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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:PPP1R13B-XRCC3 (FusionGDB2 ID:67398)

Fusion Gene Summary for PPP1R13B-XRCC3

check button Fusion gene summary
Fusion gene informationFusion gene name: PPP1R13B-XRCC3
Fusion gene ID: 67398
HgeneTgene
Gene symbol

PPP1R13B

XRCC3

Gene ID

23368

7517

Gene nameprotein phosphatase 1 regulatory subunit 13BX-ray repair cross complementing 3
SynonymsASPP1|p53BP2-like|p85CMM6
Cytomap

14q32.33

14q32.33

Type of geneprotein-codingprotein-coding
Descriptionapoptosis-stimulating of p53 protein 1apoptosis-stimulating protein of p53, 1protein phosphatase 1, regulatory (inhibitor) subunit 13BDNA repair protein XRCC3X-ray repair complementing defective repair in Chinese hamster cells 3X-ray repair cross-complementing protein 3
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000202556, ENST00000423488, 
ENST00000555391, 		ENST00000554913, 
ENST00000352127, ENST00000553264, 
ENST00000555055, ENST00000445556, 
ENST00000554974, ENST00000555832, 
Fusion gene scores* DoF score16 X 10 X 10=16002 X 3 X 3=18
# samples 223
** MAII scorelog2(22/1600*10)=-2.86249647625006
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PPP1R13B [Title/Abstract] AND XRCC3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPPP1R13B(104313635)-XRCC3(104169664), # samples:2
Anticipated loss of major functional domain due to fusion event.PPP1R13B-XRCC3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PPP1R13B-XRCC3 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
HgenePPP1R13B

GO:0072332

intrinsic apoptotic signaling pathway by p53 class mediator

11684014


check buttonFusion gene breakpoints across PPP1R13B (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 XRCC3 (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
ChimerDB4ESCATCGA-LN-A4A1PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
ChimerDB4ESCATCGA-LN-A4A1PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
ChimerDB4ESCATCGA-LN-A4A1PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
ChimerDB4UCECTCGA-B5-A3FB-01APPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-


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Fusion Gene ORF analysis for PPP1R13B-XRCC3

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-shiftENST00000202556ENST00000554913PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
Frame-shiftENST00000202556ENST00000352127PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
Frame-shiftENST00000202556ENST00000553264PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
Frame-shiftENST00000202556ENST00000555055PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
Frame-shiftENST00000202556ENST00000445556PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
5CDS-intronENST00000202556ENST00000554974PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
5CDS-intronENST00000202556ENST00000555832PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-3CDSENST00000423488ENST00000554913PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-3CDSENST00000423488ENST00000352127PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-3CDSENST00000423488ENST00000553264PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-3CDSENST00000423488ENST00000555055PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-3CDSENST00000423488ENST00000445556PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-intronENST00000423488ENST00000554974PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-intronENST00000423488ENST00000555832PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-3CDSENST00000555391ENST00000554913PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-3CDSENST00000555391ENST00000352127PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-3CDSENST00000555391ENST00000553264PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-3CDSENST00000555391ENST00000555055PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-3CDSENST00000555391ENST00000445556PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-intronENST00000555391ENST00000554974PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
intron-intronENST00000555391ENST00000555832PPP1R13Bchr14

104313635

-XRCC3chr14

104169664

-
Frame-shiftENST00000202556ENST00000554913PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
Frame-shiftENST00000202556ENST00000352127PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
Frame-shiftENST00000202556ENST00000553264PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
Frame-shiftENST00000202556ENST00000555055PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
Frame-shiftENST00000202556ENST00000445556PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
5CDS-intronENST00000202556ENST00000554974PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
5CDS-intronENST00000202556ENST00000555832PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-3CDSENST00000423488ENST00000554913PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-3CDSENST00000423488ENST00000352127PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-3CDSENST00000423488ENST00000553264PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-3CDSENST00000423488ENST00000555055PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-3CDSENST00000423488ENST00000445556PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-intronENST00000423488ENST00000554974PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-intronENST00000423488ENST00000555832PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-3CDSENST00000555391ENST00000554913PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-3CDSENST00000555391ENST00000352127PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-3CDSENST00000555391ENST00000553264PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-3CDSENST00000555391ENST00000555055PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-3CDSENST00000555391ENST00000445556PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-intronENST00000555391ENST00000554974PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
intron-intronENST00000555391ENST00000555832PPP1R13Bchr14

