Long considered “junk DNA”, retrotransposons make up approximately 46% of all human DNA and have recently been discovered to contribute to embryonic development and the progression of several diseases, including aging, neurodegeneration and cancers. Retrotransposons have been shown to be reliable markers of cell fate and tumorigenesis. While most investigation has been conducted into the deleterious effects of retrotransposon expression, with special focus on the LINE-1 family of retrotransposons causing deleterious insertions, relatively little investigation has been conducted into the potential beneficial effects of retrotransposons occurring through millions of years of co-evolution. Moreover, while some successful investigation has been conducted into the possibility of retrotransposon-targeted therapeutics on disease progression, those studies have largely focused on the indirect impact and potential of drugs targeted towards epigenetic regulation, and not directly on the impact of the retrotransposons themselves. Utilizing genomic indices taken from RepeatMasker, a database of millions of retrotransposon found in humans and mouse, we obtained all the sequences assigned to the IAPez and MT2_Mm transposons families that show massive expression in the early preimplantation embryo. Utilizing a variety of tools to analyze their expression in the 1-cell, 2-cell, 4-cell, 8-cell and morula stages of development, we were able to design effective probes and reagents against the MT2_Mm family. This work is done in tandem and validated by the characterization of a mouse model in which specific retrotransposon elements have been removed using CRISPR-Cas9. Globally, we were able to conduct a cluster and motif analysis of both families to reveal the adjacent genes these specific insertions possibly evolved to directly regulate during development and open the door for further exploration into the role of these sequences in the genome.