Hi, The issue is that the RefSeq identifier in your example has been replaced by RefSeq. If you go to:
http://www.ncbi.nlm.nih.gov/nuccore/NM_214677.1?report=genbank You will see the message: NCBI Reference Sequence: NM_214677.1 This sequence has been replaced by NR_026707. The reason you can still find a reference to it in the knownGene track on hg18 is that that track was updated in 2009 (see the "Data last updated" note at the top of the page). On the other hand, the refGene track is updated on our site every day, so this is normal. Admittedly, our error message is not very informative. I have submitted a request to our engineers to change it so that it is more obvious what the problem is. I suggest looking for the rest of your missing NMs in NCBI's Nucleotide database (http://www.ncbi.nlm.nih.gov/nuccore/) to see if they have changed or have been replaced. You should be able to find the current set of RefSeq identifiers in the Genome Browser. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 10/7/11 2:35 AM, Luqman Hakim Bin Abdul Hadi wrote: > Hi UCSC team, > > I'm noticing an inconsistency of a large scale between the Browser > andthe Table. > In particular, I have a list of NMs (refseq ids) which I need to get its coordinates using 'track: RefSeq Genes' and 'table: refGene'. For brevity, lets use NM_214677 (there are other genes in my list with the same problem) > > An error inn the Table browser led me to suspect that NM_214677 > could be missing: > "Note: 1 of the 1 given identifiers (e.g. NM_214677) have no match > intable refGene, field name or in alias table refLink, field name. Try the "describe table schema" button for more information about the table and field." > > I proceeded to try almost every possible table but I could not find NM_214677. I was beginning to resign to my fate until I checked the Genome Browser and found NM_214677 here: http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc002mie.1&hgg_prot=Q9H2X3-2&hgg_chrom=chr19&hgg_start=7734080&hgg_end=7740491&hgg_type=knownGene&db=hg18&hgsid=216140513 > > However, the link in the page (under 'Other Names for This Gene'), which I suppose should link me to another page gave me this error: > "Couldn't find NM_214677 in refLink table - database inconsistency." > > I hope a fix is already in place, otherwise is this 'normal'? Is > there any other particular way that I can search for my missing NMs? > > Thanks! > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
