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Fusion Protein:AGBL5-CHD5 |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: AGBL5-CHD5 | FusionPDB ID: 2856 | FusionGDB2.0 ID: 2856 | Hgene | Tgene | Gene symbol | AGBL5 | CHD5 | Gene ID | 60509 | 84181 |
| Gene name | ATP/GTP binding protein like 5 | chromodomain helicase DNA binding protein 6 | |
| Synonyms | CCP5|RP75 | CHD-6|CHD5|RIGB | |
| Cytomap | 2p23.3 | 20q12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cytosolic carboxypeptidase-like protein 5cytosolic carboxypeptidase 5 | chromodomain-helicase-DNA-binding protein 6ATP-dependent helicase CHD6helicase C-terminal domain- and SNF2 N-terminal domain-containing proteinradiation-induced gene B protein | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | Q8NDL9 | Q8TDI0 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000323064, ENST00000360131, | ENST00000378021, ENST00000262450, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 5 X 9 X 2=90 | 2 X 2 X 2=8 |
| # samples | 9 | 2 | |
| ** MAII score | log2(9/90*10)=0 | log2(2/8*10)=1.32192809488736 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: AGBL5 [Title/Abstract] AND CHD5 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | AGBL5(27276821)-CHD5(6214829), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | AGBL5-CHD5 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. AGBL5-CHD5 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. AGBL5-CHD5 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. AGBL5-CHD5 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 |
| Fusion gene breakpoints across AGBL5 (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 CHD5 (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 |
| ChiTaRS5.0 | N/A | BF363390 | AGBL5 | chr2 | 27276821 | - | CHD5 | chr1 | 6214829 | - |
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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) |
| ENST00000323064 | AGBL5 | chr2 | 27276821 | - | ENST00000262450 | CHD5 | chr1 | 6214829 | - | 9566 | 655 | 1162 | 2364 | 400 |
| ENST00000360131 | AGBL5 | chr2 | 27276821 | - | ENST00000262450 | CHD5 | chr1 | 6214829 | - | 9563 | 652 | 1159 | 2361 | 400 |
| 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 |
| ENST00000323064 | ENST00000262450 | AGBL5 | chr2 | 27276821 | - | CHD5 | chr1 | 6214829 | - | 0.31786445 | 0.6821355 |
| ENST00000360131 | ENST00000262450 | AGBL5 | chr2 | 27276821 | - | CHD5 | chr1 | 6214829 | - | 0.31822208 | 0.68177795 |
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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 >2856_2856_1_AGBL5-CHD5_AGBL5_chr2_27276821_ENST00000323064_CHD5_chr1_6214829_ENST00000262450_length(amino acids)=400AA_BP= MIWPPARLEPPSTRQGRFGEPLSSPMVRPWLTFPLLPAKAGGRQVFALSLWGGGSSASRCLSPAQRILKALDSVTSGGPVAPALHSRQKR MIPGRVGWGGGSTCLGATAALGLPSARGVVKGSDSCAPARRVMGPELAQETLALPCALGCLPCPPPEVEPGCPWGPGLVPFPCPWKGLPG GFLPEAALLEGVGRVLPGGGLDPVPSADPSQPQHQGLAALFPARSALTSQNHLPTCGLLESHPLPRTLPLQVGDGDGEQVRPSLGLFVCD PSPGPRSTWKAFLSLVLGPSQGRCLGVQNPGNVRKGLREKPSWAWGGGAHGLGLSSLERACLGLRGPGLGQDSPACVADTGAIAWPSLSP -------------------------------------------------------------- >2856_2856_2_AGBL5-CHD5_AGBL5_chr2_27276821_ENST00000360131_CHD5_chr1_6214829_ENST00000262450_length(amino acids)=400AA_BP= MIWPPARLEPPSTRQGRFGEPLSSPMVRPWLTFPLLPAKAGGRQVFALSLWGGGSSASRCLSPAQRILKALDSVTSGGPVAPALHSRQKR MIPGRVGWGGGSTCLGATAALGLPSARGVVKGSDSCAPARRVMGPELAQETLALPCALGCLPCPPPEVEPGCPWGPGLVPFPCPWKGLPG GFLPEAALLEGVGRVLPGGGLDPVPSADPSQPQHQGLAALFPARSALTSQNHLPTCGLLESHPLPRTLPLQVGDGDGEQVRPSLGLFVCD PSPGPRSTWKAFLSLVLGPSQGRCLGVQNPGNVRKGLREKPSWAWGGGAHGLGLSSLERACLGLRGPGLGQDSPACVADTGAIAWPSLSP -------------------------------------------------------------- |
