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Fusion Protein:CPSF6-CDK13 |
Fusion Gene and Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: CPSF6-CDK13 | FusionPDB ID: 19142 | FusionGDB2.0 ID: 19142 | Hgene | Tgene | Gene symbol | CPSF6 | CDK13 | Gene ID | 11052 | 8621 |
| Gene name | cleavage and polyadenylation specific factor 6 | cyclin dependent kinase 13 | |
| Synonyms | CFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7 | CDC2L|CDC2L5|CHDFIDD|CHED|hCDK13 | |
| Cytomap | 12q15 | 7p14.1 | |
| 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 | cyclin-dependent kinase 13CDC2-related protein kinase 5cell division cycle 2-like protein kinase 5cell division protein kinase 13cholinesterase-related cell division controller | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | Q16630 Main function of 5'-partner protein: 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}. | Q14004 Main function of 5'-partner protein: FUNCTION: Cyclin-dependent kinase which displays CTD kinase activity and is required for RNA splicing. Has CTD kinase activity by hyperphosphorylating the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit RPB1, thereby acting as a key regulator of transcription elongation. Required for RNA splicing, probably by phosphorylating SRSF1/SF2. Required during hematopoiesis. In case of infection by HIV-1 virus, interacts with HIV-1 Tat protein acetylated at 'Lys-50' and 'Lys-51', thereby increasing HIV-1 mRNA splicing and promoting the production of the doubly spliced HIV-1 protein Nef. {ECO:0000269|PubMed:16721827, ECO:0000269|PubMed:1731328, ECO:0000269|PubMed:18480452, ECO:0000269|PubMed:20952539}. | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000266679, ENST00000435070, ENST00000456847, ENST00000551516, ENST00000550987, | ENST00000181839, ENST00000340829, ENST00000484589, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 69 X 12 X 19=15732 | 5 X 6 X 2=60 |
| # samples | 71 | 6 | |
| ** MAII score | log2(71/15732*10)=-4.46973925655087 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(6/60*10)=0 | |
| Fusion gene context | PubMed: CPSF6 [Title/Abstract] AND CDK13 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Fusion neoantigen context | PubMed: CPSF6 [Title/Abstract] AND CDK13 [Title/Abstract] AND neoantigen [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | CPSF6(69656342)-CDK13(40027198), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | CPSF6-CDK13 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. CPSF6-CDK13 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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 |
| Tgene | CDK13 | GO:0070816 | phosphorylation of RNA polymerase II C-terminal domain | 20952539 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:69656342/chr7:40027198) - 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. |
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| Retention analysis results 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, are available here. |
| 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. |
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| Fusion gene breakpoints across CDK13 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Amino Acid Sequences |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| 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) |
| ENST00000551516 | CPSF6 | chr12 | 69656342 | + | ENST00000181839 | CDK13 | chr7 | 40027198 | + | 5654 | 172 | 5 | 3499 | 1164 |
| ENST00000551516 | CPSF6 | chr12 | 69656342 | + | ENST00000340829 | CDK13 | chr7 | 40027198 | + | 3895 | 172 | 5 | 3319 | 1104 |
| 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 |
| ENST00000551516 | ENST00000181839 | CPSF6 | chr12 | 69656342 | + | CDK13 | chr7 | 40027198 | + | 0.000180756 | 0.9998192 |
| ENST00000551516 | ENST00000340829 | CPSF6 | chr12 | 69656342 | + | CDK13 | chr7 | 40027198 | + | 0.000514125 | 0.99948585 |
| Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones. |
Get the fusion protein sequences from here. |
| Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
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Fusion Protein Breakpoint Sequences for CPSF6-CDK13 |
| +/-13 AA sequence from the breakpoints of the fusion protein sequences. |
| Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
| CPSF6 | chr12 | 69656342 | CDK13 | chr7 | 40027198 | 172 | 55 | ESVTESANIVIVRRRSGKSRSRSPYS |
| CPSF6 | chr12 | 69656342 | CDK13 | chr7 | 40027198 | 172 | 61 | ANIVIVRRRSGKSRSRSPYSSRHSRS |
| CPSF6 | chr12 | 69656342 | CDK13 | chr7 | 40027198 | 172 | 71 | GKSRSRSPYSSRHSRSRSRHRLSRSR |
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Potential FusionNeoAntigen Information of CPSF6-CDK13 in HLA I |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| CPSF6-CDK13_69656342_40027198.msa |
