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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-RGS9 (FusionGDB2 ID:68295)

Fusion Gene Summary for PRKCA-RGS9

check button Fusion gene summary
Fusion gene informationFusion gene name: PRKCA-RGS9
Fusion gene ID: 68295
HgeneTgene
Gene symbol

PRKCA

RGS9

Gene ID

5578

388531

Gene nameprotein kinase C alpharegulator of G protein signaling 9 binding protein
SynonymsAAG6|PKC-alpha|PKCA|PKCI+/-|PKCalpha|PRKACAPERRS|R9AP|RGS9
Cytomap

17q24.2

19q13.11

Type of geneprotein-codingprotein-coding
Descriptionprotein kinase C alpha typePKC-Aaging-associated gene 6regulator of G-protein signaling 9-binding proteinRGS9 anchor proteinRGS9-anchoring protein
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000413366, ENST00000583361, 
ENST00000443584, ENST00000449996, 
ENST00000262406, ENST00000577186, 
Fusion gene scores* DoF score44 X 23 X 14=1416813 X 16 X 5=1040
# samples 4615
** MAII scorelog2(46/14168*10)=-4.94485844580754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/1040*10)=-2.79354912253257
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PRKCA [Title/Abstract] AND RGS9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPRKCA(64637584)-RGS9(63221120), # samples:3
Anticipated loss of major functional domain due to fusion event.PRKCA-RGS9 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
PRKCA-RGS9 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PRKCA-RGS9 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PRKCA-RGS9 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PRKCA-RGS9 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
PRKCA-RGS9 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
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 buttonFusion gene breakpoints across PRKCA (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 RGS9 (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
ChimerDB4BRCATCGA-3C-AALI-01APRKCAchr17

64637584

+RGS9chr17

63221120

+
ChimerDB4BRCATCGA-GI-A2C9-01APRKCAchr17

64302245

+RGS9chr17

63115270

+
ChimerDB4BRCATCGA-3C-AALI-01APRKCAchr17

64637584

+RGS9chr17

63221120

+
ChimerDB4BRCATCGA-3C-AALI-01APRKCAchr17

64637588

+RGS9chr17

63221120

+
ChimerDB4BRCATCGA-3C-AALI-01APRKCAchr17

64637584

-RGS9chr17

63221120

+


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Fusion Gene ORF analysis for PRKCA-RGS9

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
In-frameENST00000413366ENST00000443584PRKCAchr17

