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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:EEF1A1-RPS4X

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: EEF1A1-RPS4X
FusionPDB ID: 25147
FusionGDB2.0 ID: 25147
HgeneTgene
Gene symbol

EEF1A1

RPS4X

Gene ID

1915

6191

Gene nameeukaryotic translation elongation factor 1 alpha 1ribosomal protein S4 X-linked
SynonymsCCS-3|CCS3|EE1A1|EEF-1|EEF1A|EF-Tu|EF1A|GRAF-1EF|LENG7|PTI1|eEF1A-1CCG2|DXS306|RPS4|S4|SCAR|SCR10
Cytomap

6q13

Xq13.1

Type of geneprotein-codingprotein-coding
Descriptionelongation factor 1-alpha 1CTCL tumor antigenEF-1-alpha-1EF1a-like proteincervical cancer suppressor 3elongation factor 1 alpha subunitelongation factor Tuepididymis secretory sperm binding proteineukaryotic elongation factor 1 A-1eukaryotic tran40S ribosomal protein S4, X isoformcell cycle gene 2ribosomal protein S4X isoformsingle copy abundant mRNA proteinsingle-copy abundant mRNAsmall ribosomal subunit protein eS4
Modification date2020032720200313
UniProtAcc

Q5VTE0

.
Ensembl transtripts involved in fusion geneENST idsENST00000309268, ENST00000316292, 
ENST00000331523, ENST00000491404, 
ENST00000373626, ENST00000486733, 
ENST00000316084, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score24 X 34 X 12=979220 X 17 X 7=2380
# samples 3822
** MAII scorelog2(38/9792*10)=-4.6875322343617
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(22/2380*10)=-3.43538614467065
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: EEF1A1 [Title/Abstract] AND RPS4X [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)EEF1A1(74227755)-RPS4X(71494945), # samples:1
EEF1A1(74227751)-RPS4X(71494941), # samples:1
Anticipated loss of major functional domain due to fusion event.EEF1A1-RPS4X 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.
EEF1A1-RPS4X 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.
EEF1A1-RPS4X seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
EEF1A1-RPS4X seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
EEF1A1-RPS4X seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
EEF1A1-RPS4X seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
EEF1A1-RPS4X seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneEEF1A1

GO:0071364

cellular response to epidermal growth factor stimulus

9852145

HgeneEEF1A1

GO:1900022

regulation of D-erythro-sphingosine kinase activity

18263879


check buttonFusion gene breakpoints across EEF1A1 (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 RPS4X (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
ChimerDB4Non-CancerERR188311EEF1A1chr6

74227751

-RPS4XchrX

71494941

-
ChimerDB4Non-CancerERR188410EEF1A1chr6

74227755

-RPS4XchrX

71494945

-


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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)
ENST00000316292EEF1A1chr674227755-ENST00000316084RPS4XchrX71494945-336022569922314440
ENST00000316292EEF1A1chr674227751-ENST00000316084RPS4XchrX71494941-335622569922314440

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
ENST00000316292ENST00000316084EEF1A1chr674227755-RPS4XchrX71494945-0.0007474560.9992525
ENST00000316292ENST00000316084EEF1A1chr674227751-RPS4XchrX71494941-0.0007636490.99923635

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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

>25147_25147_1_EEF1A1-RPS4X_EEF1A1_chr6_74227751_ENST00000316292_RPS4X_chrX_71494941_ENST00000316084_length(amino acids)=440AA_BP=
MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGITIDISLWKFETSKYYVTII
DAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKK
IGYNPDTVAFVPISGWNGDNMLEPSANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETG
VLKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPV

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

>25147_25147_2_EEF1A1-RPS4X_EEF1A1_chr6_74227755_ENST00000316292_RPS4X_chrX_71494945_ENST00000316084_length(amino acids)=440AA_BP=
MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGITIDISLWKFETSKYYVTII
DAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKK
IGYNPDTVAFVPISGWNGDNMLEPSANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETG
VLKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPV

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

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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/chr6:74227755/chrX:71494945)
- 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
EEF1A1

Q5VTE0

.
FUNCTION: This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. {ECO:0000250}.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
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000309268-785_242421.3333333333333463.0DomainNote=tr-type G
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000316292-675_242421.3333333333333463.0DomainNote=tr-type G
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000331523-785_242421.3333333333333463.0DomainNote=tr-type G
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000309268-785_242421.3333333333333463.0DomainNote=tr-type G
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000316292-675_242421.3333333333333463.0DomainNote=tr-type G
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000331523-785_242421.3333333333333463.0DomainNote=tr-type G
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000309268-7891_95421.3333333333333463.0Nucleotide bindingGTP
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000316292-6791_95421.3333333333333463.0Nucleotide bindingGTP
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000331523-7891_95421.3333333333333463.0Nucleotide bindingGTP
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000309268-7891_95421.3333333333333463.0Nucleotide bindingGTP
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000316292-6791_95421.3333333333333463.0Nucleotide bindingGTP
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000331523-7891_95421.3333333333333463.0Nucleotide bindingGTP
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000309268-7814_21421.3333333333333463.0RegionG1
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000309268-78153_156421.3333333333333463.0RegionG4
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000309268-78194_196421.3333333333333463.0RegionG5
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000309268-7870_74421.3333333333333463.0RegionG2
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000309268-7891_94421.3333333333333463.0RegionG3
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000316292-6714_21421.3333333333333463.0RegionG1
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000316292-67153_156421.3333333333333463.0RegionG4
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000316292-67194_196421.3333333333333463.0RegionG5
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000316292-6770_74421.3333333333333463.0RegionG2
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000316292-6791_94421.3333333333333463.0RegionG3
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000331523-7814_21421.3333333333333463.0RegionG1
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000331523-78153_156421.3333333333333463.0RegionG4
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000331523-78194_196421.3333333333333463.0RegionG5
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000331523-7870_74421.3333333333333463.0RegionG2
HgeneEEF1A1chr6:74227751chrX:71494941ENST00000331523-7891_94421.3333333333333463.0RegionG3
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000309268-7814_21421.3333333333333463.0RegionG1
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000309268-78153_156421.3333333333333463.0RegionG4
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000309268-78194_196421.3333333333333463.0RegionG5
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000309268-7870_74421.3333333333333463.0RegionG2
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000309268-7891_94421.3333333333333463.0RegionG3
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000316292-6714_21421.3333333333333463.0RegionG1
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000316292-67153_156421.3333333333333463.0RegionG4
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000316292-67194_196421.3333333333333463.0RegionG5
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000316292-6770_74421.3333333333333463.0RegionG2
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000316292-6791_94421.3333333333333463.0RegionG3
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000331523-7814_21421.3333333333333463.0RegionG1
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000331523-78153_156421.3333333333333463.0RegionG4
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000331523-78194_196421.3333333333333463.0RegionG5
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000331523-7870_74421.3333333333333463.0RegionG2
HgeneEEF1A1chr6:74227755chrX:71494945ENST00000331523-7891_94421.3333333333333463.0RegionG3
TgeneRPS4Xchr6:74227751chrX:71494941ENST000003160840742_1040264.0DomainNote=S4 RNA-binding
TgeneRPS4Xchr6:74227755chrX:71494945ENST000003160840742_1040264.0DomainNote=S4 RNA-binding

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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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
EEF1A1
RPS4X


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 EEF1A1-RPS4X


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 EEF1A1-RPS4X


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