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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:CPSF6-RBM39 (FusionGDB2 ID:19194) |
Fusion Gene Summary for CPSF6-RBM39 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CPSF6-RBM39 | Fusion gene ID: 19194 | Hgene | Tgene | Gene symbol | CPSF6 | RBM39 | Gene ID | 11052 | 9584 |
| Gene name | cleavage and polyadenylation specific factor 6 | RNA binding motif protein 39 | |
| Synonyms | CFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7 | CAPER|CAPERalpha|FSAP59|HCC1|RNPC2 | |
| Cytomap | 12q15 | 20q11.22 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cleavage 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 date | 20200313 | 20200327 | |
| UniProtAcc | Q16630 | . | |
| Ensembl transtripts involved in fusion gene | ENST00000435070, ENST00000456847, ENST00000266679, ENST00000550987, ENST00000551516, | ENST00000253363, ENST00000361162, ENST00000528062, ENST00000407261, ENST00000397370, ENST00000463098, | |
| Fusion gene scores | * DoF score | 69 X 12 X 19=15732 | 24 X 16 X 12=4608 |
| # samples | 71 | 27 | |
| ** MAII score | log2(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 breakpoint | CPSF6(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) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | CPSF6 | GO:0006397 | mRNA processing | 14690600 |
| Hgene | CPSF6 | GO:0051262 | protein tetramerization | 20695905 |
| Hgene | CPSF6 | GO:0051290 | protein heterotetramerization | 23187700 |
| Hgene | CPSF6 | GO:1990120 | messenger ribonucleoprotein complex assembly | 29276085 |
| Fusion 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. |
| Fusion 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. |
| 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | Non-Cancer | TCGA-KN-8422-11A | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
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Fusion Gene ORF analysis for CPSF6-RBM39 |
| 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. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| 3UTR-3CDS | ENST00000435070 | ENST00000253363 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-3CDS | ENST00000435070 | ENST00000361162 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-3CDS | ENST00000435070 | ENST00000528062 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-5UTR | ENST00000435070 | ENST00000407261 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-5UTR | ENST00000435070 | ENST00000397370 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-intron | ENST00000435070 | ENST00000463098 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-3CDS | ENST00000456847 | ENST00000253363 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-3CDS | ENST00000456847 | ENST00000361162 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-3CDS | ENST00000456847 | ENST00000528062 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-5UTR | ENST00000456847 | ENST00000407261 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-5UTR | ENST00000456847 | ENST00000397370 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-intron | ENST00000456847 | ENST00000463098 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-3CDS | ENST00000266679 | ENST00000253363 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-3CDS | ENST00000266679 | ENST00000361162 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-3CDS | ENST00000266679 | ENST00000528062 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-5UTR | ENST00000266679 | ENST00000407261 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-5UTR | ENST00000266679 | ENST00000397370 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 3UTR-intron | ENST00000266679 | ENST00000463098 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| intron-3CDS | ENST00000550987 | ENST00000253363 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| intron-3CDS | ENST00000550987 | ENST00000361162 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| intron-3CDS | ENST00000550987 | ENST00000528062 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| intron-5UTR | ENST00000550987 | ENST00000407261 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| intron-5UTR | ENST00000550987 | ENST00000397370 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| intron-intron | ENST00000550987 | ENST00000463098 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| Frame-shift | ENST00000551516 | ENST00000253363 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| Frame-shift | ENST00000551516 | ENST00000361162 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| Frame-shift | ENST00000551516 | ENST00000528062 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 5CDS-5UTR | ENST00000551516 | ENST00000407261 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 5CDS-5UTR | ENST00000551516 | ENST00000397370 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| 5CDS-intron | ENST00000551516 | ENST00000463098 | CPSF6 | chr12 | 69656342 | + | RBM39 | chr20 | 34326939 | - |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| DeepORF 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. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
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Fusion Genomic Features for CPSF6-RBM39 |
| FusionAI 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. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
| Distribution 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. |
| Distribution 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 |
| Go to FGviewer for the breakpoints of :-: - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| CPSF6 | . |
| 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: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes. |
| Retention 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 * 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. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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Fusion Gene Sequence for CPSF6-RBM39 |
| 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 |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs for CPSF6-RBM39 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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Related Diseases for CPSF6-RBM39 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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