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| scheitel | early pluteus larva stage to competent pluteus larva stage | |
| secondary podia | early juvenile stage to undefined | |
| secondary podia associated neuron | early juvenile stage to undefined | |
| secretory vesicle | 1-cell stage to 1-cell stage | |
| sensory neuron | undefined | |
| serotonergic neuron | undefined to competent pluteus larva stage | |
| skeletal element | mid-gastrula stage to adult stage | |
| skeletal rod | late gastrula stage to early juvenile stage | |
| small micromere | 32-cell stage to undefined | |
| small micromere descendant cell | very early blastula stage to competent pluteus larva stage | |
| somatocoel | 6-arm pluteus larva stage to 8-arm pluteus larva stage | |
| sperm aster | mature spermatozoid stage to mature spermatozoid stage | |
| spermatozoid | spermatogenesis period to spermatogenesis period | |
| spermatozoid entry point | mature oocyte stage to 1-cell stage | |
| spermatozoid flagellum | undefined | |
| spermatozoid head | undefined | |
| spermatozoid part | spermatogenesis period to spermatogenesis period | |
| sphaeridium | early juvenile stage to adult stage | |
| sphincter | prism stage to undefined | |
| sphincter muscle | 4-arm pluteus larva stage to undefined | |
| sphincter muscle cell | 4-arm pluteus larva stage to undefined | |
| spicule granule | undefined | |
| spicule rudiment | undefined | |
| spine | 8-arm pluteus larva stage to adult stage | |
| stomodeum | prism stage to undefined | |
| stone canal | 8-arm pluteus larva stage to adult stage | |
| subequatorial skeletogenic mesenchyme ring | mid-gastrula stage to undefined | |
| synaptotagmin-B neuron | undefined | |
| synaptotagmin-B-expressing neuron | late gastrula stage to adulthood | |
| syncytium | undefined |
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