For more information related to References 1 and 2, visit the Structure Definitions page.

# Description
1. TC: Tertiary Structure Codes:
  • B: Tertiary base pair: includes noncanonical pairings at the ends of helices and pairings at the ends of helices which are separated from the helix by a bulge.
  • K: Pseudoknot
  • R: Base Triple

2. CC: Comparative Support Color Codes:
  1. Strongest comparative support (red): both positions correlate best with one another in at least one sequence alignment under study using at least one of the covariation algorithms.
  2. Strong comparative support (green): the two positions have a significant correlation value for one another, although not the highest value for one another. The correlation value is within 90% of the top value.
  3. Minimal or weakly suggestive comparative support (black): some covariation observed in base pair frequency tables; in proximity to base pairs with comparative support.
  4. Invariant pair (gray): Usually invariant; has little or no positive or negative comparative support. These pairings always occur in proximity to pairs with strong comparative support.
  5. Pair not predicted with collective scoring/helix extend (blue).

3. Woese C.R., Magrum L.J., Gupta R., Siegel R.B., Stahl D.A., Kop J., Crawford N., Brosius J., Gutell R., Hogan J.J., and Noller H.F. (1980) Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Research 8:2275-2293.
4. Woese C.R., Gutell R., Gupta R., Noller H.F. (1983) Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiological Reviews 47(4):621-669.
5. Noller H.F. (1984). Structure of ribosomal RNA. Annual Review of Biochemistry 53:119-162.
6. Gutell R.R., Weiser B., Woese C.R., and Noller H.F. (1985) Comparative Anatomy of 16-S-like Ribosomal RNA. Progress in Nucleic Acid Research and Molecular Biology 32:155-216.
7. Gutell R.R., Noller H.F., Woese C.R. (1986) Higher order structure in ribosomal RNA. The EMBO Journal 5(5):1111-1113.
8. Haselman T., Camp D.G., and Fox G.E. (1989). Phylogenetic evidence for tertiary interactions in 16S-like ribosomal RNA. Nucleic Acids Research 17(6):2215-2221.
9. Woese C.R. and Gutell R.R. (1989) Evidence for several higher order structural elements in ribosomal RNA. Proceedings of the National Academy of Sciences (USA) 86:3119-3122.
10. Gutell, R.R. and Woese C.R. (1990) Higher order structural elements in ribosomal RNAs: Pseudo-knots and the use of non-canonical pairs. Proceedings of the National Academy of Sciences (USA) 87(2):663-667.
11. Woese C.R., Winker S. and Gutell R.R. (1990) Architecture of Ribosomal RNA: Constraints on the sequence of 'tetra-loops.' Proceedings of the National Academy of Sciences (USA) 87(21):8467-8471.
12. Gutell R.R. (1993). The Simplicity Behind the Elucidation of Complex Structure in Ribosomal RNA. in: The Translational Apparatus, Nierhaus K.H., Subramanian A.R., Erdmann V.A., Franceschi F., and Wittman-Liebold B (eds). pp. 477-488. Plenum Publishing Corporation. New York, New York.
13. Gutell R.R., Larsen N., and Woese C.R. (1994) Lessons from an Evolving Ribosomal RNA: 16S and 23S rRNA Structure from a Comparative Perspective. Microbiological Reviews. 58:10-26.
14. Gutell R.R. (1994) Collection of small subunit (16S and 16S-like) ribosomal RNA structures: 1994. Nucleic Acids Research 22(17):3502-3507.
15. Lodmell J.S., Gutell R.R., Dahlberg A.E. (1995) Genetic and comparative analyses reveal an alternative secondary structure in the region of nt 912 of 16S ribosomal RNA. Proceedings of the National Academy of Sciences (USA). 92(23):10555-10559.
16. Gutell R.R. (1996). Comparative Sequence Analysis and the Structure of 16S and 23S rRNA. in: Ribosomal RNA. Structure, Evolution, Processing, and Function in Protein Biosynthesis. pp. 111-128. Dahlberg A. and Zimmerman B. (eds.) CRC Press. Boca Raton.
17. Gutell R.R. Current 16S rRNA secondary structure model (1999), available from the Comparative RNA Web Site (http://www.rna.icmb.utexas.edu), and also presented in these papers (PubMed abstracts are accessible from these web pages): U-turn, A Story, and AA.AG@helix.ends.
18. Lodmell J.S. and Dahlberg A.E. (1997). A Conformational Switch in Escherichia coli 16S Ribosomal RNA During Decoding of messenger RNA. Science 277(5330):1262-1267.
19. Noller H.F., Kop J., Wheaton V., Brosius J., Gutell R.R., Kopylov A.M., Dohme F., Herr W., Stahl D.A., Gupta R., and Woese C.R. (1981) Secondary structure model for 23S ribosomal RNA. Nucleic Acids Research 9(22):6167-6189.
20. Gutell R.R. and Fox G.E. (1988) A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Research 16(supplement):r175-r269.
21. Haselman T., Gutell R.R., Jurka J., and Fox G.E. (1989) Additional Watson-Crick Interactions Suggest a Structural Core in Large Subunit Ribosomal RNA. Journal of Biomolecular Structure and Dynamics 7:181-186.
22. Gutell R.R. (1992). Evolutionary Characteristics of 16S and 23S rRNA Structures. pp. 243-309. PRESENTED AT: The Symposium -- The Origin and Evolution of Prokaryotic and Eukaryotic Cells. Shimoda, Japan. April 22-25, 1992. Hyman Hartman and Koichiro Matsuno (eds.). World Scientific Publishing Co., New Jersey. USA.
23. Gutell R.R., Power A.,Hertz G., Putz E., and Stormo G. (1992) Identifying Constraints on the Higher-Order Structure of RNA: Continued Development and Application of Comparative Sequence Analysis Methods. Nucleic Acids Research 20(21):5785-5795.
24. Gutell R.R., Schnare M.N., Gray M.W. (1992) A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucleic Acids Research 20(Supplement):2095-2109.
25. Larsen N. (1992). Higher order interactions in 23S rRNA. Proceedings of the National Academy of Sciences (USA) 89(11):5044-5048.
26. Gutell R.R., Gray M.W., and Schnare M.N. (1993) A compilation of large subunit (23S- and 23S-like) ribosomal RNA structures. Nucleic Acids Reseach. 21(13):3055-3074.
27. Gutell R.R. Current 23S rRNA secondary structure model (1999), available from the Comparative RNA Web Site (http://www.rna.icmb.utexas.edu), and also presented in these papers (PubMed abstracts are accessible from these web pages): U-turn, A Story, and AA.AG@helix.ends.
28. Leffers H., Kjems J., Ostergaard L., Larsen N., and Garrett R.A. (1987). Evolutionary Relationships Amongst Archaebacteria: A Comparative Study of 23 S Ribosomal RNAs of a Sulphur-dependent Extreme Thermophile, an Extreme Halophile and a Thermophilic Methanogen. Journal of Molecular Biology 195(1):43-61.