RNA Splicing

Join exons, remove an intron and compare the messages made from one gene.

Experimental post-catalytic human spliceosome cutaway with mint joined exons, a dark-green intron lariat and violet small nuclear RNAs surrounded by detailed grey protein machinery.

Structural referencePDB 6QDV Source 2

Experiment · A synthetic transcript

Same starting RNA. Different messages.

Choose a splice pattern, follow the RNA, then read the codons. Does losing an exon always shift the reading frame?

Splice outcome

Pre-mRNAExon sizes and introns drawn schematically

Lariat loops show excised RNA, with a branch-point linkage and a tail. Catalytic steps are combined in this overview.

RNA product

—nt

Change from exon inclusion

—nt

Downstream frame

Not yet joined

Pre-mRNA

The same pre-mRNA is the starting point for each scenario. Coloured blocks are exons; the connecting regions are introns.

1 / 4

Authored eukaryotic teaching construct: exons contain 6, 6, 9 nucleotides; retained intron 1 contains 65. These are chosen splice outcomes, not predictions of splice-site recognition, RNA stability or protein function. UTRs and RNA surveillance are omitted.

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Quick reference

The first transcript

A eukaryotic pre-mRNA can contain both exons and introns. Splicing removes introns and joins the retained exons. Exons can contain untranslated regions as well as protein-coding sequence.

An RNA machine

The spliceosome contains proteins and small nuclear RNAs. In the usual spliceosomal reaction, the intron forms a branched lariat intermediate before the flanking exons are joined.

Alternative outcomes

Regulated use of splice sites can produce different transcripts from a gene. Exon skipping may preserve or change a coding frame, depending on the boundaries. A real cell can produce a mixture of isoforms; the choices here are fixed teaching examples.

Check your understanding Optional

Does skipping an exon always cause a frameshift?

No. It depends on how the coding sequence is joined.Yes. Every exon contains exactly one codon.No. Splicing changes DNA, so translation is unaffected.

At the bench

Inspect the experimental spliceosome structure used in the Cell tour.

Open Cell

Sources and model notes

Structure-based views of resolved experimental coordinates. Cutaways, category colours, camera choices and guided highlights are authored for teaching. Coordinates remain fixed; highlights are not experimental trajectories or simulation outputs.

RCSB PDB · Spliceosome 6QDV

Human post-catalytic complex with an experimental RNA substrate.

CSHL · Alternative RNA splicing

Researcher explanation of different transcript outcomes, including SMN2.