SANTA CLARA -- Indulging linemen with contract extensions has become a habit for the 49ers, though guard Alex Boone is still holding out for one.

Defensive tackle Glenn Dorsey signed a two-year extension Tuesday, and he did so with his left arm in a brace because of a torn biceps that's jeopardized his coming season.

Dorsey's deal comes in the wake of left tackle Joe Staley's two-year extension last month. Dorsey, 29, was entering the final year of his two-year deal, whereas Boone has two years remaining.

Boone remains entrenched in a contract dispute that's kept him away through the offseason program and training camp.

The deals with Dorsey and Staley followed Colin Kaepernick's six-year pact, in which he intentionally left salary-cap room for others.

San Francisco 49ers’ Anthony Davis (76) speaks to the media at their practice facility in Santa Clara, Calif. on Monday, Aug. 5, 2013.  (Nhat V.
San Francisco 49ers' Anthony Davis (76) speaks to the media at their practice facility in Santa Clara, Calif. on Monday, Aug. 5, 2013. (Nhat V. Meyer/Bay Area News Group) ( Nhat V. Meyer )

Teammates entering the final year of their contracts include wideout Michael Crabtree, guard Mike Iupati, running back Frank Gore and cornerback Chris Culliver.

Progress is being made on Crabtree's negotiations, and an incentive-laden deal might be reached in the next two weeks, NFL Network's Ian Rapoport reported Tuesday upon visiting the 49ers facility.

Kaepernick didn't stump on Boone's or anyone else's behalf Tuesday, deferring to the front office on how the 49ers should manage their payroll.

"For me, I tried to do something where we gave them space to try to get players back," Kaepernick said. "Now, who they sign and what they do with it, that is really up to them."


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Dorsey curried enough favor in 17 months with the 49ers, making a smooth transition to nose tackle, that extending his deal shouldn't be surprising, even if he did tear the biceps in his left arm Aug. 1. The 49ers haven't decided if he'll miss the season or if he'll draw their injured-reserve/designated-for-return tag.

"Glenn is a true pro who has quickly become a valued contributor to our organization both on and off the field," general manager Trent Baalke said in a statement. "He is a quick study and a very good football player that has earned this extension, and we look forward to his future contributions."

Signed last year as a free agent out of Kansas City, Dorsey took over as the starting nose tackle once Ian Williams suffered an ankle injury in a Week 2 loss at Seattle. Williams is projected to return as this season's starter, though he started practicing only last week.

While Boone's absence has attracted national attention in potential trade scenarios, the offensive line has practiced since the spring without him -- and without right tackle Anthony Davis, who practiced Tuesday for the first time since April surgery on a torn left biceps and bone spurs in his labrum.

"It's exciting. I finally get to do what I do," said Davis, who is on track to play in the Sept. 7 opener at Dallas. He wasn't in full pads Tuesday but did wear his jersey and helmet for individual drills.

  • Boone's replacement on the starting unit has been Joe Looney, who's described by Davis as: "A smart, heady player. Looney is like a vet, mentally." Other than the recent two exhibitions, Looney hasn't started a game in his two-year career. He saw self-improvement from the exhibition opener at Baltimore to Sunday's game against Denver. "I played a little better, and there's always stuff I can get better at doing, like my pad level," Looney said.

    "We believe in Joe Looney, we believe we can win with Joe Looney," coach Jim Harbaugh said. "Joe Looney is working every day to improve, and that's what we want the whole unit doing."

  • Kaepernick said he's had no lingering effects from last season's foot injury, which did not require surgery for a chipped bone on his forefoot and a ruptured capsule in the ball of the foot. "It's a nonfactor," Kaepernick said. "It's a year-old injury now."

    Kaepernick told the Sacramento Bee he suffered the injury in a Week 2 loss at Seattle when a defender landed on his foot. The 49ers injury reports vaguely described Kaepernick's ailment as merely a "foot" injury through October, while Kaepernick coyly passed it off as a "hangnail" issue.

  • Safety Antoine Bethea was strictly an observer at practice while he undergoes the NFL's post-concussion protocol.

  • Crabtree became a father Monday and remained in his native Texas after attending the birth of Michael Crabtree III.

  • Linebacker Patrick Willis (stinger), running back LaMichael James (elbow) and nose tackle Mike Purcell (undisclosed) wore noncontact jerseys in practice.

  • Kicker Phil Dawson, who missed his two field-goal attempts Sunday, expects to take awhile to learn Levi's Stadium's kicking conditions. But he quelled the media firestorm that came Tuesday and readied himself for another solid year, leaving reporters with this line: "See you all in January."

    Sunday's Exhibition game

    San Diego (1-1) at 49ers
    (0-2), 1 p.m. FOX