Biology – Quantitative Biology – Quantitative Methods
Scientific paper
2009-11-05
International Journal of Biological Sciences (2009) 10 p
Biology
Quantitative Biology
Quantitative Methods
Scientific paper
We define new profiles based on hydropathy properties and point out specific profiles for regions surrounding splice sites. We built a set T of flanking regions of genes with 1-3 introns from 21st and 22nd chromosomes. These genes contained 313 introns and 385 exons and were extracted from GenBank. They were used in order to define hydropathy profiles. Most human introns, around 99.66%, are likely to be U2- type introns. They have highly degenerate sequence motifs and many different sequences can function as U2-type splice sites. Our new profiles allow to identify regions which have conservative biochemical features that are essential for recognition by spliceosome. We have also found differences between hydropathy profiles for U2 or U12-types of introns on sets of spice sites extracted from SpliceRack database in order to distinguish GT?AG introns belonging to U2 and U12-types. Indeed, intron type cannot be simply determined by the dinucleotide termini. We show that there is a similarity of hydropathy profiles inside intron types. On the one hand, GT?AG and GC?AG introns belonging to U2-type have resembling hydropathy profiles as well as AT?AC and GT?AG introns belonging to U12-type. On the other hand, hydropathy profiles of U2 and U12-types GT?AG introns are completely different. Finally, we define and compute a pvalue; we compare our profiles with the profiles provided by a classical method, Pictogram.
Boldina Galina
Ivashchenko Anatoly
Régnier Mireille
Turmagambetova Aizhan
No associations
LandOfFree
Using profiles based on hydropathy properties to define essential regions for splicing does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with Using profiles based on hydropathy properties to define essential regions for splicing, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Using profiles based on hydropathy properties to define essential regions for splicing will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-418337