Among those 32 lncRNA-target mRNA pairs, 5 lncRNA-target mRNA pairs (NONRATG014028.2-Pim1, NONRATG011882.2-Il15, NONRATG013497.2-Fbxw7, NONRATG011747.2-Mrps35, and MSTRG.1662-Ucp3) appeared in 901 co-expressed lncRNA-mRNA pairs with high correlation coefficients, suggesting these dysregulated lncRNA-mRNA pairs might involve in the hyperglycemia and T2D of GK rats at the age of 3 and 4 weeks. Here, UCP3 is linked to type 2 diabetes mellitus.