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Fusion Protein:IRAK2-FANCD2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: IRAK2-FANCD2
	FusionPDB ID: 40213
	FusionGDB2.0 ID: 40213
		Hgene	Tgene
	Gene symbol	IRAK2	FANCD2
	Gene ID	3656	2177
	Gene name	interleukin 1 receptor associated kinase 2	FA complementation group D2
	Synonyms	IRAK-2	FA-D2\|FA4\|FACD\|FAD\|FAD2\|FANCD
	Cytomap	3p25.3	3p25.3
	Type of gene	protein-coding	protein-coding
	Description	interleukin-1 receptor-associated kinase-like 2	Fanconi anemia group D2 proteinFanconi anemia complementation group D2
	Modification date	20200313	20200313
	UniProtAcc	O43187 Main function of 5'-partner protein: FUNCTION: Binds to the IL-1 type I receptor following IL-1 engagement, triggering intracellular signaling cascades leading to transcriptional up-regulation and mRNA stabilization. {ECO:0000269\|PubMed:10383454, ECO:0000269\|PubMed:9374458}.	Q96PS1 Main function of 5'-partner protein:
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000256458,	ENST00000431693, ENST00000438741, ENST00000383806, ENST00000287647, ENST00000383807, ENST00000419585,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 8 X 8=448	9 X 13 X 7=819
	# samples	8	11
	** MAII score	log2(8/448*10)=-2.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(11/819*10)=-2.89635992811635 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: IRAK2 [Title/Abstract] AND FANCD2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: IRAK2 [Title/Abstract] AND FANCD2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	IRAK2(10268117)-FANCD2(10133865), # samples:1
Anticipated loss of major functional domain due to fusion event.	IRAK2-FANCD2 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. IRAK2-FANCD2 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. IRAK2-FANCD2 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. IRAK2-FANCD2 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. IRAK2-FANCD2 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. IRAK2-FANCD2 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF. IRAK2-FANCD2 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted 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	FANCD2	GO:0010332	response to gamma radiation	12874027

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:10268117/chr3:10133865)
- 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 IRAK2 (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 FANCD2 (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)

ENST00000256458

IRAK2

chr3

10268117

ENST00000287647

FANCD2

chr3

10133865

2711

1362

2000

636

ENST00000256458

IRAK2

chr3

10268117

ENST00000383807

FANCD2

chr3

10133865

2609

1362

1940

616

ENST00000256458

IRAK2

chr3

10268117

ENST00000419585

FANCD2

chr3

10133865

2609

1362

1940

616

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
ENST00000256458	ENST00000287647	IRAK2	chr3	10268117	+	FANCD2	chr3	10133865	+	0.011185165	0.9888149
ENST00000256458	ENST00000383807	IRAK2	chr3	10268117	+	FANCD2	chr3	10133865	+	0.004636527	0.9953635
ENST00000256458	ENST00000419585	IRAK2	chr3	10268117	+	FANCD2	chr3	10133865	+	0.004636527	0.9953635

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 IRAK2-FANCD2

+/-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
IRAK2	chr3	10268117	FANCD2	chr3	10133865	1362	424	IPAMDNNRSPVYLIHEEKLLYWNMAV

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Potential FusionNeoAntigen Information of IRAK2-FANCD2 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.

