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Fusion Protein:TTC13-JAK2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: TTC13-JAK2
	FusionPDB ID: 94900
	FusionGDB2.0 ID: 94900
		Hgene	Tgene
	Gene symbol	TTC13	JAK2
	Gene ID	79573	3717
	Gene name	tetratricopeptide repeat domain 13	Janus kinase 2
	Synonyms	-	JTK10\|THCYT3
	Cytomap	1q42.2	9p24.1
	Type of gene	protein-coding	protein-coding
	Description	tetratricopeptide repeat protein 13TPR repeat protein 13epididymis secretory sperm binding protein	tyrosine-protein kinase JAK2JAK-2Janus kinase 2 (a protein tyrosine kinase)
	Modification date	20200313	20200329
	UniProtAcc	.	O60674 Main function of 5'-partner protein: FUNCTION: Non-receptor tyrosine kinase involved in various processes such as cell growth, development, differentiation or histone modifications. Mediates essential signaling events in both innate and adaptive immunity. In the cytoplasm, plays a pivotal role in signal transduction via its association with type I receptors such as growth hormone (GHR), prolactin (PRLR), leptin (LEPR), erythropoietin (EPOR), thrombopoietin (THPO); or type II receptors including IFN-alpha, IFN-beta, IFN-gamma and multiple interleukins (PubMed:7615558). Following ligand-binding to cell surface receptors, phosphorylates specific tyrosine residues on the cytoplasmic tails of the receptor, creating docking sites for STATs proteins (PubMed:9618263). Subsequently, phosphorylates the STATs proteins once they are recruited to the receptor. Phosphorylated STATs then form homodimer or heterodimers and translocate to the nucleus to activate gene transcription. For example, cell stimulation with erythropoietin (EPO) during erythropoiesis leads to JAK2 autophosphorylation, activation, and its association with erythropoietin receptor (EPOR) that becomes phosphorylated in its cytoplasmic domain. Then, STAT5 (STAT5A or STAT5B) is recruited, phosphorylated and activated by JAK2. Once activated, dimerized STAT5 translocates into the nucleus and promotes the transcription of several essential genes involved in the modulation of erythropoiesis. Part of a signaling cascade that is activated by increased cellular retinol and that leads to the activation of STAT5 (STAT5A or STAT5B) (PubMed:21368206). In addition, JAK2 mediates angiotensin-2-induced ARHGEF1 phosphorylation (PubMed:20098430). Plays a role in cell cycle by phosphorylating CDKN1B (PubMed:21423214). Cooperates with TEC through reciprocal phosphorylation to mediate cytokine-driven activation of FOS transcription. In the nucleus, plays a key role in chromatin by specifically mediating phosphorylation of 'Tyr-41' of histone H3 (H3Y41ph), a specific tag that promotes exclusion of CBX5 (HP1 alpha) from chromatin (PubMed:19783980). {ECO:0000269\|PubMed:12023369, ECO:0000269\|PubMed:19783980, ECO:0000269\|PubMed:20098430, ECO:0000269\|PubMed:21368206, ECO:0000269\|PubMed:21423214, ECO:0000269\|PubMed:7615558, ECO:0000269\|PubMed:9618263}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000366661, ENST00000366662, ENST00000414259,	ENST00000487310, ENST00000381652, ENST00000539801, ENST00000544510,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	5 X 8 X 3=120	22 X 26 X 9=5148
	# samples	6	15
	** MAII score	log2(6/120*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(15/5148*10)=-5.10097764772482 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: TTC13 [Title/Abstract] AND JAK2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: TTC13 [Title/Abstract] AND JAK2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	TTC13(231075132)-JAK2(5064883), # samples:3
Anticipated loss of major functional domain due to fusion event.	TTC13-JAK2 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. TTC13-JAK2 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. TTC13-JAK2 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. TTC13-JAK2 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	JAK2	GO:0010811	positive regulation of cell-substrate adhesion	10925297
Tgene	JAK2	GO:0019221	cytokine-mediated signaling pathway	8609418
Tgene	JAK2	GO:0033209	tumor necrosis factor-mediated signaling pathway	8609418
Tgene	JAK2	GO:0034612	response to tumor necrosis factor	8609418
Tgene	JAK2	GO:0035409	histone H3-Y41 phosphorylation	19783980
Tgene	JAK2	GO:0035722	interleukin-12-mediated signaling pathway	7528775
Tgene	JAK2	GO:0046677	response to antibiotic	16280321
Tgene	JAK2	GO:0050727	regulation of inflammatory response	10925297
Tgene	JAK2	GO:0060396	growth hormone receptor signaling pathway	10925297
Tgene	JAK2	GO:0070671	response to interleukin-12	7528775

