"The substance of the case got lost in the procedural tangle; even the record is not clear because transcripts are missing or blacked out".
This may be due to the possibility that some transcripts were missing from our antennal transcriptome.
When we compared the "gold standard" to our initial gene build, many transcripts were missing.
We have found that some of these transcripts are missing from RABT output completely, whereas some are present but are missing short inner exons (and thus cannot be matched back to their true counterparts).
In some cases, the 5' end of transcripts were missing and here a BLASTn search with a cut-off of e < 1 × 10-10 was carried out against the draft S. ratti genome.
Proteins potentially encoded by some of these alternatively spliced transcripts are missing SRAP N-terminal extremity but still contain SRAP amino acids 180 to 236 recognized by 743A antibody.
Among the non-exonic TARs, 3473 matched with the current rice Unigene set (Figure 1A), suggesting that those transcripts were missed from the genome annotation we used.
This was illustrated at site 3 where two MLL AFF1 fusion transcripts were missed by the MMA.
It should be noted that transcripts present in less than 3% of total transcripts were missed in some reactions.
