JuncDB: an exon-exon junction database

Abstract

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. Yet, there is currently no database that offers such comparative information. Here, we present JuncDB (http://juncdb.carmelab.huji.ac.il/), an exon-exon junction database dedicated to the comparison of architectures between orthologous transcripts. It covers nearly 40,000 sets of orthologous transcripts spanning 88 eukaryotic species. JuncDB offers a user-friendly interface, access to detailed information, instructive graphical displays of the comparative data and easy ways to download data to a local computer. In addition, JuncDB allows the analysis to be carried out either on specific genes, or at a genome-wide level for any selected group of species.

Figure 1.

JuncDB relational database simplified diagram.

Figure 2.

The phylogenetic tree of the 88 eukaryotic species in JuncDB.

Figure 3.

JuncDB browse or query results page. (A) Download the current row (set of orthologs) information; (B) Download data on all sets of orthologs on the page; (C) Detailed description of the current row (set of orthologs).

Figure 4.

The upper part of JuncDB ‘Details’ page, providing information on a particular set of orthologs. (A) Orthologs set ID; (B) Source orthology database; (C) The gene symbol associated with the set; (D) The phylogenetic tree of the species represented in the set; (E) Scheme of the exonic architecture of all transcripts in the set. Each row describes a specific transcript, a vertical line is an exon–exon junction position and each block is an exon. The number within each block is the length of the exon in the multiple alignment.

Figure 5.

The lower part of JuncDB ‘Details’ page. (A) Intron positions projected upon the mRNA multiple alignment; (B) Information of the set's transcripts; (C) Information on the set's proteins; (D) The set's transcripts multiple sequence alignment; (E) The set's proteins multiple sequence alignment.

Figure 6.

Filtering set of orthologs by species. The user can choose between ‘At least one of’, meaning it is sufficient for a set to contain at least one of the selected species, or ‘All of’, meaning the set must contain all selected species.