Warner to work with 49ers’ Kaepernick on game’s mental aspects

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Colin Kaepernick has a bazooka arm and sprinter’s speed.

Now Kurt Warner is hoping he can help the 49ers quarterback develop a football mind to match his jaw-dropping physical skills.

Warner, 43, a two-time NFL MVP, will work with Kaepernick, 27, this offseason at Exos training facility in Phoenix and the focus of their time together will be on the mental aspects of the position.

“It’s really going to be about seeing where he’s at as a quarterback,” Warner said Thursday on CBS Radio. “And seeing how far we can push it to teach him how you play the game with your mind as opposed to your arm and your legs.”

In 2014, Kaepernick made a series of highlight-reel plays, most notably a 55-yard, across-the-field touchdown pass to running back Frank Gore that he fired off his back foot in a win over the Eagles. Warner, however, wants Kaepernick to become more adept at identifying routine throws that are available, such as short, underneath tosses.

“I’m just a firm believer that, regardless of how talented you are physically, you have to be able to make the easy plays at the quarterback position to be successful,” Warner said. “You have to know what you are seeing. When a defense gives you an easy read, you have to be able to make that read and make that throw 90 percent of the time. Because you don’t get that all the time and it’s hard enough to play the position.”

Unlike Kaepernick, Warner lacked mobility. He had 286 rushing yards in his 11-year career, but was a classic pocket passer who ranks ninth in NFL history in passer rating (93.7), one spot ahead of Joe Montana. Warner hopes to help Kaepernick see what is possible if he becomes less reliant on his legs.

“He’s gotten by on athleticism and he’s made some great plays and had some great games,” Warner said. “But I think the goal is, in the time that I’m going to have with him, just to see where he’s at. What he knows about the position. And then how far we can push the envelope as far as helping him develop as a pocket passer.”

FILE - In this Aug. 13, 2005, file photo, Arizona Cardinals quarterback Kurt Warner looks for an open receiver in the first quarter against the Dallas Cowboys in Tempe, Ariz. Warner, Junior Seau and Orlando Pace are first year eligible nominees among the 15 Modern-Era Finalists that will be considered for election to the Pro Football Hall of Fame when the Hall's Selection Committee meets in Phoenix on Saturday, Jan. 31, 2015. (AP Photo/Paul Connors, File) less FILE - In this Aug. 13, 2005, file photo, Arizona Cardinals quarterback Kurt Warner looks for an open receiver in the first quarter against the Dallas Cowboys in Tempe, Ariz. Warner, Junior Seau and Orlando ... more Photo: PAUL CONNORS / Associated Press Photo: PAUL CONNORS / Associated Press Image 1 of / 1 Caption Close Warner to work with 49ers’ Kaepernick on game’s mental aspects 1 / 1 Back to Gallery

In his second full season as a starter, Kaepernick ranked 20th in the NFL in passer rating (86.4), 22nd in yards per attempt (7.0) and 24th in completion percentage (60.5).

Thinning staff: Assistant secondary coach Greg Jackson, one of the 49ers’ six defensive coaches, has joined former 49ers head coach Jim Harbaugh at the University of Michigan, according to multiple reports.

Jackson, 48, had been with the 49ers since 2011 when he reconnected with Harbaugh, his teammate for two seasons with the Chargers. Niners wide receivers coach John Morton has also traveled to Ann Arbor with Harbaugh. In addition, 49ers assistant strength coach Kevin Tolbert will go to Michigan, Fox Sports reported.

The only other coach known to have left the 49ers is co-offensive line coach Reggie Davis, who is the running backs coach at Nebraska.

Eric Branch is a San Francisco Chronicle staff writer. E-mail: ebranch@sfchronicle.com Twitter: @Eric_Branch