Cis Splicing vs. Trans Splicing

What's the Difference?

Cis splicing and trans splicing are two different mechanisms of RNA processing in eukaryotic cells. Cis splicing occurs when introns are removed from a single pre-mRNA molecule, resulting in the joining of adjacent exons. This process takes place within the same RNA molecule. On the other hand, trans splicing involves the joining of exons from two separate RNA molecules. In this mechanism, a spliceosome recognizes and removes an intron from one RNA molecule and then joins it with another RNA molecule, resulting in the formation of a mature mRNA. While cis splicing is the more common form of splicing, trans splicing is found in certain organisms and can be involved in the generation of alternative spliced transcripts.


AttributeCis SplicingTrans Splicing
DefinitionCis splicing refers to the process of splicing together adjacent exons within the same RNA molecule.Trans splicing refers to the process of splicing together exons from different RNA molecules.
OccurrenceCommon in eukaryotes.Found in some eukaryotes, including nematodes and trypanosomes.
SpliceosomeSplicing is typically carried out by the spliceosome complex.Splicing can occur with or without the involvement of the spliceosome complex.
RNA MoleculesExons are spliced together within the same RNA molecule.Exons can be spliced together from different RNA molecules.
TypesIncludes constitutive cis splicing and alternative cis splicing.Includes trans-splicing of pre-mRNA and trans-splicing of small nuclear RNA (snRNA).
FunctionRegulates gene expression, alternative splicing can generate different protein isoforms.Can generate chimeric transcripts, increase transcript diversity, and regulate gene expression.

Further Detail


Splicing is a crucial process in gene expression that involves the removal of introns and joining of exons to produce mature mRNA. While most eukaryotic organisms utilize cis splicing, a few organisms have evolved to employ trans splicing as an alternative mechanism. In this article, we will explore the attributes of cis splicing and trans splicing, highlighting their similarities and differences.

Cis Splicing

Cis splicing is the predominant form of splicing found in eukaryotes. It occurs within a single RNA molecule, where the introns are excised and the exons are joined together. The process is facilitated by the spliceosome, a complex machinery composed of small nuclear ribonucleoproteins (snRNPs) and other associated proteins. Cis splicing is a highly regulated process, ensuring the accurate removal of introns and the precise joining of exons.

One of the key advantages of cis splicing is its ability to generate multiple mRNA isoforms from a single gene. This alternative splicing mechanism allows for the production of different protein variants with distinct functions, expanding the proteomic diversity of an organism. Cis splicing also enables the removal of non-coding regions, such as introns, which can be essential for the stability and functionality of the mature mRNA.

However, cis splicing is not without its limitations. The presence of introns within genes can increase the size of the genome, requiring additional energy and resources for their maintenance. Moreover, errors in cis splicing can lead to the production of aberrant mRNA isoforms, potentially resulting in dysfunctional or non-functional proteins. Despite these drawbacks, cis splicing remains the primary splicing mechanism in most eukaryotes.

Trans Splicing

Trans splicing, on the other hand, is a less common form of splicing found in certain organisms, including some nematodes, trypanosomes, and cnidarians. Unlike cis splicing, trans splicing involves the joining of exons from separate RNA molecules. This process occurs when a spliced leader (SL) RNA, which contains a conserved sequence, is trans-spliced onto the 5' end of the pre-mRNA.

Trans splicing provides several advantages over cis splicing. Firstly, it allows for the processing of polycistronic transcripts, which contain multiple genes within a single RNA molecule. By trans-splicing each gene with a common SL RNA, individual mRNAs are generated, enabling independent regulation and translation of each gene. This mechanism is particularly advantageous for organisms with compact genomes, as it maximizes the coding potential of their limited genetic material.

Additionally, trans splicing can facilitate the repair of defective mRNAs. If a pre-mRNA contains a mutation or a premature stop codon, trans splicing can rescue the transcript by replacing the defective region with a functional exon from another RNA molecule. This process, known as trans-splicing-mediated RNA repair, ensures the production of intact and functional proteins, even in the presence of genetic abnormalities.

However, trans splicing is a more complex process compared to cis splicing. It requires the recognition of specific sequences, such as the SL RNA, and the coordination of multiple RNA molecules. This complexity makes trans splicing more prone to errors and regulatory challenges. Nevertheless, the unique advantages offered by trans splicing have allowed it to evolve and persist in certain organisms.

Similarities and Differences

While cis splicing and trans splicing differ in their mechanisms and prevalence, they share some common attributes. Both processes involve the removal of introns and the joining of exons to produce mature mRNA. They contribute to the regulation of gene expression and the generation of protein diversity. Additionally, both cis splicing and trans splicing require the involvement of specific RNA sequences and associated protein factors.

However, the key difference lies in the location of the splicing event. Cis splicing occurs within a single RNA molecule, while trans splicing involves the joining of exons from separate RNA molecules. This distinction has significant implications for the complexity and regulation of the splicing process. Cis splicing is the predominant mechanism in most eukaryotes, while trans splicing is limited to specific organisms.


In summary, cis splicing and trans splicing are two distinct mechanisms involved in the processing of pre-mRNA. Cis splicing is the more prevalent and well-studied form, occurring within a single RNA molecule and allowing for alternative splicing and removal of non-coding regions. Trans splicing, on the other hand, is a less common mechanism that involves the joining of exons from separate RNA molecules, enabling the processing of polycistronic transcripts and repair of defective mRNAs.

While cis splicing and trans splicing have their own advantages and limitations, they both contribute to the complexity and diversity of gene expression. Further research into the regulation and functional implications of these splicing mechanisms will deepen our understanding of gene regulation and the intricate processes that govern protein synthesis.

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