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. Each mucin transcript is typically made up of one long VNTR exon, which encodes the heavily glycosylated tandem-repeat domain, flanked by many shorter, non-repetitive exons that encode the cysteine-rich and other functional domains of the protein. This track shows the non-VNTR (non-repetitive) exons of each mucin transcript on the T2T-CHM13 (hs1) primary assembly.
Each item is a single exon, drawn in blue (), labeled with the gene symbol and the exon number from the source table (e.g. MUC1_exon7). The transcript accession and gene symbol are shown in the details page. The companion track Mucin VNTR exons shows the tandem-repeat exons of the same transcripts.
Mucin gene structures with their corresponding VNTR and non-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.
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 335 exons labeled as non_VNTR_exon across 14 mucin transcripts.
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=mucinsNonVntr.
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 mucinsNonVntr.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/mucinsNonVntr.bb -chrom=chr1 -start=154000000 -end=154500000 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