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Fusion Protein:SLC44A3-ABCD3

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SLC44A3-ABCD3
	FusionPDB ID: 83299
	FusionGDB2.0 ID: 83299
		Hgene	Tgene
	Gene symbol	SLC44A3	ABCD3
	Gene ID	126969	5825
	Gene name	solute carrier family 44 member 3	ATP binding cassette subfamily D member 3
	Synonyms	CTL3	ABC43\|CBAS5\|PMP70\|PXMP1\|ZWS2
	Cytomap	1p21.3	1p21.3
	Type of gene	protein-coding	protein-coding
	Description	choline transporter-like protein 3	ATP-binding cassette sub-family D member 370 kDa peroxisomal membrane proteinATP-binding cassette, sub-family D (ALD), member 3Peroxisomal membrane protein-1 (70kD)dJ824O18.1 (ATP-binding cassette, sub-family D (ALD), member 3 (PMP70, PXMP1))peroxiso
	Modification date	20200313	20200313
	UniProtAcc	.	P28288 Main function of 5'-partner protein: FUNCTION: Probable transporter involved in the transport of branched-chain fatty acids and C27 bile acids into the peroxisome; the latter function is a crucial step in bile acid biosynthesis (PubMed:25168382). The nucleotide-binding fold acts as an ATP-binding subunit with ATPase activity (PubMed:11248239). {ECO:0000269\|PubMed:11248239, ECO:0000269\|PubMed:25168382}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000530397, ENST00000271227, ENST00000446120, ENST00000467909, ENST00000527077, ENST00000529450, ENST00000532427,	ENST00000315713, ENST00000370214, ENST00000394233, ENST00000454898, ENST00000536817, ENST00000484213,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 1 X 2=4	10 X 6 X 6=360
	# samples	2	10
	** MAII score	log2(2/4*10)=2.32192809488736	log2(10/360*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SLC44A3 [Title/Abstract] AND ABCD3 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SLC44A3 [Title/Abstract] AND ABCD3 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SLC44A3(95332973)-ABCD3(94940699), # samples:1
Anticipated loss of major functional domain due to fusion event.	SLC44A3-ABCD3 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. SLC44A3-ABCD3 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. SLC44A3-ABCD3 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. SLC44A3-ABCD3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

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

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

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	ABCD3	GO:0007031	peroxisome organization	9425230

