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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:KRT20-TSC22D1 (FusionGDB2 ID:HG54474TG8848)

Fusion Gene Summary for KRT20-TSC22D1

check button Fusion gene summary
Fusion gene informationFusion gene name: KRT20-TSC22D1
Fusion gene ID: hg54474tg8848
HgeneTgene
Gene symbol

KRT20

TSC22D1

Gene ID

54474

8848

Gene namekeratin 20TSC22 domain family member 1
SynonymsCD20|CK-20|CK20|K20|KRT21Ptg-2|TGFB1I4|TSC22
Cytomap('KRT20')('TSC22D1')

17q21.2

13q14.11

Type of geneprotein-codingprotein-coding
Descriptionkeratin, type I cytoskeletal 20cytokeratin 20keratin 20, type Iprotein ITTSC22 domain family protein 1TGFB-stimulated clone 22 homologTGFbeta-stimulated clone 22cerebral protein 2regulatory protein TSC-22transcriptional regulator TSC-22transforming growth factor beta-1-induced transcript 4 proteintransforming growth fac
Modification date2020032720200313
UniProtAcc

P35900

.
Ensembl transtripts involved in fusion geneENST00000167588, 
Fusion gene scores* DoF score1 X 1 X 1=124 X 20 X 7=3360
# samples 128
** MAII scorelog2(1/1*10)=3.32192809488736log2(28/3360*10)=-3.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KRT20 [Title/Abstract] AND TSC22D1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKRT20(39032193)-TSC22D1(45111057), # samples:3
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 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


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Fusion Gene ORF analysis for KRT20-TSC22D1

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

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 KRT20-TSC22D1


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)


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Fusion Protein Features for KRT20-TSC22D1


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/:39032193/:45111057)
- 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
KRT20

P35900

.
FUNCTION: Plays a significant role in maintaining keratin filament organization in intestinal epithelia. When phosphorylated, plays a role in the secretion of mucin in the small intestine (By similarity). {ECO:0000250, ECO:0000269|PubMed:12857878, ECO:0000269|PubMed:16608857}.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 KRT20-TSC22D1


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 KRT20-TSC22D1


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 KRT20-TSC22D1


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 KRT20-TSC22D1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKRT20C0001418Adenocarcinoma1CTD_human
HgeneKRT20C0007528Cecal Neoplasms1CTD_human
HgeneKRT20C0024623Malignant neoplasm of stomach1CTD_human
HgeneKRT20C0038356Stomach Neoplasms1CTD_human
HgeneKRT20C0153437Malignant neoplasm of cecum1CTD_human
HgeneKRT20C0205641Adenocarcinoma, Basal Cell1CTD_human
HgeneKRT20C0205642Adenocarcinoma, Oxyphilic1CTD_human
HgeneKRT20C0205643Carcinoma, Cribriform1CTD_human
HgeneKRT20C0205644Carcinoma, Granular Cell1CTD_human
HgeneKRT20C0205645Adenocarcinoma, Tubular1CTD_human
HgeneKRT20C1708349Hereditary Diffuse Gastric Cancer1CTD_human
TgeneC0019207Hepatoma, Morris2CTD_human
TgeneC0019208Hepatoma, Novikoff2CTD_human
TgeneC0023904Liver Neoplasms, Experimental2CTD_human
TgeneC0086404Experimental Hepatoma2CTD_human
TgeneC0007097Carcinoma1CTD_human
TgeneC0007621Neoplastic Cell Transformation1CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0024667Animal Mammary Neoplasms1CTD_human
TgeneC0024668Mammary Neoplasms, Experimental1CTD_human
TgeneC0205696Anaplastic carcinoma1CTD_human
TgeneC0205697Carcinoma, Spindle-Cell1CTD_human
TgeneC0205698Undifferentiated carcinoma1CTD_human
TgeneC0205699Carcinomatosis1CTD_human
TgeneC1257925Mammary Carcinoma, Animal1CTD_human