Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Jan 1;33(Database issue):D135-8.
doi: 10.1093/nar/gki015.

The Small Subunit rRNA Modification Database

James A McCloskey  1 , Jef Rozenski
Affiliations

The Small Subunit rRNA Modification Database

James A McCloskey et al. Nucleic Acids Res. .

Abstract

The Small Subunit rRNA Modification Database provides a listing of reported post-transcriptionally modified nucleosides and sequence sites in small subunit rRNAs from bacteria, archaea and eukarya. Data are compiled from reports of full or partial rRNA sequences, including RNase T1 oligonucleotide catalogs reported in earlier literature in studies of phylogenetic relatedness. Options for data presentation include full sequence maps, some of which have been assembled by database curators with the aid of contemporary gene sequence data, and tabular forms organized by source organism or chemical identity of the modification. A total of 32 rRNA sequence alignments are provided, annotated with sites of modification and chemical identities of modifications if known, with provision for scrolling full sequences or user-dictated subsequences for comparative viewing for organisms of interest. The database can be accessed through the World Wide Web at http://medlib.med.utah.edu/SSUmods.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Chemical structures of presently known post-transcriptionally modified nucleosides from rRNA. A, archaea; B, bacteria; and E, eukarya. Symbols: m1A, 1-methyladenosine; m2A, 2-methyladenosine; m6A, N6-methyladenosine; Am, 2′-O-methyladenosine; m62A, N6,N6-dimethyladenosine; Im, 2′-O-methylinosine; m3C, 3-methylcytidine; m4C, N4-methlycytidine; m5C, 5-methlycytidine; Cm, 2′-O-methylcytidine; ac4C, N4-acetylcytidine; m4Cm, N4,2′-O-dimethylcytidine; m42Cm, N4,N4,2′-O-trimethylcytidine; hm5C, 5-hydroxymethylcytidine; ac4Cm, N4-acetyl-2′-O-methylcytidine; m1G, 1-methylguanosine; m2G, N2-methylguanosine; m7G, 7-methylguanosine; Gm, 2′-O-methylguanosine; m22G, N2,N2-dimethylguanosine; Ψ, pseudouridine; D, dihydrouridine; m3U, 3-methyluridine; m5U, 5-methyluridine; cm5U, 5-carboxymethyluridine; Um, 2′-O-methyluridine; m1Ψ, 1-methylpseudouridine; m3Ψ, 3-methylpseudouridine; Ψm, 2′-O-methylpseudouridine; acp3U, 3-(3-amino-3-carboxypropyl)uridine; and m1acp3Ψ, 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine.
See this image and copyright information in PMC

References

    1. Littlefield J.W. and Dunn,D.B. (1958) Natural occurrence of thymine and three methylated adenine bases in several ribonucleic acids. Nature, 181, 254–255. - PubMed
    1. Smith J.D. and Dunn,D.B. (1959) An additional sugar component of ribonucleic acids. Biochim. Biophys. Acta, 31, 573–575. - PubMed
    1. Fox G.E., Pechman,K.R. and Woese,C.R. (1977) Comparative cataloguing of 16S ribosomal RNA: molecular approach to prokaryotic systematics. Int. J. Syst. Bacteriol., 27, 44–57.
    1. Grosjean H. and Benne,R. (eds) (1998) Modification and Editing of RNA. ASM Press, Washington, DC.
    1. Wimberly B.T., Brodersen,D.E., Clemons,W.M.,Jr, Morgan-Warren,R.J., Carter,A.P., Vonrhein,C., Hartsch,T. and Ramakrishnan,V. (2000) Structure of the 30S ribosomal subunit. Nature, 407, 327–339. - PubMed

Publication types