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:95332973/chr1:94940699)
- 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 SLC44A3 (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 ABCD3 (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)
ENST00000446120	SLC44A3	chr1	95332973	-	ENST00000394233	ABCD3	chr1	94940699	+	4263	1484	110	2728	872
ENST00000446120	SLC44A3	chr1	95332973	-	ENST00000454898	ABCD3	chr1	94940699	+	3210	1484	110	3058	982
ENST00000446120	SLC44A3	chr1	95332973	-	ENST00000536817	ABCD3	chr1	94940699	+	3532	1484	110	3058	982
ENST00000446120	SLC44A3	chr1	95332973	-	ENST00000370214	ABCD3	chr1	94940699	+	4593	1484	110	3058	982
ENST00000446120	SLC44A3	chr1	95332973	-	ENST00000315713	ABCD3	chr1	94940699	+	1963	1484	110	1789	559
ENST00000271227	SLC44A3	chr1	95332973	-	ENST00000394233	ABCD3	chr1	94940699	+	4363	1584	102	2828	908
ENST00000271227	SLC44A3	chr1	95332973	-	ENST00000454898	ABCD3	chr1	94940699	+	3310	1584	102	3158	1018
ENST00000271227	SLC44A3	chr1	95332973	-	ENST00000536817	ABCD3	chr1	94940699	+	3632	1584	102	3158	1018
ENST00000271227	SLC44A3	chr1	95332973	-	ENST00000370214	ABCD3	chr1	94940699	+	4693	1584	102	3158	1018
ENST00000271227	SLC44A3	chr1	95332973	-	ENST00000315713	ABCD3	chr1	94940699	+	2063	1584	102	1889	595
ENST00000527077	SLC44A3	chr1	95332973	-	ENST00000394233	ABCD3	chr1	94940699	+	4112	1333	55	2577	840
ENST00000527077	SLC44A3	chr1	95332973	-	ENST00000454898	ABCD3	chr1	94940699	+	3059	1333	55	2907	950
ENST00000527077	SLC44A3	chr1	95332973	-	ENST00000536817	ABCD3	chr1	94940699	+	3381	1333	55	2907	950
ENST00000527077	SLC44A3	chr1	95332973	-	ENST00000370214	ABCD3	chr1	94940699	+	4442	1333	55	2907	950
ENST00000527077	SLC44A3	chr1	95332973	-	ENST00000315713	ABCD3	chr1	94940699	+	1812	1333	55	1638	527
ENST00000529450	SLC44A3	chr1	95332973	-	ENST00000394233	ABCD3	chr1	94940699	+	4213	1434	51	2678	875
ENST00000529450	SLC44A3	chr1	95332973	-	ENST00000454898	ABCD3	chr1	94940699	+	3160	1434	51	3008	985
ENST00000529450	SLC44A3	chr1	95332973	-	ENST00000536817	ABCD3	chr1	94940699	+	3482	1434	51	3008	985
ENST00000529450	SLC44A3	chr1	95332973	-	ENST00000370214	ABCD3	chr1	94940699	+	4543	1434	51	3008	985
ENST00000529450	SLC44A3	chr1	95332973	-	ENST00000315713	ABCD3	chr1	94940699	+	1913	1434	51	1739	562
ENST00000467909	SLC44A3	chr1	95332973	-	ENST00000394233	ABCD3	chr1	94940699	+	4229	1450	22	2694	890
ENST00000467909	SLC44A3	chr1	95332973	-	ENST00000454898	ABCD3	chr1	94940699	+	3176	1450	22	3024	1000
ENST00000467909	SLC44A3	chr1	95332973	-	ENST00000536817	ABCD3	chr1	94940699	+	3498	1450	22	3024	1000
ENST00000467909	SLC44A3	chr1	95332973	-	ENST00000370214	ABCD3	chr1	94940699	+	4559	1450	22	3024	1000
ENST00000467909	SLC44A3	chr1	95332973	-	ENST00000315713	ABCD3	chr1	94940699	+	1929	1450	22	1755	577
ENST00000532427	SLC44A3	chr1	95332973	-	ENST00000394233	ABCD3	chr1	94940699	+	4104	1325	83	2569	828
ENST00000532427	SLC44A3	chr1	95332973	-	ENST00000454898	ABCD3	chr1	94940699	+	3051	1325	83	2899	938
ENST00000532427	SLC44A3	chr1	95332973	-	ENST00000536817	ABCD3	chr1	94940699	+	3373	1325	83	2899	938
ENST00000532427	SLC44A3	chr1	95332973	-	ENST00000370214	ABCD3	chr1	94940699	+	4434	1325	83	2899	938
ENST00000532427	SLC44A3	chr1	95332973	-	ENST00000315713	ABCD3	chr1	94940699	+	1804	1325	83	1630	515

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
ENST00000446120	ENST00000394233	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000192287	0.9998078
ENST00000446120	ENST00000454898	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000182954	0.9998171
ENST00000446120	ENST00000536817	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000139867	0.99986017
ENST00000446120	ENST00000370214	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	9.37E-05	0.9999063
ENST00000446120	ENST00000315713	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.001704623	0.99829537
ENST00000271227	ENST00000394233	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	9.81E-05	0.9999019
ENST00000271227	ENST00000454898	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000207869	0.99979216
ENST00000271227	ENST00000536817	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000161258	0.9998387
ENST00000271227	ENST00000370214	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000111222	0.9998888
ENST00000271227	ENST00000315713	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.001334312	0.9986657
ENST00000527077	ENST00000394233	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000235428	0.9997646
ENST00000527077	ENST00000454898	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000251796	0.9997482
ENST00000527077	ENST00000536817	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000208843	0.9997912
ENST00000527077	ENST00000370214	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000143223	0.9998567
ENST00000527077	ENST00000315713	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.001721967	0.998278
ENST00000529450	ENST00000394233	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	8.09E-05	0.99991906
ENST00000529450	ENST00000454898	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	9.17E-05	0.9999083
ENST00000529450	ENST00000536817	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	7.51E-05	0.9999249
ENST00000529450	ENST00000370214	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	5.17E-05	0.99994826
ENST00000529450	ENST00000315713	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.001141503	0.99885845
ENST00000467909	ENST00000394233	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000178621	0.99982136
ENST00000467909	ENST00000454898	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000163553	0.99983644
ENST00000467909	ENST00000536817	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000128711	0.99987125
ENST00000467909	ENST00000370214	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	8.68E-05	0.9999132
ENST00000467909	ENST00000315713	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.001973782	0.9980262
ENST00000532427	ENST00000394233	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000400743	0.9995993
ENST00000532427	ENST00000454898	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000309967	0.99969006
ENST00000532427	ENST00000536817	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000275833	0.9997242
ENST00000532427	ENST00000370214	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.000193827	0.9998062
ENST00000532427	ENST00000315713	SLC44A3	chr1	95332973	-	ABCD3	chr1	94940699	+	0.004276302	0.9957237