64637584

+RGS9chr17

63221120

+
Frame-shiftENST00000413366ENST00000449996PRKCAchr17

64637584

+RGS9chr17

63221120

+
Frame-shiftENST00000413366ENST00000262406PRKCAchr17

64637584

+RGS9chr17

63221120

+
5CDS-intronENST00000413366ENST00000577186PRKCAchr17

64637584

+RGS9chr17

63221120

+
intron-3CDSENST00000583361ENST00000443584PRKCAchr17

64637584

+RGS9chr17

63221120

+
intron-3CDSENST00000583361ENST00000449996PRKCAchr17

64637584

+RGS9chr17

63221120

+
intron-3CDSENST00000583361ENST00000262406PRKCAchr17

64637584

+RGS9chr17

63221120

+
intron-intronENST00000583361ENST00000577186PRKCAchr17

64637584

+RGS9chr17

63221120

+
5CDS-intronENST00000413366ENST00000443584PRKCAchr17

64302245

+RGS9chr17

63115270

+
5CDS-intronENST00000413366ENST00000449996PRKCAchr17

64302245

+RGS9chr17

63115270

+
5CDS-intronENST00000413366ENST00000262406PRKCAchr17

64302245

+RGS9chr17

63115270

+
5CDS-intronENST00000413366ENST00000577186PRKCAchr17

64302245

+RGS9chr17

63115270

+
3UTR-intronENST00000583361ENST00000443584PRKCAchr17

64302245

+RGS9chr17

63115270

+
3UTR-intronENST00000583361ENST00000449996PRKCAchr17

64302245

+RGS9chr17

63115270

+
3UTR-intronENST00000583361ENST00000262406PRKCAchr17

64302245

+RGS9chr17

63115270

+
3UTR-intronENST00000583361ENST00000577186PRKCAchr17

64302245

+RGS9chr17

63115270

+
In-frameENST00000413366ENST00000443584PRKCAchr17

64637588

+RGS9chr17

63221120

+
Frame-shiftENST00000413366ENST00000449996PRKCAchr17

64637588

+RGS9chr17

63221120

+
Frame-shiftENST00000413366ENST00000262406PRKCAchr17

64637588

+RGS9chr17

63221120

+
5CDS-intronENST00000413366ENST00000577186PRKCAchr17

64637588

+RGS9chr17

63221120

+
intron-3CDSENST00000583361ENST00000443584PRKCAchr17

64637588

+RGS9chr17

63221120

+
intron-3CDSENST00000583361ENST00000449996PRKCAchr17

64637588

+RGS9chr17

63221120

+
intron-3CDSENST00000583361ENST00000262406PRKCAchr17

64637588

+RGS9chr17

63221120

+
intron-intronENST00000583361ENST00000577186PRKCAchr17

64637588

+RGS9chr17

63221120

+

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)
ENST00000413366PRKCAchr1764637584+ENST00000443584RGS9chr1763221120+1013426898383171
ENST00000413366PRKCAchr1764637588+ENST00000443584RGS9chr1763221120+1013426898383171

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
ENST00000413366ENST00000443584PRKCAchr1764637584+RGS9chr1763221120+0.36488340.6351166
ENST00000413366ENST00000443584PRKCAchr1764637588+RGS9chr1763221120+0.36488340.6351166

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Fusion Genomic Features for PRKCA-RGS9


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)
PRKCAchr1764637584+RGS9chr1763221119+1.32E-060.9999987
PRKCAchr1764637584+RGS9chr1763221119+1.32E-060.9999987

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 PRKCA-RGS9


check button Go to

FGviewer for the breakpoints of chr17:64637584-chr17:63221120

.
- 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
..
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: 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
HgenePRKCAchr17:64637584chr17:63221120ENST00000413366+41736_86133.33333333333334673.0Zinc fingerPhorbol-ester/DAG-type 1
HgenePRKCAchr17:64637588chr17:63221120ENST00000413366+41736_86133.33333333333334673.0Zinc fingerPhorbol-ester/DAG-type 1

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePRKCAchr17:64637584chr17:63221120ENST00000413366+417158_275133.33333333333334673.0DomainC2
HgenePRKCAchr17:64637584chr17:63221120ENST00000413366+417339_597133.33333333333334673.0DomainProtein kinase
HgenePRKCAchr17:64637584chr17:63221120ENST00000413366+417598_668133.33333333333334673.0DomainAGC-kinase C-terminal
HgenePRKCAchr17:64637588chr17:63221120ENST00000413366+417158_275133.33333333333334673.0DomainC2
HgenePRKCAchr17:64637588chr17:63221120ENST00000413366+417339_597133.33333333333334673.0DomainProtein kinase
HgenePRKCAchr17:64637588chr17:63221120ENST00000413366+417598_668133.33333333333334673.0DomainAGC-kinase C-terminal
HgenePRKCAchr17:64637584chr17:63221120ENST00000413366+417345_353133.33333333333334673.0Nucleotide bindingATP
HgenePRKCAchr17:64637588chr17:63221120ENST00000413366+417345_353133.33333333333334673.0Nucleotide bindingATP
HgenePRKCAchr17:64637584chr17:63221120ENST00000413366+417101_151133.33333333333334673.0Zinc fingerPhorbol-ester/DAG-type 2
HgenePRKCAchr17:64637588chr17:63221120ENST00000413366+417101_151133.33333333333334673.0Zinc fingerPhorbol-ester/DAG-type 2
TgeneRGS9chr17:64637584chr17:63221120ENST000002624061619219_280469.0675.0DomainNote=G protein gamma
TgeneRGS9chr17:64637584chr17:63221120ENST000002624061619298_413469.0675.0DomainRGS
TgeneRGS9chr17:64637584chr17:63221120ENST00000262406161930_105469.0675.0DomainDEP
TgeneRGS9chr17:64637584chr17:63221120ENST000004499961619219_280466.0672.0DomainNote=G protein gamma
TgeneRGS9chr17:64637584chr17:63221120ENST000004499961619298_413466.0672.0DomainRGS
TgeneRGS9chr17:64637584chr17:63221120ENST00000449996161930_105466.0672.0DomainDEP
TgeneRGS9chr17:64637588chr17:63221120ENST000002624061619219_280469.0675.0DomainNote=G protein gamma
TgeneRGS9chr17:64637588chr17:63221120ENST000002624061619298_413469.0675.0DomainRGS
TgeneRGS9chr17:64637588chr17:63221120ENST00000262406161930_105469.0675.0DomainDEP
TgeneRGS9chr17:64637588chr17:63221120ENST000004499961619219_280466.0672.0DomainNote=G protein gamma
TgeneRGS9chr17:64637588chr17:63221120ENST000004499961619298_413466.0672.0DomainRGS
TgeneRGS9chr17:64637588chr17:63221120ENST00000449996161930_105466.0672.0DomainDEP


