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Fusion Protein:RAB3IP-KCNC2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RAB3IP-KCNC2
	FusionPDB ID: 71394
	FusionGDB2.0 ID: 71394
		Hgene	Tgene
	Gene symbol	RAB3IP	KCNC2
	Gene ID	117177	3747
	Gene name	RAB3A interacting protein	potassium voltage-gated channel subfamily C member 2
	Synonyms	RABIN3\|RABIN8	KV3.2
	Cytomap	12q15	12q21.1
	Type of gene	protein-coding	protein-coding
	Description	rab-3A-interacting proteinSSX2 interacting proteinrab3A-interacting proteinrabin-3	potassium voltage-gated channel subfamily C member 2potassium channel, voltage gated Shaw related subfamily C, member 2potassium voltage-gated channel, Shaw-related subfamily, member 2shaw-like potassium channelvoltage-gated potassium channel Kv3.2
	Modification date	20200327	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000247833, ENST00000362025, ENST00000378815, ENST00000483530, ENST00000550536, ENST00000325555, ENST00000550847, ENST00000551641, ENST00000553099,	ENST00000548243, ENST00000298972, ENST00000341669, ENST00000350228, ENST00000393288, ENST00000540018, ENST00000548513, ENST00000549446, ENST00000550433,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	21 X 9 X 12=2268	15 X 5 X 6=450
	# samples	27	16
	** MAII score	log2(27/2268*10)=-3.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(16/450*10)=-1.49185309632967 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: RAB3IP [Title/Abstract] AND KCNC2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: RAB3IP [Title/Abstract] AND KCNC2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	RAB3IP(70150443)-KCNC2(75445097), # samples:1
Anticipated loss of major functional domain due to fusion event.	RAB3IP-KCNC2 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. RAB3IP-KCNC2 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. RAB3IP-KCNC2 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. RAB3IP-KCNC2 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	RAB3IP	GO:0006612	protein targeting to membrane	23382462

