Hello Can, What you are detecting are the alignment differences generated by a direct BLAT of the query sequence(s) versus the genome(s). For the Other RefSeq track, there is no special filtering or processing to generate orthologous gene structure alignments. The differences are an expected result for this type of track.
To examine more directed conservation annotation, considering alternate tracks independently or in combination with the "Other" tracks may be a better fit for your research. To date, there is no definitive, genome-wide Ortholog/COG gene mapping or grouping annotation. There are however several tracks with important information that can help solve individual region's conservation. Some suggestions: UCSC Genes (best hit in other species is noted), Conservation (4 subtracks plus codon translation), Exoniphy, Chain/Net tracks. Some of these are genome-based, some are gene based, and some a combination. Hopefully this helps to explain the data. Please feel free to contact the mailing list support team again if you would like more assistance. Warm regards, Jen UCSC Genome Browser Support On 8/16/10 11:38 AM, Can Cenik wrote: > Hi, > > I have been using the "Other RefSeq" track to compare transcript > structures between genomes. However, I realized that the transcript > structure shown in other RefSeq track does not match the original > RefSeq transcript from the target genome. > > Consider NM_022331 from the mouse genome as an example. When one looks > at the homo sapiens ortholog among the Non-Mouse Refseq genes, several > 3'UTR introns are annotated. However, when the human genome is > searched for NM_014685, the corresponding ortholog in human, no 3'UTR > introns are evident. > > I was unable to find any references to this problem in the table > schema and track descriptions. > > Thanks in advance, > Can Cenik > Harvard Medical School > Department of Biological Chemistry and Molecular Pharmacology > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
