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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:SP3-OLA1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SP3-OLA1
	FusionPDB ID: 85400
	FusionGDB2.0 ID: 85400
		Hgene	Tgene
	Gene symbol	SP3	OLA1
	Gene ID	6670	29789
	Gene name	Sp3 transcription factor	Obg like ATPase 1
	Synonyms	SPR2	DOC45\|GBP45\|GTBP9\|GTPBP9\|PTD004
	Cytomap	2q31.1	2q31.1
	Type of gene	protein-coding	protein-coding
	Description	transcription factor Sp3GC-binding transcription factor Sp3specificity protein 3	obg-like ATPase 1DNA damage-regulated overexpressed in cancer 45 proteinGTP-binding protein 9 (putative)GTP-binding protein PTD004homologous yeast-44.2 protein
	Modification date	20200313	20200313
	UniProtAcc	Q02447	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000310015, ENST00000418194, ENST00000455789, ENST00000483084,	ENST00000344357, ENST00000409546, ENST00000428402, ENST00000392560, ENST00000284719,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	12 X 8 X 9=864	14 X 8 X 7=784
	# samples	18	14
	** MAII score	log2(18/864*10)=-2.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(14/784*10)=-2.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: SP3 [Title/Abstract] AND OLA1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SP3(174819601)-OLA1(175006728), # samples:4 OLA1(175087761)-SP3(174820960), # samples:1
Anticipated loss of major functional domain due to fusion event.	OLA1-SP3 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. OLA1-SP3 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. SP3-OLA1 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. SP3-OLA1 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. SP3-OLA1 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. SP3-OLA1 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. SP3-OLA1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF. OLA1-SP3 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
Hgene	SP3	GO:0006355	regulation of transcription, DNA-templated	12560508
Hgene	SP3	GO:0045893	positive regulation of transcription, DNA-templated	12771217
Tgene	OLA1	GO:0046034	ATP metabolic process	17430889

Fusion gene breakpoints across SP3 (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 OLA1 (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	BRCA	TCGA-AO-A12F-01A	SP3	chr2	174819601	-	OLA1	chr2	175006728	-
ChimerDB4	CESC	TCGA-DS-A3LQ-01A	SP3	chr2	174819601	-	OLA1	chr2	175006728	-

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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)
ENST00000310015	SP3	chr2	174819601	-	ENST00000284719	OLA1	chr2	175006728	-	5967	2170	510	2987	825
ENST00000418194	SP3	chr2	174819601	-	ENST00000284719	OLA1	chr2	175006728	-	5616	1819	360	2636	758

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
ENST00000310015	ENST00000284719	SP3	chr2	174819601	-	OLA1	chr2	175006728	-	0.000217632	0.9997824
ENST00000418194	ENST00000284719	SP3	chr2	174819601	-	OLA1	chr2	175006728	-	0.00030224	0.9996978

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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

>85400_85400_1_SP3-OLA1_SP3_chr2_174819601_ENST00000310015_OLA1_chr2_175006728_ENST00000284719_length(amino acids)=825AA_BP=553
MRCPKHTMTAPEKPVKQEEMAALDVDSGGGGGGGGGHGEYLQQQQQHGNGAVAAAAAAQDTQPSPLALLAATCSKIGPPSPGDDEEEAAA
AAGAPAAAGATGDLASAQLGGAPNRWEVLSATPTTIKDEAGNLVQIPSAATSSGQYVLPLQNLQNQQIFSVAPGSDSSNGTVSSVQYQVI
PQIQSADGQQVQIGFTGSSDNGGINQESSQIQIIPGSNQTLLASGTPSANIQNLIPQTGQVQVQGVAIGGSSFPGQTQVVANVPLGLPGN
ITFVPINSVDLDSLGLSGSSQTMTAGINADGHLINTGQAMDSSDNSERTGERVSPDINETNTDTDLFVPTSSSSQLPVTIDSTGILQQNT
NSLTTSSGQVHSSDLQGNYIQSPVSEETQAQNIQVSTAQPVVQHLQLQESQQPTSQAQIVQGITPQTIHGVQASGQNISQQALQNLQLQL
NPGTFLIQAQTVTPSGQVTWQTFQVQGVQNLQNLQIQNTAAQQITLTPVQTLTLGQVAAGGAFTSTPVSLSTGQLPNLQTVTVNSIDSAG
IQLHPGENADSPAGAFEDDDITHVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQKKPVR
FYHDWNDKEIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALELKLQELSAEERQKYLEANMTQSA
LPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQAAGKIHTDFEKGFIMAEVMKYEDFKEEGSENAVKAAGKYRQQGRNYIVEDGD

