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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:EPB41L1-HTR3C

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: EPB41L1-HTR3C
FusionPDB ID: 26814
FusionGDB2.0 ID: 26814
HgeneTgene
Gene symbol

EPB41L1

HTR3C

Gene ID

2036

170572

Gene nameerythrocyte membrane protein band 4.1 like 15-hydroxytryptamine receptor 3C
Synonyms4.1N|MRD11-
Cytomap

20q11.23

3q27.1

Type of geneprotein-codingprotein-coding
Descriptionband 4.1-like protein 1neuron-type nonerythroid protein 4.1neuronal protein 4.15-hydroxytryptamine receptor 3C5-HT3-C5-HT3C5-hydroxytryptamine (serotonin) receptor 3, family member C5-hydroxytryptamine (serotonin) receptor 3C, ionotropic5-hydroxytryptamine receptor 3 subunit Cserotonin receptor 3C
Modification date2020031320200313
UniProtAcc

Q9H4G0

.
Ensembl transtripts involved in fusion geneENST idsENST00000202028, ENST00000338074, 
ENST00000373950, ENST00000441639, 
ENST00000373946, ENST00000373941, 
ENST00000479336, 
ENST00000318351, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score24 X 23 X 12=66244 X 7 X 4=112
# samples 345
** MAII scorelog2(34/6624*10)=-4.28409602136162
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/112*10)=-1.16349873228288
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: EPB41L1 [Title/Abstract] AND HTR3C [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)EPB41L1(34700402)-HTR3C(183773100), # samples:2
Anticipated loss of major functional domain due to fusion event.EPB41L1-HTR3C 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.
EPB41L1-HTR3C 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.
EPB41L1-HTR3C seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
EPB41L1-HTR3C 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

check buttonFusion gene breakpoints across EPB41L1 (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 HTR3C (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
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34680735

+HTR3Cchr3

183772509

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34680735

+HTR3Cchr3

183773965

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34680735

+HTR3Cchr3

183774663

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34700402

+HTR3Cchr3

183772509

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34700402

+HTR3Cchr3

183773100

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34700402

+HTR3Cchr3

183773965

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34700402

+HTR3Cchr3

183774663

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34710669

+HTR3Cchr3

183772509

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34710669

+HTR3Cchr3

183773100

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34710669

+HTR3Cchr3

183774663

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34713449

+HTR3Cchr3

183772509

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34713449

+HTR3Cchr3

183773100

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34713449

+HTR3Cchr3

183774663

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34742818

+HTR3Cchr3

183772509

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34742818

+HTR3Cchr3

183773100

+
ChimerDB4OVTCGA-13-1405-01AEPB41L1chr20

34751306

+HTR3Cchr3

183772509

+


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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)
ENST00000373946EPB41L1chr2034713449+ENST00000318351HTR3Cchr3183773100+15138401193397

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
ENST00000373946ENST00000318351EPB41L1chr2034713449+HTR3Cchr3183773100+0.022334320.97766566

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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

>26814_26814_1_EPB41L1-HTR3C_EPB41L1_chr20_34713449_ENST00000373946_HTR3C_chr3_183773100_ENST00000318351_length(amino acids)=397AA_BP=31
MVFLGRINEVEPAKGLAESLAPTERSVKDAQLQLLTSFLWMDLVWDNPFINWNPKECVGINKLTVLAENLWLPDIFIVESMDVDQTPSGL
TAYISSEGRIKYDKPMRVTSICNLDIFYFPFDQQNCTFTFSSFLYTVDSMLLGMDKEVWEITDTSRKVIQTQGEWELLGINKATPKMSMG
NNLYDQIMFYVAIRRRPSLYIINLLVPSSFLVAIDALSFYLPAESENRAPFKITLLLGYNVFLLMMNDLLPASGTPLISVYFALCLSLMV
VSLLETVFITYLLHVATTQPPPMPRWLHSLLLHCTSPGRCCPTAPQKGNKGLGLTLTHLPGPKEPGELAGKKLGPRETEPDGGSGWTKTQ

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

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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/chr20:34700402/chr3:183773100)
- 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
EPB41L1

Q9H4G0

.
FUNCTION: May function to confer stability and plasticity to neuronal membrane via multiple interactions, including the spectrin-actin-based cytoskeleton, integral membrane channels and membrane-associated guanylate kinases.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.

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
TgeneHTR3Cchr20:34713449chr3:183773100ENST0000031835119270_28278.0448.0Topological domainCytoplasmic
TgeneHTR3Cchr20:34713449chr3:183773100ENST0000031835119304_30678.0448.0Topological domainExtracellular
TgeneHTR3Cchr20:34713449chr3:183773100ENST0000031835119330_42478.0448.0Topological domainCytoplasmic
TgeneHTR3Cchr20:34713449chr3:183773100ENST0000031835119446_44778.0448.0Topological domainExtracellular
TgeneHTR3Cchr20:34713449chr3:183773100ENST0000031835119249_26978.0448.0TransmembraneHelical%3B Name%3D1
TgeneHTR3Cchr20:34713449chr3:183773100ENST0000031835119283_30378.0448.0TransmembraneHelical%3B Name%3D2
TgeneHTR3Cchr20:34713449chr3:183773100ENST0000031835119307_32978.0448.0TransmembraneHelical%3B Name%3D3
TgeneHTR3Cchr20:34713449chr3:183773100ENST0000031835119425_44578.0448.0TransmembraneHelical%3B Name%3D4

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000202028+12097_3780780.0DomainFERM
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000338074+12297_3780882.0DomainFERM
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000373941+12197_3780881.0DomainFERM
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000373946+11997_37828.0702.0DomainFERM
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000373950+12197_3780773.0DomainFERM
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000441639+11997_3780780.0DomainFERM
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000202028+120483_5410780.0RegionNote=Spectrin--actin-binding
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000202028+120746_8810780.0RegionNote=C-terminal (CTD)
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000338074+122483_5410882.0RegionNote=Spectrin--actin-binding
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000338074+122746_8810882.0RegionNote=C-terminal (CTD)
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000373941+121483_5410881.0RegionNote=Spectrin--actin-binding
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000373941+121746_8810881.0RegionNote=C-terminal (CTD)
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000373946+119483_54128.0702.0RegionNote=Spectrin--actin-binding
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000373946+119746_88128.0702.0RegionNote=C-terminal (CTD)
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000373950+121483_5410773.0RegionNote=Spectrin--actin-binding
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000373950+121746_8810773.0RegionNote=C-terminal (CTD)
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000441639+119483_5410780.0RegionNote=Spectrin--actin-binding
HgeneEPB41L1chr20:34713449chr3:183773100ENST00000441639+119746_8810780.0RegionNote=C-terminal (CTD)
TgeneHTR3Cchr20:34713449chr3:183773100ENST000003183511928_24878.0448.0Topological 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
EPB41L1
HTR3C


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 EPB41L1-HTR3C


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 EPB41L1-HTR3C


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