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|specie||scientific name||EPDnew TSSs||Additional resources for TSSs|
Promoter sequences (±100bp relative to the transcription start site (TSS)) were downloaded from the Eukaryotic Promoter Database (EPDnew).
The ElemeNT algorithm was used to predict core promoter composition, providing a score between 0 and 1 for each predicted element. ElemeNT default parameters were used for creating this data. Motifs were scanned in a ±10bp window relative to the expected motif location, based on its known distance from the TSS.
For each organism, the resulting motif predictions were converted to multiple BED files, each BED file corresponds to a single core promoter element. A custom UCSC genome browser session was generated based on the BED files.
The detected core promoter elements are denoted as gray-scaled blocks in their relevant genomic position. The blocks’ intensity represents the corresponding score (scaled from 0 to 1000, according to BED format). Since MTE, DPE and bridge elements are Inr-dependent, every prediction of these elements has been visually linked to a thin block, representing its relative Inr.
For human and fly genomes, additional sessions were created- based on GENOCODE and FlyBase annotation, respectively.