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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:SKI-ATAD3A

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SKI-ATAD3A
	FusionPDB ID: 82081
	FusionGDB2.0 ID: 82081
		Hgene	Tgene
	Gene symbol	SKI	ATAD3A
	Gene ID	6497	55210
	Gene name	SKI proto-oncogene	ATPase family AAA domain containing 3A
	Synonyms	SGS\|SKV	HAYOS
	Cytomap	1p36.33-p36.32	1p36.33
	Type of gene	protein-coding	protein-coding
	Description	ski oncogeneproto-oncogene c-Skiski oncoproteinv-ski avian sarcoma viral oncogene homolog	ATPase family AAA domain-containing protein 3A
	Modification date	20200329	20200320
	UniProtAcc	SKIDA1,C10orf140	Q9NVI7
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000378536, ENST00000478223,	ENST00000378755, ENST00000378756, ENST00000536055,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 8 X 8=896	5 X 5 X 4=100
	# samples	17	5
	** MAII score	log2(17/896*10)=-2.3979639859199 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: SKI [Title/Abstract] AND ATAD3A [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SKI(2161174)-ATAD3A(1454301), # samples:2
Anticipated loss of major functional domain due to fusion event.	SKI-ATAD3A 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. SKI-ATAD3A 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. SKI-ATAD3A 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. SKI-ATAD3A 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	SKI	GO:0000122	negative regulation of transcription by RNA polymerase II	17469184
Hgene	SKI	GO:0008285	negative regulation of cell proliferation	11430826
Hgene	SKI	GO:0014902	myotube differentiation	19008232
Hgene	SKI	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	17469184
Hgene	SKI	GO:0030514	negative regulation of BMP signaling pathway	14699069
Hgene	SKI	GO:0032926	negative regulation of activin receptor signaling pathway	14699069
Hgene	SKI	GO:0043388	positive regulation of DNA binding	15107821
Hgene	SKI	GO:0045668	negative regulation of osteoblast differentiation	14699069
Hgene	SKI	GO:0060395	SMAD protein signal transduction	12874272

Fusion gene breakpoints across SKI (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 ATAD3A (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	UCS	TCGA-N5-A59F-01A	SKI	chr1	2161174	+	ATAD3A	chr1	1454301	+
ChimerDB4	UCS	TCGA-N5-A59F	SKI	chr1	2161174	+	ATAD3A	chr1	1454301	+

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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)

ENST00000378536

SKI

chr1

2161174

ENST00000378756

ATAD3A

chr1

1454301

2971

1041

2357

761

ENST00000378536

SKI

chr1

2161174

ENST00000378755

ATAD3A

chr1

1454301

2971

1041

2357

761

ENST00000378536

SKI

chr1

2161174

ENST00000536055

ATAD3A

chr1

1454301

2973

1041

2357

761

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
ENST00000378536	ENST00000378756	SKI	chr1	2161174	+	ATAD3A	chr1	1454301	+	0.022435093	0.97756493
ENST00000378536	ENST00000378755	SKI	chr1	2161174	+	ATAD3A	chr1	1454301	+	0.022435093	0.97756493
ENST00000378536	ENST00000536055	SKI	chr1	2161174	+	ATAD3A	chr1	1454301	+	0.022460729	0.9775393

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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

>82081_82081_1_SKI-ATAD3A_SKI_chr1_2161174_ENST00000378536_ATAD3A_chr1_1454301_ENST00000378755_length(amino acids)=761AA_BP=323
MEAAAGGRGCFQPHPGLQKTLEQFHLSSMSSLGGPAAFSARWAQEAYKKESAKEAGAAAVPAPVPAATEPPPVLHLPAIQPPPPVLPGPF
FMPSDRSTERCETVLEGETISCFVVGGEKRLCLPQILNSVLRDFSLQQINAVCDELHIYCSRCTADQLEILKVMGILPFSAPSCGLITKT
DAERLCNALLYGGAYPPPCKKELAASLALGLELSERSVRVYHECFGKCKGLLVPELYSSPSAACIQCLDCRLMYPPHKFVVHSHKALENR
TCHWGFDSANWRAYILLSQDYTGKEEQARLGRCLDDVKEKFDYGNKYKRRVPRQLLNEENLRKQEESVQKQEAMRRATVEREMELRHKNE
MLRVEAEARARAKAERENADIIREQIRLKAAEHRQTVLESIRTAGTLFGEGFRAFVTDWDKVTATVAGLTLLAVGVYSAKNATLVAGRFI
EARLGKPSLVRETSRITVLEALRHPIQVSRRLLSRPQDALEGVVLSPSLEARVRDIAIATRNTKKNRSLYRNILMYGPPGTGKTLFAKKL
ALHSGMDYAIMTGGDVAPMGREGVTAMHKLFDWANTSRRGLLLFVDEADAFLRKRATEKISEDLRATLNAFLYRTGQHSNKFMLVLASNQ
PEQFDWAINDRINEMVHFDLPGQEERERLVRMYFDKYVLKPATEGKQRLKLAQFDYGRKCSEVARLTEGMSGREIAQLAVSWQATAYASE

