1. Reading Frames and ORF’s

2. Reading Frames A piece of DNA has 6 possible reading frames
It is read in blocks of 3 nucleotides – a codon 1 2 3 -1 -2 -3
Symbols used in figure
*** stop-codon
>>> start-codon in frames 1,2 or 3
<<< start-codon in frames -1,-2 or -3
))) Alternative start-codon (not important here)
((( Alternative start codon (not important here)

3. Bla A codon. 3 nucleotides
Represent a fraction of a codon. 1 or 2 nucleotides
Represents an intron
stop-codon
DNA sequence c
ATG TTC CGA T
gtccctagcgtag
AC TCA TAA
 Exon   Intron  Exon2
Sequence counter ….
mRNA sequence

4. Reading frame and reverse complement
Having a piece of DNA like:
5-TGCCATGCATAGCCCCTGCCATA-3
Forward strings & reading frames
1 : 5-TGCCATGCATAGCCCCTGCCATA-3
2 : 5-GCCATGCATAGCCCCTGCCATA-3
3 : 5-CCATGCATAGCCCCTGCCATA-3
Reverse and complement strings
-1: ATACCGTCCCCGATACGTACCGT -> 5-TATGGCAGGGGCTATGCATGGCA-3
-2: ATACCGTCCCCGATACGTACCG -> 5-TATGGCAGGGGCTATGCATGGC-3
-3: ATACCGTCCCCGATACGTACC -> 5-TATGGCAGGGGCTATGCATGG-3
Another example of
reading frames 1,2,3
on the plus strand 1 2 3

5. ORF ORF – Open Reading Frame
A continuous stretch of codons that do not contain a stop codon
There are many ORF in the human genome – NOT all of them are transcribed
Within an ORF you can look for a START codon and use prediction tools to
guess/predict if a gene or at least an exon is located within that region
Removal of intron regions in eukaryotes is a complex process (spliceosome)
Prokaryotes do NOT have the small ribonucleoproteins involved in the spliceosome so no intron regions in ex Bacteria, but as always exceptions do occur (self-splicing introns).