0923e3a1c3c53c946f553f37351d262c1c6cff6f mspeir Sun Jan 25 10:20:04 2026 -0800 minor changes from CR feedback, refs #36979 diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 7f2d9ef4f38..ed42cef9460 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -876,56 +876,57 @@ <p> <pre><code>chr1 1046829 1047018 NM_001077977_utr3_2_0_chr1_1046830_f 0 + chr1 1099124 1099325 NM_001077124_utr3_0_0_chr1_1099125_r 0 - </code></pre> </p> <p> The name column contains several pieces of information separated by underscores: <code>NM_001077124_utr3_0_0_chr1_1099125_r</code>. Here's a breakdown of that information: <ol> <li><code>NM_001077124</code> - Transcript accession <li><code>utr3</code> - will be cds or utr3/5 <li><code>0</code> - exon inFrame - This indicates the offset at the beginning of a feature (like an exon) to reach the first base of the next complete codon. <li><code>0</code> - exon outFrame - This indicates the offset remaining at the end of a feature. - <li><code>chr1_1099125</code> - chromosome and start position of the exon + <li><code>chr1_1099125</code> - start position of the exon <li><code>r</code> - strand, "r" for reverse or "-" and "f" for forward or "+" </ol> </p> <p> -Here we're going to focus on the inFrame and outFrame specifically. The values +Here, we're going to focus on the inFrame and outFrame specifically. The values typically range from 0 to 2. These numbers are a representation of where in the frame the exon starts and ends. <table> <thead> <tr> <th>Value</th> <th>Meaning</th> </tr> </thead> <tbody> <tr> <td>0</td> <td>The feature starts/ends exactly at the beginning of a codon. No offset is required.</td> </tr> <tr> <td>1</td> <td>There is 1 "extra" nucleotide before/after the complete codons start.</td> </tr> <tr> <td>2</td> <td>There are 2 "extra" nucleotides before/after the complete codons start.</td> </tr> </tbody> </table></p> <p> In the example lines above, the exons have "0" for both inFrame and outFrame because they are UTR exons.</p> <p> -Finally, it should be noted that when the amino acid output is split per exons (where a split codon is impossible to -denote), the amino acid for split codon is placed in the exon with most of the bases.</p> +Finally, it should be noted that when the amino acid output is split per exons +(where a split codon is impossible to denote), the amino acid for this split codon +is placed in the exon with most of the bases.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->