Hi Yi, The refSeq track on rn4 was created before refGene was changed to have frame data. Unfortunately, this means that this track will at times display the incorrect frame. Our developers are currently working on updating this track to include frames information.
When creating the UCSC Genes track, we collect various types of CDS evidence, including information from RefSeq, GenBank mRNAs and several protein databases. Verifying the cdsStart across several sources allows us to safely assume that the first codon of each UCSC Genes item is complete (begins in translation frame 0). During the post-processing of the alignments we add in small alignment gaps to prevent the track from getting the wrong frame when the gene or genome has 1-5 base insertions. These small gaps are displayed as solid lines as opposed to regular introns (larger alignment gaps), which are displayed as lines with arrows indicating the direction of transcription. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 9/14/10 3:48 PM, Yi Lee wrote: > Hello, > > I am looking to extract coding sequence for exons. Most genes tables, like > refGene on hg18/hg19, include a field called "exonFrames", which contains > values 0,1,2 and can be used to translate each exon start-stop genomic text > according to the right frame. So far so good. However, certain genes tracks, > including knownGene for all species, or even refGene for rn4, do not contain > that field. Moreover, because certain genes do not start with a start codon > (or, in other words, have an "incomplete start"), one cannot just assume > that cdsStart is aligned to a frame and start translating all exons > according to that. So, how does UCSC display the codon information when > zooming in to a knownGene (or a refGene in rn4)? Which table is that > information stored? Where is the missing exonFrames info? > > Thanks in advance, > Y. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
