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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:SEMA4B-CERS3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SEMA4B-CERS3
FusionPDB ID: 80308
FusionGDB2.0 ID: 80308
HgeneTgene
Gene symbol

SEMA4B

CERS3

Gene ID

10509

204219

Gene namesemaphorin 4Bceramide synthase 3
SynonymsSEMAC|SemCARCI9|LASS3
Cytomap

15q26.1

15q26.3

Type of geneprotein-codingprotein-coding
Descriptionsemaphorin-4Bsema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Bsema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, 4Bsemaphorin-Cceramide synthase 3LAG1 homolog, ceramide synthase 3LAG1 longevity assurance homolog 3dihydroceramide synthase 3sphingosine N-acyltransferase CERS3
Modification date2020031320200313
UniProtAcc.

Q8IU89

Ensembl transtripts involved in fusion geneENST idsENST00000332496, ENST00000379122, 
ENST00000411539, ENST00000560263, 
ENST00000560944, ENST00000284382, 
ENST00000394113, ENST00000538112, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score16 X 9 X 11=15848 X 7 X 7=392
# samples 2111
** MAII scorelog2(21/1584*10)=-2.91511110241349
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/392*10)=-1.83335013059055
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SEMA4B [Title/Abstract] AND CERS3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SEMA4B(90744967)-CERS3(100943070), # samples:1
SEMA4B(90761061)-CERS3(100943070), # samples:1
Anticipated loss of major functional domain due to fusion event.SEMA4B-CERS3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
SEMA4B-CERS3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
SEMA4B-CERS3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
SEMA4B-CERS3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
SEMA4B-CERS3 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
SEMA4B-CERS3 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
* 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
TgeneCERS3

GO:0046513

ceramide biosynthetic process

17977534|22038835


check buttonFusion gene breakpoints across SEMA4B (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across CERS3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4LUADTCGA-J2-A4AD-01ASEMA4Bchr15

90744967

+CERS3chr15

100943070

-
ChimerDB4LUADTCGA-J2-A4AD-01ASEMA4Bchr15

90761061

-CERS3chr15

100943070

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000379122SEMA4Bchr1590744967+ENST00000394113CERS3chr15100943070-795440142462106
ENST00000332496SEMA4Bchr1590744967+ENST00000394113CERS3chr15100943070-75239799419106
ENST00000411539SEMA4Bchr1590744967+ENST00000394113CERS3chr15100943070-7724174051135
ENST00000379122SEMA4Bchr1590761061-ENST00000284382CERS3chr15100943070-3138667142819225
ENST00000332496SEMA4Bchr1590761061-ENST00000284382CERS3chr15100943070-309562499776225
ENST00000411539SEMA4Bchr1590761061-ENST00000284382CERS3chr15100943070-3115644191796201

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
ENST00000379122ENST00000394113SEMA4Bchr1590744967+CERS3chr15100943070-0.599441050.40055895
ENST00000332496ENST00000394113SEMA4Bchr1590744967+CERS3chr15100943070-0.669695850.33030415
ENST00000411539ENST00000394113SEMA4Bchr1590744967+CERS3chr15100943070-0.602303450.3976965
ENST00000379122ENST00000284382SEMA4Bchr1590761061-CERS3chr15100943070-0.007624980.9923751
ENST00000332496ENST00000284382SEMA4Bchr1590761061-CERS3chr15100943070-0.0076690670.9923309
ENST00000411539ENST00000284382SEMA4Bchr1590761061-CERS3chr15100943070-0.0076222490.99237776

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>80308_80308_1_SEMA4B-CERS3_SEMA4B_chr15_90744967_ENST00000332496_CERS3_chr15_100943070_ENST00000394113_length(amino acids)=106AA_BP=
MTLTHSRSGGGGPRGDSGADRGAELPPVSPAEPPEPEPRDTVAPALRMLRTAMGLRSWLAAPWGALPPRPPLLLLLLLLLLLQPPPPTWA

--------------------------------------------------------------

>80308_80308_2_SEMA4B-CERS3_SEMA4B_chr15_90744967_ENST00000379122_CERS3_chr15_100943070_ENST00000394113_length(amino acids)=106AA_BP=
MTLTHSRSGGGGPRGDSGADRGAELPPVSPAEPPEPEPRDTVAPALRMLRTAMGLRSWLAAPWGALPPRPPLLLLLLLLLLLQPPPPTWA

--------------------------------------------------------------

>80308_80308_3_SEMA4B-CERS3_SEMA4B_chr15_90744967_ENST00000411539_CERS3_chr15_100943070_ENST00000394113_length(amino acids)=135AA_BP=
MIRGLSAQVGGGGCSRSSSSRSSSSGGRGGSAPHGAASQLLRPIAVRSIRRAGATVSRGSGSGGSAGLTGGSSAPRSAPESPRGPPPPDL

