(a) In eukaryotes, the cap site is the position in the gene at which transcription starts, and really should be called the “transcription initiation site”. The first nucleotide is transcribed from this site to start the nascent RNA chain. That nucleotide becomes the 5′ end of the chain, and thus the nucleotide to which the cap structure is attached.(b) In bacteria, the CAP site (note the capital letters) is a site on the DNA to which a protein factor (the Catabolite Activated Protein) binds.