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:PRKCA-IGF2BP3 (FusionGDB2 ID:68276)

Fusion Gene Summary for PRKCA-IGF2BP3

check button Fusion gene summary
Fusion gene informationFusion gene name: PRKCA-IGF2BP3
Fusion gene ID: 68276
HgeneTgene
Gene symbol

PRKCA

IGF2BP3

Gene ID

5578

10643

Gene nameprotein kinase C alphainsulin like growth factor 2 mRNA binding protein 3
SynonymsAAG6|PKC-alpha|PKCA|PKCI+/-|PKCalpha|PRKACACT98|IMP-3|IMP3|KOC|KOC1|VICKZ3
Cytomap

17q24.2

7p15.3

Type of geneprotein-codingprotein-coding
Descriptionprotein kinase C alpha typePKC-Aaging-associated gene 6insulin-like growth factor 2 mRNA-binding protein 3IGF-II mRNA-binding protein 3IGF2 mRNA-binding protein 3KH domain containing protein overexpressed in cancerVICKZ family member 3cancer/testis antigen 98
Modification date2020032720200313
UniProtAcc.

O00425

Ensembl transtripts involved in fusion geneENST00000413366, ENST00000583361, 
ENST00000258729, ENST00000491719, 
Fusion gene scores* DoF score44 X 23 X 14=141687 X 6 X 5=210
# samples 467
** MAII scorelog2(46/14168*10)=-4.94485844580754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/210*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PRKCA [Title/Abstract] AND IGF2BP3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointIGF2BP3(23381683)-PRKCA(64637473), # samples:3
PRKCA(64492401)-IGF2BP3(23358873), # samples:3
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 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 IGF2BP3 (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
ChimerDB4LUSCTCGA-33-4587-01APRKCAchr17

64492401

+IGF2BP3chr7

23358873

-
ChimerDB4LUSCTCGA-33-4587PRKCAchr17

64492401

+IGF2BP3chr7

23358873

-
ChimerDB4LUSCTCGA-33-4587-01APRKCAchr17

64492401

-IGF2BP3chr7

23358873

-


Top

Fusion Gene ORF analysis for PRKCA-IGF2BP3

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-frameENST00000413366ENST00000258729PRKCAchr17

64492401

+IGF2BP3chr7

23358873

-
5CDS-intronENST00000413366ENST00000491719PRKCAchr17

64492401

+IGF2BP3chr7

23358873

-
intron-3CDSENST00000583361ENST00000258729PRKCAchr17

64492401

+IGF2BP3chr7

23358873

-
intron-intronENST00000583361ENST00000491719PRKCAchr17

64492401

+IGF2BP3chr7

23358873

-

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)
ENST00000413366PRKCAchr1764492401+ENST00000258729IGF2BP3chr723358873-300431414850278

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
ENST00000413366ENST00000258729PRKCAchr1764492401+IGF2BP3chr723358873-0.0005991040.99940085

Top

Fusion Genomic Features for PRKCA-IGF2BP3


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)

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 PRKCA-IGF2BP3


check button Go to

FGviewer for the breakpoints of chr17:64492401-chr7:23358873

.
- 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
.IGF2BP3

O00425

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: RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). This transcript 'caging' into mRNPs allows mRNA transport and transient storage. It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. Binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. Binds to beta-actin/ACTB and MYC transcripts. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. {ECO:0000269|PubMed:16541107, ECO:0000269|PubMed:23640942}.

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
HgenePRKCAchr17:64492401chr7:23358873ENST00000413366+31736_8696.0673.0Zinc fingerPhorbol-ester/DAG-type 1
TgeneIGF2BP3chr17:64492401chr7:23358873ENST00000258729915405_470401.0580.0DomainKH 3
TgeneIGF2BP3chr17:64492401chr7:23358873ENST00000258729915487_553401.0580.0DomainKH 4

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePRKCAchr17:64492401chr7:23358873ENST00000413366+317158_27596.0673.0DomainC2
HgenePRKCAchr17:64492401chr7:23358873ENST00000413366+317339_59796.0673.0DomainProtein kinase
HgenePRKCAchr17:64492401chr7:23358873ENST00000413366+317598_66896.0673.0DomainAGC-kinase C-terminal
HgenePRKCAchr17:64492401chr7:23358873ENST00000413366+317345_35396.0673.0Nucleotide bindingATP
HgenePRKCAchr17:64492401chr7:23358873ENST00000413366+317101_15196.0673.0Zinc fingerPhorbol-ester/DAG-type 2
TgeneIGF2BP3chr17:64492401chr7:23358873ENST00000258729915195_260401.0580.0DomainKH 1
TgeneIGF2BP3chr17:64492401chr7:23358873ENST00000258729915276_343401.0580.0DomainKH 2
TgeneIGF2BP3chr17:64492401chr7:23358873ENST000002587299152_75401.0580.0DomainRRM 1
TgeneIGF2BP3chr17:64492401chr7:23358873ENST0000025872991581_156401.0580.0DomainRRM 2


