Intron positions upon the mRNA transcript are sometimes remarkably conserved even across distantly related eukaryotic species. This has made the comparison of intron–exon architectures across orthologous transcripts a very useful tool for studying various evolutionary processes. Moreover, the wide range of functions associated with introns may confer biological meaning to evolutionary changes in gene architectures.
A plant gene structure comparison and evolution database with 25 species. Annotated genes were extracted from the species and classified based on Pfam motif. Phylogenetic tree was reconstructed for each gene category integrated exon-intron and protein motif information. Both the sequences and gene structure information for each identified gene are freely available for online access on the PIECE website. The PIECE database provides a user-friendly graphical viewer that displays a gene structure pattern diagram linked to the resulting bootstrapped dendrogram for each gene family. Gene structure information can be displayed and retrieved in nucleotide sequence or in aligned protein sequence.
A database for comparing exonic architectures within sets of orthologous transcripts, offering user-friendly web interfaces and extensive visualization tools. JuncDB covers nearly 40 000 sets of orthologous transcripts spanning 88 eukaryotic species. The database can be queried and browsed, and the results are given in both textual and graphical ways. Users can query the database by providing transcript/gene/protein IDs and/or by selecting a set of species. Thus, JuncDB makes it possible to investigate the gene architecture of specific genes or compare architectures across selected species in a genome-wide fashion. By matching the comparative gene architecture data to the phylogenetic species tree, JuncDB makes it possible to infer intron gain and loss events, and therefore also to study the potential functional roles of specific introns.
Offers a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The collection of exons and introns has been extended beyond coding regions and current versions of EID contain data on untranslated regions of gene sequences as well. Intron-less genes are included as a special part of EID. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames.
Generates a fully structured local database with an intuitive user-friendly graphic interface for personal computers. GeneBase is a full parser of the National Center for Biotechnology Information (NCBI) Gene database. It allows users to do original searches, calculations and analyses of the main information about genes which are fully annotated with the ‘Gene Table’ section in NCBI Gene. Furthermore, for a subset of gene records, it integrates nucleotide sequences useful for additional elaboration with the corresponding gene-associated meta-information.
Stores information of all GenBank eukaryotic entries containing an annotated intron sequence. Features in the database include: intron nucleotide sequence, amino acid sequence of the corresponding protein, position of the introns at the amino acid level and intron phase. ExInt is accessible through a retrieval system with pointers to GenBank. The database can be searched by keywords, locus name, NID, accession number or length of the protein.
Aims to balance the goal of giving the complete picture of possible coding exons, with the need to stay grounded in terms of the verifiability of the actual function of the sequences it collects. Thus it relies on the ENSEMBL’s annotation of ‘known’ (‘known’ here being the actual annotation term used, hence the quotes) human exons as the anchor for the search and for the results presentation. To these, ExoLocator adds the search for ostensibly missing exons in orthologous protein pairs across species, using an extensive computational pipeline to narrow down the search region for the candidate exons and find a suitable template in the other species, as well as state-of-the-art implementations of pairwise alignment algorithms. The resulting complements of exons are organized in a way currently unique to ExoLocator: multiple sequence alignments, both on the nucleotide and on the peptide levels, clearly indicating the exon boundaries. The alignments can be inspected in the web-embedded viewer, downloaded or used on the spot to produce an estimate of conservation within orthologous sets, or functional divergence across paralogues.