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Fusion Protein:TRIO-ANKH

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: TRIO-ANKH
	FusionPDB ID: 94182
	FusionGDB2.0 ID: 94182
		Hgene	Tgene
	Gene symbol	TRIO	ANKH
	Gene ID	7204	56172
	Gene name	trio Rho guanine nucleotide exchange factor	ANKH inorganic pyrophosphate transport regulator
	Synonyms	ARHGEF23\|MEBAS\|MRD44\|tgat	ANK\|CCAL2\|CMDJ\|CPPDD\|HANK\|MANK\|SLC62A1
	Cytomap	5p15.2	5p15.2
	Type of gene	protein-coding	protein-coding
	Description	triple functional domain proteinPTPRF-interacting proteintriple functional domain (PTPRF interacting)	progressive ankylosis protein homologankylosis, progressive homolog
	Modification date	20200313	20200313
	UniProtAcc	TPI1 Main function of 5'-partner protein: 249	Q8IWZ3 Main function of 5'-partner protein: FUNCTION: May play a role as a scaffolding protein that may be associated with the abnormal phenotype of leukemia cells. Isoform 2 may possess an antiapoptotic effect and protect cells during normal cell survival through its regulation of caspases. {ECO:0000269\|PubMed:16098192}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000344204, ENST00000509967, ENST00000537187, ENST00000344135, ENST00000515710,	ENST00000503939, ENST00000535119, ENST00000284268,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	34 X 28 X 12=11424	13 X 11 X 7=1001
	# samples	35	14
	** MAII score	log2(35/11424*10)=-5.02856915219677 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(14/1001*10)=-2.83794324189103 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: TRIO [Title/Abstract] AND ANKH [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: TRIO [Title/Abstract] AND ANKH [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	TRIO(14287172)-ANKH(14751348), # samples:1 TRIO(14287171)-ANKH(14751347), # samples:1
Anticipated loss of major functional domain due to fusion event.	TRIO-ANKH 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. TRIO-ANKH 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:14287172/chr5:14751348)
- 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 TRIO (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 ANKH (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)
ENST00000344204	TRIO	chr5	14287172	+	ENST00000284268	ANKH	chr5	14751348	-	7920	564	24	1526	500
ENST00000537187	TRIO	chr5	14287172	+	ENST00000284268	ANKH	chr5	14751348	-	7902	546	6	1508	500
ENST00000509967	TRIO	chr5	14287172	+	ENST00000284268	ANKH	chr5	14751348	-	7901	545	152	1507	451
ENST00000344204	TRIO	chr5	14287171	+	ENST00000284268	ANKH	chr5	14751347	-	7920	564	24	1526	500
ENST00000537187	TRIO	chr5	14287171	+	ENST00000284268	ANKH	chr5	14751347	-	7902	546	6	1508	500
ENST00000509967	TRIO	chr5	14287171	+	ENST00000284268	ANKH	chr5	14751347	-	7901	545	152	1507	451

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
ENST00000344204	ENST00000284268	TRIO	chr5	14287172	+	ANKH	chr5	14751348	-	0.000469638	0.99953043
ENST00000537187	ENST00000284268	TRIO	chr5	14287172	+	ANKH	chr5	14751348	-	0.000462416	0.9995376
ENST00000509967	ENST00000284268	TRIO	chr5	14287172	+	ANKH	chr5	14751348	-	0.000704164	0.99929583
ENST00000344204	ENST00000284268	TRIO	chr5	14287171	+	ANKH	chr5	14751347	-	0.000469638	0.99953043
ENST00000537187	ENST00000284268	TRIO	chr5	14287171	+	ANKH	chr5	14751347	-	0.000462416	0.9995376
ENST00000509967	ENST00000284268	TRIO	chr5	14287171	+	ANKH	chr5	14751347	-	0.000704164	0.99929583

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 TRIO-ANKH

+/-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
TRIO	chr5	14287171	ANKH	chr5	14751347	545	131	QRTNFGSSKFEFEVVFVAILLHSHLE
TRIO	chr5	14287171	ANKH	chr5	14751347	546	180	QRTNFGSSKFEFEVVFVAILLHSHLE
TRIO	chr5	14287171	ANKH	chr5	14751347	564	180	QRTNFGSSKFEFEVVFVAILLHSHLE
TRIO	chr5	14287172	ANKH	chr5	14751348	545	131	QRTNFGSSKFEFEVVFVAILLHSHLE
TRIO	chr5	14287172	ANKH	chr5	14751348	546	180	QRTNFGSSKFEFEVVFVAILLHSHLE
TRIO	chr5	14287172	ANKH	chr5	14751348	564	180	QRTNFGSSKFEFEVVFVAILLHSHLE

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Potential FusionNeoAntigen Information of TRIO-ANKH 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.

