|
Psuedouridines of S. cervisiae 25S rRNA and
equivalent nucleotides in Haloarcula marismortui and E. coli. The
snoRNA responsible for guiding a particular modification in yeast is also
included.
|
S. cerevisiae
|
H. marismortuib
|
E. colic
|
|
snoRNA
|
Modified
position in 25S [U53879]a
|
The modified position reported in
several older publications
|
|
snR80
|
Y776
|
775
|
-1 to G738 (~A737)
|
-d
|
|
snR8
|
Y960
|
959
|
G921
|
U828
|
|
snR43
|
Y966
|
965
|
U927
|
G834
|
|
snR8
|
Y986
|
985
|
U945
|
C851
|
|
snR49
|
Y990
|
989
|
U949
|
G855
|
|
snR5
|
Y1004
|
1003
|
C963
|
U868
|
|
snR33
|
Y1042
|
1041
|
U1001e
|
A905
|
|
snR81
|
Y1052
|
1051
|
C1011
|
C915
|
|
snR44
|
Y1056
|
1055
|
C1015
|
U919
|
|
snR82
|
Y1110
|
1109
|
G1038
|
G939
|
|
snR5
|
Y1124
|
1123
|
G1052
|
G953
|
|
snR3
|
Y2129
|
2128
|
G1827
|
C1771
|
|
snR3
|
Y2133
|
2132
|
U1831
|
U1775
|
|
snR32
|
Y2191
|
2190
|
C1888
|
C1832
|
|
snR191
|
Y2258
|
2257
|
Y1956*
|
m3Y1915
|
|
snR191
|
Y2260
|
2259
|
Y1958*
|
Y1917
|
|
snR3
|
Y2264
|
2263
|
C1962*
|
G1921
|
|
snR84
|
Y2266
|
2265
|
U1964
|
U1923
|
|
snR86
|
Y2314
|
2313
|
U2012
|
U1971
|
|
snR9
|
Y2340
|
2339
|
A2038
|
C1997
|
|
snR82
|
Y2349
|
2348
|
C2047
|
C2006
|
|
snR82
|
Y2351
|
2350
|
C2049
|
C2008
|
|
snR11
|
Y2416
|
2415
|
U2115
|
U2074
|
|
snR189
|
Y2735
|
2730
|
A2402
|
G2365
|
|
snR34
|
Y2826
|
2822
|
U2492
|
Y2457
|
|
snR46
|
Y2865
|
2861
|
U2531
|
C2496
|
|
snR34
|
Y2880
|
2876
|
U2546
|
U2511
|
|
snR10
|
Y2923
|
2919
|
U2589
|
U2554
|
|
snR37
|
Y2944
|
2940
|
U2610
|
C2575
|
|
snR42
|
Y2975
|
2971
|
C2641
|
C2606
|
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.)
bNumbering in PDB entry 1JJ2. Asterisks indicate the
corresponding nucleotides not visible in the crystal structure of the large
subunit H. marismortui at 2.4 angstroms (Klein, D. J., T. M. Schmeing, P. B. Moore, and T. A. Steitz., 2001 and Ban, N., P. Nissen, J. Hansen, P. B. Moore, and T. A. Steitz., 2000). Modified nucleotides are indicated according to Kirpekar, et al. 2005.
cNumbering of modified nucleotides according to Genbank entry
J01695, annotated at the Gutell
lab Comparative RNA website.
a,b,cAligned using data from the rRNA WWW server.
dAn equivalent nucleotide is not present in 25 S rRNA; it is in expansion segment #9 (ES9), 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; Clark, C. G., B. W. Tague, V. C. Ware, and S. A. Gerbi, 1984.
eAccording to Ofengand, 2002 these are equivalent; however, he incorrectly reports as a pseudouridine in H. marismortui there and retracts in Del Campo et al., 2005.
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