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Fusion Protein:CPSF6-CDK13 |
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 | Q14004 | |
| 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 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: CPSF6 [Title/Abstract] AND CDK13 [Title/Abstract] AND fusion [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 |
| 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 Gene Sample Information |
| Fusion gene information from FusionGDB2.0. |
| 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 | STAD | TCGA-D7-8574-01A | CPSF6 | chr12 | 69656342 | + | CDK13 | chr7 | 40027198 | + |
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Fusion ORF Analysis |
| 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 |
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Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP >19142_19142_1_CPSF6-CDK13_CPSF6_chr12_69656342_ENST00000551516_CDK13_chr7_40027198_ENST00000181839_length(amino acids)=1164AA_BP=71 MADGVDHIDIYADVGEEFNQEAEYEREAENERGTGIVTETVTESVTESANIVIVRRRSGKSRSRSPYSSRHSRSRSRHRLSRSRSRHSSI SPSTLTLKSSLAAELNKNKKARAAEAARAAEAAKAAEATKAAEAAAKAAKASNTSTPTKGNTETSASASQTNHVKDVKKIKIEHAPSPSS GGTLKNDKAKTKPPLQVTKVENNLIVDKATKKAVIVGKESKSAATKEESVSLKEKTKPLTPSIGAKEKEQHVALVTSTLPPLPLPPMLPE DKEADSLRGNISVKAVKKEVEKKLRCLLADLPLPPELPGGDDLSKSPEEKKTATQLHSKRRPKICGPRYGETKEKDIDWGKRCVDKFDII GIIGEGTYGQVYKARDKDTGEMVALKKVRLDNEKEGFPITAIREIKILRQLTHQSIINMKEIVTDKEDALDFKKDKGAFYLVFEYMDHDL MGLLESGLVHFNENHIKSFMRQLMEGLDYCHKKNFLHRDIKCSNILLNNRGQIKLADFGLARLYSSEESRPYTNKVITLWYRPPELLLGE ERYTPAIDVWSCGCILGELFTKKPIFQANQELAQLELISRICGSPCPAVWPDVIKLPYFNTMKPKKQYRRKLREEFVFIPAAALDLFDYM LALDPSKRCTAEQALQCEFLRDVEPSKMPPPDLPLWQDCHELWSKKRRRQKQMGMTDDVSTIKAPRKDLSLGLDDSRTNTPQGVLPSSQL KSQGSSNVAPVKTGPGQHLNHSELAILLNLLQSKTSVNMADFVQVLNIKVNSETQQQLNKINLPAGILATGEKQTDPSTPQQESSKPLGG IQPSSQTIQPKVETDAAQAAVQSAFAVLLTQLIKAQQSKQKDVLLEERENGSGHEASLQLRPPPEPSTPVSGQDDLIQHQDMRILELTPE PDRPRILPPDQRPPEPPEPPPVTEEDLDYRTENQHVPTTSSSLTDPHAGVKAALLQLLAQHQPQDDPKREGGIDYQAGDTYVSTSDYKDN FGSSSFSSAPYVSNDGLGSSSAPPLERRSFIGNSDIQSLDNYSTASSHSGGPPQPSAFSESFPSSVAGYGDIYLNAGPMLFSGDKDHRFE -------------------------------------------------------------- >19142_19142_2_CPSF6-CDK13_CPSF6_chr12_69656342_ENST00000551516_CDK13_chr7_40027198_ENST00000340829_length(amino acids)=1104AA_BP=71 MADGVDHIDIYADVGEEFNQEAEYEREAENERGTGIVTETVTESVTESANIVIVRRRSGKSRSRSPYSSRHSRSRSRHRLSRSRSRHSSI SPSTLTLKSSLAAELNKNKKARAAEAARAAEAAKAAEATKAAEAAAKAAKASNTSTPTKGNTETSASASQTNHVKDVKKIKIEHAPSPSS GGTLKNDKAKTKPPLQVTKVENNLIVDKATKKAVIVGKESKSAATKEESVSLKEKTKPLTPSIGAKEKEQHVALVTSTLPPLPLPPMLPE DKEADSLRGNISVKAVKKEVEKKLRCLLADLPLPPELPGGDDLSKSPEEKKTATQLHSKRRPKICGPRYGETKEKDIDWGKRCVDKFDII GIIGEGTYGQVYKARDKDTGEMVALKKVRLDNEKEGFPITAIREIKILRQLTHQSIINMKEIVTDKEDALDFKKDKGAFYLVFEYMDHDL MGLLESGLVHFNENHIKSFMRQLMEGLDYCHKKNFLHRDIKCSNILLNNRGQIKLADFGLARLYSSEESRPYTNKVITLWYRPPELLLGE ERYTPAIDVWSCGCILGELFTKKPIFQANQELAQLELISRICGSPCPAVWPDVIKLPYFNTMKPKKQYRRKLREEFVFIPAAALDLFDYM LALDPSKRCTAEQALQCEFLRDVEPSKMPPPDLPLWQDCHELWSKKRRRQKQMGMTDDVSTIKAPRKDLSLGLDDSRTNTPQGVLPSSQL KSQGSSNVAPGEKQTDPSTPQQESSKPLGGIQPSSQTIQPKVETDAAQAAVQSAFAVLLTQLIKAQQSKQKDVLLEERENGSGHEASLQL RPPPEPSTPVSGQDDLIQHQDMRILELTPEPDRPRILPPDQRPPEPPEPPPVTEEDLDYRTENQHVPTTSSSLTDPHAGVKAALLQLLAQ HQPQDDPKREGGIDYQAGDTYVSTSDYKDNFGSSSFSSAPYVSNDGLGSSSAPPLERRSFIGNSDIQSLDNYSTASSHSGGPPQPSAFSE SFPSSVAGYGDIYLNAGPMLFSGDKDHRFEYSHGPIAVLANSSDPSTGPESTHPLPAKMHNYNYGGNLQENPSGPSLMHGQTWTSPAQGP -------------------------------------------------------------- |
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Fusion Protein Functional Features |
| 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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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| CPSF6 | CDK13 |
| 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: 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}. |