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Fusion Gene Sequence for PRKCA-RGS9


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.
>In-frame_ENST00000413366_ENST00000443584_TCGA-3C-AALI-01A_PRKCA_chr17_64637584_+_RGS9_chr17_63221120_length(transcript)=1013nt_BP=426nt
GAGGCAAGAGGTGGTTGGGGGGGACCATGGCTGACGTTTTCCCGGGCAACGACTCCACGGCGTCTCAGGACGTGGCCAACCGCTTCGCCC
GCAAAGGGGCGCTGAGGCAGAAGAACGTGCACGAGGTGAAGGACCACAAATTCATCGCGCGCTTCTTCAAGCAGCCCACCTTCTGCAGCC
ACTGCACCGACTTCATCTGGGGGTTTGGGAAACAAGGCTTCCAGTGCCAAGTTTGCTGTTTTGTGGTCCACAAGAGGTGCCATGAATTTG
TTACTTTTTCTTGTCCGGGTGCGGATAAGGGACCCGACACTGATGACCCCAGGAGCAAGCACAAGTTCAAAATCCACACTTACGGAAGCC
CCACCTTCTGCGATCACTGTGGGTCACTGCTCTATGGACTTATCCATCAAGGGATGAAATGTGACACCGGGCCAGCACATGGCTCCCAGC
CCCCATCTGACCGTGTACACCGGGACCTGCATGCCCCCGTCTCCTTCTAGCCCCTTCTCCTCCTCCTGCCGCTCCCCCAGGAAGCCTTTC
GCCTCACCCAGCCGCTTCATCCGGCGACCCAGCACCACCATCTGCCCCTCACCCATCAGAGTGGCCTTGGAGAGCTCATCGGGCTTGGAG
CAGAAAGGGGAGTGCAGCGGGTCCATGGCCCCCCGTGGGCCCTCTGTCACCGAGAGCAGCGAGGCCTCCCTCGACACCTCCTGGCCTCGC
AGCCGGCCCAGGGCCCCTCCTAAGGCCCGCATGGCTCTGTCCTTCAGCAGGTTTCTGAGACGAGGCTGTCTGGCCTCACCTGTCTTTGCC
AGGCTCTCACCCAAGTGCCCTGCTGTGTCCCACGGGAGGGTGCAGCCCCTGGGGGACGTGGGCCAGCAGCTGCCACGATTGAAATCCAAG
AGAGTAGCAAAGTAAGAACCCGAAGGGGACGTGCCGTATGCATGGGTGGCTGTGGGTGTGCAGGCCTCTGCATGTGAATATGCATGCTTT

