Fig. 1

Classification of transcription start sites. a Schematic overview of categories used for classification of TSSs according to their genomic context. sTSS: Sense TSSs with a annotated ORF downstream in a maximal distance of 300 nt. (n)sTSS: TSSs downstream of an ORF start, which were used to revise the translation start position (corrected ORF). pTSS: Putative TSSs assigned to annotated ORFs downstream, yet with a minimal distance of 300 nt and a maximal distance of 600 nt. iTSS: Intragenic TSSs in sense orientation. asTSS: TSSs located antisense to ORFs or UTRs. nTSS: Intergenic TSS representing possible novel transcripts. Also, possible scenarios with TSSs associated to more than one category are shown. b Number and classification of detected TSSs. TSSs belonging to rRNA, tRNA, and RNase P genes as well as false positive TSSs were removed. Two thousand three hundred fifteen manually verified TSSs were considered for classification. The Venn diagram showing overlap between the categories was generated with Venny 2.1.0 [95]. c Upper panel: Nucleotide distribution at the transcription initiating site +1 as well as at −1 and +2 based on the TSSs identified solely for the categories sTSS, pTSS, iTSS, and asTSS. The 10 TSSs assigned to both sTSS and pTSS were assumed to be sTSSs (see Results). Lower panel: Distribution of the read start coverage for TSSs assigned to the categories sTSS, pTSS, iTSS, and asTSSs. TSSs with the highest (Top 10%) and lowest coverage (Low 10%) are bold-framed. The number (n) and the average coverage (∅) for all TSSs and the top as well as low 10% is given for each category