Small addition: If using this method to extract mRNA sequences, be sure to exclude rows from kgXref that also do not have a mRNA identifier. There are only 5 of these in hg19:
mysql> select kgID, geneSymbol, description from kgXref where mRNA like ""; +------------+------------+----------------- | kgID | geneSymbol |description +------------+------------+----------------- | uc010tyt.1 | abParts | Parts of antibodies, mostly variable regions. | | uc002stl.2 | abParts | Parts of antibodies, mostly variable regions. | | uc010fhm.2 | abParts | Parts of antibodies, mostly variable regions. | | uc010ytr.1 | abParts | Parts of antibodies, mostly variable regions. | | uc011aim.1 | abParts | Parts of antibodies, mostly variable regions. | +------------+------------+----------------- 5 rows in set (0.00 sec) On 4/13/10 2:23 PM, Jennifer Jackson wrote: > Hello again, > > Yes, that would be a correct way to interpret the table contents. > > Thanks! > Jen > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 4/13/10 12:20 PM, Bio X2Y wrote: >> Hi, >> >> >> Concerning the Known Genes annotation, is it correct to say that any >> transcript whose kgxref row contains empty values for spID, spDisplayID, >> refseq and protAcc is a GenBank mRNA based transcript? >> >> >> Thanks for your help! >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
