ER17p is a synthetic peptide corresponding to the sequence P295LMIKRSKKNSLALSLT311 of the estrogen receptor alpha (ER) and initially synthesized to mimic its calmodulin binding site. ER17p was subsequently found to elicit estrogenic responses in E2-deprived ER-positive breast cancer cells, increasing proliferation and E2-dependent gene transcription. Surprisingly, in E2-supplemented media, ER17p induced apoptosis and modified the actin network, influencing thereby cell motility. Here, we report that ER17p induces a massive early (3h) transcriptional activity in breast cancer cell lines SKBR3). Remarkably, about 75% of the significantly modified transcripts were also modified by E2, confirming the pro-estrogenic profile of ER17p. The different ER spectra of the used cell lines allowed us to extract a specific ER17p signature related to ER and its variant ER36. With respect to ER, the peptide activates nuclear (cell cycle, cell proliferation, nucleic acid and protein synthesis) and extranuclear signaling pathways. In contrast, through ER36 it exerts inhibitory events on inflammation and cell cycle and inhibition of EGFR signaling. This is the first work reporting ER36 specific transcriptional effects. The fact that a number ER17p-induced transcripts is different from those activated by E2 revealed that the apoptosis and actin modifying effects of ER17p are independent from the ER-related actions of the peptide.