Primer on Reading Frames and Phase Wilson Leung08/2012.

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Primer on Reading Frames and Phase Wilson Leung08/2012

3 reading frames per strand (+ / -) Frame: base to start translation relative to the first base of the sequence 1: Start translation at first base of sequence 2: Start translation at second base of sequence 3: Start translation at third base of sequence A genomic sequence has 6 reading frames Frames

Splice donor and acceptor phases Phase: Number of bases between the complete codon and splice site – Donor phase: Number of bases between the end of last complete codon and the splice donor site (GT/GC) – Acceptor phase: Number of bases between splice acceptor site (AG) and the start of first complete codon Phase is relative to the reading frame of the exon

Phase depends on the reading frame Acceptor phase: – Phase 2 relative to frame 1 – Phase 0 relative to frame 2 – Phase 1 relative to frame 3 Splice acceptor

Compatibility of donor and acceptor site Donor and acceptor phases of adjacent exons must be compatible with each other: ( (Donor phase + Acceptor phase) % 3 ) == 0 GTAG… … … CC A AA T G CT C GA T TT P P N N V V L L D D Translation: CC A AA T G CT C GA T GTT CC A AA T CT C GA T TT

Incompatible donor and acceptor phases introduce a frame shift in the translation CC A GTAG… AA T G CT C GA T TT P P N N G G F F S S Translation: GT CC A AA T TC G ATGGTGGT TTC Phase 0 donor and phase 2 acceptor are incompatible with each other

Calculating the exon acceptor phase where: i > 1 P i = Acceptor phase of exon i L i-1 = Length of previous exon P i-1 = Acceptor phase of previous exon L i-1 - P i-1 =Previous exon length starting from the first complete codon (L i-1 - P i-1 ) % 3=Donor phase of previous exon 3 - ((L i-1 - P i-1 ) % 3)=Acceptor phase of current exon (3 - ((L i-1 - P i-1 ) % 3 )) % 3=Change to phase 0 if acceptor phase is 3

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