Jubin won 7-11, 9-11, 8-11, 11-7, 11-7, 11-9, 11-8.
No. 2 seed Devesh Karia of Gujarat, who had a wonderful outing this season, lost to qualifier Raj Mondal from West Bengal who beat him 4-1.
Earlier, another former national champion Anthony Amalraj bowed out in the second round of the main draw, losing to eighth seed Sushmit Srirarm, after comfortably leading 3-1. Sriram awon 11-9, 7-11, 7-11, 8-11, 11-9, 14-12, 11-8.
The quarterfinals in both sections will be played tonight with only the semifinals and finals slated for the morrow, the concluding day of the championships, along with the men and women's doubles finals.
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Of all the upsets on the day, Shetty's must hurt the Petroleum player the most as he was not only having a smooth ride but was even expected to defend the title he won at Patna last year.
Woefully out of the match and down 0-3, the Haryana lad played a mesmerizing game-superbly working on the angles and catching Shetty on his somewhat weak forehand and often forcing him into errors. In fact, Shetty kept pushing Jubin away from the table and it worked well for him in the first three games. The match-point shot, a curving-in forehand exemplified Jubin's fantastic play.