Most transcripts are tagged as 'protein coding', but there are some transcripts tagged as 'nonsense_mediated_decay' (NMD).
We were also interested to analyse some poorly-characterized genes, where there is little information on function or mutant phenotypes but where there is some transcript abundance information allowing an assessment to be made of the accuracy of network predictions.
Moreover, there were some unknown transcripts in the data set.
For alternative splicing, it was possible that there were some genes spliced as multiple transcripts.
However, there were some discrepancies with the quantitation of transcripts with high copy number, such as C3 (complement component 3).
In addition, there are some chimeric transcripts that would encode a complete CSNK2B protein considering that they contain all exons (1-7) of Csnk2b including the stop codon and in which the Ly6g5b nucleotide sequences will act as 3´ UTRs.
Even though there are some incomplete transcripts in the ESTs, full-length-enriched cDNA libraries are much more valuable for determining the correct structures of functional mRNA than are cDNA libraries constructed by using normal methods, because the latter rarely yield intact full-length cDNAs [ 26].
Although there was some reduction in transcripts encoding structural proteins including the flagellar protein PFR2 and tubulin, the observed reduction of just a few transcripts does not explain the global protein synthesis arrest phenotype.
The high percentage of down-regulated transcripts in the exoribonuclease mutants might be an indirect consequence of the exoribonuclease deletion, although there is some evidence that some transcripts can be protected instead of being degraded by the exoribonucleases [ 8, 9, 31, 33].
There is some evidence that chimeric transcripts can be assembled and exist in EST collections.
