Cap site Two usages are given below:

1] In eukaryotes, the cap site is position in the gene at which transcription begins, and really should be called the "transcription initiation site". The first nucleotide is transcribed from this site to begin the nascent RNA chain. That particular nucleotide becomes the 5' end of the chain, and hence the nucleotide to which the cap structure is attached



2] In the bacteria, the CAP site (note capital letters) is the site on the DNA to which a protein factor (the Catabolite Activated Protein) binds.