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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:EEF1DP3-RB1 (FusionGDB2 ID:HG196549TG5925)

Fusion Gene Summary for EEF1DP3-RB1

check button Fusion gene summary
Fusion gene informationFusion gene name: EEF1DP3-RB1
Fusion gene ID: hg196549tg5925
HgeneTgene
Gene symbol

EEF1DP3

RB1

Gene ID

196549

5925

Gene nameRB transcriptional corepressor 1
SynonymsOSRC|PPP1R130|RB|p105-Rb|p110-RB1|pRb|pp110
Cytomap('EEF1DP3')('RB1')

13q14.2

Type of geneprotein-coding
Descriptionretinoblastoma-associated proteinGOS563 exon 17 substitution mutation causes premature stopexon 17 tumor GOS561 substitution mutation causes premature stopprepro-retinoblastoma-associated proteinprotein phosphatase 1, regulatory subunit 130retinoblas
Modification date20200329
UniProtAcc

Q658K8

.
Ensembl transtripts involved in fusion geneENST00000428783, 
Fusion gene scores* DoF score7 X 2 X 5=7013 X 16 X 11=2288
# samples 727
** MAII scorelog2(7/70*10)=0log2(27/2288*10)=-3.08305573972756
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: EEF1DP3 [Title/Abstract] AND RB1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEEF1DP3(32421076)-RB1(48934153), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
TgeneRB1

GO:0043550

regulation of lipid kinase activity

16286473

TgeneRB1

GO:0045892

negative regulation of transcription, DNA-templated

10783144|12065415|19223331

TgeneRB1

GO:2000679

positive regulation of transcription regulatory region DNA binding

25100735



check button Fusion gene information
* 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-44-8120-01AEEF1DP3chr13

32421076

+RB1chr13

48934153

+


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Fusion Gene ORF analysis for EEF1DP3-RB1

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
3UTR-3CDSENST00000428783ENST00000267163EEF1DP3chr13

32421076

+RB1chr13

48934153

+
3UTR-intronENST00000428783ENST00000484879EEF1DP3chr13

32421076

+RB1chr13

48934153

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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

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Fusion Genomic Features for EEF1DP3-RB1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
EEF1DP3chr1332421076+RB1chr1348934152+1.46E-050.99998534
EEF1DP3chr1332421076+RB1chr1348934152+1.46E-050.99998534


check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for EEF1DP3-RB1


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/:32421076/:48934153)
- 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
EEF1DP3

Q658K8

.
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for EEF1DP3-RB1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for EEF1DP3-RB1


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 (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for EEF1DP3-RB1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for EEF1DP3-RB1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0035335Retinoblastoma15CGI;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0006142Malignant neoplasm of breast3CGI;CTD_human
TgeneC0149925Small cell carcinoma of lung3CGI;CTD_human;ORPHANET
TgeneC0678222Breast Carcinoma3CGI;CTD_human
TgeneC0751483Familial Retinoblastoma3CTD_human;ORPHANET
TgeneC1257931Mammary Neoplasms, Human3CTD_human
TgeneC1458155Mammary Neoplasms3CTD_human
TgeneC4704874Mammary Carcinoma, Human3CTD_human
TgeneC0029463Osteosarcoma2CTD_human;ORPHANET
TgeneC2239176Liver carcinoma2CTD_human
TgeneC0001624Adrenal Gland Neoplasms1CTD_human
TgeneC0007097Carcinoma1CTD_human
TgeneC0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneC0007786Brain Ischemia1CTD_human
TgeneC0014518Toxic Epidermal Necrolysis1CTD_human
TgeneC0019207Hepatoma, Morris1CTD_human
TgeneC0019208Hepatoma, Novikoff1CTD_human
TgeneC0023452Childhood Acute Lymphoblastic Leukemia1CTD_human
TgeneC0023453L2 Acute Lymphoblastic Leukemia1CTD_human
TgeneC0023904Liver Neoplasms, Experimental1CTD_human
TgeneC0024667Animal Mammary Neoplasms1CTD_human
TgeneC0024668Mammary Neoplasms, Experimental1CTD_human
TgeneC0027627Neoplasm Metastasis1CTD_human
TgeneC0027659Neoplasms, Experimental1CTD_human
TgeneC0030297Pancreatic Neoplasm1CTD_human
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0036920Sezary Syndrome1CTD_human
TgeneC0038325Stevens-Johnson Syndrome1CTD_human
TgeneC0086404Experimental Hepatoma1CTD_human
TgeneC0205696Anaplastic carcinoma1CTD_human
TgeneC0205697Carcinoma, Spindle-Cell1CTD_human
TgeneC0205698Undifferentiated carcinoma1CTD_human
TgeneC0205699Carcinomatosis1CTD_human
TgeneC0206686Adrenocortical carcinoma1CTD_human
TgeneC0238198Gastrointestinal Stromal Tumors1CTD_human
TgeneC0279626Squamous cell carcinoma of esophagus1CTD_human
TgeneC0346647Malignant neoplasm of pancreas1CTD_human
TgeneC0376358Malignant neoplasm of prostate1CTD_human
TgeneC0750887Adrenal Cancer1CTD_human
TgeneC0917798Cerebral Ischemia1CTD_human
TgeneC1257925Mammary Carcinoma, Animal1CTD_human
TgeneC1274933Drug-Induced Stevens Johnson Syndrome1CTD_human
TgeneC1368275Pigmented Basal Cell Carcinoma1CTD_human
TgeneC1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1CTD_human
TgeneC2608045Trilateral Retinoblastoma1GENOMICS_ENGLAND
TgeneC2930974Acute erythroleukemia1CTD_human
TgeneC2930975Acute erythroleukemia - M6a subtype1CTD_human
TgeneC2930976Acute myeloid leukemia FAB-M61CTD_human
TgeneC2930977Acute erythroleukemia - M6b subtype1CTD_human
TgeneC3151302Chromosome 13q14 deletion syndrome1ORPHANET
TgeneC3179349Gastrointestinal Stromal Sarcoma1CTD_human
TgeneC3658301Mycoplasma-Induced Stevens-Johnson Syndrome1CTD_human
TgeneC3658302Stevens-Johnson Syndrome Toxic Epidermal Necrolysis Spectrum1CTD_human
TgeneC4721806Carcinoma, Basal Cell1CTD_human