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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:TOM1L2-ATPAF2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: TOM1L2-ATPAF2
	FusionPDB ID: 92997
	FusionGDB2.0 ID: 92997
		Hgene	Tgene
	Gene symbol	TOM1L2	ATPAF2
	Gene ID	146691	91647
	Gene name	target of myb1 like 2 membrane trafficking protein	ATP synthase mitochondrial F1 complex assembly factor 2
	Synonyms	-	ATP12\|ATP12p\|LP3663\|MC5DN1
	Cytomap	17p11.2	17p11.2
	Type of gene	protein-coding	protein-coding
	Description	TOM1-like protein 2target of Myb-like protein 2target of myb1-like 2	ATP synthase mitochondrial F1 complex assembly factor 2ATP12 homolog
	Modification date	20200313	20200327
	UniProtAcc	.	Q8N5M1
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000318094, ENST00000379504, ENST00000395739, ENST00000535933, ENST00000540946, ENST00000542206, ENST00000581396, ENST00000478943, ENST00000577517,	ENST00000469327, ENST00000474627, ENST00000585101,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	16 X 13 X 7=1456	5 X 5 X 4=100
	# samples	17	5
	** MAII score	log2(17/1456*10)=-3.098403704061 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/100*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: TOM1L2 [Title/Abstract] AND ATPAF2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	TOM1L2(17810761)-ATPAF2(17928018), # samples:2
Anticipated loss of major functional domain due to fusion event.	TOM1L2-ATPAF2 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. TOM1L2-ATPAF2 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	TOM1L2	GO:0007165	signal transduction	16479011
Hgene	TOM1L2	GO:0045839	negative regulation of mitotic nuclear division	16479011

Fusion gene breakpoints across TOM1L2 (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 ATPAF2 (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 Gene Sample Information

Fusion gene information from FusionGDB2.0.

Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	HNSC	TCGA-CV-7253-01A	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-
ChimerDB4	HNSC	TCGA-CV-7253	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-
ChimerDB4	HNSC	TCGA-CV-7253	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-

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Fusion ORF Analysis

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)
ENST00000581396	TOM1L2	chr17	17810760	-	ENST00000585101	ATPAF2	chr17	17928018	-	369	234	97	336	79
ENST00000581396	TOM1L2	chr17	17810760	-	ENST00000474627	ATPAF2	chr17	17928018	-	1221	234	97	681	194
ENST00000379504	TOM1L2	chr17	17810760	-	ENST00000585101	ATPAF2	chr17	17928018	-	356	221	84	323	79
ENST00000379504	TOM1L2	chr17	17810760	-	ENST00000474627	ATPAF2	chr17	17928018	-	1208	221	84	668	194
ENST00000318094	TOM1L2	chr17	17810760	-	ENST00000585101	ATPAF2	chr17	17928018	-	356	221	84	323	79
ENST00000318094	TOM1L2	chr17	17810760	-	ENST00000474627	ATPAF2	chr17	17928018	-	1208	221	84	668	194
ENST00000395739	TOM1L2	chr17	17810760	-	ENST00000585101	ATPAF2	chr17	17928018	-	363	228	91	330	79
ENST00000395739	TOM1L2	chr17	17810760	-	ENST00000474627	ATPAF2	chr17	17928018	-	1215	228	91	675	194
ENST00000535933	TOM1L2	chr17	17810760	-	ENST00000585101	ATPAF2	chr17	17928018	-	379	244	107	346	79
ENST00000535933	TOM1L2	chr17	17810760	-	ENST00000474627	ATPAF2	chr17	17928018	-	1231	244	107	691	194
ENST00000540946	TOM1L2	chr17	17810760	-	ENST00000585101	ATPAF2	chr17	17928018	-	356	221	84	323	79
ENST00000540946	TOM1L2	chr17	17810760	-	ENST00000474627	ATPAF2	chr17	17928018	-	1208	221	84	668	194
ENST00000542206	TOM1L2	chr17	17810760	-	ENST00000585101	ATPAF2	chr17	17928018	-	359	224	87	326	79
ENST00000542206	TOM1L2	chr17	17810760	-	ENST00000474627	ATPAF2	chr17	17928018	-	1211	224	87	671	194
ENST00000581396	TOM1L2	chr17	17810761	-	ENST00000585101	ATPAF2	chr17	17928018	-	369	234	97	336	79
ENST00000581396	TOM1L2	chr17	17810761	-	ENST00000474627	ATPAF2	chr17	17928018	-	1221	234	97	681	194
ENST00000379504	TOM1L2	chr17	17810761	-	ENST00000585101	ATPAF2	chr17	17928018	-	356	221	84	323	79
ENST00000379504	TOM1L2	chr17	17810761	-	ENST00000474627	ATPAF2	chr17	17928018	-	1208	221	84	668	194
ENST00000318094	TOM1L2	chr17	17810761	-	ENST00000585101	ATPAF2	chr17	17928018	-	356	221	84	323	79
ENST00000318094	TOM1L2	chr17	17810761	-	ENST00000474627	ATPAF2	chr17	17928018	-	1208	221	84	668	194
ENST00000395739	TOM1L2	chr17	17810761	-	ENST00000585101	ATPAF2	chr17	17928018	-	363	228	91	330	79
ENST00000395739	TOM1L2	chr17	17810761	-	ENST00000474627	ATPAF2	chr17	17928018	-	1215	228	91	675	194
ENST00000535933	TOM1L2	chr17	17810761	-	ENST00000585101	ATPAF2	chr17	17928018	-	379	244	107	346	79
ENST00000535933	TOM1L2	chr17	17810761	-	ENST00000474627	ATPAF2	chr17	17928018	-	1231	244	107	691	194
ENST00000540946	TOM1L2	chr17	17810761	-	ENST00000585101	ATPAF2	chr17	17928018	-	356	221	84	323	79
ENST00000540946	TOM1L2	chr17	17810761	-	ENST00000474627	ATPAF2	chr17	17928018	-	1208	221	84	668	194
ENST00000542206	TOM1L2	chr17	17810761	-	ENST00000585101	ATPAF2	chr17	17928018	-	359	224	87	326	79
ENST00000542206	TOM1L2	chr17	17810761	-	ENST00000474627	ATPAF2	chr17	17928018	-	1211	224	87	671	194

