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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: 8315

FusionGeneSummary for CPSF3_CPSF3

check button Fusion gene summary
Fusion gene informationFusion gene name: CPSF3_CPSF3
Fusion gene ID: 8315
HgeneTgene
Gene symbol

CPSF3

CPSF3

Gene ID

51692

51692

Gene namecleavage and polyadenylation specific factor 3cleavage and polyadenylation specific factor 3
SynonymsCPSF-73|CPSF73CPSF-73|CPSF73
Cytomap

2p25.1

2p25.1

Type of geneprotein-codingprotein-coding
Descriptioncleavage and polyadenylation specificity factor subunit 3cleavage and polyadenylation specific factor 3, 73kDamRNA 3'-end-processing endonuclease CPSF-73cleavage and polyadenylation specificity factor subunit 3cleavage and polyadenylation specific factor 3, 73kDamRNA 3'-end-processing endonuclease CPSF-73
Modification date2018052320180523
UniProtAcc

Q9UKF6

Q9UKF6

Ensembl transtripts involved in fusion geneENST00000238112, ENST00000460593, 
ENST00000489403, 
ENST00000238112, 
ENST00000460593, ENST00000489403, 
Fusion gene scores* DoF score1 X 1 X 1=14 X 4 X 2=32
# samples 15
** MAII scorelog2(1/1*10)=3.32192809488736log2(5/32*10)=0.643856189774725
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CPSF3 [Title/Abstract] AND CPSF3 [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
HgeneCPSF3

GO:0006398

mRNA 3'-end processing by stem-loop binding and cleavage

18688255

TgeneCPSF3

GO:0006398

mRNA 3'-end processing by stem-loop binding and cleavage

18688255


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
ChiTaRS3.1CB135523CPSF3chr2

9593113

-CPSF3chr2

9597081

+
* 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
In-frameENST00000238112ENST00000238112CPSF3chr2

9593113

-CPSF3chr2

9597081

+
In-frameENST00000238112ENST00000460593CPSF3chr2

9593113

-CPSF3chr2

9597081

+
5CDS-intronENST00000238112ENST00000489403CPSF3chr2

9593113

-CPSF3chr2

9597081

+
In-frameENST00000460593ENST00000238112CPSF3chr2

9593113

-CPSF3chr2

9597081

+
In-frameENST00000460593ENST00000460593CPSF3chr2

9593113

-CPSF3chr2

9597081

+
5CDS-intronENST00000460593ENST00000489403CPSF3chr2

9593113

-CPSF3chr2

9597081

+
intron-3CDSENST00000489403ENST00000238112CPSF3chr2

9593113

-CPSF3chr2

9597081

+
intron-3CDSENST00000489403ENST00000460593CPSF3chr2

9593113

-CPSF3chr2

9597081

+
intron-intronENST00000489403ENST00000489403CPSF3chr2

9593113

-CPSF3chr2

9597081

+

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FusionProtFeatures for CPSF3_CPSF3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CPSF3

Q9UKF6

CPSF3

Q9UKF6

Component of the cleavage and polyadenylationspecificity factor (CPSF) complex that play a key role in pre-mRNA3'-end formation, recognizing the AAUAAA signal sequence andinteracting with poly(A) polymerase and other factors to bringabout cleavage and poly(A) addition. Has endonuclease activity,and functions as mRNA 3'-end-processing endonuclease. Alsoinvolved in the histone 3'-end pre-mRNA processing. U7 snRNP-dependent protein that induces both the 3'-endoribonucleolyticcleavage of histone pre-mRNAs and acts as a 5' to 3' exonucleasefor degrading the subsequent downstream cleavage product (DCP) ofmature histone mRNAs. Cleavage occurs after the 5'-ACCCA-3'sequence in the histone pre-mRNA leaving a 3'hydroxyl group on theupstream fragment containing the stem loop (SL) and 5' phosphateon the downstream cleavage product (DCP) starting with CUnucleotides. The U7-dependent 5' to 3' exonuclease activity isprocessive and degrades the DCP RNA substrate even after completeremoval of the U7-binding site. Binds to the downstream cleavageproduct (DCP) of histone pre-mRNAs and the cleaved DCP RNAsubstrate in a U7 snRNP dependent manner.{ECO:0000269|PubMed:14749727, ECO:0000269|PubMed:15037765,ECO:0000269|PubMed:17128255, ECO:0000269|PubMed:18688255}. Component of the cleavage and polyadenylationspecificity factor (CPSF) complex that play a key role in pre-mRNA3'-end formation, recognizing the AAUAAA signal sequence andinteracting with poly(A) polymerase and other factors to bringabout cleavage and poly(A) addition. Has endonuclease activity,and functions as mRNA 3'-end-processing endonuclease. Alsoinvolved in the histone 3'-end pre-mRNA processing. U7 snRNP-dependent protein that induces both the 3'-endoribonucleolyticcleavage of histone pre-mRNAs and acts as a 5' to 3' exonucleasefor degrading the subsequent downstream cleavage product (DCP) ofmature histone mRNAs. Cleavage occurs after the 5'-ACCCA-3'sequence in the histone pre-mRNA leaving a 3'hydroxyl group on theupstream fragment containing the stem loop (SL) and 5' phosphateon the downstream cleavage product (DCP) starting with CUnucleotides. The U7-dependent 5' to 3' exonuclease activity isprocessive and degrades the DCP RNA substrate even after completeremoval of the U7-binding site. Binds to the downstream cleavageproduct (DCP) of histone pre-mRNAs and the cleaved DCP RNAsubstrate in a U7 snRNP dependent manner.{ECO:0000269|PubMed:14749727, ECO:0000269|PubMed:15037765,ECO:0000269|PubMed:17128255, ECO:0000269|PubMed:18688255}.

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 CPSF3_CPSF3


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 CPSF3_CPSF3


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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RelatedDrugs for CPSF3_CPSF3


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 CPSF3_CPSF3


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