U12DB: a database of orthologous U12-type spliceosomal introns

Abstract

U12-type introns are spliced by the U12-dependent spliceosome and are present in the genomes of many higher eukaryotic lineages including plants, chordates and some invertebrates. However, due to their relatively recent discovery and a systematic bias against recognition of non-canonical splice sites in general, the introns defined by U12-type splice sites are under-represented in genome annotations. Such under-representation compounds the already difficult problem of determining gene structures. It also impedes attempts to study these introns genome-wide or phylum-wide. The resource described here, the U12 Intron Database (U12DB), aims to catalog the U12-type introns of completely sequenced eukaryotic genomes in a framework that groups orthologous introns with each other. This will aid further investigations into the evolution and mechanism of U12-dependent splicing as well as assist ongoing genome annotation efforts. Public access to the U12DB is available at http://genome.imim.es/cgi-bin/u12db/u12db.cgi.

Figure 1

The U12DB schema. Square rectangles are tables in MySQL. The lines connecting them represent foreign key—primary key relationships. Transcript-confirmed or annotated U12 introns from reference genomes are loaded into the query table. The introns are then associated with Ensembl or TAIR6 genes and these genes are inserted into the gene table. The Ensembl Compara database or a custom-built Inparanoid human/Arabidopsis database is then searched for orthologs. The orthologs are inserted into the gene table and assigned a gene cluster id that is stored in a separate table. Each reference intron is then mapped with Exonerate to each gene in the gene cluster to which its host gene belongs. The introns are assigned an intron cluster id and stored in the intron table. Splice site and exon information are stored in separate tables. The system is designed to be updatable so that intron and gene records are not duplicated but, instead, are updated if they are the target of a new reference intron mapping from the query set. Therefore, there is a many-to-many relationship between query and intron.

Figure 2

Representation of U12 introns in the U12DB. The total number of U12 introns and the number of each subtype are shown in the columns to the right of the species tree. Grand totals are shown at the bottom. The number of U12 introns in the database for each species does not necessarily reflect the actual number of U12 introns in its genome. Note that branch lengths are not to scale. Branch order was obtained from the NCBI taxonomy browser.

Figure 3

The U12DB multi-intron view. The search box appears on every page, including the results page, in order to allow quick navigation of the database. The donor and acceptor splice sites are color coded by type and subtype (U2: green, U12gtag: purple, U12atac: magenta). The predicted branch point consensus is highlighted in yellow and the putative polypyrimidine tract is highlighted in light blue (note that U12 introns do not generally possess a polypyrimidine tract).

Figure 4

The U12DB single-intron view. This view provides more detail on the intron returned by the query. The splice junction sequences are color-coded as in Figure 2. In addition, the user can choose to display the intronic sequence or the gene sequence. For certain species, one can also link to UCSC genome browser where a user-defined track will display the intron position. The transcript view provides a visualization of the intron with respect to the Ensembl transcripts. The transcripts are clickable and link to the corresponding ExonView in Ensembl. The U12DB introns are also clickable and link to the intron record in U12DB. This is useful in the case of two or more U12-type introns that are located in the same gene.