Hello Andrew, The gbCdnaInfo table links the Genbank accession number to the CDS information you are looking for. The CDS info is in the 'name' field of the table 'cds'. The relationship is:
gbCdnaInfo.acc --> gbCdnaInfo.cds = cds.id --> cds.name To get the information with the Table Browser, select the gbCdnaInfo table and paste a list of mRNA identifiers. You will need to strip the version number (the ".1") off first. Choose "output format: selected fields from primary and related tables". Hit "get output", select the cds.name field, and hit "get output" again. You should see a result like this: #hg19.gbCdnaInfo.acc hg19.cds.name NM_001014431 341..1783 Please let us know if you have any further questions by replying to the list at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group Andrew Yee wrote on 4/8/10 8:25 PM: > Hi, I was trying to find a table that corresponds to the mRNA information in > Genbank. > > Take for example, the entry for NM_001014431.1 in > http://www.ncbi.nlm.nih.gov/nuccore/62241012. I'd like to find a table > where the coordinates correspond to the numbers listed in the Genbank entry. > I'd like the coordinates to be given with respect to the transcript. For > example, it shows the CDS go from 341..1783. However, the tables I've found > so far at UCSC (e.g. refGene) correspond to the genomic coordinates. > > Thanks, > Andrew > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
