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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:SEMA6B-STAT3 (FusionGDB2 ID:80357)

Fusion Gene Summary for SEMA6B-STAT3

check button Fusion gene summary
Fusion gene informationFusion gene name: SEMA6B-STAT3
Fusion gene ID: 80357
HgeneTgene
Gene symbol

SEMA6B

STAT3

Gene ID

10501

6774

Gene namesemaphorin 6Bsignal transducer and activator of transcription 3
SynonymsSEM-SEMA-Y|SEMA-VIB|SEMAN|semaZADMIO|ADMIO1|APRF|HIES
Cytomap

19p13.3

17q21.2

Type of geneprotein-codingprotein-coding
Descriptionsemaphorin-6Bsema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6Bsemaphorin VIBsemaphorin Zsemaphorin-6Basignal transducer and activator of transcription 3DNA-binding protein APRFacute-phase response factor
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000301293, ENST00000586582, 
ENST00000586965, 		ENST00000264657, 
ENST00000389272, ENST00000404395, 
ENST00000585517, ENST00000588969, 
ENST00000590776, 
Fusion gene scores* DoF score1 X 1 X 1=117 X 21 X 8=2856
# samples 121
** MAII scorelog2(1/1*10)=3.32192809488736log2(21/2856*10)=-3.76553474636298
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SEMA6B [Title/Abstract] AND STAT3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSEMA6B(4562021)-STAT3(40537295), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneSTAT3

GO:0006355

regulation of transcription, DNA-templated

15664994|17344214

TgeneSTAT3

GO:0006606

protein import into nucleus

18234692

TgeneSTAT3

GO:0010507

negative regulation of autophagy

26962683

TgeneSTAT3

GO:0010628

positive regulation of gene expression

23820254

TgeneSTAT3

GO:0030522

intracellular receptor signaling pathway

17324931

TgeneSTAT3

GO:0032355

response to estradiol

12552091

TgeneSTAT3

GO:0032870

cellular response to hormone stimulus

12552091

TgeneSTAT3

GO:0033210

leptin-mediated signaling pathway

17344214

TgeneSTAT3

GO:0035278

miRNA mediated inhibition of translation

23820254

TgeneSTAT3

GO:0044320

cellular response to leptin stimulus

17344214

TgeneSTAT3

GO:0044321

response to leptin

17344214

TgeneSTAT3

GO:0045893

positive regulation of transcription, DNA-templated

19390056

TgeneSTAT3

GO:0045944

positive regulation of transcription by RNA polymerase II

17324931|27050391|31462771

TgeneSTAT3

GO:0051726

regulation of cell cycle

17344214

TgeneSTAT3

GO:0060396

growth hormone receptor signaling pathway

10925297

TgeneSTAT3

GO:0060397

JAK-STAT cascade involved in growth hormone signaling pathway

12552091

TgeneSTAT3

GO:0070102

interleukin-6-mediated signaling pathway

12359225|12552091|17324931|24429361

TgeneSTAT3

GO:1902895

positive regulation of pri-miRNA transcription by RNA polymerase II

19390056|23820254

TgeneSTAT3

GO:2000637

positive regulation of gene silencing by miRNA

23820254


check buttonFusion gene breakpoints across SEMA6B (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 STAT3 (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
ChiTaRS5.0N/ABQ374310SEMA6Bchr19

4562021

+STAT3chr17

40537295

-


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Fusion Gene ORF analysis for SEMA6B-STAT3

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
intron-intronENST00000301293ENST00000264657SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000301293ENST00000389272SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000301293ENST00000404395SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000301293ENST00000585517SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000301293ENST00000588969SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000301293ENST00000590776SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000586582ENST00000264657SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000586582ENST00000389272SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000586582ENST00000404395SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000586582ENST00000585517SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000586582ENST00000588969SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000586582ENST00000590776SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000586965ENST00000264657SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000586965ENST00000389272SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000586965ENST00000404395SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000586965ENST00000585517SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000586965ENST00000588969SEMA6Bchr19

4562021

+STAT3chr17

40537295

-
intron-intronENST00000586965ENST00000590776SEMA6Bchr19

4562021

+STAT3chr17

40537295

-

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 SEMA6B-STAT3


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)

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.

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Fusion Protein Features for SEMA6B-STAT3


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/:4562021/:40537295)
- 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 SEMA6B-STAT3


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 SEMA6B-STAT3


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 SEMA6B-STAT3


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 SEMA6B-STAT3


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