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:70150443/chr12:75445097)
- 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 RAB3IP (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 KCNC2 (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)
ENST00000247833	RAB3IP	chr12	70150443	-	ENST00000550433	KCNC2	chr12	75445097	-	3109	886	316	2088	590
ENST00000247833	RAB3IP	chr12	70150443	-	ENST00000548513	KCNC2	chr12	75445097	-	3204	886	316	2040	574
ENST00000247833	RAB3IP	chr12	70150443	-	ENST00000549446	KCNC2	chr12	75445097	-	5143	886	316	2115	599
ENST00000247833	RAB3IP	chr12	70150443	-	ENST00000298972	KCNC2	chr12	75445097	-	3165	886	316	2040	574
ENST00000247833	RAB3IP	chr12	70150443	-	ENST00000341669	KCNC2	chr12	75445097	-	3070	886	316	2088	590
ENST00000247833	RAB3IP	chr12	70150443	-	ENST00000350228	KCNC2	chr12	75445097	-	2999	886	316	1875	519
ENST00000247833	RAB3IP	chr12	70150443	-	ENST00000540018	KCNC2	chr12	75445097	-	2095	886	316	1950	544
ENST00000247833	RAB3IP	chr12	70150443	-	ENST00000393288	KCNC2	chr12	75445097	-	2436	886	316	2055	579
ENST00000378815	RAB3IP	chr12	70150443	-	ENST00000550433	KCNC2	chr12	75445097	-	2928	705	135	1907	590
ENST00000378815	RAB3IP	chr12	70150443	-	ENST00000548513	KCNC2	chr12	75445097	-	3023	705	135	1859	574
ENST00000378815	RAB3IP	chr12	70150443	-	ENST00000549446	KCNC2	chr12	75445097	-	4962	705	135	1934	599
ENST00000378815	RAB3IP	chr12	70150443	-	ENST00000298972	KCNC2	chr12	75445097	-	2984	705	135	1859	574
ENST00000378815	RAB3IP	chr12	70150443	-	ENST00000341669	KCNC2	chr12	75445097	-	2889	705	135	1907	590
ENST00000378815	RAB3IP	chr12	70150443	-	ENST00000350228	KCNC2	chr12	75445097	-	2818	705	135	1694	519
ENST00000378815	RAB3IP	chr12	70150443	-	ENST00000540018	KCNC2	chr12	75445097	-	1914	705	135	1769	544
ENST00000378815	RAB3IP	chr12	70150443	-	ENST00000393288	KCNC2	chr12	75445097	-	2255	705	135	1874	579
ENST00000483530	RAB3IP	chr12	70150443	-	ENST00000550433	KCNC2	chr12	75445097	-	2928	705	135	1907	590
ENST00000483530	RAB3IP	chr12	70150443	-	ENST00000548513	KCNC2	chr12	75445097	-	3023	705	135	1859	574
ENST00000483530	RAB3IP	chr12	70150443	-	ENST00000549446	KCNC2	chr12	75445097	-	4962	705	135	1934	599
ENST00000483530	RAB3IP	chr12	70150443	-	ENST00000298972	KCNC2	chr12	75445097	-	2984	705	135	1859	574
ENST00000483530	RAB3IP	chr12	70150443	-	ENST00000341669	KCNC2	chr12	75445097	-	2889	705	135	1907	590
ENST00000483530	RAB3IP	chr12	70150443	-	ENST00000350228	KCNC2	chr12	75445097	-	2818	705	135	1694	519
ENST00000483530	RAB3IP	chr12	70150443	-	ENST00000540018	KCNC2	chr12	75445097	-	1914	705	135	1769	544
ENST00000483530	RAB3IP	chr12	70150443	-	ENST00000393288	KCNC2	chr12	75445097	-	2255	705	135	1874	579
ENST00000550536	RAB3IP	chr12	70150443	-	ENST00000550433	KCNC2	chr12	75445097	-	3238	1015	445	2217	590
ENST00000550536	RAB3IP	chr12	70150443	-	ENST00000548513	KCNC2	chr12	75445097	-	3333	1015	445	2169	574
ENST00000550536	RAB3IP	chr12	70150443	-	ENST00000549446	KCNC2	chr12	75445097	-	5272	1015	445	2244	599
ENST00000550536	RAB3IP	chr12	70150443	-	ENST00000298972	KCNC2	chr12	75445097	-	3294	1015	445	2169	574
ENST00000550536	RAB3IP	chr12	70150443	-	ENST00000341669	KCNC2	chr12	75445097	-	3199	1015	445	2217	590
ENST00000550536	RAB3IP	chr12	70150443	-	ENST00000350228	KCNC2	chr12	75445097	-	3128	1015	445	2004	519
ENST00000550536	RAB3IP	chr12	70150443	-	ENST00000540018	KCNC2	chr12	75445097	-	2224	1015	445	2079	544
ENST00000550536	RAB3IP	chr12	70150443	-	ENST00000393288	KCNC2	chr12	75445097	-	2565	1015	445	2184	579
ENST00000362025	RAB3IP	chr12	70150443	-	ENST00000550433	KCNC2	chr12	75445097	-	3228	1005	435	2207	590
ENST00000362025	RAB3IP	chr12	70150443	-	ENST00000548513	KCNC2	chr12	75445097	-	3323	1005	435	2159	574
ENST00000362025	RAB3IP	chr12	70150443	-	ENST00000549446	KCNC2	chr12	75445097	-	5262	1005	435	2234	599
ENST00000362025	RAB3IP	chr12	70150443	-	ENST00000298972	KCNC2	chr12	75445097	-	3284	1005	435	2159	574
ENST00000362025	RAB3IP	chr12	70150443	-	ENST00000341669	KCNC2	chr12	75445097	-	3189	1005	435	2207	590
ENST00000362025	RAB3IP	chr12	70150443	-	ENST00000350228	KCNC2	chr12	75445097	-	3118	1005	435	1994	519
ENST00000362025	RAB3IP	chr12	70150443	-	ENST00000540018	KCNC2	chr12	75445097	-	2214	1005	435	2069	544
ENST00000362025	RAB3IP	chr12	70150443	-	ENST00000393288	KCNC2	chr12	75445097	-	2555	1005	435	2174	579