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:231075132/chr9:5064883)
- 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 TTC13 (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 JAK2 (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)
ENST00000366661	TTC13	chr1	231075132	-	ENST00000539801	JAK2	chr9	5064883	+	3274	908	8	3250	1080
ENST00000366661	TTC13	chr1	231075132	-	ENST00000381652	JAK2	chr9	5064883	+	4643	908	8	3250	1080
ENST00000366661	TTC13	chr1	231075132	-	ENST00000544510	JAK2	chr9	5064883	+	3309	908	8	3250	1080
ENST00000366662	TTC13	chr1	231075132	-	ENST00000539801	JAK2	chr9	5064883	+	3136	770	29	3112	1027
ENST00000366662	TTC13	chr1	231075132	-	ENST00000381652	JAK2	chr9	5064883	+	4505	770	29	3112	1027
ENST00000366662	TTC13	chr1	231075132	-	ENST00000544510	JAK2	chr9	5064883	+	3171	770	29	3112	1027
ENST00000414259	TTC13	chr1	231075132	-	ENST00000539801	JAK2	chr9	5064883	+	3138	772	31	3114	1027
ENST00000414259	TTC13	chr1	231075132	-	ENST00000381652	JAK2	chr9	5064883	+	4507	772	31	3114	1027
ENST00000414259	TTC13	chr1	231075132	-	ENST00000544510	JAK2	chr9	5064883	+	3173	772	31	3114	1027
ENST00000366661	TTC13	chr1	231075131	-	ENST00000539801	JAK2	chr9	5064882	+	3274	908	8	3250	1080
ENST00000366661	TTC13	chr1	231075131	-	ENST00000381652	JAK2	chr9	5064882	+	4643	908	8	3250	1080
ENST00000366661	TTC13	chr1	231075131	-	ENST00000544510	JAK2	chr9	5064882	+	3309	908	8	3250	1080
ENST00000366662	TTC13	chr1	231075131	-	ENST00000539801	JAK2	chr9	5064882	+	3136	770	29	3112	1027
ENST00000366662	TTC13	chr1	231075131	-	ENST00000381652	JAK2	chr9	5064882	+	4505	770	29	3112	1027
ENST00000366662	TTC13	chr1	231075131	-	ENST00000544510	JAK2	chr9	5064882	+	3171	770	29	3112	1027
ENST00000414259	TTC13	chr1	231075131	-	ENST00000539801	JAK2	chr9	5064882	+	3138	772	31	3114	1027
ENST00000414259	TTC13	chr1	231075131	-	ENST00000381652	JAK2	chr9	5064882	+	4507	772	31	3114	1027
ENST00000414259	TTC13	chr1	231075131	-	ENST00000544510	JAK2	chr9	5064882	+	3173	772	31	3114	1027
ENST00000366661	TTC13	chr1	231079552	-	ENST00000539801	JAK2	chr9	5064883	+	3046	680	8	3022	1004
ENST00000366661	TTC13	chr1	231079552	-	ENST00000381652	JAK2	chr9	5064883	+	4415	680	8	3022	1004
ENST00000366661	TTC13	chr1	231079552	-	ENST00000544510	JAK2	chr9	5064883	+	3081	680	8	3022	1004
ENST00000366661	TTC13	chr1	231090079	-	ENST00000539801	JAK2	chr9	5064883	+	2887	521	8	2863	951
ENST00000366661	TTC13	chr1	231090079	-	ENST00000381652	JAK2	chr9	5064883	+	4256	521	8	2863	951
ENST00000366661	TTC13	chr1	231090079	-	ENST00000544510	JAK2	chr9	5064883	+	2922	521	8	2863	951
ENST00000366662	TTC13	chr1	231090079	-	ENST00000539801	JAK2	chr9	5064883	+	2908	542	29	2884	951
ENST00000366662	TTC13	chr1	231090079	-	ENST00000381652	JAK2	chr9	5064883	+	4277	542	29	2884	951
ENST00000366662	TTC13	chr1	231090079	-	ENST00000544510	JAK2	chr9	5064883	+	2943	542	29	2884	951
ENST00000414259	TTC13	chr1	231090079	-	ENST00000539801	JAK2	chr9	5064883	+	2910	544	31	2886	951
ENST00000414259	TTC13	chr1	231090079	-	ENST00000381652	JAK2	chr9	5064883	+	4279	544	31	2886	951
ENST00000414259	TTC13	chr1	231090079	-	ENST00000544510	JAK2	chr9	5064883	+	2945	544	31	2886	951

