"I think about it all the time, believe me," Jackson told Sports Illustrated's Peter King on Sunday night. "No question in my mind we wanted it to happen, and no question I thought it could happen. We wanted the kid in the worst way."
The Raiders ranked Kaepernick their No. 1 quarterback in the draft (ahead of Cam Newton, Jake Locker, Blaine Gabbert, Christian Ponder and Andy Dalton) and badly wanted to move up in the second round to draft the former Nevada stud -- their first-round pick in 2011 was spent in the Richard Seymour trade.
"Coach Jackson told me before the draft they were going to do everything they could to try to get me," Kaepernick told King. "I thought there was a good chance they'd pick me. I never heard anything from the 49ers before the draft after I worked out for them (at Nevada). I just figured they weren't interested."
The Raiders weren't willing to give up a package that included a second-round pick (eventually center Stefan Wisniewski) to the New England Patriots to jump into the first slot in the second round. Instead, the San Francisco 49ers eventually made a trade with the Denver Broncos at pick No. 36.
"I don't know that he threw anything,'' Jackson said. "But he was upset. So was I. Scouting him, I fell in love with the kid. Leader, won a ton of games at Nevada, really impressive when you talked to him, strong, all the tools to win in the NFL. No doubt in my mind he was going to be good."
Of course, going to a team with a stout defense, good rushing attack and coach Jim Harbaugh as opposed to a helter-skelter organization with a dearth of talent might have had a little bit to do with Kaepernick's early accomplishments.
"I don't think too much about things like that," Kaepernick said, smiling. "But I am pretty happy how things turned out."
Follow Kevin Patra on Twitter @kpatra.