Complexity of transcriptome around a hypothetical gene. Green boxes represent exons of typical protein coding gene. Not all the sRNAs and genomic elements are in scale. CAGE tags (red lines; dots beyond the arrowheads indicate than the 3′ ends are unknown) identify TSSs or other capped molecules; the dashed lines on CAGE tags indicate that the 3′ end is not determined. Various types of transcripts are indicated by numbers: (1) protein coding mRNA transcript gene (green boxes: coding exons, gray lines, 5′ and 3′ untranslated regions); (2, a–c), antisense RNAs in various relation with the transcripts (3′–3′ overlap, full overlap, 5′–5′ overlap); (3) CAGE tags identify transcript in the 3′-UTRs, likely polyadenylated; (4) termination-associated sRNAs (TASRs); (5) exonic long-capped transcripts; (6) CAGE tags identifying TSS (exact location can vary) and may overlap PALRs; (7) PASRs (green) and tiny 18 nt long RNAs (tiRNAs, arrowhead only); (8) antisense transcription events detected by CAGE, often (but not limited to) the first exons and introns; (9) bidirectionally transcribed RNAs from core promoters; (10) ncRNA splicing isoforms only partially overlapping to coding mRNA sequences; (11) PALRs; (12) PROMPTs, unstable transcripts on upstream regulatory regions; (13) miRNAs and endogenous siRNAs (deriving mostly from other loci, not perfectly matching in most cases in animal cells); (14) other sRNAs associated to exonic-capped long transcripts. The list of different types of RNAs is continuously growing and subject to revisions and further classifications.