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1、Primer on Reading Frames and PhaseWilson Leung08/20163 reading frames per strand (+ / -)Frame: base to start translation relative to the first base of the sequence1: Start translation at first base of sequence2: Start translation at second base of sequence3: Start translation at third base of sequen
2、ceA genomic sequence has 6 reading frames123FramesA codon could be derived from nucleotides in adjacent exonsCTGAGATTT CCGGATPhase 0Phase 0Spliced mRNAGATPhase 1Phase 2Phase 2Phase 1DonorAcceptorIntronGTAG CTGAGAGATTTT CCGGAT TTT CCGGTAG CTGAGATTT CCGGTAG CTGAGAGATSplice donor and acceptor phasesPha
3、se: Number of bases between the complete codon and the splice siteDonor phase: Number of bases between the end of the last complete codon and the splice donor site (GT/GC)Acceptor phase: Number of bases between the splice acceptor site (AG) and the start of first complete codonPhase depends on the r
4、eading frame of the CDSPhase depends on the reading frameAcceptor phase:Phase 2 relative to frame 1Phase 0 relative to frame 2Phase 1 relative to frame 3Splice acceptorPhase depends on the reading frameAcceptor phase:Phase 2 relative to frame 1Phase 0 relative to frame 2Phase 1 relative to frame 3Sp
5、lice acceptorCompatibility of donor and acceptor siteDonor and acceptor phases of adjacent exons must be compatible with each other:Donor phase + acceptor phase = 0 or 3GTAG CCAAATGCTCGATTTPNVLDTranslation:CCAAATGCTCGATGTTCCAAATCTCGATTTIncompatible donor and acceptor phases introduce a frame shift i
6、n the translationCCAGTAG AATGCTCGATTTPNGFSTranslation:GTCCAAATTCGATGGTTTCPhase 0 donor site is incompatible with phase 2 acceptor siteCalculating the exon acceptor phasewhere: i 1Pi= Acceptor phase of exon i Li-1= Length of previous exonPi-1= Acceptor phase of previous exonLi-1 - Pi-1= Previous exon length starting from the first complete codon(Li-1 - Pi-1) % 3 = Donor phase of previous exon3 - (Li-1 - Pi-1 ) % 3) = Acceptor phase of current exon(3 - (Li-1 - Pi-1) % 3 ) % 3 = Change to phase 0 if acceptor phase is 3Questions?http:/
