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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:PPIL2-UBE2L3 (FusionGDB2 ID:67565)

Fusion Gene Summary for PPIL2-UBE2L3

check button Fusion gene summary
Fusion gene informationFusion gene name: PPIL2-UBE2L3
Fusion gene ID: 67565
HgeneTgene
Gene symbol

PPIL2

UBE2L3

Gene ID

23759

7332

Gene namepeptidylprolyl isomerase like 2ubiquitin conjugating enzyme E2 L3
SynonymsCYC4|CYP60|Cyp-60|UBOX7|hCyP-60E2-F1|L-UBC|UBCH7|UbcM4
Cytomap

22q11.21

22q11.21

Type of geneprotein-codingprotein-coding
DescriptionRING-type E3 ubiquitin-protein ligase PPIL2PPIaseRING-type E3 ubiquitin transferase isomerase-like 2U-box domain containing 7cyclophilin, 60kDacyclophilin-60cyclophilin-like protein CyP-60peptidyl-prolyl cis-trans isomerase-like 2peptidylprolyl ciubiquitin-conjugating enzyme E2 L3E2 ubiquitin-conjugating enzyme L3ubiquitin carrier protein L3ubiquitin conjugating enzyme E2L 3ubiquitin-conjugating enzyme E2-F1ubiquitin-conjugating enzyme UBCH7ubiquitin-protein ligase L3
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000446951, ENST00000335025, 
ENST00000398831, ENST00000406385, 
ENST00000412327, ENST00000456792, 
ENST00000492445, 		ENST00000342192, 
ENST00000458578, ENST00000545681, 
Fusion gene scores* DoF score7 X 7 X 4=19620 X 14 X 7=1960
# samples 722
** MAII scorelog2(7/196*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(22/1960*10)=-3.15527822547791
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PPIL2 [Title/Abstract] AND UBE2L3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPPIL2(22043138)-UBE2L3(21975804), # samples:1
Anticipated loss of major functional domain due to fusion event.PPIL2-UBE2L3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PPIL2-UBE2L3 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgenePPIL2

GO:0000209

protein polyubiquitination

11435423

TgeneUBE2L3

GO:0000209

protein polyubiquitination

10888878|14765125

TgeneUBE2L3

GO:0006355

regulation of transcription, DNA-templated

17003263

TgeneUBE2L3

GO:0016567

protein ubiquitination

9990509|21532592

TgeneUBE2L3

GO:0070979

protein K11-linked ubiquitination

20061386

TgeneUBE2L3

GO:0071385

cellular response to glucocorticoid stimulus

17003263


check buttonFusion gene breakpoints across PPIL2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across UBE2L3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4OVTCGA-24-1928-01APPIL2chr22

22043138

+UBE2L3chr22

21975804

+


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Fusion Gene ORF analysis for PPIL2-UBE2L3

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-3CDSENST00000446951ENST00000342192PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
3UTR-3CDSENST00000446951ENST00000458578PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
3UTR-3CDSENST00000446951ENST00000545681PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
Frame-shiftENST00000335025ENST00000545681PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
Frame-shiftENST00000398831ENST00000545681PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
Frame-shiftENST00000406385ENST00000545681PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
Frame-shiftENST00000412327ENST00000545681PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
Frame-shiftENST00000456792ENST00000545681PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
Frame-shiftENST00000492445ENST00000545681PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
In-frameENST00000335025ENST00000342192PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
In-frameENST00000335025ENST00000458578PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
In-frameENST00000398831ENST00000342192PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
In-frameENST00000398831ENST00000458578PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
In-frameENST00000406385ENST00000342192PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
In-frameENST00000406385ENST00000458578PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
In-frameENST00000412327ENST00000342192PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
In-frameENST00000412327ENST00000458578PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
In-frameENST00000456792ENST00000342192PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
In-frameENST00000456792ENST00000458578PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
In-frameENST00000492445ENST00000342192PPIL2chr22

22043138

+UBE2L3chr22

21975804

+
In-frameENST00000492445ENST00000458578PPIL2chr22

22043138

+UBE2L3chr22

21975804

+

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 PPIL2-UBE2L3


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)
PPIL2chr2222043138+UBE2L3chr2221975803+1.01E-081
PPIL2chr2222043138+UBE2L3chr2221975803+1.01E-081

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.
genomic feature

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 PPIL2-UBE2L3


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/chr22:22043138/chr22:21975804)
- 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
HgenePPIL2chr22:22043138chr22:21975804ENST00000335025+1521197_2173791569.6666666666667Coiled coilOntology_term=ECO:0000255
HgenePPIL2chr22:22043138chr22:21975804ENST00000398831+1520197_217379521.0Coiled coilOntology_term=ECO:0000255
HgenePPIL2chr22:22043138chr22:21975804ENST00000406385+1521197_2173791239.0Coiled coilOntology_term=ECO:0000255
HgenePPIL2chr22:22043138chr22:21975804ENST00000412327+1521197_217379528.0Coiled coilOntology_term=ECO:0000255
HgenePPIL2chr22:22043138chr22:21975804ENST00000492445+1521197_217379549.0Coiled coilOntology_term=ECO:0000255
HgenePPIL2chr22:22043138chr22:21975804ENST00000335025+152135_1083791569.6666666666667DomainNote=U-box
HgenePPIL2chr22:22043138chr22:21975804ENST00000398831+152035_108379521.0DomainNote=U-box
HgenePPIL2chr22:22043138chr22:21975804ENST00000406385+152135_1083791239.0DomainNote=U-box
HgenePPIL2chr22:22043138chr22:21975804ENST00000412327+152135_108379528.0DomainNote=U-box
HgenePPIL2chr22:22043138chr22:21975804ENST00000492445+152135_108379549.0DomainNote=U-box

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePPIL2chr22:22043138chr22:21975804ENST00000335025+1521278_4333791569.6666666666667DomainPPIase cyclophilin-type
HgenePPIL2chr22:22043138chr22:21975804ENST00000398831+1520278_433379521.0DomainPPIase cyclophilin-type
HgenePPIL2chr22:22043138chr22:21975804ENST00000406385+1521278_4333791239.0DomainPPIase cyclophilin-type
HgenePPIL2chr22:22043138chr22:21975804ENST00000412327+1521278_433379528.0DomainPPIase cyclophilin-type
HgenePPIL2chr22:22043138chr22:21975804ENST00000492445+1521278_433379549.0DomainPPIase cyclophilin-type
TgeneUBE2L3chr22:22043138chr22:21975804ENST00000342192242_149103155.0DomainUBC core
TgeneUBE2L3chr22:22043138chr22:21975804ENST00000458578242_149161213.0DomainUBC core
TgeneUBE2L3chr22:22043138chr22:21975804ENST00000545681132_14971123.0DomainUBC core


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Fusion Gene Sequence for PPIL2-UBE2L3


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 PPIL2-UBE2L3


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 PPIL2-UBE2L3


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 PPIL2-UBE2L3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource