163a294300cc27dbcc4b9501aac95630bb765d5f lrnassar Fri Mar 19 16:57:03 2021 -0700 Announcng GENCODE update refs #27008 #27007 #27006 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 28c19ae..a88eca3 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,66 @@ <div class="col-sm-3"> <ul> <li><a href="#2005">2005 News</a></li> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> <!-- ============= 2021 archived news ============= --> <a name="2021"></a> +<a name="032321"></a> +<h2>Mar. 23, 2020 New GENCODE gene tracks: Human V37 (hg19/hg38) - Mouse M26 +(mm39)</h2> +<p> +We are pleased to announce new GENCODE Gene annotation tracks, which correspond +to <a href="https://www.ensembl.info/2021/02/15/ensembl-103-has-been-released/" +target="_blank">Ensembl 103</a>, for three assemblies: <a target="_blank" +href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV37lift37">hg19/GRCh37</a>, +<a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38c=chr1&g=wgEncodeGencodeV37">hg38/GRCh38</a>, +and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=mm39&c=chr12&g=wgEncodeGencodeVM26">mm39/GRCm39</a>. +For human, the GENCODE V37 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="031821"></a> <h2>Mar. 18, 2021 Updated transcription start miRNA sites for human</h2> <p> We are happy to announce an update to the TS miRNA Targets track for human, <a href="/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=targetScanMiRnaSitesV72" >GRCh37/hg19</a>. This track shows conserved mammalian microRNA regulatory target sites for conserved microRNA families in the 3' UTR regions of Refseq Genes, as predicted by TargetScanHuman 7.2.</p> <p> The track items are colored based on the four classes of target sites identified in Agarwal <em>et al.</em>, 2015.</p> <table cellpadding="2"> <tbody> <tr> <td>Purple</td>