9b842af51fa1fa6ebe403f397ce52fc4448b9807 max Fri Jun 5 03:32:12 2026 -0700 docs diff --git src/hg/htdocs/goldenPath/help/query.html src/hg/htdocs/goldenPath/help/query.html index 9e2474660c0..47f4f8e7ff2 100755 --- src/hg/htdocs/goldenPath/help/query.html +++ src/hg/htdocs/goldenPath/help/query.html @@ -68,32 +68,34 @@ To jump directly to a specific exon, type the gene symbol or transcript ID followed by the exon number in one of two formats:</p> <ul> <li><code>SYMBOL exon N</code> — e.g. <code>TP53 exon 5</code> or <code>NM_000546 exon 5</code></li> <li><code>SYMBOL:e.N</code> — compact notation from the <a href="https://fusions.cancervariants.org/en/latest/" target="_blank">VICC Gene Fusion Specification</a>, e.g. <code>TP53:e.5</code> or <code>NM_000546:e.5</code>. Optionally add an intronic offset: <code>SYMBOL:e.N+offset</code> navigates <em>offset</em> bases past the 3’ end of the exon (into the downstream intron), and <code>SYMBOL:e.N-offset</code> navigates <em>offset</em> bases before the 5’ start (into the upstream intron). Useful for splice site inspection: <code>BRCA2:e.10+2</code> lands 2 bp into the intron after exon 10.</li> </ul> <p> Exon numbering is 1-based and follows transcript order (exon 1 is the 5′ exon). Genes are looked up in order: MANE, GENCODE/UCSC (knownGene), -all RefSeq, then historical RefSeq. To jump to a codon instead, right-click -any transcript in the browser and select “Zoom to codon”.</p> +all RefSeq, then historical RefSeq. To jump to a codon instead, just enter it +after the gene, e.g. "BRAF 600", use the HGVS notation (see below) or +right-click any transcript in the browser and select “Zoom to +codon”.</p> <h2>Sample queries</h2> <p> Below is a list of examples that might be used to query the Genome Browser. Note that not every query listed here will produce a result in every assembly. The list serves only to illustrate the different types of queries that can be performed. <table border="1"> <tr><th width="200">Query</th><th width="250">Genome Browser Response</th></tr> <tr> <td>chr7</td> <td>Displays all of chromosome 7</td></tr> <tr> <td>chr3:1-1000000</td> <td>Displays the first million bases of chromosome 3, counting from the p-arm telomere</td></tr> <tr>