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Fusion Protein:ITPA-SLC22A24

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ITPA-SLC22A24
	FusionPDB ID: 40647
	FusionGDB2.0 ID: 40647
		Hgene	Tgene
	Gene symbol	ITPA	SLC22A24
	Gene ID	3704	283238
	Gene name	inosine triphosphatase	solute carrier family 22 member 24
	Synonyms	C20orf37\|HLC14-06-P\|ITPase\|My049\|NTPase\|dJ794I6.3	NET46
	Cytomap	20p13	11q12.3
	Type of gene	protein-coding	protein-coding
	Description	inosine triphosphate pyrophosphataseepididymis secretory sperm binding proteininosine triphosphatase (nucleoside triphosphate pyrophosphatase)inosine triphosphate pyrophosphohydrolasenon-canonical purine NTP pyrophosphatasenon-standard purine NTP pyr	solute carrier family 22 member 24
	Modification date	20200320	20200313
	UniProtAcc	Q9BY32 Main function of 5'-partner protein: FUNCTION: Pyrophosphatase that hydrolyzes the non-canonical purine nucleotides inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) and xanthosine 5'-triphosphate (XTP) to their respective monophosphate derivatives. The enzyme does not distinguish between the deoxy- and ribose forms. Probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions. {ECO:0000255\|HAMAP-Rule:MF_03148, ECO:0000269\|PubMed:17090528}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000483354, ENST00000380113, ENST00000399838, ENST00000455664,	ENST00000417740, ENST00000326192,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	4 X 4 X 2=32	1 X 1 X 1=1
	# samples	4	1
	** MAII score	log2(4/32*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(1/1*10)=3.32192809488736
Fusion gene context	PubMed: ITPA [Title/Abstract] AND SLC22A24 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ITPA [Title/Abstract] AND SLC22A24 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ITPA(3194704)-SLC22A24(62847469), # samples:2
Anticipated loss of major functional domain due to fusion event.	ITPA-SLC22A24 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. ITPA-SLC22A24 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. ITPA-SLC22A24 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. ITPA-SLC22A24 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
Tgene	SLC22A24	GO:0008202	steroid metabolic process	31553721
Tgene	SLC22A24	GO:0035382	sterol transmembrane transport	31553721

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr20:3194704/chr11:62847469)
- 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 ITPA (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 SLC22A24 (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)
ENST00000380113	ITPA	chr20	3194704	+	ENST00000417740	SLC22A24	chr11	62847469	-	513	455	192	512	106
ENST00000455664	ITPA	chr20	3194704	+	ENST00000417740	SLC22A24	chr11	62847469	-	309	251	39	308	89
ENST00000399838	ITPA	chr20	3194704	+	ENST00000417740	SLC22A24	chr11	62847469	-	225	167	27	224	65

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
ENST00000380113	ENST00000417740	ITPA	chr20	3194704	+	SLC22A24	chr11	62847469	-	0.016302615	0.98369735
ENST00000455664	ENST00000417740	ITPA	chr20	3194704	+	SLC22A24	chr11	62847469	-	0.038803272	0.9611967
ENST00000399838	ENST00000417740	ITPA	chr20	3194704	+	SLC22A24	chr11	62847469	-	0.2908453	0.7091547

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 ITPA-SLC22A24

+/-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
ITPA	chr20	3194704	SLC22A24	chr11	62847469	167	47	CFNALGGLPGPYIKDSRNIKQEDTCM
ITPA	chr20	3194704	SLC22A24	chr11	62847469	251	71	CFNALGGLPGPYIKDSRNIKQEDTCM
ITPA	chr20	3194704	SLC22A24	chr11	62847469	455	88	CFNALGGLPGPYIKDSRNIKQEDTCM

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Potential FusionNeoAntigen Information of ITPA-SLC22A24 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.

ITPA-SLC22A24_3194704_62847469.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)
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	HLA-A30:01	YIKDSRNIK	0.9609	0.7894	11	20

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Potential FusionNeoAntigen Information of ITPA-SLC22A24 in HLA II

ITPA-SLC22A24_3194704_62847469.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)
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0305	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0305	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0305	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0305	GLPGPYIKDSRNIKQ	6	21
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0305	GGLPGPYIKDSRNIK	5	20
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0340	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0340	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0340	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0340	GLPGPYIKDSRNIKQ	6	21
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0340	GGLPGPYIKDSRNIK	5	20
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0437	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0437	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0466	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0466	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0466	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-0473	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1108	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1114	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1120	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1153	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1153	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1153	GLPGPYIKDSRNIKQ	6	21
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1153	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1168	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1168	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1169	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1173	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1173	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1173	GLPGPYIKDSRNIKQ	6	21
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1173	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1179	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1179	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1179	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1179	GLPGPYIKDSRNIKQ	6	21
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1182	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1182	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1186	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1193	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1302	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-13101	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-13101	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1310	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1310	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1316	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1323	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1329	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1329	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1333	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1333	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1333	GLPGPYIKDSRNIKQ	6	21
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1334	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1336	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1336	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1337	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1337	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1337	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1337	GLPGPYIKDSRNIKQ	6	21
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1338	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1339	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1341	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1341	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1341	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1356	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1360	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1365	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1366	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1373	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1374	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1385	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1385	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1385	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1385	GLPGPYIKDSRNIKQ	6	21
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1386	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1386	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1388	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1396	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1396	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1397	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1399	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1402	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1402	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1409	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1409	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1409	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1413	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1419	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1419	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1419	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1419	GLPGPYIKDSRNIKQ	6	21
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1424	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1424	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1430	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1430	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1430	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1441	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1441	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1446	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1447	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1447	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1447	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1449	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1451	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1451	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1451	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1457	GPYIKDSRNIKQEDT	9	24
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1489	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1494	PGPYIKDSRNIKQED	8	23
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1494	LPGPYIKDSRNIKQE	7	22
ITPA-SLC22A24	chr20	3194704	chr11	62847469	455	DRB1-1498	PGPYIKDSRNIKQED	8	23

