How Do 5` And 3` Ltr Regions Of Ltr Retrotransposon Look Like?

Question

[Biomonika (Noolean)]

I am wondering, how 5` and 3` LTR regions look like, is it just a direct repeat? Or inverted repeat?

I mean

TSD ACAAT proteincodingregion ACAAT TSD

..or..

TSD ACAAT proteincodingregion ATTGT TSD

(Actual nucleotides are just made up)

Thank you.

Answer 1

[Casey Bergman]

The long terminal repeats of a LTR retrotrapnsoson or retrovirus are direct repeats, e.g. in your scenario: "TSD ACAAT protein_coding_region ACAAT TSD". This is a hard rule with no exceptions that I am aware of, and has been implemented in several software systems, like LTRharvest: http://www.ncbi.nlm.nih.gov/pubmed/18194517

[Biomonika (Noolean)]

Thank you a lot.