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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:DPP9-LDB3 (FusionGDB2 ID:24050)

Fusion Gene Summary for DPP9-LDB3

check button Fusion gene summary
Fusion gene informationFusion gene name: DPP9-LDB3
Fusion gene ID: 24050
HgeneTgene
Gene symbol

DPP9

LDB3

Gene ID

91039

11155

Gene namedipeptidyl peptidase 9LIM domain binding 3
SynonymsDP9|DPLP9|DPP IX|DPRP-2|DPRP2CMD1C|CMH24|CMPD3|CYPHER|LDB3Z1|LDB3Z4|LVNC3|MFM4|ORACLE|PDLIM6|ZASP
Cytomap

19p13.3

10q23.2

Type of geneprotein-codingprotein-coding
Descriptiondipeptidyl peptidase 9dipeptidyl peptidase IV-related protein-2dipeptidyl peptidase IXdipeptidyl peptidase-like protein 9LIM domain-binding protein 3PDZ and LIM domain 6Z-band alternatively spliced PDZ-motif proteincardiomyopathy, dilated 1C (autosomal dominant)protein cypher
Modification date2020032020200328
UniProtAcc

Q86TI2

O75112

Ensembl transtripts involved in fusion geneENST00000262960, ENST00000594671, 
ENST00000597849, ENST00000598800, 
ENST00000601173, 		ENST00000263066, 
ENST00000310944, ENST00000352360, 
ENST00000361373, ENST00000372056, 
ENST00000372066, ENST00000429277, 
ENST00000458213, ENST00000542786, 
Fusion gene scores* DoF score8 X 10 X 3=2404 X 4 X 1=16
# samples 94
** MAII scorelog2(9/240*10)=-1.41503749927884
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/16*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: DPP9 [Title/Abstract] AND LDB3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointDPP9(4675842)-LDB3(88488299), # samples:2
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

check buttonFusion gene breakpoints across DPP9 (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 LDB3 (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/AAA972615DPP9chr19

4675842

+LDB3chr10

88488299

-
ChiTaRS5.0N/AAA994238DPP9chr19

4675842

+LDB3chr10

88488299

-


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Fusion Gene ORF analysis for DPP9-LDB3

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
intron-intronENST00000262960ENST00000263066DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000262960ENST00000310944DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000262960ENST00000352360DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000262960ENST00000361373DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000262960ENST00000372056DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000262960ENST00000372066DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000262960ENST00000429277DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000262960ENST00000458213DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000262960ENST00000542786DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000594671ENST00000263066DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000594671ENST00000310944DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000594671ENST00000352360DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000594671ENST00000361373DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000594671ENST00000372056DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000594671ENST00000372066DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000594671ENST00000429277DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000594671ENST00000458213DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000594671ENST00000542786DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000597849ENST00000263066DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000597849ENST00000310944DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000597849ENST00000352360DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000597849ENST00000361373DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000597849ENST00000372056DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000597849ENST00000372066DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000597849ENST00000429277DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000597849ENST00000458213DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000597849ENST00000542786DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000598800ENST00000263066DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000598800ENST00000310944DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000598800ENST00000352360DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000598800ENST00000361373DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000598800ENST00000372056DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000598800ENST00000372066DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000598800ENST00000429277DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000598800ENST00000458213DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000598800ENST00000542786DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000601173ENST00000263066DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000601173ENST00000310944DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000601173ENST00000352360DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000601173ENST00000361373DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000601173ENST00000372056DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000601173ENST00000372066DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000601173ENST00000429277DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000601173ENST00000458213DPP9chr19

4675842

+LDB3chr10

88488299

-
intron-intronENST00000601173ENST00000542786DPP9chr19

4675842

+LDB3chr10

88488299

-

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 DPP9-LDB3


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.

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Fusion Protein Features for DPP9-LDB3


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/:4675842/:88488299)
- 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
DPP9

Q86TI2

LDB3

O75112

FUNCTION: Dipeptidyl peptidase that cleaves off N-terminal dipeptides from proteins having a Pro or Ala residue at position 2. {ECO:0000269|PubMed:12662155, ECO:0000269|PubMed:16475979, ECO:0000269|PubMed:29382749}.FUNCTION: May function as an adapter in striated muscle to couple protein kinase C-mediated signaling via its LIM domains to the cytoskeleton. {ECO:0000305}.

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 DPP9-LDB3


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 DPP9-LDB3


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 DPP9-LDB3


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 DPP9-LDB3


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