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
ENST00000366661	ENST00000539801	TTC13	chr1	231075132	-	JAK2	chr9	5064883	+	0.000817559	0.9991824
ENST00000366661	ENST00000381652	TTC13	chr1	231075132	-	JAK2	chr9	5064883	+	0.000163512	0.99983644
ENST00000366661	ENST00000544510	TTC13	chr1	231075132	-	JAK2	chr9	5064883	+	0.000801881	0.99919814
ENST00000366662	ENST00000539801	TTC13	chr1	231075132	-	JAK2	chr9	5064883	+	0.000386289	0.9996137
ENST00000366662	ENST00000381652	TTC13	chr1	231075132	-	JAK2	chr9	5064883	+	6.75E-05	0.9999325
ENST00000366662	ENST00000544510	TTC13	chr1	231075132	-	JAK2	chr9	5064883	+	0.000377563	0.99962246
ENST00000414259	ENST00000539801	TTC13	chr1	231075132	-	JAK2	chr9	5064883	+	0.000384994	0.99961495
ENST00000414259	ENST00000381652	TTC13	chr1	231075132	-	JAK2	chr9	5064883	+	6.77E-05	0.9999323
ENST00000414259	ENST00000544510	TTC13	chr1	231075132	-	JAK2	chr9	5064883	+	0.000376356	0.99962366
ENST00000366661	ENST00000539801	TTC13	chr1	231075131	-	JAK2	chr9	5064882	+	0.000817559	0.9991824
ENST00000366661	ENST00000381652	TTC13	chr1	231075131	-	JAK2	chr9	5064882	+	0.000163512	0.99983644
ENST00000366661	ENST00000544510	TTC13	chr1	231075131	-	JAK2	chr9	5064882	+	0.000801881	0.99919814
ENST00000366662	ENST00000539801	TTC13	chr1	231075131	-	JAK2	chr9	5064882	+	0.000386289	0.9996137
ENST00000366662	ENST00000381652	TTC13	chr1	231075131	-	JAK2	chr9	5064882	+	6.75E-05	0.9999325
ENST00000366662	ENST00000544510	TTC13	chr1	231075131	-	JAK2	chr9	5064882	+	0.000377563	0.99962246
ENST00000414259	ENST00000539801	TTC13	chr1	231075131	-	JAK2	chr9	5064882	+	0.000384994	0.99961495
ENST00000414259	ENST00000381652	TTC13	chr1	231075131	-	JAK2	chr9	5064882	+	6.77E-05	0.9999323
ENST00000414259	ENST00000544510	TTC13	chr1	231075131	-	JAK2	chr9	5064882	+	0.000376356	0.99962366
ENST00000366661	ENST00000539801	TTC13	chr1	231079552	-	JAK2	chr9	5064883	+	0.000262902	0.9997371
ENST00000366661	ENST00000381652	TTC13	chr1	231079552	-	JAK2	chr9	5064883	+	6.06E-05	0.99993944
ENST00000366661	ENST00000544510	TTC13	chr1	231079552	-	JAK2	chr9	5064883	+	0.000257958	0.9997421
ENST00000366661	ENST00000539801	TTC13	chr1	231090079	-	JAK2	chr9	5064883	+	0.000389553	0.9996105
ENST00000366661	ENST00000381652	TTC13	chr1	231090079	-	JAK2	chr9	5064883	+	9.47E-05	0.9999052
ENST00000366661	ENST00000544510	TTC13	chr1	231090079	-	JAK2	chr9	5064883	+	0.000383062	0.99961686
ENST00000366662	ENST00000539801	TTC13	chr1	231090079	-	JAK2	chr9	5064883	+	0.000381649	0.9996183
ENST00000366662	ENST00000381652	TTC13	chr1	231090079	-	JAK2	chr9	5064883	+	9.45E-05	0.99990547
ENST00000366662	ENST00000544510	TTC13	chr1	231090079	-	JAK2	chr9	5064883	+	0.000376062	0.9996239
ENST00000414259	ENST00000539801	TTC13	chr1	231090079	-	JAK2	chr9	5064883	+	0.000379677	0.9996203
ENST00000414259	ENST00000381652	TTC13	chr1	231090079	-	JAK2	chr9	5064883	+	9.45E-05	0.99990547
ENST00000414259	ENST00000544510	TTC13	chr1	231090079	-	JAK2	chr9	5064883	+	0.000374345	0.9996257

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 TTC13-JAK2

+/-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
TTC13	chr1	231075131	JAK2	chr9	5064882	770	247	YKGLTFFHRGLLKEIELSSLREALSF
TTC13	chr1	231075131	JAK2	chr9	5064882	772	247	YKGLTFFHRGLLKEIELSSLREALSF
TTC13	chr1	231075131	JAK2	chr9	5064882	908	300	YKGLTFFHRGLLKEIELSSLREALSF
TTC13	chr1	231075132	JAK2	chr9	5064883	770	247	YKGLTFFHRGLLKEIELSSLREALSF
TTC13	chr1	231075132	JAK2	chr9	5064883	772	247	YKGLTFFHRGLLKEIELSSLREALSF
TTC13	chr1	231075132	JAK2	chr9	5064883	908	300	YKGLTFFHRGLLKEIELSSLREALSF
TTC13	chr1	231079552	JAK2	chr9	5064883	680	222	TLEPDRPEVFEQRAEEIELSSLREAL
TTC13	chr1	231090079	JAK2	chr9	5064883	521	171	YDEAIRHFSTMLQEIELSSLREALSF
TTC13	chr1	231090079	JAK2	chr9	5064883	542	171	YDEAIRHFSTMLQEIELSSLREALSF
TTC13	chr1	231090079	JAK2	chr9	5064883	544	171	YDEAIRHFSTMLQEIELSSLREALSF

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Potential FusionNeoAntigen Information of TTC13-JAK2 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.

