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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:PRKCA-LINC00963 (FusionGDB2 ID:HG5578TG100506190)

Fusion Gene Summary for PRKCA-LINC00963

check button Fusion gene summary
Fusion gene informationFusion gene name: PRKCA-LINC00963
Fusion gene ID: hg5578tg100506190
HgeneTgene
Gene symbol

PRKCA

LINC00963

Gene ID

5578

100506190

Gene nameprotein kinase C alphalong intergenic non-protein coding RNA 963
SynonymsAAG6|PKC-alpha|PKCA|PKCI+/-|PKCalpha|PRKACAMetaLnc9
Cytomap('PRKCA')('LINC00963')

17q24.2

9q34.11

Type of geneprotein-codingncRNA
Descriptionprotein kinase C alpha typePKC-Aaging-associated gene 6-
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000583361, ENST00000413366, 
Fusion gene scores* DoF score44 X 23 X 14=141684 X 3 X 4=48
# samples 464
** MAII scorelog2(46/14168*10)=-4.94485844580754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PRKCA [Title/Abstract] AND LINC00963 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPRKCA(64302245)-LINC00963(132265602), # 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
HgenePRKCA

GO:0006468

protein phosphorylation

10770950

HgenePRKCA

GO:0035408

histone H3-T6 phosphorylation

20228790

HgenePRKCA

GO:0043536

positive regulation of blood vessel endothelial cell migration

20011604

HgenePRKCA

GO:0090330

regulation of platelet aggregation

12724315



check button Fusion gene information
* 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
ChimerDB4LGGTCGA-HT-A617PRKCAchr17

64302245

+LINC00963chr9

132265602

+


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Fusion Gene ORF analysis for PRKCA-LINC00963

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
3UTR-3UTRENST00000583361ENST00000419300PRKCAchr17

64302245

+LINC00963chr9

132265602

+
5CDS-3UTRENST00000413366ENST00000419300PRKCAchr17

64302245

+LINC00963chr9

132265602

+

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 PRKCA-LINC00963


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)
PRKCAchr1764302245+LINC00963chr9132265601+0.0111595250.9888405
PRKCAchr1764302245+LINC00963chr9132265601+0.0111595250.9888405


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 PRKCA-LINC00963


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/:64302245/:132265602)
- 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
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 PRKCA-LINC00963


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 PRKCA-LINC00963


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 PRKCA-LINC00963


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 PRKCA-LINC00963


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePRKCAC0036341Schizophrenia2PSYGENET
HgenePRKCAC0002152Alloxan Diabetes1CTD_human
HgenePRKCAC0011853Diabetes Mellitus, Experimental1CTD_human
HgenePRKCAC0018800Cardiomegaly1CTD_human
HgenePRKCAC0021841Intestinal Neoplasms1CTD_human
HgenePRKCAC0032617Polyuria1CTD_human
HgenePRKCAC0033975Psychotic Disorders1PSYGENET
HgenePRKCAC0036337Schizoaffective Disorder1PSYGENET
HgenePRKCAC0038433Streptozotocin Diabetes1CTD_human
HgenePRKCAC0162283Nephrogenic Diabetes Insipidus1CTD_human
HgenePRKCAC0264423Asthma, Occupational1CTD_human
HgenePRKCAC0268443Acquired Nephrogenic Diabetes Insipidus1CTD_human
HgenePRKCAC0346627Intestinal Cancer1CTD_human
HgenePRKCAC0349204Nonorganic psychosis1PSYGENET
HgenePRKCAC0400966Non-alcoholic Fatty Liver Disease1CTD_human
HgenePRKCAC0677501Congenital Nephrogenic Diabetes Insipidus1CTD_human
HgenePRKCAC1383860Cardiac Hypertrophy1CTD_human
HgenePRKCAC1563705Nephrogenic Diabetes Insipidus, Type I1CTD_human
HgenePRKCAC1563706Nephrogenic Diabetes Insipidus, Type II1CTD_human
HgenePRKCAC3241937Nonalcoholic Steatohepatitis1CTD_human
HgenePRKCAC3542500ADH-Resistant Diabetes Insipidus1CTD_human