Molecular Genetics

Dr. Atif Kamran

Assistant Professor
Seed Centre,
University of The Punjab, Lahore
Introns and Exons
• Introns and exons are nucleotide sequences within a gene.
• Introns are removed by RNA splicing as RNA matures, meaning that
they are not expressed in the final messenger RNA (mRNA) product,
while exons go on to be covalently bonded to one another in order to
create mature mRNA.
• Introns can be considered as intervening sequences, and exons
as expressed sequences.

There are an average of 8.8 exons and 7.8 introns per human
gene
Introns and Exons
Exons
• Exons are nucleotide sequences in DNA and RNA that are conserved in
the creation of mature RNA.
• Exons usually include both the 5’- and 3’- untranslated regions of
mRNA, which contain start and stop codons, in addition to any protein
coding sequences.
• The term exon derives from the expressed region and was coined by
American biochemist Walter Gilbert in 1978.
• Just as the entire set of genes for a species constitutes the genome, the
entire set of exons constitutes the exome.
Exons
• Although unicellular eukaryotes such as yeast have either no introns or
very few, metazoans and especially vertebrate genomes have a large
fraction of non-coding DNA.
• For instance, in the human genome only 1.1% of the genome is spanned
by exons, whereas 24% is in introns, with 75% of the genome
being intergenic DNA:
• An intergenic region (IGR) is a stretch of DNA sequences located
between genes.
• Intergenic regions are a subset of noncoding DNA. Occasionally some intergenic
DNA acts to control genes nearby, but most of it has no currently known
function.
Exons: Size and distribution
• Across all eukaryotic genes in GenBank, there were (in 2002), on
average, 5.48 exons per gene.
• The average exon encoded 30-36 amino acids.
• While the longest exon in the human genome is 11555 bp long, several
exons have been found to be only 2 bp long.
• A single-nucleotide exon has been reported from the Arabidopsis
genome.
• Introns
• An intron (for intragenic region) is any nucleotide sequence within
a gene that is removed by RNA splicing during maturation of the final
RNA product. In other words, introns are non-coding regions of an RNA
transcript, or the DNA encoding it, that are eliminated by splicing
before translation.
• The word intron is derived from the term intragenic region, i.e. a region
inside a gene. The term intron refers to both the DNA sequence within a
gene and the corresponding sequence in RNA transcripts.
• 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
 Introns
• Introns Discovery
• 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
Phillip Allen Sharp
genes throughout organisms and viruses within all of the
biological kingdoms.
• The fact that genes were split or interrupted by introns
was discovered independently in 1977 by Phillip Allen
Sharp and Richard J. Roberts, for which they shared
the Nobel Prize in Physiology or Medicine in 1993. The
term intron was introduced by
American biochemist Walter Gilbert

Richard J. Roberts
Introns
• Introns Distribution
• 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 jawed 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/brewer'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
• Introns Size
• A particularly extreme case is the Drosophila dhc7 gene containing a
≥3.6 megabase (Mb) intron, which takes roughly three days to
transcribe.
• On the other extreme, a recent study suggests that the shortest known
eukaryotic intron length is 30 base pairs (bp) belonging to the
human MST1L gene
Introns
• Introns Classifications
• 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 (spliceosomal introns)
• Introns in nuclear and archaeal transfer RNA genes that are removed by proteins
(tRNA introns)
• Self-splicing group I introns that are removed by RNA catalysis
• Self-splicing group II introns that are removed by RNA catalysis
Introns
• Introns Classifications: 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.
Introns
• Introns Classifications: tRNA Interons
• Transfer RNA introns that depend upon proteins for removal, occur at a
specific location within the anticodon loop of un-spliced 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 gene
Introns and Exons
• Introns Classifications: Group I and II Interons
• 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.
Introns and Exons
• Introns Classifications: tRNA Interons
• In some cases, particular intron-binding proteins are involved in
splicing, acting in such a way that they 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.