d98002da63a523f6de0e7c04936e458827a3b1ee
lrnassar
  Mon Feb 7 16:13:27 2022 -0800
News release for 3 new GENCODE tracks, M28 and V39. Refs #28771 #28770 #28769

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 </div>
 
 <!-- ============= 2022 archived news ============= -->
 <a name="2022"></a>
 
+<a name="020922"></a>
+<h2>Feb. 9, 2022 &nbsp;&nbsp; New GENCODE gene tracks: Human V39 (hg19/hg38) - Mouse M28
+(mm39)</h2>
+<p>
+We are pleased to announce new GENCODE Gene annotation tracks, which correspond
+to <a href="https://www.ensembl.info/2021/12/10/ensembl-105-has-been-released/"
+target="_blank">Ensembl 105</a>, for three assemblies: <a target="_blank"
+href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV39lift37&position=default">hg19/GRCh37</a>,
+<a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&c=chr1&g=wgEncodeGencodeV39&position=default">hg38/GRCh38</a>,
+and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=mm39&c=chr12&g=wgEncodeGencodeVM28&position=default">mm39/GRCm39</a>.
+For human, the GENCODE V39 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 tracks that are not available on hg19:
+</p>
+<ul>
+  <li>2-way Pseudogenes - pseudogenes predicted by both the Yale Pseudopipe and UCSC
+      Retrofinder pipelines.</li>
+  <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>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 Lou Nassar for the development and
+release of these tracks.</p>
 
 <a name="010622"></a>
 <h2>Jan. 6, 2022 &nbsp;&nbsp; JASPAR Transcription Factor Binding Site track available for human
 and mouse</h2>
 <p>
 We are happy to announce the new JASPAR 2022 track for human
 (<a href="/cgi-bin/hgTrackUi?db=hg19&g=jaspar">GRCh37/hg19</a> and
 <a href="/cgi-bin/hgTrackUi?db=hg38&g=jaspar">GRCh38/hg38</a>) and
 mouse (<a href="/cgi-bin/hgTrackUi?db=mm39&g=jaspar">GRCm39/mm39</a> and
 <a href="/cgi-bin/hgTrackUi?db=mm10&g=jaspar">GRCm38/mm10</a>). With this release, we are also
 introducing the JASPAR 2020 track for GRCm38/mm10.
 </p>
 <p>
 These tracks represent genome-wide predicted binding sites for transcription factor binding profiles
 in the <a href="https://jaspar.genereg.net/about/" target="_blank">JASPAR CORE collection</a>.