Intron

An intron is any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene. The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of most organisms and many viruses, and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation.

The word intron is derived from the term intragenic region, i.e. a region inside a gene. Although introns are sometimes called intervening sequences, the term "intervening sequence" can refer to any of several families of internal nucleic acid sequences that are not present in the final gene product, including inteins, untranslated sequences (UTR), and nucleotides removed by RNA editing, in addition to introns.

Simple illustration of an intron and RNA splicing
Introns and the process of RNA splicing can be illustrated using a text example. Consider the following quotation from Groucho Marx:

"Outside of a dog, a book is man's best friend. Inside of a dog it's too dark to read."

To make this text look more like a nucleic acid sequence, we'll simply delete all punctuation and make all of the text uppercase. This will be our "message".

OUTSIDEOFADOGABOOKISMANSBESTFRIENDINSIDEOFADOGITSTOODARKTOREAD

If there were a single intron within this sequence, it would look something like this. In general, introns are much longer than exons. No one really knows why. OUTSIDEOFADOGABOOKISMANSBEGUITUITGLSAJSAKHDLAYSIOEYASHDKLSALKDN KLASNDKLASKGDASJKBDNKNSKDKLSANDKNSKANDKNSAKNDKSAKLDHSDJGJASBDKN SANDLNSMALVJOPDHVANVLNVKLSAKNFADNGKLHKNIUHSAFLSAFLFASFOLSANFLNK FNKDSNGOIFSGHSKDHGKDHSFIABHFIHEHRFKHLKDHSUNSIUANIDAUBIOAYICMUSF AVMASSTFRIENDINSIDEOFADOGITSTOODARKTOREAD

1. Identify exon and intron sequences
To remove the intron, the sequences corresponding to the intron and exons must be precisely identified. Here, the exon sequences are changed to bold. Note that misidentifying the boundaries between the exons and intron by even a single letter will result in a nonsensical message.

OUTSIDEOFADOGABOOKISMANSBEGUITUITGLSAJSAKHDLAYSIOEYASHDKLSALKDN KLASNDKLASKGDASJKBDNKNSKDKLSANDKNSKANDKNSAKNDKSAKLDHSDJGJASBDKN SANDLNSMALVJOPDHVANVLNVKLSAKNFADNGKLHKNIUHSAFLSAFLFASFOLSANFLNK FNKDSNGOIFSGHSKDHGKDHSFIABHFIHEHRFKHLKDHSUNSIUANIDAUBIOAYICMUSF AVMASSTFRIENDINSIDEOFADOGITSTOODARKTOREAD

2. Cleavage at intron-exon junctions
Next, the sequence must be cut precisely at the boundaries between the exons and the intron

OUTSIDEOFADOGABOOKISMANSBE GUITUITGLSAJSAKHDLAYSIOEYASHDKLSALKDN KLASNDKLASKGDASJKBDNKNSKDKLSANDKNSKANDKNSAKNDKSAKLDHSDJGJASBDKN SANDLNSMALVJOPDHVANVLNVKLSAKNFADNGKLHKNIUHSAFLSAFLFASFOLSANFLNK FNKDSNGOIFSGHSKDHGKDHSFIABHFIHEHRFKHLKDHSUNSIUANIDAUBIOAYICMUSF AVMAS STFRIENDINSIDEOFADOGITSTOODARKTOREAD

3. Link the exons together
Last, the exons must be joined together to generate the final message. (The excised intron is usually broken down to its component letters, which are then recycled.) OUTSIDEOFADOGABOOKISMANSBESTFRIENDINSIDEOFADOGITSTOODARKTOREAD

Introduction
Introns were first discovered in protein-coding genes of adenovirus, and were subsequently identified in genes encoding transfer RNA and ribosomal RNA genes. Introns are now known to occur within a wide variety of genes throughout organisms and viruses within all of the biological kingdoms.

The discovery of introns led to the Nobel Prize in Physiology or Medicine in 1993 for Phillip Allen Sharp and Richard J. Roberts. The term intron was introduced by American biochemist Walter Gilbert:

"'The notion of the cistron [...] must be replaced by that of a transcription unit containing regions which will be lost from the mature messenger - which I suggest we call introns (for intragenic regions) - alternating with regions which will be expressed - exons.' (Gilbert 1978)"

The frequency of introns within different genomes is observed to vary widely across the spectrum of biological organisms. For example, introns are extremely common within the nuclear genome of higher vertebrates (e.g. humans and mice), where protein-coding genes almost always contain multiple introns, while introns are rare within the nuclear genes of some eukaryotic microorganisms, for example baker's yeast (Saccharomyces cerevisiae). In contrast, the mitochondrial genomes of vertebrates are entirely devoid of introns, while those of eukaryotic microorganisms may contain many introns. Introns are well known in bacterial and archaeal genes, but occur more rarely than in most eukaryotic genomes.



