Exon- Definition, Structure, Splicing, Process of Splicing

Exon is defined as the segment of the eukaryotic gene that encodes a portion of the final product of the gene (protein).

Exon = Expressed region

Exon is also defined as the segment of RNA which remains after the post-transcriptional modification and which is transcribed into protein or incorporated into RNA structure- this part of the gene codes for proteins.

  • Exons are exclusively present only in the eukaryotic gene.
  • Exons are the coding regions of a gene.
  • They code for proteins and are very important segments of the gene.
  • Exons are interspaced by introns in a gene. 
  • The process of splicing (a post-transcriptional process) removes the introns (non-coding regions) and joins the exons.

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Exon Structure

  • Nucleotide sequences in DNA or RNA which are expressed are known as exons. 
  • Exons are conserved in DNA or mature RNA.
  • Exon structure includes the untranslated regions from both 5` and 3`. This includes the start and stops codons and other codons which code for proteins.
Eukaryotic Gene Structure
Eukaryotic Gene Structure


Splicing is defined as the process in which introns, the non-coding regions, are excised out of the primary mRNA, and exons are joined together in the primary transcript.

  • In this process, a pre-mRNA is formed into a mature mRNA.
  • Splicing occurs before the process of translation, before protein synthesis. 
  • It is an important process because correct protein cannot be coded without splicing. 
  • It also plays an important role in the regulation of gene expression and proteins.
  • Several methods for splicing are known, but the process mainly depends on three main factors-
  1. Type of organism
  2. Structure of RNA or intron
  3. Presence of a catalyst

Process of splicing

  1. The exon-intron junctions in the pre-mRNA have conserved sequences. The 5` end junction of the pre-mRNA has a GU sequence and the 3` end of the junction has an AG sequence. 
  2. These specific sites are known as 5` splice sites and 3` splice sites respectively. 
  3. Along with these two sites, an invariant site is also present with 15-45 nucleotides upstream of the 3` slice site. This site is rich in A bases and is known as Branch point or Branch site.
  4. Spliceosome recognizes these conserved sequences in the pre-mRNA at the respective splice sites.
  5. A spliceosome is a set of RNA-protein complexes, and each of these complexes is made up of small nuclear RNA and a protein. Collectively this small nuclear RNA and protein are known as small nuclear ribonucleotideproteins (snRNP).
  6. The important snRNPs which make up the spliceosome are U1, U2, U5, and U4-U6. (U4 and U6 are bounded together.)

Splicing Pathway

  1. The first step of splicing involves U1 and U2. U1 binds to the 5` splice site and U2 binds to the invariant site or the branch point.
  2. In the second step the remaining snRNPs bind to the earlier bound snRNPs. U5 and U4-U6 bind to the intron region and hence, now the spliceosome is assembled. 
  3. Now, the spliceosome loops out the intron, and the two ends of the introns are brought close to each other.
  4. Further U1 and U4 are released and U6 is bound to both, the 5` splice site and U2.
  5. In the next step the 5` end of the intron is cleaved and it attaches to the branch point of the intron, which is rich in A.
  6. Finally, the 3` end of the introns is also cleaved and the intron is released and further degraded by enzymes. The intron structure is called a Lariat (loop-like). 
  7. Lastly the two exons are joined together.
  8. The snRNPs are used for splicing of other introns and the process of splicing continues for the remaining introns in the pre-mRNA.

Alternative Splicing

  • Alternative splicing is the process in which different variations in the mRNA are created by joining different exons. 
  • Alternative splicing leads to isoforms of proteins.
  • This leads to changes in the chemical and biological activity of proteins. 
  • This means one gene can code for more than one type of mRNA, and more than one type of protein.

The most common types of alternative splicing are:

  1. Consecutive splicing – in this splicing process consecutive introns are spliced and consecutive exons are joined together. 
  2. Exon skipping – in this process certain exons along with their adjacent exons are excised from the pre-mRNA before translation. 
  3. Alternative 5` splice site or 3` splice site – this can be achieved by joining of exons t alternative 3` or ` splice site.
  4. Intron retention – this is achieved when some introns are retained in the mature mRNA.

Self-Splicing Introns

Self-splicing is the process in which the introns (or the RNA) can excise themselves from the pre-mRNA without any precursors and proteins.

It occurs by the mechanism of phosphoester transfer.

Image source – Self-splicing by the group I introns (pre-rRNA of Tetrahymena). (2021, July 20). The Pennsylvania State University. https://bio.libretexts.org/@go/page/9985


  • Exons are the coding regions that code for specific amino acids.
  • Exons are very important in protein formation.
  • Exons are separated by non-coding regions called introns. 
  • Removal of introns is achieved by the process of splicing.
  • Splicing involves the use of cellular machinery known as Spliceosome.
  • Due to splicing, the exons are joined together forming a complete gene with all coding regions.
  • At the end of the splicing process, a pre-mRNA is converted into a mature mRNA.
  • Alternative splicing forms protein isoforms which lead to variations in the biological and chemical activity of proteins. Hence one gene gives rise to more than one type of mRNA.
  • Some RNA molecules can undergo self-splicing. 
  • Splicing is an extremely important process in eukaryotes before translation. 


  1. https://www.news-medical.net/life-sciences/What-are-introns-and-exons.aspx
  2. Gene VIII, Benzamin Lewis 
  3. Lehninger Principles of Biochemistry – 6th ed- c2013- 
  4. https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/splicing
  5. https://www.yourgenome.org/facts/what-is-rna-splicing
  6. https://www.technologynetworks.com/genomics/articles/alternative-splicing-importance-and-definition-351813
  7. Clancy, S. (2008) RNA splicing: introns, exons, and spliceosome. Nature Education 1(1):31
  8. https://www.nature.com/scitable/topicpage/rna-splicing-introns-exons-and-spliceosome-12375/

About Author

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Nidhi Abhay Kulkarni

Nidhi Abhay Kulkarni completed her bachelor’s degree (B.Sc.) in Microbiology from Savitribai Phule Pune University. She has published two articles in the Scientific Journal. She is interested in research related to medical microbiology, molecular biology, and genetics. She also has good Laboratory and Bioinformatics skills.

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