Hello, Belinda. What you are suggesting is possible by using our Table Browser. If you are unfamiliar with the Table Browser, please check out the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
To address your first question, for each particular gene locus, there may be different isoforms, each with their own NM_XXXX number (RefSeq ID), so yes, you would need to include all NM_XXXX numbers. If you want information on only a specific group of RefSeq IDs, the Table Browser gives you the ability to specify a list of IDs. Otherwise, the Table Browser gives you the ability to specify the entire genome, a single chromosome or specific regions on one or more chromosomes and it will give you a list of IDs that occur in the regions you specify. For your second question, follow these steps: 1. From http://genome.ucsc.edu, click "Tables" in the blue navigation bar at the top of the screen. 2. Set the following: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Genes and Gene Prediction Tracks Track: RefSeq Genes Table: refGene Region: Select "genome" for the entire genome. Select "position" to specify a single chromosome or region of a chromosome. You can click the "define regions" button to specify multiple regions or click the "paste list" or "upload list" buttons to specify a list of RefSeq IDs. Output format: Selected fields from primary and related tables 3. Click the "get output" button 4. Select the fields you are interested in. If you're interested in exon information for each gene, you might check name, exonCount, exonStarts and exonEnds which will give you the RefSeq ID, number of exons and exon start and stop positions for every RefSeq ID contained in your specified region. 5. Click the "get output" button to display your results. You can experiment to find the set of options that works best for you. In answer to your third question, the positions of the RefSeq genes aren't necessarily identical between UCSC and NCBI or Ensembl, so please be aware of that if you're working with data across sites. I hope this helps! 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 Campos Fernandes Xavier Ana Belinda Sent: Monday, December 05, 2011 8:42 AM To: [email protected] Subject: [Genome] Question&Help I've a list of genes to do a Target Sequencing and now I need to create a list of NM_xxxxx number to give for the ''producion'' of capturing probes for my genes/regions of interest. However I have some questions concerning the NM_xxxx Numbers and also concerning your site/UCSC. 1st question: For each gene, do I need to introduce all the NM_xxxxx numbers corresponding to each splice variant to be sure that all exons of all coding variants will be captured? 2nd question (if yes for the 1st question): How can you get the genomic coordinates of all the exons for all the splice forms (variants) for a given gene ? In UCSC, I can only get one cDNA at a time, getting the NM number for it, but not including all exons (only the exons included in this particualr cDNA). Is there a way of getting the coordinates for all the exons of one gene, with a unique NM_xxxx number containing all exons ? Or is an NM number restricted to one isoform ? In that case where can I find the genomic coordinates of all the exons for one specific gene ??? Thank you very much for your (quick) help. 3rd question If I use another database to obtain all the NM_xxxx number (p.e. NCBI, ENSEMBL) does can be a problem for the genomic coordinates? In other word cas I do the NM_xxxx number list for exemple with Ensembl and after upload the list on UCSC and prepare the the file with all the genomic coordinates? Thank you very much for your help. Belinda Xavier Belinda Campos-Xavier, PhD Centre Hospitalier Universitaire Vaudois 1011 Lausanne Switzerland Email: [email protected] _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
