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I try to read ORFs from a gene sequence but I am not sure how to interpret a sequence with a start codon but no stop codon. Imagining I have a gene sequence like the following:

atggcagaagaaga

The gene sequence contains a start codon (atg at the beginning) but no stop codon.

Does this count as ORF or not?

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Generally speaking, every single ATG..... is not an ORF. That would be a LOT of ORFs in the genome. Not even every ATG.....STOP is an ORF. An ORF has to be transcribed...and spliced into an mRNA. Just looking through an entire genome and finding ATGs is futile for understand gene density.

More practically speaking, a sequence generated from a reverse transcribed library (mRNA to coding DNA, or cDNA) is a good source for ORFs. But, you can still be fooled by the multiple possible reading frames within a cDNA. Using software to convert all 3 possible reading frames of the ORF is an excellent way to start and make predictions. The best way to find out what is really made is to consult the literature OR put the cDNA in an expression vector and translate it in vitro. This tells you the general size of the actual protein and you can compare that kDa value to the expected weight of your ORF. Then, antibodies can be directed against portions of the protein sequence to study it in vivo.

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  • $\begingroup$ It's actually for an assignment and the task is to read ORFs from DNA. In the assignment every start with stop codon is an ORF. With your answer I am just more unsure yet. Websites like web.expasy.org/translate also count a dna with no stop codon as ORF. $\endgroup$
    – yemy
    Commented Sep 28, 2022 at 16:59
  • $\begingroup$ Darn. I hate it when biology gets confusing like this. Class assignments, depending on the level, can be almost too straightforward. Stick with the straight answer...ATG to STOP codon to find your ORFs. The Web.expasy.org/translate app is pretty weak and just meant to take sequence and find ATGs. Just like I mentioned before...futile. You could get the same answer by taking the sequence into MS Word and using the Find function to search for ATG. The only thing the app gives you is all the additional translation which doesn't mean anything if it's not a real ORF. $\endgroup$
    – Daniel Van Antwerp
    Commented Sep 28, 2022 at 18:04
  • $\begingroup$ Okay. ATG to STOP codon means that ATG without a following STOP codon is no ORF? $\endgroup$
    – yemy
    Commented Sep 28, 2022 at 18:27
  • $\begingroup$ Before I definitively say yes, tell me the size of the sequences you are being given to find an ORF. If they are really short, your instructor may just be trying to get you to find an ATG. But if they are long and some ATGs do have an in-frame stop codon and others don't, I'd say the instructor is wanting you to identify an actual ORF...ATG to STOP. $\endgroup$
    – Daniel Van Antwerp
    Commented Sep 28, 2022 at 19:20
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    $\begingroup$ Also, remember that instructors' favorite trick question is find the ORF in an mRNA sequence: A) augccg....stop or B) atgccg...stop...Tricky...tricky $\endgroup$
    – Daniel Van Antwerp
    Commented Sep 28, 2022 at 19:22

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