TRIO-ANKH_14287171_14751347.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)
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:01	FEFEVVFV	0.9895	0.9778	9	17
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B52:01	FEFEVVFV	0.9698	0.9865	9	17
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B45:01	FEFEVVFVA	0.9957	0.9319	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B50:02	FEFEVVFVA	0.9926	0.7948	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B27:02	SKFEFEVVF	0.9825	0.7843	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B39:01	SKFEFEVVF	0.981	0.9846	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B39:24	SKFEFEVVF	0.9783	0.544	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B38:01	SKFEFEVVF	0.9729	0.9912	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B38:02	SKFEFEVVF	0.9708	0.9934	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B39:13	SKFEFEVVF	0.9504	0.9798	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:01	FEFEVVFVA	0.9297	0.9711	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:01	FEVVFVAIL	0.9279	0.9121	11	20
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B14:01	SKFEFEVVF	0.8873	0.9103	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B14:02	SKFEFEVVF	0.8873	0.9103	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B39:06	FEFEVVFVA	0.7566	0.9785	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B41:01	FEFEVVFVA	0.6737	0.9871	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:10	SKFEFEVVF	0.6674	0.8613	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:18	SKFEFEVVF	0.6219	0.934	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B50:01	FEFEVVFVA	0.5887	0.9336	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:03	SKFEFEVVF	0.5767	0.9445	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:37	SKFEFEVVF	0.3509	0.8984	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:01	SKFEFEVVF	0.3082	0.9732	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B47:01	SKFEFEVVF	0.2631	0.7875	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B52:01	SKFEFEVVF	0.0404	0.9877	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B57:03	SSKFEFEVVF	0.9996	0.9928	6	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:16	SSKFEFEVVF	0.9987	0.8382	6	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:03	SSKFEFEVVF	0.9954	0.941	6	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B45:01	KFEFEVVFVA	0.9162	0.9492	8	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B50:02	KFEFEVVFVA	0.8965	0.8027	8	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B41:01	KFEFEVVFVA	0.6649	0.9613	8	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B50:01	KFEFEVVFVA	0.5969	0.827	8	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B45:01	SKFEFEVVFVA	0.9541	0.9598	7	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B50:02	SKFEFEVVFVA	0.8085	0.8163	7	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B50:01	SKFEFEVVFVA	0.7841	0.8277	7	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B40:06	FEFEVVFV	0.9999	0.7434	9	17
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B51:07	FEFEVVFV	0.9803	0.9538	9	17
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B40:06	FEFEVVFVA	0.999	0.7459	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:95	SKFEFEVVF	0.9916	0.8798	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:05	SKFEFEVVF	0.9909	0.9816	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B39:09	SKFEFEVVF	0.9863	0.6858	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:27	SKFEFEVVF	0.9831	0.9833	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B39:12	SKFEFEVVF	0.982	0.9863	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B73:01	FEFEVVFVA	0.9813	0.9794	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:29	SKFEFEVVF	0.9627	0.9787	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B39:05	SKFEFEVVF	0.9617	0.9807	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B40:03	FEFEVVFVA	0.9318	0.6212	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:19	SKFEFEVVF	0.8388	0.9214	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:46	SKFEFEVVF	0.8324	0.9658	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:10	SKFEFEVVF	0.8239	0.9876	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:67	SKFEFEVVF	0.8212	0.9845	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:80	SKFEFEVVF	0.8212	0.9845	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:21	SKFEFEVVF	0.6962	0.9751	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B40:03	SKFEFEVVF	0.4444	0.566	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C12:16	SKFEFEVVF	0.1422	0.981	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B40:06	KFEFEVVFVA	0.957	0.686	8	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B40:06	SKFEFEVVFVA	0.9636	0.7851	7	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:03	FEVVFVAI	0.9926	0.8763	11	19
