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This limitation only applied to the mammalian data, as most of the yeasts genes are not alternatively spliced.
On the other hand, among genes that are not alternatively spliced, several functions related to house-keeping, such as 'protein transport'DNA'DNA repair' and 'cell wall organization' , are over-represented.
On the other hand, an analysis of the alternative-splicing status of homologous genes from the closely related alga Chlamydomonas could show that a large fraction of the genes that are alternatively spliced in Volvox are not alternatively spliced in Chlamydomonas.
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Examination of the mouse GRK4 subfamily (GRKs 4, 5, and 6) suggests that mouse GRK4 is not alternatively spliced in a manner analogous to human or rat GRK4, whereas GRK6 undergoes extensive alternative splicing to generate three variants with distinct carboxyl termini.
TPs were grouped as Non-AS-TPs if transcripts were not alternatively spliced.
Using the above described methods, all of them are shown to be not alternatively spliced.
(B ) A gene (bed-2) with up-regulated introns (intron up) and that is not alternatively spliced (non-AS).
Constitutive splice junctions and introns were defined as junctions that were not alternatively spliced in any isoform of the UCSC knownGene track [ 26].
Furthermore, pyrimidine +3 was also seen adjacent to all β-dystrobrevin exon 13 sequences, which are also alternatively spliced[ 9], but not γ-dystrobrevin exon 13, which is not alternatively spliced (this work; [see Additional File 2]).
While IRF1 is not alternatively spliced, and a more general deficiency in intron processing is likely, it remains possible that these functions are distorted in the MEN1 knockdown cell line, as experiments to address some of them yielded negative results.
Finally, we observed that methylated honeybee genes that are also alternatively spliced were even higher conserved across species than methylated genes that were not alternatively spliced (Additional file 1: Table S1) or than alternatively spliced genes that are not methylated (Additional file 1: Table S2).
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