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To test the hypothesis that AA transporter transcripts are present in the large intestine and similarly expressed along the intestinal tract, mRNA abundance of candidate AA transporter genes solute carrier (SLC) family 7, member 9 (SLC7A9), SLC7A1, SLC7A8, and SLC43A1 encoding for b(0,+)-type AA transporter (b(0,+)AT), cationic AA transporter-1 (CAT-1), L-type AA transporter-2 (LAT-2), and L-type AA transporter-3 (LAT-3), respectively, was determined in small and large intestinal segments of the horse. Mucosa was collected from the equine small (jejunum and ileum) and large intestine (cecum, left ventral colon, and left dorsal colon), flash frozen in liquid nitrogen, and stored at -80 degrees C. Messenger RNA was isolated from tissue samples, followed by manufacture of cDNA. Relative quantitative reverse transcription-PCR was conducted using the 2(-DeltaDeltaCT) method, with glyceraldehyde-3-phosphate dehydrogenase serving as the housekeeping gene. Compared with the jejunum, cationic and neutral AA transporter SLC7A9 mRNA abundance was similar in the ileum, cecum, and large intestinal segments. Compared with the jejunum, cationic AA transporter SLC7A1 mRNA abundance was similar in the ileum and decreased in the cecum, left ventral colon, and left dorsal colon (P < 0.001). Neutral AA transporter SLC7A8 mRNA abundance decreased from the cranial to caudal end of the intestinal tract (P < 0.001). Neutral AA transporter SLC43A1 mRNA abundance was similar in the ileum and left dorsal colon and increased in the cecum (P < 0.01) and left ventral colon (P < 0.1) compared with the jejunum. Cationic and neutral AA transporter SLC7A9 mRNA abundance was similarly expressed in the large compared with small intestine, whereas cationic AA transporter SLC7A1 was of low abundance in the large intestine; neutral AA transporters SLC7A8 and SLC43A1 were differentially expressed with decreased abundance of SLC7A8 and increased abundance of SLC43A1 in the large intestine. Results indicate that the large intestine might contribute to both cationic and neutral AA uptake and absorption predominantly via transporters LAT-3 and b(0,+)AT.