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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:LSAMP-LSAMP (FusionGDB2 ID:50168)

Fusion Gene Summary for LSAMP-LSAMP

check button Fusion gene summary
Fusion gene informationFusion gene name: LSAMP-LSAMP
Fusion gene ID: 50168
HgeneTgene
Gene symbol

LSAMP

LSAMP

Gene ID

4045

4045

Gene namelimbic system associated membrane proteinlimbic system associated membrane protein
SynonymsIGLON3|LAMPIGLON3|LAMP
Cytomap

3q13.31

3q13.31

Type of geneprotein-codingprotein-coding
Descriptionlimbic system-associated membrane proteinIgLON family member 3limbic system-associated membrane proteinIgLON family member 3
Modification date2020031320200313
UniProtAcc

Q13449

Q13449

Ensembl transtripts involved in fusion geneENST00000490035, ENST00000539563, 
ENST00000498645, 		ENST00000498645, 
ENST00000490035, ENST00000539563, 
Fusion gene scores* DoF score14 X 13 X 5=91020 X 18 X 11=3960
# samples 1634
** MAII scorelog2(16/910*10)=-2.5077946401987
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(34/3960*10)=-3.54189377882927
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LSAMP [Title/Abstract] AND LSAMP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLSAMP(116163718)-LSAMP(115571468), # samples:1
LSAMP(115527614)-LSAMP(115527730), # samples:1
LSAMP(115915126)-LSAMP(115914871), # samples:1
LSAMP(115535161)-LSAMP(115559759), # samples:1
Anticipated loss of major functional domain due to fusion event.LSAMP-LSAMP seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
LSAMP-LSAMP seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
LSAMP-LSAMP seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
LSAMP-LSAMP seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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 buttonFusion gene breakpoints across LSAMP (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 LSAMP (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
ChiTaRS5.0N/AAA515979LSAMPchr3

116163718

-LSAMPchr3

115571468

-
ChiTaRS5.0N/ABE770467LSAMPchr3

115527614

+LSAMPchr3

115527730

-
ChiTaRS5.0N/ACV357692LSAMPchr3

115915126

+LSAMPchr3

115914871

-
ChiTaRS5.0N/ADA568784LSAMPchr3

115535161

-LSAMPchr3

115559759

-


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Fusion Gene ORF analysis for LSAMP-LSAMP

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-5UTRENST00000490035ENST00000498645LSAMPchr3

116163718

-LSAMPchr3

115571468

-
5CDS-5UTRENST00000539563ENST00000498645LSAMPchr3

116163718

-LSAMPchr3

115571468

-
Frame-shiftENST00000490035ENST00000490035LSAMPchr3

116163718

-LSAMPchr3

115571468

-
Frame-shiftENST00000490035ENST00000539563LSAMPchr3

116163718

-LSAMPchr3

115571468

-
Frame-shiftENST00000539563ENST00000490035LSAMPchr3

116163718

-LSAMPchr3

115571468

-
Frame-shiftENST00000539563ENST00000539563LSAMPchr3

116163718

-LSAMPchr3

115571468

-
intron-3CDSENST00000498645ENST00000490035LSAMPchr3

116163718

-LSAMPchr3

115571468

-
intron-3CDSENST00000498645ENST00000539563LSAMPchr3

116163718

-LSAMPchr3

115571468

-
intron-3UTRENST00000490035ENST00000490035LSAMPchr3

115527614

+LSAMPchr3

115527730

-
intron-3UTRENST00000498645ENST00000490035LSAMPchr3

115527614

+LSAMPchr3

115527730

-
intron-3UTRENST00000539563ENST00000490035LSAMPchr3

115527614

+LSAMPchr3

115527730

-
intron-5UTRENST00000498645ENST00000498645LSAMPchr3

116163718

-LSAMPchr3

115571468

-
intron-intronENST00000490035ENST00000490035LSAMPchr3

115915126

+LSAMPchr3

115914871

-
intron-intronENST00000490035ENST00000490035LSAMPchr3

115535161

-LSAMPchr3

115559759

-
intron-intronENST00000490035ENST00000498645LSAMPchr3

115527614

+LSAMPchr3

115527730

-
intron-intronENST00000490035ENST00000498645LSAMPchr3

115915126

+LSAMPchr3

115914871

-
intron-intronENST00000490035ENST00000498645LSAMPchr3

115535161

-LSAMPchr3

115559759

-
intron-intronENST00000490035ENST00000539563LSAMPchr3

115527614

+LSAMPchr3

115527730

-
intron-intronENST00000490035ENST00000539563LSAMPchr3

115915126

+LSAMPchr3

115914871

-
intron-intronENST00000490035ENST00000539563LSAMPchr3

115535161

-LSAMPchr3

115559759

-
intron-intronENST00000498645ENST00000490035LSAMPchr3

115915126

+LSAMPchr3

115914871

-
intron-intronENST00000498645ENST00000490035LSAMPchr3

115535161

-LSAMPchr3

115559759

-
intron-intronENST00000498645ENST00000498645LSAMPchr3

115527614

+LSAMPchr3

115527730

-
intron-intronENST00000498645ENST00000498645LSAMPchr3

115915126

+LSAMPchr3

115914871

-
intron-intronENST00000498645ENST00000498645LSAMPchr3

115535161

-LSAMPchr3

115559759

-
intron-intronENST00000498645ENST00000539563LSAMPchr3

115527614

+LSAMPchr3

115527730

-
intron-intronENST00000498645ENST00000539563LSAMPchr3

115915126

+LSAMPchr3

115914871

-
intron-intronENST00000498645ENST00000539563LSAMPchr3

115535161

-LSAMPchr3

115559759

-
intron-intronENST00000539563ENST00000490035LSAMPchr3

115915126

+LSAMPchr3

115914871

-
intron-intronENST00000539563ENST00000490035LSAMPchr3

115535161

-LSAMPchr3

115559759

-
intron-intronENST00000539563ENST00000498645LSAMPchr3

115527614

+LSAMPchr3

115527730

-
intron-intronENST00000539563ENST00000498645LSAMPchr3

115915126

+LSAMPchr3

115914871

-
intron-intronENST00000539563ENST00000498645LSAMPchr3

115535161

-LSAMPchr3

115559759

-
intron-intronENST00000539563ENST00000539563LSAMPchr3

115527614

+LSAMPchr3

115527730

-
intron-intronENST00000539563ENST00000539563LSAMPchr3

115915126

+LSAMPchr3

115914871

-
intron-intronENST00000539563ENST00000539563LSAMPchr3

115535161

-LSAMPchr3

115559759

-

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 LSAMP-LSAMP


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 LSAMP-LSAMP


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/:116163718/:115571468)
- 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
LSAMP

Q13449

LSAMP

Q13449

FUNCTION: Mediates selective neuronal growth and axon targeting. Contributes to the guidance of developing axons and remodeling of mature circuits in the limbic system. Essential for normal growth of the hyppocampal mossy fiber projection (By similarity). {ECO:0000250}.FUNCTION: Mediates selective neuronal growth and axon targeting. Contributes to the guidance of developing axons and remodeling of mature circuits in the limbic system. Essential for normal growth of the hyppocampal mossy fiber projection (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 LSAMP-LSAMP


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 LSAMP-LSAMP


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 LSAMP-LSAMP


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 LSAMP-LSAMP


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