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Specifically, a transcript tag encoding the key ABA biosynthesis enzyme 9-cis-epoxycarotenoid dioxygenase (NCED1) (RC.21240) was over-expressed in response to drought stress in both pools.
Only one transcript tagged by ESTs derived solely from a metamorphic stage was identified.
We made use of the consensus sequence (5' CACCTCTCCACCTGCC 3') of 33.15 repeat loci to explore the buffalo transcriptome and uncovered the Smoc-1 transcript tagged with this repeat.
Using transcripts tagged with a 3′-terminal deletion, it was found that recombinants contained the 3′ end derived from the replicative strand, indicating a cis-preference for initiation of negative-strand synthesis.
While deletion mutagenesis showed that the presence of the junction untranslated region (J-UTR) between the ORFs appeared to be necessary on both transcripts for recombination in this region of the genome, analysis with transcripts tagged with restriction sites showed that the J-UTR was not a hot spot for recombination compared to neighboring regions in both ORFs.
Most transcripts are tagged as 'protein coding', but there are some transcripts tagged as 'nonsense_mediated_decay' (NMD).
The tissue- and spermatozoa-specific sequence organizations in transcripts tagged with GACA/GATA repeats substantiated this hypothesis.
The gene copy number of individual genes/gene fragments corresponding to the transcripts tagged with minisatellite 33.15 was calculated using standard curve method.
The full list of all transcript tags with their annotation and assignment to GO terms is available in Additional file 3. Other relevant statistics include an average transcript tag length of 933 bp, N50 of 622 bp, 196.4× coverage (actual number of reads mapped/transcriptome length) and longest sequence of 13855 bp.
Genes (i.e. tags that matched a transcript) and tags that were only aligned to the genome were analyzed separately.
Starting with a dataset of 149,291 unique transcript tags, a second filter selecting for a project total (sum expression level all 22 libraries included in this study) of ≥10 counts was applied reducing the amount of transcript tags to 23, 649.
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