Fig. 3

TEs regulate the transcription of lncRNAs. A Genomic loci of lncRNAs and coding genes overlapping with TEs (up). Exonic sequences of lncRNAs and coding genes overlapping with TEs (down). The black dashed lines represent the ratio of TE sequences in whole genome; the red solid lines represent the ratio of coding genes overlapping with TEs; and the black and grey bars represent the ratio of lincRNA and lncNAT overlapping with TEs, respectively. B The distribution of Class I and Class II TEs in genome, lncRNAs and coding genes. C The ratio of lncRNAs with TE promoters in each species. D TE-lincRNA Osat_00007032 in rice (subspecies: Japonica). The up black line represents genome of Japonica, while the down one represents genome of Indica. The grey block between Japonica and Indica was the syntenic area between the two genomes. The locus of Osat_00007032 was signed with the red and blue bar, while the syntenic area in Indica was not found with lncRNAs or other elements. The TE upstream Osat_0000732 belonged to MERMITEJ sub-family, and was a type of DNA/Gypsy TE