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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:CLCN3-SMAD1 (FusionGDB2 ID:HG1182TG4086)

Fusion Gene Summary for CLCN3-SMAD1

check button Fusion gene summary
Fusion gene informationFusion gene name: CLCN3-SMAD1
Fusion gene ID: hg1182tg4086
HgeneTgene
Gene symbol

CLCN3

SMAD1

Gene ID

1182

4086

Gene namechloride voltage-gated channel 3SMAD family member 1
SynonymsCLC3|ClC-3BSP-1|BSP1|JV4-1|JV41|MADH1|MADR1
Cytomap('CLCN3')('SMAD1')

4q33

4q31.21

Type of geneprotein-codingprotein-coding
DescriptionH(+)/Cl(-) exchange transporter 3chloride channel 3chloride channel protein 3chloride channel, voltage-sensitive 3chloride transporter ClC-3mothers against decapentaplegic homolog 1MAD, mothers against decapentaplegic homolog 1Mad-related protein 1SMAD, mothers against DPP homolog 1TGF-beta signaling protein 1mothers against DPP homolog 1transforming growth factor-beta signaling protein
Modification date2020031320200322
UniProtAcc

P51790

.
Ensembl transtripts involved in fusion geneENST00000506924, ENST00000347613, 
ENST00000360642, ENST00000504131, 
ENST00000513761, 
Fusion gene scores* DoF score13 X 9 X 6=7026 X 6 X 6=216
# samples 167
** MAII scorelog2(16/702*10)=-2.1333991254172
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/216*10)=-1.6256044852185
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLCN3 [Title/Abstract] AND SMAD1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLCN3(170557239)-SMAD1(146474936), # samples:3
Anticipated loss of major functional domain due to fusion event.CLCN3-SMAD1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
CLCN3-SMAD1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
CLCN3-SMAD1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
CLCN3-SMAD1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
CLCN3-SMAD1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CLCN3-SMAD1 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
HgeneCLCN3

GO:1902476

chloride transmembrane transport

11274166

TgeneSMAD1

GO:0007183

SMAD protein complex assembly

9111321

TgeneSMAD1

GO:0010628

positive regulation of gene expression

19664780

TgeneSMAD1

GO:0030509

BMP signaling pathway

8653785|9389648|18548003

TgeneSMAD1

GO:0045944

positive regulation of transcription by RNA polymerase II

12270938


check buttonFusion gene breakpoints across CLCN3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across SMAD1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4BRCATCGA-AN-A04C-01ACLCN3chr4

170557239

-SMAD1chr4

146474936

+
ChimerDB4BRCATCGA-AN-A04C-01ACLCN3chr4

170557239

+SMAD1chr4

146474936

+
ChimerDB4BRCATCGA-AN-A04CCLCN3chr4

170557239

+SMAD1chr4

146474935

+


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Fusion Gene ORF analysis for CLCN3-SMAD1

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-3CDSENST00000506924ENST00000302085CLCN3chr4

