In the first step of primary RNA transcript splicing, the 2' OH on the branch point A attacks the phosphoryl group of the G in the 5' splice site. This G is the boundary between the 5' end of the intron and the 3' end of the adjacent exon. The attack leads to the breaking of the phosphodiester bond between the 3' end of the exon and the 5' end of the intron and the formation of a new phosphodiester bond between the branch point A and the 5' end of the intron.
As is illustrated in the figure above, the first splicing step breaks the primary transcript into two pieces. One piece contains the 5' end of an exon, with a new free 3' OH. The other piece is a strange looking structure that resembles a lasso and as a result is called a lariat structure. The lariat contains the intron that is still connected to a second exon.
In the second step of primary transcript splicing, the newly released 3' OH of exon 1 attacks the phosphoryl group on the 5'-most nucleotide of exon 2. The resulting phosphodiester bond is the boundary between the intron and the second exon. The final products of the reaction are the two joined exons and the intron, which is still in the lariat structure.
Alternative splicing is a way of introducing diversity to the gene products of transcription by creating multiple protein products from the same DNA sequence. Alternative splicing accomplishes this in two ways: 1) by splicing together exons from two different primary RNA transcripts in a process called trans- splicing; 2) by splicing out entire exons.
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