Fig. 3: Comparative analysis of sequence features between derived lncRNAs and their syntenic genes.

A Distribution of the sequence similarity between derived lncRNAs and their corresponding syntenic protein-coding genes. B Comparative analysis of transcript lengths (log₂-transformed) across four gene categories, statistical significance (P < 0.0001, Wilcoxon’s test) indicated for pairwise comparisons, unless indicated otherwise. C TE overlap fractions in transcripts of the four gene categories, statistical significance (P < 0.0001, Wilcoxon’s test) indicated for pairwise comparisons, unless indicated otherwise. D Detailed analysis of TE distribution in exonic and intronic regions. Paired box plots compare TE fractions in exons versus introns within each gene type (***P < 0.001 and ****P < 0.0001, Wilcoxon’s test), with statistical significance shown for both within-type and between-type comparisons (P < 0.0001, Wilcoxon’s test). E Compositional analysis of TE types (DNA transposons, LTRs, LINEs, etc.) in each gene category. Stacked bar plot shows the relative abundance of different TE classes within each gene type. Blue = derived lncRNAs (n = 4806), red = syntenic protein-coding genes (n = 6290), light blue = other lncRNAs (n = 642,885), orange = other protein-coding genes (n = 2,030,166). Error bars represent standard deviation unless otherwise indicated.