Fluorescent timer proteins, which undergo a spectral shift over time after synthesis, as well as nucleic acid compositions encoding the same, are provided. Also provided are fragments of the subject proteins and nucleic acids encoding the same, as well as antibodies to the subject proteins and transgenic cells and organisms including the subject nucleic acid molecules. The subject protein and nucleic acid compositions find use in a variety of different applications. Finally, kits for use in such applications that include the subject nucleic acid compositions are provided.