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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:SDE2-SLC22A15 (FusionGDB2 ID:79859)

Fusion Gene Summary for SDE2-SLC22A15

check button Fusion gene summary
Fusion gene informationFusion gene name: SDE2-SLC22A15
Fusion gene ID: 79859
HgeneTgene
Gene symbol

SDE2

SLC22A15

Gene ID

163859

55356

Gene nameSDE2 telomere maintenance homologsolute carrier family 22 member 15
SynonymsC1orf55|dJ671D7.1FLIPT1|PRO34686
Cytomap

1q42.12

1p13.1

Type of geneprotein-codingprotein-coding
Descriptionreplication stress response regulator SDE2UPF0667 protein C1orf55protein SDE2 homologsolute carrier family 22 member 15flipt 1fly-like putative organic ion transporter 1fly-like putative transporter 1solute carrier family 22 (organic cation transporter), member 15trans-like protein
Modification date2020031320200313
UniProtAcc

Q6IQ49

.
Ensembl transtripts involved in fusion geneENST00000272091, ENST00000481127, 
ENST00000369502, ENST00000369503, 
Fusion gene scores* DoF score2 X 2 X 2=85 X 4 X 4=80
# samples 25
** MAII scorelog2(2/8*10)=1.32192809488736log2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SDE2 [Title/Abstract] AND SLC22A15 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSDE2(226182967)-SLC22A15(116562203), # samples:1
Anticipated loss of major functional domain due to fusion event.SDE2-SLC22A15 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
SDE2-SLC22A15 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
HgeneSDE2

GO:0016485

protein processing

27906959

HgeneSDE2

GO:0016567

protein ubiquitination

27906959

HgeneSDE2

GO:0034644

cellular response to UV

27906959

HgeneSDE2

GO:0071156

regulation of cell cycle arrest

27906959


check buttonFusion gene breakpoints across SDE2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across SLC22A15 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4PRADTCGA-EJ-7784-01ASDE2chr1

226182967

-SLC22A15chr1

116562203

+


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Fusion Gene ORF analysis for SDE2-SLC22A15

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-intronENST00000272091ENST00000481127SDE2chr1

226182967

-SLC22A15chr1

116562203

+
Frame-shiftENST00000272091ENST00000369502SDE2chr1

226182967

-SLC22A15chr1

116562203

+
Frame-shiftENST00000272091ENST00000369503SDE2chr1

226182967

-SLC22A15chr1

116562203

+

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 SDE2-SLC22A15


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)
SDE2chr1226182966-SLC22A15chr1116562202+1.50E-070.9999999
SDE2chr1226182966-SLC22A15chr1116562202+1.50E-070.9999999

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for SDE2-SLC22A15


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/:226182967/:116562203)
- 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
SDE2

Q6IQ49

.
FUNCTION: Involved in both DNA replication and cell cycle control (PubMed:27906959). Unprocessed SDE2 interacts with PCNA via its PIP-box. The interaction with PCNA prevents monoubiquitination of the latter thereby inhibiting translesion DNA synthesis. The binding of SDE2 to PCNA also leads to processing of SDE2 by an unidentified deubiquitinating enzyme, cleaving off the N-terminal ubiquitin-like domain. The resulting mature SDE2 is degraded by the DCX(DTL) complex in a cell cycle- and DNA damage dependent manner (PubMed:27906959). Binding of SDE2 to PCNA is necessary to counteract damage due to ultraviolet light induced replication stress. The complete degradation of SDE2 is necessary to allow S-phase progression (PubMed:27906959). {ECO:0000269|PubMed:27906959}.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 SDE2-SLC22A15


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 SDE2-SLC22A15


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 SDE2-SLC22A15


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 SDE2-SLC22A15


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