IRAK2-FANCD2_10268117_10133865.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)
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:01	LIHEEKLLY	0.9996	0.968	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:25	LIHEEKLLY	0.9989	0.9662	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B27:05	NRSPVYLIH	0.9988	0.8286	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B27:04	NRSPVYLIH	0.9985	0.6132	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:02	LIHEEKLLY	0.997	0.9689	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:08	LIHEEKLLY	0.9892	0.8763	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:17	LIHEEKLLY	0.9882	0.9472	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:22	YLIHEEKLL	0.9789	0.6879	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:30	YLIHEEKLL	0.9751	0.7589	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:67	YLIHEEKLL	0.9751	0.7589	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:24	YLIHEEKLL	0.9751	0.7589	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:60	YLIHEEKLL	0.9748	0.7336	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:11	YLIHEEKLL	0.9733	0.7956	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:27	YLIHEEKLL	0.9435	0.6418	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:04	YLIHEEKLL	0.9321	0.7568	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:01	LIHEEKLLY	0.9302	0.9466	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:16	YLIHEEKLL	0.9112	0.6631	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:05	LIHEEKLLY	0.8673	0.7466	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:29	YLIHEEKLL	0.844	0.7645	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:20	YLIHEEKLL	0.8253	0.7621	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:38	YLIHEEKLL	0.8162	0.6349	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A24:14	VYLIHEEKL	0.8133	0.5855	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B57:01	LIHEEKLLYW	0.9999	0.9809	12	22
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:01	YLIHEEKLLY	0.9998	0.965	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B58:01	LIHEEKLLYW	0.9987	0.9552	12	22
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:25	YLIHEEKLLY	0.9975	0.9614	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:02	YLIHEEKLLY	0.9948	0.9635	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B27:14	NRSPVYLIH	0.9983	0.7266	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:07	LIHEEKLLY	0.9983	0.86	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:21	LIHEEKLLY	0.9969	0.9567	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B27:03	NRSPVYLIH	0.9774	0.8633	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:01	YLIHEEKLL	0.9751	0.7589	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:05	YLIHEEKLL	0.9673	0.5703	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:05	LIHEEKLLY	0.9645	0.9412	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:05	NRSPVYLIH	0.9597	0.915	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:27	NRSPVYLIH	0.957	0.8725	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:04	LIHEEKLLY	0.9368	0.9715	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:31	LIHEEKLLY	0.9341	0.9467	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C15:04	LIHEEKLLY	0.8331	0.928	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:10	NRSPVYLIH	0.7719	0.8658	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:67	NRSPVYLIH	0.7614	0.8348	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:80	NRSPVYLIH	0.7614	0.8348	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:46	NRSPVYLIH	0.7555	0.6377	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:10	VYLIHEEKL	0.3333	0.9741	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:80	VYLIHEEKL	0.3288	0.9623	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:67	VYLIHEEKL	0.3288	0.9623	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:29	VYLIHEEKL	0.3272	0.9777	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:13	VYLIHEEKL	0.3077	0.9518	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C03:14	LIHEEKLLY	0.2754	0.9772	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C04:14	VYLIHEEKL	0.2039	0.8903	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C12:16	NRSPVYLIH	0.0023	0.9152	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:07	YLIHEEKLLY	0.9993	0.8737	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:21	YLIHEEKLLY	0.994	0.9532	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:04	YLIHEEKLLY	0.9806	0.9703	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:05	YLIHEEKLLY	0.9633	0.9437	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:31	YLIHEEKLLY	0.9377	0.9496	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C06:17	NRSPVYLI	0.9357	0.9926	6	14
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C06:02	NRSPVYLI	0.9357	0.9926	6	14
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:27	LIHEEKLLY	0.9996	0.9705	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:125	LIHEEKLLY	0.9996	0.968	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:33	LIHEEKLLY	0.9996	0.968	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:34	LIHEEKLLY	0.9996	0.968	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:135	LIHEEKLLY	0.9995	0.9685	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:50	LIHEEKLLY	0.9994	0.9518	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:11	LIHEEKLLY	0.9992	0.9466	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:08	LIHEEKLLY	0.9989	0.9425	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B27:08	NRSPVYLIH	0.9988	0.6984	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:39	LIHEEKLLY	0.9988	0.9251	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:43	LIHEEKLLY	0.9987	0.9398	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:24	LIHEEKLLY	0.9987	0.9502	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:35	LIHEEKLLY	0.9987	0.9656	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:12	LIHEEKLLY	0.9985	0.9517	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B27:10	NRSPVYLIH	0.9984	0.8023	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:11	LIHEEKLLY	0.9972	0.9533	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:20	LIHEEKLLY	0.9731	0.9583	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:13	LIHEEKLLY	0.9661	0.5951	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-A02:14	YLIHEEKLL	0.9601	0.8016	11	20
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:28	LIHEEKLLY	0.9386	0.9553	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:23	LIHEEKLLY	0.9339	0.9131	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:20	LIHEEKLLY	0.9335	0.9577	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:77	LIHEEKLLY	0.9302	0.9466	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:17	NRSPVYLIH	0.9168	0.9388	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C03:02	LIHEEKLLY	0.9107	0.9806	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:17	LIHEEKLLY	0.8978	0.8777	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:30	LIHEEKLLY	0.8978	0.8777	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:24	LIHEEKLLY	0.8796	0.9543	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C15:09	LIHEEKLLY	0.8331	0.928	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:02	NRSPVYLIH	0.7614	0.8348	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:22	NRSPVYLIH	0.6616	0.5103	6	15
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:17	VYLIHEEKL	0.3332	0.9822	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C07:02	VYLIHEEKL	0.3288	0.9623	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C04:04	VYLIHEEKL	0.1597	0.9319	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C06:06	VYLIHEEKL	0.0416	0.9867	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C14:03	VYLIHEEKL	0.0307	0.9718	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C14:02	VYLIHEEKL	0.0307	0.9718	10	19
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C02:02	LIHEEKLLY	0.016	0.9801	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-C02:10	LIHEEKLLY	0.016	0.9801	12	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B57:10	LIHEEKLLYW	0.9999	0.9809	12	22
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:125	YLIHEEKLLY	0.9998	0.965	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:12	YLIHEEKLLY	0.9998	0.9486	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:34	YLIHEEKLLY	0.9998	0.965	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:27	YLIHEEKLLY	0.9998	0.9697	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:33	YLIHEEKLLY	0.9998	0.965	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:135	YLIHEEKLLY	0.9997	0.9663	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:50	YLIHEEKLLY	0.9997	0.9659	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B57:04	LIHEEKLLYW	0.9996	0.8454	12	22
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:35	YLIHEEKLLY	0.9994	0.9659	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:39	YLIHEEKLLY	0.9972	0.9172	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:20	YLIHEEKLLY	0.9669	0.9592	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:28	YLIHEEKLLY	0.9502	0.958	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B35:20	YLIHEEKLLY	0.9473	0.9605	11	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	HLA-B15:13	YLIHEEKLLY	0.9385	0.5855	11	21

