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. 2000 Jan 1;28(1):91-3.
doi: 10.1093/nar/28.1.91.

The intronerator: exploring introns and alternative splicing in Caenorhabditis elegans

W J Kent  1 , A M Zahler
Affiliations

The intronerator: exploring introns and alternative splicing in Caenorhabditis elegans

W J Kent et al. Nucleic Acids Res. .

Abstract

The Intronerator (http://www.cse.ucsc.edu/ approximately kent/intronerator/ ) is a set of web-based tools for exploring RNA splicing and gene structure in Caenorhabditis elegans. It includes a display of cDNA alignments with the genomic sequence, a catalog of alternatively spliced genes and a database of introns. The cDNA alignments include >100 000 ESTs and almost 1000 full-length cDNAs. ESTs from embryos and mixed stage animals as well as full-length cDNAs can be compared in the alignment display with each other and with predicted genes. The alt-splicing catalog includes 844 open reading frames for which there is evidence of alternative splicing of pre-mRNA. The intron database includes 28 478 introns, and can be searched for patterns near the splice junctions.

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Figures

Figure 1
Figure 1
Tracks Display of the region around the predicted gene ZK1127.9. Alignments of ESTs deriving from mixed stage animals (black) and embryos (green) are not in complete agreement with the Genefinder prediction (blue) and provide evidence for an alternative exon between predicted exons 1 and 2. The parts of the alignments drawn in lighter colors are regions of the ESTs with sequencing errors that do not correspond 100% with the genomic sequence.
Figure 2
Figure 2
Detailed display of alignment between the EST yk507g11.5 and the area of the genome around ZK1127.9 obtained by clicking this EST’s graphic display in Figure 1. In the upper part of the display, the blue areas represent nucleotides that match perfectly between cDNA and genomic DNA. The lighter blue areas represent the ends of matching areas. In the second area of the display, regions that are predicted to be coding exons as annotated in AceDB are in upper case. Though the EST sequence contains some sequencing errors, the alternatively spliced exon is apparent.
Figure 3
Figure 3
Display of an ORF in which an unusual intron—one which starts with GC instead of the canonical GU—is highlighted in light blue. EST evidence for alternative splicing of this gene is also shown.
See this image and copyright information in PMC

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