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I would like to know some rules about the nomenclature of Inverted Repeats DNA sequences. More in detail, I want to know what is the name of sequences between two inverted repeats.

For example, I have two genes A and B in this order: A, B, -A. The gene A is inverted duplicated and forms an inverted repeat with gene B in the middle. What do I call this gene B?

Here below are some names I found or that I thought, however, I don't consider them a good choice. Could you suggest some other names?

"intervening sequence", "in-between", "inserted", "separating", "spacer", "non-palindromic spacer", "loop", "gap".

In Wikipedia, they used the name "intervening sequence". https://en.wikipedia.org/wiki/Inverted_repeat

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  • $\begingroup$ Welecome to SE Biology. Come si chiama, como se llama, Wie heißt, comment s'appelle. But in English is is What, not How. $\endgroup$
    – David
    Apr 12 at 16:34
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    $\begingroup$ There is no "rule" or even convention, as you found from Wikipedia. Such sequences are not sufficiently important (and have no general function) to have been given a name. Intervening sequence is a description, but as it is the long form of intron, I wouldn't use it. For suggestions on how to describe it (there are problems with all of yours), SE English Language & Usage would seem more appropriate. However you will need to give an example sentence there, which should relate to the specific circumstances. $\endgroup$
    – David
    Apr 12 at 16:45
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    $\begingroup$ To add to David's points, "inverted repeats" typically described very short sequences. Even so-called "long inverted repeats" are just tens of bp long. Since you have designated sequences A and B to be genes, it would be better to described your system as "gene B flanked by inverted copies of gene A", or something like that. $\endgroup$
    – acvill
    Apr 12 at 17:09
  • $\begingroup$ Thank you David and acvill, both comments were very useful. Yes, unfortunately, I have some long Inverted repeats with many genes and kilobases long which are not common and not well described (named). I want to name them to describe a property that I think these sequences might have. I think I will use the term "internal sequences" or "sequences flanked by internal repeats" as acvill suggested. $\endgroup$ Apr 14 at 9:01

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