e9e65457cccbb63368ae37dd7bebf88921322f2c jnavarr5 Wed Jul 9 15:59:35 2025 -0700 Announcing the Unusually conserved regions track for hg38, refs #35703 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index c8838f98f11..34b185225c3 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,115 @@ <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="070925"></a> +<h2>July 09, 2025 Unusually Conserved Regions track for hg38</h2> +<p> +We are happy to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=unusualcons" +target="_blank">Unusually Conserved Regions</a> track for GRCh38/hg38. The supertrack consists of +12 tracks that show regions of unusual conservation in humans relative to other organisms. The full +list of tracks, along with item count and coverage is summarized in the following table: +</p> +<p> +<table class="stdTbl"> + <tbody><tr> + <th>Track</th> + <th>Count</th> + <th>Coverage in bp</th> + </tr> + <tr> + <td>HAQERS: Human Ancestor Quickly Evolved Regions</td> + <td>1,580</td> + <td>1,410,669</td> + </tr> + <tr> + <td>HARs: Human Accelerated Regions (HARs) merged from various + publications by the Pollard Lab</td> + <td>2,647</td> + <td>681,420</td> + </tr> + <tr> + <td>Long hConDels: Long Human Conserved Deletions - present in chimp and + macaque but deleted in humans</td> + <td>583</td> + <td>293,809</td> + </tr> + <tr> + <td>Short hConDels: Human Conserved Deletions < 40bp</td> + <td>10,032</td> + <td>1,968,123</td> + </tr> + <tr> + <td>UCNEBase Chicken - Chicken-conserved elements</td> + <td>4,351</td> + <td>1,415,142</td> + </tr> + <tr> + <td>UCNEBase Paralogs - Paralogous elements</td> + <td>987</td> + <td>215,800</td> + </tr> + <tr> + <td>UCNEBase Clusters: Ultra-conserved genomic regulatory blocks</td> + <td>239</td> + <td>199,269,634</td> + </tr> + <tr> + <td>Ultracons: Ultraconserved regions - + 100% identical in human, mouse and rat, >200bp</td> + <td>481</td> + <td>126,007</td> + </tr> + <tr> + <td>UltraZoos: Ultraconserved regions in Zoonomia alignment - + 100% identical in 235 species, >20bp</td> + <td>4,552</td> + <td>131,661</td> + </tr> + <tr> + <td>ZooHARs: Human Accelerated Regions (HARs) from Zoonomia alignments</td> + <td>312</td> + <td>49,173</td> + </tr> + <tr> + <td>Zoonomia RoCCs: Runs of contiguous phyloP constraint</td> + <td>595,536</td> + <td>26,995,284</td> + </tr><tr> + <td>Zoonomia UNICORNs: Unannotated Intergenic Constrained Regions</td> + <td>423,586</td> + <td>16,155,520</td> + </tr> +</tbody></table></p> +<p> +We would like to thank Katie Pollard, Hiram Clawson, James Xue, Matt Christmas, Carol Nguyen, +and Mark Diekhans for providing the data. We would also like to thank Max Haeussler and Jairo +Navarro for the creation and release of the tracks. +</p> + <a name="070725"></a> <h2>July 7, 2025 UCSC Genome Browser turns 25</h2> <p> July 7th marks the 25th anniversary of the human genome going online, and the start of the UCSC Genome Browser. Our visualization journey began when Jim Kent wrote the <a href = "https://hgwdev-hiram.gi.ucsc.edu/intronerator/index.html" target="_blank">Intronerator</a>, which displayed regions of C. elegans. This was the foundation for the UCSC Genome Browser as we know it now, and decades later, we are proud to continue serving our ever-growing users.<br><br> So, how has the Browser evolved over the years? </p> <ul> <li>We now have <b>165k</b> monthly users and <b>1.5M</b> users per year <li>The project is now comprised of <b>three million lines of code</b> <li>We have responded to over <b>15k</b> mailing questions from our users