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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:PVT1-MYC (FusionGDB2 ID:HG5820TG4609)

Fusion Gene Summary for PVT1-MYC

check button Fusion gene summary
Fusion gene informationFusion gene name: PVT1-MYC
Fusion gene ID: hg5820tg4609
HgeneTgene
Gene symbol

PVT1

MYC

Gene ID

5820

4609

Gene namePvt1 oncogeneMYC proto-oncogene, bHLH transcription factor
SynonymsLINC00079|MIR1204HG|NCRNA00079|onco-lncRNA-100MRTL|MYCC|bHLHe39|c-Myc
Cytomap('PVT1')('MYC')

8q24.21

8q24.21

Type of genencRNAprotein-coding
DescriptionCXCR4/PVT1 fusionHIST1H2BD/PVT1 fusionMIR1204, MIR1205, MIR1206 and MIR1207 hostOncogene PVT-1 (MYC activator)PVT1/CASC8 fusionPVT1/CCDC26 fusionPVT1/IFRD1 fusionPVT1/IRF2BP2 fusionPVT1/LINC00824 fusionPVT1/MYC fusionPVT1/NFIL3 fusionPVT1/NSMCEmyc proto-oncogene proteinavian myelocytomatosis viral oncogene homologclass E basic helix-loop-helix protein 39myc-related translation/localization regulatory factorproto-oncogene c-Myctranscription factor p64v-myc avian myelocytomatosis viral onco
Modification date2020032220200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000408388, ENST00000408388, 
Fusion gene scores* DoF score75 X 36 X 19=5130024 X 26 X 9=5616
# samples 10936
** MAII scorelog2(109/51300*10)=-5.55655878571749
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(36/5616*10)=-3.96347412397489
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PVT1 [Title/Abstract] AND MYC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPVT1(128806980)-MYC(128750494), # samples:2
PVT1(128903244)-MYC(128750494), # samples:2
PVT1(128903244)-MYC(128750497), # samples:2
PVT1(128806980)-MYC(128750497), # samples:2
PVT1(128806979)-MYC(128750493), # samples:2
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
TgeneMYC

GO:0000122

negative regulation of transcription by RNA polymerase II

9924025|19160485

TgeneMYC

GO:0006338

chromatin remodeling

21533051

TgeneMYC

GO:0006879

cellular iron ion homeostasis

9924025

TgeneMYC

GO:0006974

cellular response to DNA damage stimulus

17873522

TgeneMYC

GO:0007050

cell cycle arrest

10962037

TgeneMYC

GO:0008284

positive regulation of cell proliferation

15994933|19160485

TgeneMYC

GO:0010332

response to gamma radiation

19179467

TgeneMYC

GO:0010468

regulation of gene expression

21447833

TgeneMYC

GO:0010628

positive regulation of gene expression

15459207

TgeneMYC

GO:0032986

protein-DNA complex disassembly

19160485

TgeneMYC

GO:0035690

cellular response to drug

17873522|19179467

TgeneMYC

GO:0043280

positive regulation of cysteine-type endopeptidase activity involved in apoptotic process

19179467

TgeneMYC

GO:0045893

positive regulation of transcription, DNA-templated

10962037|17558397|18818310

TgeneMYC

GO:0045944

positive regulation of transcription by RNA polymerase II

10723141

TgeneMYC

GO:0048146

positive regulation of fibroblast proliferation

9924025|18987311

TgeneMYC

GO:0048147

negative regulation of fibroblast proliferation

10962037

TgeneMYC

GO:0050679

positive regulation of epithelial cell proliferation

18987311

TgeneMYC

GO:0051276

chromosome organization

10962037

TgeneMYC

GO:0051782

negative regulation of cell division

10962037

TgeneMYC

GO:0070371

ERK1 and ERK2 cascade

15459207

TgeneMYC

GO:0071456

cellular response to hypoxia

15459207

TgeneMYC

GO:2001022

positive regulation of response to DNA damage stimulus

19179467



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
ChimerDB4BRCATCGA-AN-A0FJ-01APVT1chr8

