What is the nucleotide sequence of this gene?

Remember that we are looking at the gene for the red-sensitive opsin in humna vision, and it's located near the bottom tip of the X chromosome. Scroll down to NCBI Reference Sequences (RefSeq). You see that mRNA (messenger RNA) and protein sequences are available, along with a GenBank sequence.

Click the entry number beside mRNA.

This is a typical GenBank nucleotide file, and a lot of it is hard to read, but a few things are clear. First note, under references, a citations to the publication of this sequence in the scientific literature. To see an abstract of the article in which this gene was described, click the PubMed link below the reference. As you see, you've been here before. There are many ways to move from one database to another, which is both a blessing and a curse. You have to keep your eyes open for useful links, and when you find a path that you think you might use again, make a note of it and bookmark the web pages. It is frustrating to know there's an easier way to do something, and not remember how you did it.

NB to GR: point back to this abstract when you get the phylogenetic tree.
to find the sequence go to this page http://www.ncbi.nlm.nih.gov/nuccore/9910525?report=genbank
Scroll to the bottom of this long page. The last thing is the sequence of this messenger RNA. You are seeing the actual list of As, Ts, Gs, and Cs that make up the message for synthesis of this opsin. But wait! You know that RNA contains no T. In most nucleotide databases, U from RNA is represented as T, to make for easy comparison of DNA and RNA sequences. This sequence information is not in the form that is most useful for searching in databases, say, searching for related genes. Let's display this entry in a form more useful for searching.

At the top of the page, beside the Display button, pull down the menu that says default (we are looking at the default entry display), and select FASTA (note that several other display options are available). Then click the Display button. You see one descriptive or "comment" line that begins with ">", followed by the nucleotide sequence. This little file is just what you need to search nucleotide databases for similar sequences. Let's keep it for future use.
This is the FASTA format of the gene OPN1LW http://www.ncbi.nlm.nih.gov/nuccore/164419729?report=fasta
Click and drag on the web page to select everything from the ">" through the last nucleotide. Be careful not to select anything else. From your browser's Edit menu, select Copy to make a copy of this information on your clipboard, for pasting elsewhere. Now start your favorite word processor, make a new document, and paste. The FASTA comment and sequence should appear. Select all of the text and change the font to Courier or Monaco -- these "typewriter" fonts make it easy to align letters into columns, because all letter are the same width. Save this file, choosing text or plain text as the file type. Call it mrnared.txt. Save it to a convenient location for the files you'll be making later. Click your browser's Back button until you return to LocusLink.