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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:CPEB3-NHP2 (FusionGDB2 ID:18960) |
Fusion Gene Summary for CPEB3-NHP2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CPEB3-NHP2 | Fusion gene ID: 18960 | Hgene | Tgene | Gene symbol | CPEB3 | NHP2 | Gene ID | 22849 | 55651 |
| Gene name | cytoplasmic polyadenylation element binding protein 3 | NHP2 ribonucleoprotein | |
| Synonyms | - | DKCB2|NHP2P|NOLA2 | |
| Cytomap | 10q23.32 | 5q35.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cytoplasmic polyadenylation element-binding protein 3CPE-BP3CPE-binding protein 3hCPEB-3 | H/ACA ribonucleoprotein complex subunit 2NHP2 ribonucleoprotein homologNHP2-like proteinnucleolar protein family A, member 2 (H/ACA small nucleolar RNPs)snoRNP protein NHP2 | |
| Modification date | 20200322 | 20200313 | |
| UniProtAcc | Q8NE35 | SNU13 | |
| Ensembl transtripts involved in fusion gene | ENST00000265997, ENST00000412050, | ENST00000274606, ENST00000314397, | |
| Fusion gene scores | * DoF score | 6 X 7 X 2=84 | 4 X 5 X 2=40 |
| # samples | 7 | 6 | |
| ** MAII score | log2(7/84*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(6/40*10)=0.584962500721156 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: CPEB3 [Title/Abstract] AND NHP2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | CPEB3(93976331)-NHP2(177577969), # samples:1 CPEB3(93976601)-NHP2(177576643), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | |||
| * 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 | CPEB3 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 20639532 |
| Hgene | CPEB3 | GO:0017148 | negative regulation of translation | 21336257|22711986 |
| Hgene | CPEB3 | GO:0060213 | positive regulation of nuclear-transcribed mRNA poly(A) tail shortening | 21336257 |
| Hgene | CPEB3 | GO:0061158 | 3'-UTR-mediated mRNA destabilization | 21336257 |
| Hgene | CPEB3 | GO:0071230 | cellular response to amino acid stimulus | 20639532|22730302 |
| Hgene | CPEB3 | GO:1900153 | positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay | 21336257 |
| Tgene | NHP2 | GO:0007004 | telomere maintenance via telomerase | 29695869 |
| Fusion gene breakpoints across CPEB3 (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 NHP2 (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 |
| ChiTaRS5.0 | N/A | EC459240 | CPEB3 | chr10 | 93976331 | - | NHP2 | chr5 | 177577969 | - |
| ChiTaRS5.0 | N/A | EC548178 | CPEB3 | chr10 | 93976601 | - | NHP2 | chr5 | 177576643 | - |
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Fusion Gene ORF analysis for CPEB3-NHP2 |
| 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 |
| intron-3CDS | ENST00000265997 | ENST00000274606 | CPEB3 | chr10 | 93976331 | - | NHP2 | chr5 | 177577969 | - |
| intron-3CDS | ENST00000412050 | ENST00000274606 | CPEB3 | chr10 | 93976331 | - | NHP2 | chr5 | 177577969 | - |
| intron-3UTR | ENST00000265997 | ENST00000274606 | CPEB3 | chr10 | 93976601 | - | NHP2 | chr5 | 177576643 | - |
| intron-3UTR | ENST00000265997 | ENST00000314397 | CPEB3 | chr10 | 93976601 | - | NHP2 | chr5 | 177576643 | - |
| intron-3UTR | ENST00000412050 | ENST00000274606 | CPEB3 | chr10 | 93976601 | - | NHP2 | chr5 | 177576643 | - |
| intron-3UTR | ENST00000412050 | ENST00000314397 | CPEB3 | chr10 | 93976601 | - | NHP2 | chr5 | 177576643 | - |
| intron-intron | ENST00000265997 | ENST00000314397 | CPEB3 | chr10 | 93976331 | - | NHP2 | chr5 | 177577969 | - |
| intron-intron | ENST00000412050 | ENST00000314397 | CPEB3 | chr10 | 93976331 | - | NHP2 | chr5 | 177577969 | - |
| 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 CPEB3-NHP2 |
| 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 CPEB3-NHP2 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:93976331/:177577969) - 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 |
| CPEB3 | NHP2 |
| FUNCTION: Sequence-specific RNA-binding protein which acts as a translational repressor in the basal unstimulated state but, following neuronal stimulation, acts as a translational activator (By similarity). In contrast to CPEB1, does not bind to the cytoplasmic polyadenylation element (CPE), a uridine-rich sequence element within the mRNA 3'-UTR, but binds to a U-rich loop within a stem-loop structure (By similarity). Required for the consolidation and maintenance of hippocampal-based long term memory (By similarity). In the basal state, binds to the mRNA 3'-UTR of the glutamate receptors GRIA2/GLUR2 mRNA and negatively regulates their translation (By similarity). Also represses the translation of DLG4, GRIN1, GRIN2A and GRIN2B (By similarity). When activated, acts as a translational activator of GRIA1 and GRIA2 (By similarity). In the basal state, suppresses SUMO2 translation but activates it following neuronal stimulation (By similarity). Binds to the 3'-UTR of TRPV1 mRNA and represses TRPV1 translation which is required to maintain normal thermoception (By similarity). Binds actin mRNA, leading to actin translational repression in the basal state and to translational activation following neuronal stimulation (By similarity). Negatively regulates target mRNA levels by binding to TOB1 which recruits CNOT7/CAF1 to a ternary complex and this leads to target mRNA deadenylation and decay (PubMed:21336257). In addition to its role in translation, binds to and inhibits the transcriptional activation activity of STAT5B without affecting its dimerization or DNA-binding activity. This, in turn, represses transcription of the STAT5B target gene EGFR which has been shown to play a role in enhancing learning and memory performance (PubMed:20639532). In contrast to CPEB1, CPEB2 and CPEB4, not required for cell cycle progression (PubMed:26398195). {ECO:0000250|UniProtKB:Q7TN99, ECO:0000269|PubMed:20639532, ECO:0000269|PubMed:21336257, ECO:0000269|PubMed:26398195}. | 128 |
| 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 CPEB3-NHP2 |
| 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 CPEB3-NHP2 |
| 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 CPEB3-NHP2 |
| 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 CPEB3-NHP2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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