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
ENST00000581396	ENST00000585101	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.06018523	0.93981475
ENST00000581396	ENST00000474627	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.007720587	0.9922794
ENST00000379504	ENST00000585101	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.05874586	0.9412542
ENST00000379504	ENST00000474627	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.007507675	0.9924924
ENST00000318094	ENST00000585101	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.05874586	0.9412542
ENST00000318094	ENST00000474627	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.007507675	0.9924924
ENST00000395739	ENST00000585101	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.061229646	0.93877035
ENST00000395739	ENST00000474627	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.007343112	0.9926569
ENST00000535933	ENST00000585101	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.081794046	0.9182059
ENST00000535933	ENST00000474627	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.008456423	0.99154353
ENST00000540946	ENST00000585101	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.05874586	0.9412542
ENST00000540946	ENST00000474627	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.007507675	0.9924924
ENST00000542206	ENST00000585101	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.06342406	0.93657595
ENST00000542206	ENST00000474627	TOM1L2	chr17	17810760	-	ATPAF2	chr17	17928018	-	0.007742947	0.9922571
ENST00000581396	ENST00000585101	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.06018523	0.93981475
ENST00000581396	ENST00000474627	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.007720587	0.9922794
ENST00000379504	ENST00000585101	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.05874586	0.9412542
ENST00000379504	ENST00000474627	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.007507675	0.9924924
ENST00000318094	ENST00000585101	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.05874586	0.9412542
ENST00000318094	ENST00000474627	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.007507675	0.9924924
ENST00000395739	ENST00000585101	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.061229646	0.93877035
ENST00000395739	ENST00000474627	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.007343112	0.9926569
ENST00000535933	ENST00000585101	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.081794046	0.9182059
ENST00000535933	ENST00000474627	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.008456423	0.99154353
ENST00000540946	ENST00000585101	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.05874586	0.9412542
ENST00000540946	ENST00000474627	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.007507675	0.9924924
ENST00000542206	ENST00000585101	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.06342406	0.93657595
ENST00000542206	ENST00000474627	TOM1L2	chr17	17810761	-	ATPAF2	chr17	17928018	-	0.007742947	0.9922571

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>92997_92997_1_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000318094_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

--------------------------------------------------------------

>92997_92997_2_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000318094_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_3_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000379504_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

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>92997_92997_4_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000379504_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_5_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000395739_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

--------------------------------------------------------------

>92997_92997_6_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000395739_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_7_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000535933_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

--------------------------------------------------------------

>92997_92997_8_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000535933_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_9_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000540946_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

--------------------------------------------------------------

>92997_92997_10_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000540946_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_11_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000542206_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

--------------------------------------------------------------

>92997_92997_12_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000542206_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_13_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000581396_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

