Rodent-specific BC1 RNA and primate-specific BC200 RNA are small non-protein coding RNAs transcribed by RNA polymerase III. However, their precise cellular functions have yet to be discovered. In the cell they are bound to proteins and form ribonucleoprotein (RNP) complexes. we developed an RNA tag-based affinity purification procedure, whereby both BC RNAs were tagged with MS2 RNA motifs in combination with the MS2 coat protein fused to the tandem affinity purification (TAP ) tag to purify the endogenously assembled BC RNP complexes using an affinity matrix. The TAP tag is a two-step affinity purification method and provides a higher purification compared to other conventional biochemical purifications. Thus, established two different transgenic mouse models, BC1MS2B+MS2TAP and BC200MS2+MS2TAP, to study the purification and transport of both BC RNAs from mouse brain. In the second part of my thesis, I have used SINE retroposed elements as tools for reconstructing the rodent phylogeny.