2015/11/17 by Allison Piovesan, Maria Caracausi, Marco Ricci +3 · 1 citation
Biochemistry, Genetics and Molecular Biology · #RNA and protein synthesis mechanisms #RNA Research and Splicing #RNA modifications and cancer
paper · pdf · doi:10.1093/dnares/dsv028
openalex publication_date 2015/11/17 · openalex created_date 2025/10/10 · openalex updated_date 2026/06/18
We have developed GeneBase, a full parser of the National Center for Biotechnology Information (NCBI) Gene database, which generates a fully structured local database with an intuitive user-friendly graphic interface for personal computers. Features of all the annotated eukaryotic genes are accessible through three main software tables, including for each entry details such as the gene summary, the gene exon/intron structure and the specific Gene Ontology attributions. The structuring of the data, the creation of additional calculation fields and the integration with nucleotide sequences allow users to make many types of comparisons and calculations that are useful for data retrieval and analysis. We provide an original example analysis of the existing introns across all the available species, through which the classic biological problem of the 'minimal intron' may find a solution using available data. Based on all currently available data, we can define the shortest known eukaryotic GT-AG intron length, setting the physical limit at the 30 base pair intron belonging to the human MST1L gene. This 'model intron' will shed light on the minimal requirement elements of recognition used for conventional splicing functioning. Remarkably, this size is indeed consistent with the sum of the splicing consensus sequence lengths.