Three possible copies of One Gene, which one is true?
How to know when a gene is true when they appear in the annotation with three possible copies.
What steps should I follow, what tools are recommended for this? And what characteristics should I take into account to discriminate the true one from the others?
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Please indicate if this is a genome that you assembled/annotated or are you looking at public genomes available in GenBank. If the information is public, indicate which gene/genome you are looking at.
When you say "true", are you referring to other copies being potential "pseudo genes". This could be checked by looking for mutations that would disrupt the coding regions(s).
There can certainly be genes that are multi-copy which can all be expressed (e.g. rRNA, histones etc) so it is not necessary that there be a single "true" gene.
Greetings, I will start by saying that I use a genome of the ncbi, this has two versions (gfa and gfc), I am consulting the pho P gene in priestia megaterium, in the annotation there are three "possible copies" of "phoP--PhoR, but in the literature and for this group this type of data has not been detected, not even in its closest neighbor which is B. subtilis. What makes me think is that only one of them must be the real one. I have the amino acid sequence of the three phoP-phoR versions. Greetings, I will start by saying that I use a genome of the ncbi, this has two versions (gfa and gfc), I am consulting the pho P gene in priestia megaterium, in the annotation there are three "possible copies" of "phoP--PhoR, but in the literature and for this group this type of data has not been detected, not even in its closest neighbor which is B. subtilis. What makes me think is that only one of them must be the real one. I have the amino acid sequence of the three phoP-phoR versions. As it should
It looks like your post text is duplicated above and then a part seems to be incomplete. You may want to fix that.
I assume you are referring to the GenBank (GCA_006094495.1) and RefSeq (GCF_006094495.1) versions of the genome. RefSeq version is manually curated and should always be used when available. In this case the RefSeq version appears to contain more genes (see https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_006094495.1/ table comparing annotations).
Check the gene annotations (https://www.ncbi.nlm.nih.gov/datasets/gene/GCF_006094495.1/ ) to see if there is evidence that all three copies are active.
In many cases they could all three be true, it's called gene duplication ;-)
you will need to provide some more context to your question to get meaningful answers ... which species for instance? how do you get to three copies? ....
I want to perform the deletion of that gene in that bacterium, to establish its function under culture conditions in different sources of phosphates. P. Megaterium is the target, In order to perform a successful KO I need to identify the functional gene and I don't know where to start doing it.
How can I detect the true function, what steps should I follow and the programs to use?