7 replies to this topic

[indoubt]

hello everybody,

what does ORF mean?

i am really stucked at this word!



so help, please!

[labrat]

ORF is a piece of DNA that begins with an initiation (methionine ATG) codon and ends with a nonsense codon. Every piece of DNA has six possible reading frames, three in each direction. The reading frame that is used determines which amino acids will be encoded by a gene. Typically only one reading frame is used in translating a gene (in eukaryotes), and this is often the longest open reading frame. Once the open reading frame is known the DNA sequence can be translated into its corresponding amino acid sequence. An open reading frame starts with an atg (Met) in most species and ends with a stop codon (taa, tag or tga).

There are many online tools which can be used to predict ORF from a piece of DNA sequence.

[indoubt]

hi labrat!

i am so glad that you replied! and thanks for your help, but i have some more doubts about ORF...hope you can share your ideas with me!


what i question are:

1. is reading frame and open reading frame the same word? this confuses me
alot!

2. why they have to add "open" before "reading frame" ?

3. besides is open reading frame an active gene?


thanks again!

[labrat]

I am sorry I didn't make it clear.

A reading frame is one of the three possible ways of reading a nucleotide sequence as a series of triplets. An open reading frame is a Reading Frame that is potentially translatable into protein.

An open reading frame predicted doesn't always represent an existing protein.

[zany]

then,do you mean that a open reading frame is a kind of reading frame that have the potential to encod a peptide?

thank you very much !

[DevGrp]

Medicine.net

Quote

Open reading frame: A long sequence of DNA that has no stop codon (no signal to stop reading) and therefore may encode part or all of a protein.

The "Open" part refers to the lack of a stop codon within the reading frame.

In practical terms when I get a DNA sequence which may encode a protein I run it through some software called vector NTi. This searches for ORFs in the 6 possible (3 forward/3 reverse) triplet frames. The default is that an ORF should start with a start codon (ATG or GTG) go on for at least 300 codons (900bp) and end in a stop codon (TAA TGA TAG). Usually 5 of the frames wont have long enough ORFs (ie closed reading frames, start codons with stops shortly afterwards) and only one of the frames will produce an ORF.

[zany]

DevGrp, on Dec 8 2004, 06:29 AM, said:

Medicine.net

Quote

Open reading frame: A long sequence of DNA that has no stop codon (no signal to stop reading) and therefore may encode part or all of a protein.

The "Open" part refers to the lack of a stop codon within the reading frame.

In practical terms when I get a DNA sequence which may encode a protein I run it through some software called vector NTi. This searches for ORFs in the 6 possible (3 forward/3 reverse) triplet frames. The default is that an ORF should start with a start codon (ATG or GTG) go on for at least 300 codons (900bp) and end in a stop codon (TAA TGA TAG). Usually 5 of the frames wont have long enough ORFs (ie closed reading frames, start codons with stops shortly afterwards) and only one of the frames will produce an ORF.

I'm confused ,sorry.

you said the ORFstarts with start codon and ends with stop codon,
then ,how does an ORF contain no stop codon?

thanx

[DevGrp]

Sorry, I could see that confusion in the definitions I got from the website

"The "Open" part refers to the lack of a stop codon WITHIN the reading frame"

Important word is "within"
open reading frame: long run of codons starting with a start ending in a stop with no stops in the middle.