MiRNA target site positions on the nucleotide level were extracted from the TarBase UCSC custom annotation tracks [21] as of August 2008.
Further, other reported transcriptome analyses may overestimate the number of novel features discovered due to the incompleteness of the reference annotation tracks used [ 20, 23, 51, 53, 75].
The annotation file used to generate the splice junctions was a non-redundant transcriptome database generated from the 8 empirically-determined transcriptome annotation tracks (UCSC, Refseq, Vega, Aceview, Ensembl, Gencode V7, CCDS and lincRNA) [ 32, 42- 48].
Projected annotations track the orientation and location of pages as the user moves them on the desktop.
A curated annotation was constructed by integrating the various annotation tracks and hand annotating individual genes.
First, the RNA-Seq analyses of human retinal RNA samples detected 75% of previously annotated exons, based on the combined annotation track used for these studies, which includes over 1 million unique exons.
This class of fragmented DNA, representing 63.91% of the detected DNA in our results, was annotated based on the D. melanogaster annotation tracks (supplementary table S1, Supplementary Material online) but was only analyzed as neighboring sequences of the detected CDSs and TE sequences.
Sequence data were annotated using ANNOVAR (v2013Jun21) and the UCSC RefGene annotation track.
Notably, this locus was not annotated as a processed pseudogene in pseudogene-related annotation tracks at UCSC Genome Brower.
The Ensembl database, however, does not have this antisense transcript annotated but it does have two genes annotated further downstream as shown in the Ensembl annotation track in Figure 4.