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
ENST00000247833	ENST00000550433	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000968421	0.99903154
ENST00000247833	ENST00000548513	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000958847	0.99904114
ENST00000247833	ENST00000549446	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000910563	0.9990895
ENST00000247833	ENST00000298972	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000969832	0.99903023
ENST00000247833	ENST00000341669	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000978437	0.99902153
ENST00000247833	ENST00000350228	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000614927	0.999385
ENST00000247833	ENST00000540018	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.002213894	0.99778605
ENST00000247833	ENST00000393288	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.001458815	0.99854124
ENST00000378815	ENST00000550433	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000819852	0.99918014
ENST00000378815	ENST00000548513	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000808786	0.9991912
ENST00000378815	ENST00000549446	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000830428	0.9991696
ENST00000378815	ENST00000298972	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000823545	0.99917644
ENST00000378815	ENST00000341669	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.00083217	0.9991678
ENST00000378815	ENST00000350228	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.00050917	0.99949086
ENST00000378815	ENST00000540018	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.001734203	0.9982658
ENST00000378815	ENST00000393288	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.001156629	0.9988433
ENST00000483530	ENST00000550433	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000819852	0.99918014
ENST00000483530	ENST00000548513	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000808786	0.9991912
ENST00000483530	ENST00000549446	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000830428	0.9991696
ENST00000483530	ENST00000298972	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000823545	0.99917644
ENST00000483530	ENST00000341669	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.00083217	0.9991678
ENST00000483530	ENST00000350228	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.00050917	0.99949086
ENST00000483530	ENST00000540018	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.001734203	0.9982658
ENST00000483530	ENST00000393288	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.001156629	0.9988433
ENST00000550536	ENST00000550433	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.00024981	0.9997502
ENST00000550536	ENST00000548513	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000246765	0.9997532
ENST00000550536	ENST00000549446	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000199872	0.99980015
ENST00000550536	ENST00000298972	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.00024945	0.99975055
ENST00000550536	ENST00000341669	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000254953	0.9997451
ENST00000550536	ENST00000350228	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000251735	0.9997483
ENST00000550536	ENST00000540018	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000568605	0.9994313
ENST00000550536	ENST00000393288	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000324641	0.9996754
ENST00000362025	ENST00000550433	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000247661	0.99975234
ENST00000362025	ENST00000548513	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000244691	0.9997553
ENST00000362025	ENST00000549446	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.00019908	0.999801
ENST00000362025	ENST00000298972	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000247606	0.99975234
ENST00000362025	ENST00000341669	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000252736	0.9997472
ENST00000362025	ENST00000350228	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000249289	0.9997507
ENST00000362025	ENST00000540018	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.000563697	0.9994363
ENST00000362025	ENST00000393288	RAB3IP	chr12	70150443	-	KCNC2	chr12	75445097	-	0.00032313	0.99967694

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 RAB3IP-KCNC2

+/-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
RAB3IP	chr12	70150443	KCNC2	chr12	75445097	1005	190	YERLKEELAKAQRFIAFASLFFILVS
RAB3IP	chr12	70150443	KCNC2	chr12	75445097	1015	190	YERLKEELAKAQRFIAFASLFFILVS
RAB3IP	chr12	70150443	KCNC2	chr12	75445097	705	190	YERLKEELAKAQRFIAFASLFFILVS
RAB3IP	chr12	70150443	KCNC2	chr12	75445097	886	190	YERLKEELAKAQRFIAFASLFFILVS

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Potential FusionNeoAntigen Information of RAB3IP-KCNC2 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.

