Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
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:CHTOP-S100A13 (FusionGDB2 ID:HG26097TG6284)

Fusion Gene Summary for CHTOP-S100A13

check button Fusion gene summary
Fusion gene informationFusion gene name: CHTOP-S100A13
Fusion gene ID: hg26097tg6284
HgeneTgene
Gene symbol

CHTOP

S100A13

Gene ID

26097

6284

Gene namechromatin target of PRMT1S100 calcium binding protein A13
SynonymsC10orf77|C1orf77|FL-SRAG|FOP|SRAG|SRAG-3|SRAG-5|pp7704-
Cytomap('CHTOP')('S100A13')

1q21.3

1q21.3

Type of geneprotein-codingprotein-coding
Descriptionchromatin target of PRMT1 proteinfriend of PRMT1 proteinsmall protein rich in arginine and glycineprotein S100-A13
Modification date2020031320200320
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000495554, ENST00000368690, 
ENST00000368694, ENST00000403433, 
ENST00000368686, ENST00000368687, 
Fusion gene scores* DoF score7 X 8 X 5=2808 X 8 X 5=320
# samples 99
** MAII scorelog2(9/280*10)=-1.63742992061529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/320*10)=-1.83007499855769
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CHTOP [Title/Abstract] AND S100A13 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCHTOP(153609129)-S100A13(153604716), # samples:3
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
HgeneCHTOP

GO:0006406

mRNA export from nucleus

23299939

HgeneCHTOP

GO:0032781

positive regulation of ATPase activity

23299939

HgeneCHTOP

GO:0051096

positive regulation of helicase activity

23299939

TgeneS100A13

GO:0043123

positive regulation of I-kappaB kinase/NF-kappaB signaling

15033494

TgeneS100A13

GO:0050703

interleukin-1 alpha secretion

12746488



check button Fusion gene information
* 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
ChimerDB4BLCATCGA-K4-A5RH-01ACHTOPchr1

153609129

-S100A13chr1

153604716

-
ChimerDB4BLCATCGA-K4-A5RH-01ACHTOPchr1

153609129

+S100A13chr1

153604716

-
ChimerDB4BLCATCGA-K4-A5RHCHTOPchr1

153609129

+S100A13chr1

153604716

-


Top

Fusion Gene ORF analysis for CHTOP-S100A13

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-5UTRENST00000495554ENST00000368699CHTOPchr1

153609129

+S100A13chr1

153604716

-
3UTR-intronENST00000495554ENST00000339556CHTOPchr1

153609129

+S100A13chr1

153604716

-
3UTR-intronENST00000495554ENST00000392622CHTOPchr1

153609129

+S100A13chr1

153604716

-
3UTR-intronENST00000495554ENST00000392623CHTOPchr1

153609129

+S100A13chr1

153604716

-
3UTR-intronENST00000495554ENST00000440685CHTOPchr1

153609129

+S100A13chr1

153604716

-
3UTR-intronENST00000495554ENST00000491177CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-5UTRENST00000368690ENST00000368699CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-5UTRENST00000368694ENST00000368699CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-5UTRENST00000403433ENST00000368699CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000368690ENST00000339556CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000368690ENST00000392622CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000368690ENST00000392623CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000368690ENST00000440685CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000368690ENST00000491177CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000368694ENST00000339556CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000368694ENST00000392622CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000368694ENST00000392623CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000368694ENST00000440685CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000368694ENST00000491177CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000403433ENST00000339556CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000403433ENST00000392622CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000403433ENST00000392623CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000403433ENST00000440685CHTOPchr1

153609129

+S100A13chr1

153604716

-
5CDS-intronENST00000403433ENST00000491177CHTOPchr1

153609129

+S100A13chr1

153604716

-
intron-5UTRENST00000368686ENST00000368699CHTOPchr1

153609129

+S100A13chr1

153604716

-
intron-5UTRENST00000368687ENST00000368699CHTOPchr1

153609129

+S100A13chr1

153604716

-
intron-intronENST00000368686ENST00000339556CHTOPchr1

153609129

+S100A13chr1

153604716

-
intron-intronENST00000368686ENST00000392622CHTOPchr1

153609129

+S100A13chr1

153604716

-
intron-intronENST00000368686ENST00000392623CHTOPchr1

153609129

+S100A13chr1

153604716

-
intron-intronENST00000368686ENST00000440685CHTOPchr1

153609129

+S100A13chr1

153604716

-
intron-intronENST00000368686ENST00000491177CHTOPchr1

153609129

+S100A13chr1

153604716

-
intron-intronENST00000368687ENST00000339556CHTOPchr1

153609129

+S100A13chr1

153604716

-
intron-intronENST00000368687ENST00000392622CHTOPchr1

153609129

+S100A13chr1

153604716

-
intron-intronENST00000368687ENST00000392623CHTOPchr1

153609129

+S100A13chr1

153604716

-
intron-intronENST00000368687ENST00000440685CHTOPchr1

153609129

+S100A13chr1

153604716

-
intron-intronENST00000368687ENST00000491177CHTOPchr1

153609129

+S100A13chr1

153604716

-

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 CHTOP-S100A13


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)


Top

Fusion Protein Features for CHTOP-S100A13


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/:153609129/:153604716)
- 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


Top

Fusion Gene Sequence for CHTOP-S100A13


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 CHTOP-S100A13


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 CHTOP-S100A13


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 CHTOP-S100A13


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