Cross-kingdom patterns of alternative splicing and splice recognition

Additional data file 1:

The data for H. sapiens were taken from a previous study [8].

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Additional data file 2:

(a) Sequence logos [41] for 3' splice sites of RIs and control introns. (b) Sequence logos [41] for 5' splice sites of RIs and control introns. For 5' splice sites, we show sequence logos for six intronic and three exonic bases. For 3' splice sites, we show sequence logos for three intronic and one exonic bases.

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Additional data file 3:

Six example organisms with large numbers of splice variants were chosen and their normalized intron and exon length distributions are plotted here. (a) CE distributions are shifted towards shorter lengths than the control exon length distribution, because of constraints on exon length imposed by ED. (b) The peak at short intron lengths is very similar in RIs and constitutive introns, because this short intron peak is primarily made up of introns recognized by ID. In contrast, almost no introns surrounding CEs have lengths close to this 'intron-definition peak' - almost all of them are spread out over a wide range of longer intron lengths, and have low values in the area of the short intron-length ID peak shown here (0-200 bp).

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Additional data file 4:

Table S1: differences in information content between RIs and controls. Table S2: intron and exon lengths from annotations. Table S3: details of our analysis of functional group enrichment of RIs.

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Additional data file 5:

A comparison of alternative splicing events for the situations where unspliced ESTs are included as well as discarded. We also include data for a higher-confidence dataset requiring a greater number of ESTs supporting each predicted alternative splicing event.

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Additional data file 6:

We include the source code for the CallReferenceGenes program, as well as the code which labels alternative splice forms. These codes can be inspected but will not be functional without the rest of the Broad Institute's Calhoun environment. These are included as Unix tar files.

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