Cargando…

Comparative Analysis of Splice Site Regions by Information Content

We have applied concepts from information theory for a comparative analysis of donor (gt) and acceptor (ag) splice site regions in the genes of five different organisms by calculating their mutual information content (relative entropy) over a selected block of nucleotides. A similar pattern that the...

Descripción completa

Detalles Bibliográficos
Autores principales: Rekha, T. Shashi, Mitra, Chanchal K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054069/
https://www.ncbi.nlm.nih.gov/pubmed/17531798
http://dx.doi.org/10.1016/S1672-0229(07)60003-5
_version_ 1782458519251845120
author Rekha, T. Shashi
Mitra, Chanchal K.
author_facet Rekha, T. Shashi
Mitra, Chanchal K.
author_sort Rekha, T. Shashi
collection PubMed
description We have applied concepts from information theory for a comparative analysis of donor (gt) and acceptor (ag) splice site regions in the genes of five different organisms by calculating their mutual information content (relative entropy) over a selected block of nucleotides. A similar pattern that the information content decreases as the block size increases was observed for both regions in all the organisms studied. This result suggests that the information required for splicing might be contained in the consensus of ~6–8 nt at both regions. We assume from our study that even though the nucleotides are showing some degrees of conservation in the flanking regions of the splice sites, certain level of variability is still tolerated, which leads the splicing process to occur normally even if the extent of base pairing is not fully satisfied. We also suggest that this variability can be compensated by recognizing different splice sites with different spliceosomal factors.
format Online
Article
Text
id pubmed-5054069
institution National Center for Biotechnology Information
language English
publishDate 2006
publisher Elsevier
record_format MEDLINE/PubMed
spelling pubmed-50540692016-10-14 Comparative Analysis of Splice Site Regions by Information Content Rekha, T. Shashi Mitra, Chanchal K. Genomics Proteomics Bioinformatics Article We have applied concepts from information theory for a comparative analysis of donor (gt) and acceptor (ag) splice site regions in the genes of five different organisms by calculating their mutual information content (relative entropy) over a selected block of nucleotides. A similar pattern that the information content decreases as the block size increases was observed for both regions in all the organisms studied. This result suggests that the information required for splicing might be contained in the consensus of ~6–8 nt at both regions. We assume from our study that even though the nucleotides are showing some degrees of conservation in the flanking regions of the splice sites, certain level of variability is still tolerated, which leads the splicing process to occur normally even if the extent of base pairing is not fully satisfied. We also suggest that this variability can be compensated by recognizing different splice sites with different spliceosomal factors. Elsevier 2006 2007-05-23 /pmc/articles/PMC5054069/ /pubmed/17531798 http://dx.doi.org/10.1016/S1672-0229(07)60003-5 Text en © 2006 Beijing Institute of Genomics http://creativecommons.org/licenses/by-nc-sa/3.0/ This is an open access article under the CC BY-NC-SA license (http://creativecommons.org/licenses/by-nc-sa/3.0/).
spellingShingle Article
Rekha, T. Shashi
Mitra, Chanchal K.
Comparative Analysis of Splice Site Regions by Information Content
title Comparative Analysis of Splice Site Regions by Information Content
title_full Comparative Analysis of Splice Site Regions by Information Content
title_fullStr Comparative Analysis of Splice Site Regions by Information Content
title_full_unstemmed Comparative Analysis of Splice Site Regions by Information Content
title_short Comparative Analysis of Splice Site Regions by Information Content
title_sort comparative analysis of splice site regions by information content
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054069/
https://www.ncbi.nlm.nih.gov/pubmed/17531798
http://dx.doi.org/10.1016/S1672-0229(07)60003-5
work_keys_str_mv AT rekhatshashi comparativeanalysisofsplicesiteregionsbyinformationcontent
AT mitrachanchalk comparativeanalysisofsplicesiteregionsbyinformationcontent