TTC13-JAK2_231075131_5064882.msa
TTC13-JAK2_231079552_5064883.msa
TTC13-JAK2_231090079_5064883.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)
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B47:01	KEIELSSL	0.997	0.6152	12	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B39:13	KEIELSSL	0.9707	0.8227	12	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B50:01	KEIELSSL	0.9279	0.6004	12	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B41:01	KEIELSSL	0.8915	0.8776	12	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B39:06	FHRGLLKEI	0.9919	0.681	6	15
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B14:02	FHRGLLKEI	0.9742	0.6595	6	15
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B14:01	FHRGLLKEI	0.9742	0.6595	6	15
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B08:01	RGLLKEIEL	0.953	0.8126	8	17
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B15:37	FHRGLLKEI	0.5228	0.552	6	15
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B27:07	HRGLLKEIEL	0.9991	0.6543	7	17
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B45:01	KEIELSSLREA	0.9999	0.788	12	23
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B50:02	KEIELSSLREA	0.9997	0.6554	12	23
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B41:01	KEIELSSLREA	0.9974	0.8155	12	23
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B50:01	KEIELSSLREA	0.9906	0.7221	12	23
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B40:06	KEIELSSL	0.9999	0.5197	12	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B39:08	KEIELSSL	0.993	0.7662	12	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-C12:16	FHRGLLKEI	0.0107	0.9643	6	15
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B39:12	HRGLLKEIEL	0.9898	0.9297	7	17
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B40:04	KEIELSSL	0.9998	0.6739	12	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B41:03	KEIELSSL	0.9736	0.5926	12	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B39:02	KEIELSSL	0.9711	0.8332	12	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B50:05	KEIELSSL	0.9279	0.6004	12	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B50:04	KEIELSSL	0.9279	0.6004	12	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B08:18	RGLLKEIEL	0.953	0.8126	8	17
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B15:09	FHRGLLKEI	0.7441	0.6874	6	15
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-C06:02	FHRGLLKEI	0.0336	0.9898	6	15
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-C06:17	FHRGLLKEI	0.0336	0.9898	6	15
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-C06:08	FHRGLLKEI	0.0323	0.9858	6	15
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B27:06	HRGLLKEIEL	0.9995	0.8694	7	17
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B27:09	HRGLLKEIEL	0.9995	0.8866	7	17
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-A02:03	LLKEIELSSL	0.9977	0.6399	10	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B15:73	LLKEIELSSL	0.9955	0.7496	10	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B15:30	LLKEIELSSL	0.9915	0.6852	10	20
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B50:05	KEIELSSLREA	0.9906	0.7221	12	23
TTC13-JAK2	chr1	231075131	chr9	5064882	908	HLA-B50:04	KEIELSSLREA	0.9906	0.7221	12	23
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:01	QRAEEIEL	0.9998	0.9128	11	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:24	QRAEEIEL	0.9998	0.6167	11	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B38:02	QRAEEIEL	0.9997	0.9687	11	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B14:02	EQRAEEIEL	0.9938	0.8019	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B14:01	EQRAEEIEL	0.9938	0.8019	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:01	EQRAEEIEL	0.9626	0.8858	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:13	EQRAEEIEL	0.9366	0.9184	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-A66:01	EVFEQRAEE	0.933	0.5106	7	16
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-A26:03	EVFEQRAEE	0.8886	0.5171	7	16
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B15:10	EQRAEEIEL	0.7755	0.5079	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B15:37	EQRAEEIEL	0.7425	0.6186	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:01	QRAEEIELSSL	0.9998	0.8407	11	22
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B38:02	QRAEEIELSSL	0.9997	0.9185	11	22
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:12	QRAEEIEL	0.9997	0.918	11	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:05	QRAEEIEL	0.9996	0.9033	11	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-C04:10	VFEQRAEEI	0.9917	0.7789	8	17
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-C04:07	VFEQRAEEI	0.9916	0.7645	8	17
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:05	EQRAEEIEL	0.9266	0.8715	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:08	EQRAEEIEL	0.8801	0.7927	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-C04:14	VFEQRAEEI	0.838	0.7937	8	17
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B14:03	EQRAEEIEL	0.7766	0.8346	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B73:01	DRPEVFEQRA	0.9906	0.9204	4	14
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:08	RAEEIELSSL	0.9518	0.8275	12	22
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:31	QRAEEIEL	0.9998	0.9136	11	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-C04:01	VFEQRAEEI	0.9916	0.7645	8	17
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-C18:01	VFEQRAEEI	0.9861	0.7953	8	17
