Using profiles based on hydropathy properties to define essential regions for splicing

Anatoly Ivashchenko 1 Galina Boldina 1, * Aizhan Turmagambetova 1, * Mireille Régnier 2
* Auteur correspondant
2 AMIB - Algorithms and Models for Integrative Biology
CNRS - Centre National de la Recherche Scientifique : UMR8623, X - École polytechnique, Inria Saclay - Ile de France, UP11 - Université Paris-Sud - Paris 11, LRI - Laboratoire de Recherche en Informatique, LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
Abstract : 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.
Type de document :
Article dans une revue
International Journal of Biological Sciences, Ivyspring International Publisher, 2009, 5, pp.13-19. 〈http://www.biolsci.org/v05p0013.htm〉
Liste complète des métadonnées

Littérature citée [17 références]  Voir  Masquer  Télécharger

https://hal.inria.fr/inria-00429780
Contributeur : Mireille Regnier <>
Soumis le : jeudi 5 novembre 2009 - 16:05:29
Dernière modification le : mercredi 25 avril 2018 - 10:45:38
Document(s) archivé(s) le : samedi 26 novembre 2016 - 13:08:08

Fichiers

BoIvRe2411.pdf
Fichiers produits par l'(les) auteur(s)

Identifiants

  • HAL Id : inria-00429780, version 1
  • ARXIV : 0911.1066

Collections

Citation

Anatoly Ivashchenko, Galina Boldina, Aizhan Turmagambetova, Mireille Régnier. Using profiles based on hydropathy properties to define essential regions for splicing. International Journal of Biological Sciences, Ivyspring International Publisher, 2009, 5, pp.13-19. 〈http://www.biolsci.org/v05p0013.htm〉. 〈inria-00429780〉

Partager

Métriques

Consultations de la notice

398

Téléchargements de fichiers

114