I am assuming that by domain, you mean protein domain? If that is the case, and if you are dealing with just 1 gene, you can first check for the presence of any protein domain in the encoded protein using a sensitive approach such as "HHpred". Which takes slightly more time than the less sensitive PfamScan at Xfam.

If indeed your protein contains 1 or more protein domains, note its coordinates. Convert these protein start-stop coordinates to CDS start-stop coordinates simply using the formula n = 3a - 2 (a = aa coord in protein, n = nt coord in CDS). Then map i.e. align, CDS coordinates or just this sequence to obtain start stop coordinates of the protein domain, on its encoding gene, using something like NCBI's SPIDEY. If this region even partially overlaps with the region you deleted in your gene, then your answer is yes. 

However, I suspect you are looking for a single piece of software that can do all of the above. Couple of options - GENEWISE by Ewan Birney, or EXONERATE by Guy Slater, available at EBI.

And this is just 1 answer, there is always more than one way to do this. If you can work on the command line, I may provide a slightly different workflow. 

Links to each suggested software may be found easily with Google searches.

Good luck!