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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:SEMA4D-NDRG1 (FusionGDB2 ID:80327)

Fusion Gene Summary for SEMA4D-NDRG1

check button Fusion gene summary
Fusion gene informationFusion gene name: SEMA4D-NDRG1
Fusion gene ID: 80327
HgeneTgene
Gene symbol

SEMA4D

NDRG1

Gene ID

10507

10397

Gene namesemaphorin 4DN-myc downstream regulated 1
SynonymsA8|BB18|C9orf164|CD100|COLL4|GR3|M-sema-G|SEMAJ|coll-4CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5
Cytomap

9q22.2

8q24.22

Type of geneprotein-codingprotein-coding
Descriptionsemaphorin-4Dsema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Dsema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, 4Dprotein NDRG1N-myc downstream-regulated gene 1 proteindifferentiation-related gene 1 proteinnickel-specific induction protein Cap43protein regulated by oxygen-1reducing agents and tunicamycin-responsive protein
Modification date2020031320200328
UniProtAcc.

Q92597

Ensembl transtripts involved in fusion geneENST00000343780, ENST00000356444, 
ENST00000420987, ENST00000422704, 
ENST00000438547, ENST00000455551, 
ENST00000339861, ENST00000420101, 
ENST00000450295, ENST00000469653, 
ENST00000323851, ENST00000354944, 
ENST00000414097, ENST00000518066, 
ENST00000518176, ENST00000537882, 
ENST00000521414, ENST00000522476, 
Fusion gene scores* DoF score4 X 5 X 3=6024 X 17 X 10=4080
# samples 526
** MAII scorelog2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(26/4080*10)=-3.9719856238304
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SEMA4D [Title/Abstract] AND NDRG1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSEMA4D(92070803)-NDRG1(134296572), # 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
HgeneSEMA4D

GO:0001934

positive regulation of protein phosphorylation

16055703

HgeneSEMA4D

GO:0007162

negative regulation of cell adhesion

15218527

HgeneSEMA4D

GO:0030335

positive regulation of cell migration

16055703

HgeneSEMA4D

GO:0071526

semaphorin-plexin signaling pathway

15218527


check buttonFusion gene breakpoints across SEMA4D (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 NDRG1 (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
ChimerDB4STADTCGA-D7-8574-01ASEMA4Dchr9

92070803

-NDRG1chr8

134296572

-


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Fusion Gene ORF analysis for SEMA4D-NDRG1

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
5UTR-5UTRENST00000343780ENST00000323851SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000343780ENST00000354944SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000343780ENST00000414097SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000343780ENST00000518066SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000343780ENST00000518176SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000343780ENST00000537882SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000356444ENST00000323851SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000356444ENST00000354944SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000356444ENST00000414097SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000356444ENST00000518066SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000356444ENST00000518176SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000356444ENST00000537882SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000420987ENST00000323851SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000420987ENST00000354944SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000420987ENST00000414097SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000420987ENST00000518066SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000420987ENST00000518176SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000420987ENST00000537882SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000422704ENST00000323851SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000422704ENST00000354944SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000422704ENST00000414097SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000422704ENST00000518066SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000422704ENST00000518176SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000422704ENST00000537882SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000438547ENST00000323851SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000438547ENST00000354944SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000438547ENST00000414097SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000438547ENST00000518066SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000438547ENST00000518176SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000438547ENST00000537882SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000455551ENST00000323851SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000455551ENST00000354944SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000455551ENST00000414097SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000455551ENST00000518066SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000455551ENST00000518176SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-5UTRENST00000455551ENST00000537882SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-intronENST00000343780ENST00000521414SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-intronENST00000343780ENST00000522476SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-intronENST00000356444ENST00000521414SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-intronENST00000356444ENST00000522476SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-intronENST00000420987ENST00000521414SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-intronENST00000420987ENST00000522476SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-intronENST00000422704ENST00000521414SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-intronENST00000422704ENST00000522476SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-intronENST00000438547ENST00000521414SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-intronENST00000438547ENST00000522476SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-intronENST00000455551ENST00000521414SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
5UTR-intronENST00000455551ENST00000522476SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000339861ENST00000323851SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000339861ENST00000354944SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000339861ENST00000414097SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000339861ENST00000518066SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000339861ENST00000518176SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000339861ENST00000537882SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000420101ENST00000323851SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000420101ENST00000354944SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000420101ENST00000414097SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000420101ENST00000518066SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000420101ENST00000518176SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000420101ENST00000537882SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000450295ENST00000323851SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000450295ENST00000354944SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000450295ENST00000414097SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000450295ENST00000518066SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000450295ENST00000518176SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000450295ENST00000537882SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000469653ENST00000323851SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000469653ENST00000354944SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000469653ENST00000414097SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000469653ENST00000518066SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000469653ENST00000518176SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-5UTRENST00000469653ENST00000537882SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-intronENST00000339861ENST00000521414SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-intronENST00000339861ENST00000522476SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-intronENST00000420101ENST00000521414SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-intronENST00000420101ENST00000522476SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-intronENST00000450295ENST00000521414SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-intronENST00000450295ENST00000522476SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-intronENST00000469653ENST00000521414SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-
intron-intronENST00000469653ENST00000522476SEMA4Dchr9

92070803

-NDRG1chr8

134296572

-

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 SEMA4D-NDRG1


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 SEMA4D-NDRG1


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/:92070803/:134296572)
- 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
.NDRG1

Q92597

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: Stress-responsive protein involved in hormone responses, cell growth, and differentiation. Acts as a tumor suppressor in many cell types. Necessary but not sufficient for p53/TP53-mediated caspase activation and apoptosis. Has a role in cell trafficking, notably of the Schwann cell, and is necessary for the maintenance and development of the peripheral nerve myelin sheath. Required for vesicular recycling of CDH1 and TF. May also function in lipid trafficking. Protects cells from spindle disruption damage. Functions in p53/TP53-dependent mitotic spindle checkpoint. Regulates microtubule dynamics and maintains euploidy. {ECO:0000269|PubMed:15247272, ECO:0000269|PubMed:15377670, ECO:0000269|PubMed:17786215, ECO:0000269|PubMed:9766676}.

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 SEMA4D-NDRG1


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 SEMA4D-NDRG1


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 SEMA4D-NDRG1


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 SEMA4D-NDRG1


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