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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:PTPRK-STAG3 (FusionGDB2 ID:70026)

Fusion Gene Summary for PTPRK-STAG3

check button Fusion gene summary
Fusion gene informationFusion gene name: PTPRK-STAG3
Fusion gene ID: 70026
HgeneTgene
Gene symbol

PTPRK

STAG3

Gene ID

5796

10734

Gene nameprotein tyrosine phosphatase receptor type Kstromal antigen 3
SynonymsR-PTP-kappa-
Cytomap

6q22.33

7q22.1

Type of geneprotein-codingprotein-coding
Descriptionreceptor-type tyrosine-protein phosphatase kappadJ480J14.2.1 (protein tyrosine phosphatase, receptor type, K (R-PTP-KAPPA, protein tyrosine phosphatase kappa , protein tyrosine phosphatase kappaprotein-tyrosine phosphatase kappaprotein-tyrosine phosphacohesin subunit SA-3SCC3 homolog 3stromalin-3
Modification date2020032220200313
UniProtAcc.

STAG3L3

Ensembl transtripts involved in fusion geneENST00000368226, ENST00000368227, 
ENST00000532331, ENST00000368213, 
ENST00000368210, ENST00000368215, 
ENST00000368207, ENST00000524481, 
ENST00000525459, 		ENST00000426455, 
ENST00000394018, ENST00000317296, 
ENST00000440830, 
Fusion gene scores* DoF score36 X 18 X 16=103682 X 2 X 1=4
# samples 482
** MAII scorelog2(48/10368*10)=-4.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/4*10)=2.32192809488736
Context

PubMed: PTPRK [Title/Abstract] AND STAG3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPTPRK(128530504)-STAG3(99800186), # 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)

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

GO:0006470

protein dephosphorylation

16263724

HgenePTPRK

GO:0007165

signal transduction

16849327

HgenePTPRK

GO:0007179

transforming growth factor beta receptor signaling pathway

15899872

HgenePTPRK

GO:0008285

negative regulation of cell proliferation

15899872|18276111

HgenePTPRK

GO:0010839

negative regulation of keratinocyte proliferation

16263724

HgenePTPRK

GO:0030336

negative regulation of cell migration

18276111

HgenePTPRK

GO:0034394

protein localization to cell surface

18276111

HgenePTPRK

GO:0034614

cellular response to reactive oxygen species

16849327

HgenePTPRK

GO:0034644

cellular response to UV

16849327

HgenePTPRK

GO:0045786

negative regulation of cell cycle

15899872

HgenePTPRK

GO:0045892

negative regulation of transcription, DNA-templated

18276111


check buttonFusion gene breakpoints across PTPRK (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 STAG3 (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
ChiTaRS5.0N/AR85198PTPRKchr6

128530504

+STAG3chr7

99800186

+


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Fusion Gene ORF analysis for PTPRK-STAG3

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
intron-3CDSENST00000368226ENST00000426455PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368226ENST00000394018PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368226ENST00000317296PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3UTRENST00000368226ENST00000440830PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368227ENST00000426455PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368227ENST00000394018PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368227ENST00000317296PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3UTRENST00000368227ENST00000440830PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000532331ENST00000426455PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000532331ENST00000394018PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000532331ENST00000317296PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3UTRENST00000532331ENST00000440830PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368213ENST00000426455PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368213ENST00000394018PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368213ENST00000317296PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3UTRENST00000368213ENST00000440830PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368210ENST00000426455PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368210ENST00000394018PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368210ENST00000317296PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3UTRENST00000368210ENST00000440830PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368215ENST00000426455PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368215ENST00000394018PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368215ENST00000317296PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3UTRENST00000368215ENST00000440830PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368207ENST00000426455PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368207ENST00000394018PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000368207ENST00000317296PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3UTRENST00000368207ENST00000440830PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000524481ENST00000426455PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000524481ENST00000394018PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000524481ENST00000317296PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3UTRENST00000524481ENST00000440830PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000525459ENST00000426455PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000525459ENST00000394018PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3CDSENST00000525459ENST00000317296PTPRKchr6

128530504

+STAG3chr7

99800186

+
intron-3UTRENST00000525459ENST00000440830PTPRKchr6

128530504

+STAG3chr7

99800186

+

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 PTPRK-STAG3


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 PTPRK-STAG3


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
.STAG3

STAG3L3

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.134

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 PTPRK-STAG3


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 PTPRK-STAG3


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 PTPRK-STAG3


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 PTPRK-STAG3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePTPRKC0025202melanoma2CTD_human
HgenePTPRKC0033578Prostatic Neoplasms1CTD_human
HgenePTPRKC0376358Malignant neoplasm of prostate1CTD_human
TgeneSTAG3C0085215Ovarian Failure, Premature1GENOMICS_ENGLAND