Top

Fusion Gene Sequence for PRKCA-IGF2BP3


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_ENST00000258729_TCGA-33-4587-01A_PRKCA_chr17_64492401_+_IGF2BP3_chr7_23358873_length(transcript)=3004nt_BP=314nt
GAGGCAAGAGGTGGTTGGGGGGGACCATGGCTGACGTTTTCCCGGGCAACGACTCCACGGCGTCTCAGGACGTGGCCAACCGCTTCGCCC
GCAAAGGGGCGCTGAGGCAGAAGAACGTGCACGAGGTGAAGGACCACAAATTCATCGCGCGCTTCTTCAAGCAGCCCACCTTCTGCAGCC
ACTGCACCGACTTCATCTGGGGGTTTGGGAAACAAGGCTTCCAGTGCCAAGTTTGCTGTTTTGTGGTCCACAAGAGGTGCCATGAATTTG
TTACTTTTTCTTGTCCGGGTGCGGATAAGGGACCCGACACTGATCAATCAGAAACGGAGACTGTTCATCTGTTTATCCCAGCTCTATCAG
TCGGTGCCATCATCGGCAAGCAGGGCCAGCACATCAAGCAGCTTTCTCGCTTTGCTGGAGCTTCAATTAAGATTGCTCCAGCGGAAGCAC
CAGATGCTAAAGTGAGGATGGTGATTATCACTGGACCACCAGAGGCTCAGTTCAAGGCTCAGGGAAGAATTTATGGAAAAATTAAAGAAG
AAAACTTTGTTAGTCCTAAAGAAGAGGTGAAACTTGAAGCTCATATCAGAGTGCCATCCTTTGCTGCTGGCAGAGTTATTGGAAAAGGAG
GCAAAACGGTGAATGAACTTCAGAATTTGTCAAGTGCAGAAGTTGTTGTCCCTCGTGACCAGACACCTGATGAGAATGACCAAGTGGTTG
TCAAAATAACTGGTCACTTCTATGCTTGCCAGGTTGCCCAGAGAAAAATTCAGGAAATTCTGACTCAGGTAAAGCAGCACCAACAACAGA
AGGCTCTGCAAAGTGGACCACCTCAGTCAAGACGGAAGTAAAGGCTCAGGAAACAGCCCACCACAGAGGCAGATGCCAAACCAAAGACAG
ATTGCTTAACCAACAGATGGGCGCTGACCCCCTATCCAGAATCACATGCACAAGTTTTTACCTAGCCAGTTGTTTCTGAGGACCAGGCAA
CTTTTGAACTCCTGTCTCTGTGAGAATGTATACTTTATGCTCTCTGAAATGTATGACACCCAGCTTTAAAACAAACAAACAAACAAACAA
AAAAAGGGTGGGGGAGGGAGGGAAAGAGAAGAGCTCTGCACTTCCCTTTGTTGTAGTCTCACAGTATAACAGATATTCTAATTCTTCTTA
ATATTCCCCCATAATGCCAGAAATTGGCTTAATGATGCTTTCACTAAATTCATCAAATAGATTGCTCCTAAATCCAATTGTTAAAATTGG
ATCAGAATAATTATCACAGGAACTTAAATGTTAAGCCATTAGCATAGAAAAACTGTTCTCAGTTTTATTTTTACCTAACACTAACATGAG
TAACCTAAGGGAAGTGCTGAATGGTGTTGGCAGGGGTATTAAACGTGCATTTTTACTCAACTACCTCAGGTATTCAGTAATACAATGAAA
AGCAAAATTGTTCCTTTTTTTTGAAAATTTTATATACTTTATAATGATAGAAGTCCAACCGTTTTTTAAAAAATAAATTTAAAATTTAAC
AGCAATCAGCTAACAGGCAAATTAAGATTTTTACTTCTGGCTGGTGACAGTAAAGCTGGAAAATTAATTTCAGGGTTTTTTGAGGCTTTT
GACACAGTTATTAGTTAAATCAAATGTTCAAAAATACGGAGCAGTGCCTAGTATCTGGAGAGCAGCACTACCATTTATTCTTTCATTTAT
AGTTGGGAAAGTTTTTGACGGTACTAACAAAGTGGTCGCAGGAGATTTTGGAACGGCTGGTTTAAATGGCTTCAGGAGACTTCAGTTTTT
TGTTTAGCTACATGATTGAATGCATAATAAATGCTTTGTGCTTCTGACTATCAATACCTAAAGAAAGTGCATCAGTGAAGAGATGCAAGA
CTTTCAACTGACTGGCAAAAAGCAAGCTTTAGCTTGTCTTATAGGATGCTTAGTTTGCCACTACACTTCAGACCAATGGGACAGTCATAG
ATGGTGTGACAGTGTTTAAACGCAACAAAAGGCTACATTTCCATGGGGCCAGCACTGTCATGAGCCTCACTAAGCTATTTTGAAGATTTT
TAAGCACTGATAAATTAAAAAAAAAAAATTAGACTCCACCTTAAGTAGTAAAGTATAACAGGATTTCTGTATACTGTGCAATCAGTTCTT
TGAAAAAAAAGTCAAAAGATAGAGAATACAAGAAAAGTTTTTGGGATATAATTTGAATGACTGTGAAAACATATGACCTTTGATAACGAA
CTCATTTGCTCACTCCTTGACAGCAAAGCCCAGTACGTACAATTGTGTTGGGTGTGGGTGGTCTCCAAGGCCACGCTGCTCTCTGAATTG
ATTTTTTGAGTTTTGTTTGTAAGATGATCACAGTCATGTTACACTGATCTAAAGGACATATATATAACCCTTTAAAAAAAAAATCACTGC
CTCATTCTTATTTCAAGATGAATTTCTATACAGACTAGATGTTTTTCTGAAGATCAATTAGACATTTTGAAAATGATTTAAAGTGTTTTC
CTTAATGTTCTCTGAAAACAAGTTTCTTTTGTAGTTTTAACCAAAAAAGTGCCCTTTTTGTCACTGGATTCTCCTAGCATTCATGATTTT
TTTTTCATACAATGAATTAAAATTGCTAAAATCATGGACTGGCTTTCTGGTTGGATTTCAGGTAAGATGTGTTTAAGGCCAGAGCTTTTC
TCAGTATTTGATTTTTTTCCCCAATATTTGATTTTTTAAAAATATACACATAGGTGCTGCATTTATATCTGCTGGTTTAAATTCTGTCAT
ATTTCACTTCTAGCCTTTTAGTATGGCAAATCATATTTTACTTTTACTTAAGCATTTGTAATTTGGAGTATCTGGTACTAGCTAAGAAAT
AATTCTATAATTGAGTTTTGTACTCACCATATATGGATCATTCCTCATGTATAATGTGCCCCAAATGCAGCTTCATTTTCCAGATACCTT

