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Fusion Protein:SIM2-GRIK1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SIM2-GRIK1
	FusionPDB ID: 81900
	FusionGDB2.0 ID: 81900
		Hgene	Tgene
	Gene symbol	SIM2	GRIK1
	Gene ID	6493	2897
	Gene name	SIM bHLH transcription factor 2	glutamate ionotropic receptor kainate type subunit 1
	Synonyms	HMC13F06\|HMC29C01\|SIM\|bHLHe15	EAA3\|EEA3\|GLR5\|GLUR5\|GluK1\|gluR-5
	Cytomap	21q22.13	21q21.3
	Type of gene	protein-coding	protein-coding
	Description	single-minded homolog 2class E basic helix-loop-helix protein 15single-minded family bHLH transcription factor 2transcription factor SIM2	glutamate receptor ionotropic, kainate 1excitatory amino acid receptor 3glutamate receptor 5
	Modification date	20200320	20200320
	UniProtAcc	.	P39086 Main function of 5'-partner protein: FUNCTION: Ionotropic glutamate receptor. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L-glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. May be involved in the transmission of light information from the retina to the hypothalamus.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000460783, ENST00000290399, ENST00000430056,	ENST00000309434, ENST00000327783, ENST00000389124, ENST00000389125, ENST00000399907, ENST00000399909, ENST00000399913, ENST00000399914, ENST00000535441, ENST00000472429,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 2 X 3=18	12 X 9 X 6=648
	# samples	4	12
	** MAII score	log2(4/18*10)=1.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(12/648*10)=-2.43295940727611 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SIM2 [Title/Abstract] AND GRIK1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SIM2 [Title/Abstract] AND GRIK1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SIM2(38072221)-GRIK1(31066382), # samples:2
Anticipated loss of major functional domain due to fusion event.	SIM2-GRIK1 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. SIM2-GRIK1 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. SIM2-GRIK1 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. SIM2-GRIK1 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/chr21:38072221/chr21:31066382)
- 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 SIM2 (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 GRIK1 (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)
ENST00000290399	SIM2	chr21	38072221	+	ENST00000327783	GRIK1	chr21	31066382	-	3817	788	613	3519	968
ENST00000290399	SIM2	chr21	38072221	+	ENST00000389125	GRIK1	chr21	31066382	-	3685	788	613	3387	924
ENST00000290399	SIM2	chr21	38072221	+	ENST00000399913	GRIK1	chr21	31066382	-	3730	788	613	3432	939
ENST00000290399	SIM2	chr21	38072221	+	ENST00000399914	GRIK1	chr21	31066382	-	3772	788	613	3474	953
ENST00000290399	SIM2	chr21	38072221	+	ENST00000535441	GRIK1	chr21	31066382	-	3439	788	613	3438	942
ENST00000290399	SIM2	chr21	38072221	+	ENST00000389124	GRIK1	chr21	31066382	-	3350	788	613	3285	890
ENST00000290399	SIM2	chr21	38072221	+	ENST00000399907	GRIK1	chr21	31066382	-	3730	788	613	3426	937
ENST00000290399	SIM2	chr21	38072221	+	ENST00000399909	GRIK1	chr21	31066382	-	3685	788	613	3381	922
ENST00000290399	SIM2	chr21	38072221	+	ENST00000309434	GRIK1	chr21	31066382	-	3433	788	613	3432	940
ENST00000430056	SIM2	chr21	38072221	+	ENST00000327783	GRIK1	chr21	31066382	-	3260	231	56	2962	968
ENST00000430056	SIM2	chr21	38072221	+	ENST00000389125	GRIK1	chr21	31066382	-	3128	231	56	2830	924
ENST00000430056	SIM2	chr21	38072221	+	ENST00000399913	GRIK1	chr21	31066382	-	3173	231	56	2875	939
ENST00000430056	SIM2	chr21	38072221	+	ENST00000399914	GRIK1	chr21	31066382	-	3215	231	56	2917	953
ENST00000430056	SIM2	chr21	38072221	+	ENST00000535441	GRIK1	chr21	31066382	-	2882	231	56	2881	942
ENST00000430056	SIM2	chr21	38072221	+	ENST00000389124	GRIK1	chr21	31066382	-	2793	231	56	2728	890
ENST00000430056	SIM2	chr21	38072221	+	ENST00000399907	GRIK1	chr21	31066382	-	3173	231	56	2869	937
ENST00000430056	SIM2	chr21	38072221	+	ENST00000399909	GRIK1	chr21	31066382	-	3128	231	56	2824	922
ENST00000430056	SIM2	chr21	38072221	+	ENST00000309434	GRIK1	chr21	31066382	-	2876	231	56	2875	940

