FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:PDLIM5-TARDBP (FusionGDB2 ID:64008)

Fusion Gene Summary for PDLIM5-TARDBP

check button Fusion gene summary
Fusion gene informationFusion gene name: PDLIM5-TARDBP
Fusion gene ID: 64008
HgeneTgene
Gene symbol

PDLIM5

TARDBP

Gene ID

10611

23435

Gene namePDZ and LIM domain 5TAR DNA binding protein
SynonymsENH|ENH1|L9|LIMALS10|TDP-43
Cytomap

4q22.3

1p36.22

Type of geneprotein-codingprotein-coding
DescriptionPDZ and LIM domain protein 5enigma homologenigma-like LIM domain proteinenigma-like PDZ and LIM domains proteinTAR DNA-binding protein 43TAR DNA-binding protein-43
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000317968, ENST00000318007, 
ENST00000359265, ENST00000380180, 
ENST00000437932, ENST00000450793, 
ENST00000504489, ENST00000508216, 
ENST00000512274, ENST00000514743, 
ENST00000538141, ENST00000542407, 
ENST00000380176, 		ENST00000240185, 
ENST00000315091, ENST00000439080, 
ENST00000480464, 
Fusion gene scores* DoF score20 X 18 X 9=32405 X 5 X 2=50
# samples 235
** MAII scorelog2(23/3240*10)=-3.81628804682761
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/50*10)=0
Context

PubMed: PDLIM5 [Title/Abstract] AND TARDBP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPDLIM5(95376414)-TARDBP(11083670), # 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
TgeneTARDBP

GO:0008380

RNA splicing

11285240

TgeneTARDBP

GO:0043922

negative regulation by host of viral transcription

7745706

TgeneTARDBP

GO:0061158

3'-UTR-mediated mRNA destabilization

28335005

TgeneTARDBP

GO:0070935

3'-UTR-mediated mRNA stabilization

17481916


check buttonFusion gene breakpoints across PDLIM5 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across TARDBP (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChiTaRS5.0N/ADA887356PDLIM5chr4

95376414

+TARDBPchr1

11083670

+


Top

Fusion Gene ORF analysis for PDLIM5-TARDBP

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
5UTR-3UTRENST00000317968ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000317968ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000318007ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000318007ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000359265ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000359265ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000380180ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000380180ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000437932ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000437932ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000450793ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000450793ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000504489ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000504489ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000508216ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000508216ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000512274ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000512274ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000514743ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000514743ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000538141ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000538141ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000542407ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-3UTRENST00000542407ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000317968ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000317968ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000318007ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000318007ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000359265ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000359265ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000380180ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000380180ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000437932ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000437932ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000450793ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000450793ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000504489ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000504489ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000508216ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000508216ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000512274ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000512274ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000514743ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000514743ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000538141ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000538141ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000542407ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
5UTR-intronENST00000542407ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
intron-3UTRENST00000380176ENST00000240185PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
intron-3UTRENST00000380176ENST00000315091PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
intron-intronENST00000380176ENST00000439080PDLIM5chr4

95376414

+TARDBPchr1

11083670

+
intron-intronENST00000380176ENST00000480464PDLIM5chr4

95376414

+TARDBPchr1

11083670

+

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

Top

Fusion Genomic Features for PDLIM5-TARDBP


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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.

Top

Fusion Protein Features for PDLIM5-TARDBP


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/:95376414/:11083670)
- 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
..
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}.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


Top

Fusion Gene Sequence for PDLIM5-TARDBP


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.

Top

Fusion Gene PPI Analysis for PDLIM5-TARDBP


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


Top

Related Drugs for PDLIM5-TARDBP


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

Top

Related Diseases for PDLIM5-TARDBP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource