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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:CSMD1-EIF3E

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CSMD1-EIF3E
FusionPDB ID: 19739
FusionGDB2.0 ID: 19739
HgeneTgene
Gene symbol

CSMD1

EIF3E

Gene ID

64478

3646

Gene nameCUB and Sushi multiple domains 1eukaryotic translation initiation factor 3 subunit E
SynonymsPPP1R24EIF3-P48|EIF3S6|INT6|eIF3-p46
Cytomap

8p23.2

8q23.1

Type of geneprotein-codingprotein-coding
DescriptionCUB and sushi domain-containing protein 1protein phosphatase 1, regulatory subunit 24eukaryotic translation initiation factor 3 subunit EeIF-3 p48eukaryotic translation initiation factor 3 subunit 6eukaryotic translation initiation factor 3 subunit E isoform 2 transcripteukaryotic translation initiation factor 3, subunit 6 (48kD)euka
Modification date2020031320200313
UniProtAcc

Q96PZ7

P60228

Ensembl transtripts involved in fusion geneENST idsENST00000400186, ENST00000520002, 
ENST00000537824, ENST00000539096, 
ENST00000542608, ENST00000602557, 
ENST00000602723, ENST00000523387, 
ENST00000519517, ENST00000220849, 
ENST00000519030, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score31 X 30 X 4=372021 X 12 X 10=2520
# samples 3221
** MAII scorelog2(32/3720*10)=-3.53915881110803
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(21/2520*10)=-3.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: CSMD1 [Title/Abstract] AND EIF3E [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CSMD1(4494863)-EIF3E(109215732), # samples:1
Anticipated loss of major functional domain due to fusion event.CSMD1-EIF3E 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.
CSMD1-EIF3E 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.
CSMD1-EIF3E 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.
CSMD1-EIF3E 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.
* 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
TgeneEIF3E

GO:0006413

translational initiation

17581632


check buttonFusion gene breakpoints across CSMD1 (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 EIF3E (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
ChimerDB4ESCATCGA-IG-A3YACSMD1chr8

4494863

-EIF3Echr8

109215732

-


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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)
ENST00000602723CSMD1chr84494863-ENST00000220849EIF3Echr8109215732-100658781863260
ENST00000602723CSMD1chr84494863-ENST00000519030EIF3Echr8109215732-96958781863260
ENST00000400186CSMD1chr84494863-ENST00000220849EIF3Echr8109215732-100658781863260
ENST00000400186CSMD1chr84494863-ENST00000519030EIF3Echr8109215732-96958781863260
ENST00000520002CSMD1chr84494863-ENST00000220849EIF3Echr8109215732-12778581901134314
ENST00000520002CSMD1chr84494863-ENST00000519030EIF3Echr8109215732-12408581901134314
ENST00000602557CSMD1chr84494863-ENST00000220849EIF3Echr8109215732-12778581901134314
ENST00000602557CSMD1chr84494863-ENST00000519030EIF3Echr8109215732-12408581901134314
ENST00000537824CSMD1chr84494863-ENST00000220849EIF3Echr8109215732-7213020578192
ENST00000537824CSMD1chr84494863-ENST00000519030EIF3Echr8109215732-6843020578192
ENST00000542608CSMD1chr84494863-ENST00000220849EIF3Echr8109215732-7213020578192
ENST00000542608CSMD1chr84494863-ENST00000519030EIF3Echr8109215732-6843020578192
ENST00000539096CSMD1chr84494863-ENST00000220849EIF3Echr8109215732-7213020578192
ENST00000539096CSMD1chr84494863-ENST00000519030EIF3Echr8109215732-6843020578192

