title: Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank.
abstract: 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.
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, BO 40126, Italy.
authors.forename: Allison
authors.initials: A
authors.lastname: Piovesan
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, BO 40126, Italy.
authors.forename: Maria
authors.initials: M
authors.lastname: Caracausi
authors.affiliation: Department of Biological, Geological and Environmental Sciences (BIGeA), University of Bologna, Bologna, BO 40126, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Ricci
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, BO 40126, Italy.
authors.forename: Pierluigi
authors.initials: P
authors.lastname: Strippoli
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, BO 40126, Italy lorenza.vitale@unibo.it.
authors.forename: Lorenza
authors.initials: L
authors.lastname: Vitale
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, BO 40126, Italy.
authors.forename: Maria Chiara
authors.initials: MC
authors.lastname: Pelleri
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D023281:Genomics; D017228:Hepatocyte Growth Factor / Q000235:genetics; D006801:Humans; D007438:Introns; D011518:Proto-Oncogene Proteins / Q000235:genetics; D014584:User-Computer Interface
chemical_list: D011518:Proto-Oncogene Proteins; C082332:macrophage stimulating protein; D017228:Hepatocyte Growth Factor
keywords: NCBI Gene; computational biology; gene data parsing; minimal intron; personal computer software