>In-frame_ENST00000413366_ENST00000258729_TCGA-33-4587-01A_PRKCA_chr17_64492401_+_IGF2BP3_chr7_23358873_length(amino acids)=278AA_start in transcript=14_stop in transcript=850
MGGTMADVFPGNDSTASQDVANRFARKGALRQKNVHEVKDHKFIARFFKQPTFCSHCTDFIWGFGKQGFQCQVCCFVVHKRCHEFVTFSC
PGADKGPDTDQSETETVHLFIPALSVGAIIGKQGQHIKQLSRFAGASIKIAPAEAPDAKVRMVIITGPPEAQFKAQGRIYGKIKEENFVS
PKEEVKLEAHIRVPSFAAGRVIGKGGKTVNELQNLSSAEVVVPRDQTPDENDQVVVKITGHFYACQVAQRKIQEILTQVKQHQQQKALQS

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

Top

Fusion Gene PPI Analysis for PRKCA-IGF2BP3


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 PRKCA-IGF2BP3


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

Top

Related Diseases for PRKCA-IGF2BP3


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
TgeneIGF2BP3C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneIGF2BP3C0031149Peritoneal Neoplasms1CTD_human
TgeneIGF2BP3C0345967Malignant mesothelioma1CTD_human
TgeneIGF2BP3C0346990Carcinomatosis of peritoneal cavity1CTD_human
TgeneIGF2BP3C2239176Liver carcinoma1CTD_human