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Xie et al. 10.1073/pnas.0604768103. |
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Supporting Table 4
Fig. 4. Number of instances in the human genome similar to HsSINE3-1 (+) and a randomized control (circles) as a function of Smith-Waterman alignment score cutoff.
Fig. 5. Alignment of a member of the HsSINE3 family that has retained sequence similar to the 5S rRNA-derived sequence of the DrSINE3 repeat. The full genomic range of the aligned human sequence in chromosome 12 (nucleotides 64746273-64746673, hg17) is shown.
Fig. 6. Relationship between similarity to consensus (Smith–Waterman alignment score) and cross-species conservation (rate of perfect conservation across HDMR) for all members of the HsSINE3 family except for HsSINE3-1 itself. Instances with significant conservation above background (49%) are shown in red (+), and others are shown in blue (circles).
Fig. 7. Relationship between the rate of perfect alignment identity across HDMR and extent of overlap with the central portion of the HsSINE3-1 element for all members of the HsSINE3 family. The central region is shown in blue and is marked (B) in Fig. 1. Instances with significant conservation above background are shown in red (+), and others are shown in blue (circles).
Fig. 8. Relationship between the rate of perfect alignment identity across HDMR and extent of overlap with the terminal portion of the HsSINE3-1 element for all members of the HsSINE3 family. The terminal is shown in violet and is marked (C) in Fig. 1. Instances with significant conservation above background are shown in red (+), and others are shown in blue (circles).
Fig. 9. Relationship between the extent of terminal and central overlap for all members of the HsSINE3 family. The central region is shown in blue and is marked (B) in Fig. 1. The terminal is shown in violet and is marked (C) in Fig. 1. Instances with significant conservation above background are shown in red (+), and others are shown in blue (circles).
Fig. 10. Alignment of a member of the GalSINE3 family that has retained sequence similar to the 5S rRNA-derived sequence of the DrSINE3 repeat as well as sequence similar to the terminal region of HsSINE3-1. The full genomic range of the aligned chicken sequence in chromosome 2 (nucleotides 86373901-86374233, galGal2) is shown.
Fig. 11. Salmon sequence (Salmo salar, GenBank accession no. AF488844) aligned to the central portion alone (A) and central and 5' end (B) of DrSINE3.
Fig. 12. Eel sequence (Anguilla japonica, GenBank accession no. AB023960) that shows significant similarity to the central portion of DrSINE3 (83% identity over 89 bp).
Fig. 13. Phylogenetic subtree. Species for which instances of SINE3-related sequence have been identified are shown in red.
Fig. 14. Alignment of different portions the coelacanth LmSINE3 consensus. (A) 5' end to an actual tRNA (Lys) and a tRNA-derived SINE element, SINE_TE. The B box that is characteristic of polIII promoters is enclosed in a box. (B) Central region to the central region of DrSINE3 and HsSINE3. (C) The 3' end of DrSINE3 and SINE_AFC, a SINE element found in chiclid fish.
Fig. 15. Alignment of genomic sequence of the blood fluke Schistosoma japonicum (GenBank accession no. AY915887) to the core region of DrSINE3. (B) Eighty-eight percent identity was found over the 72-bp.
Fig. 16. Multiple alignment (A) and HDMR conservation profile (B) for the top 75 human instances most similar to the AMCNE2 consensus. In A, human bases are color-coded. A, blue; G, green; T, red; C, orange. In B, conservation status of each base across HDMR is color-coded. Perfect four-way identity, red; four bases aligned imperfectly, black; less than four bases aligning, gray.
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