--------------------------------------------------------------

>92997_92997_14_TOM1L2-ATPAF2_TOM1L2_chr17_17810760_ENST00000581396_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_15_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000318094_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

--------------------------------------------------------------

>92997_92997_16_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000318094_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_17_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000379504_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

--------------------------------------------------------------

>92997_92997_18_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000379504_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_19_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000395739_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

--------------------------------------------------------------

>92997_92997_20_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000395739_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_21_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000535933_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

--------------------------------------------------------------

>92997_92997_22_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000535933_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_23_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000540946_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

--------------------------------------------------------------

>92997_92997_24_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000540946_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_25_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000542206_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

--------------------------------------------------------------

>92997_92997_26_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000542206_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

--------------------------------------------------------------

>92997_92997_27_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000581396_ATPAF2_chr17_17928018_ENST00000474627_length(amino acids)=194AA_BP=46
MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP
AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL

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>92997_92997_28_TOM1L2-ATPAF2_TOM1L2_chr17_17810761_ENST00000581396_ATPAF2_chr17_17928018_ENST00000585101_length(amino acids)=79AA_BP=46

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:17810761/chr17:17928018)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	ATPAF2 Q8N5M1
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.	FUNCTION: May play a role in the assembly of the F1 component of the mitochondrial ATP synthase (ATPase). {ECO:0000269\|PubMed:11410595}.

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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000318094

20_152

45.666666666666664

463.0

Domain

VHS

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000318094

219_307

45.666666666666664

463.0

Domain

GAT

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000379504

20_152

45.666666666666664

508.0

Domain

VHS

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000379504

219_307

45.666666666666664

508.0

Domain

GAT

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000395739

20_152

45.666666666666664

463.0

Domain

VHS

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000395739

219_307

45.666666666666664

463.0

Domain

GAT

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000478943

20_152

241.0

Domain

VHS

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000478943

219_307

241.0

Domain

GAT

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000581396

20_152

45.666666666666664

458.0

Domain

VHS

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000581396

219_307

45.666666666666664

458.0

Domain

GAT

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000318094

20_152

45.666666666666664

463.0

Domain

VHS

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000318094

219_307

45.666666666666664

463.0

Domain

GAT

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000379504

20_152

45.666666666666664

508.0

Domain

VHS

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000379504

219_307

45.666666666666664

508.0

Domain

GAT

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000395739

20_152

45.666666666666664

463.0

Domain

VHS

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000395739

219_307

45.666666666666664

463.0

Domain

GAT

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000478943

20_152

241.0

Domain

VHS

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000478943

219_307

241.0

Domain

GAT

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000581396

20_152

45.666666666666664

458.0

Domain

VHS

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000581396

219_307

45.666666666666664

458.0

Domain

GAT

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000318094

329_334

45.666666666666664

463.0

Motif

Note=Clathrin-binding

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000379504

329_334

45.666666666666664

508.0

Motif

Note=Clathrin-binding

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000395739

329_334

45.666666666666664

463.0

Motif

Note=Clathrin-binding

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000478943

329_334

241.0

Motif

Note=Clathrin-binding

Hgene

TOM1L2

chr17:17810760

chr17:17928018

ENST00000581396

329_334

45.666666666666664

458.0

Motif

Note=Clathrin-binding

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000318094

329_334

45.666666666666664

463.0

Motif

Note=Clathrin-binding

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000379504

329_334

45.666666666666664

508.0

Motif

Note=Clathrin-binding

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000395739

329_334

45.666666666666664

463.0

Motif

Note=Clathrin-binding

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000478943

329_334

241.0

Motif

Note=Clathrin-binding

Hgene

TOM1L2

chr17:17810761

chr17:17928018

ENST00000581396

329_334

45.666666666666664

458.0

Motif

Note=Clathrin-binding

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>247_TOM1L2_17810761_ATPAF2_17928018_ranked_0.pdb	TOM1L2	17810761	17810761	ENST00000474627	ATPAF2	chr17	17928018	-	MEFLLGNPFSTPVGQCLEKATDGSLQSEDWTLNMEICDIINETEEGYRVEEPETLVELQRNEWDPIIEWAEKRYGVEISSSTSIMGPSIP AKTREVLVSHLASYNTWALQGIEFVAAQLKSMVLTLGLIDLRLTVEQAVLLSRLEEEYQIQKWGNIEWAHDYELQELRARTAAGTLFIHL	194

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

TOM1L2_pLDDT.png

ATPAF2_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
TOM1L2
ATPAF2

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to TOM1L2-ATPAF2

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 TOM1L2-ATPAF2

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