The full-length coding sequence of rat liver-specific organic anion transporter-1 (1st-1) and its splice variant have been cloned. The full-length rat 1st-1 (designated r1st-1a) encodes a protein containing 687 amino acids and has 12-putative transmembrane domains, multiple potential N-glycosylation and phosphorylation sites. Therefore, rat 1st-1a has 35 additional amino acid residues compared to the previously reported rat 1st-1. A splice variant (designated r1st-1c) reported in this communication encodes a protein containing 654 amino acids and has 10-putative transmembrane domains. PCR analysis suggests that r1st-1a is the most abundant form in liver. Phylogenetic analysis reveals that rat 1st-1a is an ortholog of human LST-1 (hLST-1) and mouse 1st-1 (m1st-1). The r1st-1 gene is composed of 15 exons and 14 introns. Analysis of exon-intron boundary reveals that the splice variant r1st-1c lacks the entire exon 7, while the previously reported rat 1st-1 (designated herein as r1st-1b) lacks approximately half of exon 10, and the splicing has occurred through alternative usage of a splice donor site within exon 10.