First I need to suggest definitions for rational and emotion.
Rational = relating to, based on, or agreeable to reason (Merriam-Webster), which is a logical thought about how things are related; the thoughts appear in the brain.
An emotion = heart feeling, which is a reaction of the heart to what one thinks, recalls, sees, hears or experiences in other ways (my own definition).
So, emotions, which are heart reactions, are not rational, but can be partially controlled by reasoning. For example, one feels a fear of doing something, but then thinks about it and realizes it can be good to do it anyway and starts to feel hope and peace instead of fear.
On the other hand, emotions can influence rational decisions. One who sees something and finds it emotionally pleasant can start to think how to get it.
Past trauma can make you believe (in your head) that something what is generally not harmful is harmful for you, so next time, when confronted with a similar situation, you may feel fear, which can make you run away from "no reason." One could say this is an "irrational" response but it is "understandable." You can then learn how to overcome bad memories from the trauma and make your decisions in future similar situations more "intelligent." Based on this example, I claim they are thoughts and actions that can be rational (intelligent) or not, but emotions are just feelings, so they can not be rational or irrational.
You see a person, which triggers a pleasant emotion in your heart. The emotion makes you believe (in your head) that if you approach the person and start talking with him, something good will happen, so you do, and then something good actually happens, for example, you are able to reveal some bothering thoughts to him, which relieves you. Based on this example, I claim that emotions, even if they cannot be rational by themselves, can convince you to make rational decisions.
In conclusion: Thoughts (rational or irrational) are in your head and emotions in your heart. The reason for the action can start in your head or in your heart, but it is only your head that can be rational, not your heart. And emotions can help you make rational decisions.