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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:FOXJ3-GAPVD1 (FusionGDB2 ID:31068)

Fusion Gene Summary for FOXJ3-GAPVD1

Fusion gene summary

Fusion gene information	Fusion gene name: FOXJ3-GAPVD1
	Fusion gene ID: 31068
		Hgene	Tgene
	Gene symbol	FOXJ3	GAPVD1
	Gene ID	22887	26130
	Gene name	forkhead box J3	GTPase activating protein and VPS9 domains 1
	Synonyms	-	GAPEX5\|GAPex-5\|RAP6
	Cytomap	1p34.2	9q33.3
	Type of gene	protein-coding	protein-coding
	Description	forkhead box protein J3	GTPase-activating protein and VPS9 domain-containing protein 1Rab5 exchange factorRab5-activating protein 6
	Modification date	20200313	20200313
	UniProtAcc	Q9UPW0	Q14C86
	Ensembl transtripts involved in fusion gene	ENST00000361346, ENST00000361776, ENST00000372571, ENST00000372572, ENST00000372573, ENST00000545068,	ENST00000394084, ENST00000265956, ENST00000297933, ENST00000312123, ENST00000394083, ENST00000394104, ENST00000394105, ENST00000469528, ENST00000470056, ENST00000495955,
Fusion gene scores	* DoF score	22 X 19 X 13=5434	10 X 10 X 4=400
	# samples	31	10
	** MAII score	log2(31/5434*10)=-4.13167444494774 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/400*10)=-2 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: FOXJ3 [Title/Abstract] AND GAPVD1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	FOXJ3(42644888)-GAPVD1(128069803), # 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	FOXJ3	GO:0045944	positive regulation of transcription by RNA polymerase II	22740631

Fusion gene breakpoints across FOXJ3 (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 GAPVD1 (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	EC497143	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+

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Fusion Gene ORF analysis for FOXJ3-GAPVD1

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-3CDS	ENST00000361346	ENST00000394084	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-3CDS	ENST00000361776	ENST00000394084	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-3CDS	ENST00000372571	ENST00000394084	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-3CDS	ENST00000372572	ENST00000394084	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-3CDS	ENST00000372573	ENST00000394084	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-3CDS	ENST00000545068	ENST00000394084	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361346	ENST00000265956	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361346	ENST00000297933	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361346	ENST00000312123	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361346	ENST00000394083	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361346	ENST00000394104	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361346	ENST00000394105	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361346	ENST00000469528	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361346	ENST00000470056	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361346	ENST00000495955	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361776	ENST00000265956	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361776	ENST00000297933	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361776	ENST00000312123	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361776	ENST00000394083	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361776	ENST00000394104	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361776	ENST00000394105	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361776	ENST00000469528	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361776	ENST00000470056	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000361776	ENST00000495955	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372571	ENST00000265956	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372571	ENST00000297933	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372571	ENST00000312123	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372571	ENST00000394083	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372571	ENST00000394104	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372571	ENST00000394105	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372571	ENST00000469528	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372571	ENST00000470056	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372571	ENST00000495955	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372572	ENST00000265956	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372572	ENST00000297933	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372572	ENST00000312123	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372572	ENST00000394083	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372572	ENST00000394104	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372572	ENST00000394105	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372572	ENST00000469528	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372572	ENST00000470056	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372572	ENST00000495955	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372573	ENST00000265956	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372573	ENST00000297933	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372573	ENST00000312123	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372573	ENST00000394083	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372573	ENST00000394104	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372573	ENST00000394105	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372573	ENST00000469528	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372573	ENST00000470056	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000372573	ENST00000495955	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000545068	ENST00000265956	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000545068	ENST00000297933	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000545068	ENST00000312123	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000545068	ENST00000394083	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000545068	ENST00000394104	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000545068	ENST00000394105	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000545068	ENST00000469528	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000545068	ENST00000470056	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+
intron-intron	ENST00000545068	ENST00000495955	FOXJ3	chr1	42644888	+	GAPVD1	chr9	128069803	+

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 FOXJ3-GAPVD1

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 FOXJ3-GAPVD1

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:42644888/:128069803)
- 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
FOXJ3 Q9UPW0	GAPVD1 Q14C86
FUNCTION: Transcriptional activator of MEF2C involved in the regulation of adult muscle fiber type identity and skeletal muscle regeneration (By similarity). Plays an important role in spermatogenesis (By similarity). Required for the survival of spermatogonia and participates in spermatocyte meiosis (By similarity). {ECO:0000250\|UniProtKB:Q8BUR3}.	FUNCTION: Acts both as a GTPase-activating protein (GAP) and a guanine nucleotide exchange factor (GEF), and participates in various processes such as endocytosis, insulin receptor internalization or LC2A4/GLUT4 trafficking. Acts as a GEF for the Ras-related protein RAB31 by exchanging bound GDP for free GTP, leading to regulate LC2A4/GLUT4 trafficking. In the absence of insulin, it maintains RAB31 in an active state and promotes a futile cycle between LC2A4/GLUT4 storage vesicles and early endosomes, retaining LC2A4/GLUT4 inside the cells. Upon insulin stimulation, it is translocated to the plasma membrane, releasing LC2A4/GLUT4 from intracellular storage vesicles. Also involved in EGFR trafficking and degradation, possibly by promoting EGFR ubiquitination and subsequent degradation by the proteasome. Has GEF activity for Rab5 and GAP activity for Ras. {ECO:0000269\|PubMed:16410077}.

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 FOXJ3-GAPVD1

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 FOXJ3-GAPVD1

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 FOXJ3-GAPVD1

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 FOXJ3-GAPVD1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source