RNA Splicing

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A Brief Summary of RNA Splicing

For most eukaryotic introns, splicing is catalyzed by a complex of small nuclear ribonucleoproteins (snRNPs), singularly called the spliceosome. There are also self-splicing introns, or ribozymes capable of catalyzing their own excisions from the parent molecule. Spliceosomal introns are mostly interleaved between protein-coding exons. The four primary features required for splicing reside within the intron sequence:

  • a splice donor GT site (GU in pre-mRNA) at the 5' end of the intron.
  • a branch A site near the 3' end of the intron.
  • a tract/high number of pyrimidines (C and G/U).
  • a splice acceptor AG site at the 3' end of the intron.

Intron homology.jpg

The splice donor site includes an almost invariant sequence GT site (GU in pre-mRNA) at the 5'-end of the intron. The upstream exon-intron is cut right before the GT splice donor, which is embedded within a moderately conserved region. Nearing the 3'-end of the intron things become more highly conserved, and the intron is always cut just after the AG splice acceptor. Upstream from the AG splice acceptor is a region high in pyrimidines (C and G/U), the polypyrimidine tract. Further upstream from the polypyrimidine tract is the branchpoint, which includes an adenine A involved in lariat formation. The IUPAC consensus sequence for an intron is defined as:


However, 'consensus' here provides flexibility along the intronic sequence and number of nucleotides between the branchpoint and nearest 3’ acceptor, which can affect splice site selection. Point mutations in the underlying DNA or errors during transcription can activate a cryptic splice site in part of the transcript that usually is not spliced. In this way, a point mutation, which might otherwise affect only a single amino acid, can manifest as a deletion or truncation in the final protein.

mRNA splicing in two steps