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 SLC44A3-ABCD3

+/-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
SLC44A3	chr1	95332973	ABCD3	chr1	94940699	1325	414	FWCLDKYLLHLNQISLVNNFLKYGLN
SLC44A3	chr1	95332973	ABCD3	chr1	94940699	1333	426	FWCLDKYLLHLNQISLVNNFLKYGLN
SLC44A3	chr1	95332973	ABCD3	chr1	94940699	1434	461	FWCLDKYLLHLNQISLVNNFLKYGLN
SLC44A3	chr1	95332973	ABCD3	chr1	94940699	1450	476	FWCLDKYLLHLNQISLVNNFLKYGLN
SLC44A3	chr1	95332973	ABCD3	chr1	94940699	1484	458	FWCLDKYLLHLNQISLVNNFLKYGLN
SLC44A3	chr1	95332973	ABCD3	chr1	94940699	1584	494	FWCLDKYLLHLNQISLVNNFLKYGLN

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Potential FusionNeoAntigen Information of SLC44A3-ABCD3 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.

SLC44A3-ABCD3_95332973_94940699.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)
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B39:06	LHLNQISL	0.9998	0.5657	8	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B39:01	LHLNQISL	0.9996	0.8187	8	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B38:01	LHLNQISL	0.9995	0.9134	8	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B38:02	LHLNQISL	0.9995	0.9332	8	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B14:01	LHLNQISL	0.9993	0.5205	8	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B14:02	LHLNQISL	0.9993	0.5205	8	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:01	NQISLVNNF	0.9991	0.7406	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B39:06	LHLNQISLV	0.9989	0.5778	8	17
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B38:01	LHLNQISLV	0.9967	0.8343	8	17
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B38:02	LHLNQISLV	0.9963	0.8494	8	17
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:25	NQISLVNNF	0.9786	0.763	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:02	NQISLVNNF	0.9644	0.7776	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B08:01	LLHLNQISL	0.9476	0.5279	7	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B08:09	LLHLNQISL	0.9353	0.5853	7	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B18:01	NQISLVNNF	0.9048	0.7204	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B13:01	NQISLVNNF	0.8034	0.7175	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B38:01	NQISLVNNF	0.6995	0.7796	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B38:02	NQISLVNNF	0.6582	0.8191	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-A32:13	NQISLVNNF	0.4007	0.8821	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B52:01	NQISLVNNF	0.0929	0.5254	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B39:12	LHLNQISL	0.9995	0.8493	8	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B39:05	LHLNQISL	0.9993	0.7886	8	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B14:03	LHLNQISL	0.8697	0.6161	8	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B39:05	LHLNQISLV	0.996	0.7444	8	17
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:04	NQISLVNNF	0.9868	0.7268	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:21	NQISLVNNF	0.9637	0.7644	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:05	NQISLVNNF	0.9324	0.7291	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:31	NQISLVNNF	0.9235	0.7433	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B38:05	LHLNQISL	0.9995	0.9134	8	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B39:31	LHLNQISL	0.9995	0.8462	8	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B39:11	LHLNQISL	0.8558	0.7311	8	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:27	NQISLVNNF	0.9991	0.7733	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:125	NQISLVNNF	0.9991	0.7406	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:34	NQISLVNNF	0.9991	0.7406	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:33	NQISLVNNF	0.9991	0.7406	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:135	NQISLVNNF	0.9991	0.7237	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:24	NQISLVNNF	0.9984	0.6452	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:50	NQISLVNNF	0.9983	0.8528	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:53	NQISLVNNF	0.9968	0.67	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B38:05	LHLNQISLV	0.9967	0.8343	8	17
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:54	NQISLVNNF	0.9928	0.6353	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:12	NQISLVNNF	0.9918	0.7671	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:35	NQISLVNNF	0.9895	0.6724	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:39	NQISLVNNF	0.981	0.5783	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:73	LLHLNQISL	0.9526	0.6102	7	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B08:18	LLHLNQISL	0.9476	0.5279	7	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:73	NQISLVNNF	0.9256	0.5781	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:20	NQISLVNNF	0.9243	0.821	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B18:07	NQISLVNNF	0.9237	0.6729	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B18:11	NQISLVNNF	0.918	0.6822	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B18:06	NQISLVNNF	0.9165	0.7236	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B35:28	NQISLVNNF	0.91	0.8179	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:30	LLHLNQISL	0.9071	0.5937	7	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B18:05	NQISLVNNF	0.9048	0.7204	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B35:20	NQISLVNNF	0.8947	0.8303	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B18:04	NQISLVNNF	0.8881	0.7534	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B18:03	NQISLVNNF	0.872	0.7058	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B15:30	NQISLVNNF	0.8049	0.5778	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B48:02	NQISLVNNF	0.7823	0.7838	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B08:12	LLHLNQISL	0.7747	0.7192	7	16
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-B38:05	NQISLVNNF	0.6995	0.7796	11	20
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	1584	HLA-C06:06	KYLLHLNQI	0.0289	0.9576	5	14