170557239

+SMAD1chr4

146474936

+
3UTR-3CDSENST00000506924ENST00000302085CLCN3chr4

170557239

+SMAD1chr4

146474935

+
3UTR-intronENST00000506924ENST00000394092CLCN3chr4

170557239

+SMAD1chr4

146474936

+
3UTR-intronENST00000506924ENST00000394092CLCN3chr4

170557239

+SMAD1chr4

146474935

+
3UTR-intronENST00000506924ENST00000515385CLCN3chr4

170557239

+SMAD1chr4

146474936

+
3UTR-intronENST00000506924ENST00000515385CLCN3chr4

170557239

+SMAD1chr4

146474935

+
3UTR-intronENST00000506924ENST00000515527CLCN3chr4

170557239

+SMAD1chr4

146474936

+
3UTR-intronENST00000506924ENST00000515527CLCN3chr4

170557239

+SMAD1chr4

146474935

+
5CDS-intronENST00000347613ENST00000394092CLCN3chr4

170557239

+SMAD1chr4

146474936

+
5CDS-intronENST00000347613ENST00000394092CLCN3chr4

170557239

+SMAD1chr4

146474935

+
5CDS-intronENST00000347613ENST00000515385CLCN3chr4

170557239

+SMAD1chr4

146474936

+
5CDS-intronENST00000347613ENST00000515385CLCN3chr4

170557239

+SMAD1chr4

146474935

+
5CDS-intronENST00000347613ENST00000515527CLCN3chr4

170557239

+SMAD1chr4

146474936

+
5CDS-intronENST00000347613ENST00000515527CLCN3chr4

170557239

+SMAD1chr4

146474935

+
5CDS-intronENST00000360642ENST00000394092CLCN3chr4

170557239

+SMAD1chr4

146474936

+
5CDS-intronENST00000360642ENST00000394092CLCN3chr4

170557239

+SMAD1chr4

146474935

+
5CDS-intronENST00000360642ENST00000515385CLCN3chr4

170557239

+SMAD1chr4

146474936

+
5CDS-intronENST00000360642ENST00000515385CLCN3chr4

170557239

+SMAD1chr4

146474935

+
5CDS-intronENST00000360642ENST00000515527CLCN3chr4

170557239

+SMAD1chr4

146474936

+
5CDS-intronENST00000360642ENST00000515527CLCN3chr4

170557239

+SMAD1chr4

146474935

+
5CDS-intronENST00000504131ENST00000394092CLCN3chr4

170557239

+SMAD1chr4

146474936

+
5CDS-intronENST00000504131ENST00000394092CLCN3chr4

170557239

+SMAD1chr4

146474935

+
5CDS-intronENST00000504131ENST00000515385CLCN3chr4

170557239

+SMAD1chr4

146474936

+
5CDS-intronENST00000504131ENST00000515385CLCN3chr4

170557239

+SMAD1chr4

146474935

+
5CDS-intronENST00000504131ENST00000515527CLCN3chr4

170557239

+SMAD1chr4

146474936

+
5CDS-intronENST00000504131ENST00000515527CLCN3chr4

170557239

+SMAD1chr4

146474935

+
5CDS-intronENST00000513761ENST00000394092CLCN3chr4

170557239

+SMAD1chr4

146474936

+
5CDS-intronENST00000513761ENST00000394092CLCN3chr4

170557239

+SMAD1chr4

146474935

+
5CDS-intronENST00000513761ENST00000515385CLCN3chr4

170557239

+SMAD1chr4

146474936

+
5CDS-intronENST00000513761ENST00000515385CLCN3chr4

170557239

+SMAD1chr4

146474935

+
5CDS-intronENST00000513761ENST00000515527CLCN3chr4

170557239

+SMAD1chr4

146474936

+
5CDS-intronENST00000513761ENST00000515527CLCN3chr4

170557239

+SMAD1chr4

146474935

+
Frame-shiftENST00000504131ENST00000302085CLCN3chr4

170557239

+SMAD1chr4

146474936

+
Frame-shiftENST00000504131ENST00000302085CLCN3chr4

170557239

+SMAD1chr4

146474935

+
In-frameENST00000347613ENST00000302085CLCN3chr4

170557239

+SMAD1chr4

146474936

+
In-frameENST00000347613ENST00000302085CLCN3chr4

170557239

+SMAD1chr4

146474935

+
In-frameENST00000360642ENST00000302085CLCN3chr4

170557239

+SMAD1chr4

146474936

+
In-frameENST00000360642ENST00000302085CLCN3chr4

170557239

+SMAD1chr4

146474935

+
In-frameENST00000513761ENST00000302085CLCN3chr4

170557239

+SMAD1chr4

146474936

+
In-frameENST00000513761ENST00000302085CLCN3chr4

170557239

+SMAD1chr4

146474935

+

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)
ENST00000513761CLCN3chr4170557239+ENST00000302085SMAD1chr4146474936+12657195591119186
ENST00000347613CLCN3chr4170557239+ENST00000302085SMAD1chr4146474936+12607145541114186
ENST00000360642CLCN3chr4170557239+ENST00000302085SMAD1chr4146474936+12577115511111186
ENST00000513761CLCN3chr4170557239+ENST00000302085SMAD1chr4146474935+12657195591119186
ENST00000347613CLCN3chr4170557239+ENST00000302085SMAD1chr4146474935+12607145541114186
ENST00000360642CLCN3chr4170557239+ENST00000302085SMAD1chr4146474935+12577115511111186

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
ENST00000513761ENST00000302085CLCN3chr4170557239+SMAD1chr4146474936+0.0027724640.9972275
ENST00000347613ENST00000302085CLCN3chr4170557239+SMAD1chr4146474936+0.002845710.99715424
ENST00000360642ENST00000302085CLCN3chr4170557239+SMAD1chr4146474936+0.0034877220.99651223
ENST00000513761ENST00000302085CLCN3chr4170557239+SMAD1chr4146474935+0.0027724640.9972275
ENST00000347613ENST00000302085CLCN3chr4170557239+SMAD1chr4146474935+0.002845710.99715424
ENST00000360642ENST00000302085CLCN3chr4170557239+SMAD1chr4146474935+0.0034877220.99651223

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Fusion Genomic Features for CLCN3-SMAD1


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)
CLCN3chr4170557239+SMAD1chr4146474935+5.63E-060.9999944
CLCN3chr4170557239+SMAD1chr4146474935+5.63E-060.9999944
CLCN3chr4170557239+SMAD1chr4146474935+5.63E-060.9999944
CLCN3chr4170557239+SMAD1chr4146474935+5.63E-060.9999944

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.
genomic feature

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 CLCN3-SMAD1


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/chr4:170557239/chr4:146474936)
- 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
CLCN3

