Reading Frames & ORFs

Start, Stop & the Open Reading Frame

A minimal ORF starts at AUG, continues in that frame, and ends at the next stop codon.

highlighted = computed this step

Find the first AUG

The minimal rule begins at the first AUG. In this worked mRNA, that start codon begins at position 0.

start=AUG at position 0\text{start} = \text{AUG}\text{ at position } 0
Open reading frameThe ORF begins at the start codon and runs to the in-frame stop.mRNAAUGGCAUGCAAAUAAcodonsAUGGCAUGCAAAUAApeptideMACK

Translate to the next in-frame stop

From the start codon, translation reads codons in the same frame until UAA ends it. The stop codon is not an amino acid in the peptide.

UAA⟶stop\text{UAA} \longrightarrow \text{stop}
Open reading frameThe ORF begins at the start codon and runs to the in-frame stop.mRNAAUGGCAUGCAAAUAAcodonsAUGGCAUGCAAAUAApeptideMACK

The open reading frame is that stretch

The ORF spans the start through the stop, positions 0 through 15, and encodes MACK. Honesty note: real ORF finding also weighs Kozak or Shine-Dalgarno context and alternative starts; this is the minimal deterministic rule.

ORF=[0,15)⟶MACK\text{ORF}=[0,15) \longrightarrow \text{MACK}
Open reading frameThe ORF begins at the start codon and runs to the in-frame stop.mRNAAUGGCAUGCAAAUAAcodonsAUGGCAUGCAAAUAApeptideMACK