27ad7e08d0c5752b8cc1804c5e25f075c5c7d9cf gperez2 Tue Jun 24 11:47:03 2025 -0700 Updating GENCODE V47 to V48 in the newsarch, refs #35185 #35184 #35188 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 1011b8e0112..d4190fff887 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -62,31 +62,31 @@ 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 +For human, the GENCODE V48 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>