Based on the most current genome annotation, the transcription start site (TSS), initiation codon and predicted TATA box of a given locus were determined.
Most current NGS annotation tools follow the left aligned input VCF coordinates which position an indel at the most 3′ position if the coding transcript is on the reverse strand (e.g., BRCA1), but at the most 5′ position if the coding transcript is on the forward strand (e.g., BRCA2).
Another reason for the small number of annotated genes is because most of the current annotations are based on A. thaliana, B. rapa and P. trichocarpa and we already subtracted the sequences orthologous to them.
For genes with several transcript isoforms, we selected the transcript of which the current annotation extended most 3'.
As the transcriptome dataset is revised and supplemented with addtional manually curated annotations, the most current functional data will be made available to the community via the public portal and annotation tool.
The true percentage of reads that map to intergenic regions might be even lower, because some genes are most likely still missing in the current annotation and not all UTRs for all predicted genes have been annotated yet (see previous section).
The newly updated tree provides more specific grouping, most likely due to the better current annotation of the GH43 genes, as biochemical data have been reported for all proposed five phylogenetic groups after the previous tree was published.
The Ensembl probeset annotation pipeline is optimised to create a comprehensive gene expression array annotation based on the most current genome sequence and species-specific supporting data.
