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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:STAG1-NCK1 (FusionGDB2 ID:87081)

Fusion Gene Summary for STAG1-NCK1

check button Fusion gene summary
Fusion gene informationFusion gene name: STAG1-NCK1
Fusion gene ID: 87081
HgeneTgene
Gene symbol

STAG1

NCK1

Gene ID

56937

4690

Gene nameprostate transmembrane protein, androgen induced 1NCK adaptor protein 1
SynonymsSTAG1|TMEPAINCK|NCKalpha|nck-1
Cytomap

20q13.31

3q22.3

Type of geneprotein-codingprotein-coding
Descriptionprotein TMEPAIsolid tumor-associated 1 proteintransmembrane, prostate androgen induced RNAcytoplasmic protein NCK1NCK tyrosine kinaseSH2/SH3 adaptor protein NCK-alphamelanoma NCK proteinnon-catalytic region of tyrosine kinase
Modification date2020031320200327
UniProtAcc.

P16333

Ensembl transtripts involved in fusion geneENST00000236698, ENST00000383202, 
ENST00000434713, ENST00000480733, 
ENST00000536929, 		ENST00000288986, 
ENST00000481752, ENST00000469404, 
Fusion gene scores* DoF score23 X 21 X 12=57969 X 5 X 9=405
# samples 3312
** MAII scorelog2(33/5796*10)=-4.13451966531111
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/405*10)=-1.75488750216347
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: STAG1 [Title/Abstract] AND NCK1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNCK1(136664594)-STAG1(136240259), # samples:2
STAG1(136221470)-NCK1(136646826), # samples:2
Anticipated loss of major functional domain due to fusion event.NCK1-STAG1 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
NCK1-STAG1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneSTAG1

GO:0010991

negative regulation of SMAD protein complex assembly

20129061

HgeneSTAG1

GO:0030512

negative regulation of transforming growth factor beta receptor signaling pathway

24627487

HgeneSTAG1

GO:0060394

negative regulation of pathway-restricted SMAD protein phosphorylation

24627487

TgeneNCK1

GO:0033137

negative regulation of peptidyl-serine phosphorylation

14676213|16835242

TgeneNCK1

GO:0036493

positive regulation of translation in response to endoplasmic reticulum stress

14676213

TgeneNCK1

GO:0045944

positive regulation of transcription by RNA polymerase II

10026169

TgeneNCK1

GO:0060548

negative regulation of cell death

18835251

TgeneNCK1

GO:0070262

peptidyl-serine dephosphorylation

16835242

TgeneNCK1

GO:1902237

positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway

14676213

TgeneNCK1

GO:1903676

positive regulation of cap-dependent translational initiation

11959995

TgeneNCK1

GO:1903679

positive regulation of cap-independent translational initiation

11959995

TgeneNCK1

GO:1903898

negative regulation of PERK-mediated unfolded protein response

14676213

TgeneNCK1

GO:1903912

negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation

14676213|16835242

TgeneNCK1

GO:1990441

negative regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress

16835242


check buttonFusion gene breakpoints across STAG1 (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 NCK1 (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
ChimerDB4ESCATCGA-LN-A5U7STAG1chr3

136471036

-NCK1chr3

136646825

+
ChimerDB4LUSCTCGA-94-8035-01ASTAG1chr3

136221470

-NCK1chr3

136646826

+
ChimerDB4LUSCTCGA-94-8035STAG1chr3

136221470

-NCK1chr3

136646826

+


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Fusion Gene ORF analysis for STAG1-NCK1

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-5UTRENST00000236698ENST00000288986STAG1chr3

