Hi Maria, This discrepancy is likely due to the way we construct the RefSeq track. We construct this track by taking the entire mRNA sequence from Genbank and aligning it to the genome using Blat (for more information see the details page here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=refGene). In other words, we do not use the RefSeq produced annotations.
Very small exons, like those you have pointed out, are quite difficult for computer algorithms, such as blat, to align correctly to the genome. These small exons can be often included in next exon or not included at all. Hand curated tracks, such as Gencode, have a higher probability of aligning these very small exons correctly. For MYBPC3, if you turn on the Gencode track, you'll see that exons 10 and 14 are included in the annotation. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Maria elena Sana wrote, On 04/22/11 02:37: > Good morning, > I found a discrepancy among RefSeq annotation and UCSC genome browser > annotation. > For example, MYBPC3 gene (NM_000256) has 35 exons (We are sure of this > information). Two of these exons are very small and have only 3 nucleotides > (exon 10: chr11:47,368,578-47,368,580 and exon 14: > chr11:47,364,811-47,364,813). > In NCBI and Ensembl databases, I can find the correct exon counts with the > correct coordinates, while in Genome Browser, the MYBPC3 exon counts is 33, > and these small exons are reported as introns (in Tables fields too). > > How can I explain this mismatch? > > Thanx a lot, > Maria Elena > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
