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As expected, 86.5 % of these 21-nt phasiRNAs mapped to unannotated regions of the O. sativa genome.
Most of the reads mapped to unannotated regions 40-700%) probably due the scarcity of annotated elements for Anopheles gambiae.
Transcripts that mapped to unannotated regions of the T. hominis genome were screened for potential ORFs by using BLASTx to search against the nr database with an E-value threshold of 0.01.
In addition, 58.3 % of piRNAs are mapped to unannotated sequences, a portion of which may represent novel protein-coding genes, TEs, or long non-coding RNA genes (Fig. 2b).
These 135 tag types represented 114 candidate genes with 7 tag types that did not map to the genome, 5 tag types that mapped to unannotated genomic locations, and 9 genes that were associated with more than one tag type.
After removing rRNA reads, for each of the substrates tested, 74.3% to 84.2% of the reads were mapped to previously annotated coding regions, and the remaining were either upstream of a coding sequence (CDS; thus putatively identifying a 5′-untranslated region (5′-UTR)) or mapped to unannotated or potentially mis-annotated regions.
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Mapping the unigenes matching the grape genome in regions not annotated as coding sequences to the VvGI identified a further 2,663 transcripts that, together with the remaining 3,709 unigenes mapping to unannotated regions of the genome and that we considered putative novel genes, raised the grape genes represented to 21,846.
Some of this difference may be attributed to the larger proportion of unannotated sequences in An. gambiae, where at least 58.3 % of piRNAs are mapped to the unannotated part of the genome.
A few small RNA reads were mapped to previously unannotated regions, including the 70 kb and 153 kb regions of the EBV genome.
These also included 189 novel transcripts, which were mapped to the unannotated regions of the genome.
That is, specific qRT-PCR primers could not be designed due to repetition in the genome, or because the tag mapped to an unannotated transcript variant.
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CEO of Professional Science Editing for Scientists @ prosciediting.com