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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:MLXIPL-LSM2 (FusionGDB2 ID:54354)

Fusion Gene Summary for MLXIPL-LSM2

check button Fusion gene summary
Fusion gene informationFusion gene name: MLXIPL-LSM2
Fusion gene ID: 54354
HgeneTgene
Gene symbol

MLXIPL

LSM2

Gene ID

51085

57819

Gene nameMLX interacting protein likeLSM2 homolog, U6 small nuclear RNA and mRNA degradation associated
SynonymsCHREBP|MIO|MLX|MONDOB|WBSCR14|WS-bHLH|bHLHd14C6orf28|G7B|YBL026W|snRNP
Cytomap

7q11.23

6p21.33

Type of geneprotein-codingprotein-coding
Descriptioncarbohydrate-responsive element-binding proteinMlx interactorWS basic-helix-loop-helix leucine zipper proteinWilliams Beuren syndrome chromosome region 14Williams-Beuren syndrome chromosome region 14 protein 1Williams-Beuren syndrome chromosome regioU6 snRNA-associated Sm-like protein LSm2LSM2 U6 small nuclear RNA and mRNA degradation associatedLSM2 homolog, U6 small nuclear RNA associatedprotein G7bsmall nuclear ribonuclear protein D homologsnRNP core Sm-like protein Sm-x5
Modification date2020031320200320
UniProtAcc

Q9NP71

Q9Y333

Ensembl transtripts involved in fusion geneENST00000313375, ENST00000354613, 
ENST00000395189, ENST00000414749, 
ENST00000429400, ENST00000434326, 
ENST00000375661, ENST00000383391, 
ENST00000424975, ENST00000432122, 
ENST00000434125, ENST00000455705, 
ENST00000467102, ENST00000474526, 
ENST00000477511, ENST00000483453, 
ENST00000491421, ENST00000493146, 
Fusion gene scores* DoF score1 X 1 X 1=13 X 7 X 3=63
# samples 15
** MAII scorelog2(1/1*10)=3.32192809488736log2(5/63*10)=-0.333423733725192
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MLXIPL [Title/Abstract] AND LSM2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMLXIPL(73030097)-LSM2(31773419), # 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
TgeneLSM2

GO:0000244

spliceosomal tri-snRNP complex assembly

10523320

TgeneLSM2

GO:0000398

mRNA splicing, via spliceosome

28781166

TgeneLSM2

GO:0006402

mRNA catabolic process

12515382


check buttonFusion gene breakpoints across MLXIPL (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 LSM2 (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/AAA557579MLXIPLchr7

73030097

+LSM2chr6

31773419

-


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Fusion Gene ORF analysis for MLXIPL-LSM2

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-intronENST00000313375ENST00000375661MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000313375ENST00000383391MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000313375ENST00000424975MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000313375ENST00000432122MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000313375ENST00000434125MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000313375ENST00000455705MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000313375ENST00000467102MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000313375ENST00000474526MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000313375ENST00000477511MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000313375ENST00000483453MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000313375ENST00000491421MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000313375ENST00000493146MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000354613ENST00000375661MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000354613ENST00000383391MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000354613ENST00000424975MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000354613ENST00000432122MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000354613ENST00000434125MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000354613ENST00000455705MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000354613ENST00000467102MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000354613ENST00000474526MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000354613ENST00000477511MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000354613ENST00000483453MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000354613ENST00000491421MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000354613ENST00000493146MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000395189ENST00000375661MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000395189ENST00000383391MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000395189ENST00000424975MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000395189ENST00000432122MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000395189ENST00000434125MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000395189ENST00000455705MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000395189ENST00000467102MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000395189ENST00000474526MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000395189ENST00000477511MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000395189ENST00000483453MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000395189ENST00000491421MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000395189ENST00000493146MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000414749ENST00000375661MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000414749ENST00000383391MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000414749ENST00000424975MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000414749ENST00000432122MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000414749ENST00000434125MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000414749ENST00000455705MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000414749ENST00000467102MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000414749ENST00000474526MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000414749ENST00000477511MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000414749ENST00000483453MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000414749ENST00000491421MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000414749ENST00000493146MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000429400ENST00000375661MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000429400ENST00000383391MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000429400ENST00000424975MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000429400ENST00000432122MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000429400ENST00000434125MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000429400ENST00000455705MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000429400ENST00000467102MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000429400ENST00000474526MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000429400ENST00000477511MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000429400ENST00000483453MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000429400ENST00000491421MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000429400ENST00000493146MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000434326ENST00000375661MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000434326ENST00000383391MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000434326ENST00000424975MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000434326ENST00000432122MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000434326ENST00000434125MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000434326ENST00000455705MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000434326ENST00000467102MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000434326ENST00000474526MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000434326ENST00000477511MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000434326ENST00000483453MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000434326ENST00000491421MLXIPLchr7

73030097

+LSM2chr6

31773419

-
intron-intronENST00000434326ENST00000493146MLXIPLchr7

73030097

+LSM2chr6

31773419

-

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 MLXIPL-LSM2


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 MLXIPL-LSM2


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/:73030097/:31773419)
- 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
MLXIPL

Q9NP71

LSM2

Q9Y333

FUNCTION: Transcriptional repressor. Binds to the canonical and non-canonical E box sequences 5'-CACGTG-3' (By similarity). {ECO:0000250}.FUNCTION: Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA (PubMed:10523320). {ECO:0000269|PubMed:10523320, ECO:0000269|PubMed:28781166}.

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 MLXIPL-LSM2


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 MLXIPL-LSM2


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 MLXIPL-LSM2


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 MLXIPL-LSM2


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