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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:EPHA6-PHC2 (FusionGDB2 ID:26975)

Fusion Gene Summary for EPHA6-PHC2

Fusion gene summary

Fusion gene information	Fusion gene name: EPHA6-PHC2
	Fusion gene ID: 26975
		Hgene	Tgene
	Gene symbol	EPHA6	PHC2
	Gene ID	285220	1912
	Gene name	EPH receptor A6	polyhomeotic homolog 2
	Synonyms	EHK-2\|EHK2\|EK12\|EPA6\|HEK12\|PRO57066	EDR2\|HPH2\|PH2
	Cytomap	3q11.2	1p35.1
	Type of gene	protein-coding	protein-coding
	Description	ephrin type-A receptor 6EPH homology kinase 2EPH-like kinase 12ephrin receptor EphA6	polyhomeotic-like protein 2early development regulator 2 (homolog of polyhomeotic 2)early development regulatory protein 2polyhomeotic 2polyhomeotic-like 2
	Modification date	20200313	20200320
	UniProtAcc	Q9UF33	.
	Ensembl transtripts involved in fusion gene	ENST00000389672, ENST00000442602, ENST00000470610, ENST00000502694, ENST00000514100, ENST00000542517,	ENST00000257118, ENST00000373416, ENST00000373418, ENST00000373422, ENST00000419414, ENST00000431992, ENST00000485928,
Fusion gene scores	* DoF score	6 X 5 X 4=120	8 X 11 X 4=352
	# samples	7	9
	** MAII score	log2(7/120*10)=-0.777607578663552 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/352*10)=-1.96757852230762 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: EPHA6 [Title/Abstract] AND PHC2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	EPHA6(97473325)-PHC2(33789228), # 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

Fusion gene breakpoints across EPHA6 (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 PHC2 (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	BM193627	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+

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Fusion Gene ORF analysis for EPHA6-PHC2

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-intron	ENST00000389672	ENST00000257118	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000389672	ENST00000373416	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000389672	ENST00000373418	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000389672	ENST00000373422	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000389672	ENST00000419414	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000389672	ENST00000431992	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000389672	ENST00000485928	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000442602	ENST00000257118	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000442602	ENST00000373416	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000442602	ENST00000373418	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000442602	ENST00000373422	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000442602	ENST00000419414	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000442602	ENST00000431992	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000442602	ENST00000485928	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000470610	ENST00000257118	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000470610	ENST00000373416	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000470610	ENST00000373418	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000470610	ENST00000373422	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000470610	ENST00000419414	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000470610	ENST00000431992	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000470610	ENST00000485928	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000502694	ENST00000257118	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000502694	ENST00000373416	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000502694	ENST00000373418	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000502694	ENST00000373422	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000502694	ENST00000419414	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000502694	ENST00000431992	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000502694	ENST00000485928	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000514100	ENST00000257118	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000514100	ENST00000373416	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000514100	ENST00000373418	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000514100	ENST00000373422	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000514100	ENST00000419414	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000514100	ENST00000431992	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000514100	ENST00000485928	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000542517	ENST00000257118	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000542517	ENST00000373416	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000542517	ENST00000373418	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000542517	ENST00000373422	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000542517	ENST00000419414	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000542517	ENST00000431992	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+
intron-intron	ENST00000542517	ENST00000485928	EPHA6	chr3	97473325	+	PHC2	chr1	33789228	+

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 EPHA6-PHC2

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 EPHA6-PHC2

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:97473325/:33789228)
- 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
EPHA6 Q9UF33	.
FUNCTION: Receptor tyrosine kinase which binds promiscuously GPI-anchored ephrin-A family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling (By similarity). {ECO:0000250}.	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 EPHA6-PHC2

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 EPHA6-PHC2

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 EPHA6-PHC2

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 EPHA6-PHC2

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source