FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:XRN1-PRKCE (FusionGDB2 ID:99125)

Fusion Gene Summary for XRN1-PRKCE

check button Fusion gene summary
Fusion gene informationFusion gene name: XRN1-PRKCE
Fusion gene ID: 99125
HgeneTgene
Gene symbol

XRN1

PRKCE

Gene ID

54464

5581

Gene name5'-3' exoribonuclease 1protein kinase C epsilon
SynonymsSEP1PKCE|nPKC-epsilon
Cytomap

3q23

2p21

Type of geneprotein-codingprotein-coding
Description5'-3' exoribonuclease 1strand-exchange protein 1 homologprotein kinase C epsilon type
Modification date2020032920200327
UniProtAcc.

Q02156

Ensembl transtripts involved in fusion geneENST00000264951, ENST00000392981, 
ENST00000463916, ENST00000544157, 
ENST00000465074, 		ENST00000306156, 
ENST00000467135, ENST00000394874, 
Fusion gene scores* DoF score9 X 8 X 8=57611 X 12 X 7=924
# samples 1112
** MAII scorelog2(11/576*10)=-2.38856528791765
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/924*10)=-2.94485844580754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: XRN1 [Title/Abstract] AND PRKCE [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointXRN1(142089327)-PRKCE(46411874), # samples:1
Anticipated loss of major functional domain due to fusion event.XRN1-PRKCE seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
XRN1-PRKCE seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
XRN1-PRKCE seems lost the major protein functional domain in Tgene partner, which is a kinase due to the frame-shifted ORF.
XRN1-PRKCE seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
XRN1-PRKCE seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
XRN1-PRKCE seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
TgenePRKCE

GO:0006468

protein phosphorylation

18556656

TgenePRKCE

GO:0018105

peptidyl-serine phosphorylation

15695813


check buttonFusion gene breakpoints across XRN1 (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 PRKCE (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
ChimerDB4LUADTCGA-69-7979-01AXRN1chr3

142089327

-PRKCEchr2

46411874

+


Top

Fusion Gene ORF analysis for XRN1-PRKCE

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-shiftENST00000264951ENST00000306156XRN1chr3

142089327

-PRKCEchr2

46411874

+
5CDS-intronENST00000264951ENST00000467135XRN1chr3

142089327

-PRKCEchr2

46411874

+
5CDS-intronENST00000264951ENST00000394874XRN1chr3

142089327

-PRKCEchr2

46411874

+
Frame-shiftENST00000392981ENST00000306156XRN1chr3

142089327

-PRKCEchr2

46411874

+
5CDS-intronENST00000392981ENST00000467135XRN1chr3

142089327

-PRKCEchr2

46411874

+
5CDS-intronENST00000392981ENST00000394874XRN1chr3

142089327

-PRKCEchr2

46411874

+
intron-3CDSENST00000463916ENST00000306156XRN1chr3

142089327

-PRKCEchr2

46411874

+
intron-intronENST00000463916ENST00000467135XRN1chr3

142089327

-PRKCEchr2

46411874

+
intron-intronENST00000463916ENST00000394874XRN1chr3

142089327

-PRKCEchr2

46411874

+
intron-3CDSENST00000544157ENST00000306156XRN1chr3

142089327

-PRKCEchr2

46411874

+
intron-intronENST00000544157ENST00000467135XRN1chr3

142089327

-PRKCEchr2

46411874

+
intron-intronENST00000544157ENST00000394874XRN1chr3

142089327

-PRKCEchr2

46411874

+
intron-3CDSENST00000465074ENST00000306156XRN1chr3

142089327

-PRKCEchr2

46411874

+
intron-intronENST00000465074ENST00000467135XRN1chr3

142089327

-PRKCEchr2

46411874

+
intron-intronENST00000465074ENST00000394874XRN1chr3

142089327

-PRKCEchr2

46411874

+

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

Top

Fusion Genomic Features for XRN1-PRKCE


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)
XRN1chr3142089326-PRKCEchr246411873+6.66E-161
XRN1chr3142089326-PRKCEchr246411873+6.66E-161

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.

