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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:MANBA-LIMCH1 (FusionGDB2 ID:51129)

Fusion Gene Summary for MANBA-LIMCH1

check button Fusion gene summary
Fusion gene informationFusion gene name: MANBA-LIMCH1
Fusion gene ID: 51129
HgeneTgene
Gene symbol

MANBA

LIMCH1

Gene ID

4126

22998

Gene namemannosidase betaLIM and calponin homology domains 1
SynonymsMANB1LIMCH1A|LMO7B
Cytomap

4q24

4p13

Type of geneprotein-codingprotein-coding
Descriptionbeta-mannosidasebeta-mannosidase Alysosomal beta A mannosidasemannanasemannasemannosidase, beta A, lysosomalLIM and calponin homology domains-containing protein 1
Modification date2020031320200313
UniProtAcc

O00462

Q9UPQ0

Ensembl transtripts involved in fusion geneENST00000226578, ENST00000505239, 
ENST00000313860, ENST00000503057, 
ENST00000508501, ENST00000509638, 
ENST00000511496, ENST00000512632, 
ENST00000512820, ENST00000512946, 
ENST00000513024, ENST00000381753, 
ENST00000396595, ENST00000509277, 
ENST00000509454, ENST00000514096, 
ENST00000515785, 
Fusion gene scores* DoF score4 X 4 X 4=6418 X 19 X 9=3078
# samples 519
** MAII scorelog2(5/64*10)=-0.356143810225275
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/3078*10)=-4.01792190799726
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MANBA [Title/Abstract] AND LIMCH1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMANBA(103681875)-LIMCH1(41600937), # samples:3
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

check buttonFusion gene breakpoints across MANBA (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 LIMCH1 (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-22-5481-01AMANBAchr4

103681875

-LIMCH1chr4

41600937

+
ChimerDB4LUSCTCGA-22-5481MANBAchr4

103681875

-LIMCH1chr4

41600937

+


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Fusion Gene ORF analysis for MANBA-LIMCH1

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-5UTRENST00000226578ENST00000313860MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000226578ENST00000503057MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000226578ENST00000508501MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000226578ENST00000509638MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000226578ENST00000511496MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000226578ENST00000512632MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000226578ENST00000512820MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000226578ENST00000512946MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000226578ENST00000513024MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000505239ENST00000313860MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000505239ENST00000503057MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000505239ENST00000508501MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000505239ENST00000509638MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000505239ENST00000511496MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000505239ENST00000512632MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000505239ENST00000512820MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000505239ENST00000512946MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-5UTRENST00000505239ENST00000513024MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-intronENST00000226578ENST00000381753MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-intronENST00000226578ENST00000396595MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-intronENST00000226578ENST00000509277MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-intronENST00000226578ENST00000509454MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-intronENST00000226578ENST00000514096MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-intronENST00000226578ENST00000515785MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-intronENST00000505239ENST00000381753MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-intronENST00000505239ENST00000396595MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-intronENST00000505239ENST00000509277MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-intronENST00000505239ENST00000509454MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-intronENST00000505239ENST00000514096MANBAchr4

103681875

-LIMCH1chr4

41600937

+
5CDS-intronENST00000505239ENST00000515785MANBAchr4

103681875

-LIMCH1chr4

41600937

+

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 MANBA-LIMCH1


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.
genomic feature of top 1%

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Fusion Protein Features for MANBA-LIMCH1


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/:103681875/:41600937)
- 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
MANBA

O00462

LIMCH1

Q9UPQ0

FUNCTION: Exoglycosidase that cleaves the single beta-linked mannose residue from the non-reducing end of all N-linked glycoprotein oligosaccharides. {ECO:0000305|PubMed:12890191, ECO:0000305|PubMed:30552791}.FUNCTION: Actin stress fibers-associated protein that activates non-muscle myosin IIa. Activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. Through the activation of non-muscle myosin IIa, positively regulates actin stress fibers assembly and stabilizes focal adhesions. It therefore negatively regulates cell spreading and cell migration. {ECO:0000269|PubMed:28228547}.

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 MANBA-LIMCH1


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 MANBA-LIMCH1


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 MANBA-LIMCH1


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 MANBA-LIMCH1


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