I assume you are using
My questions is...
to emphasise your point after someone has misunderstood your question.
If that is the case, you could go for
I am asking if...
This would need further rewording for the remainder of the sentence. Observe below:
A: Is the monkey related to the panda?
B: The panda eats Bamboo whereas the Monkey eats Bananas.
A: I am asking if the monkey is related to the panda. (My question is, is the monkey related to the panda) you can see how the verb 'to be' has moved from the beginning of the clause - where it would be placed in a direct question - to follow the subject as it is now a reported/indirect question.
A: Oh, I'm sorry. The answer is no.
I hope this helps.