Fig. 2
From: Identification of a novel long non-coding RNA within RUNX1 intron 5
Multiple transcription start site predictions are found within chromosomal breakpoint regions of RUNX1 intron 5. Using the free online software YAPP Eukaryotic Core Promoter Predictor, the presence of core promoter elements within RUNX1 gene intron 5 (a, top panel), a region surrounding the transcription start site (TSS) of SNRPD3 gene (a, middle panel), and a gene-free region found in chromosome 1 (a, bottom panel) was analyzed. The genomic sequence of the three regions was used as input. The cutoff score considered for this analysis was 0.99. Each arrow represents the central position of initiator elements (INR) found within each region, that is, potential TSSs. Additionally, processed data from CAGE experiments performed in 35 cell types, available in the server ENCODE, was analyzed to evaluate the presence of TSSs, predicted using Hidden Markov Models (HMM) based on raw CAGE data, within RUNX1 gene intron 5 (b, left panel); a region surrounding the TSS of SNRPD3 gene (b, middle panel); and a gene-free region found in chromosome 1 (b, right panel). Each region was subdivided into 2.5-kb modules, as indicated by roman numerals. The bars indicate the total number of TSSs predicted in each respective subdivision, distinguishing between TSSs in the positive strand (black) and TSSs in the negative strand (gray)