An exon is a segment of a gene whose sequence is retained in a mature RNA transcript. The term applies both to the corresponding region of DNA and to its RNA copy. In genes that undergo RNA splicing, exons are joined together while intervening introns are removed. Exons may contain protein-coding sequences, untranslated sequences, or sequences belonging to noncoding RNAs; an exon is therefore not necessarily a region that encodes a protein. (ensembl.org)
Exons and gene structure
A transcript consists of one or more exons. In a multi-exon gene, exons are separated in the DNA by introns, but their sequences become adjacent in the processed RNA. Genes without introns can be annotated as producing single-exon transcripts. The defining feature of an exon is its inclusion in the transcript, rather than the requirement that it be separated from another exon by an intron. (ensembl.org)
For a protein-coding messenger RNA (mRNA), exonic sequence can belong to either of two principal categories:
- Coding sequence (CDS): the portion specifying the protein product.
- Untranslated regions (UTRs): sequences at the 5′ and 3′ ends of the mRNA that lie outside the main protein-coding sequence.
An individual exon may be entirely coding, entirely untranslated, or contain both coding and untranslated portions. Consequently, the boundaries of an exon need not coincide with the beginning or end of the coding sequence. Noncoding transcripts also contain exons, despite lacking a protein-coding sequence. (ensembl.org)
Exon boundaries also need not coincide with codon boundaries. A splice junction can fall between codons, after the first nucleotide of a codon, or after its second nucleotide. These positions are described as phases 0, 1, and 2, respectively. A codon interrupted by an intron in the DNA is completed when the adjacent exons are joined in RNA. Exon lengths therefore need not be multiples of three. (ensembl.org)
Formation of a mature transcript
During transcription, a gene is copied into RNA. For a typical intron-containing protein-coding gene in a eukaryote, the initial RNA contains both exonic and intronic sequences. Processing removes the introns and connects the exons, producing the continuous sequence of the mature mRNA. Splicing changes the RNA molecule; it does not excise introns from the gene’s DNA. (pmc.ncbi.nlm.nih.gov)
Most nuclear pre-mRNA splicing is carried out by the spliceosome, a complex of RNAs and proteins. Recognition of splice sites and surrounding regulatory sequences determines which exon boundaries are used. Exon selection is thus a regulated molecular process, rather than simply the removal of every sequence between fixed coding blocks. (pmc.ncbi.nlm.nih.gov)
A simplified three-exon transcript illustrates the relationship:
DNA and precursor RNA:
Exon 1 — Intron 1 — Exon 2 — Intron 2 — Exon 3
Spliced RNA:
Exon 1 — Exon 2 — Exon 3
This diagram represents sequence organization, not the coding status of each exon: any of the retained segments may include untranslated sequence. (ensembl.org)
Constitutive and alternative exons
A constitutive exon is included in all transcripts of a gene within the set being considered. An alternative exon is included in some transcript forms but not others. Through alternative splicing, one gene can produce RNAs containing different combinations of exons or different exon boundaries. (ensembl.org)
Important patterns include:
- Exon skipping: an exon is included in one transcript and omitted from another.
- Mutually exclusive exon selection: alternative transcripts use different exons at a corresponding position.
- Alternative splice-site selection: different donor or acceptor sites change the extent of an exon.
- Intron retention: a sequence removed as an intron in one transcript remains in another. (ncbi.nlm.nih.gov)
The distinction between exon and intron is therefore transcript-dependent. A genomic region can be exonic in one transcript and intronic in another, and an exon’s coding status can depend on the particular transcript being examined. An exon number or boundary is most precisely interpreted with reference to a specified transcript, not merely a gene name. (ensembl.org)
Alternative exon use can change a protein’s sequence, but not every alternatively spliced RNA produces a distinct functional protein. Some splice forms introduce a premature termination codon and become targets of nonsense-mediated decay, an RNA surveillance pathway. In these cases, alternative splicing can regulate gene expression by altering the amount of productive mRNA. (ncbi.nlm.nih.gov)
Discovery and terminology
The experimental basis of the exon–intron distinction emerged in 1977 from studies of adenovirus RNA. Researchers found that sequences adjacent in a mature viral mRNA corresponded to separated regions of the viral DNA, establishing that a gene’s RNA product could be assembled from discontinuous genomic segments. Richard J. Roberts and Phillip A. Sharp received the 1993 Nobel Prize in Physiology or Medicine for their discoveries of split genes. (pmc.ncbi.nlm.nih.gov)
Walter Gilbert introduced the terms exon and intron in his 1978 article “Why genes in pieces?” The terminology distinguished sequences expressed in the mature RNA from intervening sequences removed during processing. “Expressed” in this context should not be understood as synonymous with “translated”: untranslated and noncoding RNA sequences can also be exonic. (pmc.ncbi.nlm.nih.gov)
Evolutionary significance
The modular organization of genes permits exon shuffling, in which genomic rearrangements bring exons or groups of exons into new combinations. Such changes can contribute to the evolution of proteins with new combinations of functional regions. This is a change in genomic organization across generations, distinct from alternative splicing, which combines sequences at the RNA level. (pmc.ncbi.nlm.nih.gov)
An exon is not necessarily equivalent to a protein domain. A domain may be encoded by several exons, and exon boundaries can occur within domains. Comparative studies have found associations between exon boundaries and domain boundaries in some settings, but the inferred importance of exon shuffling depends partly on the statistical models used to evaluate those associations. Exons are processing units whose relationship to protein structural units is variable. (pmc.ncbi.nlm.nih.gov)
Annotation, sequencing, and sequence variation
In genome annotation, exon records describe the retained segments of individual transcripts. Coding-sequence records describe only their protein-coding portions. Treating the two as interchangeable excludes UTRs and noncoding exons and can misrepresent a gene’s structure. Transcript-specific annotations are also necessary when alternative splicing gives the same genomic region different roles in different RNAs. (ensembl.org)
The related term exome is widely used for the protein-coding portion of a genome, and exome sequencing focuses sequencing on those regions. This operational use is narrower than the full biological definition of exonic sequence: not every exon encodes protein, and a protein-focused exome assay is not equivalent to examining every sequence retained in every mature RNA. (genome.gov)
A mutation within an exon can have several kinds of consequence. In a coding region, it may change an amino acid, introduce a stop codon, alter the reading frame, or leave the amino-acid sequence unchanged. Other variants affect untranslated or noncoding exonic sequences, or splice-site regions. These categories describe different molecular consequences; “exonic” alone does not establish a variant’s effect. (mart.ensembl.org)
References
- Exongenome.gov
- Retrieving sequencesstatic.ensembl.org
- ensembl-cdm-docs/src/docs/exon.mdgithub.com
- Discovery of RNA splicing and genes in piecespmc.ncbi.nlm.nih.gov
- Regulation of Gene Expression by Coupling of Alternative Splicing and NMDncbi.nlm.nih.gov
- The Nobel Prize in Physiology or Medicine 1993nobelprize.org
- Why genes in pieces?nature.com
- ‘Why genes in pieces?’—revisitedpmc.ncbi.nlm.nih.gov
- Evidence for exon shuffling is sensitive to model choicepubmed.ncbi.nlm.nih.gov
- Exomegenome.gov
- Calculated consequencesmart.ensembl.org