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:02	EQRAEEIEL	0.9775	0.9185	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B15:73	EQRAEEIEL	0.9266	0.8916	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B15:30	EQRAEEIEL	0.8857	0.8265	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:11	EQRAEEIEL	0.8355	0.7208	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B15:09	EQRAEEIEL	0.5953	0.6139	10	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-A68:02	EVFEQRAEEI	0.9927	0.5891	7	17
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B40:04	FEQRAEEIEL	0.9908	0.6977	9	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B15:30	FEQRAEEIEL	0.9859	0.8756	9	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B15:73	FEQRAEEIEL	0.9852	0.8659	9	19
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B35:13	RAEEIELSSL	0.8072	0.9173	12	22
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B41:03	RAEEIELSSL	0.5959	0.5252	12	22
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B27:09	QRAEEIELSSL	0.9999	0.6025	11	22
TTC13-JAK2	chr1	231079552	chr9	5064883	680	HLA-B39:31	QRAEEIELSSL	0.9998	0.8418	11	22
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B18:01	QEIELSSL	0.9948	0.7539	12	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B39:13	QEIELSSL	0.9753	0.7736	12	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B39:13	LQEIELSSL	0.8988	0.8891	11	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B13:01	LQEIELSSL	0.7517	0.8547	11	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-A02:22	MLQEIELSSL	0.9981	0.6237	10	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-A02:27	MLQEIELSSL	0.9923	0.6582	10	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B38:01	RHFSTMLQEI	0.991	0.9383	5	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-A02:04	MLQEIELSSL	0.9906	0.5118	10	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-A02:13	MLQEIELSSL	0.9901	0.6724	10	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-A02:38	MLQEIELSSL	0.9734	0.7051	10	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B45:01	QEIELSSLREA	0.9998	0.8311	12	23
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B50:02	QEIELSSLREA	0.9997	0.6912	12	23
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B50:01	QEIELSSLREA	0.9976	0.7337	12	23
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B41:01	QEIELSSLREA	0.9965	0.9126	12	23
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B39:08	QEIELSSL	0.9896	0.82	12	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C15:06	STMLQEIEL	0.9993	0.9312	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C03:07	STMLQEIEL	0.9992	0.9678	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C03:19	STMLQEIEL	0.999	0.9902	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C03:08	STMLQEIEL	0.9988	0.8715	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C04:06	STMLQEIEL	0.9985	0.888	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C08:03	STMLQEIEL	0.9276	0.987	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B39:08	LQEIELSSL	0.8902	0.8509	11	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C02:06	STMLQEIEL	0.8461	0.9733	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B40:06	QEIELSSLREA	0.9997	0.5005	12	23
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B40:04	QEIELSSL	0.9998	0.5583	12	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B18:06	QEIELSSL	0.995	0.7584	12	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B18:05	QEIELSSL	0.9948	0.7539	12	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B18:03	QEIELSSL	0.9924	0.7461	12	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B18:08	QEIELSSL	0.9911	0.6878	12	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B18:04	QEIELSSL	0.991	0.7681	12	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B18:11	QEIELSSL	0.9889	0.7429	12	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B41:03	QEIELSSL	0.983	0.6894	12	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B39:02	QEIELSSL	0.9762	0.7777	12	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C15:05	STMLQEIEL	0.9992	0.9164	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C15:02	STMLQEIEL	0.9991	0.8987	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C03:03	STMLQEIEL	0.9988	0.9895	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C03:04	STMLQEIEL	0.9988	0.9895	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C03:17	STMLQEIEL	0.9979	0.977	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C03:05	STMLQEIEL	0.9974	0.938	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C03:06	STMLQEIEL	0.9826	0.9908	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C16:02	STMLQEIEL	0.9764	0.9915	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-A69:01	STMLQEIEL	0.9415	0.6762	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C08:01	STMLQEIEL	0.9276	0.987	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C16:01	STMLQEIEL	0.9248	0.9816	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B39:02	LQEIELSSL	0.9239	0.8888	11	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B39:11	LQEIELSSL	0.8672	0.8616	11	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B35:13	STMLQEIEL	0.8335	0.9137	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B15:73	LQEIELSSL	0.7715	0.7085	11	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C17:01	STMLQEIEL	0.7471	0.9438	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B15:30	LQEIELSSL	0.6916	0.6742	11	20
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B07:13	STMLQEIEL	0.2873	0.8381	8	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-C06:06	HFSTMLQEI	0.1813	0.9872	6	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B38:05	RHFSTMLQEI	0.991	0.9383	5	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B50:05	QEIELSSLREA	0.9976	0.7337	12	23
TTC13-JAK2	chr1	231090079	chr9	5064883	521	HLA-B50:04	QEIELSSLREA	0.9976	0.7337	12	23