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Potential FusionNeoAntigen Information of SLC44A3-ABCD3 in HLA II

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA II

FusionNeoAntigen peptide

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of SLC44A3-ABCD3

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
10716	YLLHLNQISLVNNF	SLC44A3	ABCD3	chr1	95332973	chr1	94940699	1584

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SLC44A3-ABCD3

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	10716	YLLHLNQISLVNNF	-8.85616	-8.96956
HLA-B14:02	3BVN	10716	YLLHLNQISLVNNF	-5.66423	-6.69953
HLA-B52:01	3W39	10716	YLLHLNQISLVNNF	-6.49489	-6.60829
HLA-B52:01	3W39	10716	YLLHLNQISLVNNF	-3.99785	-5.03315
HLA-A11:01	4UQ2	10716	YLLHLNQISLVNNF	-4.90759	-5.94289
HLA-A24:02	5HGA	10716	YLLHLNQISLVNNF	-7.27887	-7.39227
HLA-A24:02	5HGA	10716	YLLHLNQISLVNNF	-7.11524	-8.15054
HLA-B27:05	6PYJ	10716	YLLHLNQISLVNNF	-6.11615	-6.22955
HLA-B27:05	6PYJ	10716	YLLHLNQISLVNNF	-4.78818	-5.82348
HLA-B44:05	3DX8	10716	YLLHLNQISLVNNF	-7.22602	-7.33942
HLA-B44:05	3DX8	10716	YLLHLNQISLVNNF	-4.86671	-5.90201

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Vaccine Design for the FusionNeoAntigens of SLC44A3-ABCD3

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
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	11	20	NQISLVNNF	AACCAGATCTCTCTGGTTAATAACTTC
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	5	14	KYLLHLNQI	AAATACCTGCTCCATCTCAACCAGATC
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	7	16	LLHLNQISL	CTGCTCCATCTCAACCAGATCTCTCTG
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	8	16	LHLNQISL	CTCCATCTCAACCAGATCTCTCTG
SLC44A3-ABCD3	chr1	95332973	chr1	94940699	8	17	LHLNQISLV	CTCCATCTCAACCAGATCTCTCTGGTT

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide

FusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of SLC44A3-ABCD3

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
LUSC	SLC44A3-ABCD3	chr1	95332973	ENST00000271227	chr1	94940699	ENST00000315713	TCGA-37-A5EN-01A

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Potential target of CAR-T therapy development for SLC44A3-ABCD3

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

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000271227

213_233

494

654.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000271227

243_263

494

654.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000271227

284_304

494

654.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000271227

334_354

494

654.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000271227

34_54

494

654.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000271227

384_404

494

654.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000446120

213_233

458

618.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000446120

243_263

458

618.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000446120

284_304

458

618.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000446120

334_354

458

618.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000446120

34_54

458

618.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000446120

384_404

458

618.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000467909

213_233

446

606.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000467909

243_263

446

606.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000467909

284_304

446

606.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000467909

334_354

446

606.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000467909

34_54

446

606.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000467909

384_404

446

606.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000527077

213_233

426

586.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000527077

243_263

426

586.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000527077

284_304

426

586.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000527077

334_354

426

586.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000527077

34_54

426

586.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000527077

384_404

426

586.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000529450

213_233

461

621.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000529450

243_263

461

621.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000529450

284_304

461

621.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000529450

334_354

461

621.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000529450

34_54

461

621.0

Transmembrane

Helical

Hgene

SLC44A3

chr1:95332973

chr1:94940699

ENST00000529450

384_404

461

621.0

Transmembrane

Helical

Tgene

ABCD3

chr1:95332973

chr1:94940699

ENST00000315713

224_244

237.0

Transmembrane

Helical

Tgene

ABCD3

chr1:95332973

chr1:94940699

ENST00000315713

313_333

237.0

Transmembrane

Helical

Tgene

ABCD3

chr1:95332973

chr1:94940699

ENST00000370214

224_244

660.0

Transmembrane

Helical

Tgene

ABCD3

chr1:95332973

chr1:94940699

ENST00000370214

313_333

660.0

Transmembrane

Helical

Tgene

ABCD3

chr1:95332973

chr1:94940699

ENST00000394233

224_244

550.0

Transmembrane

Helical

Tgene

ABCD3

chr1:95332973

chr1:94940699

ENST00000394233

313_333

550.0

Transmembrane

Helical

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to SLC44A3-ABCD3

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 SLC44A3-ABCD3

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)