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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/chr2:27276821/chr1:6214829) - 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 |
| AGBL5 | CHD5 |
| FUNCTION: Metallocarboxypeptidase that mediates protein deglutamylation. Specifically catalyzes the deglutamylation of the branching point glutamate side chains generated by post-translational glutamylation in proteins such as tubulins. In contrast, it is not able to act as a long-chain deglutamylase that shortens long polyglutamate chains, a process catalyzed by AGTPBP1/CCP1, AGBL2/CCP2, AGBL3/CCP3, AGBL1/CCP4 and AGBL4/CCP6. Mediates deglutamylation of CGAS, regulating the antiviral activity of CGAS. {ECO:0000250|UniProtKB:Q09M02}. | FUNCTION: Chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. May specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3. Plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. Tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. Downstream activated genes may include CDKN2A that positively regulates the p53/TP53 pathway, which in turn, prevents cell proliferation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. {ECO:0000269|PubMed:23948251}. |
| 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 |
| Tgene | CHD5 | chr2:27276821 | chr1:6214829 | ENST00000262450 | 0 | 42 | 49_116 | 0 | 3082.3333333333335 | Compositional bias | Note=Lys-rich | |
| Tgene | CHD5 | chr2:27276821 | chr1:6214829 | ENST00000262450 | 0 | 42 | 1028_1193 | 0 | 3082.3333333333335 | Domain | Helicase C-terminal | |
| Tgene | CHD5 | chr2:27276821 | chr1:6214829 | ENST00000262450 | 0 | 42 | 497_554 | 0 | 3082.3333333333335 | Domain | Chromo 1 | |
| Tgene | CHD5 | chr2:27276821 | chr1:6214829 | ENST00000262450 | 0 | 42 | 592_653 | 0 | 3082.3333333333335 | Domain | Chromo 2 | |
| Tgene | CHD5 | chr2:27276821 | chr1:6214829 | ENST00000262450 | 0 | 42 | 712_896 | 0 | 3082.3333333333335 | Domain | Helicase ATP-binding | |
| Tgene | CHD5 | chr2:27276821 | chr1:6214829 | ENST00000262450 | 0 | 42 | 847_850 | 0 | 3082.3333333333335 | Motif | Note=DEAH box | |
| Tgene | CHD5 | chr2:27276821 | chr1:6214829 | ENST00000262450 | 0 | 42 | 725_732 | 0 | 3082.3333333333335 | Nucleotide binding | ATP | |
| Tgene | CHD5 | chr2:27276821 | chr1:6214829 | ENST00000262450 | 0 | 42 | 343_653 | 0 | 3082.3333333333335 | Region | Note=Histone-binding | |
| Tgene | CHD5 | chr2:27276821 | chr1:6214829 | ENST00000262450 | 0 | 42 | 343_390 | 0 | 3082.3333333333335 | Zinc finger | PHD-type 1 | |
| Tgene | CHD5 | chr2:27276821 | chr1:6214829 | ENST00000262450 | 0 | 42 | 416_463 | 0 | 3082.3333333333335 | Zinc finger | PHD-type 2 |
| - 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 |
| Hgene | AGBL5 | chr2:27276821 | chr1:6214829 | ENST00000323064 | - | 1 | 11 | 540_544 | 0 | 718.0 | Compositional bias | Note=Poly-Pro |
| Hgene | AGBL5 | chr2:27276821 | chr1:6214829 | ENST00000323064 | - | 1 | 11 | 651_654 | 0 | 718.0 | Compositional bias | Note=Poly-Ser |
| Hgene | AGBL5 | chr2:27276821 | chr1:6214829 | ENST00000360131 | - | 1 | 15 | 540_544 | 0 | 887.0 | Compositional bias | Note=Poly-Pro |
| Hgene | AGBL5 | chr2:27276821 | chr1:6214829 | ENST00000360131 | - | 1 | 15 | 651_654 | 0 | 887.0 | Compositional bias | Note=Poly-Ser |
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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 |
| AGBL5 | |
| CHD5 |
| - 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 AGBL5-CHD5 |
| 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 AGBL5-CHD5 |
| 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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