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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:KLF5-TMC4

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: KLF5-TMC4
FusionPDB ID: 42878
FusionGDB2.0 ID: 42878
HgeneTgene
Gene symbol

KLF5

TMC4

Gene ID

688

147798

Gene nameKruppel like factor 5transmembrane channel like 4
SynonymsBTEB2|CKLF|IKLF-
Cytomap

13q22.1

19q13.42

Type of geneprotein-codingprotein-coding
DescriptionKrueppel-like factor 5(intestinal Kruppel-like factorBTE-binding protein 2GC box binding protein 2Klf5C isoformKruppel-like factor 5 (intestinal)basic transcription element binding protein 2colon krueppel-like factorcolon kruppel-like factorepiditransmembrane channel-like protein 4testicular tissue protein Li 204
Modification date2020031320200313
UniProtAcc

Q13887

.
Ensembl transtripts involved in fusion geneENST idsENST00000377687, ENST00000539231, 
ENST00000477333, 		ENST00000476013, 
ENST00000376591, ENST00000416963, 
ENST00000301187, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score5 X 5 X 5=1253 X 3 X 1=9
# samples 73
** MAII scorelog2(7/125*10)=-0.836501267717121
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: KLF5 [Title/Abstract] AND TMC4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KLF5(73649913)-TMC4(54664070), # samples:1
Anticipated loss of major functional domain due to fusion event.KLF5-TMC4 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.
KLF5-TMC4 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.
KLF5-TMC4 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.
KLF5-TMC4 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.
KLF5-TMC4 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
KLF5-TMC4 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor 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
HgeneKLF5

GO:0045944

positive regulation of transcription by RNA polymerase II

16595680

HgeneKLF5

GO:0099156

cell-cell signaling via exosome

28408180

HgeneKLF5

GO:1902895

positive regulation of pri-miRNA transcription by RNA polymerase II

28408180


check buttonFusion gene breakpoints across KLF5 (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 TMC4 (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
ChiTaRS5.0N/ACN418033KLF5chr13

73649913

+TMC4chr19

54664070

-


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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)
ENST00000377687KLF5chr1373649913+ENST00000301187TMC4chr1954664070-371934942871804505

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
ENST00000377687ENST00000301187KLF5chr1373649913+TMC4chr1954664070-0.0016512850.9983487

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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

>42878_42878_1_KLF5-TMC4_KLF5_chr13_73649913_ENST00000377687_TMC4_chr19_54664070_ENST00000301187_length(amino acids)=505AA_BP=
MRARWGGAGESGRPEDVGVYVWKSGRVLLFVRAFENCLPLSEESTRNLPSSAGSPALSSPTQASVGEVGSAPDPRLELRPRVPMATRVLS
MSARLGPVPQPPAPQDEPVFAQLKPVLGAANPARDAALFPGEELKHAHHRPQAQPAPAQAPQPAQPPATGPRLPPEDLVQTRCEMEKYLT
PQLPPVPIIPEHKKYRRDSASVVDQFFTDTEGLPYSINMNVFLPDITHLRTGLYKSQRPCVTHIKTEPVAIFSHQSETTAPPPAPTQALP
EFTSIFSSHQTAAPEVNNIFIKQELPTPDLHLSVPTQQGHLYQLLNTPDLDMPSSTNQTAAMDTLNVSMSAAMAGLNTHTSAVPQTAVKQ
FQGMPPCTYTMPSQFLPQQATYFPPSPPSSEPGSPDRQAEMLQNLTPPPSYAATIASKLAIHNPNLPTTLPVNSQNIQPVRYNRRSNPDL

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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/chr13:73649913/chr19:54664070)
- 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
KLF5

Q13887

.
FUNCTION: Transcription factor that binds to GC box promoter elements. Activates the transcription of these genes.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
TgeneTMC4chr13:73649913chr19:54664070ENST0000030118701563_670707.0Compositional biasNote=Poly-Glu
TgeneTMC4chr13:73649913chr19:54664070ENST0000037659101563_670713.0Compositional biasNote=Poly-Glu
TgeneTMC4chr13:73649913chr19:54664070ENST000004169630863_670.0295.0Compositional biasNote=Poly-Glu
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015190_2490707.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST000003011870151_1680707.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015271_3480707.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015370_3940707.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015416_4250707.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015447_4830707.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015505_5420707.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015566_5920707.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015614_6540707.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015678_7120707.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015190_2490713.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST000003765910151_1680713.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015271_3480713.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015370_3940713.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015416_4250713.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015447_4830713.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015505_5420713.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015566_5920713.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015614_6540713.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015678_7120713.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308190_2490.0295.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST00000416963081_1680.0295.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308271_3480.0295.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308370_3940.0295.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308416_4250.0295.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308447_4830.0295.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308505_5420.0295.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308566_5920.0295.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308614_6540.0295.0Topological domainExtracellular
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308678_7120.0295.0Topological domainCytoplasmic
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015169_1890707.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015250_2700707.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015349_3690707.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015395_4150707.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015426_4460707.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015484_5040707.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015543_5650707.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015593_6130707.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000301187015655_6770707.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015169_1890713.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015250_2700713.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015349_3690713.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015395_4150713.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015426_4460713.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015484_5040713.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015543_5650713.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015593_6130713.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST00000376591015655_6770713.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308169_1890.0295.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308250_2700.0295.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308349_3690.0295.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308395_4150.0295.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308426_4460.0295.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308484_5040.0295.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308543_5650.0295.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308593_6130.0295.0TransmembraneHelical
TgeneTMC4chr13:73649913chr19:54664070ENST0000041696308655_6770.0295.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneKLF5chr13:73649913chr19:54664070ENST00000377687+14118_1260458.0Motif9aaTAD
HgeneKLF5chr13:73649913chr19:54664070ENST00000377687+14373_3970458.0Zinc fingerC2H2-type 1
HgeneKLF5chr13:73649913chr19:54664070ENST00000377687+14403_4270458.0Zinc fingerC2H2-type 2
HgeneKLF5chr13:73649913chr19:54664070ENST00000377687+14433_4550458.0Zinc fingerC2H2-type 3


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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
KLF5
TMC4


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 KLF5-TMC4


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 KLF5-TMC4


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