Hello. To obtain the sequence for exon 10 of XRCC1, you will need to navigate to that specific exon in the Browser and then use our getDNA tool to obtain the sequence. To do so, perform the following steps:
1. Open hg19 in the Browser. 2. (optional, but recommended) Click the "hide all" button just below the Browser's graphical display. 3. In the "position/search" box, type XRCC1 and hit Enter. 4. You will see many results for XRCC1. Click the one result in the "RefSeq Genes" section. 5. In the Browser's graphical display, you will see the entire gene including all 17 exons. You will need to zoom in to isolate exon 10. You can do this in two ways: 1) click and drag your mouse over a specific exon to expand that region (click and drag the coordinates at the top, not the exon itself) or 2) just click one of the "zoom in" buttons at the top of the screen. You can also use the "move" buttons at the top of the screen to shift the view left or right. 6. Make sure you are zoomed in so that only one exon is visible in the Browser. You should leave some intron space on either side so you know you're viewing the entire exon. You will see double-arrows at both sides of the Browser pointed outward. You can verify that you are looking at exon 10 if you hover over those arrows. When you hover over the left arrow, it should say "Next Exon 11/17" and when you hover over the right arrow, it should say "Prev Exon 9/17." If you are not on exon 10, you can just click one of those arrows which will take you to the next/previous exon. Note that if you click on an arrow, you may need to adjust your zoom level to again isolate the complete exon on the screen. **Note that there are potentially two sets of double arrows that can appear at the sides of the Browser. The first are the "next/previous exon" arrows mentioned above. These will appear as white arrows inline with the gene. Depending on your configuration, you may also see "next/previous item" arrows. These will appear as gray arrows above the gene. If you're not sure what is being displayed, you can check which of these are configured to display by clicking the "configure" button below the Browser's graphical display. There are checkboxes to control the display each of these items. 7. Once you are viewing exon 10 only, click the "DNA" link at the top of the screen. 8. Click the "get DNA" button. Note that if anything other than exon 10 is on the screen when you click "DNA," even just a small portion, it will give you that DNA as well. This is why it is important to isolate exon 10 only. Once you have your target sequence, you can also use our In-Silico PCR tool to help design your primers: http://genome.ucsc.edu/cgi-bin/hgPcr. 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 hitesh negi Sent: Wednesday, January 11, 2012 2:34 AM To: [email protected] Subject: [Genome] query regarding primer design-reg I have to design a primer for XRCC1 gene exon 10.. how to do i get the sequence of that particular exon in ucsc?with regardshitendra negi _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
