This dataset includes the transcriptomes of plants bearing mutations in genes enconding for three related Arabidopsis proteins: SERRATE (SE), CAP-BINDING PROTEIN 20 (CBP20) and CAP-BINDING PROTEIN 80 (CBP80). The transcriptomes were obtained by mRNA sequencing. Comparison of the RNA accumulation patterns will enable the idenfication of common patterns and uncover possible common functions of SE, CBP20 and CBP80 in regulating gene expression. Overall design: mRNA sequencing was carried out from four different plant genetypes: WT, se, cbp20 and cbp80 mutants. The aim is to compare the transcriptome of each mutant to a common WT control. Samples were prepared in triplicates form different pools of plants. WT1 is compared with se1, cbp201 and cbp801, and the same is true for replicate 2 and 3.