splice sites, the branch point, and the lariat
/ splyce sytes; branch point; LASS-oh (LARE-ee-at) /
If splicing is cutting an intron out with surgical precision, the cell needs unmistakable marks saying here is where the intron starts, here is where it ends, and here is the pivot to fold it around. Those marks are the splice sites and the branch point, and the odd loop the intron forms while being removed is the lariat — named for a cowboy's lasso.
Almost every intron begins with the two bases GU at its 5' end (the 5' splice site, also called the donor site) and ends with the two bases AG at its 3' end (the 3' splice site, or acceptor site) — this is the GU-AG rule. A short way before that 3' end sits the branch point, a specific adenine (A) nucleotide. Splicing happens in two chemical steps. First, the 2'-OH of that branch-point A attacks the 5' GU, breaking the chain there and bonding the intron's front back onto the branch A — this kinks the intron into a closed loop with a tail, the lariat. Second, the freed end of the first exon attacks the 3' AG, cutting the intron loose and joining the two exons. The intron leaves as a lariat and is then debranched and degraded.
These signals are why splicing is precise — and why it is fragile. A single mutation that destroys a GU or AG, or that creates a new GU/AG inside an exon, can make the spliceosome cut in the wrong place. Such splice-site mutations are a major and often overlooked cause of genetic disease; a base change far from any protein-coding letter can still ruin a gene by wrecking how it is spliced.
Schematically: exon1 | GU....(branch A)....AG | exon2. Step one ties the 5' GU to the branch A, forming the lariat loop; step two joins exon1 to exon2 and frees the lariat-shaped intron.
The GU-AG ends and an internal branch-point A guide two cuts; the intron exits as a looped lariat.
The GU-AG rule covers the great majority of introns but is not absolute — a rare minor class of introns uses AU-AC ends and its own minor spliceosome. The branch point joins through an unusual 2'-to-5' bond, different from the ordinary 3'-to-5' backbone, which is what makes the lariat a true loop.