+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. +
+ ++Each item is a single exon, drawn in vermillion +(), +labeled with the gene symbol and the exon number from the source table +(e.g. MUC1_exon2). The transcript accession and gene symbol are +shown in the details page. +
+ ++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 +Mucin non-VNTR exons track for +the remaining exons of the same transcripts. +
+ ++The starting file supp2_exons.txt was downloaded from the +publication's supplementary material and converted to bigGenePred by +the script described in the +makeDoc, which uses the converter in +src/hg/makeDb/scripts/mucins. 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 VNTR_exon +(one VNTR exon per mucin transcript that has one; MUC16 and MUC7 do +not carry a VNTR exon in this annotation). +
+ ++The data can be explored interactively in table format with the +Table Browser or the +Data Integrator and exported from +there to spreadsheet or tab-sep tables. From scripts, the data can be +accessed through our API, +track=mucinsVntr. +
+ ++For automated download and analysis, the annotation is stored in a +bigBed file that can be downloaded from +our download server. The file for this track is +called mucinsVntr.bb. Individual regions or the whole +annotation can be obtained using the tool bigBedToBed, 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 +here. +The tool can also be used to obtain features within a given range, e.g. +bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hs1/locusSpec/mucins/mucinsVntr.bb -chrom=chr11 -start=0 -end=2000000 stdout. +
+ ++Thanks to the Eichler lab and the authors of the source publication +for making the curated mucin annotation available. +
+ ++Plender EG, Prodanov T, Hsieh P, Nizamis E, Harvey WT, Sulovari A, Munson KM, Kaufman EJ, +O'Neal WK, Valdmanis PN et al. + +Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B. +Am J Hum Genet. 2024 Aug 8;111(8):1700-1716. +PMID: 38991590; PMC: PMC11344006 +
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