99db113e49bd1dd42a3040eaed1e61188a117ecf max Wed May 13 05:44:18 2026 -0700 mucins: new locus-specific mucin VNTR/non-VNTR exon track on hs1 (alpha) Adds a new 'Locus-specific' container in the genes group with two bigGenePred subtracks (mucinsVntr, mucinsNonVntr) derived from Plender et al. 2024 supplementary table 2. The .ra and HTML files live under trackDb/human/ so future locus-specific tracks can share them; hs1 picks them up via include ../mucins.ra alpha. refs #37540 diff --git src/hg/makeDb/trackDb/human/mucinsVntr.html src/hg/makeDb/trackDb/human/mucinsVntr.html new file mode 100644 index 00000000000..3041bf9da9c --- /dev/null +++ src/hg/makeDb/trackDb/human/mucinsVntr.html @@ -0,0 +1,98 @@ +<h2>Description</h2> + +<p> +Mucins are large secreted or membrane-tethered glycoproteins that coat +the epithelial surfaces of the airway, gut, and reproductive tract and +form the protective mucus layer. Most mucin genes contain at least one +long exon made up of a tandem array of short, near-identical sequence +units that encode the proline/threonine/serine-rich (PTS) repeats of +the protein. Because the number of repeat units varies between +individuals, these regions are called variable number tandem repeats +(VNTRs). This track shows the VNTR exon of each mucin transcript on the +T2T-CHM13 (hs1) primary assembly. +</p> + +<h2>Display Conventions and Configuration</h2> + +<p> +Each item is a single exon, drawn in vermillion +(<span style="display:inline-block; background-color:#D55E00; width:18px; height:12px; vertical-align:middle;"></span>), +labeled with the gene symbol and the exon number from the source table +(e.g. <i>MUC1_exon2</i>). The transcript accession and gene symbol are +shown in the details page. +</p> + +<h2>Methods</h2> + +<p> +Mucin gene structures with their corresponding VNTR exons were +catalogued in a long-read sequencing study of the human mucin gene +family. The annotations on the T2T-CHM13 primary assembly were curated +manually from the gene models used in the supplementary tables of that +work; for each transcript, exons were labeled as VNTR or non-VNTR based +on whether they encode the tandem-repeat PTS domain. See the +<a href="hgTrackUi?g=mucinsNonVntr">Mucin non-VNTR exons</a> track for +the remaining exons of the same transcripts. +</p> + +<p> +The starting file <tt>supp2_exons.txt</tt> was downloaded from the +publication's supplementary material and converted to bigGenePred by +the script described in the +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hs1/mucins.txt" +target="_blank">makeDoc</a>, which uses the converter in +<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/mucins" +target="_blank">src/hg/makeDb/scripts/mucins</a>. Each exon row in the +source becomes a single-block bigGenePred entry; coordinates in the +source file are 0-based half-open and were passed through unchanged. +This subtrack contains the 12 exons labeled as <tt>VNTR_exon</tt> +(one VNTR exon per mucin transcript that has one; MUC16 and MUC7 do +not carry a VNTR exon in this annotation). +</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-sep tables. From scripts, the data can be +accessed through our <a href="https://api.genome.ucsc.edu">API</a>, +track=<i>mucinsVntr</i>. +</p> + +<p> +For automated download and analysis, the annotation is stored in a +bigBed file that can be downloaded from +<a href="http://hgdownload.soe.ucsc.edu/gbdb/hs1/locusSpec/mucins/" +target="_blank">our download server</a>. The file for this track is +called <tt>mucinsVntr.bb</tt>. Individual regions or the whole +annotation can be obtained using the 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. +<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hs1/locusSpec/mucins/mucinsVntr.bb -chrom=chr11 -start=0 -end=2000000 stdout</tt>. +</p> + +<h2>Credits</h2> + +<p> +Thanks to the Eichler lab and the authors of the source publication +for making the curated mucin annotation available. +</p> + +<h2>References</h2> + + +<p> +Plender EG, Prodanov T, Hsieh P, Nizamis E, Harvey WT, Sulovari A, Munson KM, Kaufman EJ, +O'Neal WK, Valdmanis PN <em>et al</em>. +<a href="https://linkinghub.elsevier.com/retrieve/pii/S0002-9297(24)00213-1" target="_blank"> +Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B</a>. +<em>Am J Hum Genet</em>. 2024 Aug 8;111(8):1700-1716. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/38991590" target="_blank">38991590</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11344006/" target="_blank">PMC11344006</a> +</p> +