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:LCN2-LMX1B (FusionGDB2 ID:44255)

Fusion Gene Summary for LCN2-LMX1B

check button Fusion gene summary
Fusion gene informationFusion gene name: LCN2-LMX1B
Fusion gene ID: 44255
HgeneTgene
Gene symbol

LCN2

LMX1B

Gene ID

3934

4010

Gene namelipocalin 2LIM homeobox transcription factor 1 beta
Synonyms24p3|MSFI|NGAL|p25LMX1.2|NPS1
Cytomap

9q34.11

9q33.3

Type of geneprotein-codingprotein-coding
Descriptionneutrophil gelatinase-associated lipocalin25 kDa alpha-2-microglobulin-related subunit of MMP-9migration-stimulating factor inhibitoroncogene 24p3siderocalin LCN2LIM homeobox transcription factor 1-betaLIM/homeobox protein 1.2LMX-1.2
Modification date2020032920200313
UniProtAcc

P80188

O60663

Ensembl transtripts involved in fusion geneENST00000277480, ENST00000372998, 
ENST00000373013, ENST00000373017, 
ENST00000470902, ENST00000540948, 
ENST00000355497, ENST00000373474, 
ENST00000425646, ENST00000526117, 
ENST00000561065, 
Fusion gene scores* DoF score6 X 5 X 4=1208 X 7 X 5=280
# samples 710
** MAII scorelog2(7/120*10)=-0.777607578663552
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/280*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LCN2 [Title/Abstract] AND LMX1B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLCN2(130915405)-LMX1B(129458117), # samples:1
LCN2(130915405)-LMX1B(129458118), # 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
HgeneLCN2

GO:0042742

defense response to bacterium

27780864

HgeneLCN2

GO:0097577

sequestering of iron ion

27780864

TgeneLMX1B

GO:0006355

regulation of transcription, DNA-templated

10767331


check buttonFusion gene breakpoints across LCN2 (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 LMX1B (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
ChimerDB4OVTCGA-09-2045-01ALCN2chr9

130915405

+LMX1Bchr9

129458118

+
ChimerDB4OVTCGA-09-2045LCN2chr9

130915405

+LMX1Bchr9

129458117

+


Top

Fusion Gene ORF analysis for LCN2-LMX1B

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-3CDSENST00000277480ENST00000355497LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000277480ENST00000355497LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000277480ENST00000373474LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000277480ENST00000373474LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000277480ENST00000425646LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000277480ENST00000425646LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000277480ENST00000526117LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000277480ENST00000526117LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000277480ENST00000561065LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000277480ENST00000561065LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000372998ENST00000355497LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000372998ENST00000355497LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000372998ENST00000373474LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000372998ENST00000373474LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000372998ENST00000425646LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000372998ENST00000425646LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000372998ENST00000526117LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000372998ENST00000526117LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000372998ENST00000561065LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000372998ENST00000561065LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000373013ENST00000355497LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000373013ENST00000355497LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000373013ENST00000373474LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000373013ENST00000373474LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000373013ENST00000425646LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000373013ENST00000425646LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000373013ENST00000526117LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000373013ENST00000526117LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000373013ENST00000561065LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000373013ENST00000561065LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000373017ENST00000355497LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000373017ENST00000355497LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000373017ENST00000373474LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000373017ENST00000373474LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000373017ENST00000425646LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000373017ENST00000425646LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000373017ENST00000526117LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000373017ENST00000526117LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000373017ENST00000561065LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000373017ENST00000561065LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000470902ENST00000355497LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000470902ENST00000355497LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000470902ENST00000373474LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000470902ENST00000373474LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000470902ENST00000425646LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000470902ENST00000425646LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000470902ENST00000526117LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000470902ENST00000526117LCN2chr9

130915405

+LMX1Bchr9

129458117

+
3UTR-3CDSENST00000470902ENST00000561065LCN2chr9

130915405

+LMX1Bchr9

129458118

+
3UTR-3CDSENST00000470902ENST00000561065LCN2chr9

130915405

+LMX1Bchr9

129458117

+
intron-3CDSENST00000540948ENST00000355497LCN2chr9

130915405

+LMX1Bchr9

129458118

+
intron-3CDSENST00000540948ENST00000355497LCN2chr9

130915405

+LMX1Bchr9

129458117

+
intron-3CDSENST00000540948ENST00000373474LCN2chr9

130915405

+LMX1Bchr9

129458118

+
intron-3CDSENST00000540948ENST00000373474LCN2chr9

130915405

+LMX1Bchr9

129458117

+
intron-3CDSENST00000540948ENST00000425646LCN2chr9

130915405

+LMX1Bchr9

129458118

+
intron-3CDSENST00000540948ENST00000425646LCN2chr9

130915405

+LMX1Bchr9

129458117

+
intron-3CDSENST00000540948ENST00000526117LCN2chr9

130915405

+LMX1Bchr9

129458118

+
intron-3CDSENST00000540948ENST00000526117LCN2chr9

130915405

+LMX1Bchr9

129458117

+
intron-3CDSENST00000540948ENST00000561065LCN2chr9

130915405

+LMX1Bchr9

129458118

+
intron-3CDSENST00000540948ENST00000561065LCN2chr9

130915405

+LMX1Bchr9

129458117

+

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 LCN2-LMX1B


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)
LCN2chr9130915405+LMX1Bchr9129458117+0.280996050.719004
LCN2chr9130915405+LMX1Bchr9129458117+0.280996050.719004
LCN2chr9130915405+LMX1Bchr9129458117+0.280996050.719004
LCN2chr9130915405+LMX1Bchr9129458117+0.280996050.719004

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%

Top

Fusion Protein Features for LCN2-LMX1B


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/:130915405/:129458117)
- 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
LCN2

P80188

LMX1B

O60663

FUNCTION: Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development (PubMed:12453413, PubMed:27780864, PubMed:20581821). Binds iron through association with 2,3-dihydroxybenzoic acid (2,3-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis (By similarity). Involved in innate immunity; limits bacterial proliferation by sequestering iron bound to microbial siderophores, such as enterobactin (PubMed:27780864). Can also bind siderophores from M.tuberculosis (PubMed:15642259, PubMed:21978368). {ECO:0000250|UniProtKB:P11672, ECO:0000269|PubMed:12453413, ECO:0000269|PubMed:15642259, ECO:0000269|PubMed:20581821, ECO:0000269|PubMed:21978368, ECO:0000269|PubMed:27780864}.FUNCTION: Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels.

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 LCN2-LMX1B


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 LCN2-LMX1B


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 LCN2-LMX1B


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 LCN2-LMX1B


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