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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:PKMYT1-FLYWCH1 (FusionGDB2 ID:65764)

Fusion Gene Summary for PKMYT1-FLYWCH1

check button Fusion gene summary
Fusion gene informationFusion gene name: PKMYT1-FLYWCH1
Fusion gene ID: 65764
HgeneTgene
Gene symbol

PKMYT1

FLYWCH1

Gene ID

9088

84256

Gene nameprotein kinase, membrane associated tyrosine/threonine 1FLYWCH-type zinc finger 1
SynonymsMYT1|PPP1R126-
Cytomap

16p13.3

16p13.3

Type of geneprotein-codingprotein-coding
Descriptionmembrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinasemyt1 kinaseprotein phosphatase 1, regulatory subunit 126FLYWCH-type zinc finger-containing protein 1
Modification date2020031320200313
UniProtAcc

Q99640

Q4VC44

Ensembl transtripts involved in fusion geneENST00000571102, ENST00000262300, 
ENST00000431515, ENST00000440027, 
ENST00000573944, ENST00000574385, 
ENST00000574730, 		ENST00000253928, 
ENST00000399667, ENST00000416288, 
ENST00000570752, 
Fusion gene scores* DoF score6 X 6 X 5=1802 X 2 X 2=8
# samples 72
** MAII scorelog2(7/180*10)=-1.36257007938471
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/8*10)=1.32192809488736
Context

PubMed: PKMYT1 [Title/Abstract] AND FLYWCH1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPKMYT1(3019889)-FLYWCH1(2964177), # 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
HgenePKMYT1

GO:0010923

negative regulation of phosphatase activity

19389623


check buttonFusion gene breakpoints across PKMYT1 (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 FLYWCH1 (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
ChimerDB4CESCTCGA-EK-A2PI-01APKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+


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Fusion Gene ORF analysis for PKMYT1-FLYWCH1

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
5UTR-5UTRENST00000571102ENST00000253928PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
5UTR-5UTRENST00000571102ENST00000399667PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
5UTR-5UTRENST00000571102ENST00000416288PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
5UTR-intronENST00000571102ENST00000570752PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000262300ENST00000253928PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000262300ENST00000399667PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000262300ENST00000416288PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000431515ENST00000253928PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000431515ENST00000399667PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000431515ENST00000416288PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000440027ENST00000253928PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000440027ENST00000399667PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000440027ENST00000416288PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000573944ENST00000253928PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000573944ENST00000399667PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000573944ENST00000416288PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000574385ENST00000253928PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000574385ENST00000399667PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000574385ENST00000416288PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000574730ENST00000253928PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000574730ENST00000399667PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-5UTRENST00000574730ENST00000416288PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-intronENST00000262300ENST00000570752PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-intronENST00000431515ENST00000570752PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-intronENST00000440027ENST00000570752PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-intronENST00000573944ENST00000570752PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-intronENST00000574385ENST00000570752PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+
intron-intronENST00000574730ENST00000570752PKMYT1chr16

3019889

-FLYWCH1chr16

2964177

+

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 PKMYT1-FLYWCH1


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)
PKMYT1chr163019888-FLYWCH1chr162964176+0.723602350.2763976
PKMYT1chr163019888-FLYWCH1chr162964176+0.723602350.2763976

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.
genomic feature of top 1%

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Fusion Protein Features for PKMYT1-FLYWCH1


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:3019889/:2964177)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PKMYT1

Q99640

FLYWCH1

Q4VC44

FUNCTION: Acts as a negative regulator of entry into mitosis (G2 to M transition) by phosphorylation of the CDK1 kinase specifically when CDK1 is complexed to cyclins. Mediates phosphorylation of CDK1 predominantly on 'Thr-14'. Also involved in Golgi fragmentation. May be involved in phosphorylation of CDK1 on 'Tyr-15' to a lesser degree, however tyrosine kinase activity is unclear and may be indirect. May be a downstream target of Notch signaling pathway during eye development. {ECO:0000269|PubMed:10373560, ECO:0000269|PubMed:9001210}.

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 PKMYT1-FLYWCH1


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 PKMYT1-FLYWCH1


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 PKMYT1-FLYWCH1


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 PKMYT1-FLYWCH1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource