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The 49ers have allowed six passing touchdowns in six games this season, yet none of those scoring plays went for 20-plus yards.

Moreover, San Francisco is the only team in the NFL to not surrender a 20-plus yard touchdown pass this season. Only three of such passes have been completed against the 49ers all year, the third-fewest in the league.

Deep passing plays come into focus this Thursday night when the 49ers face a Seattle Seahawks team led by rookie quarterback Russell Wilson, a nimble quarterback who’s shown a knack for extending plays with his legs and then finishing them with deep vertical passes.

Just ask the New England Patriots. The defending AFC champions were defeated 24-23 last week in Seattle at the hands of Wilson’s Seahawks. The rookie signal-caller completed two of his three touchdown passes with less than eight minutes remaining in the game, including a 46-yard, game-winning touchdown pass to Sidney Rice with 1:18 left in the fourth quarter.

Wilson also tossed three passes against the Patriots that traveled 46 yards or more.

In doing so, the third-round draft pick out of Wisconsin has impressed coaches and players league-wide with his play-making ability.

“Been very impressed with him,” 49ers defensive coordinator Vic Fangio said this week. “He’s obviously very athletic, very fast. He’s got 4.52-speed in the 40, which is extremely fast for a quarterback.

“He’s elusive. He’s a creator when he’s moving. When things will break down, you’ll see him move all the way around, go anywhere on the field. And he’s got a strong arm. He throws the deep ball extremely well, as you guys saw last week against New England.”

Wilson threw for a career-high 293 yards against the Patriots and posted a career-best 133.7 passer rating. The breakout performance further underscores how much Wilson has meant to Seattle’s first-place status through six weeks.

In four wins this season, Wilson has a 107.6 rating with seven touchdown passes and two interceptions. In two losses, however, Wilson has a 51.0 rating with one touchdown and four interceptions.

“He’s been playing great for those guys,” 49ers All-Pro linebacker Patrick Willis said. “He’s a very elusive guy, scrambles really well and can throw the deep ball. We really have to make sure we play great team defense and when he does scramble or get outside the pocket, we have to get to him.

“He certainly poses a threat with his scramble ability. We’ve got to keep him in the pocket and not let him get loose.”

Wilson’s recent emergence (85.6 quarterback rating and 62.5 completion percentage, ranked No. 17 and No. 16, respectively in the NFL) lends itself to an emerging trend of strong quarterback play throughout the NFL this season.

Through six weeks of action, quarterbacks league-wide have averaged an 86.3 quarterback rating and a completion percentage of 61.9. Both figures are on pace to be highest of any season in NFL history. Both statistics would surpass league records set in 2011 (84.3 passer rating) and 2007 (61.2 completion percentage).

The 49ers have never lost back-to-back games under Jim Harbaugh. Following four regular season defeats, Harbaugh’s team has allowed a combined 11 points.

In order for San Francisco to keep the trend intact Thursday night, the defense will have to limit Wilson’s production.

“He keeps plays alive,” said 49ers cornerback Chris Culliver, who faced Wilson in college when the Seahawks quarterback played for N.C. State. “I know I’ll have to cover my man for a long time.”

Culliver believes the 49ers pass defense has improved in the unit’s second season under Fangio. San Francisco has allowed the fourth-fewest passing yards this season (1,099 yards) and the second-fewest yards per game (183.0).

In comparison to 2011, the unit’s first season playing under Fangio, San Francisco finished the regular season ranked No. 16 in both passing yards allowed and passing yards allowed per game.

“We just have to put everything together,” Culliver said. “We’re hard to stop if we can get everything together, but it’s better than last year.”

Culliver hopes he’s able to record an interception against Wilson unlike his last outing against the Seahawks quarterback.

“When he played for N.C. State,” Culliver recalled, “he almost threw me a pick, but I dropped it. Well, he threw me a pick, I dropped it.”

Despite the bitter memory, Culliver respects Seattle’s 5-foot-11 quarterback’s rise to the starting lineup.

“Always respect a guy for that,” Culliver said. “He’s a good quarterback, same way as he was in college, mobile, run around, try to get of pressure, try to get away for defensive ends. He sets them up real good.”

If the 49ers are able to disrupt Wilson’s production and win on Thursday it would give San Francisco a four-game winning streak over its rivals from the Pacific Northwest. It would also mark the franchise’s longest current winning streak against a division opponent.

Fortunately for the 49ers, opponents have a 35.4 quarterback rating on passes over 21 yards this season, second-lowest in the league.

If Wilson takes the easy money and looks to complete check-down passes, the 49ers have to be prepared to tackle all of Seattle’s play-makers.

Even Wilson if the quarterback decides to scramble.

“I think he’s a pretty confident and poised guy,” Fangio said of Wilson. “He handles the situations good. I think he handles if he’s ever involved in a bad play, he comes right back. He had great experiences in college playing in two different places, playing in front of big crowds. He’s got that, like you said, it’s hard to measure or quantify it, but he’s got the intangibles.”

Fangio doesn’t see Wilson’s size being an issue either. San Francisco’s defensive coordinator said he hasn’t seen any more of Wilson’s passes being batted at the line of scrimmage than anybody else in the NFL.

“I’ve been impressed with him,” Fangio said. “I think he’ll be their quarterback for a long time and credit to them for seeing through his height and picking him.”

Now, it’s a matter of if, and how many times, the 49ers are able to pick Wilson on Thursday night.