P51790

.
FUNCTION: [Isoform 1]: Strongly outwardly rectifying, electrogenic H(+)/Cl(-)exchanger which mediates the exchange of chloride ions against protons (By similarity). The CLC channel family contains both chloride channels and proton-coupled anion transporters that exchange chloride or another anion for protons (PubMed:29845874). The presence of conserved gating glutamate residues is typical for family members that function as antiporters (PubMed:29845874). {ECO:0000250|UniProtKB:P51791, ECO:0000303|PubMed:29845874}.; FUNCTION: [Isoform 2]: Strongly outwardly rectifying, electrogenic H(+)/Cl(-)exchanger which mediates the exchange of chloride ions against protons. {ECO:0000269|PubMed:11967229}.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
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+21428_2953867.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+21446_4753867.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+21228_2953792.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+21246_4753792.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+21328_2953819.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+21346_4753819.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+21428_2953867.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+21446_4753867.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+21228_2953792.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+21246_4753792.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+21328_2953819.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+21346_4753819.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
TgeneSMAD1chr4:170557239chr4:146474935ENST0000030208547418_428332466.0RegionL3 loop
TgeneSMAD1chr4:170557239chr4:146474935ENST0000039409247418_428332466.0RegionL3 loop
TgeneSMAD1chr4:170557239chr4:146474935ENST0000051538547418_428332466.0RegionL3 loop
TgeneSMAD1chr4:170557239chr4:146474936ENST0000030208547418_428332466.0RegionL3 loop
TgeneSMAD1chr4:170557239chr4:146474936ENST0000039409247418_428332466.0RegionL3 loop
TgeneSMAD1chr4:170557239chr4:146474936ENST0000051538547418_428332466.0RegionL3 loop

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214658_72253867.0DomainCBS 1
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214755_81253867.0DomainCBS 2
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212658_72253792.0DomainCBS 1
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212755_81253792.0DomainCBS 2
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213658_72253819.0DomainCBS 1
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213755_81253819.0DomainCBS 2
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214658_72253867.0DomainCBS 1
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214755_81253867.0DomainCBS 2
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212658_72253792.0DomainCBS 1
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212755_81253792.0DomainCBS 2
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213658_72253819.0DomainCBS 1
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213755_81253819.0DomainCBS 2
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214241_24853867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214313_32553867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214329_33753867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214572_58653867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214590_60153867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214602_60553867.0IntramembraneNote%3DLoop between two helices
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212241_24853792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212313_32553792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212329_33753792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212572_58653792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212590_60153792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212602_60553792.0IntramembraneNote%3DLoop between two helices
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213241_24853819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213313_32553819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213329_33753819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213572_58653819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213590_60153819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213602_60553819.0IntramembraneNote%3DLoop between two helices
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214241_24853867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214313_32553867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214329_33753867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214572_58653867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214590_60153867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214602_60553867.0IntramembraneNote%3DLoop between two helices
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212241_24853792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212313_32553792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212329_33753792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212572_58653792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212590_60153792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212602_60553792.0IntramembraneNote%3DLoop between two helices
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213241_24853819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213313_32553819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213329_33753819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213572_58653819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213590_60153819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213602_60553819.0IntramembraneNote%3DLoop between two helices
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214238_24253867.0MotifSelectivity filter part_1
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214280_28453867.0MotifSelectivity filter part_2
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214525_52953867.0MotifSelectivity filter part_3
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+21471_7553867.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212238_24253792.0MotifSelectivity filter part_1
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212280_28453792.0MotifSelectivity filter part_2
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212525_52953792.0MotifSelectivity filter part_3
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+21271_7553792.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213238_24253819.0MotifSelectivity filter part_1
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213280_28453819.0MotifSelectivity filter part_2
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213525_52953819.0MotifSelectivity filter part_3
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+21371_7553819.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214238_24253867.0MotifSelectivity filter part_1
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214280_28453867.0MotifSelectivity filter part_2
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214525_52953867.0MotifSelectivity filter part_3
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+21471_7553867.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212238_24253792.0MotifSelectivity filter part_1
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212280_28453792.0MotifSelectivity filter part_2
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212525_52953792.0MotifSelectivity filter part_3
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+21271_7553792.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213238_24253819.0MotifSelectivity filter part_1
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213280_28453819.0MotifSelectivity filter part_2
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213525_52953819.0MotifSelectivity filter part_3