--------------------------------------------------------------

>80308_80308_4_SEMA4B-CERS3_SEMA4B_chr15_90761061_ENST00000332496_CERS3_chr15_100943070_ENST00000284382_length(amino acids)=225AA_BP=175
MTLTHSRSGGGGPRGDSGADRGAELPPVSPAEPPEPEPRDTVAPALRMLRTAMGLRSWLAAPWGALPPRPPLLLLLLLLLLLQPPPPTWA
LSPRISLPLGSEERPFLRFEAEHISNYTALLLSRDGRTLYVGAREALFALSSNLSFLPGGEYQELLWGADAEKKQQCSFKGKDPQSIQDV

--------------------------------------------------------------

>80308_80308_5_SEMA4B-CERS3_SEMA4B_chr15_90761061_ENST00000379122_CERS3_chr15_100943070_ENST00000284382_length(amino acids)=225AA_BP=175
MTLTHSRSGGGGPRGDSGADRGAELPPVSPAEPPEPEPRDTVAPALRMLRTAMGLRSWLAAPWGALPPRPPLLLLLLLLLLLQPPPPTWA
LSPRISLPLGSEERPFLRFEAEHISNYTALLLSRDGRTLYVGAREALFALSSNLSFLPGGEYQELLWGADAEKKQQCSFKGKDPQSIQDV

--------------------------------------------------------------

>80308_80308_6_SEMA4B-CERS3_SEMA4B_chr15_90761061_ENST00000411539_CERS3_chr15_100943070_ENST00000284382_length(amino acids)=201AA_BP=151
MPPVSPAEPPEPEPRDTVAPALRMLRTAMGLRSWLAAPWGALPPRPPLLLLLLLLLLLQPPPPTWALSPRISLPLGSEERPFLRFEAEHI
SNYTALLLSRDGRTLYVGAREALFALSSNLSFLPGGEYQELLWGADAEKKQQCSFKGKDPQSIQDVRSDDEDYEEEEEEEEEEATKGKEM

--------------------------------------------------------------

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Fusion Protein Functional Features


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/chr15:90744967/chr15:100943070)
- 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
.CERS3

Q8IU89

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: Ceramide synthase that catalyzes formation of ceramide from sphinganine and acyl-CoA substrates, with high selectivity toward very-long (C22:0-C24:0) and ultra long chain (more than C26:0) as acyl donor (PubMed:17977534, PubMed:22038835, PubMed:26887952). It is crucial for the synthesis of ultra long-chain ceramides in the epidermis, to maintain epidermal lipid homeostasis and terminal differentiation (PubMed:23754960). {ECO:0000269|PubMed:17977534, ECO:0000269|PubMed:22038835, ECO:0000269|PubMed:23754960, ECO:0000269|PubMed:26887952}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneCERS3chr15:90744967chr15:100943070ENST000002843821113346_355333.0384.0Compositional biasNote=Poly-Glu
TgeneCERS3chr15:90744967chr15:100943070ENST000003941131214346_355333.0384.0Compositional biasNote=Poly-Glu
TgeneCERS3chr15:90744967chr15:100943070ENST000005381121113346_355333.0384.0Compositional biasNote=Poly-Glu
TgeneCERS3chr15:90761061chr15:100943070ENST000002843821113346_355333.0384.0Compositional biasNote=Poly-Glu
TgeneCERS3chr15:90761061chr15:100943070ENST000003941131214346_355333.0384.0Compositional biasNote=Poly-Glu
TgeneCERS3chr15:90761061chr15:100943070ENST000005381121113346_355333.0384.0Compositional biasNote=Poly-Glu

