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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:SMIM4-DMD (FusionGDB2 ID:84187)

Fusion Gene Summary for SMIM4-DMD

check button Fusion gene summary
Fusion gene informationFusion gene name: SMIM4-DMD
Fusion gene ID: 84187
HgeneTgene
Gene symbol

SMIM4

DMD

Gene ID

440957

1756

Gene namesmall integral membrane protein 4dystrophin
SynonymsC3orf78BMD|CMD3B|DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85
Cytomap

3p21.1

Xp21.2-p21.1

Type of geneprotein-codingprotein-coding
Descriptionsmall integral membrane protein 4UPF0640 protein C3orf78dystrophin
Modification date2020031320200329
UniProtAcc

Q8WVI0

P11532

Ensembl transtripts involved in fusion geneENST00000477703, ENST00000307106, 
ENST00000482728, ENST00000476842, 
ENST00000288447, ENST00000343523, 
ENST00000357033, ENST00000359836, 
ENST00000361471, ENST00000378677, 
ENST00000378680, ENST00000378702, 
ENST00000378707, ENST00000378723, 
ENST00000445312, ENST00000474231, 
ENST00000541735, 
Fusion gene scores* DoF score7 X 4 X 3=8435 X 39 X 12=16380
# samples 741
** MAII scorelog2(7/84*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(41/16380*10)=-5.32016763702292
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMIM4 [Title/Abstract] AND DMD [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMIM4(52574542)-DMD(31976243), # 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 buttonFusion gene breakpoints across SMIM4 (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 DMD (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/ABP432767SMIM4chr3

52574542

+DMDchrX

31976243

-


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Fusion Gene ORF analysis for SMIM4-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
3UTR-intronENST00000477703ENST00000288447SMIM4chr3

52574542

+DMDchrX

31976243

-
3UTR-intronENST00000477703ENST00000343523SMIM4chr3

52574542

+DMDchrX

31976243

-
3UTR-intronENST00000477703ENST00000357033SMIM4chr3

52574542

+DMDchrX

31976243

-
3UTR-intronENST00000477703ENST00000359836SMIM4chr3

52574542

+DMDchrX

31976243

-
3UTR-intronENST00000477703ENST00000361471SMIM4chr3

52574542

+DMDchrX

31976243

-
3UTR-intronENST00000477703ENST00000378677SMIM4chr3

52574542

+DMDchrX

31976243

-
3UTR-intronENST00000477703ENST00000378680SMIM4chr3

52574542

+DMDchrX

31976243

-
3UTR-intronENST00000477703ENST00000378702SMIM4chr3

52574542

+DMDchrX

31976243

-
3UTR-intronENST00000477703ENST00000378707SMIM4chr3

52574542

+DMDchrX

31976243

-
3UTR-intronENST00000477703ENST00000378723SMIM4chr3

52574542

+DMDchrX

31976243

-
3UTR-intronENST00000477703ENST00000445312SMIM4chr3

52574542

+DMDchrX

31976243

-
3UTR-intronENST00000477703ENST00000474231SMIM4chr3

52574542

+DMDchrX

31976243

-
3UTR-intronENST00000477703ENST00000541735SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000288447SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000343523SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000357033SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000359836SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000361471SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000378677SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000378680SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000378702SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000378707SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000378723SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000445312SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000474231SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000307106ENST00000541735SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000288447SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000343523SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000357033SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000359836SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000361471SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000378677SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000378680SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000378702SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000378707SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000378723SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000445312SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000474231SMIM4chr3

52574542

+DMDchrX

31976243

-
5CDS-intronENST00000482728ENST00000541735SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000288447SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000343523SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000357033SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000359836SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000361471SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000378677SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000378680SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000378702SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000378707SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000378723SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000445312SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000474231SMIM4chr3

52574542

+DMDchrX

31976243

-
intron-intronENST00000476842ENST00000541735SMIM4chr3

52574542

+DMDchrX

31976243

-

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 SMIM4-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)

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 SMIM4-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/:52574542/:31976243)
- 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
SMIM4

Q8WVI0

DMD

P11532

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 SMIM4-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 SMIM4-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 SMIM4-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

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Related Diseases for SMIM4-DMD


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