bd5ebb2dc0b10ad589ed54c3319da1fac28d2b26 max Wed May 7 06:38:51 2025 -0700 adding html to genePred exon mouseover, refs #33749 diff --git src/hg/htdocs/goldenPath/help/codonPhase.html src/hg/htdocs/goldenPath/help/codonPhase.html new file mode 100755 index 00000000000..2f01ce0c0e7 --- /dev/null +++ src/hg/htdocs/goldenPath/help/codonPhase.html @@ -0,0 +1,38 @@ +<!DOCTYPE html> +<!--#set var="TITLE" value="Genome Browser Codon Phase Display" --> +<!--#set var="ROOT" value="../.." --> + +<!-- Relative paths to support mirror sites with non-standard GB docs install --> +<!--#include virtual="$ROOT/inc/gbPageStart.html" --> + +<h1>Codon phases shown on the Genome Browser</h1> +<p> +Gene transcript tracks, for example NCBI RefSeq and Gencode, show the codon phase of exons on mouse +over. The text looks like this:<p> + +<div style='border: 1px solid black; width:400px; background-color:#EEE; padding:3px'> +<b>Transcript:</b> ENST00000297261.7<br> +<b>Strand:</b> -<br> +<b>Exon:</b> Exon 2 of 3<br> +<b>Codon phase:</b> start 0, end 1: out-of-frame exon<br> +</div> + +<p> +The codon phase specifies where in the coding sequence the intron falls in the codon that separates two exons: +<p> +<ul> + <li>Phase 0: before the first nucleotide, cleanly between two codons. + <li>Phase 1: between the first and the second nucleotide + <li>Phase 2: between the second and third nucleotide +</ul> +</p> + +<p>This means that: +<ul> + <li>The start phase of an exon is always the same as the end phase of the previous exon. + <li>An exon where the end and start phases are identical can be removed without destroying the reading frame: in-frame exon. + <li>An exon where start and end phases differ cannot be removed without destroying the reading frame: out-of-frame exon. +</ul> +</p> + +<!--#include virtual="$ROOT/inc/gbPageEnd.html" -->