Synaptoporin, also known as synaptophysin 2 and p38-2, is highly homologous to synaptophysin 1 but encoded by a different gene. Like synaptopysin 1, synaptoporin contains four transmembrane regions and a short cytoplasmic tail. Unlike synaptophysin 1, it is not glycosylated.
The distributions of synaptophysin 1 and synaptoporin are different. Synaptophysin 1 is more uniformly expressed whereas synaptoporin is particularly enriched in mossy fiber synapses in the hippocampus. It is thus an excellent marker for subsets of synapses.