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

>85400_85400_2_SP3-OLA1_SP3_chr2_174819601_ENST00000418194_OLA1_chr2_175006728_ENST00000284719_length(amino acids)=758AA_BP=486
MLAATCSKIGPPSPGDDEEEAAAAAGAPAAAGATGDLASAQLGGAPNRWEVLSATPTTIKDEAGNLVQIPSAATSSGQYVLPLQNLQNQQ
IFSVAPGSDSSNGTVSSVQYQVIPQIQSADGQQVQIGFTGSSDNGGINQESSQIQIIPGSNQTLLASGTPSANIQNLIPQTGQVQVQGVA
IGGSSFPGQTQVVANVPLGLPGNITFVPINSVDLDSLGLSGSSQTMTAGINADGHLINTGQAMDSSDNSERTGERVSPDINETNTDTDLF
VPTSSSSQLPVTIDSTGILQQNTNSLTTSSGQVHSSDLQGNYIQSPVSEETQAQNIQVSTAQPVVQHLQLQESQQPTSQAQIVQGITPQT
IHGVQASGQNISQQALQNLQLQLNPGTFLIQAQTVTPSGQVTWQTFQVQGVQNLQNLQIQNTAAQQITLTPVQTLTLGQVAAGGAFTSTP
VSLSTGQLPNLQTVTVNSIDSAGIQLHPGENADSPAGAFEDDDITHVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDKLEKVAVRGGDKK
LKPEYDIMCKVKSWVIDQKKPVRFYHDWNDKEIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALE
LKLQELSAEERQKYLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQAAGKIHTDFEKGFIMAEVMKYEDFKEEGS

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

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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/chr2:174819601/chr2:175006728)
- 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
SP3 Q02447	.
FUNCTION: Transcriptional factor that can act as an activator or repressor depending on isoform and/or post-translational modifications. Binds to GT and GC boxes promoter elements. Competes with SP1 for the GC-box promoters. Weak activator of transcription but can activate a number of genes involved in different processes such as cell-cycle regulation, hormone-induction and house-keeping. {ECO:0000269\|PubMed:10391891, ECO:0000269\|PubMed:11812829, ECO:0000269\|PubMed:12419227, ECO:0000269\|PubMed:12837748, ECO:0000269\|PubMed:15247228, ECO:0000269\|PubMed:15494207, ECO:0000269\|PubMed:15554904, ECO:0000269\|PubMed:16781829, ECO:0000269\|PubMed:17548428, ECO:0000269\|PubMed:18187045, ECO:0000269\|PubMed:18617891, ECO:0000269\|PubMed:9278495}.	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.

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

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000310015

21_31

546.3333333333334

782.0

Compositional bias

Note=Poly-Gly

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000310015

35_39

546.3333333333334

782.0

Compositional bias

Note=Poly-Gln

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000310015

44_100

546.3333333333334

782.0

Compositional bias

Note=Ala-rich

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000455789

21_31

493.3333333333333

729.0

Compositional bias

Note=Poly-Gly

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000455789

35_39

493.3333333333333

729.0

Compositional bias

Note=Poly-Gln

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000455789

44_100

493.3333333333333

729.0

Compositional bias

Note=Ala-rich

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000310015

461_469

546.3333333333334

782.0

Motif

9aaTAD

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000455789

461_469

493.3333333333333

729.0

Motif

9aaTAD

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000310015

138_237

546.3333333333334

782.0

Region

Note=Transactivation domain (Gln-rich)

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000310015

350_499

546.3333333333334

782.0

Region

Note=Transactivation domain (Gln-rich)

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000455789

138_237

493.3333333333333

729.0

Region

Note=Transactivation domain (Gln-rich)