| 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. |
| - 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 |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000266679 | + | 10 | 11 | 208_398 | 590.0 | 701.3333333333334 | Compositional bias | Note=Pro-rich |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000266679 | + | 10 | 11 | 490_551 | 590.0 | 701.3333333333334 | Compositional bias | Note=Arg-rich |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000435070 | + | 9 | 10 | 208_398 | 553.0 | 2111.0 | Compositional bias | Note=Pro-rich |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000435070 | + | 9 | 10 | 490_551 | 553.0 | 2111.0 | Compositional bias | Note=Arg-rich |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000266679 | + | 10 | 11 | 202_206 | 590.0 | 701.3333333333334 | Motif | GAR |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000435070 | + | 9 | 10 | 202_206 | 553.0 | 2111.0 | Motif | GAR |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000266679 | + | 10 | 11 | 358_551 | 590.0 | 701.3333333333334 | Region | (Microbial infection) Binds to HIV-1 capsid protein p24 (CA) |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000266679 | + | 10 | 11 | 404_551 | 590.0 | 701.3333333333334 | Region | Sufficient for nuclear speckle localization |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000266679 | + | 10 | 11 | 405_551 | 590.0 | 701.3333333333334 | Region | Necessary for RNA-binding |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000266679 | + | 10 | 11 | 510_551 | 590.0 | 701.3333333333334 | Region | Sufficient for nuclear targeting |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000266679 | + | 10 | 11 | 81_161 | 590.0 | 701.3333333333334 | Region | Necessary for nuclear paraspeckles localization |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000435070 | + | 9 | 10 | 358_551 | 553.0 | 2111.0 | Region | (Microbial infection) Binds to HIV-1 capsid protein p24 (CA) |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000435070 | + | 9 | 10 | 404_551 | 553.0 | 2111.0 | Region | Sufficient for nuclear speckle localization |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000435070 | + | 9 | 10 | 405_551 | 553.0 | 2111.0 | Region | Necessary for RNA-binding |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000435070 | + | 9 | 10 | 510_551 | 553.0 | 2111.0 | Region | Sufficient for nuclear targeting |
| Hgene | CPSF6 | chr12:69656342 | chr7:40027198 | ENST00000435070 | + | 9 | 10 | 81_161 | 553.0 | 2111.0 | Region | Necessary for nuclear paraspeckles localization |
| Tgene | CDK13 | chr12:69656342 | chr7:40027198 | ENST00000181839 | 0 | 14 | 705_998 | 403.6666666666667 | 1513.0 | Domain | Protein kinase | |
| Tgene | CDK13 | chr12:69656342 | chr7:40027198 | ENST00000340829 | 0 | 14 | 705_998 | 403.6666666666667 | 1453.0 | Domain | Protein kinase | |
| Tgene | CDK13 | chr12:69656342 | chr7:40027198 | ENST00000181839 | 0 | 14 | 711_719 | 403.6666666666667 | 1513.0 | Nucleotide binding | ATP | |
| Tgene | CDK13 | chr12:69656342 | chr7:40027198 | ENST00000340829 | 0 | 14 | 711_719 | 403.6666666666667 | 1453.0 | Nucleotide binding | ATP |
| - 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 Protein-Protein Interaction |
| 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 from validated records (BIOGRID-3.4.160) |
| Gene | PPI interactors |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| CPSF6 | |
| CDK13 |
| - Retained interactions in fusion protein (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost interactions due to fusion (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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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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