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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:TSPAN3-PSTPIP1 (FusionGDB2 ID:94090)

Fusion Gene Summary for TSPAN3-PSTPIP1

check button Fusion gene summary
Fusion gene informationFusion gene name: TSPAN3-PSTPIP1
Fusion gene ID: 94090
HgeneTgene
Gene symbol

TSPAN3

PSTPIP1

Gene ID

10099

9051

Gene nametetraspanin 3proline-serine-threonine phosphatase interacting protein 1
SynonymsTM4-A|TM4SF8|TSPAN-3CD2BP1|CD2BP1L|CD2BP1S|H-PIP|PAPAS|PSTPIP
Cytomap

15q24.3

15q24.3

Type of geneprotein-codingprotein-coding
Descriptiontetraspanin-3tetraspan 3tetraspan TM4SFtetraspanin TM4-Atransmembrane 4 superfamily member 8proline-serine-threonine phosphatase-interacting protein 1CD2 antigen-binding protein 1CD2 cytoplasmic tail-binding proteinCD2-binding protein 1PEST phosphatase-interacting protein 1truncated proline-serine-threonine phosphatase interacting protein 1
Modification date2020032220200315
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000267970, ENST00000346495, 
ENST00000424443, ENST00000561277, 
ENST00000559494, ENST00000558745, 
ENST00000558394, 		ENST00000558012, 
ENST00000267939, ENST00000379595, 
ENST00000559295, ENST00000557995, 
Fusion gene scores* DoF score13 X 10 X 7=9103 X 3 X 2=18
# samples 143
** MAII scorelog2(14/910*10)=-2.70043971814109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: TSPAN3 [Title/Abstract] AND PSTPIP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTSPAN3(77344727)-PSTPIP1(77310489), # samples:1
TSPAN3(77339131)-PSTPIP1(77310489), # 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

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.

check buttonFusion gene breakpoints across PSTPIP1 (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
ChimerDB4SKCMTCGA-EE-A2MQ-06ATSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
ChimerDB4SKCMTCGA-EE-A2MQ-06ATSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+


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Fusion Gene ORF analysis for TSPAN3-PSTPIP1

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
In-frameENST00000267970ENST00000558012TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000267970ENST00000267939TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000267970ENST00000379595TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000267970ENST00000559295TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
5CDS-intronENST00000267970ENST00000557995TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000346495ENST00000558012TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000346495ENST00000267939TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000346495ENST00000379595TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000346495ENST00000559295TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
5CDS-intronENST00000346495ENST00000557995TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000424443ENST00000558012TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000424443ENST00000267939TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000424443ENST00000379595TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000424443ENST00000559295TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
5CDS-intronENST00000424443ENST00000557995TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
Frame-shiftENST00000561277ENST00000558012TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
Frame-shiftENST00000561277ENST00000267939TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
Frame-shiftENST00000561277ENST00000379595TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
Frame-shiftENST00000561277ENST00000559295TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
5CDS-intronENST00000561277ENST00000557995TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000559494ENST00000558012TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000559494ENST00000267939TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000559494ENST00000379595TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
In-frameENST00000559494ENST00000559295TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
5CDS-intronENST00000559494ENST00000557995TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
Frame-shiftENST00000558745ENST00000558012TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
Frame-shiftENST00000558745ENST00000267939TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
Frame-shiftENST00000558745ENST00000379595TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
Frame-shiftENST00000558745ENST00000559295TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
5CDS-intronENST00000558745ENST00000557995TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000558394ENST00000558012TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000558394ENST00000267939TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000558394ENST00000379595TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000558394ENST00000559295TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
intron-intronENST00000558394ENST00000557995TSPAN3chr15