Tgene

OLA1

chr2:174819601

chr2:175006728

ENST00000284719

304_387

124.33333333333333

397.0

Domain

TGS

Tgene

OLA1

chr2:174819601

chr2:175006728

ENST00000344357

23_283

239.0

Domain

OBG-type G

Tgene

OLA1

chr2:174819601

chr2:175006728

ENST00000344357

304_387

239.0

Domain

TGS

Tgene

OLA1

chr2:174819601

chr2:175006728

ENST00000428402

304_387

124.33333333333333

279.0

Domain

TGS

Tgene

OLA1

chr2:174819601

chr2:175006728

ENST00000284719

267_274

124.33333333333333

397.0

Motif

Nuclear export signal

Tgene

OLA1

chr2:174819601

chr2:175006728

ENST00000344357

267_274

239.0

Motif

Nuclear export signal

Tgene

OLA1

chr2:174819601

chr2:175006728

ENST00000428402

267_274

124.33333333333333

279.0

Motif

Nuclear export signal

Tgene

OLA1

chr2:174819601

chr2:175006728

ENST00000344357

32_37

239.0

Nucleotide binding

ATP

- 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

SP3

chr2:174819601

chr2:175006728

ENST00000310015

534_620

546.3333333333334

782.0

Region

Note=Repressor domain

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000455789

350_499

493.3333333333333

729.0

Region

Note=Transactivation domain (Gln-rich)

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000455789

534_620

493.3333333333333

729.0

Region

Note=Repressor domain

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000310015

621_645

546.3333333333334

782.0

Zinc finger

C2H2-type 1

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000310015

651_675

546.3333333333334

782.0

Zinc finger

C2H2-type 2

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000310015

681_703

546.3333333333334

782.0

Zinc finger

C2H2-type 3

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000455789

621_645

493.3333333333333

729.0

Zinc finger

C2H2-type 1

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000455789

651_675

493.3333333333333

729.0

Zinc finger

C2H2-type 2

Hgene

SP3

chr2:174819601

chr2:175006728

ENST00000455789

681_703

493.3333333333333

729.0

Zinc finger

C2H2-type 3

Tgene

OLA1

chr2:174819601

chr2:175006728

ENST00000284719

23_283

124.33333333333333

397.0

Domain

OBG-type G

Tgene

OLA1

chr2:174819601

chr2:175006728

ENST00000428402

23_283

124.33333333333333

279.0

Domain

OBG-type G

Tgene

OLA1

chr2:174819601

chr2:175006728

ENST00000284719

32_37

124.33333333333333

397.0

Nucleotide binding

ATP

Tgene

OLA1

chr2:174819601

chr2:175006728

ENST00000428402

32_37

124.33333333333333

279.0

Nucleotide binding

ATP

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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 >>>1608_SP3_174819601_OLA1_175006728_ranked_0.pdb	SP3	174819601	174819601	ENST00000284719	OLA1	chr2	175006728	-	MRCPKHTMTAPEKPVKQEEMAALDVDSGGGGGGGGGHGEYLQQQQQHGNGAVAAAAAAQDTQPSPLALLAATCSKIGPPSPGDDEEEAAA AAGAPAAAGATGDLASAQLGGAPNRWEVLSATPTTIKDEAGNLVQIPSAATSSGQYVLPLQNLQNQQIFSVAPGSDSSNGTVSSVQYQVI PQIQSADGQQVQIGFTGSSDNGGINQESSQIQIIPGSNQTLLASGTPSANIQNLIPQTGQVQVQGVAIGGSSFPGQTQVVANVPLGLPGN ITFVPINSVDLDSLGLSGSSQTMTAGINADGHLINTGQAMDSSDNSERTGERVSPDINETNTDTDLFVPTSSSSQLPVTIDSTGILQQNT NSLTTSSGQVHSSDLQGNYIQSPVSEETQAQNIQVSTAQPVVQHLQLQESQQPTSQAQIVQGITPQTIHGVQASGQNISQQALQNLQLQL NPGTFLIQAQTVTPSGQVTWQTFQVQGVQNLQNLQIQNTAAQQITLTPVQTLTLGQVAAGGAFTSTPVSLSTGQLPNLQTVTVNSIDSAG IQLHPGENADSPAGAFEDDDITHVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQKKPVR FYHDWNDKEIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALELKLQELSAEERQKYLEANMTQSA LPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQAAGKIHTDFEKGFIMAEVMKYEDFKEEGSENAVKAAGKYRQQGRNYIVEDGD	825

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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.

SP3_pLDDT.png

OLA1_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
SP3
OLA1

- 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 SP3-OLA1

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 SP3-OLA1

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