[...]... along as well zoom in and out of a chromosomal region 4 Use the selection boxes below to select which track you wish to visualize and in which format, and click refresh Tracks are organized by categories: mapping and sequencing tracks, phenotypes and disease association, gene and gene prediction tracks, mRNA and EST tracks, expression, regulation, comparative genomics, and variation and repeats (Not all... contrasts with the other mucins in showing little variation (43) Multiple bands are detected in DNA digested with 1 Mucin Methods: Genes Encoding Mucins 19 several enzymes (e.g Mspl, Pstl, and Taql) Relatively infrequent variant patterns involving the presence or absence of one or more small bands were detected with PstI and TaqI A single large band is detected with EcoRI (27 kb) and with HindIII (25... JER58 for MUC5AC (32), and the cDNA reported in 33 for MUC6, and, when used, JER57 for MUC5B 1 Mucin Methods: Genes Encoding Mucins 9 (34) Label 25 ng by random primed labelling utilizing [a-32P] dCTP and the Amersham Megaprime™ DNA Labeling System using the solutions and protocol provided (GE Healthcare) 14 Prehybridize the filters in a plastic box in 200 mL of 6× SCC, 5× Denhardt’s, and 0.5% (w/v) SDS... Chapter 1 Mucin Methods: Genes Encoding Mucins and Their Genetic Variation with a Focus on Gel-Forming Mucins Karine Rousseau and Dallas M Swallow Abstract Mucin genes encode the polypeptide backbone of the mucin glycoproteins which are expressed on all epithelial surfaces and are major constituents of the mucus layer Mucins are, thus, expressed at the interface between the external and the internal... impact on susceptibility to inflammatory disease, and to an array of studies to examine allelic association with inflammatory and epithelial disorders (Table 2) However, while there are many, now standard, tools for studying genes and their expression, the 1 Mucin Methods: Genes Encoding Mucins 3 Table 1 Tandem repeat characteristics of the secreted gel-forming mucins Size of the TR unit Mucin gene in bp... in this chapter In addition, methods and approaches that have been used successfully are described Key words: MUC gene, Tandem repeat domain, Polymorphism, SNP, Disease association 1 Introduction As is seen elsewhere in this volume, mucins are extracellular proteins containing large domains that are rich in serine and threonine residues and are heavily O-glycosylated, and they are mainly expressed... conservation of the location of the exon/intron boundaries and following the rules for end and start of intron sequences ag/gt Figure 3 shows the amino acid sequence of human MUC2, MUC5AC, MUC6, and MUC5B mucins highlighting the position of the introns 8 Inspect and check all the exons 9 Copy and paste the entire sequence, delete all intronic sequences, and translate 10 Submit this translation to the NCBI... in gel formation, and which some would argue were the only true mucins (i.e critical to the formation of mucus gels) Four of these, MUC6, MUC2, MUC5AC, and MUC5B, are located on chromosome 11p15.5 and form a gene complex while the fifth mucin gene, MUC19, is located on chromosome 12q12 (1, 2) The four 11p15.5 gelforming mucins are closely related and all five share common structural and functional characteristics... to the end of the tandem repeat region of MUC5AC and is continuous until the end of the gene The presence of this gap in the genomic sequence and the similarity of MUC5AC and MUC5B results in errors in annotation and confusion of the Refseq and Uniprot sequences Importantly, the protein sequences A7Y9J9 and NIEHS 4586 are erroneous composites of MUC5AC and MUC5B 32 MUC5B is the fourth gene of the MUC... Ann, D K., and Wu, R (2004) Genome-wide search and identification of a novel gel-forming mucin MUC19/Muc19 in glandular tissues Am J Respir Cell Mol Biol 30, 155–165 3 Thornton, D J., Rousseau, K., and McGuckin, M A (2008) Structure and function of the polymeric mucins in airways mucus Annu Rev Physiol 70, 459–486 4 Swallow, D M., Gendler, S., Griffiths, B., Corney, G., Taylor-Papadimitriou, J., and Bramwell, . http://www.springer.com/series/7651 Mucins Methods and Protocols Edited by Michael A. McGuckin Immunity, Infection and Infl ammation Program, Mater Medical. the challenges of the isolation and biochemical analysis of mucin glycoproteins and methods for detecting and quantifying mucins. The next two chapters