Ribose methylated nucleotides 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

The modified position is reported with following number in Lowe Database (July 2006 version)

snR74

Am28

 

 

A33

snR51

Am100

 

 

A116

U14

Cm414

 

 

C342

snR52

Am420

 

 

G348

snR87

Am436

 

 

A364

snR41

Am541

 

 

A495

snR77

Um578

 

 

U531

snR47

Am619

 

 

A572

snR53

Am796

 

 

-d

snR54

Am974

975

973

G763

snR79

Cm1007

1008

1006

C796

snR41

Gm1126

1127

1123

G902

snR55

Um1269

1267

1265

U1049

snR40

Gm1271

1269

1267

C1051

snR56

Gm1428

1427

1425

A1197

snR57

Gm1572

1571

1570

U1335

snR70

Cm1639

1638

1637

m4Cm1402

a Sequence 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 as 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 #6 (ES6), 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; Alkemar and Nygård, 2006; Clark, C. G., B. W. Tague, V. C. Ware, and S. A. Gerbi, 1984.

 

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