136221470

-NCK1chr3

136646826

+
5CDS-5UTRENST00000236698ENST00000481752STAG1chr3

136221470

-NCK1chr3

136646826

+
5CDS-5UTRENST00000383202ENST00000288986STAG1chr3

136221470

-NCK1chr3

136646826

+
5CDS-5UTRENST00000383202ENST00000481752STAG1chr3

136221470

-NCK1chr3

136646826

+
5CDS-5UTRENST00000434713ENST00000288986STAG1chr3

136221470

-NCK1chr3

136646826

+
5CDS-5UTRENST00000434713ENST00000481752STAG1chr3

136221470

-NCK1chr3

136646826

+
5CDS-intronENST00000236698ENST00000469404STAG1chr3

136221470

-NCK1chr3

136646826

+
5CDS-intronENST00000383202ENST00000469404STAG1chr3

136221470

-NCK1chr3

136646826

+
5CDS-intronENST00000434713ENST00000469404STAG1chr3

136221470

-NCK1chr3

136646826

+
5UTR-5UTRENST00000236698ENST00000288986STAG1chr3

136471036

-NCK1chr3

136646825

+
5UTR-5UTRENST00000236698ENST00000481752STAG1chr3

136471036

-NCK1chr3

136646825

+
5UTR-5UTRENST00000383202ENST00000288986STAG1chr3

136471036

-NCK1chr3

136646825

+
5UTR-5UTRENST00000383202ENST00000481752STAG1chr3

136471036

-NCK1chr3

136646825

+
5UTR-5UTRENST00000434713ENST00000288986STAG1chr3

136471036

-NCK1chr3

136646825

+
5UTR-5UTRENST00000434713ENST00000481752STAG1chr3

136471036

-NCK1chr3

136646825

+
5UTR-5UTRENST00000480733ENST00000288986STAG1chr3

136471036

-NCK1chr3

136646825

+
5UTR-5UTRENST00000480733ENST00000481752STAG1chr3

136471036

-NCK1chr3

136646825

+
5UTR-intronENST00000236698ENST00000469404STAG1chr3

136471036

-NCK1chr3

136646825

+
5UTR-intronENST00000383202ENST00000469404STAG1chr3

136471036

-NCK1chr3

136646825

+
5UTR-intronENST00000434713ENST00000469404STAG1chr3

136471036

-NCK1chr3

136646825

+
5UTR-intronENST00000480733ENST00000469404STAG1chr3

136471036

-NCK1chr3

136646825

+
intron-5UTRENST00000480733ENST00000288986STAG1chr3

136221470

-NCK1chr3

136646826

+
intron-5UTRENST00000480733ENST00000481752STAG1chr3

136221470

-NCK1chr3

136646826

+
intron-5UTRENST00000536929ENST00000288986STAG1chr3

136471036

-NCK1chr3

136646825

+
intron-5UTRENST00000536929ENST00000288986STAG1chr3

136221470

-NCK1chr3

136646826

+
intron-5UTRENST00000536929ENST00000481752STAG1chr3

136471036

-NCK1chr3

136646825

+
intron-5UTRENST00000536929ENST00000481752STAG1chr3

136221470

-NCK1chr3

136646826

+
intron-intronENST00000480733ENST00000469404STAG1chr3

136221470

-NCK1chr3

136646826

+
intron-intronENST00000536929ENST00000469404STAG1chr3

136471036

-NCK1chr3

136646825

+
intron-intronENST00000536929ENST00000469404STAG1chr3

136221470

-NCK1chr3

136646826

+

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 STAG1-NCK1


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)
STAG1chr3136221469-NCK1chr3136646825+2.41E-060.9999976
STAG1chr3136221469-NCK1chr3136646825+2.41E-060.9999976
STAG1chr3136471036-NCK1chr3136646825+2.17E-081
STAG1chr3136221469-NCK1chr3136646825+2.41E-060.9999976
STAG1chr3136221469-NCK1chr3136646825+2.41E-060.9999976
STAG1chr3136471036-NCK1chr3136646825+2.17E-081

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 STAG1-NCK1


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/:136664594/:136240259)
- 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
.NCK1

P16333

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: Adapter protein which associates with tyrosine-phosphorylated growth factor receptors, such as KDR and PDGFRB, or their cellular substrates. Maintains low levels of EIF2S1 phosphorylation by promoting its dephosphorylation by PP1. Plays a role in the DNA damage response, not in the detection of the damage by ATM/ATR, but for efficient activation of downstream effectors, such as that of CHEK2. Plays a role in ELK1-dependent transcriptional activation in response to activated Ras signaling. Modulates the activation of EIF2AK2/PKR by dsRNA. May play a role in cell adhesion and migration through interaction with ephrin receptors. {ECO:0000269|PubMed:10026169, ECO:0000269|PubMed:16835242, ECO:0000269|PubMed:17803907, ECO:0000269|PubMed:18835251, ECO:0000269|PubMed:23358419, ECO:0000269|PubMed:9430661}.

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 STAG1-NCK1


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 STAG1-NCK1


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 STAG1-NCK1


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 STAG1-NCK1


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