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

>82081_82081_2_SKI-ATAD3A_SKI_chr1_2161174_ENST00000378536_ATAD3A_chr1_1454301_ENST00000378756_length(amino acids)=761AA_BP=323
MEAAAGGRGCFQPHPGLQKTLEQFHLSSMSSLGGPAAFSARWAQEAYKKESAKEAGAAAVPAPVPAATEPPPVLHLPAIQPPPPVLPGPF
FMPSDRSTERCETVLEGETISCFVVGGEKRLCLPQILNSVLRDFSLQQINAVCDELHIYCSRCTADQLEILKVMGILPFSAPSCGLITKT
DAERLCNALLYGGAYPPPCKKELAASLALGLELSERSVRVYHECFGKCKGLLVPELYSSPSAACIQCLDCRLMYPPHKFVVHSHKALENR
TCHWGFDSANWRAYILLSQDYTGKEEQARLGRCLDDVKEKFDYGNKYKRRVPRQLLNEENLRKQEESVQKQEAMRRATVEREMELRHKNE
MLRVEAEARARAKAERENADIIREQIRLKAAEHRQTVLESIRTAGTLFGEGFRAFVTDWDKVTATVAGLTLLAVGVYSAKNATLVAGRFI
EARLGKPSLVRETSRITVLEALRHPIQVSRRLLSRPQDALEGVVLSPSLEARVRDIAIATRNTKKNRSLYRNILMYGPPGTGKTLFAKKL
ALHSGMDYAIMTGGDVAPMGREGVTAMHKLFDWANTSRRGLLLFVDEADAFLRKRATEKISEDLRATLNAFLYRTGQHSNKFMLVLASNQ
PEQFDWAINDRINEMVHFDLPGQEERERLVRMYFDKYVLKPATEGKQRLKLAQFDYGRKCSEVARLTEGMSGREIAQLAVSWQATAYASE

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

>82081_82081_3_SKI-ATAD3A_SKI_chr1_2161174_ENST00000378536_ATAD3A_chr1_1454301_ENST00000536055_length(amino acids)=761AA_BP=323
MEAAAGGRGCFQPHPGLQKTLEQFHLSSMSSLGGPAAFSARWAQEAYKKESAKEAGAAAVPAPVPAATEPPPVLHLPAIQPPPPVLPGPF
FMPSDRSTERCETVLEGETISCFVVGGEKRLCLPQILNSVLRDFSLQQINAVCDELHIYCSRCTADQLEILKVMGILPFSAPSCGLITKT
DAERLCNALLYGGAYPPPCKKELAASLALGLELSERSVRVYHECFGKCKGLLVPELYSSPSAACIQCLDCRLMYPPHKFVVHSHKALENR
TCHWGFDSANWRAYILLSQDYTGKEEQARLGRCLDDVKEKFDYGNKYKRRVPRQLLNEENLRKQEESVQKQEAMRRATVEREMELRHKNE
MLRVEAEARARAKAERENADIIREQIRLKAAEHRQTVLESIRTAGTLFGEGFRAFVTDWDKVTATVAGLTLLAVGVYSAKNATLVAGRFI
EARLGKPSLVRETSRITVLEALRHPIQVSRRLLSRPQDALEGVVLSPSLEARVRDIAIATRNTKKNRSLYRNILMYGPPGTGKTLFAKKL
ALHSGMDYAIMTGGDVAPMGREGVTAMHKLFDWANTSRRGLLLFVDEADAFLRKRATEKISEDLRATLNAFLYRTGQHSNKFMLVLASNQ
PEQFDWAINDRINEMVHFDLPGQEERERLVRMYFDKYVLKPATEGKQRLKLAQFDYGRKCSEVARLTEGMSGREIAQLAVSWQATAYASE

