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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 20146

FusionGeneSummary for LRP4_CELF1

check button Fusion gene summary
Fusion gene informationFusion gene name: LRP4_CELF1
Fusion gene ID: 20146
HgeneTgene
Gene symbol

LRP4

CELF1

Gene ID

4038

10658

Gene nameLDL receptor related protein 4CUGBP Elav-like family member 1
SynonymsCLSS|CMS17|LRP-4|LRP10|MEGF7|SOST2BRUNOL2|CUG-BP|CUGBP|CUGBP1|EDEN-BP|NAB50|NAPOR|hNab50
Cytomap

11p11.2

11p11.2

Type of geneprotein-codingprotein-coding
Descriptionlow-density lipoprotein receptor-related protein 4multiple epidermal growth factor-like domains 7CUGBP Elav-like family member 150 kDa nuclear polyadenylated RNA-binding proteinCELF-1CUG RNA-binding proteinCUG triplet repeat RNA-binding protein 1CUG-BP- and ETR-3-like factor 1CUG-BP1EDEN-BP homologRNA-binding protein BRUNOL-2bruno-like 2bru
Modification date2018051920180523
UniProtAcc

O75096

Q92879

Ensembl transtripts involved in fusion geneENST00000378623, ENST00000395290, 
ENST00000358597, ENST00000395292, 
ENST00000310513, ENST00000361904, 
ENST00000539455, ENST00000531165, 
ENST00000532048, 
Fusion gene scores* DoF score4 X 4 X 4=646 X 7 X 3=126
# samples 48
** MAII scorelog2(4/64*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/126*10)=-0.655351828612554
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LRP4 [Title/Abstract] AND CELF1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneLRP4

GO:0001822

kidney development

20381006

HgeneLRP4

GO:0060173

limb development

20381006

HgeneLRP4

GO:0090090

negative regulation of canonical Wnt signaling pathway

20093106

TgeneCELF1

GO:0006376

mRNA splice site selection

11158314

TgeneCELF1

GO:0043484

regulation of RNA splicing

16946708


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVOVTCGA-13-A5FT-01ALRP4chr11

46905422

-CELF1chr11

47510576

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
Frame-shiftENST00000378623ENST00000395290LRP4chr11

46905422

-CELF1chr11

47510576

-
5CDS-intronENST00000378623ENST00000358597LRP4chr11

46905422

-CELF1chr11

47510576

-
5CDS-5UTRENST00000378623ENST00000395292LRP4chr11

46905422

-CELF1chr11

47510576

-
5CDS-5UTRENST00000378623ENST00000310513LRP4chr11

46905422

-CELF1chr11

47510576

-
5CDS-5UTRENST00000378623ENST00000361904LRP4chr11

46905422

-CELF1chr11

47510576

-
5CDS-intronENST00000378623ENST00000539455LRP4chr11

46905422

-CELF1chr11

47510576

-
5CDS-intronENST00000378623ENST00000531165LRP4chr11

46905422

-CELF1chr11

47510576

-
5CDS-intronENST00000378623ENST00000532048LRP4chr11

46905422

-CELF1chr11

47510576

-

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FusionProtFeatures for LRP4_CELF1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LRP4

