AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes
The mRNA translation defines the composition of the cell proteome in all forms of life and diseases. In this process, precise selection of the mRNA translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for triplet decoding. We have gathered and curated all pu...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2025-12-01
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| Series: | RNA Biology |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/15476286.2025.2465196 |
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| author | Vincent G. Osnaya Laura Gómez-Romero Gabriel Moreno-Hagelsieb Greco Hernández |
| author_facet | Vincent G. Osnaya Laura Gómez-Romero Gabriel Moreno-Hagelsieb Greco Hernández |
| author_sort | Vincent G. Osnaya |
| collection | DOAJ |
| description | The mRNA translation defines the composition of the cell proteome in all forms of life and diseases. In this process, precise selection of the mRNA translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for triplet decoding. We have gathered and curated all published TIS consensus context sequences. We also included the TIS consensus context from novel 538 fungal genomes available from NCBI’s RefSeq database. To do so, we wrote ad hoc programs in PERL to find and extract the TIS for each annotated gene, plus ten bases upstream and three downstream. For each genome, the sequences around the TIS of each gene were obtained, and the consensus was further calculated according to the Cavener rules and by the LOGOS algorithm. We created AUGcontext DB, a portal with a comprehensive collection of TIS context sequences across eukaryotes in a range from −10 to + 6. The compilation covers species of 30 vertebrates, 17 invertebrates, 25 plants, 14 fungi, and 11 protists studied in silico; 23 experimental studies; data on biotechnology; and the discovery of 8 diseases associated with specific mutations. Additionally, TIS context sequences of cellular IRESs were included. AUGcontext DB belongs to the National Institute of Cancer (Instituto Nacional de Cancerología, INCan), Mexico, and is freely available at http://108.161.138.77:8096/. Our catalogue allows us to do comparative studies between species, may help improve the diagnosis of certain diseases, and will be key to maximize the production of recombinant proteins. |
| format | Article |
| id | doaj-art-c0b05db821ca43fd85ce09bc6ab0723c |
| institution | DOAJ |
| issn | 1547-6286 1555-8584 |
| language | English |
| publishDate | 2025-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | RNA Biology |
| spelling | doaj-art-c0b05db821ca43fd85ce09bc6ab0723c2025-08-20T03:21:42ZengTaylor & Francis GroupRNA Biology1547-62861555-85842025-12-012211510.1080/15476286.2025.2465196AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotesVincent G. Osnaya0Laura Gómez-Romero1Gabriel Moreno-Hagelsieb2Greco Hernández3mRNA and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City, MexicoBioinformatics Department, National Institute of Genomic Medicine, Mexico City, MexicoDepartment of Biology, Wilfrid Laurier University, Waterloo, ON, CanadamRNA and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City, MexicoThe mRNA translation defines the composition of the cell proteome in all forms of life and diseases. In this process, precise selection of the mRNA translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for triplet decoding. We have gathered and curated all published TIS consensus context sequences. We also included the TIS consensus context from novel 538 fungal genomes available from NCBI’s RefSeq database. To do so, we wrote ad hoc programs in PERL to find and extract the TIS for each annotated gene, plus ten bases upstream and three downstream. For each genome, the sequences around the TIS of each gene were obtained, and the consensus was further calculated according to the Cavener rules and by the LOGOS algorithm. We created AUGcontext DB, a portal with a comprehensive collection of TIS context sequences across eukaryotes in a range from −10 to + 6. The compilation covers species of 30 vertebrates, 17 invertebrates, 25 plants, 14 fungi, and 11 protists studied in silico; 23 experimental studies; data on biotechnology; and the discovery of 8 diseases associated with specific mutations. Additionally, TIS context sequences of cellular IRESs were included. AUGcontext DB belongs to the National Institute of Cancer (Instituto Nacional de Cancerología, INCan), Mexico, and is freely available at http://108.161.138.77:8096/. Our catalogue allows us to do comparative studies between species, may help improve the diagnosis of certain diseases, and will be key to maximize the production of recombinant proteins.https://www.tandfonline.com/doi/10.1080/15476286.2025.2465196Translation initiation siteKozak motiftranslational controlfungal translationAUG codon |
| spellingShingle | Vincent G. Osnaya Laura Gómez-Romero Gabriel Moreno-Hagelsieb Greco Hernández AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes RNA Biology Translation initiation site Kozak motif translational control fungal translation AUG codon |
| title | AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes |
| title_full | AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes |
| title_fullStr | AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes |
| title_full_unstemmed | AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes |
| title_short | AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes |
| title_sort | augcontext db a comprehensive catalog of the mrna aug initiator codon context across eukaryotes |
| topic | Translation initiation site Kozak motif translational control fungal translation AUG codon |
| url | https://www.tandfonline.com/doi/10.1080/15476286.2025.2465196 |
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