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Gene Sequence Viewer

You can get to the Gene Sequence Viewer from the Protein Page by clicking either the gene track, or the View nucleotide and 3-frame translation link.

With this viewer you can see:

• The nucleotide sequence
• The three reading frame translation
• Introns and exons
• A transcript of the resulting protein after splicing

The Gene Sequence Viewer includes several display options. Depending upon on how you get to the viewer, one or more of the display options will be turned on by default. These options include:

• Display genomic coordinates shows the coordinates relative to the start of the gene for each line in the sequence
• Display 3-frame translation shows the nucleotide sequence of the gene and its translations in the three reading frames possible in the plus direction
• Display sequence ruler marks shows a dot above every tenth base-pair
• Display width lets you set the number of bases to be displayed in one line across the page. You will probably want to set this to a width that suits your printer
• Upstream/downstream padding allows you to specify how many bases upstream and downstream of the gene are displayed

Additionally, text color and style indicate:

• Gray upstream or downstream padding
• Red coding regions
• Blue untranslated regions, or UTRs (noncoding exon sequences)
• Black introns
• Lower-case repeats identified by Repeat Masker

Text color shading indicate:

• The transcribed frame of a coding sequence is highlighted with alternating colors (green or purple) to visualize the alignment.
• In cases where no frame shows the correct amino acid (i.e. at splice junctions where a codon spans the intron) the 2 amino acids in the frame of the exon are shown in bold rose, suggesting that the translation frame does not give the correct amino acid.

To change the display settings, select one or more check-box options, edit the default base-pair (bp) settings and click Update Display.

Understanding Coordinates

When you select View with Coordinates, two coordinates will appear for each line of sequence. Coordinates are always relative to the frame of the sequence being viewed.

For positive (+) strand features, the left coordinate indicates the start of the block of sequence and the right coordinate indicates the position of the last base in the preceding block of sequence.

For negative (-) strand features, the left coordinate indicates the base position of the first displayed base (last base on the - strand) and the right coordinate indicates the position of the last displayed base (first base on the - strand).

For example; a scaffold of length n where the - strand is the reverse complement of the + strand:

+ strand, aka 5'-3' strand: 1 ATCG........AGGTA n
- strand, aka 3'-5' strand: n TAGC........TCCAT 1

For example; a block on the + strand starting at position 53 and ending at position 62 on a scaffold of length 62:

+ strand: 53 ATCGATCGAT 62
- strand: 10 TAGCTAGCTA 1