Can Animal protein has different domain from the same protein in different translation frames?

Question

[javiersg]

Good morning/evening/night

I was using the ORFFInder (NCBI). Then i blastp to biggest selected the ORFs to check the domains. This case the whole protein domains are splitted in the two ORFs (and in different frames +1, +3). I wonder if someone has read something in literature. The strange (or not) that the sequences are from RNA-seq. It should have without introns (hypothetically). I am thinking it is about problems in the assembly or a natural processes.

Have someone saw this in animal proteins? is it normal? I know in viruses is so normal in different frames, different proteins. But it is the same protein. Other option is that the first codon stop is not used, then the translation continues. But it is in different frames (+1,+3).

Regards.

Answer 1

[lieven.sterck]

In an ORF (in the sense of mRNA, where thus the protein is translated from) there can only be one biological correct reading frame. I have never known otherwise.

What can happen in this particular case (you are using DNA sequence as input for the blast, right?) is that the assembly introduced a frameshift in your sequence (this is not so uncommon) and as a consequence it will look you have protein sequence derived from different reading frames. This is thus merely a technical artefact.

if you align your input sequences back to your assembled sequence you might be able to pinpoint the location and correct it. Alternatively you can run some ORF finding software on it that can detect and correct frameshifts (eg. FrameD, but there will be other as well). An alternative to the alternative is that you dig in manually and correct (eg. by introducing 1 or 2 Ns) the sequence somewhere arbitrary (but most likely in the proximity of that stop codon) such that you end up with a single continuous protein.

[javiersg]

Thanks lieven.sterck. I will follow your advise.

I have discovered new topics, such as there are 'pseudogenes' are not pseudo.

Olfactory receptor pseudo-pseudogenes https://www.nature.com/articles/nature19824

The small ORFs haave a huge potential. Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703645/

Regards

[lieven.sterck]

yes indeed. "True" pseudogenes are a possibility as well. Are you using genomics as input or are we talking transcriptome here (assembly artefact will be more likely than pseudogene when it's transcriptome data).

And yes again, there are indeed 'pseudogenes' that seem to be functional but then the question is of course whether they are 'true' pseudogene in the classical sense of the term.

[javiersg]

Sorry, Yes it is transcriptome sequence. Probably the artifact.

Regards.