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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:CDK7-PPWD1 (FusionGDB2 ID:15305) |
Fusion Gene Summary for CDK7-PPWD1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CDK7-PPWD1 | Fusion gene ID: 15305 | Hgene | Tgene | Gene symbol | CDK7 | PPWD1 | Gene ID | 1022 | 23398 |
| Gene name | cyclin dependent kinase 7 | peptidylprolyl isomerase domain and WD repeat containing 1 | |
| Synonyms | CAK|CAK1|CDKN7|HCAK|MO15|STK1|p39MO15 | - | |
| Cytomap | 5q13.2 | 5q12.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cyclin-dependent kinase 739 KDa protein kinaseCDK-activating kinase 1TFIIH basal transcription factor complex kinase subunitcell division protein kinase 7cyclin-dependent kinase 7 (MO15 homolog, Xenopus laevis, cdk-activating kinase)homolog of Xenop | peptidylprolyl isomerase domain and WD repeat-containing protein 1epididymis secretory sperm binding proteinspliceosome-associated cyclophilin | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | P50613 | . | |
| Ensembl transtripts involved in fusion gene | ENST00000513629, ENST00000256443, ENST00000514676, ENST00000502604, | ENST00000261308, ENST00000535264, ENST00000538977, | |
| Fusion gene scores | * DoF score | 6 X 1 X 3=18 | 4 X 3 X 5=60 |
| # samples | 7 | 6 | |
| ** MAII score | log2(7/18*10)=1.95935801550265 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(6/60*10)=0 | |
| Context | PubMed: CDK7 [Title/Abstract] AND PPWD1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | CDK7(68531280)-PPWD1(64863340), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | CDK7-PPWD1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF. CDK7-PPWD1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. CDK7-PPWD1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. CDK7-PPWD1 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF. CDK7-PPWD1 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 | CDK7 | GO:0006366 | transcription by RNA polymerase II | 9852112 |
| Hgene | CDK7 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 8692841 |
| Tgene | PPWD1 | GO:0000413 | protein peptidyl-prolyl isomerization | 20676357 |
| Fusion gene breakpoints across CDK7 (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 PPWD1 (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 | STAD | TCGA-CD-5813-01A | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
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Fusion Gene ORF analysis for CDK7-PPWD1 |
| 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 | ENST00000513629 | ENST00000261308 | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
| 3UTR-3CDS | ENST00000513629 | ENST00000535264 | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
| 3UTR-intron | ENST00000513629 | ENST00000538977 | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
| 5CDS-intron | ENST00000256443 | ENST00000538977 | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
| 5CDS-intron | ENST00000514676 | ENST00000538977 | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
| 5UTR-3CDS | ENST00000502604 | ENST00000261308 | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
| 5UTR-3CDS | ENST00000502604 | ENST00000535264 | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
| 5UTR-intron | ENST00000502604 | ENST00000538977 | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
| Frame-shift | ENST00000256443 | ENST00000261308 | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
| Frame-shift | ENST00000256443 | ENST00000535264 | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
| Frame-shift | ENST00000514676 | ENST00000261308 | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
| Frame-shift | ENST00000514676 | ENST00000535264 | CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863340 | + |
| 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 CDK7-PPWD1 |
| 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) |
| CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863339 | + | 1.93E-07 | 0.99999976 |
| CDK7 | chr5 | 68531280 | + | PPWD1 | chr5 | 64863339 | + | 1.93E-07 | 0.99999976 |
| 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 CDK7-PPWD1 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:68531280/:64863340) - 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 |
| CDK7 | . |
| FUNCTION: Serine/threonine kinase involved in cell cycle control and in RNA polymerase II-mediated RNA transcription. Cyclin-dependent kinases (CDKs) are activated by the binding to a cyclin and mediate the progression through the cell cycle. Each different complex controls a specific transition between 2 subsequent phases in the cell cycle. Required for both activation and complex formation of CDK1/cyclin-B during G2-M transition, and for activation of CDK2/cyclins during G1-S transition (but not complex formation). CDK7 is the catalytic subunit of the CDK-activating kinase (CAK) complex. Phosphorylates SPT5/SUPT5H, SF1/NR5A1, POLR2A, p53/TP53, CDK1, CDK2, CDK4, CDK6 and CDK11B/CDK11. CAK activates the cyclin-associated kinases CDK1, CDK2, CDK4 and CDK6 by threonine phosphorylation, thus regulating cell cycle progression. CAK complexed to the core-TFIIH basal transcription factor activates RNA polymerase II by serine phosphorylation of the repetitive C-terminal domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter and elongation of the transcripts. Phosphorylation of POLR2A in complex with DNA promotes transcription initiation by triggering dissociation from DNA. Its expression and activity are constant throughout the cell cycle. Upon DNA damage, triggers p53/TP53 activation by phosphorylation, but is inactivated in turn by p53/TP53; this feedback loop may lead to an arrest of the cell cycle and of the transcription, helping in cell recovery, or to apoptosis. Required for DNA-bound peptides-mediated transcription and cellular growth inhibition. {ECO:0000269|PubMed:10024882, ECO:0000269|PubMed:11113184, ECO:0000269|PubMed:16327805, ECO:0000269|PubMed:17373709, ECO:0000269|PubMed:17386261, ECO:0000269|PubMed:17901130, ECO:0000269|PubMed:19015234, ECO:0000269|PubMed:19071173, ECO:0000269|PubMed:19136461, ECO:0000269|PubMed:19450536, ECO:0000269|PubMed:19667075, ECO:0000269|PubMed:20360007, ECO:0000269|PubMed:9372954, ECO:0000269|PubMed:9840937}. | 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}. |
| 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 CDK7-PPWD1 |
| 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 CDK7-PPWD1 |
| 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 CDK7-PPWD1 |
| 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 CDK7-PPWD1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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