RAB3IP-KCNC2_70150443_75445097.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)
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:02	QRFIAFASL	0.9999	0.5916	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:07	QRFIAFASL	0.9999	0.5358	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:05	QRFIAFASL	0.9999	0.8401	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:04	QRFIAFASL	0.9999	0.732	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B44:03	EELAKAQRF	0.9992	0.9107	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B39:06	QRFIAFASL	0.9991	0.7665	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B14:01	QRFIAFASL	0.9988	0.6174	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B39:01	QRFIAFASL	0.9988	0.9688	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B14:02	QRFIAFASL	0.9988	0.6174	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B38:02	QRFIAFASL	0.9976	0.9763	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B18:01	EELAKAQRF	0.997	0.7379	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B15:10	QRFIAFASL	0.9213	0.6168	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B14:01	AKAQRFIAF	0.9027	0.7036	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B14:02	AKAQRFIAF	0.9027	0.7036	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B15:37	QRFIAFASL	0.8865	0.5798	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-A24:14	RFIAFASLF	0.7779	0.6362	12	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B15:18	AKAQRFIAF	0.7033	0.716	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B15:03	AKAQRFIAF	0.6663	0.7613	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B07:10	QRFIAFASL	0.3559	0.5102	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B47:01	AKAQRFIAF	0.2182	0.5608	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:02	QRFIAFASLF	0.9999	0.6202	11	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:05	QRFIAFASLF	0.9999	0.8126	11	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:04	QRFIAFASLF	0.9999	0.7461	11	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:07	QRFIAFASLF	0.9997	0.5857	11	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B44:03	KEELAKAQRF	0.998	0.8784	4	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:07	AQRFIAFASL	0.9936	0.5321	10	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:04	AQRFIAFASL	0.9935	0.6641	10	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:04	QRFIAFASLFF	0.9999	0.7334	11	22
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:02	QRFIAFASLFF	0.9999	0.5894	11	22
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:14	QRFIAFASL	0.9999	0.769	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:05	QRFIAFASL	0.9994	0.9627	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:95	QRFIAFASL	0.9992	0.7028	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:27	QRFIAFASL	0.9991	0.9378	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:29	QRFIAFASL	0.999	0.939	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B39:09	QRFIAFASL	0.999	0.7292	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:13	QRFIAFASL	0.9989	0.8872	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B39:12	QRFIAFASL	0.9985	0.9709	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:46	QRFIAFASL	0.9975	0.8311	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B39:05	QRFIAFASL	0.9971	0.9618	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:19	QRFIAFASL	0.9955	0.6461	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:03	QRFIAFASL	0.9925	0.8549	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:10	QRFIAFASL	0.9925	0.9489	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:05	AKAQRFIAF	0.9922	0.9601	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:80	QRFIAFASL	0.9919	0.9221	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:67	QRFIAFASL	0.9919	0.9221	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:27	AKAQRFIAF	0.9832	0.9561	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B73:01	QRFIAFASL	0.9776	0.5617	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:19	AKAQRFIAF	0.924	0.759	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B39:12	AKAQRFIAF	0.8942	0.7752	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:80	AKAQRFIAF	0.8922	0.9557	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:67	AKAQRFIAF	0.8922	0.9557	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:46	AKAQRFIAF	0.8858	0.8818	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:10	AKAQRFIAF	0.8656	0.9624	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B14:03	QRFIAFASL	0.6578	0.8007	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C12:16	QRFIAFASL	0.4391	0.959	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C12:16	AKAQRFIAF	0.403	0.9507	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B14:03	AKAQRFIAF	0.334	0.7189	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:14	QRFIAFASLF	0.9999	0.7473	11	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:03	QRFIAFASLF	0.9981	0.8261	11	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:03	QRFIAFASLFF	0.9986	0.7995	11	22
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C16:01	KAQRFIAF	0.9993	0.9328	9	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C14:02	RFIAFASL	0.9453	0.9777	12	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C14:03	RFIAFASL	0.9453	0.9777	12	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:10	QRFIAFASL	0.9999	0.8445	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:06	QRFIAFASL	0.9999	0.7468	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:08	QRFIAFASL	0.9999	0.7641	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:09	QRFIAFASL	0.9998	0.7966	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:01	QRFIAFASL	0.9993	0.65	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B44:07	EELAKAQRF	0.9992	0.9107	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B44:26	EELAKAQRF	0.9992	0.9107	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B44:13	EELAKAQRF	0.9992	0.9107	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B39:31	QRFIAFASL	0.9987	0.969	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:17	QRFIAFASL	0.9986	0.9561	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B18:04	EELAKAQRF	0.9977	0.7542	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B18:07	EELAKAQRF	0.9977	0.7052	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B18:05	EELAKAQRF	0.997	0.7379	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B18:08	EELAKAQRF	0.9969	0.7557	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B18:06	EELAKAQRF	0.9962	0.7449	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:01	AKAQRFIAF	0.9956	0.6578	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B18:03	EELAKAQRF	0.994	0.7211	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C06:08	QRFIAFASL	0.992	0.9823	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:02	QRFIAFASL	0.9919	0.9221	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B18:11	EELAKAQRF	0.991	0.6469	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:17	AKAQRFIAF	0.9021	0.9623	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:02	AKAQRFIAF	0.8922	0.9557	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:22	QRFIAFASL	0.8769	0.8105	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C07:22	AKAQRFIAF	0.858	0.6419	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B15:09	QRFIAFASL	0.8264	0.7954	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C06:08	AKAQRFIAF	0.5644	0.9913	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B15:68	AKAQRFIAF	0.5583	0.6101	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B48:02	AKAQRFIAF	0.5538	0.8506	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B41:03	EELAKAQRF	0.5347	0.5592	5	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C06:17	QRFIAFASL	0.3669	0.9921	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C06:02	QRFIAFASL	0.3669	0.9921	11	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B15:54	AKAQRFIAF	0.3568	0.8326	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C06:02	AKAQRFIAF	0.2734	0.9924	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C06:17	AKAQRFIAF	0.2734	0.9924	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B15:53	AKAQRFIAF	0.1779	0.8495	8	17
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C14:02	RFIAFASLF	0.0684	0.98	12	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-C14:03	RFIAFASLF	0.0684	0.98	12	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:10	QRFIAFASLF	0.9999	0.8575	11	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:08	QRFIAFASLF	0.9999	0.7421	11	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:06	QRFIAFASLF	0.9997	0.7784	11	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:09	QRFIAFASLF	0.9996	0.801	11	21
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B44:26	KEELAKAQRF	0.998	0.8784	4	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B44:07	KEELAKAQRF	0.998	0.8784	4	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B44:13	KEELAKAQRF	0.998	0.8784	4	14
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:08	AQRFIAFASL	0.9948	0.6813	10	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:06	AQRFIAFASL	0.9923	0.6819	10	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:09	AQRFIAFASL	0.9915	0.7428	10	20
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:08	QRFIAFASLFF	0.9999	0.7156	11	22
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	HLA-B27:06	KAQRFIAFASL	0.998	0.7169	9	20

