Cryptic splice site

The selection of appropriate introns is important for efficient RNA processing and to eliminate the utilization of the cryptic splice site in the coding region. Introns with splice sites and branch points that closely match the established consensus sequences are spliced more efficiently and accurately than ones that do not. Several introns have been used widely in mammalian expression vectors, including the second intron of the rabbit, 0-globin gene (O Hare et al., 1981), and intron A of CMV (Hartikka et al., 1996). Some expression vectors include a hybrid intron, e.g., the 5 portion of an adenovirus sequence and the 3 portion of an immunoglobulin sequence (Choi et al., 1991). 

Relatively expensive on a large scale, presence of cryptic splice sites in large inserts may lead to inactivation of RNA transcript... 

Messenger RNA (mRNA) processing (cryptic splice sites, consensus sequence, poly A addition site, etc.)... 

Figure 1. Molecular structure of the mouse short-chain acyl-CoA dehydrogenase gene including the deletion mutation found in BALB/cByJ mice. Adapted and redrawn from previous publications."- A. The fine genomic structure of the deletion mutation, b. Molecular structure of the approximately normal size Acads mRNA from the mutant allele. This consists of an RNA copy of the deleted gene sequence with no splicing, c. Molecular structure of the short Acads mRNA from the mutant allele. This consists of a missplked mRNA from exon 8 to a cryptic splice site in exon 10.

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