Hi Alessandra, It is possible the literature is referring to the hg18 assembly and you are using the hg19 assembly for your analysis. Or it could be an exon numbering off-by-one error. The CDS FASTA files start at exon 1, it's possible the literature reference is starting at zero.
Hopefully this information is helpful and answers your question. Please contact us again at [email protected] if you have additional questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 12/16/2011 9:59 AM, Alessandra Breschi wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