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+21371_7553819.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214689_69153867.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214796_79953867.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212689_69153792.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212796_79953792.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213689_69153819.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213796_79953819.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214689_69153867.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214796_79953867.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212689_69153792.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212796_79953792.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213689_69153819.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213796_79953819.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+2141_12553867.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214625_81853867.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+2121_12553792.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212625_81853792.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+2131_12553819.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213625_81853819.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+2141_12553867.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214625_81853867.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+2121_12553792.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212625_81853792.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+2131_12553819.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213625_81853819.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214126_16353867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214209_23253867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214258_27653867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214282_30153867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214349_36753867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214391_41653867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214423_44353867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214500_52053867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214525_54453867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214606_62453867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212126_16353792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212209_23253792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212258_27653792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212282_30153792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212349_36753792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212391_41653792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212423_44353792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212500_52053792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212525_54453792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212606_62453792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213126_16353819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213209_23253819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213258_27653819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213282_30153819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213349_36753819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213391_41653819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213423_44353819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213500_52053819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213525_54453819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213606_62453819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214126_16353867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214209_23253867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214258_27653867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214282_30153867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214349_36753867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214391_41653867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214423_44353867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214500_52053867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214525_54453867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214606_62453867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212126_16353792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212209_23253792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212258_27653792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212282_30153792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212349_36753792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212391_41653792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212423_44353792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212500_52053792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212525_54453792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212606_62453792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213126_16353819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213209_23253819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213258_27653819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213282_30153819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213349_36753819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213391_41653819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213423_44353819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213500_52053819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213525_54453819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213606_62453819.0TransmembraneHelical
TgeneSMAD1chr4:170557239chr4:146474935ENST0000030208547198_201332466.0Compositional biasNote=Poly-Ser
TgeneSMAD1chr4:170557239chr4:146474935ENST000003020854739_45332466.0Compositional biasNote=Poly-Lys
TgeneSMAD1chr4:170557239chr4:146474935ENST0000039409247198_201332466.0Compositional biasNote=Poly-Ser
TgeneSMAD1chr4:170557239chr4:146474935ENST000003940924739_45332466.0Compositional biasNote=Poly-Lys
TgeneSMAD1chr4:170557239chr4:146474935ENST0000051538547198_201332466.0Compositional biasNote=Poly-Ser
TgeneSMAD1chr4:170557239chr4:146474935ENST000005153854739_45332466.0Compositional biasNote=Poly-Lys
TgeneSMAD1chr4:170557239chr4:146474936ENST0000030208547198_201332466.0Compositional biasNote=Poly-Ser
TgeneSMAD1chr4:170557239chr4:146474936ENST000003020854739_45332466.0Compositional biasNote=Poly-Lys
TgeneSMAD1chr4:170557239chr4:146474936ENST0000039409247198_201332466.0Compositional biasNote=Poly-Ser
TgeneSMAD1chr4:170557239chr4:146474936ENST000003940924739_45332466.0Compositional biasNote=Poly-Lys
TgeneSMAD1chr4:170557239chr4:146474936ENST0000051538547198_201332466.0Compositional biasNote=Poly-Ser
TgeneSMAD1chr4:170557239chr4:146474936ENST000005153854739_45332466.0Compositional biasNote=Poly-Lys
TgeneSMAD1chr4:170557239chr4:146474935ENST000003020854712_136332466.0DomainMH1
TgeneSMAD1chr4:170557239chr4:146474935ENST0000030208547271_465332466.0DomainMH2
TgeneSMAD1chr4:170557239chr4:146474935ENST000003940924712_136332466.0DomainMH1
TgeneSMAD1chr4:170557239chr4:146474935ENST0000039409247271_465332466.0DomainMH2
TgeneSMAD1chr4:170557239chr4:146474935ENST000005153854712_136332466.0DomainMH1
TgeneSMAD1chr4:170557239chr4:146474935ENST0000051538547271_465332466.0DomainMH2
TgeneSMAD1chr4:170557239chr4:146474936ENST000003020854712_136332466.0DomainMH1
TgeneSMAD1chr4:170557239chr4:146474936ENST0000030208547271_465332466.0DomainMH2
TgeneSMAD1chr4:170557239chr4:146474936ENST000003940924712_136332466.0DomainMH1
TgeneSMAD1chr4:170557239chr4:146474936ENST0000039409247271_465332466.0DomainMH2
TgeneSMAD1chr4:170557239chr4:146474936ENST000005153854712_136332466.0DomainMH1
TgeneSMAD1chr4:170557239chr4:146474936ENST0000051538547271_465332466.0DomainMH2