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

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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/chr1:2161174/chr1:1454301)
- 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
SKI SKIDA1,C10orf140	ATAD3A Q9NVI7
908	FUNCTION: Essential for mitochondrial network organization, mitochondrial metabolism and cell growth at organism and cellular level. May play an important role in mitochondrial protein synthesis. May also participate in mitochondrial DNA replication. May bind to mitochondrial DNA D-loops and contribute to nucleoid stability. Required for enhanced channeling of cholesterol for hormone-dependent steroidogenesis. Involved in mitochondrial-mediated antiviral innate immunity (PubMed:31522117). {ECO:0000269\|PubMed:17210950, ECO:0000269\|PubMed:20154147, ECO:0000269\|PubMed:22453275, ECO:0000269\|PubMed:31522117}.

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

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000536055

139_267

69.0

508.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000378755

400_407

196.0

635.0

Nucleotide binding

ATP

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000378756

400_407

148.0

587.0

Nucleotide binding

ATP

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000536055

400_407

69.0

508.0

Nucleotide binding

ATP

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000378755

338_353

196.0

635.0

Region

Note=S100B-binding

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000378756

338_353

148.0

587.0

Region

Note=S100B-binding

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000536055

338_353

69.0

508.0

Region

Note=S100B-binding

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000378755

313_634

196.0

635.0

Topological domain

Mitochondrial matrix

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000378756

313_634

148.0

587.0

Topological domain

Mitochondrial matrix

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000536055

313_634

69.0

508.0

Topological domain

Mitochondrial matrix

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000378755

295_312

196.0

635.0

Transmembrane

Helical

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000378756

295_312

148.0

587.0

Transmembrane

Helical

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000536055

295_312

69.0

508.0

Transmembrane

Helical

- 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

SKI

chr1:2161174

chr1:1454301

ENST00000378536

536_710

323.0

729.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000378755

139_267

196.0

635.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000378756

139_267

148.0

587.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000378755

2_294

196.0

635.0

Topological domain

Mitochondrial intermembrane

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000378756

2_294

148.0

587.0

Topological domain

Mitochondrial intermembrane

Tgene

ATAD3A

chr1:2161174

chr1:1454301

ENST00000536055

2_294

69.0

508.0

Topological domain

Mitochondrial intermembrane

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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 >>>1532_SKI_2161174_ATAD3A_1454301_ranked_0.pdb	SKI	2161174	2161174	ENST00000536055	ATAD3A	chr1	1454301	+	MEAAAGGRGCFQPHPGLQKTLEQFHLSSMSSLGGPAAFSARWAQEAYKKESAKEAGAAAVPAPVPAATEPPPVLHLPAIQPPPPVLPGPF FMPSDRSTERCETVLEGETISCFVVGGEKRLCLPQILNSVLRDFSLQQINAVCDELHIYCSRCTADQLEILKVMGILPFSAPSCGLITKT DAERLCNALLYGGAYPPPCKKELAASLALGLELSERSVRVYHECFGKCKGLLVPELYSSPSAACIQCLDCRLMYPPHKFVVHSHKALENR TCHWGFDSANWRAYILLSQDYTGKEEQARLGRCLDDVKEKFDYGNKYKRRVPRQLLNEENLRKQEESVQKQEAMRRATVEREMELRHKNE MLRVEAEARARAKAERENADIIREQIRLKAAEHRQTVLESIRTAGTLFGEGFRAFVTDWDKVTATVAGLTLLAVGVYSAKNATLVAGRFI EARLGKPSLVRETSRITVLEALRHPIQVSRRLLSRPQDALEGVVLSPSLEARVRDIAIATRNTKKNRSLYRNILMYGPPGTGKTLFAKKL ALHSGMDYAIMTGGDVAPMGREGVTAMHKLFDWANTSRRGLLLFVDEADAFLRKRATEKISEDLRATLNAFLYRTGQHSNKFMLVLASNQ PEQFDWAINDRINEMVHFDLPGQEERERLVRMYFDKYVLKPATEGKQRLKLAQFDYGRKCSEVARLTEGMSGREIAQLAVSWQATAYASE	761

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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.

SKI_pLDDT.png

ATAD3A_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
SKI
ATAD3A

- 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 SKI-ATAD3A

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 SKI-ATAD3A

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