How to align genomic sequence with corresponding amino acid sequence
Have a look at exonerate's protein2genome!
From the documentation:


  Aligning a protein to genomic sequence:
  
  Similarly, it is possible to align a protein sequence to the genome, (similar to GeneWise, but with
  heuristics).
  
  exonerate --model protein2genome query.fasta target.fasta 
  
  This model will allow introns in the alignment, but also allow frameshifts, and
  exon phase changes when a codon is split by an intron.