Pseudouridines of S. cerevisiae SSU rRNA and equivalent nucleotides in E. coli. The snoRNA responsible for guiding a particular modification in yeast is also included.

 

S. cerevisiae

E. colic

snoRNA

Modified position in 18S [U53879] a

The modified position reported in several older publicationsb

 

snR44

Ψ106

 

G122

snR49

Ψ120

 

C135

snR49

Ψ211

 

-d

snR49

Ψ302

 

C233

snR189

Ψ466

 

C395

snR161

Ψ632

 

G585

snR80

Ψ759

 

-e

snR161

Ψ766

 

-e

snR31

Ψ999

1000

U788

snR85

Ψ1181

1179

U956

snR36

Ψ1187

1185

C962

snR35

m1acp3Ψ1191

1189

m2G966

snR83

Ψ1290

1289

U1070

snR83

Ψ1415

1414

G1184

aSequence from Johnston, M., L. Hillier, L. Riles, K. Albermann, B. Andre, W. Ansorge, V. Benes, M. Bruckner, H. Delius, E. Dubois, A. Dusterhoft, K. D. Entian, M. Floeth, A. Goffeau, U. Hebling, K. Heumann, D. Heuss-Neitzel, H. Hilbert, F. Hilger, K. Kleine, P. Kotter, E. J. Louis, F. Messenguy, H. W. Mewes, J. D. Hoheisel, and et al. 1997. accessible at the Saccharomyces Genome Database (Issel-Tarver, L., K. R. Christie, K. Dolinski, R. Andrada, R. Balakrishnan, C. A. Ball, G. Binkley, S. Dong, S. S. Dwight, D. G. Fisk, M. Harris, M. Schroeder, A. Sethuraman, K. Tse, S. Weng, D. Botstein, and J. M. Cherry. 2002.), secondary structure annotated at the Gutell lab Comparative RNA website (Cannone, J. J., S. Subramanian, M. N. Schnare, J. R. Collett, L. M. D'Souza, Y. Du, B. Feng, N. Lin, L. V. Madabusi, K. M. Muller, N. Pande, Z. Shang, N. Yu, and R. R. Gutell et al., 2002.)

bPublications such as Bakin and Ofengand, 1995 and others that refer to that one for the sequence and numbering of rRNA.

cNumbering used in PDB entry 2AVY. Modified nucleotides are indicated according to sequence (Genbank entry J01695) annotated at the Gutell lab Comparative RNA website.

a,cAligned using data from the rRNA WWW server.

dAn equivalent nucleotide is not present in 16 S rRNA; it is in eukaryotic expansion segment #3 (ES3), see Gerbi, S.A. 1996. Expansion segments: Regions of variable size that interrupt the universal core secondary structure of ribosomal RNA. In Ribosomal RNA—Structure, evolution, processing, and function in protein synthesis (eds. R.A. Zimmermann and A.E. Dahlberg), pp.71-87. CRC Press, Boca Raton, FL; Alkemar and Nygård, 2003; Alkemar and Nygård, 2004.

eAn equivalent nucleotide is not present in 16 S rRNA; it is in eukaryotic expansion segment #6 (ES6), see Gerbi, 1996; Alkemar and Nygård, 2003; Alkemar and Nygård, 2004; Alkemar and Nygård, 2006; Clark, C. G., B. W. Tague, V. C. Ware, and S. A. Gerbi, 1984.

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