Yes, eukaryotes have introns. They are a defining feature of eukaryotic genomes, present across animals, plants, fungi, and protists. The average human gene contains 8 to 9 introns, and 95 to 100% of human genes that span more than one exon produce multiple versions of their RNA through a process that depends entirely on introns being there in the first place.
What Introns Actually Are
Introns are stretches of DNA within a gene that do not code for protein. When a gene is read and copied into RNA, the introns are included in the initial transcript. Before that RNA can be used to build a protein, the introns must be cut out and the remaining pieces, called exons, are stitched together. The finished RNA then travels out of the nucleus to be translated into protein.
This cutting and stitching is handled by a molecular machine called the spliceosome, which is built from five small RNA molecules and more than 150 proteins. The process happens in two precise chemical steps. First, a specific spot within the intron loops back and cuts the connection at the beginning of the intron, forming a lasso-shaped loop. Then the loose end of the upstream exon attacks the far edge of the intron, joining the two exons together and releasing the intron loop as waste. All eukaryotic genomes rely on this same basic machinery.
How Many Introns Human Genes Contain
The human genome is heavily populated with introns. The average protein-coding gene has 8 to 9 of them, and genes with 3 to 6 introns are the most common group, making up over 30% of all human genes. Only about 2% of human genes have zero introns. At the extreme end, the gene for titin (the largest known protein, found in muscle) contains more than 300 introns.
Still, over 600 human genes are intronless. Many of these belong to a family called G protein-coupled receptors, which are involved in detecting signals like light, hormones, and odors. Histone genes, which package DNA, are another well-known group that typically lacks introns. So while introns are the norm in eukaryotic genomes, they are not universal within every single gene.
Why Introns Exist
Introns trace back to the last common ancestor of all eukaryotes. The leading explanation for how they got there involves an ancient invasion of self-splicing genetic elements from bacteria into early eukaryotic cells. Over billions of years, those self-splicing elements evolved into the introns we see today, now dependent on the spliceosome rather than splicing themselves.
Maintaining introns is expensive. Cells spend energy copying them every time a gene is read, and they need a massive molecular machine to remove them precisely. The fact that introns have persisted across such a long evolutionary timeline suggests they provide real advantages that outweigh the cost. The most significant of those advantages is alternative splicing.
Alternative Splicing and Protein Diversity
Introns make it possible for a single gene to produce multiple different proteins. By including or skipping certain exons, or by choosing slightly different cut points, cells can rearrange the same gene’s output into a variety of RNA messages. This process, called alternative splicing, is one of the main sources of protein diversity in complex organisms.
The scale is striking. A single human gene called KCNMA1 (involved in controlling electrical signals in cells) can generate more than 500 different RNA versions from one stretch of DNA. In fruit flies, a gene called Dscam can theoretically produce over 38,000 distinct RNA forms, each encoding a slightly different protein used in wiring the nervous system. These aren’t rare exceptions. High-throughput sequencing studies show that 95 to 100% of multi-exon human genes undergo alternative splicing, and the number of protein versions per gene can range from two to several thousand.
This is part of why the human genome can encode a vastly more complex body than its roughly 20,000 protein-coding genes might suggest. Introns provide the raw material for cells to multiply protein options without needing more genes.
Not All Eukaryotes Have the Same Intron Load
While all eukaryotic genomes carry introns, the number varies enormously between species. Vertebrates and land plants tend to be intron-rich. Baker’s yeast (Saccharomyces cerevisiae), on the other hand, has lost most of its introns over evolutionary time and is often used as a model for studying intron depletion. An analysis of 1,700 species found that certain intron-generating elements were present in about 5% of genomes and were especially common in aquatic lineages.
This variation reflects different evolutionary pressures. Organisms with small, streamlined genomes and rapid reproduction, like yeast, tend to shed introns. Organisms with larger genomes and more complex bodies tend to retain or even gain them.
What Happens When Splicing Goes Wrong
Because introns must be removed with exact precision, mutations at splice sites can cause serious genetic diseases. A mutation that disrupts the signal marking where an intron begins or ends can cause the splicing machinery to skip an exon, include part of an intron, or use the wrong cut site entirely. The result is often a defective or missing protein.
The list of diseases linked to splicing mutations is long: cystic fibrosis, Duchenne and Becker muscular dystrophy, spinal muscular atrophy, neurofibromatosis type 1, Ehlers-Danlos syndrome, hemophilia B, and familial dysautonomia, among others. In neurofibromatosis type 1, about 69% of the splicing-related mutations in the responsible gene disrupt regulatory sequences that guide exon selection, causing entire exons to be skipped.
Some of these mutations occur deep within introns, far from the exon boundaries, yet still disrupt splicing. One of the most common mutations causing cystic fibrosis in certain populations sits nearly 2,500 nucleotides inside an intron. Mutations at the start of an intron (the donor site) are roughly 1.5 times more common than those at the end (the acceptor site), based on a meta-analysis of 478 splicing mutations across 38 genes.
Understanding these errors has opened the door to targeted therapies. Treatments for spinal muscular atrophy and Duchenne muscular dystrophy now use molecules designed to redirect the splicing machinery, forcing it to include or skip specific exons to produce a functional protein. These therapies work precisely because introns and their splicing signals are predictable enough to manipulate.
Prokaryotes Handle Things Differently
Bacteria and archaea (prokaryotes) occasionally contain self-splicing introns, but these are mechanistically different from the spliceosomal introns found in eukaryotes. Prokaryotic introns remove themselves without needing a spliceosome. They are also far less common. Spliceosomal introns, the kind that require 150-plus proteins to remove and that enable alternative splicing, are a eukaryotic innovation. This distinction is one of the fundamental differences between the two domains of life at the molecular level.