Synthetic Biology Parts, Devices and Applications

Mammals

Budding
yeast

Exon definition

Intron definition

Exon ISS

U2 65 35

U2AF

YNYURAY

UACUAAC

Y(n) YAG

U(n) YAG

30 nt

ESE ESS GU ISE Exon

Exon

U1

5 ′ splice site

5 ′ splice site

3 ′ splice site

3 ′ splice site

Branch site

Branch site

Poly(Y)

tract

Poly(U)

tract

GURAGU

Exon GUAUGU

U1 U2

Figure 7.1 Conserved sequence elements of mammalian and budding yeast pre-mRNAs. Exons (cylinders) are separated
by introns (lines). The consensus sequences in mammals and budding yeast at the 5′ splice site, branch site, and 3′ splice
site are as indicated. N is any nucleotide, R is purine, and Y is pyrimidine. Mammals contain a polypyrimidine-rich stretch;
S. cerevisiae contains a polyuridine-rich stretch. Both are located between the branch site and the 3′ splice site. In
mammals, cross-exon complexes are formed during early stages of spliceosome assembly, while in S. cerevisiae the introns
are defined. The spliceosomal snRNPs U1 and U2 (green) are shown interacting with the splice sites. Mammals additionally
have the U2 auxiliary factor (U2AF), U2AF65 and U2AF35 (green) interacting with the 3′ splice site. They also use auxiliary
regulatory elements that either enhance the splicing process, namely, exonic and intronic splicing enhancers (ESE and ISE,
dark green cylinders), or inhibit spliceosome assembly, such as exonic and intronic splicing silencers (ESS and ISS, red
cylinders). These elements are often bound by SR proteins and hnRNPs.