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Potential FusionNeoAntigen Information of RAB3IP-KCNC2 in HLA II

RAB3IP-KCNC2_70150443_75445097.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)
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-0804	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-0820	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-0820	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-0828	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-0831	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1103	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1104	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1104	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1106	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1106	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1113	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1117	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1117	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1118	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1125	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1125	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1135	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1135	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1138	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1138	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1141	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1142	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1143	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1143	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1144	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1144	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1146	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1146	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1147	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1147	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1150	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1152	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1152	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1154	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1154	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1156	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1157	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1158	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1158	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1159	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1160	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1160	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1163	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1167	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1176	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1177	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1177	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1178	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1178	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1183	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1184	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1184	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1185	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1188	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1189	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1189	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1192	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1192	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1306	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1309	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1311	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1311	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1318	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1318	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1324	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1342	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1342	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1376	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1376	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1405	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1405	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1408	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1408	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1411	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1411	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1412	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1415	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1418	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1418	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1423	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1423	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1434	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1437	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1443	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1443	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1445	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1445	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1456	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1456	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1459	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1459	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1464	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1464	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1472	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1472	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1481	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1484	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1491	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1491	LKEELAKAQRFIAFA	3	18
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1495	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1496	KEELAKAQRFIAFAS	4	19
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	886	DRB1-1496	LKEELAKAQRFIAFA	3	18

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Fusion breakpoint peptide structures of RAB3IP-KCNC2

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
1873	ELAKAQRFIAFASL	RAB3IP	KCNC2	chr12	70150443	chr12	75445097	886

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RAB3IP-KCNC2

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	1873	ELAKAQRFIAFASL	-7.15543	-7.26883
HLA-B14:02	3BVN	1873	ELAKAQRFIAFASL	-4.77435	-5.80965
HLA-B52:01	3W39	1873	ELAKAQRFIAFASL	-6.80875	-6.92215
HLA-B52:01	3W39	1873	ELAKAQRFIAFASL	-4.20386	-5.23916
HLA-A11:01	4UQ2	1873	ELAKAQRFIAFASL	-7.5194	-8.5547
HLA-A11:01	4UQ2	1873	ELAKAQRFIAFASL	-6.9601	-7.0735
HLA-A24:02	5HGA	1873	ELAKAQRFIAFASL	-7.52403	-7.63743
HLA-A24:02	5HGA	1873	ELAKAQRFIAFASL	-5.82433	-6.85963
HLA-B27:05	6PYJ	1873	ELAKAQRFIAFASL	-3.28285	-4.31815
HLA-B44:05	3DX8	1873	ELAKAQRFIAFASL	-5.91172	-6.94702
HLA-B44:05	3DX8	1873	ELAKAQRFIAFASL	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of RAB3IP-KCNC2