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
ENST00000290399	ENST00000327783	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.001465306	0.9985347
ENST00000290399	ENST00000389125	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.001598476	0.9984016
ENST00000290399	ENST00000399913	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.001462795	0.9985372
ENST00000290399	ENST00000399914	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.001388497	0.99861145
ENST00000290399	ENST00000535441	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.002689552	0.9973105
ENST00000290399	ENST00000389124	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.003558856	0.9964412
ENST00000290399	ENST00000399907	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.001567464	0.9984326
ENST00000290399	ENST00000399909	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.001680275	0.9983197
ENST00000290399	ENST00000309434	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.002210595	0.9977894
ENST00000430056	ENST00000327783	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.000434778	0.9995652
ENST00000430056	ENST00000389125	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.000627834	0.9993722
ENST00000430056	ENST00000399913	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.000552447	0.9994475
ENST00000430056	ENST00000399914	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.000454187	0.99954575
ENST00000430056	ENST00000535441	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.00102782	0.9989722
ENST00000430056	ENST00000389124	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.001522738	0.9984773
ENST00000430056	ENST00000399907	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.000665867	0.99933416
ENST00000430056	ENST00000399909	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.000743056	0.9992569
ENST00000430056	ENST00000309434	SIM2	chr21	38072221	+	GRIK1	chr21	31066382	-	0.000923387	0.9990766

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 SIM2-GRIK1

+/-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
SIM2	chr21	38072221	GRIK1	chr21	31066382	231	58	TTSYLKMRAVFPEGGIFETVENEPVN
SIM2	chr21	38072221	GRIK1	chr21	31066382	788	58	TTSYLKMRAVFPEGGIFETVENEPVN

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Potential FusionNeoAntigen Information of SIM2-GRIK1 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.