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Fusion Gene Sequence for CLCN3-SMAD1


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.
>16988_16988_1_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000347613_SMAD1_chr4_146474935_ENST00000302085_length(transcript)=1260nt_BP=714nt
GTCACGCGTCGACGCTGGGGCGTACCTTTCGGGCTCCTGACTCCTGCCGCTTCTCTTCCCCTTCCGTGGGTCAGGGCCGGTCCGGTCCGG
AACCTGCAGCCCCTTTCCCAGTGTTCTAGTTCGCCCGTGACCCGGAATAATGAGCAAGGAGGGTGTGGTGGGTTGAAAGCCATCCTACTT
TACTCCCGAGTTAGAGCATGGATTCAGTTTTAGTCTTAAGGGGGAAGTGAGATTGGAGATTTTTATTTTTAATTTTGGGCAGAAGCAGGT
TGACTCTAGGGATCTCCAGAGCGAGAGGATTTAACTTCATGTTGCTCCCGTGTTTGAAGGAGGACAATAAAAGTCCCACCGGGCAAAATT
TTCGTAACCTCTGCGGTAGAAAACGTCAGGTATCTTTTAAATCGCGATAGTTTTCGCTGTGTCAGGCTTTCTTCGGTGGAGCTCCGAGGG
TAGCTAGGTTCTAGGTTTGAAACAGATGCAGAATCCAAAGGCAGCGCAAAAAACAGCCACCGATTTTGCTATGTCTCTGAGCTGCGAGAT
AATCAGACAGCTAAATGGAGTCTGAGCAGCTGTTCCATAGAGGCTACTATAGAAACAGCTACAACAGTATAACAAGTGCAAGTAGTGATG
AGGAACTTTTAGATGGAGCAGGTGTTATTATGGACTTTCAAACATCTGAAGATGACAATTTATTAGATGGTGACACTGCAGTTGGAGTTC
ATCTTTATTATGTTGGAGGGGAGGTGTATGCCGAATGCCTTAGTGACAGTAGCATCTTTGTGCAAAGTCGGAACTGCAACTACCATCATG
GATTTCATCCTACTACTGTTTGCAAGATCCCTAGTGGGTGTAGTCTGAAAATTTTTAACAACCAAGAATTTGCTCAGTTATTGGCACAGT
CTGTGAACCATGGATTTGAGACAGTCTATGAGCTTACAAAAATGTGTACTATACGTATGAGCTTTGTGAAGGGCTGGGGAGCAGAATACC
ACCGCCAGGATGTTACTAGCACCCCCTGCTGGATTGAGATACATCTGCACGGCCCCCTCCAGTGGCTGGATAAAGTTCTTACTCAAATGG
GTTCACCTCATAATCCTATTTCATCTGTATCTTAAATGGCCCCAGGCATCTGCCTCTGGAAAACTATTGAGCCTTGCATGTACTTGAAGG
ATGGATGAGTCAGACACGATTGAGAACTGACAAAGGAGCCTTGATAATACTTGACCTCTGTGACCAACTGTTGGATTCAGAAATTTAAAC


>16988_16988_1_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000347613_SMAD1_chr4_146474935_ENST00000302085_length(amino acids)=186AA_BP=53
MESEQLFHRGYYRNSYNSITSASSDEELLDGAGVIMDFQTSEDDNLLDGDTAVGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPT
TVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHN
PISSVS

--------------------------------------------------------------
>16988_16988_2_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000347613_SMAD1_chr4_146474936_ENST00000302085_length(transcript)=1260nt_BP=714nt
GTCACGCGTCGACGCTGGGGCGTACCTTTCGGGCTCCTGACTCCTGCCGCTTCTCTTCCCCTTCCGTGGGTCAGGGCCGGTCCGGTCCGG
AACCTGCAGCCCCTTTCCCAGTGTTCTAGTTCGCCCGTGACCCGGAATAATGAGCAAGGAGGGTGTGGTGGGTTGAAAGCCATCCTACTT
TACTCCCGAGTTAGAGCATGGATTCAGTTTTAGTCTTAAGGGGGAAGTGAGATTGGAGATTTTTATTTTTAATTTTGGGCAGAAGCAGGT
TGACTCTAGGGATCTCCAGAGCGAGAGGATTTAACTTCATGTTGCTCCCGTGTTTGAAGGAGGACAATAAAAGTCCCACCGGGCAAAATT
TTCGTAACCTCTGCGGTAGAAAACGTCAGGTATCTTTTAAATCGCGATAGTTTTCGCTGTGTCAGGCTTTCTTCGGTGGAGCTCCGAGGG
TAGCTAGGTTCTAGGTTTGAAACAGATGCAGAATCCAAAGGCAGCGCAAAAAACAGCCACCGATTTTGCTATGTCTCTGAGCTGCGAGAT
AATCAGACAGCTAAATGGAGTCTGAGCAGCTGTTCCATAGAGGCTACTATAGAAACAGCTACAACAGTATAACAAGTGCAAGTAGTGATG
AGGAACTTTTAGATGGAGCAGGTGTTATTATGGACTTTCAAACATCTGAAGATGACAATTTATTAGATGGTGACACTGCAGTTGGAGTTC
ATCTTTATTATGTTGGAGGGGAGGTGTATGCCGAATGCCTTAGTGACAGTAGCATCTTTGTGCAAAGTCGGAACTGCAACTACCATCATG
GATTTCATCCTACTACTGTTTGCAAGATCCCTAGTGGGTGTAGTCTGAAAATTTTTAACAACCAAGAATTTGCTCAGTTATTGGCACAGT
CTGTGAACCATGGATTTGAGACAGTCTATGAGCTTACAAAAATGTGTACTATACGTATGAGCTTTGTGAAGGGCTGGGGAGCAGAATACC
ACCGCCAGGATGTTACTAGCACCCCCTGCTGGATTGAGATACATCTGCACGGCCCCCTCCAGTGGCTGGATAAAGTTCTTACTCAAATGG
GTTCACCTCATAATCCTATTTCATCTGTATCTTAAATGGCCCCAGGCATCTGCCTCTGGAAAACTATTGAGCCTTGCATGTACTTGAAGG
ATGGATGAGTCAGACACGATTGAGAACTGACAAAGGAGCCTTGATAATACTTGACCTCTGTGACCAACTGTTGGATTCAGAAATTTAAAC


