Conservation-based prediction of the transcription regulatory region of the SCN1A gene

A challenge in identifying the transcription regulatory region is that the locations of eukaryotic transcriptional elements are often diverse among different genes. SCN1A, a disease-related sodium channel gene, has a complex 5′-untranslated region and diverse mRNA transcripts, which might be driven by different promoters. By cross-species sequence comparison and bioinformatics analysis, human 5′-untranslated exons were found to be conserved within the region of 200 kb upstream of the 5′ flanking regions of SCN1A in higher mammals, but not in lower mammals and non-mammals. The core promoter elements (INR, DPE, and TATA) were found in the regions flanking different 5′-untranslated exons, suggesting that these sequences (from −45 to +35) might be targeted as core promoters. The nucleotide identity rate of these core promoter sequences are different, and the conservation level of the upstream region of each core promoter varies distinctly, implicating different regulatory mechanisms of the four promoters which exist in the nervous system.