KLF and octamer binding sites are highly enriched in stem cell gene promoters. (A) A Clover analysis was used to identify over-represented transcription factor binding sites within the promoter sequences of all stem cell genes identified in Table 1. Representative gene promoters are shown, indicating KLF-A binding sites (pink), octamer sites (ATGCWAAT) (green) and extended Oct4 binding sites (Oct4-Loh)(cyan) . (B) Clover output for 2 kb of promoter sequence of murine Zfp42/Rex1. The positions and sequences corresponding to PWMs for KLF-A, octamer and Oct4 occupancy sites are indicated in the table and colour coded in the sequence. The positions are relative to the transcriptional start site. (C) ECR Browser output of conserved sequence identity between mouse and rat in the promoter and part of the first intron of the Zfp42 gene. The blue arrows indicate the direction of transcription. Yellow indicates the extent of the first (non-coding) exon, pink indicates regions of sequence conservation in the first intron and red indicates regions of sequence conservation in the 5' upstream region. rVISTA was used to find all of the KLF-A and octamer sites in the murine gene (Murine only) and conserved sites between mouse and rat (Conserved mouse, rat).