Hello Prashanth, No, the name field in the refGene table can have multiple entries for the same name. To get an idea of how often this occurs, you can select the refGene table in the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), then hit the "describe table schema" button. On the next page, click the "values" link under the info column of the name row.
More information about the RefSeq names and how they are generated is available on the RefSeq site at NCBI: http://www.ncbi.nlm.nih.gov/RefSeq/ -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/20/08 3:25 PM, Prashanth Athri wrote: > Dear all, > > I had written earlier about dealing with multiple entries for a particular > gene in refGene for which a part of your response was: > > >> We simply download the RefSeq mRNAs and align >> them to the genome using BLAT. In some cases there are gene >> families that have several isoforms. That may be what you >> are seeing. In the Ref Gene track, we do NOT make at attempt to >> filter any of the annotations by choosing the "best" one, or >> a "representative" isoform. >> > > My question is: > With respect to gene families that have several isoforms, will the second > field in the ref Gene table, titled ³name² be a unique identifier (It is > usually of the form NM_12334) ? As in lets say some gene XYZ has two > isoforms, is it always true that the ³name² field will be different for > these two isoforms? > > Thanks in advance, > Prashanth > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
