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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:SEMA3C-CNTNAP2

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SEMA3C-CNTNAP2
FusionPDB ID: 80279
FusionGDB2.0 ID: 80279
HgeneTgene
Gene symbol

SEMA3C

CNTNAP2

Gene ID

10512

26047

Gene namesemaphorin 3Ccontactin associated protein 2
SynonymsSEMAE|SemEAUTS15|CASPR2|CDFE|NRXN4|PTHSL1
Cytomap

7q21.11

7q35-q36.1

Type of geneprotein-codingprotein-coding
Descriptionsemaphorin-3Csema Esema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Csemaphorin Econtactin-associated protein-like 2cell recognition molecule Caspr2contactin associated protein like 2homolog of Drosophila neurexin IV
Modification date2020031320200313
UniProtAcc.

Q9UHC6

Ensembl transtripts involved in fusion geneENST idsENST00000265361, ENST00000419255, 
ENST00000536800, ENST00000544525, 
ENST00000487621, 
ENST00000463592, 
ENST00000361727, ENST00000538075, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 5 X 5=17530 X 34 X 9=9180
# samples 836
** MAII scorelog2(8/175*10)=-1.12928301694497
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(36/9180*10)=-4.6724253419715
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SEMA3C [Title/Abstract] AND CNTNAP2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SEMA3C(80545995)-CNTNAP2(148112509), # samples:3
Anticipated loss of major functional domain due to fusion event.SEMA3C-CNTNAP2 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.
SEMA3C-CNTNAP2 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.
SEMA3C-CNTNAP2 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
SEMA3C-CNTNAP2 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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

check buttonFusion gene breakpoints across SEMA3C (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 CNTNAP2 (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
ChimerDB4BRCATCGA-E2-A1LL-01ASEMA3Cchr7

80545995

-CNTNAP2chr7

148112509

+


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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)
ENST00000265361SEMA3Cchr780545995-ENST00000361727CNTNAP2chr7148112509+6247665505864119
ENST00000265361SEMA3Cchr780545995-ENST00000538075CNTNAP2chr7148112509+1189665505864119

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
ENST00000265361ENST00000361727SEMA3Cchr780545995-CNTNAP2chr7148112509+0.044047190.95595276
ENST00000265361ENST00000538075SEMA3Cchr780545995-CNTNAP2chr7148112509+0.0448774470.95512253

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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

>80279_80279_1_SEMA3C-CNTNAP2_SEMA3C_chr7_80545995_ENST00000265361_CNTNAP2_chr7_148112509_ENST00000361727_length(amino acids)=119AA_BP=53
MISFNLGIFPWILTCISEEMAFRTICVLVGVFICSICVKGSSQPQARVYLTFDGVIAVVIFTILCTLVFLIRYMFRHKGTYHTNEAKGAE

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

>80279_80279_2_SEMA3C-CNTNAP2_SEMA3C_chr7_80545995_ENST00000265361_CNTNAP2_chr7_148112509_ENST00000538075_length(amino acids)=119AA_BP=53
MISFNLGIFPWILTCISEEMAFRTICVLVGVFICSICVKGSSQPQARVYLTFDGVIAVVIFTILCTLVFLIRYMFRHKGTYHTNEAKGAE

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

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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/chr7:80545995/chr7:148112509)
- 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
.CNTNAP2

Q9UHC6

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: Required for gap junction formation (Probable). Required, with CNTNAP1, for radial and longitudinal organization of myelinated axons. Plays a role in the formation of functional distinct domains critical for saltatory conduction of nerve impulses in myelinated nerve fibers. Demarcates the juxtaparanodal region of the axo-glial junction. {ECO:0000250|UniProtKB:Q9CPW0, ECO:0000305|PubMed:33238150}.

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
TgeneCNTNAP2chr7:80545995chr7:148112509ENST0000036172722241284_13311265.33333333333331332.0Topological domainCytoplasmic
TgeneCNTNAP2chr7:80545995chr7:148112509ENST0000036172722241263_12831265.33333333333331332.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSEMA3Cchr7:80545995chr7:148112509ENST00000265361-218724_74534.333333333333336752.0Compositional biasNote=Arg/Lys-rich (basic)
HgeneSEMA3Cchr7:80545995chr7:148112509ENST00000419255-218724_74534.333333333333336752.0Compositional biasNote=Arg/Lys-rich (basic)
HgeneSEMA3Cchr7:80545995chr7:148112509ENST00000265361-21828_51134.333333333333336752.0DomainSema
HgeneSEMA3Cchr7:80545995chr7:148112509ENST00000265361-218571_65534.333333333333336752.0DomainNote=Ig-like C2-type
HgeneSEMA3Cchr7:80545995chr7:148112509ENST00000419255-21828_51134.333333333333336752.0DomainSema
HgeneSEMA3Cchr7:80545995chr7:148112509ENST00000419255-218571_65534.333333333333336752.0DomainNote=Ig-like C2-type
TgeneCNTNAP2chr7:80545995chr7:148112509ENST0000036172722241055_12141265.33333333333331332.0DomainLaminin G-like 4
TgeneCNTNAP2chr7:80545995chr7:148112509ENST000003617272224216_3681265.33333333333331332.0DomainLaminin G-like 1
TgeneCNTNAP2chr7:80545995chr7:148112509ENST000003617272224401_5521265.33333333333331332.0DomainLaminin G-like 2
TgeneCNTNAP2chr7:80545995chr7:148112509ENST000003617272224554_5911265.33333333333331332.0DomainEGF-like 1
TgeneCNTNAP2chr7:80545995chr7:148112509ENST000003617272224592_7981265.33333333333331332.0DomainFibrinogen C-terminal
TgeneCNTNAP2chr7:80545995chr7:148112509ENST000003617272224799_9631265.33333333333331332.0DomainLaminin G-like 3
TgeneCNTNAP2chr7:80545995chr7:148112509ENST000003617272224963_10021265.33333333333331332.0DomainEGF-like 2
TgeneCNTNAP2chr7:80545995chr7:148112509ENST00000361727222428_12621265.33333333333331332.0Topological domainExtracellular


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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
SEMA3C
CNTNAP2


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 SEMA3C-CNTNAP2


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 SEMA3C-CNTNAP2


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