Hi, Where can I find the gene id number for uc007mkn (or 2310004N24Rik) gene? The gene id for this gene is "69535". I looked into kgXref and knownGene, both files do not have that.
Thanks, perdeep -----Original Message----- From: Hiram Clawson [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 22, 2008 1:44 PM To: Mehta, Perdeep Subject: Re: [Genome] finding coordinates of genes I have been informed by a colleague here that the kgXref table is better than even kgAlias: mysql> select * from kgXref where geneSymbol='2310004N24Rik'\G *************************** 1. row *************************** kgID: uc007mkn.1 mRNA: BC027639 spID: Q9D7K2 spDisplayID: Q9D7K2_MOUSE geneSymbol: 2310004N24Rik refseq: protAcc: description: Adult male tongue cDNA, RIKEN full-length enriched library, clone:2310004N24 product:hypothetical protein, full insert sequence (CRL-1722 L5178Y-R cDNA, RIKEN full-length enriched library, clone:I730043L06 product:hypothetical protein, full insert sequence) (2310004N24Rik protein). Mehta, Perdeep wrote: > Thank you so much! > > I already have the ucsc identifier for this gene and this should work. > > Thanks for also letting me know about another useful file kgAlias.txt. > > perdeep > > -----Original Message----- > From: Hiram Clawson [mailto:[EMAIL PROTECTED] > Sent: Wednesday, October 22, 2008 12:41 PM > To: Mehta, Perdeep > Cc: '[email protected]' > Subject: Re: [Genome] finding coordinates of genes > > Good Morning Perdeep: > > The knownGene.txt file has genes listed by their UCSC identification. > Look for the name uc007mkn in the knownGene.txt file: > > uc007mkn.1 chr11 + 116060202 116076632 116066204 > 116076391 4 > 116060202,116066158,116066924,116076152, > 116060297,116066293,116067082,116076632, Q9D7K2 uc007mkn.1 > > You can see the name relationships in the kgAlias.txt file: > uc007mkn.1 2310004N24Rik > uc007mkn.1 BC027639 > uc007mkn.1 Q9D7K2 > uc007mkn.1 Q9D7K2_MOUSE > > You can link all this information together in the table browser. > Use the output format: "selected fields from primary and related tables" > > --Hiram > > Mehta, Perdeep wrote: >> Hi, >> >> I have a mouse gene id like, 2310004N24Rik, I want to get the coordinates of >> its gene structure. This gene displays in UCSC genome browser on antisense >> strand of chr11 when searching a sequence with BLAT, but when I look into >> the downloaded mouse knownGene.txt file it does not have this entry. >> Apparently the gene structure coordinates looks like to have been stored >> other than the above mentioned file since UCSC's genome browser does display >> the gene structure for this. >> >> Which file would have the gene structure coordinates for 2310004N24Rik gene? >> >> Thanks for any help. >> perdeep >> >> Perdeep K. Mehta, PhD >> Research Informatics, Information Sciences Division >> St. Jude Children's Research Hospital >> 262 Danny Thomas Place >> Memphis, TN 38105-2794 >> Tel: 901-595 3774 >> http://www.hatwellcenter.org/ >> >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> http://www.soe.ucsc.edu/mailman/listinfo/genome >> > > > > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
