Fig. 4

HSat1A 3′ RACE analysis. A Agarose gel corresponding to HSat1A 3′ RACE-amplified transcripts (left); molecular weight (right). A size distribution plot is presented for the graphical representation of HSat1A reads. Assembled transcripts contained HSat1A peaks corresponding to multiples of the 42-monomer. From the total of HSat1A sequences, 16,332 sequences were found to be unique (blue in plot). The bar chart (top right corner) shows the high representation of unique sequences, visible in the distribution of counts/sequence. A and B (round) sequences are representative of the identified peaks and are displayed in B. B HSat1A tandem transcript organization. In a universe of 200 nucleotides, it is possible to reconstruct transcripts of longer lengths with smaller sequences. The black arrow points to the longer represented read (structure explored in C). C HSat1A read structure analyzed in the light of the consensus mammalian poly(A) signal. Different colors display HSat1A monomers HSat1A are organized in alternative A (17 nt) and B (25 nt); strikethrough nucleotides in the figure. Sequences that may function as poly(A) signal hexamers [72] are highlighted in bold. Shades of gray correspond to the sequence that functions as the recognition of the poly(A) signal in the absence of the canonical hexamer element [A(A/U)UAAA]. Nucleotides located at the site of optimal 3′ cleavage, named the poly(A) site, are underlined. Arrows point to the largest number of duplicates that are cleaved at that nucleotide position (bold for the largest most abundant). Dots represent the cleavage location of duplicates that contain a difference ≥ 1 nucleotide from the previous sequence. The cleavage positions address the possible occurrence of alternative polyadenylation, resulting in the observable variation of transcript length. D HSat1A transcript cluster membership. Colors determine the range (bp) between sequences of the same cluster. E Phylogenetic tree depicting transcript variability, constructed from the multiple alignment between the center sequences of each cluster. Clusters can be grouped accordingly to their distance (groups a–r). Orange dots represent clusters with more than 50 elements