>16988_16988_2_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000347613_SMAD1_chr4_146474936_ENST00000302085_length(amino acids)=186AA_BP=53
MESEQLFHRGYYRNSYNSITSASSDEELLDGAGVIMDFQTSEDDNLLDGDTAVGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPT
TVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHN
PISSVS

--------------------------------------------------------------
>16988_16988_3_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000360642_SMAD1_chr4_146474935_ENST00000302085_length(transcript)=1257nt_BP=711nt
ACGCGTCGACGCTGGGGCGTACCTTTCGGGCTCCTGACTCCTGCCGCTTCTCTTCCCCTTCCGTGGGTCAGGGCCGGTCCGGTCCGGAAC
CTGCAGCCCCTTTCCCAGTGTTCTAGTTCGCCCGTGACCCGGAATAATGAGCAAGGAGGGTGTGGTGGGTTGAAAGCCATCCTACTTTAC
TCCCGAGTTAGAGCATGGATTCAGTTTTAGTCTTAAGGGGGAAGTGAGATTGGAGATTTTTATTTTTAATTTTGGGCAGAAGCAGGTTGA
CTCTAGGGATCTCCAGAGCGAGAGGATTTAACTTCATGTTGCTCCCGTGTTTGAAGGAGGACAATAAAAGTCCCACCGGGCAAAATTTTC
GTAACCTCTGCGGTAGAAAACGTCAGGTATCTTTTAAATCGCGATAGTTTTCGCTGTGTCAGGCTTTCTTCGGTGGAGCTCCGAGGGTAG
CTAGGTTCTAGGTTTGAAACAGATGCAGAATCCAAAGGCAGCGCAAAAAACAGCCACCGATTTTGCTATGTCTCTGAGCTGCGAGATAAT
CAGACAGCTAAATGGAGTCTGAGCAGCTGTTCCATAGAGGCTACTATAGAAACAGCTACAACAGTATAACAAGTGCAAGTAGTGATGAGG
AACTTTTAGATGGAGCAGGTGTTATTATGGACTTTCAAACATCTGAAGATGACAATTTATTAGATGGTGACACTGCAGTTGGAGTTCATC
TTTATTATGTTGGAGGGGAGGTGTATGCCGAATGCCTTAGTGACAGTAGCATCTTTGTGCAAAGTCGGAACTGCAACTACCATCATGGAT
TTCATCCTACTACTGTTTGCAAGATCCCTAGTGGGTGTAGTCTGAAAATTTTTAACAACCAAGAATTTGCTCAGTTATTGGCACAGTCTG
TGAACCATGGATTTGAGACAGTCTATGAGCTTACAAAAATGTGTACTATACGTATGAGCTTTGTGAAGGGCTGGGGAGCAGAATACCACC
GCCAGGATGTTACTAGCACCCCCTGCTGGATTGAGATACATCTGCACGGCCCCCTCCAGTGGCTGGATAAAGTTCTTACTCAAATGGGTT
CACCTCATAATCCTATTTCATCTGTATCTTAAATGGCCCCAGGCATCTGCCTCTGGAAAACTATTGAGCCTTGCATGTACTTGAAGGATG
GATGAGTCAGACACGATTGAGAACTGACAAAGGAGCCTTGATAATACTTGACCTCTGTGACCAACTGTTGGATTCAGAAATTTAAAC

>16988_16988_3_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000360642_SMAD1_chr4_146474935_ENST00000302085_length(amino acids)=186AA_BP=53
MESEQLFHRGYYRNSYNSITSASSDEELLDGAGVIMDFQTSEDDNLLDGDTAVGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPT
TVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHN
PISSVS

