Hello, Hong. You can do this by using our Table Browser. If you're unfamiliar with the Table Browser, please see the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
1. From http://genome.ucsc.edu, select "Tables" from the blue navigation bar at the top of the screen. 2. Select the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Genes and Gene Prediction Tracks Track: RefSeq Genes Table: refGene 3. If you have a list of RefSeq IDs that you want annotated, on the "identifiers" line, click the "paste list" or "upload list" button to use your list of identifiers. If you want the annotation for all genes in a specific region, on the "region" line, you can click "genome" for the entire genome, "position" to define a single specific region or "define regions" to define multiple regions. 4. Set "output" to "all fields from selected table" to list all fields in your output or to "selected fields from primary or related tables" to select only certain fields in your output 5. Click the "get output" button (if you selected "selected fields from primary or related tables" in step 4, the next screen will allow you to select the fields you want in your output) 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 xu hong Sent: Friday, April 20, 2012 9:35 PM To: [email protected] Subject: [Genome] how could I get RefSeq gene annotations from UCSC database? Hi UCSC genome browser, May I ask you a question, how could I get RefSeq gene annotations from UCSC database? For example, the example of annotation we need is that: name chrom strand txStart txEnd cdsStart cdsEnd exonCount NR_024540 chr1 - 4224 19233 19233 19233 11 NM_001005484 chr1 + 58953 59871 58953 59871 1 NM_001005277 chr1 + 357521 358460 357521 358460 1 NM_001005221 chr1 + 357521 358460 357521 358460 1 NM_001005224 chr1 + 357521 358460 357521 358460 1 NM_001005277 chr1 - 610958 611897 610958 611897 1 NM_001005221 chr1 - 610958 611897 610958 611897 1 NM_001005224 chr1 - 610958 611897 610958 611897 1 NR_024321 chr1 - 751449 752765 752765 752765 1 NR_015368 chr1 + 752926 779603 779603 779603 7 NM_152486 chr1 + 850983 869824 851184 869396 14 NM_015658 chr1 - 869445 884542 869936 884483 19 NM_198317 chr1 + 885829 890958 885936 890434 12 NM_032129 chr1 + 891739 900347 891774 899818 16 NM_021170 chr1 - 924205 925415 924301 925216 4 NM_001142467 chr1 - 924207 925415 924301 925216 3 NM_005101 chr1 + 938709 939782 938816 939721 2 NM_198576 chr1 + 945365 981355 945415 980224 36 NM_017891 chr1 - 1007060 1041599 1008135 1016786 10 NM_001130045 chr1 + 1099148 1123176 1104458 1123090 16 NM_153254 chr1 + 1104939 1111106 1105296 1110385 9 NM_004195 chr1 - 1128750 1131952 1129086 1131814 5 Thanks. Best Regards, Hong Xu _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
