We bought a house for Rs 40lakhs/- by taking housing loan for Rs 35lakhs/-, however the property was registered only for Rs 15lakhs/-(this is the amount in the sale deed).Now we are planning to sell the house for Rs 43lakhs/- , the buyer is going to transfer the housing loan (for Rs 33lakhs/-) on his name and pay us the rest. In this case what will the capital gain? Will that be Rs 28lakhs/-(43 - 15)? How does housing loan fit into all this? Any comment would be really helpful.
Capital Gains and Registration Department are two different entities, they do pass information between each other (especially to the IT department), but by and large they are not bothered about the registered value at all.
However these are the points to be considered prior to calculating Capital Gains
The income tax department publishes an indexation calculator every year, and so the year of your purchase and sale would come into the picture.
In addition to registered value you can add a few related expenses, like brokerage, registration charges etc.
It is not clear from your question as to if the transactions are conducted in different financial years, but legally if you buy a house at 15 lakhs (declared legally) and sell it at 45 lakhs then yes you will pay tax, but the exact amount will depend on many factors including the two mentioned above, please feel free to add the details and I shall amend the answer accordingly