In both prokaryotes and eukaryotes, newly synthesized proteins contain signals determining their ultimate destination. In eukaryotes, the presence of a particular kind of signal sequence in the protein determines that the ribosome not remain free in the cytosol during translation but is directed to the endoplasmic reticulum. Signal sequences are typically on the order of approximately twenty residues in length. They are cleaved from the rest of the protein within the lumen of the ER. Such proteins synthesized on the endoplasmic reticulum become bound in the lumen of the ER, entering the endomembrane system, including eventually the Golgi complex, for modification, sorting, and delivery. Secretory and membrane proteins are synthesized on the rough ER.

Cells specialized for the manufacture of secretory proteins, such as the cells within the pancreas that produce digestive enzymes, contain large quantities of rough ER.