--------------------------------------------------------------
>16988_16988_4_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000360642_SMAD1_chr4_146474936_ENST00000302085_length(transcript)=1257nt_BP=711nt
ACGCGTCGACGCTGGGGCGTACCTTTCGGGCTCCTGACTCCTGCCGCTTCTCTTCCCCTTCCGTGGGTCAGGGCCGGTCCGGTCCGGAAC
CTGCAGCCCCTTTCCCAGTGTTCTAGTTCGCCCGTGACCCGGAATAATGAGCAAGGAGGGTGTGGTGGGTTGAAAGCCATCCTACTTTAC
TCCCGAGTTAGAGCATGGATTCAGTTTTAGTCTTAAGGGGGAAGTGAGATTGGAGATTTTTATTTTTAATTTTGGGCAGAAGCAGGTTGA
CTCTAGGGATCTCCAGAGCGAGAGGATTTAACTTCATGTTGCTCCCGTGTTTGAAGGAGGACAATAAAAGTCCCACCGGGCAAAATTTTC
GTAACCTCTGCGGTAGAAAACGTCAGGTATCTTTTAAATCGCGATAGTTTTCGCTGTGTCAGGCTTTCTTCGGTGGAGCTCCGAGGGTAG
CTAGGTTCTAGGTTTGAAACAGATGCAGAATCCAAAGGCAGCGCAAAAAACAGCCACCGATTTTGCTATGTCTCTGAGCTGCGAGATAAT
CAGACAGCTAAATGGAGTCTGAGCAGCTGTTCCATAGAGGCTACTATAGAAACAGCTACAACAGTATAACAAGTGCAAGTAGTGATGAGG
AACTTTTAGATGGAGCAGGTGTTATTATGGACTTTCAAACATCTGAAGATGACAATTTATTAGATGGTGACACTGCAGTTGGAGTTCATC
TTTATTATGTTGGAGGGGAGGTGTATGCCGAATGCCTTAGTGACAGTAGCATCTTTGTGCAAAGTCGGAACTGCAACTACCATCATGGAT
TTCATCCTACTACTGTTTGCAAGATCCCTAGTGGGTGTAGTCTGAAAATTTTTAACAACCAAGAATTTGCTCAGTTATTGGCACAGTCTG
TGAACCATGGATTTGAGACAGTCTATGAGCTTACAAAAATGTGTACTATACGTATGAGCTTTGTGAAGGGCTGGGGAGCAGAATACCACC
GCCAGGATGTTACTAGCACCCCCTGCTGGATTGAGATACATCTGCACGGCCCCCTCCAGTGGCTGGATAAAGTTCTTACTCAAATGGGTT
CACCTCATAATCCTATTTCATCTGTATCTTAAATGGCCCCAGGCATCTGCCTCTGGAAAACTATTGAGCCTTGCATGTACTTGAAGGATG
GATGAGTCAGACACGATTGAGAACTGACAAAGGAGCCTTGATAATACTTGACCTCTGTGACCAACTGTTGGATTCAGAAATTTAAAC

>16988_16988_4_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000360642_SMAD1_chr4_146474936_ENST00000302085_length(amino acids)=186AA_BP=53
MESEQLFHRGYYRNSYNSITSASSDEELLDGAGVIMDFQTSEDDNLLDGDTAVGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPT
TVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHN
PISSVS

--------------------------------------------------------------
>16988_16988_5_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000513761_SMAD1_chr4_146474935_ENST00000302085_length(transcript)=1265nt_BP=719nt
GTGACGTCACGCGTCGACGCTGGGGCGTACCTTTCGGGCTCCTGACTCCTGCCGCTTCTCTTCCCCTTCCGTGGGTCAGGGCCGGTCCGG
TCCGGAACCTGCAGCCCCTTTCCCAGTGTTCTAGTTCGCCCGTGACCCGGAATAATGAGCAAGGAGGGTGTGGTGGGTTGAAAGCCATCC
TACTTTACTCCCGAGTTAGAGCATGGATTCAGTTTTAGTCTTAAGGGGGAAGTGAGATTGGAGATTTTTATTTTTAATTTTGGGCAGAAG
CAGGTTGACTCTAGGGATCTCCAGAGCGAGAGGATTTAACTTCATGTTGCTCCCGTGTTTGAAGGAGGACAATAAAAGTCCCACCGGGCA
AAATTTTCGTAACCTCTGCGGTAGAAAACGTCAGGTATCTTTTAAATCGCGATAGTTTTCGCTGTGTCAGGCTTTCTTCGGTGGAGCTCC
GAGGGTAGCTAGGTTCTAGGTTTGAAACAGATGCAGAATCCAAAGGCAGCGCAAAAAACAGCCACCGATTTTGCTATGTCTCTGAGCTGC
GAGATAATCAGACAGCTAAATGGAGTCTGAGCAGCTGTTCCATAGAGGCTACTATAGAAACAGCTACAACAGTATAACAAGTGCAAGTAG
TGATGAGGAACTTTTAGATGGAGCAGGTGTTATTATGGACTTTCAAACATCTGAAGATGACAATTTATTAGATGGTGACACTGCAGTTGG
AGTTCATCTTTATTATGTTGGAGGGGAGGTGTATGCCGAATGCCTTAGTGACAGTAGCATCTTTGTGCAAAGTCGGAACTGCAACTACCA
TCATGGATTTCATCCTACTACTGTTTGCAAGATCCCTAGTGGGTGTAGTCTGAAAATTTTTAACAACCAAGAATTTGCTCAGTTATTGGC
ACAGTCTGTGAACCATGGATTTGAGACAGTCTATGAGCTTACAAAAATGTGTACTATACGTATGAGCTTTGTGAAGGGCTGGGGAGCAGA
ATACCACCGCCAGGATGTTACTAGCACCCCCTGCTGGATTGAGATACATCTGCACGGCCCCCTCCAGTGGCTGGATAAAGTTCTTACTCA
AATGGGTTCACCTCATAATCCTATTTCATCTGTATCTTAAATGGCCCCAGGCATCTGCCTCTGGAAAACTATTGAGCCTTGCATGTACTT
GAAGGATGGATGAGTCAGACACGATTGAGAACTGACAAAGGAGCCTTGATAATACTTGACCTCTGTGACCAACTGTTGGATTCAGAAATT
TAAAC

>16988_16988_5_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000513761_SMAD1_chr4_146474935_ENST00000302085_length(amino acids)=186AA_BP=53
MESEQLFHRGYYRNSYNSITSASSDEELLDGAGVIMDFQTSEDDNLLDGDTAVGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPT
TVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHN
PISSVS

