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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: 28872

FusionGeneSummary for PRPF40B_CDH4

check button Fusion gene summary
Fusion gene informationFusion gene name: PRPF40B_CDH4
Fusion gene ID: 28872
HgeneTgene
Gene symbol

PRPF40B

CDH4

Gene ID

25766

1002

Gene namepre-mRNA processing factor 40 homolog Bcadherin 4
SynonymsHYPCCAD4|R-CAD|RCAD
Cytomap

12q13.12

20q13.33

Type of geneprotein-codingprotein-coding
Descriptionpre-mRNA-processing factor 40 homolog BHuntingtin interacting protein CPRP40 pre-mRNA processing factor 40 homolog Bhuntingtin yeast partner Ccadherin-4R-cadherincadherin 4, type 1, R-cadherin (retinal)cadherin 4, type 1, preproproteinretinal cadherin
Modification date2018052420180523
UniProtAcc

Q6NWY9

P55283

Ensembl transtripts involved in fusion geneENST00000508736, ENST00000548825, 
ENST00000261897, ENST00000380281, 
ENST00000360469, ENST00000543233, 
Fusion gene scores* DoF score6 X 6 X 4=14410 X 6 X 6=360
# samples 610
** MAII scorelog2(6/144*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/360*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PRPF40B [Title/Abstract] AND CDH4 [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

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
TCGARVSARCTCGA-DX-A1KZ-01APRPF40Bchr12

49962506

+CDH4chr20

60448784

+
* 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
intron-3CDSENST00000508736ENST00000360469PRPF40Bchr12

49962506

+CDH4chr20

60448784

+
intron-3CDSENST00000508736ENST00000543233PRPF40Bchr12

49962506

+CDH4chr20

60448784

+
intron-3CDSENST00000548825ENST00000360469PRPF40Bchr12

49962506

+CDH4chr20

60448784

+
intron-3CDSENST00000548825ENST00000543233PRPF40Bchr12

49962506

+CDH4chr20

60448784

+
intron-3CDSENST00000261897ENST00000360469PRPF40Bchr12

49962506

+CDH4chr20

60448784

+
intron-3CDSENST00000261897ENST00000543233PRPF40Bchr12

49962506

+CDH4chr20

60448784

+
intron-3CDSENST00000380281ENST00000360469PRPF40Bchr12

49962506

+CDH4chr20

60448784

+
intron-3CDSENST00000380281ENST00000543233PRPF40Bchr12

49962506

+CDH4chr20

60448784

+

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FusionProtFeatures for PRPF40B_CDH4


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PRPF40B

Q6NWY9

CDH4

P55283

May be involved in pre-mRNA splicing.{ECO:0000269|PubMed:9700202}. Cadherins are calcium-dependent cell adhesion proteins.They preferentially interact with themselves in a homophilicmanner in connecting cells; cadherins may thus contribute to thesorting of heterogeneous cell types. May play an important role inretinal development.

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 PRPF40B_CDH4


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 PRPF40B_CDH4


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
PRPF40BHTT, MECP2, MFAP1, P4HB, RBM25, SF3A3, SRRM2, MYEF2, RGS9, GNB5CDH4CDH2, CDK5RAP3, FUS, UBE2I, CTNNA3, MTNR1B


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 PRPF40B_CDH4


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 PRPF40B_CDH4


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