Frequency Analysis of the Splice Site Regions in Different Organisms

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doi doi:10.2390/biecoll-jib-2007-85
submission May 02, 2007
published October 01, 2007

T. Shashi Rekha and Chanchal K Mitra

Correspondence should be addressed to:
Chanchal K Mitra
University of Hyderabad, Hyderabad 500 046, India


We have carried out a comparative analysis of the sub-sequences of size six| ten at the (donor| acceptor) splice site regions of five different organisms. The frequency analysis of the unique sub-sequences at the donor and acceptor regions suggests that the distribution of their occurrence is approximately exponential. We have observed that the number of unique sub-sequences (occurring with different frequencies) at the donor region are less than at the acceptor, suggesting that the sub-sequences at the acceptor region are more variable. The sub-sequences with high percentage of occurrence (uniqueness) are considered to be highly involved in splicing. Our analysis suggests that sub-sequences of length ~6-8 nucleotides (nt) at the splice sites - with six bases in intron (including the two central, conserved dinucleotides) and two bases in exon are optimal for the efficient assembly and binding of the spliceosomal complex during the process of splicing. The score pattern obtained by the alignment of the nucleotides at the donor region with the acceptor and vice-versa also suggests that a single sub-sequence at the donor region have different degree of similarity with sub-sequences at the acceptor thus determining that the donor sub-sequences are more crucial in pairing with the corresponding acceptor sub-sequences during the process of splicing.


T. Shashi Rekha and Chanchal K Mitra. Frequency Analysis of the Splice Site Regions in Different Organisms. Journal of Integrative Bioinformatics, 4(2):85, 2007. Online Journal:
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