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
ENST00000602723ENST00000220849CSMD1chr84494863-EIF3Echr8109215732-0.0017994090.99820054
ENST00000602723ENST00000519030CSMD1chr84494863-EIF3Echr8109215732-0.001614640.9983854
ENST00000400186ENST00000220849CSMD1chr84494863-EIF3Echr8109215732-0.0017994090.99820054
ENST00000400186ENST00000519030CSMD1chr84494863-EIF3Echr8109215732-0.001614640.9983854
ENST00000520002ENST00000220849CSMD1chr84494863-EIF3Echr8109215732-0.0021464690.99785346
ENST00000520002ENST00000519030CSMD1chr84494863-EIF3Echr8109215732-0.001639020.99836093
ENST00000602557ENST00000220849CSMD1chr84494863-EIF3Echr8109215732-0.0021464690.99785346
ENST00000602557ENST00000519030CSMD1chr84494863-EIF3Echr8109215732-0.001639020.99836093
ENST00000537824ENST00000220849CSMD1chr84494863-EIF3Echr8109215732-0.0014349660.998565
ENST00000537824ENST00000519030CSMD1chr84494863-EIF3Echr8109215732-0.0016946680.9983053
ENST00000542608ENST00000220849CSMD1chr84494863-EIF3Echr8109215732-0.0014349660.998565
ENST00000542608ENST00000519030CSMD1chr84494863-EIF3Echr8109215732-0.0016946680.9983053
ENST00000539096ENST00000220849CSMD1chr84494863-EIF3Echr8109215732-0.0014349660.998565
ENST00000539096ENST00000519030CSMD1chr84494863-EIF3Echr8109215732-0.0016946680.9983053

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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

>19739_19739_1_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000400186_EIF3E_chr8_109215732_ENST00000220849_length(amino acids)=260AA_BP=168
MQWLGTRCYEREASRAPRPSGGVGCAAGLGTGLSLRLALPSGDYLAPLIALPSSEEPSVSRACGVSADMTAWRRFQSLLLLLGLLVLCAR
LLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANCTWIIITGERNRIQLSFHTFALEEDFDILSVYDGQPQQGNLKVSMLADKLNMTPE

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

>19739_19739_2_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000400186_EIF3E_chr8_109215732_ENST00000519030_length(amino acids)=260AA_BP=168
MQWLGTRCYEREASRAPRPSGGVGCAAGLGTGLSLRLALPSGDYLAPLIALPSSEEPSVSRACGVSADMTAWRRFQSLLLLLGLLVLCAR
LLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANCTWIIITGERNRIQLSFHTFALEEDFDILSVYDGQPQQGNLKVSMLADKLNMTPE

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

>19739_19739_3_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000520002_EIF3E_chr8_109215732_ENST00000220849_length(amino acids)=314AA_BP=222
MPPLQVSPGCARSSPRFSPSRSLAALVPSCPARPALVPGPGPASPGLRARSSSALQWLGTRCYEREASRAPRPSGGVGCAAGLGTGLSLR
LALPSGDYLAPLIALPSSEEPSVSRACGVSADMTAWRRFQSLLLLLGLLVLCARLLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANC
TWIIITGERNRIQLSFHTFALEEDFDILSVYDGQPQQGNLKVSMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPY

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

>19739_19739_4_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000520002_EIF3E_chr8_109215732_ENST00000519030_length(amino acids)=314AA_BP=222
MPPLQVSPGCARSSPRFSPSRSLAALVPSCPARPALVPGPGPASPGLRARSSSALQWLGTRCYEREASRAPRPSGGVGCAAGLGTGLSLR
LALPSGDYLAPLIALPSSEEPSVSRACGVSADMTAWRRFQSLLLLLGLLVLCARLLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANC
TWIIITGERNRIQLSFHTFALEEDFDILSVYDGQPQQGNLKVSMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPY

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

>19739_19739_5_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000537824_EIF3E_chr8_109215732_ENST00000220849_length(amino acids)=192AA_BP=100
MTAWRRFQSLLLLLGLLVLCARLLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANCTWIIITGERNRIQLSFHTFALEEDFDILSVYD
GQPQQGNLKVSMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQMLAMNIEKKLNQNSRSE

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

>19739_19739_6_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000537824_EIF3E_chr8_109215732_ENST00000519030_length(amino acids)=192AA_BP=100
MTAWRRFQSLLLLLGLLVLCARLLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANCTWIIITGERNRIQLSFHTFALEEDFDILSVYD
GQPQQGNLKVSMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQMLAMNIEKKLNQNSRSE

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

>19739_19739_7_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000539096_EIF3E_chr8_109215732_ENST00000220849_length(amino acids)=192AA_BP=100
MTAWRRFQSLLLLLGLLVLCARLLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANCTWIIITGERNRIQLSFHTFALEEDFDILSVYD
GQPQQGNLKVSMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQMLAMNIEKKLNQNSRSE

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

>19739_19739_8_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000539096_EIF3E_chr8_109215732_ENST00000519030_length(amino acids)=192AA_BP=100
MTAWRRFQSLLLLLGLLVLCARLLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANCTWIIITGERNRIQLSFHTFALEEDFDILSVYD
GQPQQGNLKVSMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQMLAMNIEKKLNQNSRSE

