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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:LRWD1-CUX1 (FusionGDB2 ID:50152)

Fusion Gene Summary for LRWD1-CUX1

check button Fusion gene summary
Fusion gene informationFusion gene name: LRWD1-CUX1
Fusion gene ID: 50152
HgeneTgene
Gene symbol

LRWD1

CUX1

Gene ID

222229

1523

Gene nameleucine rich repeats and WD repeat domain containing 1cut like homeobox 1
SynonymsCENP-33|ORCACASP|CDP|CDP/Cut|CDP1|COY1|CUTL1|CUX|Clox|Cux/CDP|GDDI|GOLIM6|Nbla10317|p100|p110|p200|p75
Cytomap

7q22.1

7q22.1

Type of geneprotein-codingprotein-coding
Descriptionleucine-rich repeat and WD repeat-containing protein 1ORC-associated proteincentromere protein 33origin recognition complex-associated proteintesticular tissue protein Li 4protein CASPHomeobox protein cut-like 1CCAAT displacement proteinCUX1 gene Alternatively Spliced Productcut homologgolgi integral membrane protein 6homeobox protein cux-1putative protein product of Nbla10317
Modification date2020031320200320
UniProtAcc

Q9UFC0

P39880

Ensembl transtripts involved in fusion geneENST00000292616, ENST00000560541, 
ENST00000292535, ENST00000360264, 
ENST00000425244, ENST00000546411, 
ENST00000549414, ENST00000550008, 
ENST00000556210, ENST00000292538, 
ENST00000393824, ENST00000437600, 
ENST00000547394, 
Fusion gene scores* DoF score3 X 4 X 3=3626 X 23 X 9=5382
# samples 329
** MAII scorelog2(3/36*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(29/5382*10)=-4.21401758562548
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LRWD1 [Title/Abstract] AND CUX1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLRWD1(102105607)-CUX1(101916637), # samples:1
LRWD1(102105625)-CUX1(101916637), # samples:1
Anticipated loss of major functional domain due to fusion event.LRWD1-CUX1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
LRWD1-CUX1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
LRWD1-CUX1 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
LRWD1-CUX1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
LRWD1-CUX1 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
LRWD1-CUX1 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
HgeneLRWD1

GO:0071169

establishment of protein localization to chromatin

20932478


check buttonFusion gene breakpoints across LRWD1 (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 CUX1 (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
ChimerDB4STADTCGA-BR-A4QI-01ALRWD1chr7

102105607

+CUX1chr7

101916637

+
ChimerDB4STADTCGA-BR-A4QI-01ALRWD1chr7

102105625

+CUX1chr7

101916637

+


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Fusion Gene ORF analysis for LRWD1-CUX1

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-3UTRENST00000292616ENST00000560541LRWD1chr7