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Potential FusionNeoAntigen Information of TTC13-JAK2 in HLA II

TTC13-JAK2_231090079_5064883.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)
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0403	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0415	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0427	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0436	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0437	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0437	YDEAIRHFSTMLQEI	0	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0437	EAIRHFSTMLQEIEL	2	17
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0439	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0440	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0441	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0442	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0442	YDEAIRHFSTMLQEI	0	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0444	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0446	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0450	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0452	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0453	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0453	YDEAIRHFSTMLQEI	0	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0455	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0456	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0456	YDEAIRHFSTMLQEI	0	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0458	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0458	YDEAIRHFSTMLQEI	0	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0459	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0459	YDEAIRHFSTMLQEI	0	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0460	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0465	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0465	YDEAIRHFSTMLQEI	0	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0468	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0471	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0473	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0473	YDEAIRHFSTMLQEI	0	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0475	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0478	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0485	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0488	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-0488	YDEAIRHFSTMLQEI	0	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-1410	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-1457	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-1457	YDEAIRHFSTMLQEI	0	15
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB1-1521	DEAIRHFSTMLQEIE	1	16
TTC13-JAK2	chr1	231090079	chr9	5064883	521	DRB5-0204	DEAIRHFSTMLQEIE	1	16

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Fusion breakpoint peptide structures of TTC13-JAK2

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
2405	FHRGLLKEIELSSL	TTC13	JAK2	chr1	231075131	chr9	5064882	908

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
3316	HFSTMLQEIELSSL	TTC13	JAK2	chr1	231090079	chr9	5064883	521

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
6605	PEVFEQRAEEIELS	TTC13	JAK2	chr1	231079552	chr9	5064883	680

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TTC13-JAK2

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	2405	FHRGLLKEIELSSL	-7.14497	-7.33947
HLA-B14:02	3BVN	2405	FHRGLLKEIELSSL	-3.08951	-3.84401
HLA-B52:01	3W39	2405	FHRGLLKEIELSSL	-6.33358	-6.52808
HLA-B52:01	3W39	2405	FHRGLLKEIELSSL	-4.26077	-5.01527
HLA-A24:02	5HGA	2405	FHRGLLKEIELSSL	-8.36912	-8.56362
HLA-A24:02	5HGA	2405	FHRGLLKEIELSSL	-7.96079	-8.71529
HLA-B44:05	3DX8	2405	FHRGLLKEIELSSL	-5.68867	-5.88317
HLA-B44:05	3DX8	2405	FHRGLLKEIELSSL	-5.05897	-5.81347
HLA-A02:01	6TDR	2405	FHRGLLKEIELSSL	-2.46164	-3.21614
HLA-B14:02	3BVN	3316	HFSTMLQEIELSSL	-7.9962	-8.1096
HLA-B14:02	3BVN	3316	HFSTMLQEIELSSL	-5.70842	-6.74372
HLA-B52:01	3W39	3316	HFSTMLQEIELSSL	-6.83737	-6.95077
HLA-B52:01	3W39	3316	HFSTMLQEIELSSL	-4.4836	-5.5189
HLA-A11:01	4UQ2	3316	HFSTMLQEIELSSL	-10.0067	-10.1201
HLA-A11:01	4UQ2	3316	HFSTMLQEIELSSL	-9.03915	-10.0745
HLA-A24:02	5HGA	3316	HFSTMLQEIELSSL	-6.56204	-6.67544
HLA-A24:02	5HGA	3316	HFSTMLQEIELSSL	-5.42271	-6.45801
HLA-B44:05	3DX8	3316	HFSTMLQEIELSSL	-7.85648	-8.89178
HLA-B44:05	3DX8	3316	HFSTMLQEIELSSL	-5.3978	-5.5112
HLA-A02:01	6TDR	3316	HFSTMLQEIELSSL	-3.37154	-4.40684
HLA-B14:02	3BVN	6605	PEVFEQRAEEIELS	-7.9962	-8.1096
HLA-B14:02	3BVN	6605	PEVFEQRAEEIELS	-5.70842	-6.74372
HLA-B52:01	3W39	6605	PEVFEQRAEEIELS	-6.83737	-6.95077
HLA-B52:01	3W39	6605	PEVFEQRAEEIELS	-4.4836	-5.5189
HLA-A11:01	4UQ2	6605	PEVFEQRAEEIELS	-10.0067	-10.1201
HLA-A11:01	4UQ2	6605	PEVFEQRAEEIELS	-9.03915	-10.0745
HLA-A24:02	5HGA	6605	PEVFEQRAEEIELS	-6.56204	-6.67544
HLA-A24:02	5HGA	6605	PEVFEQRAEEIELS	-5.42271	-6.45801
HLA-B44:05	3DX8	6605	PEVFEQRAEEIELS	-7.85648	-8.89178
HLA-B44:05	3DX8	6605	PEVFEQRAEEIELS	-5.3978	-5.5112
HLA-A02:01	6TDR	6605	PEVFEQRAEEIELS	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of TTC13-JAK2

