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The homology between two exons in a pair was identified using the bl2seq implementation of TBLASTN.
The age difference between two exons in a pair confirms this observation.
To verify whether exons were present but unidentified in some species, we screened target regions (intronic region between two exons) in sequenced genomes available in Genbank.
19 of 26 old pairs show significantly high similarity between two exons in a pair, while no exon duplication event can be detected in the 21 young pairs.
Our observation that the distances between two exons in strongly-correlated pairs are shorter than in loosely-correlated pairs supports this hypothesis.
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To avoid amplification of contaminating genomic DNA, one of the two primers or the probe was placed at the junction between two exons, or in a different exon.
To avoid amplification of contaminating genomic DNA, one of the two primers was designed to be located at the junction between two exons or in a different exon.
To study the coordination between alternative exons, we performed a large scale analysis of the correlation (coordination) between the two exons in an adjacent cassette exon pair.
Specific primer pairs were placed in different exons and a dye-labelled probe was placed over the boundary between the two exons in the amplicon.
We employed a correlation coefficient to measure the interaction between the two exons in such a pair and observed that the exons show various interaction patterns.
Then the ratio of dN and of dS between the two exons in a given species has been determined (fig. 2).
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