63656c54eadd4f059fd7ac184c57f53d2081db29
gperez2
  Tue Feb 13 14:09:51 2024 -0800
Announcing the release of All GENCODE for hg38, hg19 (V45), and mm39 (VM34). refs #32411 #32413 #32412

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 <p>You can sign-up to get these announcements via our 
 <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a>
 email list. We send around one short announcement email every two weeks.</p>
 
 <p>Smaller software changes are not announced here.  A summary of the three-weekly release changes can be 
 <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. 
 For the full list of our daily code changes head to <a
 href="https://github.com/ucscGenomeBrowser/kent/commits/master"
 target=_blank>our GitHub page</a>.</p>
 
 <!-- ============= 2024 archived news ============= -->
 <a name="2024"></a>
 
+<a name="021424"></a>
+<h2>Feb. 14, 2024 &nbsp;&nbsp; New GENCODE gene tracks: Human V45 (hg19/hg38) - Mouse VM34
+(mm39)</h2>
+<p>
+We are happy to announce new GENCODE Gene annotation tracks, which correspond
+to <a href="https://www.ensembl.info/2024/01/11/ensembl-111-has-been-released/"
+target="_blank">Ensembl 111</a>, for three assemblies: <a target="_blank"
+href="/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV45lift37">hg19/GRCh37</a>,
+<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV45">hg38/GRCh38</a>,
+and
+<a target="_blank" href="/cgi-bin/hgTrackUi?db=mm39&c=chr12&g=wgEncodeGencodeVM34">mm39/GRCm39</a>.
+<a target="_blank" href="https://www.gencodegenes.org/">GENCODE</a> provides gene annotations with
+high accuracy based on biological evidence and for the benefit of biomedical research and genome
+interpretation. For human, the GENCODE V45 annotations were mapped to hg38/GRCh38 and then back-mapped
+to the hg19/GRCh37 assembly. For all three assemblies, the gene sets contain the
+following tracks:</p>
+<ul>
+  <li>
+      Basic - a subset of the <em>Comprehensive set</em>.</li>
+  <li>
+      Comprehensive - all GENCODE coding and non-coding transcript annotations, including
+      polymorphic pseudogenes. This includes both manual and automatic annotations.</li>
+  <li>
+      Pseudogenes - all annotations except polymorphic pseudogenes.</li>
+</ul>
+<p>
+The hg38 and mm39 assemblies also include the following track that is not available on hg19:
+</p>
+<ul>
+  <li>
+      PolyA - polyA signals and sites manually annotated on the genome based on transcribed
+      evidence (ESTs and cDNAs) of 3' end of transcripts containing at least 3 A's not matching the
+      genome.</li>
+</ul>
+<p>
+Details on each release can be found on the <a target="_blank"
+href="https://www.gencodegenes.org/">GENCODE site</a>. This includes <a target="_blank"
+href="https://www.gencodegenes.org/human/stats.html">statistics on each release</a>.
+</p>
+<p>
+We would like to thank the <a target="_blank"
+href="https://www.gencodegenes.org/pages/gencode.html">GENCODE project</a> for providing these
+annotations. We would also like to thank Mark Diekhans and Gerardo Perez for the development and
+release of these tracks.</p>
+
 <a name="021224"></a>
 <h2>Feb. 12, 2024 &nbsp;&nbsp; Variants of Concern SARS-CoV-2 track updated with Omicron
 variants</h2>
 <p>
 We are happy to announce an update to the <a href="/cgi-bin/hgTrackUi?db=wuhCor1&position=default&g=variantMuts"
 target="_blank">Variants of Concern</a> track to include the latest WHO-designated variants of
 concern (VOC). The evolving SARS-CoV-2 virus has been a challenge for everyone, and we are humbled
 to continue providing public data and our high-quality genetics research tools, now updated with the
 latest COVID variant information.</p>
 <p>
 In this update, the following Omicron variants were added to the
 Variants of Concern track:</p>
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