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:05	FEFEVVFV	0.9895	0.9778	9	17
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:06	FEFEVVFV	0.9871	0.9815	9	17
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:03	FEFEVVFV	0.9851	0.9754	9	17
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C15:02	GSSKFEFEV	0.9992	0.9581	5	14
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:01	SKFEFEVVF	0.9937	0.8787	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B40:04	FEFEVVFVA	0.9876	0.9619	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-A25:01	EVVFVAILL	0.9857	0.8516	12	21
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B27:08	SKFEFEVVF	0.983	0.8877	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B27:06	SKFEFEVVF	0.9825	0.8632	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B39:02	SKFEFEVVF	0.9817	0.9816	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B39:31	SKFEFEVVF	0.9795	0.9852	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B38:05	SKFEFEVVF	0.9729	0.9912	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:04	FEFEVVFVA	0.9376	0.9748	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:08	FEFEVVFVA	0.9349	0.9692	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:17	SKFEFEVVF	0.9346	0.9888	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:05	FEFEVVFVA	0.9297	0.9711	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:05	FEVVFVAIL	0.9279	0.9121	11	20
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:06	FEVVFVAIL	0.9248	0.9274	11	20
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:06	FEFEVVFVA	0.9236	0.9756	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:03	FEFEVVFVA	0.9133	0.9704	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:03	FEVVFVAIL	0.9101	0.9035	11	20
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:08	FEVVFVAIL	0.9085	0.9178	11	20
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:22	SKFEFEVVF	0.8454	0.8618	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C07:02	SKFEFEVVF	0.8212	0.9845	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:11	SKFEFEVVF	0.7665	0.9739	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B48:02	SKFEFEVVF	0.7109	0.9739	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B35:28	SKFEFEVVF	0.7057	0.9754	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:11	FEFEVVFVA	0.6795	0.9426	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B50:04	FEFEVVFVA	0.5887	0.9336	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B50:05	FEFEVVFVA	0.5887	0.9336	9	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:09	SKFEFEVVF	0.5552	0.6209	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:06	SKFEFEVVF	0.402	0.9748	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:04	SKFEFEVVF	0.4007	0.9751	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C06:08	SKFEFEVVF	0.3961	0.9968	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:03	SKFEFEVVF	0.3785	0.9697	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:07	SKFEFEVVF	0.3415	0.9605	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:05	SKFEFEVVF	0.3082	0.9732	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B18:08	SKFEFEVVF	0.3071	0.9733	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:54	SKFEFEVVF	0.1529	0.9772	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:53	SKFEFEVVF	0.1477	0.9788	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:68	SKFEFEVVF	0.1395	0.9026	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C06:02	SKFEFEVVF	0.1007	0.9972	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-C06:17	SKFEFEVVF	0.1007	0.9972	7	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:68	SSKFEFEVVF	0.9987	0.9072	6	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B15:54	SSKFEFEVVF	0.9983	0.979	6	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B48:02	SSKFEFEVVF	0.9833	0.9718	6	16
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B50:04	KFEFEVVFVA	0.5969	0.827	8	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B50:05	KFEFEVVFVA	0.5969	0.827	8	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B50:05	SKFEFEVVFVA	0.7841	0.8277	7	18
TRIO-ANKH	chr5	14287171	chr5	14751347	564	HLA-B50:04	SKFEFEVVFVA	0.7841	0.8277	7	18

