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Database Commons - The tmRNA website

The tmRNA website

Citations: 300

z-index 13.20

Short name The tmRNA website
Full name The tmRNA website
Description tmRNA is a bacterial RNA molecule with dual tRNA-like and mRNA-like properties. It forms an RNA-protein complex with ribosomal protein S1,elongation factor Tu,and the dedicated protein SmpB.
URL http://bioinformatics.sandia.gov/tmrna/
Year founded 1998
Last update & version 10/22/2013    v1.0
Availability Free to all users
University/Institution hosted Sandia National Laboratories
Address Sandia National Laboratories,Department of Systems Biology,Livermore,CA 94551,USA
City Livermore
Province/State CA
Country/Region United States
Contact name Kelly P. Williams
Contact email kpwilli@sandia.gov
Data type(s)
Major organism(s)
Keyword(s)
  • dedicated protein
  • elongation factor
  • ribosomal protein
  • rna-protein complex
  • tmrna
Publication(s)
  • The tmRNA website. [PMID: 25378311]

    Corey M Hudson, Kelly P Williams
    Nucleic acids research 2015:43(Database issue)
    Citation (to be updated)

    Abstract: The transfer-messenger RNA (tmRNA) and its partner protein SmpB act together in resolving problems arising when translating bacterial ribosomes reach the end of mRNA with no stop codon. Their genes have been found in nearly all bacterial genomes and in some organelles. The tmRNA Website serves tmRNA sequences, alignments and feature annotations, and has recently moved to http://bioinformatics.sandia.gov/tmrna/. New features include software used to find the sequences, an update raising the number of unique tmRNA sequences from 492 to 1716, and a database of SmpB sequences which are served along with the tmRNA sequence from the same organism. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts. [PMID: 14681369]

    Pulcherie Gueneau de Novoa, Kelly P Williams
    Nucleic acids research 2004:32(Database issue)
    102 Citations (Google Scholar as of 2016-04-28)

    Abstract: tmRNA combines tRNA- and mRNA-like properties and ameliorates problems arising from stalled ribosomes. Research on the mechanism, structure and biology of tmRNA is served by the tmRNA website (http://www.indiana.edu/~ tmrna), a collection of sequences, alignments, secondary structures and other information. Because many of these sequences are not in GenBank, a BLAST server has been added; another new feature is an abbreviated alignment for the tRNA-like domain only. Many tmRNA sequences from plastids have been added, five found in public sequence data and another 10 generated by direct sequencing; detection in early-branching members of the green plastid lineage brings coverage to all three primary plastid lineages. The new sequences include the shortest known tmRNA sequence. While bacterial tmRNAs usually have a lone pseudoknot upstream of the mRNA segment and a string of three or four pseudoknots downstream, plastid tmRNAs collectively show loss of pseudoknots at both postions. The pseudoknot-string region is also too short to contain the usual pseudoknot number in another new entry, the tmRNA sequence from a bacterial endosymbiont of insect cells, Tremblaya princeps. Pseudoknots may optimize tmRNA function in free-living bacteria, yet become dispensible when the endosymbiotic lifestyle relaxes selective pressure for fast growth.

  • The tmRNA Website: invasion by an intron. [PMID: 11752287]

    Kelly P Williams
    Nucleic acids research 2002:30(1)
    67 Citations (Google Scholar as of 2016-04-28)

    Abstract: tmRNA (also known as 10Sa RNA or SsrA) plays a central role in an unusual mode of translation, whereby a stalled ribosome switches from a problematic mRNA to a short reading frame within tmRNA during translation of a single polypeptide chain. Research on the mechanism, structure and biology of tmRNA is served by the tmRNA Website, a collection of sequences for tmRNA and the encoded proteolysis-inducing peptide tags, alignments, careful documentation and other information; the URL is http://www.indiana.edu/~tmrna. Four pseudoknots are usually present in each tmRNA, so the database is rich with information on pseudoknot variability. Since last year it has doubled (227 tmRNA sequences as of September 2001), a sequence alignment for the tmRNA cofactor SmpB has been included, and genomic data for Clostridium botulinum has revealed a group I (subgroup IA3) intron interrupting the tmRNA T-loop.

