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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:STK38L-CTNND1 (FusionGDB2 ID:87539)

Fusion Gene Summary for STK38L-CTNND1

check button Fusion gene summary
Fusion gene informationFusion gene name: STK38L-CTNND1
Fusion gene ID: 87539
HgeneTgene
Gene symbol

STK38L

CTNND1

Gene ID

23012

100528016

Gene nameserine/threonine kinase 38 likeTMX2-CTNND1 readthrough (NMD candidate)
SynonymsNDR2CAS|CTNND1|p120(cas)|p120(ctn)
Cytomap

12p11.23

11q12.1

Type of geneprotein-codingncRNA
Descriptionserine/threonine-protein kinase 38-likeNDR2 protein kinasenuclear Dbf2-related 2nuclear Dbf2-related kinase 2Cadherin-associated Src substrateCatenin delta-1TMX2-CTNND1 readthrough (non-protein coding)p120 catenin
Modification date2020031320200313
UniProtAcc.

O60716

Ensembl transtripts involved in fusion geneENST00000389032, ENST00000539577, 
ENST00000360682, ENST00000361391, 
ENST00000361796, ENST00000399039, 
ENST00000524630, ENST00000529919, 
ENST00000361332, ENST00000399050, 
ENST00000415361, ENST00000426142, 
ENST00000428599, ENST00000526357, 
ENST00000526938, ENST00000528232, 
ENST00000528621, ENST00000529986, 
ENST00000530094, ENST00000530748, 
ENST00000532463, ENST00000532787, 
ENST00000532844, ENST00000534579, 
ENST00000358694, ENST00000525902, 
ENST00000526772, ENST00000527467, 
ENST00000529526, ENST00000529873, 
ENST00000531014, ENST00000532245, 
ENST00000532649, ENST00000533667, 
Fusion gene scores* DoF score9 X 5 X 5=22517 X 21 X 10=3570
# samples 925
** MAII scorelog2(9/225*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(25/3570*10)=-3.83592407425437
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: STK38L [Title/Abstract] AND CTNND1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSTK38L(27397265)-CTNND1(57561482), # 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
HgeneSTK38L

GO:0006468

protein phosphorylation

15037617|15067004

HgeneSTK38L

GO:0035556

intracellular signal transduction

15067004


check buttonFusion gene breakpoints across STK38L (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 CTNND1 (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
ChimerDB4STADTCGA-HU-A4GT-01ASTK38Lchr12

27397265

+CTNND1chr11

57561482

+


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Fusion Gene ORF analysis for STK38L-CTNND1

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-3CDSENST00000389032ENST00000360682STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-3CDSENST00000389032ENST00000361391STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-3CDSENST00000389032ENST00000361796STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-3CDSENST00000389032ENST00000399039STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-3CDSENST00000389032ENST00000524630STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-3CDSENST00000389032ENST00000529919STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-3CDSENST00000539577ENST00000360682STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-3CDSENST00000539577ENST00000361391STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-3CDSENST00000539577ENST00000361796STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-3CDSENST00000539577ENST00000399039STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-3CDSENST00000539577ENST00000524630STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-3CDSENST00000539577ENST00000529919STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000361332STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000399050STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000415361STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000426142STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000428599STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000526357STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000526938STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000528232STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000528621STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000529986STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000530094STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000530748STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000532463STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000532787STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000532844STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000389032ENST00000534579STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000361332STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000399050STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000415361STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000426142STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000428599STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000526357STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000526938STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000528232STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000528621STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000529986STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000530094STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000530748STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000532463STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000532787STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000532844STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-5UTRENST00000539577ENST00000534579STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000389032ENST00000358694STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000389032ENST00000525902STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000389032ENST00000526772STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000389032ENST00000527467STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000389032ENST00000529526STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000389032ENST00000529873STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000389032ENST00000531014STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000389032ENST00000532245STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000389032ENST00000532649STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000389032ENST00000533667STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000539577ENST00000358694STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000539577ENST00000525902STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000539577ENST00000526772STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000539577ENST00000527467STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000539577ENST00000529526STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000539577ENST00000529873STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000539577ENST00000531014STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000539577ENST00000532245STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000539577ENST00000532649STK38Lchr12

27397265

+CTNND1chr11

57561482

+
5UTR-intronENST00000539577ENST00000533667STK38Lchr12

27397265

+CTNND1chr11

57561482

+

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 STK38L-CTNND1


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)
STK38Lchr1227397265+CTNND1chr1157561481+7.90E-080.9999999
STK38Lchr1227397265+CTNND1chr1157561481+7.90E-080.9999999

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 STK38L-CTNND1


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/:27397265/:57561482)
- 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
.CTNND1

O60716

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: Key regulator of cell-cell adhesion that associates with and regulates the cell adhesion properties of both C-, E- and N-cadherins, being critical for their surface stability (PubMed:14610055, PubMed:20371349). Beside cell-cell adhesion, regulates gene transcription through several transcription factors including ZBTB33/Kaiso2 and GLIS2, and the activity of Rho family GTPases and downstream cytoskeletal dynamics (PubMed:10207085, PubMed:20371349). Implicated both in cell transformation by SRC and in ligand-induced receptor signaling through the EGF, PDGF, CSF-1 and ERBB2 receptors (PubMed:17344476). {ECO:0000269|PubMed:10207085, ECO:0000269|PubMed:14610055, ECO:0000269|PubMed:17344476, ECO:0000269|PubMed:20371349}.

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 STK38L-CTNND1


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 STK38L-CTNND1


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 STK38L-CTNND1


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 STK38L-CTNND1


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