f9b9f5835f0254f949b4b863b9dc906ff69fbd92 gperez2 Fri Sep 8 13:30:18 2023 -0700 Updating news announcement for GENCODE KnownGene V44 and VM33, refs #30840 #30841 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index dcc29d9..e7d7777 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,39 +52,44 @@ <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> <!-- ============= 2023 archived news ============= --> <a name="2023"></a> <a name="090723"></a> -<h2>Sep. 07, 2023 GENCODE Genes V44 for human (hg38) and VM33 for mouse (mm39)</h2> +<h2>Sep. 07, 2023 New GENCODE "KnownGene" V44 for human (hg38) and VM33 for mouse (mm39)</h2> <p> We are pleased to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg38&g=knownGene&c=chrX">GENCODE V44 (hg38)</a> and the -<a href="/cgi-bin/hgTrackUi?db=mm39&g=knownGene&c=chrX">GENCODE VM33 (mm39)</a> tracks. -The track description pages for these tracks contain options -for configuring the display such as also showing non-coding genes, splice variants, and pseudogenes. -Different tags and labels may also be toggled.</p> +<a href="/cgi-bin/hgTrackUi?db=mm39&g=knownGene&c=chrX">GENCODE VM33 (mm39)</a> gene tracks. +The GENCODE "KnownGene" V44 for hg38 and VM33 gene tracks were built using a UCSC +pipeline (KnownGene) and the GENCODE comprehensive gene set to generate high-quality manual +annotations merged with evidence-based automated annotations. The GENCODE "KnownGene" +tracks are our default gene tracks, which have extensive associations to external sources. This +allows for additional metadata on every item as well as external links. The track description pages +contain options for configuring the display, such as showing non-coding genes, splice variants, and +pseudogenes. The track description pages for these tracks contain options for configuring the +display such as also showing non-coding genes, splice variants, and pseudogenes.</p> <p> Below is a summary of the contents found in each release. For more details visit the <a target="_blank" href="https://www.gencodegenes.org/">GENCODE site</a>.</p> <p> <table class="stdTbl"> <tr><th COLSPAN=4>GENCODE v44 Release Stats</th></tr> <tr align=left><th>Genes</th><th>Observed</th><th>Transcripts</th><th>Observed</th></tr> <tr align=left><td>Protein-coding genes</td><td>19,396</td><td>Protein-coding transcripts</td><td>89,067</td></tr> <tr align=left><td>Long non-coding RNA genes</td><td>19,922</td><td><font size="-1">- full length protein-coding</font></td><td>63,968</td></tr> <tr align=left><td>Small non-coding RNA genes</td><td>7,566</td><td><font size="-1">- partial length protein-coding</font></td><td>25,099</td></tr> <tr align=left><td>Pseudogenes</td><td>14,735</td><td>Nonsense mediated decay transcripts</td><td>21,384</td></tr> <tr align=left><td>Immunoglobulin/T-cell receptor gene segments</td><td>647</td><td>Long non-coding RNA loci transcripts</td><td>58,246</td></tr> <tr align=left><td>Total No of distinct translations</td><td>65,342</td><td>Genes that have more than one distinct translations</td><td>13,594</td></tr> </table><BR>