I've a list of genes to do a Target Sequencing and now I need to create a list of NM_xxxxx number to give for the ''producion'' of capturing probes for my genes/regions of interest. However I have some questions concerning the NM_xxxx Numbers and also concerning your site/UCSC. 1st question: For each gene, do I need to introduce all the NM_xxxxx numbers corresponding to each splice variant to be sure that all exons of all coding variants will be captured? 2nd question (if yes for the 1st question): How can you get the genomic coordinates of all the exons for all the splice forms (variants) for a given gene ? In UCSC, I can only get one cDNA at a time, getting the NM number for it, but not including all exons (only the exons included in this particualr cDNA). Is there a way of getting the coordinates for all the exons of one gene, with a unique NM_xxxx number containing all exons ? Or is an NM number restricted to one isoform ? In that case where can I find the genomic coordinates of all the exons for one specific gene ??? Thank you very much for your (quick) help. 3rd question If I use another database to obtain all the NM_xxxx number (p.e. NCBI, ENSEMBL) does can be a problem for the genomic coordinates? In other word cas I do the NM_xxxx number list for exemple with Ensembl and after upload the list on UCSC and prepare the the file with all the genomic coordinates? Thank you very much for your help. Belinda Xavier Belinda Campos-Xavier, PhD Centre Hospitalier Universitaire Vaudois 1011 Lausanne Switzerland Email: [email protected]
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