--------------------------------------------------------------
>16988_16988_6_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000513761_SMAD1_chr4_146474936_ENST00000302085_length(transcript)=1265nt_BP=719nt
GTGACGTCACGCGTCGACGCTGGGGCGTACCTTTCGGGCTCCTGACTCCTGCCGCTTCTCTTCCCCTTCCGTGGGTCAGGGCCGGTCCGG
TCCGGAACCTGCAGCCCCTTTCCCAGTGTTCTAGTTCGCCCGTGACCCGGAATAATGAGCAAGGAGGGTGTGGTGGGTTGAAAGCCATCC
TACTTTACTCCCGAGTTAGAGCATGGATTCAGTTTTAGTCTTAAGGGGGAAGTGAGATTGGAGATTTTTATTTTTAATTTTGGGCAGAAG
CAGGTTGACTCTAGGGATCTCCAGAGCGAGAGGATTTAACTTCATGTTGCTCCCGTGTTTGAAGGAGGACAATAAAAGTCCCACCGGGCA
AAATTTTCGTAACCTCTGCGGTAGAAAACGTCAGGTATCTTTTAAATCGCGATAGTTTTCGCTGTGTCAGGCTTTCTTCGGTGGAGCTCC
GAGGGTAGCTAGGTTCTAGGTTTGAAACAGATGCAGAATCCAAAGGCAGCGCAAAAAACAGCCACCGATTTTGCTATGTCTCTGAGCTGC
GAGATAATCAGACAGCTAAATGGAGTCTGAGCAGCTGTTCCATAGAGGCTACTATAGAAACAGCTACAACAGTATAACAAGTGCAAGTAG
TGATGAGGAACTTTTAGATGGAGCAGGTGTTATTATGGACTTTCAAACATCTGAAGATGACAATTTATTAGATGGTGACACTGCAGTTGG
AGTTCATCTTTATTATGTTGGAGGGGAGGTGTATGCCGAATGCCTTAGTGACAGTAGCATCTTTGTGCAAAGTCGGAACTGCAACTACCA
TCATGGATTTCATCCTACTACTGTTTGCAAGATCCCTAGTGGGTGTAGTCTGAAAATTTTTAACAACCAAGAATTTGCTCAGTTATTGGC
ACAGTCTGTGAACCATGGATTTGAGACAGTCTATGAGCTTACAAAAATGTGTACTATACGTATGAGCTTTGTGAAGGGCTGGGGAGCAGA
ATACCACCGCCAGGATGTTACTAGCACCCCCTGCTGGATTGAGATACATCTGCACGGCCCCCTCCAGTGGCTGGATAAAGTTCTTACTCA
AATGGGTTCACCTCATAATCCTATTTCATCTGTATCTTAAATGGCCCCAGGCATCTGCCTCTGGAAAACTATTGAGCCTTGCATGTACTT
GAAGGATGGATGAGTCAGACACGATTGAGAACTGACAAAGGAGCCTTGATAATACTTGACCTCTGTGACCAACTGTTGGATTCAGAAATT
TAAAC

>16988_16988_6_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000513761_SMAD1_chr4_146474936_ENST00000302085_length(amino acids)=186AA_BP=53
MESEQLFHRGYYRNSYNSITSASSDEELLDGAGVIMDFQTSEDDNLLDGDTAVGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPT
TVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHN
PISSVS

--------------------------------------------------------------

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Fusion Gene PPI Analysis for CLCN3-SMAD1


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 CLCN3-SMAD1


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 CLCN3-SMAD1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLCN3C0017638Glioma1CTD_human
HgeneCLCN3C0024623Malignant neoplasm of stomach1CTD_human
HgeneCLCN3C0038356Stomach Neoplasms1CTD_human
HgeneCLCN3C0235874Disease Exacerbation1CTD_human
HgeneCLCN3C0259783mixed gliomas1CTD_human
HgeneCLCN3C0555198Malignant Glioma1CTD_human
HgeneCLCN3C1708349Hereditary Diffuse Gastric Cancer1CTD_human
HgeneCLCN3C2931822Nasopharyngeal carcinoma1CTD_human
TgeneC0009171Cocaine Abuse1CTD_human
TgeneC0038587Substance Withdrawal Syndrome1CTD_human
TgeneC0086189Drug Withdrawal Symptoms1CTD_human
TgeneC0087169Withdrawal Symptoms1CTD_human
TgeneC0152171Idiopathic pulmonary hypertension1GENOMICS_ENGLAND
TgeneC0236736Cocaine-Related Disorders1CTD_human
TgeneC0340543Familial primary pulmonary hypertension1GENOMICS_ENGLAND
TgeneC0600427Cocaine Dependence1CTD_human
TgeneC11509292-oxo-hept-3-ene-1,7-dioate hydratase activity1GENOMICS_ENGLAND
TgeneC3203102Idiopathic pulmonary arterial hypertension1GENOMICS_ENGLAND