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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:CHP1-SMAD3 (FusionGDB2 ID:HG11261TG4088)

Fusion Gene Summary for CHP1-SMAD3

check button Fusion gene summary
Fusion gene informationFusion gene name: CHP1-SMAD3
Fusion gene ID: hg11261tg4088
HgeneTgene
Gene symbol

CHP1

SMAD3

Gene ID

11261

4088

Gene namecalcineurin like EF-hand protein 1SMAD family member 3
SynonymsCHP|SLC9A1BP|SPAX9|Sid470p|p22|p24HSPC193|HsT17436|JV15-2|LDS1C|LDS3|MADH3
Cytomap('CHP1')('SMAD3')

15q15.1

15q22.33

Type of geneprotein-codingprotein-coding
Descriptioncalcineurin B homologous protein 1EF-hand calcium-binding domain-containing protein p22SLC9A1 binding proteincalcineurin B homologcalcineurin B-like proteincalcineurin homologous proteincalcium binding protein P22calcium-binding protein CHPcalciummothers against decapentaplegic homolog 3MAD homolog 3MAD, mothers against decapentaplegic homolog 3SMA- and MAD-related protein 3SMAD, mothers against DPP homolog 3hMAD-3hSMAD3mad homolog JV15-2mad protein homologmad3mothers against DPP homolog
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000558351, ENST00000334660, 
ENST00000560397, 
Fusion gene scores* DoF score11 X 13 X 7=10016 X 8 X 3=144
# samples 158
** MAII scorelog2(15/1001*10)=-2.73840756834011
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/144*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CHP1 [Title/Abstract] AND SMAD3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCHP1(41555081)-SMAD3(67482751), # samples:2
Anticipated loss of major functional domain due to fusion event.CHP1-SMAD3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CHP1-SMAD3 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
CHP1-SMAD3 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
HgeneCHP1

GO:0010923

negative regulation of phosphatase activity

10593895

HgeneCHP1

GO:0032088

negative regulation of NF-kappaB transcription factor activity

10593895

HgeneCHP1

GO:0032417

positive regulation of sodium:proton antiporter activity

8901634|11350981

HgeneCHP1

GO:0042308

negative regulation of protein import into nucleus

10593895

HgeneCHP1

GO:0051453

regulation of intracellular pH

8901634|15035633

HgeneCHP1

GO:0070885

negative regulation of calcineurin-NFAT signaling cascade

10593895

TgeneSMAD3

GO:0000122

negative regulation of transcription by RNA polymerase II

8774881

TgeneSMAD3

GO:0006357

regulation of transcription by RNA polymerase II

21947082

TgeneSMAD3

GO:0007179

transforming growth factor beta receptor signaling pathway

9732876|18548003|21947082

TgeneSMAD3

GO:0007183

SMAD protein complex assembly

9111321|10823886

TgeneSMAD3

GO:0010628

positive regulation of gene expression

21307346

TgeneSMAD3

GO:0010718

positive regulation of epithelial to mesenchymal transition

21307346

TgeneSMAD3

GO:0030308

negative regulation of cell growth

8774881

TgeneSMAD3

GO:0045429

positive regulation of nitric oxide biosynthetic process

27038547

TgeneSMAD3

GO:0045599

negative regulation of fat cell differentiation

19816956

TgeneSMAD3

GO:0045893

positive regulation of transcription, DNA-templated

9111321|9311995|9732876

TgeneSMAD3

GO:0045944

positive regulation of transcription by RNA polymerase II

8774881|18832382

TgeneSMAD3

GO:0051481

negative regulation of cytosolic calcium ion concentration

27038547

TgeneSMAD3

GO:0071560

cellular response to transforming growth factor beta stimulus

12902338

TgeneSMAD3

GO:1901203

positive regulation of extracellular matrix assembly

21307346



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
ChimerDB4OVTCGA-29-1702-01ACHP1chr15

41555081

+SMAD3chr15

67482751

+
ChimerDB4OVTCGA-29-1702-01ACHP1chr15

41556433

+SMAD3chr15

67482751

+


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Fusion Gene ORF analysis for CHP1-SMAD3

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-3CDSENST00000558351ENST00000327367CHP1chr15

