Transits of hot Jupiters in X-rays and the ultraviolet have been shown to be both deeper and more variable than the corresponding optical transits. This variability has been attributed to hot Jupiters having extended atmospheres at these wavelengths. Using resolved images of the Sun from NASAs Solar Dynamics Observatory spanning 3.5 years of Solar Cycle 24 we simulate transit light curves of a hot Jupiter to investigate the impact of Solar like activity on our ability to reliably recover properties of the planets atmosphere in soft X-rays (94 {AA}), the UV (131-1700 {AA}), and the optical (4500 {AA}). We find that for stars with similar activity levels to the Sun, the impact of stellar activity results in the derived radius of the planet in soft X-ray/EUV to be underestimated by up-to 25% or overestimated by up-to 50% depending on whether the planet occults active regions. We also find that in up-to 70% of the X-ray light curves the planet transits over bright star spots. In the far ultraviolet (1600 & 1700 {AA}), we find the mean recovered value of the planet-to-star radius ratio to be over-estimated by up-to 20%. For optical transits we are able to consistently recover the correct planetary radius. We also address the implications of our results for transits of WASP-12b and HD 189733b at short wavelengths.
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