102105607

+CUX1chr7

101916637

+
5CDS-intronENST00000292616ENST00000292535LRWD1chr7

102105607

+CUX1chr7

101916637

+
5CDS-intronENST00000292616ENST00000360264LRWD1chr7

102105607

+CUX1chr7

101916637

+
5CDS-intronENST00000292616ENST00000425244LRWD1chr7

102105607

+CUX1chr7

101916637

+
5CDS-intronENST00000292616ENST00000546411LRWD1chr7

102105607

+CUX1chr7

101916637

+
5CDS-intronENST00000292616ENST00000549414LRWD1chr7

102105607

+CUX1chr7

101916637

+
5CDS-intronENST00000292616ENST00000550008LRWD1chr7

102105607

+CUX1chr7

101916637

+
5CDS-intronENST00000292616ENST00000556210LRWD1chr7

102105607

+CUX1chr7

101916637

+
Frame-shiftENST00000292616ENST00000292538LRWD1chr7

102105607

+CUX1chr7

101916637

+
Frame-shiftENST00000292616ENST00000393824LRWD1chr7

102105607

+CUX1chr7

101916637

+
Frame-shiftENST00000292616ENST00000437600LRWD1chr7

102105607

+CUX1chr7

101916637

+
Frame-shiftENST00000292616ENST00000547394LRWD1chr7

102105607

+CUX1chr7

101916637

+
intron-3CDSENST00000292616ENST00000292538LRWD1chr7

102105625

+CUX1chr7

101916637

+
intron-3CDSENST00000292616ENST00000393824LRWD1chr7

102105625

+CUX1chr7

101916637

+
intron-3CDSENST00000292616ENST00000437600LRWD1chr7

102105625

+CUX1chr7

101916637

+
intron-3CDSENST00000292616ENST00000547394LRWD1chr7

102105625

+CUX1chr7

101916637

+
intron-3UTRENST00000292616ENST00000560541LRWD1chr7

102105625

+CUX1chr7

101916637

+
intron-intronENST00000292616ENST00000292535LRWD1chr7

102105625

+CUX1chr7

101916637

+
intron-intronENST00000292616ENST00000360264LRWD1chr7

102105625

+CUX1chr7

101916637

+
intron-intronENST00000292616ENST00000425244LRWD1chr7

102105625

+CUX1chr7

101916637

+
intron-intronENST00000292616ENST00000546411LRWD1chr7

102105625

+CUX1chr7

101916637

+
intron-intronENST00000292616ENST00000549414LRWD1chr7

102105625

+CUX1chr7

101916637

+
intron-intronENST00000292616ENST00000550008LRWD1chr7

102105625

+CUX1chr7

101916637

+
intron-intronENST00000292616ENST00000556210LRWD1chr7

102105625

+CUX1chr7

101916637

+

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 LRWD1-CUX1


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)
LRWD1chr7102105607+CUX1chr7101916636+0.0002688110.9997311
LRWD1chr7102105607+CUX1chr7101916636+0.0002688110.9997311

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 LRWD1-CUX1


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/:102105607/:101916637)
- 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
LRWD1

Q9UFC0

CUX1

P39880

FUNCTION: Required for G1/S transition. Recruits and stabilizes the origin recognition complex (ORC) onto chromatin during G1 to establish pre-replication complex (preRC) and to heterochromatic sites in post-replicated cells. Binds a combination of DNA and histone methylation repressive marks on heterochromatin. Binds histone H3 and H4 trimethylation marks H3K9me3, H3K27me3 and H4K20me3 in a cooperative manner with DNA methylation. Required for silencing of major satellite repeats. May be important ORC2, ORC3 and ORC4 stability. {ECO:0000269|PubMed:20850016, ECO:0000269|PubMed:20932478, ECO:0000269|PubMed:21029866, ECO:0000269|PubMed:22427655, ECO:0000269|PubMed:22645314}.FUNCTION: Transcription factor involved in the control of neuronal differentiation in the brain. Regulates dendrite development and branching, and dendritic spine formation in cortical layers II-III. Also involved in the control of synaptogenesis. In addition, it has probably a broad role in mammalian development as a repressor of developmentally regulated gene expression. May act by preventing binding of positively-activing CCAAT factors to promoters. Component of nf-munr repressor; binds to the matrix attachment regions (MARs) (5' and 3') of the immunoglobulin heavy chain enhancer. Represses T-cell receptor (TCR) beta enhancer function by binding to MARbeta, an ATC-rich DNA sequence located upstream of the TCR beta enhancer. Binds to the TH enhancer; may require the basic helix-loop-helix protein TCF4 as a coactivator. {ECO:0000250|UniProtKB:P53564}.; FUNCTION: [CDP/Cux p110]: Plays a role in cell cycle progression, in particular at the G1/S transition. As cells progress into S phase, a fraction of CUX1 molecules is proteolytically processed into N-terminally truncated proteins of 110 kDa. While CUX1 only transiently binds to DNA and carries the CCAAT-displacement activity, CDP/Cux p110 makes a stable interaction with DNA and stimulates expression of genes such as POLA1. {ECO:0000269|PubMed:15099520}.

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 LRWD1-CUX1


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 LRWD1-CUX1


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 LRWD1-CUX1


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 LRWD1-CUX1


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