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From what I know, the two names are used interchangeably and I haven't found any resource which says otherwise either. Is there at all any difference, is there a transit peptide that is not a signal peptide or vice versa?

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Signal peptides are typically at the N terminus of a protein and are processed by the translocon machinery and are cleaved off after sorting through the membranes of organelles in the secretory system:

  • endoplasmic reticulum
  • Golgi apparatus
  • ER-Golgi transition vesicles
  • plasma membrane
  • lysosomes

Transit peptides target the protein to other subcellular organelles such as (from UniProt):

  • Mitochondrion
  • Apicoplast
  • Chromoplast
  • Chloroplast
  • Cyanelle
  • Thylakoid
  • Amyloplast
  • Peroxisome
  • Glyoxysome
  • Hydrogenosome

N-terminal transit peptides are quite rare. C-terminal transit peptide motifs are much more common. UniProt holds transit peptides as a discrete controlled vocabulary, separate from signal peptides.

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