  • The tmRNA website. [PMID: 10592213]

    K P Williams
    Nucleic acids research 2000:28(1)
    47 Citations (Google Scholar as of 2016-04-28)

    Abstract: The tmRNA Website collects all available tmRNA sequences into a single public resource, along with alignments and a guide to searching for new sequences. Over the last year, several sequences have been updated or newly found by monitoring ongoing genome sequencing projects; tmRNA sequence data from 70 species are now available. New features include: color-coding of sequences to mark suggested base-paired regions, a list of the literature concerning tmRNA, careful crediting of tmRNA sequence identifications, and a split browser window. Updates are very frequent. The tmRNA Website has a new URL: http:www.indiana.edu/tmrna

  • The tmRNA website. [PMID: 9847167]

    K P Williams
    Nucleic acids research 1999:27(1)
    42 Citations (Google Scholar as of 2016-04-28)

    Abstract: tmRNA (10Sa RNA) has a central role in trans -translation, in which a peptide tag encoded in tmRNA is added to the abnormally short protein product of a broken mRNA, as a signal for proteolysis of the entire tagged protein. The tmRNA website was established in 1997 as a resource for phylogenetic considerations of tmRNA structure and function. Since then, three partial tmRNA sequences have been completed, and sequences from 13 more species have been identified. Forty-six species from 10 bacterial phyla and chloroplasts are now represented in the database. Provisional sequence alignments and predicted proteolysis tag sequences are provided, as well as a literature review and a guide to searching for new tmRNA sequences. The tmRNA website is accessible via WWW at a new URL: http://sunflower.bio.indiana.edu/kwilliam/tmRNA /home.html

  • The tmRNA Website. [PMID: 9399824]

    K P Williams, D P Bartel
    Nucleic acids research 1998:26(1)
    42 Citations (Google Scholar as of 2016-04-28)

    Abstract: tmRNA (also known as 10Sa RNA) is so-named for its dual tRNA-like and mRNA-like nature. It is employed in a remarkable trans -translation process to add a C-terminal peptide tag to the incomplete protein product of a broken mRNA; the tag targets the abnormal protein for proteolysis. tmRNA sequences have been identified in genomes of diverse bacterial phyla, including the most deeply branching. They have also been identified in plastids of the 'red' lineage. The tmRNA Website (http://www.wi.mit. edu/bartel/tmRNA/home ) contains a database currently including sequences from 37 species, with provisional alignments, as well as the tentatively predicted proteolysis tag sequences. A brief review and guide to the literature is also provided.

