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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:KLF13-DTX2 (FusionGDB2 ID:42858)

Fusion Gene Summary for KLF13-DTX2

check button Fusion gene summary
Fusion gene informationFusion gene name: KLF13-DTX2
Fusion gene ID: 42858
HgeneTgene
Gene symbol

KLF13

DTX2

Gene ID

51621

113878

Gene nameKruppel like factor 13deltex E3 ubiquitin ligase 2
SynonymsBTEB3|FKLF2|NSLP1|RFLAT-1|RFLAT1RNF58
Cytomap

15q13.3

7q11.23

Type of geneprotein-codingprotein-coding
DescriptionKrueppel-like factor 13BTE-binding protein 3RANTES factor of late activated T lymphocytes-1basic transcription element binding protein 3novel Sp1-like zinc finger transcription factor 1transcription factor BTEB3transcription factor NSLP1probable E3 ubiquitin-protein ligase DTX2RING-type E3 ubiquitin transferase DTX2deltex 2, E3 ubiquitin ligasedeltex homolog 2deltex2hDTX2protein deltex-2ring finger protein 58zinc ion binding protein
Modification date2020031320200313
UniProtAcc

Q9Y2Y9

Q86UW9

Ensembl transtripts involved in fusion geneENST00000307145, ENST00000500533, 
ENST00000560473, 		ENST00000472426, 
ENST00000307569, ENST00000324432, 
ENST00000413936, ENST00000430490, 
ENST00000446600, ENST00000446820, 
Fusion gene scores* DoF score3 X 4 X 2=241 X 2 X 1=2
# samples 52
** MAII scorelog2(5/24*10)=1.05889368905357
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(2/2*10)=3.32192809488736
Context

PubMed: KLF13 [Title/Abstract] AND DTX2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKLF13(31619992)-DTX2(76109738), # 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 KLF13 (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 DTX2 (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
ChimerDB4OVTCGA-24-1425-01AKLF13chr15

31619992

+DTX2chr7

76109738

+
ChimerDB4OVTCGA-24-1425KLF13chr15

31619992

+DTX2chr7

76092861

+


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Fusion Gene ORF analysis for KLF13-DTX2

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
5CDS-3UTRENST00000307145ENST00000472426KLF13chr15

31619992

+DTX2chr7

76109738

+
5CDS-5UTRENST00000307145ENST00000307569KLF13chr15

31619992

+DTX2chr7

76109738

+
5CDS-5UTRENST00000307145ENST00000307569KLF13chr15

31619992

+DTX2chr7

76092861

+
5CDS-5UTRENST00000307145ENST00000324432KLF13chr15

31619992

+DTX2chr7

76109738

+
5CDS-5UTRENST00000307145ENST00000324432KLF13chr15

31619992

+DTX2chr7

76092861

+
5CDS-5UTRENST00000307145ENST00000413936KLF13chr15

31619992

+DTX2chr7

76109738

+
5CDS-5UTRENST00000307145ENST00000430490KLF13chr15

31619992

+DTX2chr7

76109738

+
5CDS-5UTRENST00000307145ENST00000430490KLF13chr15

31619992

+DTX2chr7

76092861

+
5CDS-5UTRENST00000307145ENST00000446600KLF13chr15

31619992

+DTX2chr7

76092861

+
5CDS-intronENST00000307145ENST00000413936KLF13chr15

31619992

+DTX2chr7

76092861

+
5CDS-intronENST00000307145ENST00000446600KLF13chr15

31619992

+DTX2chr7

76109738

+
5CDS-intronENST00000307145ENST00000446820KLF13chr15

31619992

+DTX2chr7

76109738

+
5CDS-intronENST00000307145ENST00000446820KLF13chr15

31619992

+DTX2chr7

76092861

+
5CDS-intronENST00000307145ENST00000472426KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-3UTRENST00000500533ENST00000472426KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-3UTRENST00000560473ENST00000472426KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-5UTRENST00000500533ENST00000307569KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-5UTRENST00000500533ENST00000307569KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-5UTRENST00000500533ENST00000324432KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-5UTRENST00000500533ENST00000324432KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-5UTRENST00000500533ENST00000413936KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-5UTRENST00000500533ENST00000430490KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-5UTRENST00000500533ENST00000430490KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-5UTRENST00000500533ENST00000446600KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-5UTRENST00000560473ENST00000307569KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-5UTRENST00000560473ENST00000307569KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-5UTRENST00000560473ENST00000324432KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-5UTRENST00000560473ENST00000324432KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-5UTRENST00000560473ENST00000413936KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-5UTRENST00000560473ENST00000430490KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-5UTRENST00000560473ENST00000430490KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-5UTRENST00000560473ENST00000446600KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-intronENST00000500533ENST00000413936KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-intronENST00000500533ENST00000446600KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-intronENST00000500533ENST00000446820KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-intronENST00000500533ENST00000446820KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-intronENST00000500533ENST00000472426KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-intronENST00000560473ENST00000413936KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-intronENST00000560473ENST00000446600KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-intronENST00000560473ENST00000446820KLF13chr15

31619992

+DTX2chr7

76109738

+
intron-intronENST00000560473ENST00000446820KLF13chr15

31619992

+DTX2chr7

76092861

+
intron-intronENST00000560473ENST00000472426KLF13chr15

31619992

+DTX2chr7

76092861

+

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 KLF13-DTX2


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)
KLF13chr1531619992+DTX2chr776092861+5.86E-050.99994147
KLF13chr1531619992+DTX2chr776109737+1.03E-060.9999989
KLF13chr1531619992+DTX2chr776092861+5.86E-050.99994147
KLF13chr1531619992+DTX2chr776109737+1.03E-060.9999989

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.
genomic feature of top 1%

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Fusion Protein Features for KLF13-DTX2


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/:31619992/:76109738)
- 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
KLF13

Q9Y2Y9

DTX2

Q86UW9

FUNCTION: Represses transcription by binding to the BTE site, a GC-rich DNA element, in competition with the activator SP1. It also represses transcription by interacting with the corepressor Sin3A and HDAC1. Activates RANTES expression in T-cells. {ECO:0000269|PubMed:11477107}.FUNCTION: Regulator of Notch signaling, a signaling pathway involved in cell-cell communications that regulates a broad spectrum of cell-fate determinations. Probably acts both as a positive and negative regulator of Notch, depending on the developmental and cell context. Mediates the antineural activity of Notch, possibly by inhibiting the transcriptional activation mediated by MATCH1. Functions as a ubiquitin ligase protein in vitro, suggesting that it may regulate the Notch pathway via some ubiquitin ligase activity.

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 KLF13-DTX2


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 KLF13-DTX2


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 KLF13-DTX2


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 KLF13-DTX2


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