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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:CLNS1A-XRCC6 (FusionGDB2 ID:17267)

Fusion Gene Summary for CLNS1A-XRCC6

check button Fusion gene summary
Fusion gene informationFusion gene name: CLNS1A-XRCC6
Fusion gene ID: 17267
HgeneTgene
Gene symbol

CLNS1A

XRCC6

Gene ID

1207

2547

Gene namechloride nucleotide-sensitive channel 1AX-ray repair cross complementing 6
SynonymsCLCI|CLNS1B|IClnCTC75|CTCBF|G22P1|KU70|ML8|TLAA
Cytomap

11q14.1

22q13.2

Type of geneprotein-codingprotein-coding
Descriptionmethylosome subunit pIClnchloride channel regulatory proteinchloride channel, nucleotide sensitive 1Achloride conductance regulatory protein IClnchloride ion current inducer proteini(Cln)reticulocyte pIClnreticulocyte protein IClnX-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
Modification date2020031320200329
UniProtAcc

P54105

.
Ensembl transtripts involved in fusion geneENST00000263309, ENST00000525064, 
ENST00000525428, ENST00000528364, 
ENST00000532069, ENST00000533957, 
ENST00000359308, ENST00000360079, 
ENST00000402580, ENST00000405506, 
ENST00000405878, ENST00000428575, 
Fusion gene scores* DoF score13 X 12 X 5=7805 X 5 X 2=50
# samples 164
** MAII scorelog2(16/780*10)=-2.28540221886225
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/50*10)=-0.321928094887362
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLNS1A [Title/Abstract] AND XRCC6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLNS1A(77327196)-XRCC6(42018780), # samples:1
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
HgeneCLNS1A

GO:0000387

spliceosomal snRNP assembly

18984161

TgeneXRCC6

GO:0002218

activation of innate immune response

28712728

TgeneXRCC6

GO:0045860

positive regulation of protein kinase activity

22504299

TgeneXRCC6

GO:0045893

positive regulation of transcription, DNA-templated

12145306

TgeneXRCC6

GO:0071480

cellular response to gamma radiation

26359349

TgeneXRCC6

GO:0097680

double-strand break repair via classical nonhomologous end joining

24095731


check buttonFusion gene breakpoints across CLNS1A (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 XRCC6 (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
ChiTaRS5.0N/ABG034646CLNS1Achr11

77327196

-XRCC6chr22

42018780

+


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Fusion Gene ORF analysis for CLNS1A-XRCC6

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
intron-intronENST00000263309ENST00000359308CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000263309ENST00000360079CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000263309ENST00000402580CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000263309ENST00000405506CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000263309ENST00000405878CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000263309ENST00000428575CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000525064ENST00000359308CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000525064ENST00000360079CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000525064ENST00000402580CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000525064ENST00000405506CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000525064ENST00000405878CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000525064ENST00000428575CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000525428ENST00000359308CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000525428ENST00000360079CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000525428ENST00000402580CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000525428ENST00000405506CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000525428ENST00000405878CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000525428ENST00000428575CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000528364ENST00000359308CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000528364ENST00000360079CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000528364ENST00000402580CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000528364ENST00000405506CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000528364ENST00000405878CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000528364ENST00000428575CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000532069ENST00000359308CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000532069ENST00000360079CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000532069ENST00000402580CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000532069ENST00000405506CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000532069ENST00000405878CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000532069ENST00000428575CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000533957ENST00000359308CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000533957ENST00000360079CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000533957ENST00000402580CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000533957ENST00000405506CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000533957ENST00000405878CLNS1Achr11

77327196

-XRCC6chr22

42018780

+
intron-intronENST00000533957ENST00000428575CLNS1Achr11

77327196

-XRCC6chr22

42018780

+

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 CLNS1A-XRCC6


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 CLNS1A-XRCC6


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/:77327196/:42018780)
- 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
CLNS1A

P54105

.
FUNCTION: Involved in both the assembly of spliceosomal snRNPs and the methylation of Sm proteins (PubMed:21081503, PubMed:18984161). Chaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. May also indirectly participate in cellular volume control by activation of a swelling-induced chloride conductance pathway. {ECO:0000269|PubMed:10330151, ECO:0000269|PubMed:11713266, ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:21081503}.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 CLNS1A-XRCC6


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 CLNS1A-XRCC6


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 CLNS1A-XRCC6


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 CLNS1A-XRCC6


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