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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:SPATA4-DMD (FusionGDB2 ID:HG132851TG1756)

Fusion Gene Summary for SPATA4-DMD

check button Fusion gene summary
Fusion gene informationFusion gene name: SPATA4-DMD
Fusion gene ID: hg132851tg1756
HgeneTgene
Gene symbol

SPATA4

DMD

Gene ID

132851

1756

Gene namespermatogenesis associated 4dystrophin
SynonymsCFAP178|FAP178|SPEF1B|TSARG2BMD|CMD3B|DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85
Cytomap('SPATA4')('DMD')

4q34.2

Xp21.2-p21.1

Type of geneprotein-codingprotein-coding
Descriptionspermatogenesis-associated protein 4testis and spermatogenesis cell related protein 2testis spermatocyte apoptosis-related gene 2 proteindystrophin
Modification date2020031320200329
UniProtAcc.

P11532

Ensembl transtripts involved in fusion geneENST00000280191, ENST00000515234, 
Fusion gene scores* DoF score1 X 1 X 1=135 X 39 X 12=16380
# samples 141
** MAII scorelog2(1/1*10)=3.32192809488736log2(41/16380*10)=-5.32016763702292
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SPATA4 [Title/Abstract] AND DMD [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSPATA4(177112226)-DMD(32510149), # 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
TgeneDMD

GO:0043043

peptide biosynthetic process

16000376



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/AFN070660SPATA4chr4

177112226

+DMDchrX

32510149

-


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Fusion Gene ORF analysis for SPATA4-DMD

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-intronENST00000280191ENST00000288447SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000280191ENST00000343523SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000280191ENST00000357033SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000280191ENST00000359836SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000280191ENST00000361471SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000280191ENST00000378677SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000280191ENST00000378680SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000280191ENST00000378702SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000280191ENST00000378707SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000280191ENST00000378723SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000280191ENST00000445312SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000280191ENST00000474231SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000280191ENST00000541735SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000288447SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000343523SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000357033SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000359836SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000361471SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000378677SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000378680SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000378702SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000378707SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000378723SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000445312SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000474231SPATA4chr4

177112226

+DMDchrX

32510149

-
intron-intronENST00000515234ENST00000541735SPATA4chr4

177112226

+DMDchrX

32510149

-

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 SPATA4-DMD


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)


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Fusion Protein Features for SPATA4-DMD


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/:177112226/:32510149)
- 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
.DMD

P11532

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: Anchors the extracellular matrix to the cytoskeleton via F-actin. Ligand for dystroglycan. Component of the dystrophin-associated glycoprotein complex which accumulates at the neuromuscular junction (NMJ) and at a variety of synapses in the peripheral and central nervous systems and has a structural function in stabilizing the sarcolemma. Also implicated in signaling events and synaptic transmission. {ECO:0000250|UniProtKB:P11531, ECO:0000269|PubMed:16710609}.

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 SPATA4-DMD


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 SPATA4-DMD


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 SPATA4-DMD


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneDMDP11532DB15593GolodirsenInducerBiotechApproved

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Related Diseases for SPATA4-DMD


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0013264Muscular Dystrophy, Duchenne18CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0917713Becker Muscular Dystrophy13CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC3542021Duchenne and Becker Muscular Dystrophy11CTD_human
TgeneC0026850Muscular Dystrophy4CTD_human
TgeneC3668940Dmd-Associated Dilated Cardiomyopathy4CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0033141Cardiomyopathies, Primary3CTD_human
TgeneC0036529Myocardial Diseases, Secondary3CTD_human
TgeneC0878544Cardiomyopathies3CTD_human;GENOMICS_ENGLAND
TgeneC0006663Calcinosis1CTD_human
TgeneC0007193Cardiomyopathy, Dilated1CTD_human
TgeneC0018800Cardiomegaly1CTD_human
TgeneC0023269leiomyosarcoma1CTD_human
TgeneC0026851Muscular Dystrophy, Animal1CTD_human
TgeneC0027540Necrosis1CTD_human
TgeneC0027626Neoplasm Invasiveness1CTD_human
TgeneC0027627Neoplasm Metastasis1CTD_human
TgeneC0032460Polycystic Ovary Syndrome1CTD_human
TgeneC0038220Status Epilepticus1CTD_human
TgeneC0151786Muscle Weakness1CTD_human
TgeneC0205815Leiomyosarcoma, Epithelioid1CTD_human
TgeneC0205816Leiomyosarcoma, Myxoid1CTD_human
TgeneC0206656Embryonal Rhabdomyosarcoma1CTD_human
TgeneC0238198Gastrointestinal Stromal Tumors1CTD_human
TgeneC0242973Ventricular Dysfunction1CTD_human
TgeneC0263628Tumoral calcinosis1CTD_human
TgeneC0270823Petit mal status1CTD_human
TgeneC0311335Grand Mal Status Epilepticus1CTD_human
TgeneC0340427Familial dilated cardiomyopathy1ORPHANET
TgeneC0393734Complex Partial Status Epilepticus1CTD_human
TgeneC0521174Microcalcification1CTD_human
TgeneC0751522Status Epilepticus, Subclinical1CTD_human
TgeneC0751523Non-Convulsive Status Epilepticus1CTD_human
TgeneC0751524Simple Partial Status Epilepticus1CTD_human
TgeneC1136382Sclerocystic Ovaries1CTD_human
TgeneC1383860Cardiac Hypertrophy1CTD_human
TgeneC1449563Cardiomyopathy, Familial Idiopathic1CTD_human
TgeneC2931498Mental Retardation, X-Linked 11ORPHANET
TgeneC3179349Gastrointestinal Stromal Sarcoma1CTD_human