ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization

Abstract

Alternative splicing (AS) is now emerging as a major mechanism contributing to the expansion of the transcriptome and proteome complexity of multicellular organisms. The fact that a single gene locus may give rise to multiple mRNAs and protein isoforms, showing both major and subtle structural variations, is an exceptionally versatile tool in the optimization of the coding capacity of the eukaryotic genome. The huge and continuously increasing number of genome and transcript sequences provides an essential information source for the computational detection of genes AS pattern. However, much of this information is not optimally or comprehensively used in gene annotation by current genome annotation pipelines. We present here a web resource implementing the ASPIC algorithm which we developed previously for the investigation of AS of user submitted genes, based on comparative analysis of available transcript and genome data from a variety of species. The ASPIC web resource provides graphical and tabular views of the splicing patterns of all full-length mRNA isoforms compatible with the detected splice sites of genes under investigation as well as relevant structural and functional annotation. The ASPIC web resource-available at http://www.caspur.it/ASPIC/--is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility.

Figure 1

(a) Snapshot of the gene view for the human HNRPR gene showing the gene structure and detected introns numbered progressively. Constitutive and alternative exons are shown in yellow and green respectively. (b) Sample transcript view showing the inferred structure of assembled alternative transcripts starting from the reference transcript and reporting the annotation of the 5′-UTR, CDS, 3′-UTR and poly(A) tail.

Figure 2

Sample intron table for the human HNRPR gene showing the relative and absolute coordinates of each detected intron, their lengths, the number of supporting ESTs, the donor and acceptor sites and the alignment quality (overall mismatch percentage) near to intron boundaries.

Figure 3

Transcript table for the first 10 alternative transcripts of the human HNRPR gene, showing: the transcript ID, number of exons, length, CDS annotation, occurrence of the CCDS start/stop, inferred protein length and variant type. The variant type provides information on the type of splicing events and their gene (E, exon; I, intron) and mRNA locations (5utr, CDS or 3utr).