104313636

-XRCC3chr14

104169664

-
Frame-shiftENST00000202556ENST00000554913PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
Frame-shiftENST00000202556ENST00000352127PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
Frame-shiftENST00000202556ENST00000553264PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
Frame-shiftENST00000202556ENST00000555055PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
Frame-shiftENST00000202556ENST00000445556PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
5CDS-intronENST00000202556ENST00000554974PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
5CDS-intronENST00000202556ENST00000555832PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-3CDSENST00000423488ENST00000554913PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-3CDSENST00000423488ENST00000352127PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-3CDSENST00000423488ENST00000553264PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-3CDSENST00000423488ENST00000555055PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-3CDSENST00000423488ENST00000445556PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-intronENST00000423488ENST00000554974PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-intronENST00000423488ENST00000555832PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-3CDSENST00000555391ENST00000554913PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-3CDSENST00000555391ENST00000352127PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-3CDSENST00000555391ENST00000553264PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-3CDSENST00000555391ENST00000555055PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-3CDSENST00000555391ENST00000445556PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-intronENST00000555391ENST00000554974PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-
intron-intronENST00000555391ENST00000555832PPP1R13Bchr14

104313636

-XRCC3chr14

104174996

-

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 PPP1R13B-XRCC3


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.

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Fusion Protein Features for PPP1R13B-XRCC3


check button Go to

FGviewer for the breakpoints of :-:

.
- 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
..
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: 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.

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 PPP1R13B-XRCC3


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 PPP1R13B-XRCC3


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 PPP1R13B-XRCC3


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 PPP1R13B-XRCC3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneXRCC3C0007114Malignant neoplasm of skin2CTD_human
TgeneXRCC3C0037286Skin Neoplasms2CTD_human
TgeneXRCC3C0006142Malignant neoplasm of breast1CTD_human
TgeneXRCC3C0014859Esophageal Neoplasms1CTD_human
TgeneXRCC3C0018671Head and Neck Neoplasms1CTD_human
TgeneXRCC3C0018675Head Neoplasms1CTD_human
TgeneXRCC3C0023176Lead Poisoning1CTD_human
TgeneXRCC3C0024623Malignant neoplasm of stomach1CTD_human
TgeneXRCC3C0024668Mammary Neoplasms, Experimental1CTD_human
TgeneXRCC3C0025202melanoma1CTD_human
TgeneXRCC3C0025500Mesothelioma1CTD_human
TgeneXRCC3C0027533Neck Neoplasms1CTD_human
TgeneXRCC3C0027626Neoplasm Invasiveness1CTD_human
TgeneXRCC3C0038356Stomach Neoplasms1CTD_human
TgeneXRCC3C0278996Malignant Head and Neck Neoplasm1CTD_human
TgeneXRCC3C0546837Malignant neoplasm of esophagus1CTD_human
TgeneXRCC3C0678222Breast Carcinoma1CTD_human
TgeneXRCC3C0746787Cancer of Neck1CTD_human
TgeneXRCC3C0751177Cancer of Head1CTD_human
TgeneXRCC3C0887900Upper Aerodigestive Tract Neoplasms1CTD_human
TgeneXRCC3C1257931Mammary Neoplasms, Human1CTD_human
TgeneXRCC3C1368275Pigmented Basal Cell Carcinoma1CTD_human
TgeneXRCC3C1458155Mammary Neoplasms1CTD_human
TgeneXRCC3C1708349Hereditary Diffuse Gastric Cancer1CTD_human
TgeneXRCC3C3151417MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 61CTD_human;UNIPROT
TgeneXRCC3C4704874Mammary Carcinoma, Human1CTD_human
TgeneXRCC3C4721806Carcinoma, Basal Cell1CTD_human