| Potential FusionNeoAntigen Information * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
| Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | HLA-A30:08 | RSPYSSRHSR | 0.9772 | 0.7658 | 5 | 15 |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | HLA-A74:03 | RSPYSSRHSR | 0.9766 | 0.5027 | 5 | 15 |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | HLA-A74:09 | RSPYSSRHSR | 0.9766 | 0.5027 | 5 | 15 |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | HLA-A74:11 | RSPYSSRHSR | 0.9766 | 0.5027 | 5 | 15 |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | HLA-B27:05 | SRSPYSSRHSR | 0.9997 | 0.8122 | 4 | 15 |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | HLA-B27:14 | SRSPYSSRHSR | 0.9997 | 0.7821 | 4 | 15 |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | HLA-B27:10 | SRHSRSRSR | 0.9822 | 0.9175 | 10 | 19 |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | HLA-A30:01 | RSPYSSRHSR | 0.9829 | 0.8957 | 5 | 15 |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | HLA-A74:01 | RSPYSSRHSR | 0.9766 | 0.5027 | 5 | 15 |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | HLA-B27:10 | SRSPYSSRHSR | 0.9995 | 0.8633 | 4 | 15 |
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Potential FusionNeoAntigen Information of CPSF6-CDK13 in HLA II |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| CPSF6-CDK13_69656342_40027198.msa |
| Potential FusionNeoAntigen Information * We used NetMHCIIpan v4.1 (%rank<0.5). |
| Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | DRB1-1186 | RSPYSSRHSRSRSRH | 5 | 20 |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | DRB1-1316 | RSPYSSRHSRSRSRH | 5 | 20 |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 | DRB5-0103 | RSPYSSRHSRSRSRH | 5 | 20 |
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Fusion breakpoint peptide structures of CPSF6-CDK13 |
| 3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
| File name | BPseq | Hgene | Tgene | Hchr | Hbp | Tchr | Tbp | AAlen |
| 8908 | SPYSSRHSRSRSRH | CPSF6 | CDK13 | chr12 | 69656342 | chr7 | 40027198 | 172 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CPSF6-CDK13 |
| Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens * We used Glide to predict the interaction between HLAs and neoantigens. |
| HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
| HLA-B14:02 | 3BVN | 8908 | SPYSSRHSRSRSRH | -5.68384 | -5.79564 |
| HLA-B14:02 | 3BVN | 8908 | SPYSSRHSRSRSRH | -3.56904 | -4.61214 |
| HLA-B52:01 | 3W39 | 8908 | SPYSSRHSRSRSRH | -6.63523 | -6.74703 |
| HLA-B52:01 | 3W39 | 8908 | SPYSSRHSRSRSRH | -5.62878 | -6.67188 |
| HLA-A11:01 | 4UQ2 | 8908 | SPYSSRHSRSRSRH | -5.4101 | -6.4532 |
| HLA-A11:01 | 4UQ2 | 8908 | SPYSSRHSRSRSRH | -4.27122 | -4.38302 |
| HLA-A24:02 | 5HGA | 8908 | SPYSSRHSRSRSRH | -9.1657 | -10.2088 |
| HLA-A24:02 | 5HGA | 8908 | SPYSSRHSRSRSRH | -4.66063 | -4.77243 |
| HLA-B44:05 | 3DX8 | 8908 | SPYSSRHSRSRSRH | -5.55787 | -6.60097 |
| HLA-B44:05 | 3DX8 | 8908 | SPYSSRHSRSRSRH | -4.40408 | -4.51588 |
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Vaccine Design for the FusionNeoAntigens of CPSF6-CDK13 |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 10 | 19 | SRHSRSRSR | CGTTAGAAGACGGTCTGGAAAATCCCG |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 4 | 15 | SRSPYSSRHSR | GAGCGCGAATATCGTCATCGTTAGAAGACGGTC |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 5 | 15 | RSPYSSRHSR | CGCGAATATCGTCATCGTTAGAAGACGGTC |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
| CPSF6-CDK13 | chr12 | 69656342 | chr7 | 40027198 | 5 | 20 | RSPYSSRHSRSRSRH | CGCGAATATCGTCATCGTTAGAAGACGGTCTGGAAAATCCCGAAG |
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Information of the samples that have these potential fusion neoantigens of CPSF6-CDK13 |
| These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens. |
| Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
| STAD | CPSF6-CDK13 | chr12 | 69656342 | ENST00000551516 | chr7 | 40027198 | ENST00000181839 | TCGA-D7-8574-01A |
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Potential target of CAR-T therapy development for CPSF6-CDK13 |
| Predicted 3D structure. We used RoseTTAFold. |
| 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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features * Minus value of BPloci means that the break point is located before the CDS. |
| - In-frame and retained 'Transmembrane'. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Subcellular localization prediction of the transmembrane domain retained fusion proteins * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
| Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
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Related Drugs to CPSF6-CDK13 |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to CPSF6-CDK13 |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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