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In humans, alkaline mucus is present in several organs and provides protection by way of its alkalinity and high viscosity. Alkaline mucus exists in the human eye, stomach, saliva, and cervix.

In the stomach, alkaline mucus is secreted by gastric glands in the mucosa layer of the stomach wall. Secretion of alkaline mucus is necessary to protect the mucus epithelium of the stomach from acids released during digestion. Ulcers can develop as a result of damage caused to the mucosal barrier. Duodenal ulcers have been shown to develop in sites that are in direct contact with pepsin and acids. To prevent damage and protect the mucus epithelium, alkaline mucus secretions increase in the digestive system when food is being eaten.

In the cervix, alkaline mucus has been shown to possess bactericidal properties to protect the cervix, uterus, peritoneal cavity, and vagina from microbes.