Classification
Splicing of all intron-containing RNA molecules is superficially similar, as described above. However, different types of introns were identified through the examination of intron structure by DNA sequence analysis, together with genetic and biochemical analysis of RNA splicing reactions.

At least four distinct classes of introns have been identified.
 * Introns in nuclear protein-coding genes that are removed by spliceosomes
 * Introns in nuclear and archaeal transfer RNA genes that are removed by proteins (tRNA splicing enzymes)
 * Self-splicing group I introns that are removed by RNA catalysis.
 * Self-splicing group II introns that are removed by RNA catalysis

Group III introns are proposed to be a fifth family, but little is known about the biochemical apparatus that mediates their splicing. They appear to be related to group II introns, and possibly to spliceosomal introns.

Nuclear pre-mRNA introns (spliceosomal introns) are characterized by specific intron sequences located at the boundaries between introns and exons. These sequences are recognized by spliceosomal RNA molecules when the splicing reactions are initiated. In addition, they contain a branch point, a particular nucleotide sequence near the 3' end of the intron that becomes covalently linked to the 5' end of the intron during the splicing process, generating a branched (lariat) intron. Apart from these three short conserved elements, nuclear pre-mRNA intron sequences are highly variable. Nuclear pre-mRNA introns are often much longer than their surrounding exons.

Group I and group II introns are found in genes encoding proteins (messenger RNA), transfer RNA and ribosomal RNA in a very wide range of living organisms., Following transcription into RNA, group I and group II introns also make extensive internal interactions that allow them to fold into a specific, complex three-dimensional architecture. These complex architectures allow some group I and group II introns to be self-splicing, that is, the intron-containing RNA molecule can rearrange its own covalent structure so as to precisely remove the intron and link the exons together in the correct order. In some cases, particular intron-binding proteins are involved in splicing, acting in such a way that the assist the intron in folding into the three-dimensional structure that is necessary for self-splicing activity. Group I and group II introns are distinguished by different sets of internal conserved sequences and folded structures, and by the fact that splicing of RNA molecules containing group II introns generates branched introns (like those of spliceosomal RNAs), while group I introns use a non-encoded guanosine nucleotide (typically GTP) to initiate splicing, adding it on to the 5'-end of the excised intron.

Transfer RNA introns that depend upon proteins for removal occur at a specific location within the anticodon loop of unspliced tRNA precursors, and are removed by a tRNA splicing endonuclease. The exons are then linked together by a second protein, the tRNA splicing ligase. Note that self-splicing introns are also sometimes found within tRNA genes.

Biological functions and evolution
As a first approximation, it is possible to view introns as unimportant sequences whose only function is to be removed from an unspliced precursor RNA in order to generate the functional mRNA, rRNA or tRNA product. However, it is now well-established that some introns themselves encode specific proteins or can be further processed after splicing to generate noncoding RNA molecules. Alternative splicing is widely used to generate multiple proteins from a single gene. Furthermore, some introns represent mobile genetic elements and may be regarded as examples of selfish DNA.

The biological origins of introns are obscure. After the initial discovery of introns in protein-coding genes of the eukaryotic nucleus, there was significant debate as to whether introns in modern-day organisms were inherited from a common ancient ancestor (termed the introns-early hypothesis), or whether they appeared in genes rather recently in the evolutionary process (termed the introns-late hypothesis). Another theory is that the spliceosome and the intron-exon structure of genes is a relic of the RNA world (the introns-first hypothesis). There is still considerable debate about the extent to which of these hypotheses is most correct. The popular consensus at the moment is that introns arose within the eukaryote lineage as selfish elements.

Early studies of genomic DNA sequences from a wide range of organisms show that the intron-exon structure of homologous genes in different organisms can vary widely. More recent studies of entire eukaryotic genomes have now shown that the lengths and density (introns/gene) of introns varies considerably between related species. For example, while the human genome contains an average of 8.4 introns/gene (139,418 in the genome), the unicellular fungus Encephalitozoon cuniculi contains only 0.0075 introns/gene (15 introns in the genome). Since eukaryotes arose from a common ancestor (Common descent), there must have been extensive gain and/or loss of introns during evolutionary time. This process is thought to be subject to selection, with a tendency towards intron gain in larger species due to their smaller population sizes, and the converse in smaller (particularly unicellular) species. Biological factors also influence which genes in a genome lose or accumulate introns.

Alternative splicing of introns within a gene acts to introduce greater variability of protein sequences translated from a single gene, allowing multiple related proteins to be generated from a single gene and a single precursor mRNA transcript. The control of alternative RNA splicing is performed by complex network of signaling molecules that respond to a wide range of intracellular and extracellular signals.

Introns contain several short sequences that are important for efficient splicing, such as acceptor and donor sites at either end of the intron as well as a branch point site, which are required for proper splicing by the spliceosome. Some introns are known to enhance the expression of the gene that they are contained in by a process known as intron-mediated enhancement (IME).