Hello, Dan.
You received those results because you were only looking at the 3' UTR exons for uc002lqg.2. Please see my Table Browser results below for both of the genes you have referenced: For uc010drt.1, there are 3 total exons: chr19 680714 680879 uc010drt.1_utr3_0_0_chr19_680715_f 0 + chr19 681332 681560 uc010drt.1_utr3_1_0_chr19_681333_f 0 + chr19 681649 683392 uc010drt.1_utr3_2_0_chr19_681650_f 0 + The hgGene page for uc010drt.1 is here: http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc010drt.1 <http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc010drt.1&hgg_prot=&hgg_chr om=chr19&hgg_start=680714&hgg_end=683392&hgg_type=knownGene&db=hg19> &hgg_prot=&hgg_chrom=chr19&hgg_start=680714&hgg_end=683392&hgg_type=knownGen e&db=hg19 For uc002lqg.2, there are 8 total exons (the 3' UTR is part of the first coding exon and the 5' UTR is part of the last coding exon): chr19 896502 897436 uc002lqg.2_utr3_0_0_chr19_896503_r 0 - chr19 897436 897540 uc002lqg.2_cds_0_0_chr19_897437_r 0 - chr19 899439 899495 uc002lqg.2_cds_1_0_chr19_899440_r 0 - chr19 899600 899686 uc002lqg.2_cds_2_0_chr19_899601_r 0 - chr19 900060 900146 uc002lqg.2_cds_3_0_chr19_900061_r 0 - chr19 900828 900952 uc002lqg.2_cds_4_0_chr19_900829_r 0 - chr19 901421 901546 uc002lqg.2_cds_5_0_chr19_901422_r 0 - chr19 901975 902130 uc002lqg.2_cds_6_0_chr19_901976_r 0 - chr19 913086 913157 uc002lqg.2_cds_7_0_chr19_913087_r 0 - chr19 913157 913225 uc002lqg.2_utr5_7_0_chr19_913158_r 0 - The hgGene page for uc002lqg.2 is here: http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc002lqg.2 <http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc002lqg.2&hgg_prot=Q96D70&h gg_chrom=chr19&hgg_start=896502&hgg_end=913225&hgg_type=knownGene&db=hg19> &hgg_prot=Q96D70&hgg_chrom=chr19&hgg_start=896502&hgg_end=913225&hgg_type=kn ownGene&db=hg19 When considering the total number of exons in a gene, it is important to look at the 3' UTR exons, the coding exons and the 5' UTR exons. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group From: [email protected] [mailto:[email protected]] On Behalf Of Dan Morton Sent: Wednesday, March 28, 2012 11:03 AM To: [email protected] Cc: [email protected] Subject: Re: [Genome] 3' UTR - Sequence Type Number 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
