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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:PEMT-NEU3 (FusionGDB2 ID:63865)

Fusion Gene Summary for PEMT-NEU3

check button Fusion gene summary
Fusion gene informationFusion gene name: PEMT-NEU3
Fusion gene ID: 63865
HgeneTgene
Gene symbol

PEMT

NEU3

Gene ID

10400

10825

Gene namephosphatidylethanolamine N-methyltransferaseneuraminidase 3
SynonymsPEAMT|PEMPT|PEMT2|PLMT|PNMTSIAL3
Cytomap

17p11.2

11q13.4

Type of geneprotein-codingprotein-coding
Descriptionphosphatidylethanolamine N-methyltransferasephospholipid methyltransferasesialidase-3N-acetyl-alpha-neuraminidase 3ganglioside sialidasemembrane sialidasesialidase 3 (membrane sialidase)
Modification date2020032020200313
UniProtAcc.

Q9UQ49

Ensembl transtripts involved in fusion geneENST00000395782, ENST00000395783, 
ENST00000435340, ENST00000255389, 
ENST00000395781, ENST00000484838, 
ENST00000294064, ENST00000531509, 
ENST00000544263, ENST00000529024, 
ENST00000532963, ENST00000531619, 
ENST00000545272, ENST00000526068, 
ENST00000534628, 
Fusion gene scores* DoF score11 X 7 X 6=4623 X 1 X 3=9
# samples 113
** MAII scorelog2(11/462*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PEMT [Title/Abstract] AND NEU3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPEMT(17494845)-NEU3(74705554), # samples:3
Anticipated loss of major functional domain due to fusion event.PEMT-NEU3 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PEMT-NEU3 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism 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
TgeneNEU3

GO:0005975

carbohydrate metabolic process

12730204

TgeneNEU3

GO:0006689

ganglioside catabolic process

10861246

TgeneNEU3

GO:0009313

oligosaccharide catabolic process

10861246


check buttonFusion gene breakpoints across PEMT (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 NEU3 (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-AR-A0TZ-01APEMTchr17

17494845

-NEU3chr11

74705554

+
ChimerDB4BRCATCGA-AR-A0TZ-01APEMTchr17

17494845

-NEU3chr11

74705554

+
ChimerDB4BRCATCGA-AR-A0TZ-01APEMTchr17

17494845

-NEU3chr11

74705554

+


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Fusion Gene ORF analysis for PEMT-NEU3

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
intron-3CDSENST00000395782ENST00000294064PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-3CDSENST00000395782ENST00000531509PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-5UTRENST00000395782ENST00000544263PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000395782ENST00000529024PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000395782ENST00000532963PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000395782ENST00000531619PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000395782ENST00000545272PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000395782ENST00000526068PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000395782ENST00000534628PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-3CDSENST00000395783ENST00000294064PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-3CDSENST00000395783ENST00000531509PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-5UTRENST00000395783ENST00000544263PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000395783ENST00000529024PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000395783ENST00000532963PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000395783ENST00000531619PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000395783ENST00000545272PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000395783ENST00000526068PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000395783ENST00000534628PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-3CDSENST00000435340ENST00000294064PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-3CDSENST00000435340ENST00000531509PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-5UTRENST00000435340ENST00000544263PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000435340ENST00000529024PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000435340ENST00000532963PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000435340ENST00000531619PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000435340ENST00000545272PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000435340ENST00000526068PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000435340ENST00000534628PEMTchr17

17494845

-NEU3chr11

74705554

+
Frame-shiftENST00000255389ENST00000294064PEMTchr17

17494845

-NEU3chr11

74705554

+
Frame-shiftENST00000255389ENST00000531509PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-5UTRENST00000255389ENST00000544263PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-intronENST00000255389ENST00000529024PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-intronENST00000255389ENST00000532963PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-intronENST00000255389ENST00000531619PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-intronENST00000255389ENST00000545272PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-intronENST00000255389ENST00000526068PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-intronENST00000255389ENST00000534628PEMTchr17

17494845

-NEU3chr11

74705554

+
Frame-shiftENST00000395781ENST00000294064PEMTchr17

17494845

-NEU3chr11

74705554

+
Frame-shiftENST00000395781ENST00000531509PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-5UTRENST00000395781ENST00000544263PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-intronENST00000395781ENST00000529024PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-intronENST00000395781ENST00000532963PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-intronENST00000395781ENST00000531619PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-intronENST00000395781ENST00000545272PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-intronENST00000395781ENST00000526068PEMTchr17

17494845

-NEU3chr11

74705554

+
5CDS-intronENST00000395781ENST00000534628PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-3CDSENST00000484838ENST00000294064PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-3CDSENST00000484838ENST00000531509PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-5UTRENST00000484838ENST00000544263PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000484838ENST00000529024PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000484838ENST00000532963PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000484838ENST00000531619PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000484838ENST00000545272PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000484838ENST00000526068PEMTchr17

17494845

-NEU3chr11

74705554

+
intron-intronENST00000484838ENST00000534628PEMTchr17

17494845

-NEU3chr11

74705554

+

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 PEMT-NEU3


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)
PEMTchr1717494844-NEU3chr1174705553+1.09E-060.9999989
PEMTchr1717494844-NEU3chr1174705553+1.09E-060.9999989

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 PEMT-NEU3


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.NEU3

Q9UQ49

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Exo-alpha-sialidase that catalyzes the hydrolytic cleavage of the terminal sialic acid (N-acetylneuraminic acid, Neu5Ac) of a glycan moiety in the catabolism of glycolipids, glycoproteins and oligosacharides. Displays high catalytic efficiency for gangliosides including alpha-(2->3)-sialylated GD1a and GM3 and alpha-(2->8)-sialylated GD3 (PubMed:11298736, PubMed:15847605, PubMed:10861246, PubMed:20511247, PubMed:28646141, PubMed:10405317, PubMed:12011038). Plays a role in the regulation of transmembrane signaling through the modulation of ganglioside content of the lipid bilayer and by direct interaction with signaling receptors, such as EGFR (PubMed:17334392, PubMed:25922362). Desialylates EGFR and activates downstream signaling in proliferating cells (PubMed:25922362). Contributes to clathrin-mediated endocytosis by regulating sorting of endocytosed receptors to early and recycling endosomes (PubMed:26251452). {ECO:0000269|PubMed:10405317, ECO:0000269|PubMed:10861246, ECO:0000269|PubMed:11298736, ECO:0000269|PubMed:12011038, ECO:0000269|PubMed:15847605, ECO:0000269|PubMed:17334392, ECO:0000269|PubMed:20511247, ECO:0000269|PubMed:25922362, ECO:0000269|PubMed:26251452, ECO:0000269|PubMed:28646141}.

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 PEMT-NEU3


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 PEMT-NEU3


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 PEMT-NEU3


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 PEMT-NEU3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePEMTC0036341Schizophrenia2PSYGENET
HgenePEMTC0023890Liver Cirrhosis1CTD_human
HgenePEMTC0239946Fibrosis, Liver1CTD_human
HgenePEMTC0400966Non-alcoholic Fatty Liver Disease1CTD_human
HgenePEMTC3241937Nonalcoholic Steatohepatitis1CTD_human