Hi Yongsheng, UCSC Genes doesn't include experimental RefSeq Genes (we only use NM_ and NR_ identifiers, described here: http://www.ncbi.nlm.nih.gov/projects/RefSeq/key.html#accessions).
Also, as you can see from the first step in the process of creating the UCSC Genes track (copied from the UCSC Genes track description Methods section) we align these RNAs with BLAT and keep only those with alignments with 98% or higher identity: "1. RefSeq and GenBank RNAs are aligned to the genome with BLAT, keeping only the best alignments for each RNA and discarding alignments of less than 98% identity." I hope this information is helpful. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Yongsheng Bai wrote, On 03/04/11 08:11: > Hello, > > Just to make sure that UCSC knownGene annotation includes all of RefSeq + > Others... > > Thanks, > Yongsheng > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
