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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:TSPAN3-CHRNA3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TSPAN3-CHRNA3
FusionPDB ID: 94751
FusionGDB2.0 ID: 94751
HgeneTgene
Gene symbol

TSPAN3

CHRNA3

Gene ID

10099

1136

Gene nametetraspanin 3cholinergic receptor nicotinic alpha 3 subunit
SynonymsTM4-A|TM4SF8|TSPAN-3BAIPRCK|LNCR2|NACHRA3|PAOD2
Cytomap

15q24.3

15q25.1

Type of geneprotein-codingprotein-coding
Descriptiontetraspanin-3tetraspan 3tetraspan TM4SFtetraspanin TM4-Atransmembrane 4 superfamily member 8neuronal acetylcholine receptor subunit alpha-3cholinergic receptor, nicotinic alpha 3cholinergic receptor, nicotinic, alpha 3 (neuronal)cholinergic receptor, nicotinic, alpha polypeptide 3neuronal nicotinic acetylcholine receptor, alpha3 subunit
Modification date2020032220200313
UniProtAcc.

P32297

Ensembl transtripts involved in fusion geneENST idsENST00000267970, ENST00000346495, 
ENST00000424443, ENST00000558745, 
ENST00000559494, ENST00000561277, 
ENST00000558394, 		ENST00000559941, 
ENST00000326828, ENST00000348639, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 10 X 7=9105 X 4 X 3=60
# samples 145
** MAII scorelog2(14/910*10)=-2.70043971814109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: TSPAN3 [Title/Abstract] AND CHRNA3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TSPAN3(77339131)-CHRNA3(78894606), # samples:2
Anticipated loss of major functional domain due to fusion event.TSPAN3-CHRNA3 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
TgeneCHRNA3

GO:0007165

signal transduction

8906617


check buttonFusion gene breakpoints across TSPAN3 (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 CHRNA3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4LUADTCGA-NJ-A55O-01ATSPAN3chr15

77339131

-CHRNA3chr15

78894606

-
ChimerDB4LUADTCGA-NJ-A55O-01ATSPAN3chr15

77344727

-CHRNA3chr15

78894606

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000558745TSPAN3chr1577344727-ENST00000348639CHRNA3chr1578894606-18967447301836368
ENST00000558745TSPAN3chr1577344727-ENST00000326828CHRNA3chr1578894606-31847447301884384

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
ENST00000558745ENST00000348639TSPAN3chr1577344727-CHRNA3chr1578894606-0.0081181250.9918819
ENST00000558745ENST00000326828TSPAN3chr1577344727-CHRNA3chr1578894606-0.0016602920.99833965

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>94751_94751_1_TSPAN3-CHRNA3_TSPAN3_chr15_77344727_ENST00000558745_CHRNA3_chr15_78894606_ENST00000326828_length(amino acids)=384AA_BP=2
MQLFSAVGDFQVDDKTKALLKYTGEVTWIPPAIFKSSCKIDVTYFPFDYQNCTMKFGSWSYDKAKIDLVLIGSSMNLKDYWESGEWAIIK
APGYKHDIKYNCCEEIYPDITYSLYIRRLPLFYTINLIIPCLLISFLTVLVFYLPSDCGEKVTLCISVLLSLTVFLLVITETIPSTSLVI
PLIGEYLLFTMIFVTLSIVITVFVLNVHYRTPTTHTMPSWVKTVFLNLLPRVMFMTRPTSNEGNAQKPRPLYGAELSNLNCFSRAESKGC
KEGYPCQDGMCGYCHHRRIKISNFSANLTRSSSSESVDAVLSLSALSPEIKEAIQSVKYIAENMKAQNEAKEIQDDWKYVAMVIDRIFLW