SIM2-GRIK1_38072221_31066382.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)
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:01	AVFPEGGIF	0.9894	0.9918	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:25	AVFPEGGIF	0.9866	0.9956	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:02	AVFPEGGIF	0.9839	0.9967	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:17	AVFPEGGIF	0.9688	0.996	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:16	AVFPEGGIF	0.9541	0.9942	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:03	FPEGGIFET	0.9324	0.9948	10	19
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:03	AVFPEGGIF	0.8533	0.9879	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:04	FPEGGIFET	0.8289	0.9976	10	19
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:02	FPEGGIFET	0.8289	0.9976	10	19
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B46:01	AVFPEGGIF	0.7856	0.902	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-A32:13	AVFPEGGIF	0.5348	0.994	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:01	RAVFPEGGIF	0.9947	0.9744	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:17	RAVFPEGGIF	0.9911	0.99	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:25	RAVFPEGGIF	0.9907	0.9863	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:16	RAVFPEGGIF	0.9906	0.988	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:03	FPEGGIFETV	0.986	0.9937	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B51:02	FPEGGIFETV	0.9827	0.9789	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:02	FPEGGIFETV	0.9814	0.998	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:04	FPEGGIFETV	0.9814	0.998	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B27:02	MRAVFPEGGIF	0.9999	0.6131	6	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B27:04	MRAVFPEGGIF	0.9999	0.8301	6	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B54:01	FPEGGIFET	0.995	0.8777	10	19
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:21	AVFPEGGIF	0.9831	0.9898	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:07	AVFPEGGIF	0.9816	0.98	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:05	AVFPEGGIF	0.9337	0.9788	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:31	AVFPEGGIF	0.9299	0.9816	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-C15:04	AVFPEGGIF	0.8422	0.9921	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:12	FPEGGIFET	0.8289	0.9976	10	19
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:04	AVFPEGGIF	0.7724	0.9968	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-C03:14	AVFPEGGIF	0.5184	0.9961	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B54:01	FPEGGIFETV	0.9987	0.9547	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:07	RAVFPEGGIF	0.9917	0.9284	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:12	FPEGGIFETV	0.9814	0.998	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B56:04	FPEGGIFETV	0.9573	0.9225	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B51:08	FPEGGIFETV	0.8663	0.9517	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-C14:03	VFPEGGIF	0.9279	0.9931	9	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-C14:02	VFPEGGIF	0.9279	0.9931	9	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:33	AVFPEGGIF	0.9894	0.9918	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:34	AVFPEGGIF	0.9894	0.9918	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:125	AVFPEGGIF	0.9894	0.9918	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:08	AVFPEGGIF	0.9888	0.9846	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:135	AVFPEGGIF	0.9887	0.994	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:27	AVFPEGGIF	0.9886	0.9938	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:11	AVFPEGGIF	0.9886	0.9865	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:43	AVFPEGGIF	0.9868	0.9838	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:39	AVFPEGGIF	0.9862	0.9912	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:50	AVFPEGGIF	0.9853	0.9922	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:24	AVFPEGGIF	0.9844	0.9968	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:35	AVFPEGGIF	0.9776	0.9947	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:12	AVFPEGGIF	0.967	0.9807	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:13	AVFPEGGIF	0.9623	0.9898	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:53	AVFPEGGIF	0.9607	0.9907	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-C03:02	AVFPEGGIF	0.9603	0.9959	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:20	AVFPEGGIF	0.9411	0.9872	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:20	AVFPEGGIF	0.9223	0.9892	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:28	AVFPEGGIF	0.9152	0.9882	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B55:02	FPEGGIFET	0.8891	0.6003	10	19
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-C15:09	AVFPEGGIF	0.8422	0.9921	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:09	FPEGGIFET	0.8289	0.9976	10	19
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:54	AVFPEGGIF	0.8261	0.9887	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-A32:01	AVFPEGGIF	0.7899	0.9974	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-C12:02	AVFPEGGIF	0.7646	0.9944	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-A25:01	AVFPEGGIF	0.7559	0.9881	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:68	AVFPEGGIF	0.6768	0.9629	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:73	AVFPEGGIF	0.67	0.9969	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:30	AVFPEGGIF	0.5534	0.997	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-C02:10	AVFPEGGIF	0.363	0.9973	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-C02:02	AVFPEGGIF	0.363	0.9973	8	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:27	RAVFPEGGIF	0.9948	0.9776	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:33	RAVFPEGGIF	0.9947	0.9744	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:125	RAVFPEGGIF	0.9947	0.9744	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:34	RAVFPEGGIF	0.9947	0.9744	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:135	RAVFPEGGIF	0.9946	0.9827	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:24	RAVFPEGGIF	0.9944	0.9908	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:39	RAVFPEGGIF	0.9921	0.9698	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:22	FPEGGIFETV	0.9913	0.9169	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:35	RAVFPEGGIF	0.9905	0.9813	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B15:50	RAVFPEGGIF	0.9867	0.9733	7	17
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B35:09	FPEGGIFETV	0.9814	0.998	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B59:01	FPEGGIFETV	0.9727	0.9606	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B51:05	FPEGGIFETV	0.9661	0.8163	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B51:14	FPEGGIFETV	0.962	0.9633	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B51:09	FPEGGIFETV	0.959	0.9794	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B56:02	FPEGGIFETV	0.9573	0.9225	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B51:13	FPEGGIFETV	0.9499	0.8971	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B51:29	FPEGGIFETV	0.9222	0.9544	10	20
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	HLA-B27:08	MRAVFPEGGIF	0.9998	0.7894	6	17

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Potential FusionNeoAntigen Information of SIM2-GRIK1 in HLA II

SIM2-GRIK1_38072221_31066382.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)
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0469	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0701	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0703	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0705	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0706	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0707	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0708	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0709	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0711	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0712	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0713	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0714	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0715	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0716	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0717	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-0719	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-1527	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-1529	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-1534	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-1602	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-1611	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-1614	PEGGIFETVENEPVN	11	26
SIM2-GRIK1	chr21	38072221	chr21	31066382	788	DRB1-1616	PEGGIFETVENEPVN	11	26

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Fusion breakpoint peptide structures of SIM2-GRIK1

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
6000	MRAVFPEGGIFETV	SIM2	GRIK1	chr21	38072221	chr21	31066382	788

