Download Levels of Protein Structure - CBS

Reading Frames
and
ORF’s
1
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)
http://www.cbs.dtu.dk/services/VirtualRibosome/
2
Bla
A codon. 3 nucleotides
Represent a fraction of a codon. 1 or 2 nucleotides
Represents an intron
123
DNA sequence
c
1
123
1
23
ATG TTC CGA T gtccctagcgtag AC

Sequence counter
123
234

Exon 1
567 8910 11 ….
mRNA sequence
3
123
stop-codon
TCA TAA
Intron  Exon2
Reading frame and
reverse complement
Having a piece of DNA like:
TGCCATGCATAGCCCCTGCCATATCT
Forward strings & reading frames
1 : TGCCATGCATAGCCCCTGCCATATCT
2 : GCCATGCATAGCCCCTGCCATATCT
3 :
CCATGCATAGCCCCTGCCATATCT
Reverse and complement strings
-1: TCTATACCGTCCCCGATACGTACCGT -> AGATATGGCAGGGGCTATGCATGGCT
-2: CTATACCGTCCCCGATACGTACCGT -> GATATGGCAGGGGCTATGCATGGCT
-3:
TATACCGTCCCCGATACGTACCGT -> ATATGGCAGGGGCTATGCATGGCT
ORF
ORF – Open Reading Frame
A piece of DNA going from STOP to STOP
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).
5