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Potential FusionNeoAntigen Information of TRIO-ANKH 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 TRIO-ANKH

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
9016	SSKFEFEVVFVAIL	TRIO	ANKH	chr5	14287171	chr5	14751347	564

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TRIO-ANKH

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	9016	SSKFEFEVVFVAIL	-7.15543	-7.26883
HLA-B14:02	3BVN	9016	SSKFEFEVVFVAIL	-4.77435	-5.80965
HLA-B52:01	3W39	9016	SSKFEFEVVFVAIL	-6.80875	-6.92215
HLA-B52:01	3W39	9016	SSKFEFEVVFVAIL	-4.20386	-5.23916
HLA-A11:01	4UQ2	9016	SSKFEFEVVFVAIL	-7.5194	-8.5547
HLA-A11:01	4UQ2	9016	SSKFEFEVVFVAIL	-6.9601	-7.0735
HLA-A24:02	5HGA	9016	SSKFEFEVVFVAIL	-7.52403	-7.63743
HLA-A24:02	5HGA	9016	SSKFEFEVVFVAIL	-5.82433	-6.85963
HLA-B27:05	6PYJ	9016	SSKFEFEVVFVAIL	-3.28285	-4.31815
HLA-B44:05	3DX8	9016	SSKFEFEVVFVAIL	-5.91172	-6.94702
HLA-B44:05	3DX8	9016	SSKFEFEVVFVAIL	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of TRIO-ANKH

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
TRIO-ANKH	chr5	14287171	chr5	14751347	11	19	FEVVFVAI	TTTGAGGTTGTTTTTGTAGCCATT
TRIO-ANKH	chr5	14287171	chr5	14751347	11	20	FEVVFVAIL	TTTGAGGTTGTTTTTGTAGCCATTTTG
TRIO-ANKH	chr5	14287171	chr5	14751347	12	21	EVVFVAILL	GAGGTTGTTTTTGTAGCCATTTTGCTT
TRIO-ANKH	chr5	14287171	chr5	14751347	5	14	GSSKFEFEV	GGCAGTTCTAAATTTGAATTTGAGGTT
TRIO-ANKH	chr5	14287171	chr5	14751347	6	16	SSKFEFEVVF	AGTTCTAAATTTGAATTTGAGGTTGTTTTT
TRIO-ANKH	chr5	14287171	chr5	14751347	7	16	SKFEFEVVF	TCTAAATTTGAATTTGAGGTTGTTTTT
TRIO-ANKH	chr5	14287171	chr5	14751347	7	18	SKFEFEVVFVA	TCTAAATTTGAATTTGAGGTTGTTTTTGTAGCC
TRIO-ANKH	chr5	14287171	chr5	14751347	8	18	KFEFEVVFVA	AAATTTGAATTTGAGGTTGTTTTTGTAGCC
TRIO-ANKH	chr5	14287171	chr5	14751347	9	17	FEFEVVFV	TTTGAATTTGAGGTTGTTTTTGTA
TRIO-ANKH	chr5	14287171	chr5	14751347	9	18	FEFEVVFVA	TTTGAATTTGAGGTTGTTTTTGTAGCC

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 TRIO-ANKH

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
LUSC	TRIO-ANKH	chr5	14287171	ENST00000344204	chr5	14751347	ENST00000284268	TCGA-34-5241-01A

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Potential target of CAR-T therapy development for TRIO-ANKH

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

ANKH

chr5:14287171

chr5:14751347

ENST00000284268

190_210

493.0

Transmembrane

Helical

Tgene

ANKH

chr5:14287171

chr5:14751347

ENST00000284268

327_347

493.0

Transmembrane

Helical

Tgene

ANKH

chr5:14287171

chr5:14751347

ENST00000284268

351_371

493.0

Transmembrane

Helical

Tgene

ANKH

chr5:14287171

chr5:14751347

ENST00000284268

404_426

493.0

Transmembrane

Helical

Tgene

ANKH

chr5:14287171

chr5:14751347

ENST00000284268

430_452

493.0

Transmembrane

Helical

Tgene

ANKH

chr5:14287172

chr5:14751348

ENST00000284268

190_210

493.0

Transmembrane

Helical

Tgene

ANKH

chr5:14287172

chr5:14751348

ENST00000284268

327_347

493.0

Transmembrane

Helical

Tgene

ANKH

chr5:14287172

chr5:14751348

ENST00000284268

351_371

493.0

Transmembrane

Helical

Tgene

ANKH

chr5:14287172

chr5:14751348

ENST00000284268

404_426

493.0

Transmembrane

Helical

Tgene

ANKH

chr5:14287172

chr5:14751348

ENST00000284268

430_452

493.0

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 TRIO-ANKH

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 TRIO-ANKH

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)