Hi Ilana, mm9/mm10 refer to the reference assembly, which is completely independent from the gene annotations made on that assembly.
RefSeq is one gene annotation track; and is one that is updated every day on our site. The status of Snhg12 was probably changed due to continued research, however, this didn't require a change to the reference assembly (mm9), only to the annotation. So, the mm9 assembly hasn't been updated, but the annotations for it have. For more information on RefSeq, see: http://www.ncbi.nlm.nih.gov/books/NBK21091/ The revision history for Snhg12 can be seen here: http://www.ncbi.nlm.nih.gov/nuccore/NR_024127.1?report=girevhist Also helpful...genome assembly vs. gene annotation: Genome Assembly: http://en.wikipedia.org/wiki/Genome_project#Genome_assembly Gene annotations: http://en.wikipedia.org/wiki/Genome_project#Genome_annotation Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 8/29/11 7:44 AM, Ilana Livyatan wrote: > Hello, > I'm attaching previous correspondence below with the background for this > question: > > I've been following a certain gen, Snhg12, in mouse mm9 for a while and am > perplexed by how UCSC manages its tables. > > Initially I downloaded the refGene.sql and refGene.txt files from the mouse > downloads page and copied them into my local MySQL version of UCSC (I have a > couple tables stored locally for quick and easy access). > > This table (from about 2 years ago) doesn't contain the Snhg12 gene. > I later came across the gene in the UCSC browser and noticed it was Refseq > provisional status (light blue). > > I assumed that's why I don't see it in my local refGene table, but I asked > about it below to see if I might find it somewhere. > > Upon receiving the answer I tried Vanessa's suggestion (below) which worked. > The Snhg12 gene was in the results with provisional status. > > I recently retried Vanessa's suggestion and noticed that the status has been > updated to "Validated" in both the table browser and the genome browser. > > So I have three different results for Snhg12 depending on when and how I > access the data, yet all of them belong to the same 'mm9' version! > > Isn't this a litle problematic? Is there a reason why these changes aren't > saved up for 'mm10'? > > The implications for my research and perhaps others' as well is that when we > say 'mm9' it isn't the same thing and something that was 'intergenic' one day > is now an 'exon' for example. > > Am I missing something here? I'm just trying to do as precise research as > possible so as not to mislead... > > Thanks, > > Ilana > > > > **************************************************************** > Dear Ilana, > > Please see this previously answered mailing list question that tells how to > get > the status data using the table browser: > > https://lists.soe.ucsc.edu/pipermail/genome/2008-January/015354.html > > The data that you are looking for is located in this table: "refSeqStatus" in > the mm9 database. > > Hope this helps! If you have further questions, please contact the mailing > list > ([email protected]). > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > ----- Original Message ----- > From: "Ilana Livyatan"<[email protected]> > To: [email protected] > Sent: Thursday, February 24, 2011 1:56:58 AM > Subject: [Genome] Getting Provisional Refseq genes > > Hi, > I've downloaded the mysql versions of refgene mm9 and have a local database > going. I noticed that this version doesn't include the provisional > annotations. They do appear in the genome browser as a track with lighter > blue > color. > How do I access and download these provisional Refseq annotations? > I don't want all the UCSC known genes which seem to include these provisionals > but a way to identify them as a separate group. > > Thanks for the help! > > Ilana Livyatan > Dr. Eran Meshorer's Lab > Department of Genetics > Room 2-544, Givat Ram > The Hebrew University of Jerusalem > Jerusalem, 91904 ISRAEL > Tel: 972-2-6585143 Fax: 972-2-6586975 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
