A second-round draft pick out of Nevada in 2011, Kaepernick has thrived under former NFL quarterback Jim Harbaugh — and the coach has said how much he wants the mobile, strong-armed QB around for the long haul. Accomplishing an extension before the season is a big deal as the team begins its first year in $1.2 billion Levi’s Stadium at team headquarters.

“I really expect a real breakout year for Colin. Athletically, he looks bionic,” Harbaugh said during the organized team activity last week. “If you all remember ‘The Six Million Dollar Man,’ that’s what it looks like to me. He’s very gifted and he always has been. He has the look and feel of a guy who’s really going to break out, even more so than he already has. I’m really excited about everything about his game right now.”

Greetings and kind words came via Twitter posts from teammates.

“Congrats to my boy @kaepernick7 on the extension! (hashtag)deserving (hashtag)hardestworkingdudeiknow,” wrote fullback Bruce Miller.

In a sensational playoff debut in January 2013 against Green Bay, Kap — as they call him — used his speedy legs to run for a quarterback playoff-record 181 yards and a pair of touchdowns. Then, in a season-opening win against the Packers last September, the strong-armed San Francisco QB threw for a career-best 412 yards and three scores.

“Colin’s hard work and dedication have played an integral role in the recent success of the 49ers organization,” 49ers general manager Trent Baalke said in a statement. “His work ethic, leadership and on-field production have positively influenced our team, and we look forward to his continued growth in all areas. Our organization always looks to reward our players for their contributions and commitment to the team.”

Harbaugh remained optimistic of getting a new deal done, while Kaepernick said his only focus was on football and he was leaving it to his agents to do the rest. The quarterback had said he sought a “fair” deal.

He is regularly the first to arrive at work each morning and the last one off the field.

Kaepernick has completed 382 of 639 passes for 5,046 yards and 31 touchdowns. He also has started all six postseason games in which he has appeared, earning four wins and passing for 1,374 yards and seven touchdowns.

Kaepernick said last week he hopes a Miami investigation from April that names him will soon be over. He said that matter didn’t affect his thoughts about whether it would affect the extension.

“That wasn’t something I was worried about,” Kaepernick said. “I let my agents handle all the talking.”

Last month, Miami Police released two calls to a 911 dispatcher saying a woman identifying herself as Jesus was lying naked in a bed and refusing to leave. The callers said the woman wanted to spend time with a third man who wasn’t there.

Police say the players also involved in the case are 49ers wide receiver Quinton Patton and Seahawks receiver Ricardo Lockette. None of them has been charged with any wrongdoing.

“We’re just really thrilled for the Kaepernick family. They’re amazing people,” agent Scott Smith said after Kaepernick’s news conference. “We’re just so happy for them. We’re really grateful of all the hard work the 49ers put into it.”

So, about his timely sock selection?

“To be honest, one of my friends gave them to me, gave me a box of socks,” he said. “No idea what brand or what company, but they were in my drawer.”

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