Citing my own thesis in the extracted paper I am going to extract a paper from my MSc thesis. But I am not sure how to point out that this paper is the synopsis of my thesis. What is your suggestion? In which section should I refer to the thesis, in introduction or related works? Is it allowed to insert some part of my thesis to my paper without modification?
This would be an excellent question to ask your advisor, who will be familiar with the norms of your field.

If your thesis is already finished by the time you submit your paper, treat it as you would any other reference. In particular, you may want to cite it if you wish to refer the reader there for more details on certain points.

In my opinion, it's not necessary to explicitly state that the paper is extracted from your thesis, though you could if you want. (If it's your first major paper, people will probably assume it's from a thesis anyway.) Normally the place to mention this would be either at the end of the introduction, or at the end of the paper.