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Fusion Protein:ACTR5-IPO13

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ACTR5-IPO13
	FusionPDB ID: 1876
	FusionGDB2.0 ID: 1876
		Hgene	Tgene
	Gene symbol	ACTR5	IPO13
	Gene ID	79913	9670
	Gene name	actin related protein 5	importin 13
	Synonyms	Arp5\|INO80M	IMP13\|KAP13\|LGL2\|RANBP13
	Cytomap	20q11.23	1p34.1
	Type of gene	protein-coding	protein-coding
	Description	actin-related protein 5ARP5 actin related protein 5 homologINO80 complex subunit MhARP5sarcoma antigen NY-SAR-16	importin-13Ran binding protein 13karyopherin 13late gestation lung 2ran-binding protein 13
	Modification date	20200313	20200327
	UniProtAcc	Q9H9F9 Main function of 5'-partner protein: FUNCTION: Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Involved in DNA double-strand break repair and UV-damage excision repair. {ECO:0000269\|PubMed:19014934, ECO:0000269\|PubMed:20855601}.	O94829 Main function of 5'-partner protein: FUNCTION: Functions in nuclear protein import as nuclear transport receptor. Serves as receptor for nuclear localization signals (NLS) in cargo substrates. Is thought to mediate docking of the importin/substrate complex to the nuclear pore complex (NPC) through binding to nucleoporin and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to the importin, the importin/substrate complex dissociates and importin is re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus (By similarity). Mediates the nuclear import of UBC9, the RBM8A/MAGOH complex, PAX6 and probably other members of the paired homeobox family. Also mediates nuclear export of eIF-1A, and the cytoplasmic release of eIF-1A is triggered by the loading of import substrates onto IPO13. {ECO:0000250, ECO:0000269\|PubMed:11447110, ECO:0000269\|PubMed:15143176}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000243903,	ENST00000492152, ENST00000372339, ENST00000372343,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 5 X 5=150	4 X 4 X 3=48
	# samples	6	4
	** MAII score	log2(6/150*10)=-1.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: ACTR5 [Title/Abstract] AND IPO13 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ACTR5 [Title/Abstract] AND IPO13 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ACTR5(37383817)-IPO13(44423073), # samples:1
Anticipated loss of major functional domain due to fusion event.	ACTR5-IPO13 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. ACTR5-IPO13 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	IPO13	GO:0006606	protein import into nucleus	15964792

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr20:37383817/chr1:44423073)
- 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 ACTR5 (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 IPO13 (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)

ENST00000243903

ACTR5

chr20

37383817

ENST00000372343

IPO13

chr1

44423073

2870

1030

2529

842

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
ENST00000243903	ENST00000372343	ACTR5	chr20	37383817	+	IPO13	chr1	44423073	+	0.005220547	0.99477947

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 ACTR5-IPO13

+/-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
ACTR5	chr20	37383817	IPO13	chr1	44423073	1030	342	QLDQERLDRLLYVQHTEALLYGFQSI

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Potential FusionNeoAntigen Information of ACTR5-IPO13 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.

