Pairs of azimuthal intensity decrements at near symmetric locations have been seen in a number of protoplanetary disks. They are most commonly interpreted as the two shadows cast by a highly misaligned inner disk. Direct evidence of such an inner disk, however, remain largely illusive, except in rare cases. In 2012, a pair of such shadows were discovered in scattered light observations of the near face-on disk around 2MASS J16042165-2130284, a transitional object with a cavity $sim$60 AU in radius. The star itself is a `dipper, with quasi-periodic dimming events on its light curve, commonly hypothesized as caused by extinctions by transiting dusty structures in the inner disk. Here, we report the detection of a gas disk inside the cavity using ALMA observations with $sim0$farcs2 angular resolution. A twisted butterfly pattern is found in the moment 1 map of CO (3-2) emission line towards the center, which is the key signature of a high misalignment between the inner and outer disks. In addition, the counterparts of the shadows are seen in both dust continuum emission and gas emission maps, consistent with these regions being cooler than their surroundings. Our findings strongly support the hypothesized misaligned-inner-disk origin of the shadows in the J1604-2130 disk. Finally, the inclination of inner disk would be close to -45 $^{circ}$ in contrast with 45 $^{circ}$; it is possible that its internal asymmetric structures cause the variations on the light curve of the host star.
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