The CORE database includes a list of core promoter elements/motifs located around annotated transcription start sites (TSSs) of ten species, namely:
Drosophila melanogaster (dm6)
Homo sapiens (hg38)
Macaca mulatta (rheMac8)
Mus musculus (mm10)
Rattus norvegicus (rn6)
Gallus gallus (galGal5)
Canis familiaris (canFam3)
Apis mellifera (amel5)
Danio rerio (danRer7)
Caenorhabditis elegans (ce6)
Promoter sequences (±100bp relative to the TSSs) were downloaded from the Eukaryotic Promoter Database (EPDnew) at https://epd.expasy.org/epd/EPDnew_database.php.
ElemeNT 2023 was used to predict 16 core promoter elements/motifs – GAGA, BREu, TATA box, BREd, XCPE1, XCPE2, Ohler Motif 1, dTCT, hTCT, BBCABW, hInr, dInr, MTE, bridge, DPE and Pause button.
For each analyzed transcript, the existence of a putative core promoter at the expected position relative to the TSS is indicated. If a putative element exists, its relative position and search score are denoted (position, score). If more than one putative element exists, all the possible elements are indicated, with a semicolon separator. For DPE, MTE and Bridge elements the denoted position is of the associated Inr, as these elements are functional only at the precise position relative to the Inr. Motifs were scanned using a ±10bp window relative to the expected motif location, based on its known distance from the TSS. The motif search was normalized to the species GC-content.
The parameters used in the ElemeNT run are listed in the sheet ‘ElemeNT run parameters’.
The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. Dreos, R., Ambrosini, G., Groux, R., Périer, R., Bucher, P. Nucleic Acids Res. (2017) 45:D51-55; PUBMED 27899657