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
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	10	20	AQRFIAFASL	GCTCAGAGGTTTATTGCTTTTGCTTCTTTA
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	11	20	QRFIAFASL	CAGAGGTTTATTGCTTTTGCTTCTTTA
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	11	21	QRFIAFASLF	CAGAGGTTTATTGCTTTTGCTTCTTTATTC
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	11	22	QRFIAFASLFF	CAGAGGTTTATTGCTTTTGCTTCTTTATTCTTC
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	12	20	RFIAFASL	AGGTTTATTGCTTTTGCTTCTTTA
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	12	21	RFIAFASLF	AGGTTTATTGCTTTTGCTTCTTTATTC
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	4	14	KEELAKAQRF	AAAGAAGAACTCGCAAAAGCTCAGAGGTTT
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	5	14	EELAKAQRF	GAAGAACTCGCAAAAGCTCAGAGGTTT
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	8	17	AKAQRFIAF	GCAAAAGCTCAGAGGTTTATTGCTTTT
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	9	17	KAQRFIAF	AAAGCTCAGAGGTTTATTGCTTTT
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	9	20	KAQRFIAFASL	AAAGCTCAGAGGTTTATTGCTTTTGCTTCTTTA

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
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	3	18	LKEELAKAQRFIAFA	TTAAAAGAAGAACTCGCAAAAGCTCAGAGGTTTATTGCTTTTGCT
RAB3IP-KCNC2	chr12	70150443	chr12	75445097	4	19	KEELAKAQRFIAFAS	AAAGAAGAACTCGCAAAAGCTCAGAGGTTTATTGCTTTTGCTTCT

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Information of the samples that have these potential fusion neoantigens of RAB3IP-KCNC2

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
SARC	RAB3IP-KCNC2	chr12	70150443	ENST00000247833	chr12	75445097	ENST00000298972	TCGA-DX-A1L3-01A

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Potential target of CAR-T therapy development for RAB3IP-KCNC2

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

KCNC2

chr12:70150443

chr12:75445097

ENST00000298972

230_250

599.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000298972

284_303

599.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000298972

314_334

599.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000298972

346_368

599.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000298972

382_402

599.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000298972

453_473

599.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000341669

230_250

630.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000341669

284_303

630.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000341669

314_334

630.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000341669

346_368

630.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000341669

382_402

630.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000341669

453_473

630.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000350228

230_250

543.6666666666666

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000350228

284_303

543.6666666666666

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000350228

314_334

543.6666666666666

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000350228

346_368

543.6666666666666

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000350228

382_402

543.6666666666666

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000350228

453_473

543.6666666666666

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000393288

230_250

619.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000393288

284_303

619.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000393288

314_334

619.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000393288

346_368

619.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000393288

382_402

619.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000393288

453_473

619.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000540018

230_250

584.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000540018

284_303

584.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000540018

314_334

584.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000540018

346_368

584.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000540018

382_402

584.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000540018

453_473

584.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000548513

230_250

477.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000548513

284_303

477.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000548513

314_334

477.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000548513

346_368

477.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000548513

382_402

477.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000548513

453_473

477.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000549446

230_250

639.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000549446

284_303

639.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000549446

314_334

639.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000549446

346_368

639.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000549446

382_402

639.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000549446

453_473

639.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000550433

230_250

630.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000550433

284_303

630.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000550433

314_334

630.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000550433

346_368

630.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000550433

382_402

630.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:70150443

chr12:75445097

ENST00000550433

453_473

630.0

Transmembrane

Helical%3B Name%3DSegment S6

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 RAB3IP-KCNC2

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 RAB3IP-KCNC2

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)