0adde15fcc0c841a234ab2ea86a4a8fdbef3d49b
markd
  Fri Dec 12 01:51:06 2025 -0800
switch recount3 intron track to color items by splice junction motif #34886

diff --git src/hg/makeDb/trackDb/recount3.html src/hg/makeDb/trackDb/recount3.html
index dc46a70417a..22489068208 100644
--- src/hg/makeDb/trackDb/recount3.html
+++ src/hg/makeDb/trackDb/recount3.html
@@ -15,31 +15,31 @@
 </p>
 <p>
 These tracks display the recount3 intron data, including split read counts and splice junction motifs.
 </p>
 
 <h2>Display Conventions</h2>
 <p>
 Intron items are colored based on splice junction motifs and read support (darker colors indicate higher coverage).
 Split read counts and splice motifs are shown on mouseover.
 By default, only introns with a minimum read count of 10,000 are shown. This setting can be changed
 on the track configuration page.
 </p>
 <p>
 The intron items are color-coded:
 <ul>
-  <li><b><font color="#00008b">Blue</font></b> GT donors and AG acceptors (CT and AC on
+  <li><b><font color="#00bfff">Sky blue</font></b> GT donors and AG acceptors (CT and AC on
 the minus strand)</li>
   <li><b><font color="#00ced1">Turquoise</font></b> GC donors (GT on the minus strand)</li>
   <li><b><font color="#ff8c00">Orange</font></b> AT donors and AC acceptors (GT and GT on the
 minus strand)</li>
   <li><b><font color="#a9a9a9">Grey</font></b> Non-canonical junction motifs. These could be sequencing errors, polymorphisms, or very rare U12 introns.</li>
 </ul>
 </p>
 
 <p>
 Introns can be filtered by:
 <ul>
   <li><b>read count</b> - Number of split reads supporting the intron. The default is a minimum of 10,000 reads.</li>
   <li><b>intron size</b> - Length of the intron. The default is 30 to 100,000.</li>
   <li><b>splice junction motif</b> - The motif is specified in the form <em>GT/AG</em>, with canonical motifs being uppercase and unknown motifs being lowercase.
     The default is no filtering.</li>