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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:SPATA7-GABRA3

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SPATA7-GABRA3
	FusionPDB ID: 85586
	FusionGDB2.0 ID: 85586
		Hgene	Tgene
	Gene symbol	SPATA7	GABRA3
	Gene ID	55812	2556
	Gene name	spermatogenesis associated 7	gamma-aminobutyric acid type A receptor subunit alpha3
	Synonyms	HEL-S-296\|HSD-3.1\|HSD3\|LCA3	-
	Cytomap	14q31.3	Xq28
	Type of gene	protein-coding	protein-coding
	Description	spermatogenesis-associated protein 7epididymis secretory protein Li 296epididymis secretory sperm binding proteinspermatogenesis-associated protein HSD3	gamma-aminobutyric acid receptor subunit alpha-3GABA(A) receptor subunit alpha-3GABA(A) receptor, alpha 3gamma-aminobutyric acid (GABA) A receptor, alpha 3gamma-aminobutyric acid type A receptor alpha3 subunitgamma-animobutyric acid (GABA) A receptor
	Modification date	20200328	20200313
	UniProtAcc	.	P34903
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000045347, ENST00000356583, ENST00000393545, ENST00000556553, ENST00000554102,	ENST00000497894, ENST00000535043, ENST00000370314,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 3 X 3=27	8 X 6 X 6=288
	# samples	3	7
	** MAII score	log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(7/288*10)=-2.04064198449735 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: SPATA7 [Title/Abstract] AND GABRA3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SPATA7(88904247)-GABRA3(151337035), # samples:1
Anticipated loss of major functional domain due to fusion event.	SPATA7-GABRA3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. SPATA7-GABRA3 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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

Fusion gene breakpoints across SPATA7 (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 GABRA3 (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-A7-A4SA-01A	SPATA7	chr14	88904247	-	GABRA3	chrX	151337035	-

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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)
ENST00000393545	SPATA7	chr14	88904247	-	ENST00000535043	GABRA3	chrX	151337035	-	2393	2057	289	2022	577
ENST00000356583	SPATA7	chr14	88904247	-	ENST00000370314	GABRA3	chrX	151337035	-	4179	1849	175	1812	545
ENST00000045347	SPATA7	chr14	88904247	-	ENST00000370314	GABRA3	chrX	151337035	-	3611	1281	0	1616	538

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
ENST00000393545	ENST00000535043	SPATA7	chr14	88904247	-	GABRA3	chrX	151337035	-	0.002710931	0.99728906
ENST00000356583	ENST00000370314	SPATA7	chr14	88904247	-	GABRA3	chrX	151337035	-	0.001053594	0.99894637
ENST00000045347	ENST00000370314	SPATA7	chr14	88904247	-	GABRA3	chrX	151337035	-	0.001822319	0.99817765

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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

>85586_85586_1_SPATA7-GABRA3_SPATA7_chr14_88904247_ENST00000045347_GABRA3_chrX_151337035_ENST00000370314_length(amino acids)=538AA_BP=427
MDGSRRVRATSVLPRYGPPCLFKGHLSTKSNAFCTDSSSLRLSTLQLVKNHMAVHYNKILSAKAAVDCSVPVSVSTSIKYADQQRREKLK
KELAQCEKEFKLTKTAMRANYKNNSKSLFNTLQKPSGEPQIEDDMLKEEMNGFSSFARSLVPSSERLHLSLHKSSKVITNGPEKNSSSSP
SSVDYAASGPRKLSSGALYGRRPRSTFPNSHRFQLVISKAPSGDLLDKHSELFSNKQLPFTPRTLKTEAKSFLSQYRYYTPAKRKKDFTD
QRIEAETQTELSFKSELGTAETKNMTDSEMNIKQASNCVTYDAKEKIAPLPLEGHDSTWDEIKDDALQHSSPRAMCQYSLKPPSTRKIYS
DEEELLYLSFIEDVTDEILKLGLFSNRFLERLFERHIKQNKHLEEEKMRHLLHVLKVDLGCTSEENSKKTPAAPAKKTSTTFNIVGTTYP

