Morals vary from country to country, and hare are some of Japan's manners.
In this video, you can learn 5 points of the etiquette on the train and also, these etiquettes are same as other transportation.
How to Use Trains in Japan | japan-guide.com
https://www.youtube.com/watch?v=aW_sw77sqvE
In addition to what was mentioned in this video, these are two marks that you should remember when you use public transportation.
The Help Mark is worn by people who may require assistance, even if their conditions are not readily apparent.
This mark indicates that the person is pregnant.
If you see marks like these, please give up priority seats.
In Japanese food courts, there are no janitors all the time so you have to clean up what you've finished.
In Japan, leave some stuffs (ex: handkerchief, eco bag...) if you see that, it means reserved so you can't sit there.
If you want to throw something away, throw it the trash can at the station or convenience store.
Sometimes there are trash cans at convenience stores and stations, but especially at convenience stores and stations in big cities, it's hard to find trash cans. If you can't find it, take it home yourself.
Please order new drink after you finished your drink.
If you do this to someone you meet at bar or Izakaya, it's polite.
Thank you for trying to understand Japanese manners!