Learn Portuguese (Portugal): O comboio parte às sete em ponto.

Yes, you can use sai (from the verb sair, meaning to leave or go out). However, partir (to depart) is the standard and most natural verb to use for scheduled public transport like trains, flights, and buses.

Why is there a grave accent on às in às sete?

The word às is a contraction of the preposition a (at) and the feminine plural article as (the). In Portuguese, you always use the definite article when stating the hour, so "at seven" translates literally to "at the seven hours." The grave accent marks this contraction.

I have seen the word trem for train before. Why does this sentence use comboio?

Comboio is the standard word for train in Portugal. If you have seen trem, that is the word used in Brazilian Portuguese. Since you are learning European Portuguese, you should always use comboio.

How does the phrase em ponto work?

Em ponto literally translates to "in point," but it is the standard fixed expression for saying a time is "on the dot" or "exactly." You can add it after any exact hour, such as às duas em ponto (at exactly two o'clock).