Expression levels of the identified TSS for the three genes. Dot plots showing the expression level of each promoter in TPM values in all brain regions, and selected other samples (based on expression level). The novel promoter pA@Foxg1 is the most highly expressed Foxg1 TSS in mouse primary cells and brain tissue (a), with the highest expression in cortical neurons (1018 TPM) and neonate hippocampus (435 TPM). Among mouse cells, we find high levels of p1@ Foxg1 expressed in hippocampal neurons and fibroblast cell line. In human samples (panel b) the highest expression of FOXG1 is seen from p1@FOXG1 in fetal temporal lobe (292 TPM), among primary cells in neurons (149 TPM) and among cell lines in medulloblastoma cell line (184 TPM). For mouse Mecp2, the highest expression of p1@Mecp2 is in striatal neurons (77 TPM) and cerebellar granule cells (70 TPM) and among mouse tissues (panel c) the maximum expression is seen in neonate corpus striatum (65 TPM) and adult cerebellum (52 TPM). For human, the highest expression of p1@MECP2 is found in cancer cell lines including breast carcinoma cell line (119 TPM) (panel d). In human brain the highest expression of p1@MECP2 is found in the temporal lobe (63 TPM). The two promoters of Cdkl5 in mouse are co-expressed with highest expression in adult cortex in the brain and raphe neurons among primary cells (panel e). In humans (panel f) the two promoters are expressed differentially with transcripts arising from p1 over-represented. p1@CDKL5 expression is highest in the newborn medial frontal gyrus and in neurons. In human cancer cell lines, CDKL5 is generally expressed at low levels (less than 10 TPM) from either of the promoters (p1 > p2), with a few exceptions (Additional file 1: Table S1, Additional file 3: Figure S1f).