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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:XRCC6-UBE2D2 (FusionGDB2 ID:99790)

Fusion Gene Summary for XRCC6-UBE2D2

check button Fusion gene summary
Fusion gene informationFusion gene name: XRCC6-UBE2D2
Fusion gene ID: 99790
HgeneTgene
Gene symbol

XRCC6

UBE2D2

Gene ID

2547

7322

Gene nameX-ray repair cross complementing 6ubiquitin conjugating enzyme E2 D2
SynonymsCTC75|CTCBF|G22P1|KU70|ML8|TLAAE2(17)KB2|PUBC1|UBC4|UBC4/5|UBCH4|UBCH5B
Cytomap

22q13.2

5q31.2

Type of geneprotein-codingprotein-coding
DescriptionX-ray repair cross-complementing protein 65'-dRP lyase Ku705'-deoxyribose-5-phosphate lyase Ku7070 kDa subunit of Ku antigenATP-dependent DNA helicase 2 subunit 1ATP-dependent DNA helicase II, 70 kDa subunitCTC box binding factor 75 kDa subunitDNA ubiquitin-conjugating enzyme E2 D2(E3-independent) E2 ubiquitin-conjugating enzyme D2E2 ubiquitin-conjugating enzyme D2p53-regulated ubiquitin-conjugating enzyme 1ubiquitin carrier protein D2ubiquitin conjugating enzyme E2D 2ubiquitin-conjugating en
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000359308, ENST00000360079, 
ENST00000402580, ENST00000405506, 
ENST00000405878, ENST00000428575, 
ENST00000253815, ENST00000398733, 
ENST00000505548, ENST00000511725, 
Fusion gene scores* DoF score12 X 10 X 8=96022 X 8 X 13=2288
# samples 1535
** MAII scorelog2(15/960*10)=-2.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(35/2288*10)=-2.70866022494606
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: XRCC6 [Title/Abstract] AND UBE2D2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointXRCC6(42033795)-UBE2D2(138994171), # 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
HgeneXRCC6

GO:0002218

activation of innate immune response

28712728

HgeneXRCC6

GO:0045860

positive regulation of protein kinase activity

22504299

HgeneXRCC6

GO:0045893

positive regulation of transcription, DNA-templated

12145306

HgeneXRCC6

GO:0071480

cellular response to gamma radiation

26359349

HgeneXRCC6

GO:0097680

double-strand break repair via classical nonhomologous end joining

24095731

TgeneUBE2D2

GO:0000209

protein polyubiquitination

15247280

TgeneUBE2D2

GO:0016567

protein ubiquitination

9990509|14593114

TgeneUBE2D2

GO:0051865

protein autoubiquitination

21068390

TgeneUBE2D2

GO:0070936

protein K48-linked ubiquitination

20061386


check buttonFusion gene breakpoints across XRCC6 (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 UBE2D2 (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
ChimerDB4LGGTCGA-DU-6402-01AXRCC6chr22

42033795

+UBE2D2chr5

138994171

+
ChimerDB4LGGTCGA-DU-6402XRCC6chr22

42033795

+UBE2D2chr5

138994171

+


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Fusion Gene ORF analysis for XRCC6-UBE2D2

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
Frame-shiftENST00000359308ENST00000253815XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000359308ENST00000398733XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000359308ENST00000505548XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000359308ENST00000511725XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000360079ENST00000253815XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000360079ENST00000398733XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000360079ENST00000505548XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000360079ENST00000511725XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000402580ENST00000253815XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000402580ENST00000398733XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000402580ENST00000505548XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000402580ENST00000511725XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000405506ENST00000253815XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000405506ENST00000398733XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000405506ENST00000505548XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000405506ENST00000511725XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000405878ENST00000253815XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000405878ENST00000398733XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000405878ENST00000505548XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000405878ENST00000511725XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000428575ENST00000253815XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000428575ENST00000398733XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000428575ENST00000505548XRCC6chr22

42033795

+UBE2D2chr5

138994171

+
Frame-shiftENST00000428575ENST00000511725XRCC6chr22

42033795

+UBE2D2chr5

138994171

+

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 XRCC6-UBE2D2


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)
XRCC6chr2242033795+UBE2D2chr5138994170+2.70E-060.99999726
XRCC6chr2242033795+UBE2D2chr5138994170+2.70E-060.99999726
XRCC6chr2242033795+UBE2D2chr5138994170+2.70E-060.99999726
XRCC6chr2242033795+UBE2D2chr5138994170+2.70E-060.99999726

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.
genomic feature of top 1%

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Fusion Protein Features for XRCC6-UBE2D2


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/:42033795/:138994171)
- 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 XRCC6-UBE2D2


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 XRCC6-UBE2D2


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 XRCC6-UBE2D2


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 XRCC6-UBE2D2


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