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