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Finally, analysis of allelic variations between transcript sequences of several Hevea clones could be useful for the development of functional molecular markers.
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NCBI's UniGene contains gene-oriented clusters of transcript sequences obtained by alignments between transcript sequences and genomic sequences originating from the same gene.
Finding exact alignments between probe and transcript sequences was used to attribute signal intensities of probes to transcript (or gene) expression.
However, it is important to be aware that, as for any analysis of transcript data, the major difference between several studies lies in the number of transcript sequences considered.
A total of 6,788 sequences out of the 9,766 representative transcripts were removed yielding 2,978 representative transcripts that were stitched together by inserting Ns between the representative sequences to generate a set of concatenated transcript sequences (CTS).
Marked differences in transcript size (>0.5 kb) between the Northern blots and the database sequences were found for eight genes, suggesting the presence of additional transcript sequences in these genes.
To identify ortholog gene pairs between japonica and indica, we performed BLAT searches of the 35,293 japonica Nipponbare transcript sequences against the 93-11 BGI 2003-08-01 genome sequence [ 15].
The annotated transcript sequences here reported represent a significant improvement of the genomic information available for this species.
The sequences of RFLP probes were compared with RAP2 transcript sequences using BLASTN searches (Altschul et al. 1997).
In order to find the common transcripts between sets of assembled sequences for P. kurrooa at 15°C and 25°C, the assembled transcript sequences for both the conditions were search against each other using BLASTN with E-value threshold of 10-5.
Comparison between the cDNA transcript sequence and corresponding genomic sequence revealed that all of the intron/exon boundaries of the five alternatively spliced transcripts are flanked by canonical AG/GT donor and acceptor splice sites [59].
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