Hello Steve, Thank you for your detailed response.
I am wondering why then when I have a gene like below: chr19 | 896502 | 897436 | uc002lqg.2_utr3_0_0_chr19_896503_r | 0 | - uc002lqg.2 | chr19 | - | 896502 | 913225 | 897436 | 913157 | 8 | 896502,899439,899600,900060,900828,901421,901975,913086, | 897540,899495,899686,900146,900952,901546,902130,913225, | Q96D70 | uc002lqg.2 why does this only have 3' UTR result when it has 8 exons. Im sorry if I am just not understanding this. Thanks, Dan On Wed, Mar 28, 2012 at 1:36 PM, Steve Heitner <[email protected]> wrote: > Hello, Dan. > > Please see this previously-answered mailing list question for a good > explanation of Sequence Type Number: > https://lists.soe.ucsc.edu/pipermail/genome/2011-March/025223.html > > In response to your question about why exon data is not used for every > gene, > exon coordinates are used for every gene. It may not always be obvious > because some genes only contain one exon while others, such as in your > example, contain multiple exons. In the case of a gene with multiple > exons, > the Sequence Type Number becomes more apparent, as you noticed. > > In response to your question about knowing when you need a Sequence Type > Number, the public MySql table and the Table Browser have no notion of a > Sequence Type Number - the mysql table has one row per transcript and the > Table Browser breaks out the tx{Start,End}, cds{Start,End}, strand and > exon{Starts,Ends} coordinates into a series of per-exon coords (with CDS > parts of exons clipped off). > > Please contact us again at [email protected] if you have any further > questions. > > --- > Steve Heitner > UCSC Genome Bioinformatics Group > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Dan Morton > Sent: Tuesday, March 27, 2012 6:30 PM > To: [email protected] > Subject: [Genome] 3' UTR - Sequence Type Number > > When downloading 3' UTR data for a particular range I get the following > results related to "uc010drt.1" > > chr19 | 680714 | 680879 | uc010drt.1_utr3_0_0_chr19_680715_f > | 0 | + | 165 > chr19 | 681332 | 681560 | uc010drt.1_utr3_1_0_chr19_681333_f > | 0 | + | 228 > chr19 | 681649 | 683392 | uc010drt.1_utr3_2_0_chr19_681650_f > | 0 | + | 1743 > > I noticed the "Sequence Type Number" for this gene increments for this > gene. > Indicating that exon data is used? > - Why is exon data not used for every gene and how do I know when? > > After downloading and looking through the website src I discovered that > this > number is related to something called extraSize and a trackQualifier. > > When using the genome public mysql server how do I know when I need a > "Sequence Type Number". > > I know this is a lot to ask, and helpful information will greatly > appreciated. > > Thanks, > Dan > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
