1995fb5512978d502812e7693d5d487bea61f507 gperez2 Wed Sep 23 15:26:14 2026 -0700 Updating the ncOrfs description pages: Restructuring gencNcOrfs.html's Description and Display Conventions sections and cleaning up wording. Updating the Description section of fiveUltraUorfs.html. Updating ncOrfs.html's GENCODE and 5ULTRA sections to match their subtrack pages and trimming the GENCODE summary. Minor updates to ncOrfs.ra. Refs #37649 diff --git src/hg/makeDb/trackDb/human/hg38/fiveUltraUorfs.html src/hg/makeDb/trackDb/human/hg38/fiveUltraUorfs.html index 9527065f7fe..27d0fa9075f 100644 --- src/hg/makeDb/trackDb/human/hg38/fiveUltraUorfs.html +++ src/hg/makeDb/trackDb/human/hg38/fiveUltraUorfs.html @@ -1,150 +1,157 @@ <h2>Description</h2> <p> This track shows 22,567 upstream open reading frames (uORFs) in the 5' untranslated regions (5' UTRs) of human protein-coding genes, compiled as part of the <a href="https://github.com/mchaldebas/5ULTRA" target="_blank">5ULTRA</a> pipeline for annotating 5' UTR variants. The uORFs are defined on <a href="../cgi-bin/hgTrackUi?db=hg38&g=mane">MANE Select</a> transcripts, which provide a single well-supported, clinically relevant transcript per gene matched between Ensembl/GENCODE and RefSeq. Only ATG-initiated uORFs are included. </p> <p> uORFs are short open reading frames found upstream of the main protein-coding sequence. When a ribosome scans from the 5' cap, it may translate a uORF before reaching the main start codon, which often reduces production of the downstream protein. Genetic variants that create, disrupt, -or alter uORFs can therefore change protein output and contribute to disease, particularly when they -affect genes where tight translational control is critical. +or alter uORFs can therefore change protein output and contribute to disease. </p> <p> Each uORF is classified into one of three types based on the position of its stop codon relative to the main CDS start: </p> <ul> - <li>A <b>non-overlapping</b> uORF has its stop codon upstream of the main CDS start. After - the ribosome finishes translating the uORF it may re-initiate at the CDS or disengage, - reducing overall protein output.</li> + <li>A <b>non-overlapping</b> uORF has its stop codon upstream of the main CDS start.</li> <li>An <b>overlapping</b> uORF has its stop codon within the CDS but in a different reading - frame. The ribosome traverses the CDS start codon without recognizing it, which prevents - initiation of the main protein and typically causes a stronger inhibitory effect.</li> - <li>An <b>N-terminal extension</b> is an upstream ATG that is in-frame with the main CDS and - has no intervening stop codon. The resulting protein has an extended N-terminal sequence. - Variants that convert an overlapping uORF into an N-terminal extension change the protein - product rather than merely suppressing translation.</li> + frame.</li> + <li>An <b>N-terminal extension</b> is an upstream ATG that is in-frame with the main CDS, with + no stop codon between the two start codons, producing a protein with an extended + N-terminus.</li> </ul> <h2>Display Conventions and Configuration</h2> <p> -Items are colored by Kozak consensus strength, using the same color scheme as all other subtracks +Items are colored by Kozak context strength, using the same color scheme as all other subtracks in this collection: </p> -<p> -<span style="display:inline-block; background-color:#F5A623; width:18px; height:12px; vertical-align:middle;"></span> <b>Strong</b> – A/G at position −3 and G at position +4<br> -<span style="display:inline-block; background-color:#5B9BD5; width:18px; height:12px; vertical-align:middle;"></span> <b>Moderate</b> – only one of those two positions matches<br> -<span style="display:inline-block; background-color:#A9A9A9; width:18px; height:12px; vertical-align:middle;"></span> <b>Weak</b> – neither position matches<br> -<span style="display:inline-block; background-color:#D3D3D3; width:18px; height:12px; vertical-align:middle;"></span> <b>no context</b> – Kozak context not available -</p> +<table class="stdTbl"> + <tr> + <th style="background-color:#F5A623;width:1.5em"> </th> + <td><b>Strong</b>: both position −3 (A/G) and position +4 (G) match.</td> + </tr> + <tr> + <th style="background-color:#5B9BD5;width:1.5em"> </th> + <td><b>Moderate</b>: only one of position −3 (A/G) or position +4 (G) matches.</td> + </tr> + <tr> + <th style="background-color:#A9A9A9;width:1.5em"> </th> + <td><b>Weak</b>: neither position −3 (A/G) nor position +4 (G) matches.</td> + </tr> + <tr> + <th style="background-color:#D3D3D3;width:1.5em"> </th> + <td><b>No context</b>: Kozak context not available.