Fig. 2

Assorted conventions for regions, start, end, and strands. This figure shows two hypothetical features on a DNA sequence (labeled chr1), on either the forward strand (orange) or reverse strand (blue). Using the INSDC location string notation, these regions are “1050..2080” and “complement(1050..2080)” respectively if implicitly given in terms of the reference chr1. Using the GTF/GFF3 family of formats, regardless of the strand these two locations are described with s t a r t=1050 and e n d=2080, and in general, s t a r t≤e n d. Biologically speaking, in terms of transcription, the start of a genomic feature is strand dependent. For the forward strand feature (orange), the start is 1050 while the reverse strand feature (blue) starts from 2080