Fig. 1

Summary of RE sequence features and associated grades in p53retriever. a Grade: classification of REs reflecting associated functional scores. The color code matching the 5 different grades will be maintained in all figures. b Mismatch label: classification of mismatches in different positions. High penalties are given to mismatches located in the core consensus sequence (label A and B), lower penalties are given when mismatches are gradually distant from the core (label C and D). Label O is given to a site without mismatches. Mismatches group penalties: different penalties are attributed to groups of mismatches according to how they are scattered or grouped along the site. c Schematic representation of the main rules on which p53retriever search algorithm is based. The full list of rules is listed in Additional file 1. The p53 consensus sequence is presented, grouping dinucleotide motifs that were revealed to provide a specific impact on transactivation potentials, based on our previous studies (see text for details) [28]. Penalties are indicated by an increment in the number of the “-” symbol and a color code broadly matching the grade scale. Single mismatches are more penalized when affecting a base in the internal portion of the RE, as indicated. On the contrary, the AT motif at the center of the CWWG core is a positive feature, particularly in the case of non-canonical REs (3Q = 3Q sites and half sites)