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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:PTP4A1-EYS (FusionGDB2 ID:69703)

Fusion Gene Summary for PTP4A1-EYS

check button Fusion gene summary
Fusion gene informationFusion gene name: PTP4A1-EYS
Fusion gene ID: 69703
HgeneTgene
Gene symbol

PTP4A1

EYS

Gene ID

7803

346007

Gene nameprotein tyrosine phosphatase 4A1eyes shut homolog
SynonymsHH72|PRL-1|PRL1|PTP(CAAX1)|PTPCAAX1C6orf178|C6orf179|C6orf180|EGFL10|EGFL11|RP25|SPAM|bA166P24.2|bA307F22.3|bA74E24.1|dJ1018A4.2|dJ22I17.2|dJ303F19.1
Cytomap

6q12

6q12

Type of geneprotein-codingprotein-coding
Descriptionprotein tyrosine phosphatase type IVA 1PVT1/PTP4A1 fusionphosphatase of regenerating liver 1protein tyrosine phosphatase type IVA protein 1protein tyrosine phosphatase type IVA, member 1protein-tyrosine phosphatase of regenerating liver 1protein eyes shut homologEGF-like-domain, multiple 10EGF-like-domain, multiple 11epidermal growth factor-like protein 10epidermal growth factor-like protein 11protein spacemaker homolog
Modification date2020032020200313
UniProtAcc.

Q5T1H1

Ensembl transtripts involved in fusion geneENST00000370651, ENST00000370650, 
ENST00000578299, ENST00000473334, 
ENST00000503581, ENST00000370621, 
ENST00000370616, ENST00000393380, 
ENST00000342421, ENST00000370618, 
ENST00000486069, 
Fusion gene scores* DoF score6 X 4 X 5=12036 X 24 X 15=12960
# samples 738
** MAII scorelog2(7/120*10)=-0.777607578663552
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(38/12960*10)=-5.09192248944104
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PTP4A1 [Title/Abstract] AND EYS [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPTP4A1(64286890)-EYS(65532715), # samples:4
Anticipated loss of major functional domain due to fusion event.PTP4A1-EYS seems lost the major protein functional domain in Hgene partner, which is a essential gene 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID

check buttonFusion gene breakpoints across PTP4A1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4BRCATCGA-E9-A2JS-01APTP4A1chr6

64286890

+EYSchr6

65532715

-
ChimerDB4BRCATCGA-E9-A2JSPTP4A1chr6

64286890

+EYSchr6

65532715

-
ChimerDB4BRCATCGA-E9-A2JS-01APTP4A1chr6

64286890

+EYSchr6

65532715

-
ChimerDB4BRCATCGA-E9-A2JS-01APTP4A1chr6

64286890

-EYSchr6

65532715

-


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Fusion Gene ORF analysis for PTP4A1-EYS

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shiftENST00000370651ENST00000503581PTP4A1chr6

64286890

+EYSchr6

65532715

-
Frame-shiftENST00000370651ENST00000370621PTP4A1chr6

64286890

+EYSchr6

65532715

-
Frame-shiftENST00000370651ENST00000370616PTP4A1chr6

64286890

+EYSchr6

65532715

-
5CDS-intronENST00000370651ENST00000393380PTP4A1chr6

64286890

+EYSchr6

65532715

-
5CDS-intronENST00000370651ENST00000342421PTP4A1chr6

64286890

+EYSchr6

65532715

-
5CDS-intronENST00000370651ENST00000370618PTP4A1chr6

64286890

+EYSchr6

65532715

-
5CDS-intronENST00000370651ENST00000486069PTP4A1chr6

64286890

+EYSchr6

65532715

-
Frame-shiftENST00000370650ENST00000503581PTP4A1chr6

64286890

+EYSchr6

65532715

-
Frame-shiftENST00000370650ENST00000370621PTP4A1chr6

64286890

+EYSchr6

65532715

-
Frame-shiftENST00000370650ENST00000370616PTP4A1chr6

64286890

+EYSchr6

65532715

-
5CDS-intronENST00000370650ENST00000393380PTP4A1chr6

64286890

+EYSchr6

65532715

-
5CDS-intronENST00000370650ENST00000342421PTP4A1chr6

64286890

+EYSchr6

65532715

-
5CDS-intronENST00000370650ENST00000370618PTP4A1chr6

64286890

+EYSchr6

65532715

-
5CDS-intronENST00000370650ENST00000486069PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-3CDSENST00000578299ENST00000503581PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-3CDSENST00000578299ENST00000370621PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-3CDSENST00000578299ENST00000370616PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-intronENST00000578299ENST00000393380PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-intronENST00000578299ENST00000342421PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-intronENST00000578299ENST00000370618PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-intronENST00000578299ENST00000486069PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-3CDSENST00000473334ENST00000503581PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-3CDSENST00000473334ENST00000370621PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-3CDSENST00000473334ENST00000370616PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-intronENST00000473334ENST00000393380PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-intronENST00000473334ENST00000342421PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-intronENST00000473334ENST00000370618PTP4A1chr6

64286890

+EYSchr6

65532715

-
intron-intronENST00000473334ENST00000486069PTP4A1chr6

64286890

+EYSchr6

65532715

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for PTP4A1-EYS


check buttonFusionAI 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.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution 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.

check buttonDistribution 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 PTP4A1-EYS


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.EYS

Q5T1H1

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: Required to maintain the integrity of photoreceptor cells (PubMed:18836446). Specifically required for normal morphology of the photoreceptor ciliary pocket, and might thus facilitate protein trafficking between the photoreceptor inner and outer segments via the transition zone (By similarity). {ECO:0000250|UniProtKB:B8JI71, ECO:0000269|PubMed:18836446}.

check buttonRetention 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for PTP4A1-EYS


check button 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 PTP4A1-EYS


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for PTP4A1-EYS


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for PTP4A1-EYS


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePTP4A1C0001973Alcoholic Intoxication, Chronic2PSYGENET
TgeneEYSC1864446Retinitis Pigmentosa 255CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneEYSC0035334Retinitis Pigmentosa1CTD_human;GENOMICS_ENGLAND