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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:SKI-PRKCZ (FusionGDB2 ID:81516)

Fusion Gene Summary for SKI-PRKCZ

check button Fusion gene summary
Fusion gene informationFusion gene name: SKI-PRKCZ
Fusion gene ID: 81516
HgeneTgene
Gene symbol

SKI

PRKCZ

Gene ID

6497

5590

Gene nameSKI proto-oncogeneprotein kinase C zeta
SynonymsSGS|SKVPKC-ZETA|PKC2
Cytomap

1p36.33-p36.32

1p36.33

Type of geneprotein-codingprotein-coding
Descriptionski oncogeneproto-oncogene c-Skiski oncoproteinv-ski avian sarcoma viral oncogene homologprotein kinase C zeta typenPKC-zeta
Modification date2020032920200327
UniProtAcc

SKI

.
Ensembl transtripts involved in fusion geneENST00000378536, ENST00000478223, 
ENST00000400921, ENST00000400920, 
ENST00000479263, 
Fusion gene scores* DoF score14 X 8 X 8=8967 X 6 X 7=294
# samples 1710
** MAII scorelog2(17/896*10)=-2.3979639859199
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/294*10)=-1.55581615506164
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SKI [Title/Abstract] AND PRKCZ [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPRKCZ(1991030)-SKI(2234416), # samples:1
PRKCZ(2106752)-SKI(2234417), # samples:1
SKI(2161174)-PRKCZ(2087434), # samples:2
SKI(2161174)-PRKCZ(2066701), # samples:2
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
HgeneSKI

GO:0000122

negative regulation of transcription by RNA polymerase II

17469184

HgeneSKI

GO:0008285

negative regulation of cell proliferation

11430826

HgeneSKI

GO:0014902

myotube differentiation

19008232

HgeneSKI

GO:0030512

negative regulation of transforming growth factor beta receptor signaling pathway

17469184

HgeneSKI

GO:0030514

negative regulation of BMP signaling pathway

14699069

HgeneSKI

GO:0032926

negative regulation of activin receptor signaling pathway

14699069

HgeneSKI

GO:0043388

positive regulation of DNA binding

15107821

HgeneSKI

GO:0045668

negative regulation of osteoblast differentiation

14699069

HgeneSKI

GO:0060395

SMAD protein signal transduction

12874272

TgenePRKCZ

GO:0006468

protein phosphorylation

10770950|17313651

TgenePRKCZ

GO:0018105

peptidyl-serine phosphorylation

15069075


check buttonFusion gene breakpoints across SKI (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 PRKCZ (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
ChimerDB4STADTCGA-BR-8373SKIchr1

2235541

+PRKCZchr1

2066700

+
ChimerDB4BLCATCGA-4Z-AA7QSKIchr1

2161174

+PRKCZchr1

2087434

+
ChimerDB4STADTCGA-BR-8373-01ASKIchr1

2235541

+PRKCZchr1

2066701

+
ChimerDB4BLCATCGA-4Z-AA7Q-01ASKIchr1

2161174

-PRKCZchr1

2087434

+
ChimerDB4BRCATCGA-A7-A26G-01ASKIchr1

2161174

-PRKCZchr1

2066701

+
ChimerDB4BRCATCGA-E9-A1NA-01ASKIchr1

2161174

-PRKCZchr1

2066701

+


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Fusion Gene ORF analysis for SKI-PRKCZ

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
5CDS-5UTRENST00000378536ENST00000400921SKIchr1