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Fusion breakpoint peptide structures of ITPA-SLC22A24

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
2945	GLPGPYIKDSRNIK	ITPA	SLC22A24	chr20	3194704	chr11	62847469	455

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ITPA-SLC22A24

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	2945	GLPGPYIKDSRNIK	-6.80686	-6.92026
HLA-B14:02	3BVN	2945	GLPGPYIKDSRNIK	-5.01234	-6.04764
HLA-B52:01	3W39	2945	GLPGPYIKDSRNIK	-6.71251	-6.82591
HLA-B52:01	3W39	2945	GLPGPYIKDSRNIK	-4.13165	-5.16695
HLA-A11:01	4UQ2	2945	GLPGPYIKDSRNIK	-4.31699	-4.43039
HLA-A11:01	4UQ2	2945	GLPGPYIKDSRNIK	-4.19959	-5.23489
HLA-A24:02	5HGA	2945	GLPGPYIKDSRNIK	-7.74913	-7.86253
HLA-A24:02	5HGA	2945	GLPGPYIKDSRNIK	-5.75888	-6.79418
HLA-B27:03	6PZ5	2945	GLPGPYIKDSRNIK	10001	10000
HLA-B44:05	3DX8	2945	GLPGPYIKDSRNIK	-4.89721	-5.01061
HLA-B44:05	3DX8	2945	GLPGPYIKDSRNIK	-3.74482	-4.78012
HLA-A02:01	6TDR	2945	GLPGPYIKDSRNIK	-5.01451	-6.04981

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Vaccine Design for the FusionNeoAntigens of ITPA-SLC22A24

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
ITPA-SLC22A24	chr20	3194704	chr11	62847469	11	20	YIKDSRNIK	CTACATAAAAGATTCAAGAAACATAAA

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
ITPA-SLC22A24	chr20	3194704	chr11	62847469	5	20	GGLPGPYIKDSRNIK	TGGAGGGCTCCCCGGCCCCTACATAAAAGATTCAAGAAACATAAA
ITPA-SLC22A24	chr20	3194704	chr11	62847469	6	21	GLPGPYIKDSRNIKQ	AGGGCTCCCCGGCCCCTACATAAAAGATTCAAGAAACATAAAGCA
ITPA-SLC22A24	chr20	3194704	chr11	62847469	7	22	LPGPYIKDSRNIKQE	GCTCCCCGGCCCCTACATAAAAGATTCAAGAAACATAAAGCAGGA
ITPA-SLC22A24	chr20	3194704	chr11	62847469	8	23	PGPYIKDSRNIKQED	CCCCGGCCCCTACATAAAAGATTCAAGAAACATAAAGCAGGAAGA
ITPA-SLC22A24	chr20	3194704	chr11	62847469	9	24	GPYIKDSRNIKQEDT	CGGCCCCTACATAAAAGATTCAAGAAACATAAAGCAGGAAGATAC

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Information of the samples that have these potential fusion neoantigens of ITPA-SLC22A24

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
BRCA	ITPA-SLC22A24	chr20	3194704	ENST00000380113	chr11	62847469	ENST00000417740	TCGA-PL-A8LX-01A

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Potential target of CAR-T therapy development for ITPA-SLC22A24

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

SLC22A24

chr20:3194704

chr11:62847469

ENST00000326192

146_166

323.0

Transmembrane

Helical

Tgene

SLC22A24

chr20:3194704

chr11:62847469

ENST00000326192

16_36

323.0

Transmembrane

Helical

Tgene

SLC22A24

chr20:3194704

chr11:62847469

ENST00000326192

188_208

323.0

Transmembrane

Helical

Tgene

SLC22A24

chr20:3194704

chr11:62847469

ENST00000326192

234_254

323.0

Transmembrane

Helical

Tgene

SLC22A24

chr20:3194704

chr11:62847469

ENST00000326192

260_280

323.0

Transmembrane

Helical

Tgene

SLC22A24

chr20:3194704

chr11:62847469

ENST00000326192

350_370

323.0

Transmembrane

Helical

Tgene

SLC22A24

chr20:3194704

chr11:62847469

ENST00000326192

380_400

323.0

Transmembrane

Helical

Tgene

SLC22A24

chr20:3194704

chr11:62847469

ENST00000326192

407_427

323.0

Transmembrane

Helical

Tgene

SLC22A24

chr20:3194704

chr11:62847469

ENST00000326192

435_455

323.0

Transmembrane

Helical

Tgene

SLC22A24

chr20:3194704

chr11:62847469

ENST00000326192

496_516

323.0

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 ITPA-SLC22A24

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 ITPA-SLC22A24

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)