>In-frame_ENST00000413366_ENST00000443584_TCGA-3C-AALI-01A_PRKCA_chr17_64637584_+_RGS9_chr17_63221120_length(amino acids)=171AA_start in transcript=898_stop in transcript=383
MDFNRGSCWPTSPRGCTLPWDTAGHLGESLAKTGEARQPRLRNLLKDRAMRALGGALGRLRGQEVSREASLLSVTEGPRGAMDPLHSPFC

--------------------------------------------------------------
>In-frame_ENST00000413366_ENST00000443584_TCGA-3C-AALI-01A_PRKCA_chr17_64637588_+_RGS9_chr17_63221120_length(transcript)=1013nt_BP=426nt
GAGGCAAGAGGTGGTTGGGGGGGACCATGGCTGACGTTTTCCCGGGCAACGACTCCACGGCGTCTCAGGACGTGGCCAACCGCTTCGCCC
GCAAAGGGGCGCTGAGGCAGAAGAACGTGCACGAGGTGAAGGACCACAAATTCATCGCGCGCTTCTTCAAGCAGCCCACCTTCTGCAGCC
ACTGCACCGACTTCATCTGGGGGTTTGGGAAACAAGGCTTCCAGTGCCAAGTTTGCTGTTTTGTGGTCCACAAGAGGTGCCATGAATTTG
TTACTTTTTCTTGTCCGGGTGCGGATAAGGGACCCGACACTGATGACCCCAGGAGCAAGCACAAGTTCAAAATCCACACTTACGGAAGCC
CCACCTTCTGCGATCACTGTGGGTCACTGCTCTATGGACTTATCCATCAAGGGATGAAATGTGACACCGGGCCAGCACATGGCTCCCAGC
CCCCATCTGACCGTGTACACCGGGACCTGCATGCCCCCGTCTCCTTCTAGCCCCTTCTCCTCCTCCTGCCGCTCCCCCAGGAAGCCTTTC
GCCTCACCCAGCCGCTTCATCCGGCGACCCAGCACCACCATCTGCCCCTCACCCATCAGAGTGGCCTTGGAGAGCTCATCGGGCTTGGAG
CAGAAAGGGGAGTGCAGCGGGTCCATGGCCCCCCGTGGGCCCTCTGTCACCGAGAGCAGCGAGGCCTCCCTCGACACCTCCTGGCCTCGC
AGCCGGCCCAGGGCCCCTCCTAAGGCCCGCATGGCTCTGTCCTTCAGCAGGTTTCTGAGACGAGGCTGTCTGGCCTCACCTGTCTTTGCC
AGGCTCTCACCCAAGTGCCCTGCTGTGTCCCACGGGAGGGTGCAGCCCCTGGGGGACGTGGGCCAGCAGCTGCCACGATTGAAATCCAAG
AGAGTAGCAAAGTAAGAACCCGAAGGGGACGTGCCGTATGCATGGGTGGCTGTGGGTGTGCAGGCCTCTGCATGTGAATATGCATGCTTT

>In-frame_ENST00000413366_ENST00000443584_TCGA-3C-AALI-01A_PRKCA_chr17_64637588_+_RGS9_chr17_63221120_length(amino acids)=171AA_start in transcript=898_stop in transcript=383
MDFNRGSCWPTSPRGCTLPWDTAGHLGESLAKTGEARQPRLRNLLKDRAMRALGGALGRLRGQEVSREASLLSVTEGPRGAMDPLHSPFC

--------------------------------------------------------------

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Fusion Gene PPI Analysis for PRKCA-RGS9


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-RGS9


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-RGS9


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
TgeneRGS9C0013386Dyskinesia, Drug-Induced2CTD_human
TgeneRGS9C0751088Dyskinesia, Medication-Induced2CTD_human
TgeneRGS9C0033937Psychoses, Drug1CTD_human
TgeneRGS9C0033941Psychoses, Substance-Induced1CTD_human
TgeneRGS9C0036341Schizophrenia1CTD_human
TgeneRGS9C1842073Prolonged Electroretinal Response Suppression1CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT