Hello Anna, You can get UCSC Genes exon coordinates for your LocusLink (a.k.a. Entrez Gene) identifiers using the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables). Select the following options:
clade: Mammal genome: Human assembly: Feb. 2009 (GRCh37/hg19) group: Genes and Gene Prediction Tracks track: UCSC Genes table: knownGene region: genome Now hit "filter: create." Under "Linked Tables," select the knownToLocusLink table and hit the "Allow Filtering Using Fields in Checked Tables" button. In the hg19.knownToLocusLink based filters section, paste your list of identifiers in the "value does match" box and hit submit. (The box is small, but it will accept a list of identifiers.) Now choose "output format: selected fields from primary and related tables" and hit "get output." From knownGene, select chrom, strand, exonStarts, and exonEnds, and any other fields you would like to see in the output. Then scroll down and select the knownToLocusLink table again and hit "Allow Selection from Checked Tables." Check the box next to "value" to see your LocusLink identifier in the output. Hit "get output." The result should be the exon coordinates for the gene identifiers that you entered. It's possible to do something similar to get RefSeq Gene exon coordinates if you prefer, but you would need to first convert the LocusLink identifiers to RefSeq Gene identifiers (using either the Table Browser and the refLink table or an online conversion tool such as DAVID: http://david.abcc.ncifcrf.gov/conversion2.jsp). You would then select RefSeq Genes in the Table Browser and enter the list of identifiers in the "identifiers (names/accessions): paste list" section. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 4/12/12 2:48 PM, [email protected] wrote: > > Hi, > > Does anyone know how to get the exon coordinates of a set of human genes if > you have the > LocusLink ID of these genes? Thanks in advance for any help. > > Anna > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
