Kaepernick is heading into the final year of his contract. If an extension isn't signed now, however, he can be franchised next year if an accord isn't made.
Both sides are interested in doing an extension now and have begun talking. But there is no timeline set. It has been widely discussed that the last big quarterback deal signed will be the starting point of discussion. Chicago's Jay Cutler signed a seven-year, $126 million deal in January. It is team friendly and the Bears can get out of it after three years.
I think Cutler's deal is comparable to what Kaepernick will be looking for (and for what he will get) in terms of yearly average. Kaepernick will likely command, at least, $18 million a year. Unlike Cutler (who has been inconsistent and who turns 31 in April), Kaepernick is just 26 and he is a proven winner. He is 21-8 as an NFL starter and has played in two NFC title games and a Super Bowl already.
I suspect that when Kaepernick's deal is completed he will have earned much more real money than Cutler.