Hi Denise, Please see this previously answered mailing list question, which explains what happens when you enter an identifier into the position/search box: https://lists.soe.ucsc.edu/pipermail/genome/2006-March/010032.html . The search is querying several tables that contain RefSeq identifiers, and in the example cases, is returning UCSC Genes. Please note that the RefSeq track is updated daily, and the UCSC genes track (on hg19) was last updated in 2009. If you would like to retrieve positions of the UCSC Genes displayed on the browser search results, then you will need to go through the kgXref or knownToRefSeq tables, then use the knownGene table to get actual positions. You could use the Table Browser to view table relationships (set table to 'refGene' then click the 'view table schema' button).
I hope this answers your question. Please contact us again at [email protected] if you require further assistance. Best, Luvina --- Luvina Guruvadoo UCSC Genome Bioinformatics Group Denise Mauldin wrote: > Hello all, > > I've downloaded information from the MySQL server via the command: > > echo "use hg19; select rg.name, rg.chrom, rg.strand, rg.txStart, > rg.txEnd, rg.exonStarts, rg.exonEnds from refGene rg;" | mysql > --user=genome --host=genome-mysql.cse.ucsc.edu -A -B > > hg19_refseq_positions.txt > > There are several refseq IDs that do not have entries in this file, > but if you put that refseq ID into the browser will get a result. > > NM_001081472, NM_001144763, NM_001144765, NM_001145027, NM_002978, NM_020359, > NM_022564, NM_130389, NM_152300, NM_152929, NM_152930, NM_173164, NR_001444 > > How does the genome browser have results for these refseq IDs but the > refGene table does not contain entries for them? > How do I get positions for these refseq IDs if they're being retrieved > from a table other than refGene? > > Thanks, > Denise > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
