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Each alignment was parsed into a set of splice junction coordinates.
An example of the set of splice variants seen for the Runx2 is shown in the Figure S1.
Commitment for a given set of splice sites appears to be enhanced by protein cross-talk across each exon, a process called exon definition [8], and by repression of numerous pseudosplice sites that are usually present in primary transcripts [9].
The complete set of splice sites was divided into training/testing sets of sizes 10 90%, for each set three samples were drawn.
These additional splice variants are included in Ensembl and so are imported into UniProtKB and are used to supplement the set of splice variants identified by UniProtKB curators.
We used both sources of evidence in our alignments to the human genome, with the same set of splice sites based on RefSeq transcripts as we used for the targeted alignment method.
Similar(49)
The dynamic interplay between chromatin structure, transcription and splicing might explain why some genes are alternatively spliced in different cell types that contain the same or a similar set of splicing regulators and as such might represent an efficient method for global splicing regulation during development and cell differentiation.
Previously, we have analyzed a large set of splice-site disrupting polymorphisms observed in modern human populations [ 15].
Do all constitutively spliced exons utilize the same set of splicing factors?
Combining the two methods provided a significant increase in the total set of splicing changes identified in the mutant mice.
10.7554/eLife.01201.008 Figure 5. PTBP2 regulates a large set of splicing targets important to neuronal development and function.
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