FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:LPP-ST6GAL1 (FusionGDB2 ID:49336)

Fusion Gene Summary for LPP-ST6GAL1

check button Fusion gene summary
Fusion gene informationFusion gene name: LPP-ST6GAL1
Fusion gene ID: 49336
HgeneTgene
Gene symbol

LPP

ST6GAL1

Gene ID

4026

6480

Gene nameLIM domain containing preferred translocation partner in lipomaST6 beta-galactoside alpha-2,6-sialyltransferase 1
Synonyms-SIAT1|ST6GalI|ST6N
Cytomap

3q27.3-q28

3q27.3

Type of geneprotein-codingprotein-coding
Descriptionlipoma-preferred partnerLIM proteinlipoma preferred partnerbeta-galactoside alpha-2,6-sialyltransferase 1B-cell antigen CD75CMP-N-acetylneuraminate beta-galactosamide alpha-2,6-sialyltransferaseCMP-N-acetylneuraminate-beta-galactosamide-alpha-2,6-sialyltransferase 1ST6 N-acetylgalactosaminide alpha-2,6-sialyl
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000448637, ENST00000312675, 
ENST00000543006, ENST00000471917, 
ENST00000169298, ENST00000457772, 
ENST00000448044, ENST00000487031, 
Fusion gene scores* DoF score41 X 30 X 15=1845013 X 13 X 3=507
# samples 5215
** MAII scorelog2(52/18450*10)=-5.14896538280667
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/507*10)=-1.75702324650746
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LPP [Title/Abstract] AND ST6GAL1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLPP(187871809)-ST6GAL1(186790637), # samples:2
ST6GAL1(186681714)-LPP(188583988), # 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
TgeneST6GAL1

GO:0006054

N-acetylneuraminate metabolic process

23999306

TgeneST6GAL1

GO:0018279

protein N-linked glycosylation via asparagine

23999306

TgeneST6GAL1

GO:0097503

sialylation

23999306


check buttonFusion gene breakpoints across LPP (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 ST6GAL1 (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
ChimerDB4LUSCTCGA-66-2756LPPchr3

187871809

+ST6GAL1chr3

186790637

+
ChimerDB4LUSCTCGA-66-2756LPPchr3

187926106

+ST6GAL1chr3

186790637

+
ChimerDB4LUSCTCGA-66-2756-01ALPPchr3

187871809

-ST6GAL1chr3

186790637

+
ChiTaRS5.0N/ABM919650LPPchr3

187871809

+ST6GAL1chr3

186790631

+


Top

Fusion Gene ORF analysis for LPP-ST6GAL1

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-3CDSENST00000448637ENST00000169298LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000448637ENST00000457772LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000448637ENST00000448044LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-intronENST00000448637ENST00000487031LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000312675ENST00000169298LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000312675ENST00000457772LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000312675ENST00000448044LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-intronENST00000312675ENST00000487031LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000543006ENST00000169298LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000543006ENST00000457772LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000543006ENST00000448044LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-intronENST00000543006ENST00000487031LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000471917ENST00000169298LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000471917ENST00000457772LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000471917ENST00000448044LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-intronENST00000471917ENST00000487031LPPchr3

187871809

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000448637ENST00000169298LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000448637ENST00000457772LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000448637ENST00000448044LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-intronENST00000448637ENST00000487031LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000312675ENST00000169298LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000312675ENST00000457772LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000312675ENST00000448044LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-intronENST00000312675ENST00000487031LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000543006ENST00000169298LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000543006ENST00000457772LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000543006ENST00000448044LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-intronENST00000543006ENST00000487031LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000471917ENST00000169298LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000471917ENST00000457772LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000471917ENST00000448044LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-intronENST00000471917ENST00000487031LPPchr3

187926106

+ST6GAL1chr3

186790637

+
intron-3CDSENST00000448637ENST00000169298LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-3CDSENST00000448637ENST00000457772LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-3CDSENST00000448637ENST00000448044LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-intronENST00000448637ENST00000487031LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-3CDSENST00000312675ENST00000169298LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-3CDSENST00000312675ENST00000457772LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-3CDSENST00000312675ENST00000448044LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-intronENST00000312675ENST00000487031LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-3CDSENST00000543006ENST00000169298LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-3CDSENST00000543006ENST00000457772LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-3CDSENST00000543006ENST00000448044LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-intronENST00000543006ENST00000487031LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-3CDSENST00000471917ENST00000169298LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-3CDSENST00000471917ENST00000457772LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-3CDSENST00000471917ENST00000448044LPPchr3

187871809

+ST6GAL1chr3

186790631

+
intron-intronENST00000471917ENST00000487031LPPchr3

187871809

+ST6GAL1chr3

186790631

+

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

Top

Fusion Genomic Features for LPP-ST6GAL1


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.

Top

Fusion Protein Features for LPP-ST6GAL1


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
..
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: 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.

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


Top

Fusion Gene Sequence for LPP-ST6GAL1


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.

Top

Fusion Gene PPI Analysis for LPP-ST6GAL1


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


Top

Related Drugs for LPP-ST6GAL1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for LPP-ST6GAL1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLPPC0087031Juvenile-Onset Still Disease1CTD_human
HgeneLPPC3495559Juvenile arthritis1CTD_human
HgeneLPPC3714758Juvenile psoriatic arthritis1CTD_human
HgeneLPPC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneLPPC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human
TgeneST6GAL1C0001969Alcoholic Intoxication1PSYGENET
TgeneST6GAL1C0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
TgeneST6GAL1C0162820Dermatitis, Allergic Contact1CTD_human
TgeneST6GAL1C0337677Moderate drinker1PSYGENET