162	-5.31502
HLA-B52:01	3W39	7346	QKKTEGYQLRAHAV	-6.03049	-6.14389
HLA-B52:01	3W39	7346	QKKTEGYQLRAHAV	-5.12323	-6.15853
HLA-A24:02	5HGA	7346	QKKTEGYQLRAHAV	-9.81198	-9.92538
HLA-A24:02	5HGA	7346	QKKTEGYQLRAHAV	-7.16433	-8.19963
HLA-B44:05	3DX8	7346	QKKTEGYQLRAHAV	-6.46131	-6.57471
HLA-B44:05	3DX8	7346	QKKTEGYQLRAHAV	-3.08576	-4.12106
HLA-A02:01	6TDR	7346	QKKTEGYQLRAHAV	-5.03933	-5.15273

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Vaccine Design for the FusionNeoAntigens of SPECC1L-CDH4

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
SPECC1L-CDH4	chr22	24765288	chr20	60427809	12	20	YQLRAHAV	CAGCTCCGAGCCCACGCTGTGGAC
SPECC1L-CDH4	chr22	24765288	chr20	60427809	9	19	TEGYQLRAHA	GAAGGCTATCAGCTCCGAGCCCACGCTGTG

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
SPECC1L-CDH4	chr22	24765288	chr20	60427809	10	25	EGYQLRAHAVDMNGN	GGCTATCAGCTCCGAGCCCACGCTGTGGACATGAATGGCAACAAG
SPECC1L-CDH4	chr22	24765288	chr20	60427809	11	26	GYQLRAHAVDMNGNK	TATCAGCTCCGAGCCCACGCTGTGGACATGAATGGCAACAAGGTG
SPECC1L-CDH4	chr22	24765288	chr20	60427809	7	22	KKTEGYQLRAHAVDM	AAAACAGAAGGCTATCAGCTCCGAGCCCACGCTGTGGACATGAAT
SPECC1L-CDH4	chr22	24765288	chr20	60427809	8	23	KTEGYQLRAHAVDMN	ACAGAAGGCTATCAGCTCCGAGCCCACGCTGTGGACATGAATGGC
SPECC1L-CDH4	chr22	24765288	chr20	60427809	9	24	TEGYQLRAHAVDMNG	GAAGGCTATCAGCTCCGAGCCCACGCTGTGGACATGAATGGCAAC

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Information of the samples that have these potential fusion neoantigens of SPECC1L-CDH4

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
OV	SPECC1L-CDH4	chr22	24765288	ENST00000314328	chr20	60427809	ENST00000360469	TCGA-30-1714

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Potential target of CAR-T therapy development for SPECC1L-CDH4

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

Tgene

CDH4

chr22:24765288

chr20:60427809

ENST00000360469

735_756

917.0

Transmembrane

Helical

Tgene

CDH4

chr22:24765288

chr20:60427809

ENST00000543233

735_756

843.0

Transmembrane

Helical

Tgene

CDH4

chr22:24765288

chr20:60427810

ENST00000360469

735_756

917.0

Transmembrane

Helical

Tgene

CDH4

chr22:24765288

chr20:60427810

ENST00000543233

735_756

843.0

Transmembrane

Helical

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 SPECC1L-CDH4

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 SPECC1L-CDH4

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)