128806980

+MYCchr8

128752642

+
ChimerDB4BRCATCGA-AN-A0FJ-01APVT1chr8

128808254

+MYCchr8

128752642

+
ChimerDB4BRCATCGA-AQ-A54N-01APVT1chr8

128806980

+MYCchr8

128750494

+
ChimerDB4CESCTCGA-C5-A2M1-01APVT1chr8

128873729

+MYCchr8

128752932

+
ChimerDB4CESCTCGA-C5-A2M1-01APVT1chr8

128903244

+MYCchr8

128750494

+
ChimerDB4CESCTCGA-C5-A2M1-01APVT1chr8

128903244

+MYCchr8

128750497

+
ChimerDB4CESCTCGA-EA-A3HQ-01APVT1chr8

128806979

+MYCchr8

128750493

+
ChimerDB4CESCTCGA-EA-A3HQ-01APVT1chr8

128806979

+MYCchr8

128750496

+
ChimerDB4CESCTCGA-EA-A3HQ-01APVT1chr8

128808253

+MYCchr8

128750493

+
ChimerDB4CESCTCGA-LP-A5U2-01APVT1chr8

128806979

+MYCchr8

128750493

+
ChimerDB4LUADTCGA-38-4630-01APVT1chr8

128903244

+MYCchr8

128750494

+
ChimerDB4LUADTCGA-38-4630-01APVT1chr8

128903244

+MYCchr8

128750497

+
ChimerDB4SKCMTCGA-EE-A2M6-06APVT1chr8

128806980

+MYCchr8

128750494

+
ChimerDB4SKCMTCGA-EE-A2M6-06APVT1chr8

128806980

+MYCchr8

128750497

+
ChimerKB4..PVT1chr8

128902834

+MYCchr8

128902834

+


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Fusion Gene ORF analysis for PVT1-MYC

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-3CDSENST00000408388ENST00000259523PVT1chr8

