Hi Ann, Sorry for the delayed response. We suggest you try contacting the mailing list (http://reproductivegenomics.jax.org/mailing_list.html) at the Jackson Laboratory to see if you can obtain the sequences and positions from for the DMit microsatellite markers.
Once you have those, go to the main page on our site. Click on "Tables" from the blue navigation bar to get to our table browser. Set the clade, genome, and assembly. Set the following: track: "UCSC Genes" table: "knownGene" region: "position" and click on "define regions." Paste your regions in the box and click "submit" output format: "all fields from selected table" click "get output" The result is the record for your gene. The exon/intron boundaries can be deduced from the exonStarts and exonEnds fields. If there are many fields in the record that you don't need, you can hit the back button and change the output format to "selected fields from primary and related tables." Click "get output" and select the fields you wish to see in your results, be sure to include exonStarts and exonEnds since these fields contain the data you asked about. Also, you may be interested in UCSC In-Silico PCR for mapping PCR products. To get to it, click on "PCR" from the blue navigation bar. Hope this helps! If you have further questions related to the Genome Browser, please contact the mailing list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Ann Eileen Miller Baker" <[email protected]> To: [email protected] Sent: Wednesday, March 16, 2011 7:53:57 PM Subject: [Genome] pls reply to [email protected] pls reply to [email protected] because I am unclear how to access the normal channel where replies are put (1) How can I find mouse DMit (microsatellite loci) amplified sequences? (url) (2) alleles at inbred strains for DMit microsatellite loci? (url) (3) How can I find which DMit microsatellite loci are in - introns - exons - recombination hot spots _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
