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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:RYK-CEP63 (FusionGDB2 ID:78298)

Fusion Gene Summary for RYK-CEP63

check button Fusion gene summary
Fusion gene informationFusion gene name: RYK-CEP63
Fusion gene ID: 78298
HgeneTgene
Gene symbol

RYK

CEP63

Gene ID

6259

80254

Gene namereceptor like tyrosine kinasecentrosomal protein 63
SynonymsD3S3195|JTK5|JTK5A|RYK1SCKL6
Cytomap

3q22.2

3q22.2

Type of geneprotein-codingprotein-coding
Descriptiontyrosine-protein kinase RYKJTK5A protein tyrosine kinasehydroxyaryl-protein kinasecentrosomal protein of 63 kDacentrosomal protein 63kDacentrosome protein CEP63
Modification date2020031320200328
UniProtAcc.

Q96MT8

Ensembl transtripts involved in fusion geneENST00000296084, ENST00000427044, 
ENST00000484106, 		ENST00000332047, 
ENST00000354446, ENST00000337090, 
ENST00000504013, ENST00000383229, 
ENST00000513612, ENST00000606977, 
Fusion gene scores* DoF score9 X 10 X 6=5406 X 7 X 3=126
# samples 127
** MAII scorelog2(12/540*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/126*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RYK [Title/Abstract] AND CEP63 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRYK(133969266)-CEP63(134250686), # samples:1
Anticipated loss of major functional domain due to fusion event.RYK-CEP63 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
RYK-CEP63 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
RYK-CEP63 seems lost the major protein functional domain in Tgene 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
HgeneRYK

GO:0006468

protein phosphorylation

10454588

HgeneRYK

GO:0043410

positive regulation of MAPK cascade

10454588


check buttonFusion gene breakpoints across RYK (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 CEP63 (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
ChimerDB4OVTCGA-25-1625RYKchr3

133969266

-CEP63chr3

134250686

+


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Fusion Gene ORF analysis for RYK-CEP63

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-shiftENST00000296084ENST00000332047RYKchr3

133969266

-CEP63chr3

134250686

+
Frame-shiftENST00000296084ENST00000354446RYKchr3

133969266

-CEP63chr3

134250686

+
Frame-shiftENST00000296084ENST00000337090RYKchr3

133969266

-CEP63chr3

134250686

+
5CDS-3UTRENST00000296084ENST00000504013RYKchr3

133969266

-CEP63chr3

134250686

+
5CDS-3UTRENST00000296084ENST00000383229RYKchr3

133969266

-CEP63chr3

134250686

+
5CDS-3UTRENST00000296084ENST00000513612RYKchr3

133969266

-CEP63chr3

134250686

+
5CDS-3UTRENST00000296084ENST00000606977RYKchr3

133969266

-CEP63chr3

134250686

+
5UTR-3CDSENST00000427044ENST00000332047RYKchr3

133969266

-CEP63chr3

134250686

+
5UTR-3CDSENST00000427044ENST00000354446RYKchr3

133969266

-CEP63chr3

134250686

+
5UTR-3CDSENST00000427044ENST00000337090RYKchr3

133969266

-CEP63chr3

134250686

+
5UTR-3UTRENST00000427044ENST00000504013RYKchr3

133969266

-CEP63chr3

134250686

+
5UTR-3UTRENST00000427044ENST00000383229RYKchr3

133969266

-CEP63chr3

134250686

+
5UTR-3UTRENST00000427044ENST00000513612RYKchr3

133969266

-CEP63chr3

134250686

+
5UTR-3UTRENST00000427044ENST00000606977RYKchr3

133969266

-CEP63chr3

134250686

+
intron-3CDSENST00000484106ENST00000332047RYKchr3

133969266

-CEP63chr3

134250686

+
intron-3CDSENST00000484106ENST00000354446RYKchr3

133969266

-CEP63chr3

134250686

+
intron-3CDSENST00000484106ENST00000337090RYKchr3

133969266

-CEP63chr3

134250686

+
intron-3UTRENST00000484106ENST00000504013RYKchr3

133969266

-CEP63chr3

134250686

+
intron-3UTRENST00000484106ENST00000383229RYKchr3

133969266

-CEP63chr3

134250686

+
intron-3UTRENST00000484106ENST00000513612RYKchr3

133969266

-CEP63chr3

134250686

+
intron-3UTRENST00000484106ENST00000606977RYKchr3

133969266

-CEP63chr3

134250686

+

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 RYK-CEP63


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)
RYKchr3133969266-CEP63chr3134250686+3.83E-121
RYKchr3133969266-CEP63chr3134250686+3.83E-121

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 RYK-CEP63


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
.CEP63

Q96MT8

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 for normal spindle assembly. Plays a key role in mother-centriole-dependent centriole duplication; the function seems also to involve CEP152, CDK5RAP2 and WDR62 through a stepwise assembled complex at the centrosome that recruits CDK2 required for centriole duplication. Reported to be required for centrosomal recruitment of CEP152; however, this function has been questioned (PubMed:21983783, PubMed:26297806). Also recruits CDK1 to centrosomes (PubMed:21406398). Plays a role in DNA damage response. Following DNA damage, such as double-strand breaks (DSBs), is removed from centrosomes; this leads to the inactivation of spindle assembly and delay in mitotic progression (PubMed:21406398). {ECO:0000269|PubMed:21406398, ECO:0000269|PubMed:21983783, ECO:0000269|PubMed:26297806}.

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 RYK-CEP63


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 RYK-CEP63


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 RYK-CEP63


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 RYK-CEP63


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRYKC0008925Cleft Palate1CTD_human
HgeneRYKC0043094Weight Gain1CTD_human
HgeneRYKC0376634Craniofacial Abnormalities1CTD_human
HgeneRYKC1837218Cleft palate, isolated1CTD_human
TgeneCEP63C3553582SECKEL SYNDROME 63GENOMICS_ENGLAND
TgeneCEP63C0025958Microcephaly2CTD_human;GENOMICS_ENGLAND
TgeneCEP63C0431350Primary microcephaly1GENOMICS_ENGLAND
TgeneCEP63C0920296Developmental reading disorder1GENOMICS_ENGLAND
TgeneCEP63C1956147Microlissencephaly1CTD_human
TgeneCEP63C3853041Severe Congenital Microcephaly1CTD_human