ACTR5-IPO13_37383817_44423073.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)
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:01	VQHTEALLY	0.9999	0.6697	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:25	VQHTEALLY	0.9908	0.8683	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-A02:13	LLYVQHTEA	0.9853	0.5806	9	18
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:02	VQHTEALLY	0.9697	0.8969	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B08:09	LLYVQHTEA	0.9031	0.7841	9	18
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:03	VQHTEALLY	0.6466	0.6282	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B18:01	VQHTEALLY	0.6122	0.6926	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:10	LYVQHTEAL	0.4773	0.5203	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:18	VQHTEALLY	0.4718	0.5492	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:01	YVQHTEALLY	0.9991	0.5891	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:25	YVQHTEALLY	0.9958	0.7641	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:02	YVQHTEALLY	0.9928	0.7888	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C03:19	YVQHTEAL	0.9997	0.9757	11	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C03:07	YVQHTEALL	0.9979	0.9305	11	20
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C04:06	YVQHTEALL	0.9917	0.9206	11	20
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B73:01	DRLLYVQHT	0.9855	0.5976	7	16
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:04	VQHTEALLY	0.9763	0.6904	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:21	VQHTEALLY	0.9699	0.8355	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:05	VQHTEALLY	0.909	0.7135	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:31	VQHTEALLY	0.8215	0.7293	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C12:16	LYVQHTEAL	0.5813	0.9535	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B14:03	LYVQHTEAL	0.5682	0.7445	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C07:05	LYVQHTEAL	0.5446	0.951	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C07:67	LYVQHTEAL	0.5331	0.9084	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C07:80	LYVQHTEAL	0.5331	0.9084	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C07:13	LYVQHTEAL	0.5328	0.9022	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C07:27	LYVQHTEAL	0.5321	0.9264	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B39:12	LYVQHTEAL	0.5046	0.8444	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C07:10	LYVQHTEAL	0.501	0.9456	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C03:14	VQHTEALLY	0.4968	0.9478	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C07:29	LYVQHTEAL	0.4961	0.8376	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C07:19	LYVQHTEAL	0.4807	0.6732	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C07:46	LYVQHTEAL	0.471	0.7923	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C15:04	VQHTEALLY	0.4415	0.8759	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C04:14	LYVQHTEAL	0.3045	0.8606	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:21	YVQHTEALLY	0.9935	0.7311	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:05	YVQHTEALLY	0.978	0.5788	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:31	YVQHTEALLY	0.9764	0.5841	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:04	YVQHTEALLY	0.9638	0.607	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B73:01	DRLLYVQHTEA	0.9994	0.7081	7	18
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C03:03	YVQHTEAL	0.9998	0.9713	11	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C03:04	YVQHTEAL	0.9998	0.9713	11	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C03:06	YVQHTEAL	0.9946	0.9742	11	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B07:13	YVQHTEAL	0.8941	0.7582	11	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:125	VQHTEALLY	0.9999	0.6697	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:135	VQHTEALLY	0.9999	0.6648	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:27	VQHTEALLY	0.9999	0.6974	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:34	VQHTEALLY	0.9999	0.6697	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:33	VQHTEALLY	0.9999	0.6697	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:50	VQHTEALLY	0.9998	0.639	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:35	VQHTEALLY	0.9995	0.638	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:24	VQHTEALLY	0.9994	0.6326	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:12	VQHTEALLY	0.9987	0.6231	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C03:04	YVQHTEALL	0.9981	0.9662	11	20
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C03:03	YVQHTEALL	0.9981	0.9662	11	20
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-A02:03	LLYVQHTEA	0.9939	0.6331	9	18
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:39	VQHTEALLY	0.991	0.7431	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:53	VQHTEALLY	0.984	0.6157	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C03:06	YVQHTEALL	0.9718	0.9695	11	20
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:20	VQHTEALLY	0.9069	0.8223	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:54	VQHTEALLY	0.8886	0.5677	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B35:28	VQHTEALLY	0.8693	0.8437	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B18:11	VQHTEALLY	0.8433	0.6571	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B35:20	VQHTEALLY	0.8171	0.8555	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C03:67	LYVQHTEAL	0.7968	0.9625	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B18:04	VQHTEALLY	0.7514	0.7066	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:13	VQHTEALLY	0.7343	0.6293	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B18:07	VQHTEALLY	0.6329	0.628	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B18:08	VQHTEALLY	0.6296	0.5817	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B18:05	VQHTEALLY	0.6122	0.6926	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C17:01	YVQHTEALL	0.6052	0.9166	11	20
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B18:06	VQHTEALLY	0.5997	0.6932	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C07:02	LYVQHTEAL	0.5331	0.9084	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C07:17	LYVQHTEAL	0.5039	0.9368	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C12:02	VQHTEALLY	0.4989	0.8991	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C07:04	LYVQHTEAL	0.4976	0.9055	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C15:09	VQHTEALLY	0.4415	0.8759	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B48:02	VQHTEALLY	0.3712	0.8009	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C04:04	LYVQHTEAL	0.2791	0.8631	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C06:06	LYVQHTEAL	0.2307	0.9873	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C14:02	LYVQHTEAL	0.218	0.9649	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C14:03	LYVQHTEAL	0.218	0.9649	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:09	LYVQHTEAL	0.1984	0.758	10	19
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C02:02	VQHTEALLY	0.1374	0.924	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-C02:10	VQHTEALLY	0.1374	0.924	12	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:27	YVQHTEALLY	0.9991	0.6267	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:33	YVQHTEALLY	0.9991	0.5891	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:34	YVQHTEALLY	0.9991	0.5891	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:125	YVQHTEALLY	0.9991	0.5891	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:135	YVQHTEALLY	0.999	0.5835	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:12	YVQHTEALLY	0.999	0.592	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:50	YVQHTEALLY	0.9985	0.6091	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:35	YVQHTEALLY	0.9978	0.5354	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:53	YVQHTEALLY	0.9965	0.5368	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:24	YVQHTEALLY	0.9954	0.5694	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:39	YVQHTEALLY	0.9951	0.6014	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:20	YVQHTEALLY	0.9793	0.7147	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:54	YVQHTEALLY	0.9773	0.5068	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B35:20	YVQHTEALLY	0.9724	0.7675	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B35:28	YVQHTEALLY	0.9697	0.7459	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B48:02	YVQHTEALLY	0.7189	0.7012	11	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:24	VQHTEALLYGF	1	0.7535	12	23
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:135	LYVQHTEALLY	0.9912	0.6976	10	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B15:20	LYVQHTEALLY	0.9632	0.8142	10	21
ACTR5-IPO13	chr20	37383817	chr1	44423073	1030	HLA-B35:28	LYVQHTEALLY	0.9508	0.845	10	21