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSEMA4Bchr15:90744967chr15:100943070ENST00000379122+216758_78147.333333333333336738.0Compositional biasNote=Pro-rich
HgeneSEMA4Bchr15:90761061chr15:100943070ENST00000379122-416758_781123.0738.0Compositional biasNote=Pro-rich
HgeneSEMA4Bchr15:90744967chr15:100943070ENST00000379122+21647_52347.333333333333336738.0DomainSema
HgeneSEMA4Bchr15:90744967chr15:100943070ENST00000379122+216525_57947.333333333333336738.0DomainNote=PSI
HgeneSEMA4Bchr15:90744967chr15:100943070ENST00000379122+216604_66347.333333333333336738.0DomainNote=Ig-like C2-type
HgeneSEMA4Bchr15:90761061chr15:100943070ENST00000379122-41647_523123.0738.0DomainSema
HgeneSEMA4Bchr15:90761061chr15:100943070ENST00000379122-416525_579123.0738.0DomainNote=PSI
HgeneSEMA4Bchr15:90761061chr15:100943070ENST00000379122-416604_663123.0738.0DomainNote=Ig-like C2-type
HgeneSEMA4Bchr15:90744967chr15:100943070ENST00000379122+21644_71747.333333333333336738.0Topological domainExtracellular
HgeneSEMA4Bchr15:90744967chr15:100943070ENST00000379122+216739_83747.333333333333336738.0Topological domainCytoplasmic
HgeneSEMA4Bchr15:90761061chr15:100943070ENST00000379122-41644_717123.0738.0Topological domainExtracellular
HgeneSEMA4Bchr15:90761061chr15:100943070ENST00000379122-416739_837123.0738.0Topological domainCytoplasmic
HgeneSEMA4Bchr15:90744967chr15:100943070ENST00000379122+216718_73847.333333333333336738.0TransmembraneHelical
HgeneSEMA4Bchr15:90761061chr15:100943070ENST00000379122-416718_738123.0738.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000002843821113130_331333.0384.0DomainTLC
TgeneCERS3chr15:90744967chr15:100943070ENST000003941131214130_331333.0384.0DomainTLC
TgeneCERS3chr15:90744967chr15:100943070ENST000005381121113130_331333.0384.0DomainTLC
TgeneCERS3chr15:90761061chr15:100943070ENST000002843821113130_331333.0384.0DomainTLC
TgeneCERS3chr15:90761061chr15:100943070ENST000003941131214130_331333.0384.0DomainTLC
TgeneCERS3chr15:90761061chr15:100943070ENST000005381121113130_331333.0384.0DomainTLC
TgeneCERS3chr15:90744967chr15:100943070ENST00000284382111366_127333.0384.0RegionHomeobox-like
TgeneCERS3chr15:90744967chr15:100943070ENST00000394113121466_127333.0384.0RegionHomeobox-like
TgeneCERS3chr15:90744967chr15:100943070ENST00000538112111366_127333.0384.0RegionHomeobox-like
TgeneCERS3chr15:90761061chr15:100943070ENST00000284382111366_127333.0384.0RegionHomeobox-like
TgeneCERS3chr15:90761061chr15:100943070ENST00000394113121466_127333.0384.0RegionHomeobox-like
TgeneCERS3chr15:90761061chr15:100943070ENST00000538112111366_127333.0384.0RegionHomeobox-like
TgeneCERS3chr15:90744967chr15:100943070ENST000002843821113319_383333.0384.0Topological domainCytoplasmic
TgeneCERS3chr15:90744967chr15:100943070ENST000003941131214319_383333.0384.0Topological domainCytoplasmic
TgeneCERS3chr15:90744967chr15:100943070ENST000005381121113319_383333.0384.0Topological domainCytoplasmic
TgeneCERS3chr15:90761061chr15:100943070ENST000002843821113319_383333.0384.0Topological domainCytoplasmic
TgeneCERS3chr15:90761061chr15:100943070ENST000003941131214319_383333.0384.0Topological domainCytoplasmic
TgeneCERS3chr15:90761061chr15:100943070ENST000005381121113319_383333.0384.0Topological domainCytoplasmic
TgeneCERS3chr15:90744967chr15:100943070ENST000002843821113139_159333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000002843821113174_194333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000002843821113205_225333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000002843821113264_284333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000002843821113298_318333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST00000284382111332_52333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000003941131214139_159333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000003941131214174_194333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000003941131214205_225333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000003941131214264_284333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000003941131214298_318333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST00000394113121432_52333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000005381121113139_159333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000005381121113174_194333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000005381121113205_225333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000005381121113264_284333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST000005381121113298_318333.0384.0TransmembraneHelical
TgeneCERS3chr15:90744967chr15:100943070ENST00000538112111332_52333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000002843821113139_159333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000002843821113174_194333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000002843821113205_225333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000002843821113264_284333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000002843821113298_318333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST00000284382111332_52333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000003941131214139_159333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000003941131214174_194333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000003941131214205_225333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000003941131214264_284333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000003941131214298_318333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST00000394113121432_52333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000005381121113139_159333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000005381121113174_194333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000005381121113205_225333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000005381121113264_284333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST000005381121113298_318333.0384.0TransmembraneHelical
TgeneCERS3chr15:90761061chr15:100943070ENST00000538112111332_52333.0384.0TransmembraneHelical


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
SEMA4B
CERS3


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to SEMA4B-CERS3


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to SEMA4B-CERS3


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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