Furthermore, in higher eukaryotes, several molecular mechanisms such as alternative splicing, alternative transcriptional initiation points, alternative polyadenylation and RNA editing compensate for the difference between the number of genes and expressed transcripts and proteins. Alternative splicing events taking place at donor or acceptor sites located in close proximity to the conventional splice sites, give rise to mRNAs which differ by a few nucleotides. The events leading to such subtle splice variants involve the utilization of alternative donor or acceptor splice sites, since polymorphisms on the corresponding splice sites eliminate these subtle alternative splicing events. Concerning the molecular mechanisms involved, it has been proposed that the tandem pairs of alternative splice sites generally resemble normal splice sites. It appears that intrinsic properties of the spliceosome substances favor alternative splicing on tandem sites. Subtle alternative splice sites bearing a NAGNAG motif have been shown to be the most frequent since approximately 2000 alternative spliced acceptors of this type have been observed in humans. The most common distance length between two splice sites is 4 nucleotides long at the donor site. It has been suggested, though, that their frameshift impact gives rise to products that are predicted as non-sense mediated targets. It has been shown that alternative splicing occurring at NAGNAG sites generates important differences between the proteomes of mammalian tissues. This fact implies that the evolutionary paths of mammalian proteins are highly affected by the attribution of introns within the coding sequences of the genes. NAGNAG events observed in human tissues are often tightly regulated by sequence-specific determinants. Alternative splicing at tandem sites constitutes a subtle mechanism which allows the modification of protein products without affecting the stability of the existing transcripts. This fact seems to exert an accelerating force on protein evolution at exon-exon boundaries. Recent experimental data have added a novel perspective in the transcriptome analysis by revealing an important group of transcripts termed long non coding RNAs. lncRNAs are regulatory RNAs exceeding the length of 200 nucleotides. Large-scale sequencing and prediction analyses of full length cDNA libraries have revealed that lncRNAs constitute an important portion of the total human transcriptome with an ever-rising number of reports reaching 23,000 transcripts. Even though the mechanisms of lncRNAs biogenesis are quite diverse, their transcription and splicing are mediated similarly to protein-coding mRNAs, with the majority of them being 59 capped and polyadenylated. Concerning their function, lncRNAs seem to take part in transcriptional and posttranscriptional regulation, epigenetic regulation by recruiting chromatin remodelling, whereas they seem to implicate in tumorigenesis mechanisms.