O75096

CELF1

Q92879

Mediates SOST-dependent inhibition of bone formation.Functions as a specific facilitator of SOST-mediated inhibition ofWnt signaling. Plays a key role in the formation and themaintenance of the neuromuscular junction (NMJ), the synapsebetween motor neuron and skeletal muscle. Directly binds AGRIN andrecruits it to the MUSK signaling complex. Mediates the AGRIN-induced phosphorylation of MUSK, the kinase of the complex. Theactivation of MUSK in myotubes induces the formation of NMJ byregulating different processes including the transcription ofspecific genes and the clustering of AChR in the postsynapticmembrane. Alternatively, may be involved in the negativeregulation of the canonical Wnt signaling pathway, being able toantagonize the LRP6-mediated activation of this pathway. Moregenerally, has been proposed to function as a cell surfaceendocytic receptor binding and internalizing extracellular ligandsfor degradation by lysosomes. May play an essential role in theprocess of digit differentiation (By similarity).{ECO:0000250|UniProtKB:Q8VI56, ECO:0000269|PubMed:20381006,ECO:0000269|PubMed:21471202}. RNA-binding protein implicated in the regulation ofseveral post-transcriptional events. Involved in pre-mRNAalternative splicing, mRNA translation and stability. Mediatesexon inclusion and/or exclusion in pre-mRNA that are subject totissue-specific and developmentally regulated alternativesplicing. Specifically activates exon 5 inclusion of cardiacisoforms of TNNT2 during heart remodeling at the juvenile to adulttransition. Acts as both an activator and repressor of a pair ofcoregulated exons: promotes inclusion of the smooth muscle (SM)exon but exclusion of the non-muscle (NM) exon in actinin pre-mRNAs. Activates SM exon 5 inclusion by antagonizing therepressive effect of PTB. Promotes exclusion of exon 11 of theINSR pre-mRNA. Inhibits, together with HNRNPH1, insulin receptor(IR) pre-mRNA exon 11 inclusion in myoblast. Increases translationand controls the choice of translation initiation codon of CEBPBmRNA. Increases mRNA translation of CEBPB in aging liver (Bysimilarity). Increases translation of CDKN1A mRNA by antagonizingthe repressive effect of CALR3. Mediates rapid cytoplasmic mRNAdeadenylation. Recruits the deadenylase PARN to the poly(A) tailof EDEN-containing mRNAs to promote their deadenylation. Requiredfor completion of spermatogenesis (By similarity). Binds to (CUG)ntriplet repeats in the 3'-UTR of transcripts such as DMPK and toBruno response elements (BREs). Binds to muscle-specific splicingenhancer (MSE) intronic sites flanking the alternative exon 5 ofTNNT2 pre-mRNA. Binds to AU-rich sequences (AREs or EDEN-like)localized in the 3'-UTR of JUN and FOS mRNAs. Binds to the IR RNA.Binds to the 5'-region of CDKN1A and CEBPB mRNAs. Binds with the5'-region of CEBPB mRNA in aging liver. May be a specificregulator of miRNA biogenesis. Binds to primary microRNA pri-MIR140 and, with CELF2, negatively regulates the processing tomature miRNA (PubMed:28431233). {ECO:0000250,ECO:0000269|PubMed:10536163, ECO:0000269|PubMed:11124939,ECO:0000269|PubMed:11158314, ECO:0000269|PubMed:12649496,ECO:0000269|PubMed:12799066, ECO:0000269|PubMed:14726956,ECO:0000269|PubMed:16601207, ECO:0000269|PubMed:16946708,ECO:0000269|PubMed:28431233}.

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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FusionGeneSequence for LRP4_CELF1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for LRP4_CELF1


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
LRP4DFNB31, ARRB1, PID1, BEND7, VASP, ZSCAN26, ZNF621, ZFP41, EXOSC5, LRPAP1, ZNF354C, GDF10, ZNF331, ZNF408, ZNF398, ZNF224, ZNF669, FCGRT, ZNF816, SOST, TYW3, ZNF556, ZBBX, ZNF214, ZNF563CELF1PPBP, FUBP1, TOM1L1, USP10, ELAVL1, APP, HNRNPC, RALY, TARDBP, RPA3, RPA2, RPA1, BMI1, CDK8, MKNK2, KIF2A, MAPK3, VPS26A, CCDC88A, CERK, CEP170P1, TRIM25, G3BP1


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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RelatedDrugs for LRP4_CELF1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for LRP4_CELF1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLRP4C3280402SCLEROSTEOSIS 22UNIPROT
HgeneLRP4C0039075Syndactyly1CTD_human;HPO
HgeneLRP4C0040427Tooth Abnormalities1CTD_human
HgeneLRP4C1859309Syndactyly Cenani Lenz type1CTD_human;ORPHANET;UNIPROT
HgeneLRP4C4225377MYASTHENIC SYNDROME, CONGENITAL, 171UNIPROT