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Potential FusionNeoAntigen Information of IRAK2-FANCD2 in HLA II

IRAK2-FANCD2_10268117_10133865.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)
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	DRB1-1503	NRSPVYLIHEEKLLY	6	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	DRB1-1523	NRSPVYLIHEEKLLY	6	21
IRAK2-FANCD2	chr3	10268117	chr3	10133865	1362	DRB1-1523	RSPVYLIHEEKLLYW	7	22

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Fusion breakpoint peptide structures of IRAK2-FANCD2

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
6364	NRSPVYLIHEEKLL	IRAK2	FANCD2	chr3	10268117	chr3	10133865	1362

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of IRAK2-FANCD2

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	6364	NRSPVYLIHEEKLL	-7.15543	-7.26883
HLA-B14:02	3BVN	6364	NRSPVYLIHEEKLL	-4.77435	-5.80965
HLA-B52:01	3W39	6364	NRSPVYLIHEEKLL	-6.80875	-6.92215
HLA-B52:01	3W39	6364	NRSPVYLIHEEKLL	-4.20386	-5.23916
HLA-A11:01	4UQ2	6364	NRSPVYLIHEEKLL	-7.5194	-8.5547
HLA-A11:01	4UQ2	6364	NRSPVYLIHEEKLL	-6.9601	-7.0735
HLA-A24:02	5HGA	6364	NRSPVYLIHEEKLL	-7.52403	-7.63743
HLA-A24:02	5HGA	6364	NRSPVYLIHEEKLL	-5.82433	-6.85963
HLA-B27:05	6PYJ	6364	NRSPVYLIHEEKLL	-3.28285	-4.31815
HLA-B44:05	3DX8	6364	NRSPVYLIHEEKLL	-5.91172	-6.94702
HLA-B44:05	3DX8	6364	NRSPVYLIHEEKLL	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of IRAK2-FANCD2

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
IRAK2-FANCD2	chr3	10268117	chr3	10133865	10	19	VYLIHEEKL	GTTTACCTGATTCATGAAGAGAAACTC
IRAK2-FANCD2	chr3	10268117	chr3	10133865	11	20	YLIHEEKLL	TACCTGATTCATGAAGAGAAACTCCTC
IRAK2-FANCD2	chr3	10268117	chr3	10133865	11	21	YLIHEEKLLY	TACCTGATTCATGAAGAGAAACTCCTCTAC
IRAK2-FANCD2	chr3	10268117	chr3	10133865	12	21	LIHEEKLLY	CTGATTCATGAAGAGAAACTCCTCTAC
IRAK2-FANCD2	chr3	10268117	chr3	10133865	12	22	LIHEEKLLYW	CTGATTCATGAAGAGAAACTCCTCTACTGG
IRAK2-FANCD2	chr3	10268117	chr3	10133865	6	14	NRSPVYLI	AACCGAAGCCCGGTTTACCTGATT
IRAK2-FANCD2	chr3	10268117	chr3	10133865	6	15	NRSPVYLIH	AACCGAAGCCCGGTTTACCTGATTCAT

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
IRAK2-FANCD2	chr3	10268117	chr3	10133865	6	21	NRSPVYLIHEEKLLY	AACCGAAGCCCGGTTTACCTGATTCATGAAGAGAAACTCCTCTAC
IRAK2-FANCD2	chr3	10268117	chr3	10133865	7	22	RSPVYLIHEEKLLYW	CGAAGCCCGGTTTACCTGATTCATGAAGAGAAACTCCTCTACTGG

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Information of the samples that have these potential fusion neoantigens of IRAK2-FANCD2

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
UCEC	IRAK2-FANCD2	chr3	10268117	ENST00000256458	chr3	10133865	ENST00000287647	TCGA-FI-A2EX-01A

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Potential target of CAR-T therapy development for IRAK2-FANCD2

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 IRAK2-FANCD2

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 IRAK2-FANCD2

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)