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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:CPSF6-RBM39 (FusionGDB2 ID:19182)

Fusion Gene Summary for CPSF6-RBM39

check button Fusion gene summary
Fusion gene informationFusion gene name: CPSF6-RBM39
Fusion gene ID: 19182
HgeneTgene
Gene symbol

CPSF6

RBM39

Gene ID

11052

9584

Gene namecleavage and polyadenylation specific factor 6RNA binding motif protein 39
SynonymsCFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7CAPER|CAPERalpha|FSAP59|HCC1|RNPC2
Cytomap

12q15

20q11.22

Type of geneprotein-codingprotein-coding
Descriptioncleavage and polyadenylation specificity factor subunit 6CPSF 68 kDa subunitcleavage and polyadenylation specific factor 6, 68kDacleavage and polyadenylation specificity factor 68 kDa subunitcleavage factor Im complex 68 kDa subunitpre-mRNA cleavage RNA-binding protein 39CAPER alphaRNA-binding region (RNP1, RRM) containing 2coactivator of activating protein-1 and estrogen receptorsepididymis secretory sperm binding proteinfunctional spliceosome-associated protein 59hepatocellular carcinoma prot
Modification date2020031320200327
UniProtAcc

Q16630

.
Ensembl transtripts involved in fusion geneENST00000266679, ENST00000435070, 
ENST00000456847, ENST00000551516, 
ENST00000550987, 		ENST00000253363, 
ENST00000361162, ENST00000528062, 
ENST00000397370, ENST00000407261, 
ENST00000463098, 
Fusion gene scores* DoF score69 X 12 X 19=1573224 X 16 X 12=4608
# samples 7127
** MAII scorelog2(71/15732*10)=-4.46973925655087
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(27/4608*10)=-4.09310940439148
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CPSF6 [Title/Abstract] AND RBM39 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCPSF6(69656342)-RBM39(34326939), # samples:1
Anticipated loss of major functional domain due to fusion event.CPSF6-RBM39 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CPSF6-RBM39 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneCPSF6

GO:0006397

mRNA processing

14690600

HgeneCPSF6

GO:0051262

protein tetramerization

20695905

HgeneCPSF6

GO:0051290

protein heterotetramerization

23187700

HgeneCPSF6

GO:1990120

messenger ribonucleoprotein complex assembly

29276085


check buttonFusion gene breakpoints across CPSF6 (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 RBM39 (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
ChimerDB4Non-CancerTCGA-KN-8422-11ACPSF6chr12

69656342

+RBM39chr20

34326939

-


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Fusion Gene ORF analysis for CPSF6-RBM39

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-3CDSENST00000266679ENST00000253363CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-3CDSENST00000266679ENST00000361162CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-3CDSENST00000266679ENST00000528062CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-3CDSENST00000435070ENST00000253363CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-3CDSENST00000435070ENST00000361162CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-3CDSENST00000435070ENST00000528062CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-3CDSENST00000456847ENST00000253363CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-3CDSENST00000456847ENST00000361162CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-3CDSENST00000456847ENST00000528062CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-5UTRENST00000266679ENST00000397370CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-5UTRENST00000266679ENST00000407261CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-5UTRENST00000435070ENST00000397370CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-5UTRENST00000435070ENST00000407261CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-5UTRENST00000456847ENST00000397370CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-5UTRENST00000456847ENST00000407261CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-intronENST00000266679ENST00000463098CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-intronENST00000435070ENST00000463098CPSF6chr12

69656342

+RBM39chr20

34326939

-
3UTR-intronENST00000456847ENST00000463098CPSF6chr12

69656342

+RBM39chr20

34326939

-
5CDS-5UTRENST00000551516ENST00000397370CPSF6chr12

69656342

+RBM39chr20

34326939

-
5CDS-5UTRENST00000551516ENST00000407261CPSF6chr12

69656342

+RBM39chr20

34326939

-
5CDS-intronENST00000551516ENST00000463098CPSF6chr12

69656342

+RBM39chr20

34326939

-
Frame-shiftENST00000551516ENST00000253363CPSF6chr12

69656342

+RBM39chr20

34326939

-
Frame-shiftENST00000551516ENST00000361162CPSF6chr12

69656342

+RBM39chr20

34326939

-
Frame-shiftENST00000551516ENST00000528062CPSF6chr12

69656342

+RBM39chr20

34326939

-
intron-3CDSENST00000550987ENST00000253363CPSF6chr12

69656342

+RBM39chr20

34326939

-
intron-3CDSENST00000550987ENST00000361162CPSF6chr12

69656342

+RBM39chr20

34326939

-
intron-3CDSENST00000550987ENST00000528062CPSF6chr12

69656342

+RBM39chr20

34326939

-
intron-5UTRENST00000550987ENST00000397370CPSF6chr12

69656342

+RBM39chr20

34326939

-
intron-5UTRENST00000550987ENST00000407261CPSF6chr12

69656342

+RBM39chr20

34326939

-
intron-intronENST00000550987ENST00000463098CPSF6chr12

69656342

+RBM39chr20

34326939

-

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 CPSF6-RBM39


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)

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.

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Fusion Protein Features for CPSF6-RBM39


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/:69656342/:34326939)
- 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
CPSF6

Q16630

.
FUNCTION: Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs (PubMed:9659921, PubMed:8626397, PubMed:14690600, PubMed:29276085). CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals) (PubMed:9659921, PubMed:8626397, PubMed:14690600). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation (PubMed:23187700, PubMed:29276085). The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) for a huge number of pre-mRNAs (PubMed:20695905, PubMed:29276085). CPSF6 enhances NUDT21/CPSF5 binding to 5'-UGUA-3' elements localized upstream of pA signals and promotes RNA looping, and hence activates directly the mRNA 3'-processing machinery (PubMed:15169763, PubMed:29276085, PubMed:21295486). Plays a role in mRNA export (PubMed:19864460). {ECO:0000269|PubMed:14690600, ECO:0000269|PubMed:15169763, ECO:0000269|PubMed:19864460, ECO:0000269|PubMed:20695905, ECO:0000269|PubMed:21295486, ECO:0000269|PubMed:23187700, ECO:0000269|PubMed:29276085, ECO:0000269|PubMed:8626397, ECO:0000269|PubMed:9659921}.; FUNCTION: (Microbial infection) Binds HIV-1 capsid-nucleocapsid (HIV-1 CA-NC) complexes and might thereby promote the integration of the virus in the nucleus of dividing cells (in vitro). {ECO:0000269|PubMed:24130490}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 CPSF6-RBM39


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 CPSF6-RBM39


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 CPSF6-RBM39


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 CPSF6-RBM39


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