128808254

+MYCchr8

128752642

+
3UTR-3CDSENST00000408388ENST00000377970PVT1chr8

128808254

+MYCchr8

128752642

+
3UTR-3CDSENST00000408388ENST00000524013PVT1chr8

128808254

+MYCchr8

128752642

+
3UTR-5UTRENST00000408388ENST00000259523PVT1chr8

128808253

+MYCchr8

128750493

+
3UTR-5UTRENST00000408388ENST00000377970PVT1chr8

128808253

+MYCchr8

128750493

+
3UTR-5UTRENST00000408388ENST00000524013PVT1chr8

128808253

+MYCchr8

128750493

+
intron-3CDSENST00000408388ENST00000259523PVT1chr8

128806980

+MYCchr8

128752642

+
intron-3CDSENST00000408388ENST00000377970PVT1chr8

128806980

+MYCchr8

128752642

+
intron-3CDSENST00000408388ENST00000524013PVT1chr8

128806980

+MYCchr8

128752642

+
intron-5UTRENST00000408388ENST00000259523PVT1chr8

128806980

+MYCchr8

128750494

+
intron-5UTRENST00000408388ENST00000259523PVT1chr8

128903244

+MYCchr8

128750494

+
intron-5UTRENST00000408388ENST00000259523PVT1chr8

128903244

+MYCchr8

128750497

+
intron-5UTRENST00000408388ENST00000259523PVT1chr8

128806979

+MYCchr8

128750496

+
intron-5UTRENST00000408388ENST00000259523PVT1chr8

128806979

+MYCchr8

128750493

+
intron-5UTRENST00000408388ENST00000259523PVT1chr8

128806980

+MYCchr8

128750497

+
intron-5UTRENST00000408388ENST00000377970PVT1chr8

128806980

+MYCchr8

128750494

+
intron-5UTRENST00000408388ENST00000377970PVT1chr8

128903244

+MYCchr8

128750494

+
intron-5UTRENST00000408388ENST00000377970PVT1chr8

128903244

+MYCchr8

128750497

+
intron-5UTRENST00000408388ENST00000377970PVT1chr8

128806979

+MYCchr8

128750496

+
intron-5UTRENST00000408388ENST00000377970PVT1chr8

128806979

+MYCchr8

128750493

+
intron-5UTRENST00000408388ENST00000377970PVT1chr8

128806980

+MYCchr8

128750497

+
intron-5UTRENST00000408388ENST00000524013PVT1chr8

128806980

+MYCchr8

128750494

+
intron-5UTRENST00000408388ENST00000524013PVT1chr8

128903244

+MYCchr8

128750494

+
intron-5UTRENST00000408388ENST00000524013PVT1chr8

128903244

+MYCchr8

128750497

+
intron-5UTRENST00000408388ENST00000524013PVT1chr8

128806979

+MYCchr8

128750496

+
intron-5UTRENST00000408388ENST00000524013PVT1chr8

128806979

+MYCchr8

128750493

+
intron-5UTRENST00000408388ENST00000524013PVT1chr8

128806980

+MYCchr8

128750497

+
intron-intronENST00000408388ENST00000259523PVT1chr8

128873729

+MYCchr8

128752932

+
intron-intronENST00000408388ENST00000259523PVT1chr8

128902834

+MYCchr8

128902834

+
intron-intronENST00000408388ENST00000377970PVT1chr8

128873729

+MYCchr8

128752932

+
intron-intronENST00000408388ENST00000377970PVT1chr8

128902834

+MYCchr8

128902834

+
intron-intronENST00000408388ENST00000524013PVT1chr8

128873729

+MYCchr8

128752932

+
intron-intronENST00000408388ENST00000524013PVT1chr8

128902834

+MYCchr8

128902834

+

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 PVT1-MYC


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 PVT1-MYC


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/:128806980/:128750494)
- 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 PVT1-MYC


