Thanks. I was just trying to avoid mixing the two databases. Hopefully they are updated at the same time to get most comparable current annotations.
Thanks anyway for your reply. perdeep -----Original Message----- From: Pauline Fujita [mailto:[EMAIL PROTECTED] Sent: Tuesday, November 04, 2008 5:41 PM To: Mehta, Perdeep Cc: 'Hiram Clawson'; '[email protected]' Subject: Re: [Genome] finding coordinates of genes Hello Perdeep, The ID "69535" is an entrez gene ID for the non-RefSeq gene uc007mkn.1. We only have entrez gene IDs for records that are RefSeq genes. As such we don't have the identifier "69535" in our tables. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Mehta, Perdeep wrote: > 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 > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
