71a74c027754ea2606ca4d6bcadc73c107dc3062 gperez2 Tue Jun 24 10:34:47 2025 -0700 Announcing the release of All GENCODE for hg38, hg19 (V48), and mm39 (VM37). refs #35185 #35184 #35188 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 231689a30e9..1011b8e0112 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,67 @@ <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 found <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 our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2025 archived news ============= --> <a name="2025"></a> +<a name="062425"></a> +<h2>June 24, 2025 New GENCODE gene tracks: Human V48 (hg19/hg38) - Mouse M37 +(mm39)</h2> +<p> +We are happy to announce new GENCODE Gene annotation tracks, which correspond +to <a href="https://www.ensembl.info/2025/05/07/ensembl-114-has-been-released/" +target="_blank">Ensembl 114</a>, for three assemblies: <a target="_blank" +href="../../cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV48lift37&position=default">hg19/GRCh37</a>, +<a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV48&position=default">hg38/GRCh38</a>, +and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=mm39&g=wgEncodeGencodeVM37&position=default">mm39/GRCm39</a>. +For human, the GENCODE V47 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><b>Basic</b> - a subset of the <em>Comprehensive set</em>.</li> + <li><b>Comprehensive</b> - all GENCODE coding and non-coding transcript annotations, including + polymorphic pseudogenes. This includes both manual and automatic annotations.</li> + <li><b>Pseudogenes</b> - 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> + <b>PolyA</b> - 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 Gerardo Perez for the development and +release of these tracks.</p> + + <a name="061125"></a> <h2>June 11, 2025 EVA SNP release 7 for 40 assemblies</h2> <p> We are happy to announce the release of the EVA SNP Release 7 tracks for 40 assemblies, which now includes <a href="../cgi-bin/hgTrackUi?db=bosTau9&g=evaSnp7&position=default" target="_blank">bosTau9</a>, <a href="../cgi-bin/hgTrackUi?db=ce11&g=evaSnp7&position=default" target="_blank">ce11</a>, and <a href="../cgi-bin/hgTrackUi?db=rn6&g=evaSnp7&position=default" target="_blank">rn6</a>. These tracks contain mappings of single nucleotide variants and small insertions and deletions (indels) — collectively Simple Nucleotide Variants (SNVs) — from the European Variation Archive (<a href="https://www.ebi.ac.uk/eva/" target="_blank">EVA</a>) Release 7. The full list of assemblies that contain the EVA SNP release 7 track is below:</p> <p> <div class="container">