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

>19739_19739_9_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000542608_EIF3E_chr8_109215732_ENST00000220849_length(amino acids)=192AA_BP=100
MTAWRRFQSLLLLLGLLVLCARLLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANCTWIIITGERNRIQLSFHTFALEEDFDILSVYD
GQPQQGNLKVSMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQMLAMNIEKKLNQNSRSE

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

>19739_19739_10_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000542608_EIF3E_chr8_109215732_ENST00000519030_length(amino acids)=192AA_BP=100
MTAWRRFQSLLLLLGLLVLCARLLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANCTWIIITGERNRIQLSFHTFALEEDFDILSVYD
GQPQQGNLKVSMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQMLAMNIEKKLNQNSRSE

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

>19739_19739_11_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000602557_EIF3E_chr8_109215732_ENST00000220849_length(amino acids)=314AA_BP=222
MPPLQVSPGCARSSPRFSPSRSLAALVPSCPARPALVPGPGPASPGLRARSSSALQWLGTRCYEREASRAPRPSGGVGCAAGLGTGLSLR
LALPSGDYLAPLIALPSSEEPSVSRACGVSADMTAWRRFQSLLLLLGLLVLCARLLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANC
TWIIITGERNRIQLSFHTFALEEDFDILSVYDGQPQQGNLKVSMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPY

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

>19739_19739_12_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000602557_EIF3E_chr8_109215732_ENST00000519030_length(amino acids)=314AA_BP=222
MPPLQVSPGCARSSPRFSPSRSLAALVPSCPARPALVPGPGPASPGLRARSSSALQWLGTRCYEREASRAPRPSGGVGCAAGLGTGLSLR
LALPSGDYLAPLIALPSSEEPSVSRACGVSADMTAWRRFQSLLLLLGLLVLCARLLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANC
TWIIITGERNRIQLSFHTFALEEDFDILSVYDGQPQQGNLKVSMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPY

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

>19739_19739_13_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000602723_EIF3E_chr8_109215732_ENST00000220849_length(amino acids)=260AA_BP=168
MQWLGTRCYEREASRAPRPSGGVGCAAGLGTGLSLRLALPSGDYLAPLIALPSSEEPSVSRACGVSADMTAWRRFQSLLLLLGLLVLCAR
LLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANCTWIIITGERNRIQLSFHTFALEEDFDILSVYDGQPQQGNLKVSMLADKLNMTPE

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

>19739_19739_14_CSMD1-EIF3E_CSMD1_chr8_4494863_ENST00000602723_EIF3E_chr8_109215732_ENST00000519030_length(amino acids)=260AA_BP=168
MQWLGTRCYEREASRAPRPSGGVGCAAGLGTGLSLRLALPSGDYLAPLIALPSSEEPSVSRACGVSADMTAWRRFQSLLLLLGLLVLCAR
LLTAAKGQNCGGLVQGPNGTIESPGFPHGYPNYANCTWIIITGERNRIQLSFHTFALEEDFDILSVYDGQPQQGNLKVSMLADKLNMTPE

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

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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/chr8:4494863/chr8:109215732)
- 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
CSMD1

Q96PZ7

EIF3E

P60228

FUNCTION: Potential suppressor of squamous cell carcinomas.FUNCTION: Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis (PubMed:17581632, PubMed:25849773, PubMed:27462815). The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre-initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation (PubMed:17581632). The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression (PubMed:25849773). Required for nonsense-mediated mRNA decay (NMD); may act in conjunction with UPF2 to divert mRNAs from translation to the NMD pathway (PubMed:17468741). May interact with MCM7 and EPAS1 and regulate the proteasome-mediated degradation of these proteins (PubMed:17310990, PubMed:17324924). {ECO:0000255|HAMAP-Rule:MF_03004, ECO:0000269|PubMed:17310990, ECO:0000269|PubMed:17324924, ECO:0000269|PubMed:17468741, ECO:0000269|PubMed:17581632, ECO:0000269|PubMed:25849773, ECO:0000269|PubMed:27462815}.

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

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneEIF3Echr8:4494863chr8:109215732ENST00000220849913221_398353.6666666666667446.0DomainPCI


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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
CSMD1
EIF3E


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 CSMD1-EIF3E


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 CSMD1-EIF3E


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