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3D Ribosomal Modification Maps Database

Database of maps showing the sites of modified rRNA nucleotides. Access to the rRNA sequences, secondary structures both with modification sites indicated, 3D modification maps and the supporting tables of equivalent nucleotides for rRNA from model organisms including yeast, arabidopsis, e. coli and human is provided. This database complements the Yeast snoRNA Database at UMass-Amherst and relies on linking to some content from that database, as well as to others by colleagues in related fields. Therefore, please be very cognizant as to the source when citing information obtained herein. Locations of modified rRNA nucleotides within the 3D structure of the ribosome.

URL: http://people.biochem.umass.edu/fournierlab/3dmodmap/

Resource ID: nif-0000-00552     Resource Type: Resource     Version: Latest Version

Keywords

human, plant, arabidopsis, ribosome, eukaryote, eubacteria, archaea, eukarya

Additional Resource Types

database

Supercategory

Resource

Related To

Resource:Yeast snoRNA Database

Abbreviation

3D rRNA modification maps

Parent Organization

Funding Information

U.S. Public Health Service, GM19351

Species

yeast, arabidopsis, escherichia coli, human

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am March 6, 2013

Originated From

SciCrunch

Changes from Previous Version

First Version

Version 1

Created 2 years ago by Anonymous

The 3D rRNA modification maps database: with interactive tools for ribosome analysis.

  • Piekna-Przybylska D
  • Nucleic Acids Res.
  • 2008 15

The 3D rRNA modification maps database is the first general resource of information about the locations of modified nucleotides within the 3D structure of the full ribosome, with mRNA and tRNAs in the A-, P- and E-sites. The database supports analyses for several model organisms, including higher eukaryotes, and enables users to construct 3D maps for other organisms. Data are provided for human and plant (Arabidopsis) ribosomes, and for other representative organisms from eubacteria, archaea and eukarya. Additionally, the database integrates information about positions of modifications within rRNA sequences and secondary structures, as well as links to other databases and resources about modifications and their biosynthesis. Displaying positions of modified nucleotides is fully manageable. Views of each modified nucleotide are controlled by individual buttons and buttons also control the visibility of different ribosomal molecular components. A section called 'Paint Your Own' enables the user to create a 3D modification map for rRNA from any organism where sites of modification are known. This section also provides capabilities for visualizing nucleotides of interest in rRNA or tRNA, as well as particular amino acids in ribosomal proteins. The database can be accessed at http://people.biochem.umass.edu/fournierlab/3dmodmap/