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
TTC13-JAK2	chr1	231075131	chr9	5064882	10	20	LLKEIELSSL	CTTCTGAAGGAAATTGAACTTAGCTCATTA
TTC13-JAK2	chr1	231075131	chr9	5064882	12	20	KEIELSSL	AAGGAAATTGAACTTAGCTCATTA
TTC13-JAK2	chr1	231075131	chr9	5064882	12	23	KEIELSSLREA	AAGGAAATTGAACTTAGCTCATTAAGGGAAGCT
TTC13-JAK2	chr1	231075131	chr9	5064882	6	15	FHRGLLKEI	TTTCACAGAGGACTTCTGAAGGAAATT
TTC13-JAK2	chr1	231075131	chr9	5064882	7	17	HRGLLKEIEL	CACAGAGGACTTCTGAAGGAAATTGAACTT
TTC13-JAK2	chr1	231075131	chr9	5064882	8	17	RGLLKEIEL	AGAGGACTTCTGAAGGAAATTGAACTT
TTC13-JAK2	chr1	231079552	chr9	5064883	10	19	EQRAEEIEL	CGAGCAGAAGAAATTGAACTTAGCTCA
TTC13-JAK2	chr1	231079552	chr9	5064883	11	19	QRAEEIEL	GCAGAAGAAATTGAACTTAGCTCA
TTC13-JAK2	chr1	231079552	chr9	5064883	11	22	QRAEEIELSSL	GCAGAAGAAATTGAACTTAGCTCATTAAGGGAA
TTC13-JAK2	chr1	231079552	chr9	5064883	12	22	RAEEIELSSL	GAAGAAATTGAACTTAGCTCATTAAGGGAA
TTC13-JAK2	chr1	231079552	chr9	5064883	4	14	DRPEVFEQRA	CCAGAGGTATTTGAGCAGCGAGCAGAAGAA
TTC13-JAK2	chr1	231079552	chr9	5064883	7	16	EVFEQRAEE	TTTGAGCAGCGAGCAGAAGAAATTGAA
TTC13-JAK2	chr1	231079552	chr9	5064883	7	17	EVFEQRAEEI	TTTGAGCAGCGAGCAGAAGAAATTGAACTT
TTC13-JAK2	chr1	231079552	chr9	5064883	8	17	VFEQRAEEI	GAGCAGCGAGCAGAAGAAATTGAACTT
TTC13-JAK2	chr1	231079552	chr9	5064883	9	19	FEQRAEEIEL	CAGCGAGCAGAAGAAATTGAACTTAGCTCA
TTC13-JAK2	chr1	231090079	chr9	5064883	10	20	MLQEIELSSL	ATGCTTCAGGAAATTGAACTTAGCTCATTA
TTC13-JAK2	chr1	231090079	chr9	5064883	11	20	LQEIELSSL	CTTCAGGAAATTGAACTTAGCTCATTA
TTC13-JAK2	chr1	231090079	chr9	5064883	12	20	QEIELSSL	CAGGAAATTGAACTTAGCTCATTA
TTC13-JAK2	chr1	231090079	chr9	5064883	12	23	QEIELSSLREA	CAGGAAATTGAACTTAGCTCATTAAGGGAAGCT
TTC13-JAK2	chr1	231090079	chr9	5064883	5	15	RHFSTMLQEI	CGGCATTTTTCAACAATGCTTCAGGAAATT
TTC13-JAK2	chr1	231090079	chr9	5064883	6	15	HFSTMLQEI	CATTTTTCAACAATGCTTCAGGAAATT
TTC13-JAK2	chr1	231090079	chr9	5064883	8	17	STMLQEIEL	TCAACAATGCTTCAGGAAATTGAACTT

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
TTC13-JAK2	chr1	231090079	chr9	5064883	0	15	YDEAIRHFSTMLQEI	TATGATGAAGCAATACGGCATTTTTCAACAATGCTTCAGGAAATT
TTC13-JAK2	chr1	231090079	chr9	5064883	1	16	DEAIRHFSTMLQEIE	GATGAAGCAATACGGCATTTTTCAACAATGCTTCAGGAAATTGAA
TTC13-JAK2	chr1	231090079	chr9	5064883	2	17	EAIRHFSTMLQEIEL	GAAGCAATACGGCATTTTTCAACAATGCTTCAGGAAATTGAACTT