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

>85586_85586_2_SPATA7-GABRA3_SPATA7_chr14_88904247_ENST00000356583_GABRA3_chrX_151337035_ENST00000370314_length(amino acids)=545AA_BP=
MDGSRRVRATSVLPRYGPPCLFKGHLSTKSNAAVDCSVPVSVSTSIKYADQQRREKLKKELAQCEKEFKLTKTAMRANYKNNSKSLFNTL
QKPSGEPQIEDDMLKEEMNGFSSFARSLVPSSERLHLSLHKSSKVITNGPEKNSSSSPSSVDYAASGPRKLSSGALYGRRPRSTFPNSHR
FQLVISKAPSGDLLDKHSELFSNKQLPFTPRTLKTEAKSFLSQYRYYTPAKRKKDFTDQRIEAETQTELSFKSELGTAETKNMTDSEMNI
KQASNCVTYDAKEKIAPLPLEGHDSTWDEIKDDALQHSSPRAMCQYSLKPPSTRKIYSDEEELLYLSFIEDVTDEILKLGLFSNRFLERL
FERHIKQNKHLEEVKQNDVDMLNVFDFEKAGNSEPNELKNESEVTIQQERQQYQKALDMLLSAPKDENEIFPSPTEFFMPIYKSKHSEGV
IIQQVNDETNLETSTLDENHPSISDSLTDRETSVNVIEGDSDPEKVEISNGLCGLNTSPSQSVQFSSVKGDNNHDMELSTLKIMEMSIED

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

>85586_85586_3_SPATA7-GABRA3_SPATA7_chr14_88904247_ENST00000393545_GABRA3_chrX_151337035_ENST00000535043_length(amino acids)=577AA_BP=
MDGSRRVRATSVLPRYGPPCLFKGHLSTKSNAFCTDSSSLRLSTLQLVKNHMAVHYNKILSAKAAVDCSVPVSVSTSIKYADQQRREKLK
KELAQCEKEFKLTKTAMRANYKNNSKSLFNTLQKPSGEPQIEDDMLKEEMNGFSSFARSLVPSSERLHLSLHKSSKVITNGPEKNSSSSP
SSVDYAASGPRKLSSGALYGRRPRSTFPNSHRFQLVISKAPSGDLLDKHSELFSNKQLPFTPRTLKTEAKSFLSQYRYYTPAKRKKDFTD
QRIEAETQTELSFKSELGTAETKNMTDSEMNIKQASNCVTYDAKEKIAPLPLEGHDSTWDEIKDDALQHSSPRAMCQYSLKPPSTRKIYS
DEEELLYLSFIEDVTDEILKLGLFSNRFLERLFERHIKQNKHLEEVKQNDVDMLNVFDFEKAGNSEPNELKNESEVTIQQERQQYQKALD
MLLSAPKDENEIFPSPTEFFMPIYKSKHSEGVIIQQVNDETNLETSTLDENHPSISDSLTDRETSVNVIEGDSDPEKVEISNGLCGLNTS

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

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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/chr14:88904247/chrX:151337035)
- 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
.	GABRA3 P34903
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: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel.

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

GABRA3

chr14:88904247

chrX:151337035

ENST00000370314

458_479

381.0

493.0

Transmembrane

Helical

Tgene

GABRA3

chr14:88904247

chrX:151337035

ENST00000535043

458_479

381.0

493.0

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

Tgene

GABRA3

chr14:88904247

chrX:151337035

ENST00000370314

29_276

381.0

493.0

Topological domain

Extracellular

Tgene

GABRA3

chr14:88904247

chrX:151337035

ENST00000370314

360_457

381.0

493.0

Topological domain

Cytoplasmic

Tgene

GABRA3

chr14:88904247

chrX:151337035

ENST00000535043

29_276

381.0

493.0

Topological domain

Extracellular

Tgene

GABRA3

chr14:88904247

chrX:151337035

ENST00000535043

360_457

381.0

493.0

Topological domain

Cytoplasmic

Tgene

GABRA3

chr14:88904247

chrX:151337035

ENST00000370314

277_298

381.0

493.0

Transmembrane

Helical

Tgene

GABRA3

chr14:88904247

chrX:151337035

ENST00000370314

304_325

381.0

493.0

Transmembrane

Helical

Tgene

GABRA3

chr14:88904247

chrX:151337035

ENST00000370314

338_359

381.0

493.0

Transmembrane

Helical

Tgene

GABRA3

chr14:88904247

chrX:151337035

ENST00000535043

277_298

381.0

493.0

Transmembrane

Helical

Tgene

GABRA3

chr14:88904247

chrX:151337035

ENST00000535043

304_325

381.0

493.0

Transmembrane

Helical

Tgene

GABRA3

chr14:88904247

chrX:151337035

ENST00000535043

338_359

381.0

493.0

Transmembrane

Helical

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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
SPATA7
GABRA3

- 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 SPATA7-GABRA3

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 SPATA7-GABRA3

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