Internal domains are 91% similar, and the LTRs are 81-88% similar.
these identities are enough to attribute the same family name to this TE. To refer to a particular instance of this TE in your species, best practice is to follow the nomenclature guidelines of http://www.nature.com/nrg/journal/v8/n12/full/nrg2165.html section "Naming system and name format"
May I ask one more question...
Which way is more appropriate to do, if I identified a full length construct in other people sequenced BAC sequence available in NCBI? In my study identified sequences are similar to this BAC region, but my sequences are too short to detect LTRs. (Element is present in several BAC clones, but it is not analyzed and not annotated as transposable element in RE databases). So, should I ask permission to use BAC sequences available?
Hi Angelika. Since the sequence was deposited into NCBI Genbank, it is public and you can use it to whatever you want without need for permission.
Regards
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