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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:STAG2-GRIA3 (FusionGDB2 ID:HG10735TG2892)

Fusion Gene Summary for STAG2-GRIA3

check button Fusion gene summary
Fusion gene informationFusion gene name: STAG2-GRIA3
Fusion gene ID: hg10735tg2892
HgeneTgene
Gene symbol

STAG2

GRIA3

Gene ID

10735

2892

Gene namestromal antigen 2glutamate ionotropic receptor AMPA type subunit 3
SynonymsMKMS|NEDXCF|SA-2|SA2|SCC3B|bA517O1.1GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94
Cytomap('STAG2')('GRIA3')

Xq25

Xq25

Type of geneprotein-codingprotein-coding
Descriptioncohesin subunit SA-2SCC3 homolog 2glutamate receptor 3AMPA-selective glutamate receptor 3dJ1171F9.1gluR-3glutamate receptor Cglutamate receptor subunit 3glutamate receptor, ionotrophic, AMPA 3glutamate receptor, ionotropic, AMPA 3
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000218089, ENST00000354548, 
ENST00000371144, ENST00000371145, 
ENST00000371157, ENST00000371160, 
ENST00000469481, 
Fusion gene scores* DoF score14 X 16 X 7=15686 X 6 X 2=72
# samples 206
** MAII scorelog2(20/1568*10)=-2.97085365434048
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/72*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: STAG2 [Title/Abstract] AND GRIA3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSTAG2(123164975)-GRIA3(122459877), # samples:3
Anticipated loss of major functional domain due to fusion event.STAG2-GRIA3 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
STAG2-GRIA3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
STAG2-GRIA3 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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


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
ChimerDB4LUADTCGA-55-7913-01BSTAG2chrX

123164975

-GRIA3chrX

122459877

+
ChimerDB4LUADTCGA-55-7913-01BSTAG2chrX

123164975

+GRIA3chrX

122459877

+


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Fusion Gene ORF analysis for STAG2-GRIA3

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-intronENST00000218089ENST00000371264STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000218089ENST00000371266STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000218089ENST00000479118STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000354548ENST00000371264STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000354548ENST00000371266STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000354548ENST00000479118STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000371144ENST00000371264STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000371144ENST00000371266STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000371144ENST00000479118STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000371145ENST00000371264STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000371145ENST00000371266STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000371145ENST00000479118STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000371157ENST00000371264STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000371157ENST00000371266STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000371157ENST00000479118STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000371160ENST00000371264STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000371160ENST00000371266STAG2chrX

123164975

+GRIA3chrX

122459877

+
5CDS-intronENST00000371160ENST00000479118STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000218089ENST00000264357STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000218089ENST00000371251STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000218089ENST00000371256STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000218089ENST00000541091STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000218089ENST00000542149STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000354548ENST00000264357STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000354548ENST00000371251STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000354548ENST00000371256STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000354548ENST00000541091STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000354548ENST00000542149STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371144ENST00000264357STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371144ENST00000371251STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371144ENST00000371256STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371144ENST00000541091STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371144ENST00000542149STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371145ENST00000264357STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371145ENST00000371251STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371145ENST00000371256STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371145ENST00000541091STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371145ENST00000542149STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371157ENST00000264357STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371157ENST00000371251STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371157ENST00000371256STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371157ENST00000541091STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371157ENST00000542149STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371160ENST00000264357STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371160ENST00000371251STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371160ENST00000371256STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371160ENST00000541091STAG2chrX

123164975

+GRIA3chrX

122459877

+
Frame-shiftENST00000371160ENST00000542149STAG2chrX

123164975

+GRIA3chrX

122459877

+
intron-3CDSENST00000469481ENST00000264357STAG2chrX

123164975

+GRIA3chrX

122459877

+
intron-3CDSENST00000469481ENST00000371251STAG2chrX

123164975

+GRIA3chrX

122459877

+
intron-3CDSENST00000469481ENST00000371256STAG2chrX

123164975

+GRIA3chrX

122459877

+
intron-3CDSENST00000469481ENST00000541091STAG2chrX

123164975

+GRIA3chrX

122459877

+
intron-3CDSENST00000469481ENST00000542149STAG2chrX

123164975

+GRIA3chrX

122459877

+
intron-intronENST00000469481ENST00000371264STAG2chrX

123164975

+GRIA3chrX

122459877

+
intron-intronENST00000469481ENST00000371266STAG2chrX

123164975

+GRIA3chrX

122459877

+
intron-intronENST00000469481ENST00000479118STAG2chrX

123164975

+GRIA3chrX

122459877

+

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 STAG2-GRIA3


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)
STAG2chrX123164975+GRIA3chrX122459876+3.43E-081
STAG2chrX123164975+GRIA3chrX122459876+3.43E-081


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 STAG2-GRIA3


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/:123164975/:122459877)
- 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
..
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: 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 STAG2-GRIA3


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 STAG2-GRIA3


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 STAG2-GRIA3


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 STAG2-GRIA3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSTAG2C0005684Malignant neoplasm of urinary bladder3CGI;CTD_human
HgeneSTAG2C0005695Bladder Neoplasm3CGI;CTD_human
HgeneSTAG2C4310830Xq25 TRIPLICATION SYNDROME2ORPHANET
HgeneSTAG2C4311049Xq25 DUPLICATION SYNDROME2ORPHANET
HgeneSTAG2C0007138Carcinoma, Transitional Cell1CTD_human
HgeneSTAG2C0018798Congenital Heart Defects1GENOMICS_ENGLAND
HgeneSTAG2C0023466Leukemia, Monocytic, Chronic1CTD_human
HgeneSTAG2C0023470Myeloid Leukemia1CTD_human
HgeneSTAG2C0025958Microcephaly1GENOMICS_ENGLAND
HgeneSTAG2C0456070Growth delay1GENOMICS_ENGLAND
HgeneSTAG2C0557874Global developmental delay1GENOMICS_ENGLAND
HgeneSTAG2C1384666hearing impairment1GENOMICS_ENGLAND
HgeneSTAG2C1860789Leukemia, Megakaryoblastic, of Down Syndrome1CTD_human
HgeneSTAG2C2713368Hematopoetic Myelodysplasia1CTD_human
HgeneSTAG2C3463824MYELODYSPLASTIC SYNDROME1CTD_human
HgeneSTAG2C3714756Intellectual Disability1GENOMICS_ENGLAND
HgeneSTAG2C4021817Abnormality of head or neck1GENOMICS_ENGLAND
TgeneC0796250PARTINGTON X-LINKED MENTAL RETARDATION SYNDROME6CLINGEN
TgeneC0005586Bipolar Disorder5PSYGENET
TgeneC0011581Depressive disorder3PSYGENET
TgeneC0011570Mental Depression2PSYGENET
TgeneC0036341Schizophrenia2PSYGENET
TgeneC0016722Frigidity1CTD_human
TgeneC0020594Hypoactive Sexual Desire Disorder1CTD_human
TgeneC0029261Orgasmic Disorder1CTD_human
TgeneC0033953Psychosexual Disorders1CTD_human
TgeneC0036902Sexual Arousal Disorder1CTD_human
TgeneC1862939AMYOTROPHIC LATERAL SCLEROSIS 11CTD_human
TgeneC1862941Amyotrophic Lateral Sclerosis, Sporadic1CTD_human
TgeneC2678051MENTAL RETARDATION, X-LINKED 94 (disorder)1CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC4551993Amyotrophic Lateral Sclerosis, Familial1CTD_human