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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:SH3PXD2A-MAP1S (FusionGDB2 ID:81511)

Fusion Gene Summary for SH3PXD2A-MAP1S

check button Fusion gene summary
Fusion gene informationFusion gene name: SH3PXD2A-MAP1S
Fusion gene ID: 81511
HgeneTgene
Gene symbol

SH3PXD2A

MAP1S

Gene ID

9644

55201

Gene nameSH3 and PX domains 2Amicrotubule associated protein 1S
SynonymsFISH|SH3MD1|TKS5BPY2IP1|C19orf5|MAP8|VCY2IP-1|VCY2IP1
Cytomap

10q24.33

19p13.11

Type of geneprotein-codingprotein-coding
DescriptionSH3 and PX domain-containing protein 2ASH3 multiple domains 1adapter protein TKS5adaptor protein TKS5five SH3 domain-containing proteintyrosine kinase substrate with five SH3 domainsmicrotubule-associated protein 1SBPY2-interacting protein 1MAP-1SVCY2-interacting protein 1microtubule-associated protein 8variable charge Y chromosome 2-interacting protein 1
Modification date2020031320200313
UniProtAcc.

Q66K74

Ensembl transtripts involved in fusion geneENST00000355946, ENST00000369774, 
ENST00000427662, ENST00000315994, 
ENST00000538130, ENST00000540321, 
ENST00000544059, ENST00000597681, 
ENST00000324096, 
Fusion gene scores* DoF score12 X 20 X 12=28806 X 6 X 6=216
# samples 298
** MAII scorelog2(29/2880*10)=-3.31194400631474
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/216*10)=-1.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SH3PXD2A [Title/Abstract] AND MAP1S [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSH3PXD2A(105452786)-MAP1S(17845082), # samples:3
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
HgeneSH3PXD2A

GO:0006801

superoxide metabolic process

19755710

TgeneMAP1S

GO:0010848

regulation of chromatin disassembly

12762840


check buttonFusion gene breakpoints across SH3PXD2A (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 MAP1S (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
ChimerDB4UCECTCGA-A5-A2K4-01ASH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
ChimerDB4UCECTCGA-A5-A2K4SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+


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Fusion Gene ORF analysis for SH3PXD2A-MAP1S

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-intronENST00000355946ENST00000544059SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
5CDS-intronENST00000355946ENST00000544059SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
5CDS-intronENST00000355946ENST00000597681SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
5CDS-intronENST00000355946ENST00000597681SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
5CDS-intronENST00000369774ENST00000544059SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
5CDS-intronENST00000369774ENST00000544059SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
5CDS-intronENST00000369774ENST00000597681SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
5CDS-intronENST00000369774ENST00000597681SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
5CDS-intronENST00000427662ENST00000544059SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
5CDS-intronENST00000427662ENST00000544059SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
5CDS-intronENST00000427662ENST00000597681SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
5CDS-intronENST00000427662ENST00000597681SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
5UTR-3CDSENST00000315994ENST00000324096SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
5UTR-3CDSENST00000315994ENST00000324096SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
5UTR-intronENST00000315994ENST00000544059SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
5UTR-intronENST00000315994ENST00000544059SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
5UTR-intronENST00000315994ENST00000597681SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
5UTR-intronENST00000315994ENST00000597681SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
Frame-shiftENST00000355946ENST00000324096SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
Frame-shiftENST00000355946ENST00000324096SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
Frame-shiftENST00000369774ENST00000324096SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
Frame-shiftENST00000369774ENST00000324096SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
Frame-shiftENST00000427662ENST00000324096SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
Frame-shiftENST00000427662ENST00000324096SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
intron-3CDSENST00000538130ENST00000324096SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
intron-3CDSENST00000538130ENST00000324096SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
intron-3CDSENST00000540321ENST00000324096SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
intron-3CDSENST00000540321ENST00000324096SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
intron-intronENST00000538130ENST00000544059SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
intron-intronENST00000538130ENST00000544059SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
intron-intronENST00000538130ENST00000597681SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
intron-intronENST00000538130ENST00000597681SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
intron-intronENST00000540321ENST00000544059SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
intron-intronENST00000540321ENST00000544059SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+
intron-intronENST00000540321ENST00000597681SH3PXD2Achr10

105452786

-MAP1Schr19

17845082

+
intron-intronENST00000540321ENST00000597681SH3PXD2Achr10

105452785

-MAP1Schr19

17845081

+

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 SH3PXD2A-MAP1S


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)
SH3PXD2Achr10105452785-MAP1Schr1917845081+2.12E-070.99999976
SH3PXD2Achr10105452785-MAP1Schr1917845081+2.12E-070.99999976
SH3PXD2Achr10105452785-MAP1Schr1917845081+2.12E-070.99999976
SH3PXD2Achr10105452785-MAP1Schr1917845081+2.12E-070.99999976

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 SH3PXD2A-MAP1S


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/:105452786/:17845082)
- 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
.MAP1S

Q66K74

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: Microtubule-associated protein that mediates aggregation of mitochondria resulting in cell death and genomic destruction (MAGD). Plays a role in anchoring the microtubule organizing center to the centrosomes. Binds to DNA. Plays a role in apoptosis. Involved in the formation of microtubule bundles (By similarity). {ECO:0000250, ECO:0000269|PubMed:15899810, ECO:0000269|PubMed:17234756}.

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 SH3PXD2A-MAP1S


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 SH3PXD2A-MAP1S


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 SH3PXD2A-MAP1S


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 SH3PXD2A-MAP1S


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