Top

Fusion Protein Features for XRN1-PRKCE


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
.PRKCE

Q02156

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: Calcium-independent, phospholipid- and diacylglycerol (DAG)-dependent serine/threonine-protein kinase that plays essential roles in the regulation of multiple cellular processes linked to cytoskeletal proteins, such as cell adhesion, motility, migration and cell cycle, functions in neuron growth and ion channel regulation, and is involved in immune response, cancer cell invasion and regulation of apoptosis. Mediates cell adhesion to the extracellular matrix via integrin-dependent signaling, by mediating angiotensin-2-induced activation of integrin beta-1 (ITGB1) in cardiac fibroblasts. Phosphorylates MARCKS, which phosphorylates and activates PTK2/FAK, leading to the spread of cardiomyocytes. Involved in the control of the directional transport of ITGB1 in mesenchymal cells by phosphorylating vimentin (VIM), an intermediate filament (IF) protein. In epithelial cells, associates with and phosphorylates keratin-8 (KRT8), which induces targeting of desmoplakin at desmosomes and regulates cell-cell contact. Phosphorylates IQGAP1, which binds to CDC42, mediating epithelial cell-cell detachment prior to migration. In HeLa cells, contributes to hepatocyte growth factor (HGF)-induced cell migration, and in human corneal epithelial cells, plays a critical role in wound healing after activation by HGF. During cytokinesis, forms a complex with YWHAB, which is crucial for daughter cell separation, and facilitates abscission by a mechanism which may implicate the regulation of RHOA. In cardiac myocytes, regulates myofilament function and excitation coupling at the Z-lines, where it is indirectly associated with F-actin via interaction with COPB1. During endothelin-induced cardiomyocyte hypertrophy, mediates activation of PTK2/FAK, which is critical for cardiomyocyte survival and regulation of sarcomere length. Plays a role in the pathogenesis of dilated cardiomyopathy via persistent phosphorylation of troponin I (TNNI3). Involved in nerve growth factor (NFG)-induced neurite outgrowth and neuron morphological change independently of its kinase activity, by inhibition of RHOA pathway, activation of CDC42 and cytoskeletal rearrangement. May be involved in presynaptic facilitation by mediating phorbol ester-induced synaptic potentiation. Phosphorylates gamma-aminobutyric acid receptor subunit gamma-2 (GABRG2), which reduces the response of GABA receptors to ethanol and benzodiazepines and may mediate acute tolerance to the intoxicating effects of ethanol. Upon PMA treatment, phosphorylates the capsaicin- and heat-activated cation channel TRPV1, which is required for bradykinin-induced sensitization of the heat response in nociceptive neurons. Is able to form a complex with PDLIM5 and N-type calcium channel, and may enhance channel activities and potentiates fast synaptic transmission by phosphorylating the pore-forming alpha subunit CACNA1B (CaV2.2). In prostate cancer cells, interacts with and phosphorylates STAT3, which increases DNA-binding and transcriptional activity of STAT3 and seems to be essential for prostate cancer cell invasion. Downstream of TLR4, plays an important role in the lipopolysaccharide (LPS)-induced immune response by phosphorylating and activating TICAM2/TRAM, which in turn activates the transcription factor IRF3 and subsequent cytokines production. In differentiating erythroid progenitors, is regulated by EPO and controls the protection against the TNFSF10/TRAIL-mediated apoptosis, via BCL2. May be involved in the regulation of the insulin-induced phosphorylation and activation of AKT1. Phosphorylates NLRP5/MATER and may thereby modulate AKT pathway activation in cumulus cells (PubMed:19542546). {ECO:0000269|PubMed:11884385, ECO:0000269|PubMed:1374067, ECO:0000269|PubMed:15355962, ECO:0000269|PubMed:16757566, ECO:0000269|PubMed:17603037, ECO:0000269|PubMed:17875639, ECO:0000269|PubMed:17875724, ECO:0000269|PubMed:19542546}.

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


Top

Fusion Gene Sequence for XRN1-PRKCE


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.

Top

Fusion Gene PPI Analysis for XRN1-PRKCE


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


Top

Related Drugs for XRN1-PRKCE


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgenePRKCEQ02156DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgenePRKCEQ02156DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational

Top

Related Diseases for XRN1-PRKCE


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgenePRKCEC0020429Hyperalgesia3CTD_human
TgenePRKCEC0458247Allodynia3CTD_human
TgenePRKCEC0751211Hyperalgesia, Primary3CTD_human
TgenePRKCEC0751212Hyperalgesia, Secondary3CTD_human
TgenePRKCEC0751213Tactile Allodynia3CTD_human
TgenePRKCEC0751214Hyperalgesia, Thermal3CTD_human
TgenePRKCEC2936719Mechanical Allodynia3CTD_human
TgenePRKCEC0002152Alloxan Diabetes1CTD_human
TgenePRKCEC0009402Colorectal Carcinoma1CTD_human;UNIPROT
TgenePRKCEC0009404Colorectal Neoplasms1CTD_human
TgenePRKCEC0011853Diabetes Mellitus, Experimental1CTD_human
TgenePRKCEC0011881Diabetic Nephropathy1CTD_human
TgenePRKCEC0013146Drug abuse1CTD_human
TgenePRKCEC0013170Drug habituation1CTD_human
TgenePRKCEC0013222Drug Use Disorders1CTD_human
TgenePRKCEC0017667Nodular glomerulosclerosis1CTD_human
TgenePRKCEC0023903Liver neoplasms1CTD_human
TgenePRKCEC0027051Myocardial Infarction1CTD_human
TgenePRKCEC0029231Organic Mental Disorders, Substance-Induced1CTD_human
TgenePRKCEC0033141Cardiomyopathies, Primary1CTD_human
TgenePRKCEC0036529Myocardial Diseases, Secondary1CTD_human
TgenePRKCEC0038433Streptozotocin Diabetes1CTD_human
TgenePRKCEC0038580Substance Dependence1CTD_human
TgenePRKCEC0038586Substance Use Disorders1CTD_human
TgenePRKCEC0151744Myocardial Ischemia1CTD_human
TgenePRKCEC0236969Substance-Related Disorders1CTD_human
TgenePRKCEC0242231Coronary Stenosis1CTD_human
TgenePRKCEC0345904Malignant neoplasm of liver1CTD_human
TgenePRKCEC0400966Non-alcoholic Fatty Liver Disease1CTD_human
TgenePRKCEC0740858Substance abuse problem1CTD_human
TgenePRKCEC0878544Cardiomyopathies1CTD_human
TgenePRKCEC1510472Drug Dependence1CTD_human
TgenePRKCEC3241937Nonalcoholic Steatohepatitis1CTD_human
TgenePRKCEC4316881Prescription Drug Abuse1CTD_human
TgenePRKCEC4721453Peripheral Nervous System Diseases1CTD_human