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SIM2-GRIK1

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	6000	MRAVFPEGGIFETV	-7.9962	-8.1096
HLA-B14:02	3BVN	6000	MRAVFPEGGIFETV	-5.70842	-6.74372
HLA-B52:01	3W39	6000	MRAVFPEGGIFETV	-6.83737	-6.95077
HLA-B52:01	3W39	6000	MRAVFPEGGIFETV	-4.4836	-5.5189
HLA-A11:01	4UQ2	6000	MRAVFPEGGIFETV	-10.0067	-10.1201
HLA-A11:01	4UQ2	6000	MRAVFPEGGIFETV	-9.03915	-10.0745
HLA-A24:02	5HGA	6000	MRAVFPEGGIFETV	-6.56204	-6.67544
HLA-A24:02	5HGA	6000	MRAVFPEGGIFETV	-5.42271	-6.45801
HLA-B44:05	3DX8	6000	MRAVFPEGGIFETV	-7.85648	-8.89178
HLA-B44:05	3DX8	6000	MRAVFPEGGIFETV	-5.3978	-5.5112
HLA-A02:01	6TDR	6000	MRAVFPEGGIFETV	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of SIM2-GRIK1

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
SIM2-GRIK1	chr21	38072221	chr21	31066382	10	19	FPEGGIFET	TCCCCGAAGGAGGGATTTTTGAAACAG
SIM2-GRIK1	chr21	38072221	chr21	31066382	10	20	FPEGGIFETV	TCCCCGAAGGAGGGATTTTTGAAACAGTGG
SIM2-GRIK1	chr21	38072221	chr21	31066382	6	17	MRAVFPEGGIF	TGCGCGCCGTCTTCCCCGAAGGAGGGATTTTTG
SIM2-GRIK1	chr21	38072221	chr21	31066382	7	17	RAVFPEGGIF	GCGCCGTCTTCCCCGAAGGAGGGATTTTTG
SIM2-GRIK1	chr21	38072221	chr21	31066382	8	17	AVFPEGGIF	CCGTCTTCCCCGAAGGAGGGATTTTTG
SIM2-GRIK1	chr21	38072221	chr21	31066382	9	17	VFPEGGIF	TCTTCCCCGAAGGAGGGATTTTTG

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
SIM2-GRIK1	chr21	38072221	chr21	31066382	11	26	PEGGIFETVENEPVN	CCGAAGGAGGGATTTTTGAAACAGTGGAAAATGAGCCTGTTAATG

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Information of the samples that have these potential fusion neoantigens of SIM2-GRIK1

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
LIHC	SIM2-GRIK1	chr21	38072221	ENST00000290399	chr21	31066382	ENST00000309434	TCGA-RC-A6M3-01A

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Potential target of CAR-T therapy development for SIM2-GRIK1

Predicted 3D structure. We used RoseTTAFold.

412_SIM2-GRIK1_t000_.e2e.pdb

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

GRIK1

chr21:38072221

chr21:31066382

ENST00000389125

577_597

906.0

Transmembrane

Helical

Tgene

GRIK1

chr21:38072221

chr21:31066382

ENST00000389125

654_674

906.0

Transmembrane

Helical

Tgene

GRIK1

chr21:38072221

chr21:31066382

ENST00000389125

835_855

906.0

Transmembrane

Helical

Tgene

GRIK1

chr21:38072221

chr21:31066382

ENST00000399907

577_597

919.0

Transmembrane

Helical

Tgene

GRIK1

chr21:38072221

chr21:31066382

ENST00000399907

654_674

919.0

Transmembrane

Helical

Tgene

GRIK1

chr21:38072221

chr21:31066382

ENST00000399907

835_855

919.0

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
SIM2	chr21	38072221	ENST00000290399	GRIK1	chr21	31066382	ENST00000309434
SIM2	chr21	38072221	ENST00000290399	GRIK1	chr21	31066382	ENST00000327783
SIM2	chr21	38072221	ENST00000290399	GRIK1	chr21	31066382	ENST00000389124
SIM2	chr21	38072221	ENST00000290399	GRIK1	chr21	31066382	ENST00000389125
SIM2	chr21	38072221	ENST00000290399	GRIK1	chr21	31066382	ENST00000399907
SIM2	chr21	38072221	ENST00000290399	GRIK1	chr21	31066382	ENST00000399909
SIM2	chr21	38072221	ENST00000290399	GRIK1	chr21	31066382	ENST00000399913
SIM2	chr21	38072221	ENST00000290399	GRIK1	chr21	31066382	ENST00000399914
SIM2	chr21	38072221	ENST00000290399	GRIK1	chr21	31066382	ENST00000535441

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Related Drugs to SIM2-GRIK1

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 SIM2-GRIK1

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)