Hi Phenix, The UCSC Genes set is created in part by considering many mRNA sequences. See details about the pipeline here:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene The mRNA sequence you get by clicking the "mRNA (may differ from genome)" link on the details page of a UCSC Gene (or by looking in the table knownGeneMrna) is a representative mRNA sequence that is chosen because it most closely matches the gene prediction generated by the UCSC Genes pipeline. In the next data update of the UCSC Genes track, we are going to include a table, in addition to the knownGeneMrna table, that contains sequence generated from the reference genome using the gene model. (This table will be called "knownGeneTxMrna.") I hope this helps explain the UCSC Genes track. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/16/11 6:55 PM, Phenix Hydra wrote: > Dear Luvina Guruvadoo or someone others, > > > > I get the mRNA sequence of uc001aoe.1 from the web source. It starts > with “gttgggggcag...”. But the genome sequence of the first exon > starts with “gtccct...”. I have compared the two sequences. The exon > sequence has an additional 42 bp sequence on the 5’ end. Is that a > mistake or just some genomic phenomenon I don’t know? > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
