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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:ST3GAL3-KDM4A (FusionGDB2 ID:86941)

Fusion Gene Summary for ST3GAL3-KDM4A

check button Fusion gene summary
Fusion gene informationFusion gene name: ST3GAL3-KDM4A
Fusion gene ID: 86941
HgeneTgene
Gene symbol

ST3GAL3

KDM4A

Gene ID

6487

9682

Gene nameST3 beta-galactoside alpha-2,3-sialyltransferase 3lysine demethylase 4A
SynonymsEIEE15|MRT12|SIAT6|ST3GALII|ST3Gal III|ST3GalIII|ST3NJHDM3A|JMJD2|JMJD2A|TDRD14A
Cytomap

1p34.1

1p34.2-p34.1

Type of geneprotein-codingprotein-coding
DescriptionCMP-N-acetylneuraminate-beta-1,4-galactoside alpha-2,3-sialyltransferaseGal beta-1,3(4)GlcNAc alpha-2,3 sialyltransferasealpha 2,3-ST 3alpha 2,3-sialyltransferase IIIalpha-2,3-sialyltransferase IIsialyltransferase 6 (N-acetyllacosaminide alpha 2,3-silysine-specific demethylase 4AjmjC domain-containing histone demethylation protein 3Ajumonji C domain-containing histone demethylase 3Ajumonji domain containing 2jumonji domain containing 2Ajumonji domain-containing protein 2Alysine (K)-specific dem
Modification date2020031320200313
UniProtAcc.

O75164

Ensembl transtripts involved in fusion geneENST00000262915, ENST00000330208, 
ENST00000335430, ENST00000347631, 
ENST00000351035, ENST00000353126, 
ENST00000361392, ENST00000361400, 
ENST00000372374, ENST00000372375, 
ENST00000372377, ENST00000545417, 
ENST00000332628, ENST00000361746, 
ENST00000361812, ENST00000372362, 
ENST00000372365, ENST00000372366, 
ENST00000372367, ENST00000372368, 
ENST00000372369, ENST00000372372, 
ENST00000461375, ENST00000528371, 
ENST00000531451, ENST00000531816, 
ENST00000531993, ENST00000533933, 
ENST00000372396, ENST00000463151, 
Fusion gene scores* DoF score11 X 9 X 8=7924 X 4 X 3=48
# samples 124
** MAII scorelog2(12/792*10)=-2.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ST3GAL3 [Title/Abstract] AND KDM4A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKDM4A(44137546)-ST3GAL3(44201903), # samples:1
ST3GAL3(44173364)-KDM4A(44169288), # 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
TgeneKDM4A

GO:0016577

histone demethylation

16024779

TgeneKDM4A

GO:0045892

negative regulation of transcription, DNA-templated

16024779

TgeneKDM4A

GO:0070544

histone H3-K36 demethylation

21914792


check buttonFusion gene breakpoints across ST3GAL3 (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 KDM4A (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
ChimerDB4BRCATCGA-PL-A8LZ-01AST3GAL3chr1

44173364

-KDM4Achr1

44169288

+


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Fusion Gene ORF analysis for ST3GAL3-KDM4A

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-3CDSENST00000262915ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-3CDSENST00000330208ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-3CDSENST00000335430ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-3CDSENST00000347631ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-3CDSENST00000351035ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-3CDSENST00000353126ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-3CDSENST00000361392ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-3CDSENST00000361400ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-3CDSENST00000372374ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-3CDSENST00000372375ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-3CDSENST00000372377ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-3CDSENST00000545417ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-intronENST00000262915ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-intronENST00000330208ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-intronENST00000335430ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-intronENST00000347631ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-intronENST00000351035ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-intronENST00000353126ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-intronENST00000361392ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-intronENST00000361400ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-intronENST00000372374ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-intronENST00000372375ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-intronENST00000372377ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
5UTR-intronENST00000545417ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000332628ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000361746ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000361812ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000372362ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000372365ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000372366ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000372367ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000372368ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000372369ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000372372ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000461375ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000528371ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000531451ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000531816ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000531993ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-3CDSENST00000533933ENST00000372396ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000332628ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000361746ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000361812ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000372362ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000372365ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000372366ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000372367ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000372368ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000372369ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000372372ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000461375ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000528371ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000531451ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000531816ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000531993ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+
intron-intronENST00000533933ENST00000463151ST3GAL3chr1

44173364

-KDM4Achr1

44169288

+

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 ST3GAL3-KDM4A


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)

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.

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Fusion Protein Features for ST3GAL3-KDM4A


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/:44137546/:44201903)
- 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
.KDM4A

O75164

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: Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code (PubMed:26741168). Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively. {ECO:0000269|PubMed:16024779, ECO:0000269|PubMed:16603238, ECO:0000269|PubMed:26741168}.; FUNCTION: [Isoform 2]: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain. {ECO:0000269|PubMed:21694756}.

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 ST3GAL3-KDM4A


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 ST3GAL3-KDM4A


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 ST3GAL3-KDM4A


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 ST3GAL3-KDM4A


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