41555081

+SMAD3chr15

67482751

+
3UTR-3CDSENST00000558351ENST00000327367CHP1chr15

41556433

+SMAD3chr15

67482751

+
3UTR-intronENST00000558351ENST00000439724CHP1chr15

41555081

+SMAD3chr15

67482751

+
3UTR-intronENST00000558351ENST00000439724CHP1chr15

41556433

+SMAD3chr15

67482751

+
3UTR-intronENST00000558351ENST00000537194CHP1chr15

41555081

+SMAD3chr15

67482751

+
3UTR-intronENST00000558351ENST00000537194CHP1chr15

41556433

+SMAD3chr15

67482751

+
3UTR-intronENST00000558351ENST00000540846CHP1chr15

41555081

+SMAD3chr15

67482751

+
3UTR-intronENST00000558351ENST00000540846CHP1chr15

41556433

+SMAD3chr15

67482751

+
3UTR-intronENST00000558351ENST00000559092CHP1chr15

41555081

+SMAD3chr15

67482751

+
3UTR-intronENST00000558351ENST00000559092CHP1chr15

41556433

+SMAD3chr15

67482751

+
5CDS-intronENST00000334660ENST00000439724CHP1chr15

41555081

+SMAD3chr15

67482751

+
5CDS-intronENST00000334660ENST00000537194CHP1chr15

41555081

+SMAD3chr15

67482751

+
5CDS-intronENST00000334660ENST00000540846CHP1chr15

41555081

+SMAD3chr15

67482751

+
5CDS-intronENST00000334660ENST00000559092CHP1chr15

41555081

+SMAD3chr15

67482751

+
5CDS-intronENST00000560397ENST00000439724CHP1chr15

41555081

+SMAD3chr15

67482751

+
5CDS-intronENST00000560397ENST00000537194CHP1chr15

41555081

+SMAD3chr15

67482751

+
5CDS-intronENST00000560397ENST00000540846CHP1chr15

41555081

+SMAD3chr15

67482751

+
5CDS-intronENST00000560397ENST00000559092CHP1chr15

41555081

+SMAD3chr15

67482751

+
Frame-shiftENST00000334660ENST00000327367CHP1chr15

41555081

+SMAD3chr15

67482751

+
Frame-shiftENST00000560397ENST00000327367CHP1chr15

41555081

+SMAD3chr15

67482751

+
intron-3CDSENST00000334660ENST00000327367CHP1chr15

41556433

+SMAD3chr15

67482751

+
intron-3CDSENST00000560397ENST00000327367CHP1chr15

41556433

+SMAD3chr15

67482751

+
intron-intronENST00000334660ENST00000439724CHP1chr15

41556433

+SMAD3chr15

67482751

+
intron-intronENST00000334660ENST00000537194CHP1chr15

41556433

+SMAD3chr15

67482751

+
intron-intronENST00000334660ENST00000540846CHP1chr15

41556433

+SMAD3chr15

67482751

+
intron-intronENST00000334660ENST00000559092CHP1chr15

41556433

+SMAD3chr15

67482751

+
intron-intronENST00000560397ENST00000439724CHP1chr15

41556433

+SMAD3chr15

67482751

+
intron-intronENST00000560397ENST00000537194CHP1chr15

41556433

+SMAD3chr15

67482751

+
intron-intronENST00000560397ENST00000540846CHP1chr15

41556433

+SMAD3chr15

67482751

+
intron-intronENST00000560397ENST00000559092CHP1chr15

41556433

+SMAD3chr15

67482751

+

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 CHP1-SMAD3


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)
CHP1chr1541556433+SMAD3chr1567482750+0.0102247350.9897753
CHP1chr1541555081+SMAD3chr1567482750+9.09E-060.99999094
CHP1chr1541556433+SMAD3chr1567482750+0.0102247350.9897753
CHP1chr1541555081+SMAD3chr1567482750+9.09E-060.99999094


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 CHP1-SMAD3


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/:41555081/:67482751)
- 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 CHP1-SMAD3


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 CHP1-SMAD3


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 CHP1-SMAD3


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 CHP1-SMAD3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC3151087LOEYS-DIETZ SYNDROME 38CLINGEN;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC4707243Familial thoracic aortic aneurysm and aortic dissection5CLINGEN;GENOMICS_ENGLAND
TgeneC0029408Degenerative polyarthritis2CTD_human
TgeneC0086743Osteoarthrosis Deformans2CTD_human
TgeneC0376634Craniofacial Abnormalities2CTD_human
TgeneC2697932Loeys-Dietz Syndrome2CTD_human;GENOMICS_ENGLAND
TgeneC0002949Aneurysm, Dissecting1CTD_human
TgeneC0003486Aortic Aneurysm1CTD_human
TgeneC0009171Cocaine Abuse1CTD_human
TgeneC0009402Colorectal Carcinoma1CTD_human;UNIPROT
TgeneC0009404Colorectal Neoplasms1CTD_human
TgeneC0010346Crohn Disease1CTD_human
TgeneC0023267Fibroid Tumor1CTD_human
TgeneC0023890Liver Cirrhosis1CTD_human
TgeneC0023891Liver Cirrhosis, Alcoholic1CTD_human
TgeneC0029410Osteoarthritis of hip1CTD_human
TgeneC0034067Pulmonary Emphysema1GENOMICS_ENGLAND
TgeneC0041956Ureteral obstruction1CTD_human
TgeneC0042133Uterine Fibroids1CTD_human
TgeneC0042138Uterine Neoplasms1CTD_human
TgeneC0087031Juvenile-Onset Still Disease1CTD_human
TgeneC0153567Uterine Cancer1CTD_human
TgeneC0156147Crohn's disease of large bowel1CTD_human
TgeneC0236736Cocaine-Related Disorders1CTD_human
TgeneC0239946Fibrosis, Liver1CTD_human
TgeneC0267380Crohn's disease of the ileum1CTD_human
TgeneC0340643Dissection of aorta1CTD_human
TgeneC0600427Cocaine Dependence1CTD_human
TgeneC0600519Ventricular Remodeling1CTD_human
TgeneC0600520Left Ventricle Remodeling1CTD_human
TgeneC0678202Regional enteritis1CTD_human
TgeneC0949272IIeocolitis1CTD_human
TgeneC1836635Loeys-Dietz Aortic Aneurysm Syndrome1CTD_human
TgeneC3495559Juvenile arthritis1CTD_human
TgeneC3714758Juvenile psoriatic arthritis1CTD_human
TgeneC4277533Dissection, Blood Vessel1CTD_human
TgeneC4551955Loeys-Dietz Syndrome, Type 1a1CTD_human
TgeneC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
TgeneC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human