S-adenosyl-L-methionine-dependent methyltransferase that mediates N(3)-methylcytidine modification of residue 32 of the tRNA anticodon loop of tRNA(Thr) (PubMed:27354703). Does not catalyze N(3)-methylcytidine modification of tRNA(Ser) (PubMed:27354703). cytidine(32) in tRNA(Thr) + S-adenosyl-L-methionine = H(+) + N(3)-methylcytidine(32) in tRNA(Thr) + S-adenosyl-L-homocysteine Cells lacking trm140 show abolished N(3)-methylcytidine modification in tRNA(Thr) (PubMed:27354703). Cells lacking trm140 and trm141 show abolished N(3)-methylcytidine modification in tRNAs (tRNA(Ser) and tRNA(Thr)) (PubMed:27354703). Belongs to the methyltransferase superfamily. METL family.