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Information of the samples that have these potential fusion neoantigens of TTC13-JAK2

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	TTC13-JAK2	chr1	231079552	ENST00000366661	chr9	5064883	ENST00000381652	TCGA-E9-A22D-01A
BRCA	TTC13-JAK2	chr1	231090079	ENST00000366661	chr9	5064883	ENST00000381652	TCGA-E9-A22D-01A
BRCA	TTC13-JAK2	chr1	231075131	ENST00000366661	chr9	5064882	ENST00000381652	TCGA-E9-A22D

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Potential target of CAR-T therapy development for TTC13-JAK2

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 TTC13-JAK2

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 TTC13-JAK2

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
Tgene	JAK2	C0032463	Polycythemia Vera	12	CTD_human;ORPHANET;UNIPROT
Tgene	JAK2	C0040028	Thrombocythemia, Essential	10	CTD_human;ORPHANET
Tgene	JAK2	C0001815	Primary Myelofibrosis	9	CGI;CTD_human;GENOMICS_ENGLAND;ORPHANET
Tgene	JAK2	C3489628	Thrombocytosis, Autosomal Dominant	8	CTD_human
Tgene	JAK2	C0019154	Hepatic Vein Thrombosis	3	CTD_human;ORPHANET
Tgene	JAK2	C0856761	Budd-Chiari Syndrome	3	CTD_human;ORPHANET
Tgene	JAK2	C0009324	Ulcerative Colitis	2	CTD_human
Tgene	JAK2	C0027022	Myeloproliferative disease	2	CTD_human
Tgene	JAK2	C0151744	Myocardial Ischemia	2	CTD_human
Tgene	JAK2	C0836924	Thrombocytosis	2	CTD_human
Tgene	JAK2	C3281125	THROMBOCYTHEMIA 3	2	UNIPROT
Tgene	JAK2	C0000786	Spontaneous abortion	1	CTD_human
Tgene	JAK2	C0000822	Abortion, Tubal	1	CTD_human
Tgene	JAK2	C0006663	Calcinosis	1	CTD_human
Tgene	JAK2	C0007873	Uterine Cervical Neoplasm	1	CTD_human
Tgene	JAK2	C0018824	Heart valve disease	1	CTD_human
Tgene	JAK2	C0019207	Hepatoma, Morris	1	CTD_human
Tgene	JAK2	C0019208	Hepatoma, Novikoff	1	CTD_human
Tgene	JAK2	C0021368	Inflammation	1	CTD_human
Tgene	JAK2	C0023418	leukemia	1	CTD_human
Tgene	JAK2	C0023467	Leukemia, Myelocytic, Acute	1	CGI;CTD_human;UNIPROT
Tgene	JAK2	C0023893	Liver Cirrhosis, Experimental	1	CTD_human
Tgene	JAK2	C0023904	Liver Neoplasms, Experimental	1	CTD_human
Tgene	JAK2	C0025472	Mesenteric Vascular Occlusion	1	CTD_human
Tgene	JAK2	C0026998	Acute Myeloid Leukemia, M1	1	CTD_human
Tgene	JAK2	C0032461	Polycythemia	1	CTD_human
Tgene	JAK2	C0032962	Pregnancy Complications	1	CTD_human
Tgene	JAK2	C0033578	Prostatic Neoplasms	1	CTD_human
Tgene	JAK2	C0040038	Thromboembolism	1	CTD_human
Tgene	JAK2	C0042487	Venous Thrombosis	1	CTD_human
Tgene	JAK2	C0086404	Experimental Hepatoma	1	CTD_human
Tgene	JAK2	C0149871	Deep Vein Thrombosis	1	CTD_human
Tgene	JAK2	C0263628	Tumoral calcinosis	1	CTD_human
Tgene	JAK2	C0376358	Malignant neoplasm of prostate	1	CTD_human
Tgene	JAK2	C0400966	Non-alcoholic Fatty Liver Disease	1	CTD_human
Tgene	JAK2	C0521174	Microcalcification	1	CTD_human
Tgene	JAK2	C1527405	Erythrocytosis	1	CTD_human
Tgene	JAK2	C1879321	Acute Myeloid Leukemia (AML-M2)	1	CTD_human
Tgene	JAK2	C3241937	Nonalcoholic Steatohepatitis	1	CTD_human
Tgene	JAK2	C3495676	Anorectal Malformations	1	GENOMICS_ENGLAND
Tgene	JAK2	C3830362	Early Pregnancy Loss	1	CTD_human
Tgene	JAK2	C4048328	cervical cancer	1	CTD_human
Tgene	JAK2	C4303761	Familial thrombocytosis	1	ORPHANET
Tgene	JAK2	C4552766	Miscarriage	1	CTD_human

	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)