Fig. 1
From: Subtype classification and functional annotation of L1Md retrotransposon promoters
Application of monomer detection pipeline on various mouse genome assemblies reveals potential species-specific monomer subtypes. In this figure, genome names are abbreviated using the initials of their corresponding species name, except for mm10. They are: rn (Rattus norvegicus), mc (M. caroli), ms (M. spretus), mmc (M. m. castaneus), mmm (M. m. musculus), and mmd (M. m. domesticus). a Workflow of the monomer detection starting from a single consensus sequence. b Count of identified monomers in six mouse genomes. For each monomer type in all genomes, its corresponding consensus sequence reported in previous literature was used as the starting heuristic. c Length distribution of detected Type A monomers within the range of 180 – 220 bp. d Percentage of reads detected to share sequence similarity with L1 ORF2, Type A monomer and the A monomer subtype with a specific 7-bp insertion, respectively. Error bars indicate ±SD