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Potential FusionNeoAntigen Information of ACTR5-IPO13 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 ACTR5-IPO13

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
4863	LDRLLYVQHTEALL	ACTR5	IPO13	chr20	37383817	chr1	44423073	1030

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ACTR5-IPO13

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	4863	LDRLLYVQHTEALL	-7.9962	-8.1096
HLA-B14:02	3BVN	4863	LDRLLYVQHTEALL	-5.70842	-6.74372
HLA-B52:01	3W39	4863	LDRLLYVQHTEALL	-6.83737	-6.95077
HLA-B52:01	3W39	4863	LDRLLYVQHTEALL	-4.4836	-5.5189
HLA-A11:01	4UQ2	4863	LDRLLYVQHTEALL	-10.0067	-10.1201
HLA-A11:01	4UQ2	4863	LDRLLYVQHTEALL	-9.03915	-10.0745
HLA-A24:02	5HGA	4863	LDRLLYVQHTEALL	-6.56204	-6.67544
HLA-A24:02	5HGA	4863	LDRLLYVQHTEALL	-5.42271	-6.45801
HLA-B44:05	3DX8	4863	LDRLLYVQHTEALL	-7.85648	-8.89178
HLA-B44:05	3DX8	4863	LDRLLYVQHTEALL	-5.3978	-5.5112
HLA-A02:01	6TDR	4863	LDRLLYVQHTEALL	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of ACTR5-IPO13

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
ACTR5-IPO13	chr20	37383817	chr1	44423073	10	19	LYVQHTEAL	TATGTGCAGCACACAGAGGCCCTCCTC
ACTR5-IPO13	chr20	37383817	chr1	44423073	10	21	LYVQHTEALLY	TATGTGCAGCACACAGAGGCCCTCCTCTACGGC
ACTR5-IPO13	chr20	37383817	chr1	44423073	11	19	YVQHTEAL	GTGCAGCACACAGAGGCCCTCCTC
ACTR5-IPO13	chr20	37383817	chr1	44423073	11	20	YVQHTEALL	GTGCAGCACACAGAGGCCCTCCTCTAC
ACTR5-IPO13	chr20	37383817	chr1	44423073	11	21	YVQHTEALLY	GTGCAGCACACAGAGGCCCTCCTCTACGGC
ACTR5-IPO13	chr20	37383817	chr1	44423073	12	21	VQHTEALLY	CAGCACACAGAGGCCCTCCTCTACGGC
ACTR5-IPO13	chr20	37383817	chr1	44423073	12	23	VQHTEALLYGF	CAGCACACAGAGGCCCTCCTCTACGGCTTCCAA
ACTR5-IPO13	chr20	37383817	chr1	44423073	7	16	DRLLYVQHT	CGACTGCTATATGTGCAGCACACAGAG
ACTR5-IPO13	chr20	37383817	chr1	44423073	7	18	DRLLYVQHTEA	CGACTGCTATATGTGCAGCACACAGAGGCCCTC
ACTR5-IPO13	chr20	37383817	chr1	44423073	9	18	LLYVQHTEA	CTATATGTGCAGCACACAGAGGCCCTC

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 ACTR5-IPO13

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
STAD	ACTR5-IPO13	chr20	37383817	ENST00000243903	chr1	44423073	ENST00000372343	TCGA-D7-A4YV

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Potential target of CAR-T therapy development for ACTR5-IPO13

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 ACTR5-IPO13

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 ACTR5-IPO13

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)