Hi Ann, Yes, you can recognize the first intron and the first coding exon from the Table Browser output.
I am looking at the previous answer in this thread to see how you have the Table Browser set up: https://lists.soe.ucsc.edu/pipermail/genome/2011-August/026907.html If you had the "One FASTA record per region..." selected in the Table Browser when you downloaded data, the following should work: For each gene in your output files, the first (that is, the one on the 5' end) intron is simply the first block of sequence listed for that gene in your "introns" file. The first coding exon is simply the first exon listed for that gene in your "CDS exons" file. The first intron or coding exon is listed first regardless of the gene being on the negative or positive strand. (This is contrary to what Katrina said before: "For genes on the - strand, your script will have to determine which of the regions has the highest intron/exon number and pull that as the first intron or exon." Sorry for the confusion.) Additionally, there will be a "_0" appended to the first block of sequence output for each gene. So, for example, your intron and exon files should each have several blocks of sequence, each beginning with headers (lines that begin with ">"), like this: >hg19_knownGene_uc002yow.1_0 range=chr21:32638326-32639288 5'pad=0 3'pad=0 strand=- repeatMasking=none (sequence) >hg19_knownGene_uc002yow.1_1 range=chr21:32624058-32624505 5'pad=0 3'pad=0 strand=- repeatMasking=none (sequence) >hg19_knownGene_uc002yow.1_2 range=chr21:32617804-32617976 5'pad=0 3'pad=0 strand=- repeatMasking=none (sequence) etc. The blocks with the same identifier (uc002yow.1) contain sequence for one gene. The first intron in that gene (if you are looking at the introns file) or exon (if you are looking at the exons file), is the block with the "_0" after it, and it is listed first. I hope this helps explain the output from the Table Browser. If you have further questions, please reply to [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/1/11 6:01 PM, Ann Eileen Miller Baker wrote: > 1Dc11 > Is there a way to RECOGNIZE the FIRST INTRON and FIRST CODING EXON from all > output of the TABLE BROWSER? I include the past history of this question in > earlier > emails (attached; recall this is for ca. 6600 DMIT microsatellite loci > discovered by > Bill Dietrich and his colleagues - I deduce from Brooke's answer that there > is no way to distinguish the first intron from other introns; the first > coding exon from other coding exons. > Thanks for your help now and in the past, > Ann > > > On Thu, Aug 25, 2011 at 1:04 PM, Brooke Rhead<[email protected]> wrote: > >> Hello Ann, >> >> The Table Browser does not have an option to limit output to only the >> first intron or first coding exon. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> On 08/25/11 10:00, Ann Eileen Miller Baker wrote: >> >>> 25Au11 >>> Please answer below. I am aware that the table browser delivers >>> for mouse DMIT microsatellite loci overlapping introns, exons, coding >>> exons, >>> and UTR, but I am asking if there is any way to customize this listing to >>> include FIRST INTRON; FIRST CODING EXON. >>> Thanks, >>> Ann >>> >>> ---------- Forwarded message ---------- >>> From: Ann Eileen Miller Baker<[email protected]> >>> Date: Sun, Aug 21, 2011 at 3:45 PM >>> Subject: identifying "first intron", "first coding exon" >>> To: [email protected] >>> >>> >>> 21Au11 >>> Dear UCSC genomics team, >>> When determining genomic elements (UTR, exons, coding exons, introns) >>> co-occuring with DMIT microsatellite loci, >>> <<Is there a way to specify requesting first intron, first coding exon>>? >>> Thanks, >>> Ann >>> ______________________________**_________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >>> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
