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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:LGALS3-HN1L (FusionGDB2 ID:44541)

Fusion Gene Summary for LGALS3-HN1L

check button Fusion gene summary
Fusion gene informationFusion gene name: LGALS3-HN1L
Fusion gene ID: 44541
HgeneTgene
Gene symbol

LGALS3

HN1L

Gene ID

3958

90861

Gene namegalectin 3Jupiter microtubule associated homolog 2
SynonymsCBP35|GAL3|GALBP|GALIG|L31|LGALS2|MAC2C16orf34|HN1L|L11
Cytomap

14q22.3

16p13.3

Type of geneprotein-codingprotein-coding
Descriptiongalectin-335 kDa lectinIgE-binding proteinMAC-2 antigenadvanced glycation end-product receptor 3carbohydrate-binding protein 35epididymis secretory sperm binding proteingalactose-specific lectin 3laminin-binding proteinlectin L-29lectin, galactojupiter microtubule associated homolog 2CRAMP_1 likeHN1 likeHN1-like proteinhematological and neurological expressed 1 likehematological and neurological expressed 1-like protein
Modification date2020032220200313
UniProtAcc

P17931

.
Ensembl transtripts involved in fusion geneENST00000553755, ENST00000254301, 
ENST00000554715, 		ENST00000382710, 
ENST00000382711, ENST00000569765, 
ENST00000248098, ENST00000561516, 
ENST00000562684, ENST00000569256, 
Fusion gene scores* DoF score18 X 6 X 8=86414 X 10 X 9=1260
# samples 1815
** MAII scorelog2(18/864*10)=-2.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/1260*10)=-3.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LGALS3 [Title/Abstract] AND HN1L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLGALS3(55596018)-HN1L(1735440), # 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
HgeneLGALS3

GO:0002548

monocyte chemotaxis

10925302

HgeneLGALS3

GO:0030593

neutrophil chemotaxis

10925302

HgeneLGALS3

GO:0031334

positive regulation of protein complex assembly

24846175

HgeneLGALS3

GO:0045806

negative regulation of endocytosis

19706535

HgeneLGALS3

GO:0048245

eosinophil chemotaxis

10925302

HgeneLGALS3

GO:0048246

macrophage chemotaxis

10925302

HgeneLGALS3

GO:0050918

positive chemotaxis

10925302

HgeneLGALS3

GO:0070232

regulation of T cell apoptotic process

8692888

HgeneLGALS3

GO:0071674

mononuclear cell migration

10925302

HgeneLGALS3

GO:0071677

positive regulation of mononuclear cell migration

10925302

HgeneLGALS3

GO:0090280

positive regulation of calcium ion import

10925302

HgeneLGALS3

GO:1903078

positive regulation of protein localization to plasma membrane

24846175

HgeneLGALS3

GO:2001200

positive regulation of dendritic cell differentiation

16116184

HgeneLGALS3

GO:2001237

negative regulation of extrinsic apoptotic signaling pathway

22761016


check buttonFusion gene breakpoints across LGALS3 (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 HN1L (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
ChimerDB4Non-CancerTCGA-BR-6802-11ALGALS3chr14

55596018

+HN1Lchr16

1735440

+


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Fusion Gene ORF analysis for LGALS3-HN1L

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
3UTR-5UTRENST00000553755ENST00000382710LGALS3chr14

55596018

+HN1Lchr16

1735440

+
3UTR-5UTRENST00000553755ENST00000382711LGALS3chr14

55596018

+HN1Lchr16

1735440

+
3UTR-5UTRENST00000553755ENST00000569765LGALS3chr14

55596018

+HN1Lchr16

1735440

+
3UTR-intronENST00000553755ENST00000248098LGALS3chr14

55596018

+HN1Lchr16

1735440

+
3UTR-intronENST00000553755ENST00000561516LGALS3chr14

55596018

+HN1Lchr16

1735440

+
3UTR-intronENST00000553755ENST00000562684LGALS3chr14

55596018

+HN1Lchr16

1735440

+
3UTR-intronENST00000553755ENST00000569256LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-5UTRENST00000254301ENST00000382710LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-5UTRENST00000254301ENST00000382711LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-5UTRENST00000254301ENST00000569765LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-5UTRENST00000554715ENST00000382710LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-5UTRENST00000554715ENST00000382711LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-5UTRENST00000554715ENST00000569765LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-intronENST00000254301ENST00000248098LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-intronENST00000254301ENST00000561516LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-intronENST00000254301ENST00000562684LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-intronENST00000254301ENST00000569256LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-intronENST00000554715ENST00000248098LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-intronENST00000554715ENST00000561516LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-intronENST00000554715ENST00000562684LGALS3chr14

55596018

+HN1Lchr16

1735440

+
5UTR-intronENST00000554715ENST00000569256LGALS3chr14

55596018

+HN1Lchr16

1735440

+

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 LGALS3-HN1L


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)
LGALS3chr1455596018+HN1Lchr161735439+9.60E-050.99990404
LGALS3chr1455596018+HN1Lchr161735439+9.60E-050.99990404

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 LGALS3-HN1L


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/:55596018/:1735440)
- 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
LGALS3

P17931

.
FUNCTION: Galactose-specific lectin which binds IgE. May mediate with the alpha-3, beta-1 integrin the stimulation by CSPG4 of endothelial cells migration. Together with DMBT1, required for terminal differentiation of columnar epithelial cells during early embryogenesis (By similarity). In the nucleus: acts as a pre-mRNA splicing factor. Involved in acute inflammatory responses including neutrophil activation and adhesion, chemoattraction of monocytes macrophages, opsonization of apoptotic neutrophils, and activation of mast cells. Together with TRIM16, coordinates the recognition of membrane damage with mobilization of the core autophagy regulators ATG16L1 and BECN1 in response to damaged endomembranes. {ECO:0000250, ECO:0000269|PubMed:15181153, ECO:0000269|PubMed:19594635, ECO:0000269|PubMed:19616076, ECO:0000269|PubMed:27693506}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (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 LGALS3-HN1L


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 LGALS3-HN1L


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 LGALS3-HN1L


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 LGALS3-HN1L


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