FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:RBFA-XRCC5 (FusionGDB2 ID:72182)

Fusion Gene Summary for RBFA-XRCC5

check button Fusion gene summary
Fusion gene informationFusion gene name: RBFA-XRCC5
Fusion gene ID: 72182
HgeneTgene
Gene symbol

RBFA

XRCC5

Gene ID

79863

7520

Gene nameribosome binding factor AX-ray repair cross complementing 5
SynonymsC18orf22|HsT169KARP-1|KARP1|KU80|KUB2|Ku86|NFIV
Cytomap

18q23

2q35

Type of geneprotein-codingprotein-coding
Descriptionputative ribosome-binding factor A, mitochondrialribosome binding factor A (putative)X-ray repair cross-complementing protein 586 kDa subunit of Ku antigenATP-dependent DNA helicase 2 subunit 2ATP-dependent DNA helicase II 80 kDa subunitCTC box-binding factor 85 kDa subunitCTC85CTCBFDNA repair protein XRCC5Ku autoantigen, 80kDaKu
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000306735, ENST00000586847, 
ENST00000262197, 		ENST00000392133, 
ENST00000392132, ENST00000471649, 
Fusion gene scores* DoF score6 X 7 X 6=2529 X 6 X 5=270
# samples 810
** MAII scorelog2(8/252*10)=-1.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/270*10)=-1.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RBFA [Title/Abstract] AND XRCC5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRBFA(77802219)-XRCC5(217054948), # samples:3
Anticipated loss of major functional domain due to fusion event.RBFA-XRCC5 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
RBFA-XRCC5 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgeneXRCC5

GO:0002218

activation of innate immune response

28712728

TgeneXRCC5

GO:0006303

double-strand break repair via nonhomologous end joining

26359349

TgeneXRCC5

GO:0045860

positive regulation of protein kinase activity

22504299

TgeneXRCC5

GO:0071480

cellular response to gamma radiation

26359349


check buttonFusion gene breakpoints across RBFA (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 XRCC5 (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-FG-A711-01ARBFAchr18

77802219

+XRCC5chr2

217054948

+
ChimerDB4LGGTCGA-FG-A711RBFAchr18

77802219

+XRCC5chr2

217054948

+
ChimerDB4LGGTCGA-FG-A711RBFAchr18

77794653

+XRCC5chr2

217054948

+
ChimerDB4LGGTCGA-FG-A711-01ARBFAchr18

77802219

-XRCC5chr2

217054948

+


Top

Fusion Gene ORF analysis for RBFA-XRCC5

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-shiftENST00000306735ENST00000392133RBFAchr18

77802219

+XRCC5chr2

217054948

+
Frame-shiftENST00000306735ENST00000392132RBFAchr18

77802219

+XRCC5chr2

217054948

+
5CDS-intronENST00000306735ENST00000471649RBFAchr18

77802219

+XRCC5chr2

217054948

+
intron-3CDSENST00000586847ENST00000392133RBFAchr18

77802219

+XRCC5chr2

217054948

+
intron-3CDSENST00000586847ENST00000392132RBFAchr18

77802219

+XRCC5chr2

217054948

+
intron-intronENST00000586847ENST00000471649RBFAchr18

77802219

+XRCC5chr2

217054948

+
intron-3CDSENST00000262197ENST00000392133RBFAchr18

77802219

+XRCC5chr2

217054948

+
intron-3CDSENST00000262197ENST00000392132RBFAchr18

77802219

+XRCC5chr2

217054948

+
intron-intronENST00000262197ENST00000471649RBFAchr18

77802219

+XRCC5chr2

217054948

+
Frame-shiftENST00000306735ENST00000392133RBFAchr18

77794653

+XRCC5chr2

217054948

+
Frame-shiftENST00000306735ENST00000392132RBFAchr18

77794653

+XRCC5chr2

217054948

+
5CDS-intronENST00000306735ENST00000471649RBFAchr18

77794653

+XRCC5chr2

217054948

+
3UTR-3CDSENST00000586847ENST00000392133RBFAchr18

77794653

+XRCC5chr2

217054948

+
3UTR-3CDSENST00000586847ENST00000392132RBFAchr18

77794653

+XRCC5chr2

217054948

+
3UTR-intronENST00000586847ENST00000471649RBFAchr18

77794653

+XRCC5chr2

217054948

+
Frame-shiftENST00000262197ENST00000392133RBFAchr18

77794653

+XRCC5chr2

217054948

+
Frame-shiftENST00000262197ENST00000392132RBFAchr18

77794653

+XRCC5chr2

217054948

+
5CDS-intronENST00000262197ENST00000471649RBFAchr18

77794653

+XRCC5chr2

217054948

+

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

Top

Fusion Genomic Features for RBFA-XRCC5


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)
RBFAchr1877794653+XRCC5chr2217054947+7.31E-050.9999269
RBFAchr1877802219+XRCC5chr2217054947+3.02E-070.99999964
RBFAchr1877802219+XRCC5chr2217054947+3.02E-070.99999964
RBFAchr1877794653+XRCC5chr2217054947+7.31E-050.9999269
RBFAchr1877802219+XRCC5chr2217054947+3.02E-070.99999964
RBFAchr1877802219+XRCC5chr2217054947+3.02E-070.99999964

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.

Top

Fusion Protein Features for RBFA-XRCC5


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


Top

Fusion Gene Sequence for RBFA-XRCC5


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.

Top

Fusion Gene PPI Analysis for RBFA-XRCC5


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


Top

Related Drugs for RBFA-XRCC5


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for RBFA-XRCC5


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneXRCC5C0001973Alcoholic Intoxication, Chronic1PSYGENET
TgeneXRCC5C0152013Adenocarcinoma of lung (disorder)1CTD_human
TgeneXRCC5C0678306alcohol sensitivity1PSYGENET