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 PVT1-MYC


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 PVT1-MYC


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 PVT1-MYC


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePVT1C0019829Hodgkin Disease1CTD_human
HgenePVT1C0152266Mixed Cellularity Hodgkin Lymphoma1CTD_human
HgenePVT1C0152267Hodgkin lymphoma, lymphocyte depletion1CTD_human
HgenePVT1C0162538Immunoglobulin A deficiency (disorder)1CTD_human
HgenePVT1C0220597Adult Hodgkin Lymphoma1CTD_human
HgenePVT1C1266194Lymphocyte Rich Classical Hodgkin Lymphoma1CTD_human
HgenePVT1C1334968Nodular Lymphocyte Predominant Hodgkin Lymphoma1CTD_human
TgeneC0007102Malignant tumor of colon4CTD_human
TgeneC0009375Colonic Neoplasms4CTD_human
TgeneC2239176Liver carcinoma4CTD_human
TgeneC0007621Neoplastic Cell Transformation3CTD_human
TgeneC0019207Hepatoma, Morris3CTD_human
TgeneC0019208Hepatoma, Novikoff3CTD_human
TgeneC0023904Liver Neoplasms, Experimental3CTD_human
TgeneC0033578Prostatic Neoplasms3CTD_human
TgeneC0086404Experimental Hepatoma3CTD_human
TgeneC0376358Malignant neoplasm of prostate3CTD_human
TgeneC0023903Liver neoplasms2CTD_human
TgeneC0024121Lung Neoplasms2CTD_human
TgeneC0024623Malignant neoplasm of stomach2CTD_human
TgeneC0038356Stomach Neoplasms2CTD_human
TgeneC0152013Adenocarcinoma of lung (disorder)2CTD_human
TgeneC0235874Disease Exacerbation2CTD_human
TgeneC0242379Malignant neoplasm of lung2CTD_human
TgeneC0345904Malignant neoplasm of liver2CTD_human
TgeneC1708349Hereditary Diffuse Gastric Cancer2CTD_human
TgeneC0001418Adenocarcinoma1CTD_human
TgeneC0005684Malignant neoplasm of urinary bladder1CTD_human
TgeneC0005695Bladder Neoplasm1CTD_human
TgeneC0006826Malignant Neoplasms1CGI;CTD_human
TgeneC0007097Carcinoma1CTD_human
TgeneC0007129Merkel cell carcinoma1CTD_human
TgeneC0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneC0007137Squamous cell carcinoma1CTD_human
TgeneC0007194Hypertrophic Cardiomyopathy1CTD_human
TgeneC0007873Uterine Cervical Neoplasm1CTD_human
TgeneC0008924Cleft upper lip1CTD_human
TgeneC0008925Cleft Palate1CTD_human
TgeneC0009402Colorectal Carcinoma1CTD_human
TgeneC0009404Colorectal Neoplasms1CTD_human
TgeneC0014170Endometrial Neoplasms1CTD_human
TgeneC0015695Fatty Liver1CTD_human
TgeneC0017636Glioblastoma1CTD_human
TgeneC0018923Hemangiosarcoma1CTD_human
TgeneC0023467Leukemia, Myelocytic, Acute1CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0025149Medulloblastoma1CTD_human
TgeneC0026998Acute Myeloid Leukemia, M11CTD_human
TgeneC0027627Neoplasm Metastasis1CTD_human
TgeneC0027651Neoplasms1CTD_human
TgeneC0027819Neuroblastoma1CGI;CTD_human
TgeneC0029463Osteosarcoma1CTD_human
TgeneC0030297Pancreatic Neoplasm1CTD_human
TgeneC0079744Diffuse Large B-Cell Lymphoma1CTD_human
TgeneC0085413Polycystic Kidney, Autosomal Dominant1CTD_human
TgeneC0086692Benign Neoplasm1CTD_human
TgeneC0149721Left Ventricular Hypertrophy1CTD_human
TgeneC0205641Adenocarcinoma, Basal Cell1CTD_human
TgeneC0205642Adenocarcinoma, Oxyphilic1CTD_human
TgeneC0205643Carcinoma, Cribriform1CTD_human
TgeneC0205644Carcinoma, Granular Cell1CTD_human
TgeneC0205645Adenocarcinoma, Tubular1CTD_human
TgeneC0205696Anaplastic carcinoma1CTD_human
TgeneC0205697Carcinoma, Spindle-Cell1CTD_human
TgeneC0205698Undifferentiated carcinoma1CTD_human
TgeneC0205699Carcinomatosis1CTD_human
TgeneC0205833Medullomyoblastoma1CTD_human
TgeneC0206093Neuroectodermal Tumors1CTD_human
TgeneC0278510Childhood Medulloblastoma1CTD_human
TgeneC0278876Adult Medulloblastoma1CTD_human
TgeneC0333704Chromosome Breaks1CTD_human
TgeneC0334588Giant Cell Glioblastoma1CTD_human
TgeneC0346647Malignant neoplasm of pancreas1CTD_human
TgeneC0376628Chromosome Breakage1CTD_human
TgeneC0476089Endometrial Carcinoma1CTD_human
TgeneC0751291Desmoplastic Medulloblastoma1CTD_human
TgeneC0887850Polycystic Kidney, Type 1 Autosomal Dominant Disease1CTD_human
TgeneC0919267ovarian neoplasm1CTD_human
TgeneC1140680Malignant neoplasm of ovary1CTD_human
TgeneC1176475Ductal Carcinoma1CTD_human
TgeneC1275668Melanotic medulloblastoma1CTD_human
TgeneC1621958Glioblastoma Multiforme1CTD_human
TgeneC1837218Cleft palate, isolated1CTD_human
TgeneC1879321Acute Myeloid Leukemia (AML-M2)1CTD_human
TgeneC2711227Steatohepatitis1CTD_human
TgeneC2713368Hematopoetic Myelodysplasia1CTD_human
TgeneC2751306Polycystic kidney disease, type 21CTD_human
TgeneC3463824MYELODYSPLASTIC SYNDROME1CTD_human
TgeneC4048328cervical cancer1CTD_human
TgeneC4551472Hypertrophic obstructive cardiomyopathy1CTD_human