</td> + </tr> +</table> <p> -Because all uORFs in this set are ATG-initiated, the non-ATG category does not apply here. -uORF type (Non-Overlapping, Overlapping, N-terminal extension) is shown in the mouseover and -can be used as a filter. +uORFs can span multiple exons. Each uORF borrows its exon/intron structure from an overlapping +MANE Select transcript. If no MANE transcript has introns that match the uORF's endpoints, the +GENCODE comprehensive annotation is used instead. The source transcript is recorded in the +<b>intronsSource</b> field (<tt>none</tt> if no matching transcript was found). </p> <p> -The exon/intron structure is projected from the overlapping MANE Select transcript so that uORFs -spanning multiple exons are drawn correctly. If no suitable MANE transcript could provide intron -boundaries at the exact uORF endpoints, the GENCODE comprehensive annotation is used as a fallback. -The source transcript ID is recorded in the <b>intronsSource</b> field -(<tt>none</tt> if no host transcript was found in either pool). +The track can be filtered by: </p> +<ul> + <li>uORF type</li> + <li>Kozak strength</li> +</ul> <p> -Mouseover shows the gene symbol, uORF type, rank within the gene, Kozak strength, and the donor -transcript used for intron structure. The track can be filtered by uORF type and by Kozak strength -(Strong, Moderate, Weak). +<b>Mouseover</b> shows the gene symbol, uORF type, rank within the gene, Kozak strength, and the +donor transcript used for intron structure. </p> <h2>Data Access</h2> <p> The data can be explored interactively in table format with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our <a href="https://api.genome.ucsc.edu">API</a>, track=<i>fiveUltraUorfs</i>. </p> <p> For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/ncOrfs/fiveUltraUorfs/" target="_blank">our download server</a>. The file for this track is called <tt>fiveUltraUorfs.bb</tt>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain features within a given range, e.g. </p> <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/ncOrfs/fiveUltraUorfs/fiveUltraUorfs.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt> <p> The original uORF reference set is distributed with the <a href="https://github.com/mchaldebas/5ULTRA" target="_blank">5ULTRA software package</a> and can be obtained by installing the package and running <tt>5ULTRA-download-data</tt>. </p> <h2>Methods</h2> <p> -Chaldebas et al. compiled a reference set of uORFs from two sources: the Ribo-uORF database -(501,554 translated uORFs supported by 1,495 ribosome profiling datasets) and the uORFdb database -of computationally predicted uORFs. Only ATG-initiated uORFs were retained. +Chaldebas et al. compiled a reference set of uORFs from three sources: the Ribo-uORF database +(501,554 translated uORFs supported by 1,495 ribosome profiling datasets), the uORFdb database +of computationally predicted uORFs, and the sorfs.org database. Only ATG-initiated uORFs were retained. These were mapped to the 5' UTRs of 18,775 MANE Select protein-coding transcripts from GENCODE v45 basic annotation, yielding 22,567 uORFs. Of these, 8,067 (35.7%) have direct ribosome profiling support. Each uORF was classified as Non-Overlapping, Overlapping, or N-terminal extension based on the relationship between its stop codon and the main CDS start. See Chaldebas et al. 2026 for full details. </p> <p> The uORF reference BED file was obtained from the <a href="https://github.com/mchaldebas/5ULTRA" target="_blank">5ULTRA GitHub repository</a> (installed via <tt>5ULTRA-download-data</tt>; file <tt>uORFs.MANE.hg38.bed</tt>). -Colors were remapped to the Okabe-Ito colorblind-safe palette. To recover exon/intron structure +Colors were remapped to distinguish Kozak strength (see Display Conventions). To recover exon/intron structure for uORFs that span introns, each feature was projected onto an overlapping MANE Select transcript using the <tt>addIntrons.py</tt> script in the kent source tree; a GENCODE v49 comprehensive bigBed was used as fallback when no MANE candidate could provide intact boundaries at the uORF endpoints. Of 22,567 uORFs, 3,861 received multi-block exon structure from MANE, 9 from GENCODE fallback, and 45 overlapped a GENCODE transcript but had no introns within the uORF range; 18,652 remain as single-exon features whose genomic span contains no intron from any known host. Build steps are recorded in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/ncOrfs.txt" target="_blank">makedoc</a>; the processing scripts are at <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/ncOrfs" target="_blank">src/hg/makeDb/scripts/ncOrfs/</a>. </p> <h2>Credits</h2> <p> Thanks to Matthieu Chaldebas and the 5ULTRA team for making the uORF reference data publicly available as part of the 5ULTRA package. </p> <h2>References</h2> <p> Chaldebas M, Ponsin K, Bohlen J, Conil C, Mourelatos H, Stenson PD, Cooper DN, Abel L, Casanova JL, Cobat A <em>et al</em>. <a href="https://linkinghub.elsevier.com/retrieve/pii/S0002-9297(26)00106-0" target="_blank"> Genome-wide detection of human 5' UTR variants that impact protein translation</a>. <em>Am J Hum Genet</em>. 2026 Apr 2;113(4):809-827. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/41881026" target="_blank">41881026</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13087467/" target="_blank">PMC13087467</a> </p>