Hi, I am about to perform a screening about exon skipping/inclusion related to relevant diseases. Therefore, I would really like to know the correct exon numbers as they are referred to in the literature. I figured out to obtain the exon numbering, without transcript redundancies, by using the exon structure of the "knownCanonical" table in the UCSC Genes track, and taking the numbers as indexed by CDS FASTA alignment (by selecting only human alignment). I would like to do in an automatic, given a list of gene_names and exon_numbers, retrieve the coordinates, to perform the screening on a considerable number of exons. Unfortunately, I have preliminary checked the numbers of the exons that I obtain in this way starting with an example well commented in the literature. I tried to get the coordinate of the exon 10 of the microtubule-associated protein tau (MAPT) (e.g. PUBMED ID: 18678901). Passing through the procedure that I above mentioned, I obtain that exon 10 has coordinates: chr17:44073765-44074030 (strand +). Instead, the exon 10 to which the literature referred has coordinates: chr17:44087676-44087768 (strand +), that with my procedure is pointed as exon 11.
I would be very thankful if you could tell me what I am missing in my querying the table browser, so that I can apply the correction in an automatic retrieval. Thanks in advance. Best regards, Alessandra Breschi _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
