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Recent observations have revealed that most proto-planetary discs show a pattern of bright rings and dark gaps. However, most of the high-resolution observations have focused only on the continuum emission. In this Paper we present high-resolution ALMA band 7 (0.89mm) observations of the disc around the star CI Tau in the $^{12}$CO & $^{13}$CO $J=3$-2 and CS $J=7$-6 emission lines. Our recent work demonstrated that the disc around CI Tau contains three gaps and rings in continuum emission, and we look for their counterparts in the gas emission. While we find no counterpart of the third gap and ring in $^{13}$CO, the disc has a gap in emission at the location of the second continuum ring (rather than gap). We demonstrate that this is mostly an artefact of the continuum subtraction, although a residual gap still remains after accounting for this effect. Through radiative transfer modelling we propose this is due to the inner disc shadowing the outer parts of the disc and making them colder. This raises a note of caution in mapping high-resolution gas emission lines observations to the gas surface density - while possible, this needs to be done carefully. In contrast to $^{13}$CO, CS emission shows instead a ring morphology, most likely due to chemical effects. Finally, we note that $^{12}$CO is heavily absorbed by the foreground preventing any morphological study using this line.