77344727

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000267970ENST00000558012TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000267970ENST00000267939TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000267970ENST00000379595TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000267970ENST00000559295TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-intronENST00000267970ENST00000557995TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000346495ENST00000558012TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000346495ENST00000267939TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000346495ENST00000379595TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000346495ENST00000559295TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-intronENST00000346495ENST00000557995TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000424443ENST00000558012TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000424443ENST00000267939TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000424443ENST00000379595TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000424443ENST00000559295TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-intronENST00000424443ENST00000557995TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000561277ENST00000558012TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000561277ENST00000267939TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000561277ENST00000379595TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000561277ENST00000559295TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-intronENST00000561277ENST00000557995TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000559494ENST00000558012TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000559494ENST00000267939TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000559494ENST00000379595TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000559494ENST00000559295TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-intronENST00000559494ENST00000557995TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000558745ENST00000558012TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000558745ENST00000267939TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000558745ENST00000379595TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000558745ENST00000559295TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-intronENST00000558745ENST00000557995TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000558394ENST00000558012TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000558394ENST00000267939TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000558394ENST00000379595TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-3CDSENST00000558394ENST00000559295TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+
intron-intronENST00000558394ENST00000557995TSPAN3chr15

77339131

-PSTPIP1chr15

77310489

+

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 TSPAN3-PSTPIP1


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)
TSPAN3chr1577344726-PSTPIP1chr1577310488+0.0001348410.9998652
TSPAN3chr1577344726-PSTPIP1chr1577310488+0.0001348410.9998652

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 TSPAN3-PSTPIP1


check button Go to

FGviewer for the breakpoints of chr15:77344727-chr15:77310489

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
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: 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.

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
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000267970-67107_212223.0254.0Topological domainExtracellular
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000267970-671_11223.0254.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000267970-6733_50223.0254.0Topological domainExtracellular
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000267970-6772_85223.0254.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000346495-561_11198.0229.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000346495-5633_50198.0229.0Topological domainExtracellular
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000346495-5672_85198.0229.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000424443-561_11159.0190.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000424443-5633_50159.0190.0Topological domainExtracellular
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000424443-5672_85159.0190.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000267970-6712_32223.0254.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000267970-6751_71223.0254.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000267970-6786_106223.0254.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000346495-5612_32198.0229.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000346495-5651_71198.0229.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000346495-5686_106198.0229.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000424443-5612_32159.0190.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000424443-5651_71159.0190.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000424443-5686_106159.0190.0TransmembraneHelical
TgenePSTPIP1chr15:77344727chr15:77310489ENST00000558012015166_21212.0417.0Coiled coilOntology_term=ECO:0000255
TgenePSTPIP1chr15:77344727chr15:77310489ENST00000559295014166_21212.0398.0Coiled coilOntology_term=ECO:0000255
TgenePSTPIP1chr15:77344727chr15:77310489ENST00000558012015359_41612.0417.0DomainSH3
TgenePSTPIP1chr15:77344727chr15:77310489ENST00000559295014359_41612.0398.0DomainSH3

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000267970-67234_253223.0254.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000346495-56107_212198.0229.0Topological domainExtracellular
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000346495-56234_253198.0229.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000424443-56107_212159.0190.0Topological domainExtracellular
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000424443-56234_253159.0190.0Topological domainCytoplasmic
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000267970-67213_233223.0254.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000346495-56213_233198.0229.0TransmembraneHelical
HgeneTSPAN3chr15:77344727chr15:77310489ENST00000424443-56213_233159.0190.0TransmembraneHelical
TgenePSTPIP1chr15:77344727chr15:77310489ENST000005580120155_26412.0417.0DomainF-BAR
TgenePSTPIP1chr15:77344727chr15:77310489ENST000005592950145_26412.0398.0DomainF-BAR


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Fusion Gene Sequence for TSPAN3-PSTPIP1


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 TSPAN3-PSTPIP1


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 TSPAN3-PSTPIP1


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 TSPAN3-PSTPIP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgenePSTPIP1C1858361Pyogenic Arthritis, Pyoderma Gangrenosum and Acne6CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgenePSTPIP1C0001144Acne Vulgaris1CTD_human
TgenePSTPIP1C0023893Liver Cirrhosis, Experimental1CTD_human
TgenePSTPIP1C0085652Pyoderma Gangrenosum1CTD_human
TgenePSTPIP1C0162836Hidradenitis Suppurativa1CTD_human
TgenePSTPIP1C0702166Acne1CTD_human
TgenePSTPIP1C1860229Hyperzincemia and Hypercalprotectinemia1ORPHANET
TgenePSTPIP1C3860213Autoinflammatory disorder1GENOMICS_ENGLAND