Figure 2.

The first intron plays a key role in several mechanisms regulating gene expression. The presence of intron-mediated enhancement (IME) motif within the first intron determines the TSS and increases gene expression. Phosphorylation status of polymerase II (Pol II) carboxy-terminal domain (CTD) varies during transcription. Ser-5P Pol II poses at the exon–intron junction. The first intron inhibits transcription of uaRNA by recruiting termination factors that confer promoter directionality. The presence of uORF within the mRNA transcript might negatively affect the translation efficiency of main ORF by forming the secondary structure or by ribosome stalling. Another layer of gene expression control is mediated through miRNA/TE encoded within intronic DNA. Alternatively, the intronic sequence is complementary to miRNA.