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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:APTX-SNRPD2 (FusionGDB2 ID:5728)

Fusion Gene Summary for APTX-SNRPD2

Fusion gene summary

Fusion gene information	Fusion gene name: APTX-SNRPD2
	Fusion gene ID: 5728
		Hgene	Tgene
	Gene symbol	APTX	SNRPD2
	Gene ID	54840	6633
	Gene name	aprataxin	small nuclear ribonucleoprotein D2 polypeptide
	Synonyms	AOA\|AOA1\|AXA1\|EAOH\|EOAHA\|FHA-HIT	SMD2\|SNRPD1\|Sm-D2
	Cytomap	9p21.1	19q13.32
	Type of gene	protein-coding	protein-coding
	Description	aprataxinforkhead-associated domain histidine triad-like protein	small nuclear ribonucleoprotein Sm D2small nuclear ribonucleoprotein D2 polypeptide 16.5kDasnRNP core protein D2
	Modification date	20200320	20200322
	UniProtAcc	Q7Z2E3	.
	Ensembl transtripts involved in fusion gene	ENST00000309615, ENST00000379813, ENST00000379817, ENST00000379819, ENST00000379825, ENST00000397172, ENST00000436040, ENST00000463596, ENST00000468275, ENST00000473270, ENST00000476858,	ENST00000342669, ENST00000391932, ENST00000585392, ENST00000587367, ENST00000587579, ENST00000588301, ENST00000588599, ENST00000590212,
Fusion gene scores	* DoF score	10 X 9 X 6=540	11 X 10 X 4=440
	# samples	12	12
	** MAII score	log2(12/540*10)=-2.16992500144231 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(12/440*10)=-1.87446911791614 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: APTX [Title/Abstract] AND SNRPD2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	APTX(32986029)-SNRPD2(46190718), # samples:1
Anticipated loss of major functional domain due to fusion event.

* 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	APTX	GO:0000012	single strand break repair	17519253
Hgene	APTX	GO:0042542	response to hydrogen peroxide	15044383
Tgene	SNRPD2	GO:0000387	spliceosomal snRNP assembly	18984161
Tgene	SNRPD2	GO:0000398	mRNA splicing, via spliceosome	28076346

Fusion gene breakpoints across APTX (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 SNRPD2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChiTaRS5.0	N/A	AA536202	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+

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Fusion Gene ORF analysis for APTX-SNRPD2

Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
intron-3UTR	ENST00000309615	ENST00000342669	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-3UTR	ENST00000379813	ENST00000342669	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-3UTR	ENST00000379817	ENST00000342669	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-3UTR	ENST00000379819	ENST00000342669	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-3UTR	ENST00000379825	ENST00000342669	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-3UTR	ENST00000397172	ENST00000342669	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-3UTR	ENST00000436040	ENST00000342669	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-3UTR	ENST00000463596	ENST00000342669	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-3UTR	ENST00000468275	ENST00000342669	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-3UTR	ENST00000473270	ENST00000342669	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-3UTR	ENST00000476858	ENST00000342669	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000309615	ENST00000391932	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000309615	ENST00000585392	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000309615	ENST00000587367	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000309615	ENST00000587579	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000309615	ENST00000588301	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000309615	ENST00000588599	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000309615	ENST00000590212	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379813	ENST00000391932	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379813	ENST00000585392	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379813	ENST00000587367	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379813	ENST00000587579	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379813	ENST00000588301	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379813	ENST00000588599	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379813	ENST00000590212	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379817	ENST00000391932	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379817	ENST00000585392	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379817	ENST00000587367	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379817	ENST00000587579	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379817	ENST00000588301	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379817	ENST00000588599	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379817	ENST00000590212	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379819	ENST00000391932	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379819	ENST00000585392	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379819	ENST00000587367	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379819	ENST00000587579	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379819	ENST00000588301	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379819	ENST00000588599	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379819	ENST00000590212	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379825	ENST00000391932	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379825	ENST00000585392	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379825	ENST00000587367	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379825	ENST00000587579	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379825	ENST00000588301	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379825	ENST00000588599	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000379825	ENST00000590212	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000397172	ENST00000391932	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000397172	ENST00000585392	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000397172	ENST00000587367	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000397172	ENST00000587579	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000397172	ENST00000588301	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000397172	ENST00000588599	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000397172	ENST00000590212	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000436040	ENST00000391932	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000436040	ENST00000585392	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000436040	ENST00000587367	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000436040	ENST00000587579	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000436040	ENST00000588301	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000436040	ENST00000588599	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000436040	ENST00000590212	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000463596	ENST00000391932	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000463596	ENST00000585392	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000463596	ENST00000587367	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000463596	ENST00000587579	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000463596	ENST00000588301	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000463596	ENST00000588599	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000463596	ENST00000590212	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000468275	ENST00000391932	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000468275	ENST00000585392	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000468275	ENST00000587367	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000468275	ENST00000587579	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000468275	ENST00000588301	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000468275	ENST00000588599	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000468275	ENST00000590212	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000473270	ENST00000391932	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000473270	ENST00000585392	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000473270	ENST00000587367	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000473270	ENST00000587579	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000473270	ENST00000588301	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000473270	ENST00000588599	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000473270	ENST00000590212	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000476858	ENST00000391932	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000476858	ENST00000585392	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000476858	ENST00000587367	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000476858	ENST00000587579	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000476858	ENST00000588301	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000476858	ENST00000588599	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+
intron-intron	ENST00000476858	ENST00000590212	APTX	chr9	32986029	-	SNRPD2	chr19	46190718	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)

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

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Fusion Genomic Features for APTX-SNRPD2

FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for APTX-SNRPD2

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:32986029/:46190718)
- 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
APTX Q7Z2E3	.
FUNCTION: DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair and base excision repair (PubMed:15380105, PubMed:15044383, PubMed:16964241, PubMed:17276982, PubMed:24362567). Resolves abortive DNA ligation intermediates formed either at base excision sites, or when DNA ligases attempt to repair non-ligatable breaks induced by reactive oxygen species (PubMed:16964241, PubMed:24362567). Catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined (PubMed:16964241, PubMed:17276982, PubMed:24362567). Also able to hydrolyze adenosine 5'-monophosphoramidate (AMP-NH(2)) and diadenosine tetraphosphate (AppppA), but with lower catalytic activity (PubMed:16547001). Likewise, catalyzes the release of 3'-linked guanosine (DNAppG) and inosine (DNAppI) from DNA, but has higher specific activity with 5'-linked adenosine (AppDNA) (By similarity). {ECO:0000250\|UniProtKB:O74859, ECO:0000269\|PubMed:15044383, ECO:0000269\|PubMed:15380105, ECO:0000269\|PubMed:16547001, ECO:0000269\|PubMed:16964241, ECO:0000269\|PubMed:17276982, ECO:0000269\|PubMed:24362567}.	FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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.

- In-frame and 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

- In-frame and 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

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Fusion Gene Sequence for APTX-SNRPD2

For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for APTX-SNRPD2

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 (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for APTX-SNRPD2

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for APTX-SNRPD2

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source