Hello, I checked the Genbank record at NCBI and this RefSeq moved from Provisional to Validated on 09-APR-2009.
new: http://www.ncbi.nlm.nih.gov/nuccore/226443148 old: http://www.ncbi.nlm.nih.gov/nuccore/14249381 From a bit of analysis, it appears the underlying sequence changed a bit. If I take the original sequence as noted in the current RefSeq record in the line: "On Apr 9, 2009 this sequence version replaced gi:14249381", and run a BLAT on the UCSC Browser using all defaults, I get the original alignment coordinates that you list from Jan 2009. This should clear things up for the UCSC Browser content. Specific questions about this sequence's content (ie: why it changed, implications) would probably be best directed at the RefSeq team at NCBI. From a quick look, it seems that they are working on better defining variants, but that is just an impression from the data thread in the record. For the UCSC Browser's RefSeq track, the Genbank data is used as published. We are not involved in the curation process. Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group Dhiral Phadke wrote: > I downloaded a table of refseq genes from the UCSC Table Browser using this > parameters: > Genome: human > •Assembly: Mar 2006 > •Group: genes and gene prediction tracks > •Track: RefSeq Genes > •Table: refGene > > I had downloaded the genes table in January 2009. I had not saved the > information about exon boundaries in the table at that time. I entered the > same parameters and downloaded the table again today to include the exon > boundaries information. I noticed that some of the genes have a different TSS > start and end compared to the genes in the table from January 2009. Please > can you explain why this is so. I used the March 20006 assembly for both the > downloads. > > Example (gene ABHD14B): > > entry from table downloaded in Jan 2009: > #name chrom strand txStart txEnd name2 > NM_032750 chr3 - 51977570 51983070 ABHD14B > > entry from table downloaded today: > #name chrom strand txStart txEnd name2 > NM_032750 chr3 - 51977566 51983686 ABHD14B > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
