Getting a Sequence
It's very easy to get the DNA sequence when you are viewing a region in the UCSC Genome browser. There are multiple ways to do it.
- The fastest way to get the DNA sequence for a specific gene is to right-click on the graphic gene view in the GENCODE Comprehensive Transcript section and select Get DNA for [gene name]
- To get DNA for the whole region you're viewing, go to the top of the page, and use the View menu to get DNA for the entire region shown in the browser (not just the gene--unless the gene you're viewing takes up the whole view window).
- A new page will open, on this page you can add bases up- or downstream, change masking options and use the button to custom color your DNA sequence
- In this example, I'll color all RefSeq gene exons blue, and underline and color all SNPs red and click submit
- So my sequence is colored to show exons and SNPs
Getting a Sequence in FASTA Format
- To get genomic sequence, or mRNA or protein sequences for the region you're viewing in FASTA format, go back to the GENCODE Comprehensive Transcript Set portion of the viewer and click anywhere on a gene transcript to open the detailed Description and Page Index page.
- Now go to the section marked Sequence and Links to Tools and Databases
- Click on Genomic Sequence to get the DNA sequence
- You will be taken to a page called Get Genomic Sequence Near Gene. This is very much like the Get DNA page described above, but it has more sequence extension and formatting options, but no color options
- This output is a FASTA file that you can copy or save for use in other applications.
- If you choose mRNA or Protein sequences, you will merely get the FASTA formatted sequence, with no additional options for adding bases or masking.