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

>94751_94751_2_TSPAN3-CHRNA3_TSPAN3_chr15_77344727_ENST00000558745_CHRNA3_chr15_78894606_ENST00000348639_length(amino acids)=368AA_BP=2
MQLFSAVGDFQVDDKTKALLKYTGEVTWIPPAIFKSSCKIDVTYFPFDYQNCTMKFGSWSYDKAKIDLVLIGSSMNLKDYWESGEWAIIK
APGYKHDIKYNCCEEIYPDITYSLYIRRLPLFYTINLIIPCLLISFLTVLVFYLPSDCGEKVTLCISVLLSLTVFLLVITETIPSTSLVI
PLIGEYLLFTMIFVTLSIVITVFVLNVHYRTPTTHTMPSWVKTVFLNLLPRVMFMTRPTSNEGNAQKPRPLYGAELSNLNCFSRAESKGC
KEGYPCQDGMCGYCHHRRIKISNFSANLTRSSSSESVDAVLSLSALSPEIKEAIQSVKYIAENMKAQNEAKEEQKAQEIQQLKRKEKSTE

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

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Fusion Protein Functional Features


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/chr15:77339131/chr15:78894606)
- 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
.CHRNA3

P32297

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: After binding acetylcholine, the AChR responds by an extensive change in conformation that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane. {ECO:0000269|PubMed:31708116}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000267970-67107_212223.0254.0Topological domainExtracellular
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000267970-671_11223.0254.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000267970-6733_50223.0254.0Topological domainExtracellular
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000267970-6772_85223.0254.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000346495-561_11198.0229.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000346495-5633_50198.0229.0Topological domainExtracellular
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000346495-5672_85198.0229.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000424443-561_11159.0190.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000424443-5633_50159.0190.0Topological domainExtracellular
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000424443-5672_85159.0190.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000267970-6712_32223.0254.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000267970-6751_71223.0254.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000267970-6786_106223.0254.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000346495-5612_32198.0229.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000346495-5651_71198.0229.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000346495-5686_106198.0229.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000424443-5612_32159.0190.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000424443-5651_71159.0190.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000424443-5686_106159.0190.0TransmembraneHelical
TgeneCHRNA3chr15:77344727chr15:78894606ENST0000032682836329_477125.66666666666667506.0Topological domainCytoplasmic
TgeneCHRNA3chr15:77344727chr15:78894606ENST0000034863936329_477125.66666666666667490.0Topological domainCytoplasmic
TgeneCHRNA3chr15:77344727chr15:78894606ENST0000032682836241_265125.66666666666667506.0TransmembraneHelical
TgeneCHRNA3chr15:77344727chr15:78894606ENST0000032682836273_291125.66666666666667506.0TransmembraneHelical
TgeneCHRNA3chr15:77344727chr15:78894606ENST0000032682836307_328125.66666666666667506.0TransmembraneHelical
TgeneCHRNA3chr15:77344727chr15:78894606ENST0000032682836478_497125.66666666666667506.0TransmembraneHelical
TgeneCHRNA3chr15:77344727chr15:78894606ENST0000034863936241_265125.66666666666667490.0TransmembraneHelical
TgeneCHRNA3chr15:77344727chr15:78894606ENST0000034863936273_291125.66666666666667490.0TransmembraneHelical
TgeneCHRNA3chr15:77344727chr15:78894606ENST0000034863936307_328125.66666666666667490.0TransmembraneHelical
TgeneCHRNA3chr15:77344727chr15:78894606ENST0000034863936478_497125.66666666666667490.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000267970-67234_253223.0254.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000346495-56107_212198.0229.0Topological domainExtracellular
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000346495-56234_253198.0229.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000424443-56107_212159.0190.0Topological domainExtracellular
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000424443-56234_253159.0190.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000267970-67213_233223.0254.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000346495-56213_233198.0229.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:78894606ENST00000424443-56213_233159.0190.0TransmembraneHelical
TgeneCHRNA3chr15:77344727chr15:78894606ENST000003268283632_240125.66666666666667506.0Topological domainExtracellular
TgeneCHRNA3chr15:77344727chr15:78894606ENST000003486393632_240125.66666666666667490.0Topological domainExtracellular


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
TSPAN3
CHRNA3


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to TSPAN3-CHRNA3


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to TSPAN3-CHRNA3


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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