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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:PCNA-PAX3 (FusionGDB2 ID:HG5111TG5077)

Fusion Gene Summary for PCNA-PAX3

check button Fusion gene summary
Fusion gene informationFusion gene name: PCNA-PAX3
Fusion gene ID: hg5111tg5077
HgeneTgene
Gene symbol

PCNA

PAX3

Gene ID

5111

5077

Gene nameproliferating cell nuclear antigenpaired box 3
SynonymsATLD2CDHS|HUP2|WS1|WS3
Cytomap('PCNA')('PAX3')

20p12.3

2q36.1

Type of geneprotein-codingprotein-coding
Descriptionproliferating cell nuclear antigenDNA polymerase delta auxiliary proteincyclinpaired box protein Pax-3paired box homeotic gene 3paired domain gene 3paired domain gene HuP2transcriptional factor PAX3
Modification date2020032720200313
UniProtAcc.

P23760

Ensembl transtripts involved in fusion geneENST00000379143, ENST00000379160, 
Fusion gene scores* DoF score5 X 5 X 1=258 X 11 X 3=264
# samples 59
** MAII scorelog2(5/25*10)=1
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(9/264*10)=-1.55254102302878
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PCNA [Title/Abstract] AND PAX3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPCNA(5095604)-PAX3(223143686), # 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
HgenePCNA

GO:0006298

mismatch repair

11005803

HgenePCNA

GO:0019985

translesion synthesis

20129063

HgenePCNA

GO:0032077

positive regulation of deoxyribonuclease activity

19443450

HgenePCNA

GO:0034644

cellular response to UV

24939902

TgenePAX3

GO:0045893

positive regulation of transcription, DNA-templated

11863357

TgenePAX3

GO:0045944

positive regulation of transcription by RNA polymerase II

11863357



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
ChiTaRS5.0N/ABI857100PCNAchr20

5095604

-PAX3chr2

223143686

-


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Fusion Gene ORF analysis for PCNA-PAX3

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-intronENST00000379143ENST00000258387PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379143ENST00000336840PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379143ENST00000344493PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379143ENST00000350526PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379143ENST00000392069PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379143ENST00000392070PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379143ENST00000409551PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379143ENST00000409828PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379143ENST00000464706PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379160ENST00000258387PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379160ENST00000336840PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379160ENST00000344493PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379160ENST00000350526PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379160ENST00000392069PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379160ENST00000392070PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379160ENST00000409551PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379160ENST00000409828PCNAchr20

5095604

-PAX3chr2

223143686

-
5CDS-intronENST00000379160ENST00000464706PCNAchr20

5095604

-PAX3chr2

223143686

-

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 PCNA-PAX3


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)


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Fusion Protein Features for PCNA-PAX3


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/:5095604/:223143686)
- 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
.PAX3

P23760

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: Transcription factor that may regulate cell proliferation, migration and apoptosis. Involved in neural development and myogenesis. Transcriptional activator of MITF, acting synergistically with SOX10 (PubMed:21965087). {ECO:0000269|PubMed:16951170, ECO:0000269|PubMed:21965087}.

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 PCNA-PAX3


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 PCNA-PAX3


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 PCNA-PAX3


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 PCNA-PAX3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePCNAC0007102Malignant tumor of colon2CTD_human
HgenePCNAC0009375Colonic Neoplasms2CTD_human
HgenePCNAC0001418Adenocarcinoma1CTD_human
HgenePCNAC0006118Brain Neoplasms1CTD_human
HgenePCNAC0017668Focal glomerulosclerosis1CTD_human
HgenePCNAC0022116Ischemia1CTD_human
HgenePCNAC0024121Lung Neoplasms1CTD_human
HgenePCNAC0027659Neoplasms, Experimental1CTD_human
HgenePCNAC0030246Pustulosis of Palms and Soles1CTD_human
HgenePCNAC0033860Psoriasis1CTD_human
HgenePCNAC0086432Hyalinosis, Segmental Glomerular1CTD_human
HgenePCNAC0153633Malignant neoplasm of brain1CTD_human
HgenePCNAC0205641Adenocarcinoma, Basal Cell1CTD_human
HgenePCNAC0205642Adenocarcinoma, Oxyphilic1CTD_human
HgenePCNAC0205643Carcinoma, Cribriform1CTD_human
HgenePCNAC0205644Carcinoma, Granular Cell1CTD_human
HgenePCNAC0205645Adenocarcinoma, Tubular1CTD_human
HgenePCNAC0206624Hepatoblastoma1CTD_human
HgenePCNAC0242379Malignant neoplasm of lung1CTD_human
HgenePCNAC0496899Benign neoplasm of brain, unspecified1CTD_human
HgenePCNAC0750974Brain Tumor, Primary1CTD_human
HgenePCNAC0750977Recurrent Brain Neoplasm1CTD_human
HgenePCNAC0750979Primary malignant neoplasm of brain1CTD_human
HgenePCNAC1527390Neoplasms, Intracranial1CTD_human
HgenePCNAC4014676ATAXIA-TELANGIECTASIA-LIKE DISORDER 21ORPHANET;UNIPROT
TgeneC1847800Waardenburg Syndrome Type 133CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0079661Klein's Syndrome16CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC3266898Waardenburg Syndrome12CLINGEN;CTD_human;GENOMICS_ENGLAND
TgeneC1852510Craniofacial deafness hand syndrome5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0038219Status Dysraphicus4CTD_human
TgeneC0080178Spina Bifida4CTD_human
TgeneC0266508Rachischisis4CTD_human
TgeneC0011999Diastematomyelia3CTD_human
TgeneC0027794Neural Tube Defects3CTD_human
TgeneC0027806Neurenteric Cyst3CTD_human
TgeneC0080218Tethered Cord Syndrome3CTD_human
TgeneC0152234Iniencephaly3CTD_human
TgeneC0152426Craniorachischisis3CTD_human
TgeneC0266453Exencephaly3CTD_human
TgeneC0344479Spinal Cord Myelodysplasia3CTD_human
TgeneC0599973Waardenburg Anophthalmia Syndrome3ORPHANET
TgeneC0702169Acrania3CTD_human
TgeneC0206655Alveolar rhabdomyosarcoma2CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC0011052Prelingual Deafness1CTD_human
TgeneC0011053Deafness1CTD_human
TgeneC0018566Congenital Hand Deformities1CTD_human
TgeneC0086395Hearing Loss, Extreme1CTD_human
TgeneC0205944Sarcoma, Epithelioid1CTD_human
TgeneC0205945Sarcoma, Spindle Cell1CTD_human
TgeneC0265541Cranioschisis1CTD_human
TgeneC0376634Craniofacial Abnormalities1CTD_human
TgeneC0497552Congenital neurologic anomalies1CTD_human
TgeneC0581883Complete Hearing Loss1CTD_human
TgeneC0751068Deafness, Acquired1CTD_human
TgeneC1261473Sarcoma1CTD_human
TgeneC1710096Sinonasal undifferentiated carcinoma1CTD_human
TgeneC3665473Bilateral Deafness1CTD_human
TgeneC4082305Deaf Mutism1CTD_human