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:CPSF3L-SCNN1D (FusionGDB2 ID:19123)

Fusion Gene Summary for CPSF3L-SCNN1D

check button Fusion gene summary
Fusion gene informationFusion gene name: CPSF3L-SCNN1D
Fusion gene ID: 19123
HgeneTgene
Gene symbol

CPSF3L

SCNN1D

Gene ID

54973

6339

Gene nameintegrator complex subunit 11sodium channel epithelial 1 subunit delta
SynonymsCPSF3L|CPSF73L|INT11|RC-68|RC68ENaCd|ENaCdelta|SCNED|dNaCh
Cytomap

1p36.33

1p36.33

Type of geneprotein-codingprotein-coding
Descriptionintegrator complex subunit 11CPSF3-like proteincleavage and polyadenylation specific factor 3-likecleavage and polyadenylation-specific factor 3-like proteinprotein related to CPSF subunits of 68 kDarelated to CPSF subunits 68 kDaamiloride-sensitive sodium channel subunit deltadelta-ENaCdelta-NaCHepithelial Na(+) channel subunit deltanonvoltage-gated sodium channel 1 subunit deltasodium channel epithelial 1 delta subunitsodium channel, non-voltage-gated 1, delta subunitsodi
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000411962, ENST00000419704, 
ENST00000421495, ENST00000435064, 
ENST00000450926, ENST00000540437, 
ENST00000545578, ENST00000462432, 
ENST00000400928, ENST00000467651, 
ENST00000325425, ENST00000338555, 
ENST00000379116, 
Fusion gene scores* DoF score8 X 8 X 6=3843 X 3 X 3=27
# samples 103
** MAII scorelog2(10/384*10)=-1.94110631094643
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CPSF3L [Title/Abstract] AND SCNN1D [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCPSF3L(1248889)-SCNN1D(1225651), # samples:1
Anticipated loss of major functional domain due to fusion event.CPSF3L-SCNN1D seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CPSF3L-SCNN1D seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
HgeneCPSF3L

GO:0016180

snRNA processing

16239144


check buttonFusion gene breakpoints across CPSF3L (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 SCNN1D (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 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
ChimerDB4STADTCGA-HU-A4GH-01ACPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+


Top

Fusion Gene ORF analysis for CPSF3L-SCNN1D

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
5CDS-intronENST00000411962ENST00000400928CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000411962ENST00000467651CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000419704ENST00000400928CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000419704ENST00000467651CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000421495ENST00000400928CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000421495ENST00000467651CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000435064ENST00000400928CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000435064ENST00000467651CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000450926ENST00000400928CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000450926ENST00000467651CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000540437ENST00000400928CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000540437ENST00000467651CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000545578ENST00000400928CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5CDS-intronENST00000545578ENST00000467651CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5UTR-3CDSENST00000462432ENST00000325425CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5UTR-3CDSENST00000462432ENST00000338555CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5UTR-3CDSENST00000462432ENST00000379116CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5UTR-intronENST00000462432ENST00000400928CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
5UTR-intronENST00000462432ENST00000467651CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
Frame-shiftENST00000540437ENST00000325425CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
Frame-shiftENST00000540437ENST00000338555CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
Frame-shiftENST00000540437ENST00000379116CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
Frame-shiftENST00000545578ENST00000325425CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
Frame-shiftENST00000545578ENST00000338555CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
Frame-shiftENST00000545578ENST00000379116CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000411962ENST00000325425CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000411962ENST00000338555CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000411962ENST00000379116CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000419704ENST00000325425CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000419704ENST00000338555CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000419704ENST00000379116CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000421495ENST00000325425CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000421495ENST00000338555CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000421495ENST00000379116CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000435064ENST00000325425CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000435064ENST00000338555CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000435064ENST00000379116CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000450926ENST00000325425CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000450926ENST00000338555CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+
In-frameENST00000450926ENST00000379116CPSF3Lchr1

1248889

-SCNN1Dchr1

1225651

+

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 CPSF3L-SCNN1D


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)
CPSF3Lchr11248888-SCNN1Dchr11225650+0.61579460.38420537
CPSF3Lchr11248888-SCNN1Dchr11225650+0.61579460.38420537

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%

Top

Fusion Protein Features for CPSF3L-SCNN1D


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/chr1:1248889/chr1:1225651)
- 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
HgeneCPSF3Lchr1:1248889chr1:1225651ENST00000419704-81568_73246500.0MotifNote=HXHXDH motif
HgeneCPSF3Lchr1:1248889chr1:1225651ENST00000435064-101768_73347601.0MotifNote=HXHXDH motif
HgeneCPSF3Lchr1:1248889chr1:1225651ENST00000450926-101768_73325579.0MotifNote=HXHXDH motif
HgeneCPSF3Lchr1:1248889chr1:1225651ENST00000540437-121968_73353607.0MotifNote=HXHXDH motif
HgeneCPSF3Lchr1:1248889chr1:1225651ENST00000545578-111868_73318572.0MotifNote=HXHXDH motif
TgeneSCNN1Dchr1:1248889chr1:1225651ENST00000325425815716_802456705.0Topological domainCytoplasmic
TgeneSCNN1Dchr1:1248889chr1:1225651ENST00000338555815716_802390639.0Topological domainCytoplasmic
TgeneSCNN1Dchr1:1248889chr1:1225651ENST00000400928714716_802390639.0Topological domainCytoplasmic
TgeneSCNN1Dchr1:1248889chr1:1225651ENST00000325425815695_715456705.0TransmembraneHelical%3B Name%3D2
TgeneSCNN1Dchr1:1248889chr1:1225651ENST00000338555815695_715390639.0TransmembraneHelical%3B Name%3D2
TgeneSCNN1Dchr1:1248889chr1:1225651ENST00000400928714695_715390639.0TransmembraneHelical%3B Name%3D2

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneSCNN1Dchr1:1248889chr1:1225651ENST000003254258151_250456705.0Topological domainCytoplasmic
TgeneSCNN1Dchr1:1248889chr1:1225651ENST00000325425815272_694456705.0Topological domainExtracellular
TgeneSCNN1Dchr1:1248889chr1:1225651ENST000003385558151_250390639.0Topological domainCytoplasmic
TgeneSCNN1Dchr1:1248889chr1:1225651ENST00000338555815272_694390639.0Topological domainExtracellular
TgeneSCNN1Dchr1:1248889chr1:1225651ENST000004009287141_250390639.0Topological domainCytoplasmic
TgeneSCNN1Dchr1:1248889chr1:1225651ENST00000400928714272_694390639.0Topological domainExtracellular
TgeneSCNN1Dchr1:1248889chr1:1225651ENST00000325425815251_271456705.0TransmembraneHelical%3B Name%3D1
TgeneSCNN1Dchr1:1248889chr1:1225651ENST00000338555815251_271390639.0TransmembraneHelical%3B Name%3D1
TgeneSCNN1Dchr1:1248889chr1:1225651ENST00000400928714251_271390639.0TransmembraneHelical%3B Name%3D1


Top

Fusion Gene Sequence for CPSF3L-SCNN1D


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 CPSF3L-SCNN1D


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 CPSF3L-SCNN1D


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 CPSF3L-SCNN1D


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