2235541

+PRKCZchr1

2066700

+
5CDS-5UTRENST00000378536ENST00000400920SKIchr1

2235541

+PRKCZchr1

2066700

+
5CDS-intronENST00000378536ENST00000479263SKIchr1

2235541

+PRKCZchr1

2066700

+
intron-5UTRENST00000478223ENST00000400921SKIchr1

2235541

+PRKCZchr1

2066700

+
intron-5UTRENST00000478223ENST00000400920SKIchr1

2235541

+PRKCZchr1

2066700

+
intron-intronENST00000478223ENST00000479263SKIchr1

2235541

+PRKCZchr1

2066700

+
In-frameENST00000378536ENST00000400921SKIchr1

2161174

+PRKCZchr1

2087434

+
In-frameENST00000378536ENST00000400920SKIchr1

2161174

+PRKCZchr1

2087434

+
5CDS-3UTRENST00000378536ENST00000479263SKIchr1

2161174

+PRKCZchr1

2087434

+
intron-3CDSENST00000478223ENST00000400921SKIchr1

2161174

+PRKCZchr1

2087434

+
intron-3CDSENST00000478223ENST00000400920SKIchr1

2161174

+PRKCZchr1

2087434

+
intron-3UTRENST00000478223ENST00000479263SKIchr1

2161174

+PRKCZchr1

2087434

+
5CDS-5UTRENST00000378536ENST00000400921SKIchr1

2235541

+PRKCZchr1

2066701

+
5CDS-5UTRENST00000378536ENST00000400920SKIchr1

2235541

+PRKCZchr1

2066701

+
5CDS-intronENST00000378536ENST00000479263SKIchr1

2235541

+PRKCZchr1

2066701

+
intron-5UTRENST00000478223ENST00000400921SKIchr1

2235541

+PRKCZchr1

2066701

+
intron-5UTRENST00000478223ENST00000400920SKIchr1

2235541

+PRKCZchr1

2066701

+
intron-intronENST00000478223ENST00000479263SKIchr1

2235541

+PRKCZchr1

2066701

+
5CDS-5UTRENST00000378536ENST00000400921SKIchr1

2161174

-PRKCZchr1

2066701

+
5CDS-5UTRENST00000378536ENST00000400920SKIchr1

2161174

-PRKCZchr1

2066701

+
5CDS-intronENST00000378536ENST00000479263SKIchr1

2161174

-PRKCZchr1

2066701

+
intron-5UTRENST00000478223ENST00000400921SKIchr1

2161174

-PRKCZchr1

2066701

+
intron-5UTRENST00000478223ENST00000400920SKIchr1

2161174

-PRKCZchr1

2066701

+
intron-intronENST00000478223ENST00000479263SKIchr1

2161174

-PRKCZchr1

2066701

+

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 SKI-PRKCZ


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)
SKIchr12235541+PRKCZchr12066700+0.0041723220.9958276
SKIchr12235541+PRKCZchr12066700+0.0041723220.9958276
SKIchr12161174+PRKCZchr12087433+1.53E-050.99998474
SKIchr12235541+PRKCZchr12066700+0.0041723220.9958276
SKIchr12235541+PRKCZchr12066700+0.0041723220.9958276
SKIchr12161174+PRKCZchr12087433+1.53E-050.99998474

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 SKI-PRKCZ


check button Go to

FGviewer for the breakpoints of chr1:2161174-chr1:2087434

.
- 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
SKI

SKI

.
908FUNCTION: 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.

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
TgenePRKCZchr1:2161174chr1:2087434ENST00000400920515252_518109.0410.0DomainProtein kinase
TgenePRKCZchr1:2161174chr1:2087434ENST00000400920515519_590109.0410.0DomainAGC-kinase C-terminal
TgenePRKCZchr1:2161174chr1:2087434ENST00000400921515252_518109.0410.0DomainProtein kinase
TgenePRKCZchr1:2161174chr1:2087434ENST00000400921515519_590109.0410.0DomainAGC-kinase C-terminal
TgenePRKCZchr1:2161174chr1:2087434ENST00000400920515258_266109.0410.0Nucleotide bindingATP
TgenePRKCZchr1:2161174chr1:2087434ENST00000400921515258_266109.0410.0Nucleotide bindingATP
TgenePRKCZchr1:2161174chr1:2087434ENST00000400920515130_180109.0410.0Zinc fingerPhorbol-ester/DAG-type
TgenePRKCZchr1:2161174chr1:2087434ENST00000400921515130_180109.0410.0Zinc fingerPhorbol-ester/DAG-type

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSKIchr1:2161174chr1:2087434ENST00000378536+17536_710323.0729.0Coiled coilOntology_term=ECO:0000255
TgenePRKCZchr1:2161174chr1:2087434ENST0000040092051515_98109.0410.0DomainPB1
TgenePRKCZchr1:2161174chr1:2087434ENST0000040092151515_98109.0410.0DomainPB1


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Fusion Gene Sequence for SKI-PRKCZ


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 SKI-PRKCZ


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
TgenePRKCZchr1:2161174chr1:2087434ENST0000040092051579_145109.0410.0SQSTM1
TgenePRKCZchr1:2161174chr1:2087434ENST0000040092151579_145109.0410.0SQSTM1


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 SKI-PRKCZ


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 SKI-PRKCZ


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSKIC1321551Shprintzen-Goldberg syndrome4CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneSKIC1842870Chromosome 1p36 Deletion Syndrome2ORPHANET
HgeneSKIC0003486Aortic Aneurysm1CTD_human
HgeneSKIC0011999Diastematomyelia1CTD_human
HgeneSKIC0027794Neural Tube Defects1CTD_human
HgeneSKIC0027806Neurenteric Cyst1CTD_human
HgeneSKIC0080218Tethered Cord Syndrome1CTD_human
HgeneSKIC0151491Congenital musculoskeletal anomalies1CTD_human
HgeneSKIC0152234Iniencephaly1CTD_human
HgeneSKIC0152426Craniorachischisis1CTD_human
HgeneSKIC0266453Exencephaly1CTD_human
HgeneSKIC0344479Spinal Cord Myelodysplasia1CTD_human
HgeneSKIC0376634Craniofacial Abnormalities1CTD_human
HgeneSKIC0702169Acrania1CTD_human
TgenePRKCZC0005586Bipolar Disorder1PSYGENET
TgenePRKCZC0018800Cardiomegaly1CTD_human
TgenePRKCZC0020429Hyperalgesia1CTD_human
TgenePRKCZC0023418leukemia1CTD_human
TgenePRKCZC0033578Prostatic Neoplasms1CTD_human
TgenePRKCZC0376358Malignant neoplasm of prostate1CTD_human
TgenePRKCZC0458247Allodynia1CTD_human
TgenePRKCZC0751211Hyperalgesia, Primary1CTD_human
TgenePRKCZC0751212Hyperalgesia, Secondary1CTD_human
TgenePRKCZC0751213Tactile Allodynia1CTD_human
TgenePRKCZC0751214Hyperalgesia, Thermal1CTD_human
TgenePRKCZC1383860Cardiac Hypertrophy1CTD_human
TgenePRKCZC1839839MAJOR AFFECTIVE DISORDER 21PSYGENET
TgenePRKCZC2936719Mechanical Allodynia1CTD_human