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Accessibility

Rate of accessibility:
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200 OK2018-06-19
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200 OK2018-06-12
200 OK2018-06-08
200 OK2018-06-05
200 OK2018-06-01
200 OK2018-05-29
200 OK2018-05-25
200 OK2018-05-22
200 OK2018-05-18
200 OK2018-05-15
200 OK2018-05-11
200 OK2018-05-08
200 OK2018-05-04
200 OK2018-05-01
200 OK2018-04-27
200 OK2018-04-24
200 OK2018-04-20
200 OK2018-04-17
200 OK2018-04-13
200 OK2018-04-10
200 OK2018-04-06
200 OK2018-04-03
200 OK2018-02-27
200 OK2018-02-23
200 OK2018-02-20
200 OK2018-02-16
200 OK2018-02-13
200 OK2018-02-09
200 OK2018-02-06
200 OK2018-02-02
200 OK2018-01-30
200 OK2018-01-26
200 OK2018-01-23
200 OK2018-01-19
200 OK2018-01-16
200 OK2018-01-12
200 OK2018-01-09
200 OK2018-01-05
200 OK2018-01-02
200 OK2017-12-29
200 OK2017-12-26
200 OK2017-12-22
200 OK2017-12-19
200 OK2017-12-15
200 OK2017-12-12
200 OK2017-12-08
200 OK2017-12-05
200 OK2017-12-01
200 OK2017-11-28
200 OK2017-11-24
200 OK2017-11-21
200 OK2017-11-17
200 OK2017-11-14
200 OK2017-11-10
200 OK2017-11-07
200 OK2017-11-03
200 OK2017-10-31
200 OK2017-10-27
200 OK2017-10-24
200 OK2017-10-20
200 OK2017-10-17
200 OK2017-10-13
200 OK2017-10-10
200 OK2017-10-06
200 OK2017-10-03
200 OK2017-09-29
200 OK2017-09-26
200 OK2017-09-22
200 OK2017-09-19
200 OK2017-09-15
200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
200 OK2017-08-25
200 OK2017-08-22
200 OK2017-08-18
200 OK2017-08-15
200 OK2017-08-11
200 OK2017-08-08
200 OK2017-08-04
200 OK2017-08-01
200 OK2017-07-28
200 OK2017-07-25
200 OK2017-07-21
200 OK2017-07-18
200 OK2017-07-14
200 OK2017-07-04
200 OK2017-06-30
200 OK2017-06-27
200 OK2017-06-23
200 OK2017-06-20
200 OK2017-06-16
200 OK2017-06-13
200 OK2017-06-09
200 OK2017-06-06
200 OK2017-06-02
200 OK2017-05-30
200 OK2017-05-26
200 OK2017-05-23
200 OK2017-05-19
200 OK2017-05-16
200 OK2017-05-12
200 OK2017-05-09
200 OK2017-05-05
200 OK2017-05-02
200 OK2017-04-28
200 OK2017-04-25
200 OK2017-04-21
200 OK2017-04-18
200 OK2017-04-14
200 OK2017-04-11
200 OK2017-04-07
200 OK2017-04-04
200 OK2017-03-31
200 OK2017-03-28
200 OK2017-03-24
200 OK2017-03-21
200 OK2017-03-17
200 OK2017-03-14
200 OK2017-03-10
200 OK2017-03-07
200 OK2017-03-03
200 OK2017-02-28
200 OK2017-02-24
200 OK2017-02-21
200 OK2017-02-17
200 OK2017-02-14
200 OK2017-02-10
200 OK2017-02-07
200 OK2017-02-03
200 OK2017-01-31
200 OK2017-01-27
200 OK2017-01-24
200 OK2017-01-20
200 OK2017-01-17
200 OK2017-01-13
200 OK2017-01-10
200 OK2017-01-06
200 OK2017-01-03
200 OK2016-12-30
200 OK2016-12-27
200 OK2016-12-23
200 OK2016-12-20
200 OK2016-12-16
200 OK2016-12-13
200 OK2016-12-09
200 OK2016-12-06
200 OK2016-12-02
200 OK2016-11-29
200 OK2016-11-25
200 OK2016-11-22
200 OK2016-11-18
200 OK2016-11-15
200 OK2016-11-11
200 OK2016-11-08
200 OK2016-11-04
200 OK2016-11-01
200 OK2016-10-28
200 OK2016-10-25
200 OK2016-10-21
200 OK2016-10-18
200 OK2016-10-14
200 OK2016-10-11
200 OK2016-10-07
200 OK2016-10-04
200 OK2016-09-30
200 OK2016-09-27
200 OK2016-09-23
200 OK2016-09-20
200 OK2016-09-16
200 OK2016-09-13
200 OK2016-09-09
200 OK2016-09-06
200 OK2016-09-02
200 OK2016-08-30
200 OK2016-08-26
200 OK2016-08-23
200 OK2016-08-19
200 OK2016-08-16
200 OK2016-08-12
200 OK2016-08-09
200 OK2016-08-05
200 OK2016-08-02
200 OK2016-07-29
200 OK2016-07-26
200 OK2016-07-22
200 OK2016-07-19
200 OK2016-07-15
200 OK2016-07-12
200 OK2016-07-08
200 OK2016-07-05
200 OK2016-07-01
200 OK2016-06-28
200 OK2016-06-24
200 OK2016-06-21
200 OK2016-06-17
200 OK2016-06-14
200 OK2016-06-10
200 OK2016-06-07
200 OK2016-06-03
200 OK2016-05-31
200 OK2016-05-27
200 OK2016-05-24
200 OK2016-05-20
200 OK2016-05-17
200 OK2016-05-13
200 OK2016-05-10
200 OK2016-05-06
200 OK2016-05-03
200 OK2016-04-29
200 OK2016-04-26
200 OK2016-04-22
200 OK2016-04-19
200 OK2016-04-15
200 OK2016-04-12
200 OK2016-04-08
200 OK2016-04-05
200 OK2016-04-01
200 OK2016-03-29
200 OK2016-03-28
200 OK2016-03-25
200 OK2016-03-23
200 OK2016-03-21
200 OK2016-03-18
200 OK2016-03-16
200 OK2016-03-14
200 OK2016-03-11
200 OK2016-03-09
200 OK2016-03-07
200 OK2016-03-04
200 OK2016-03-02
200 OK2016-02-29
200 OK2016-02-26
200 OK2016-02-24
200 OK2016-02-22
200 OK2016-02-19
200 OK2016-02-17
200 OK2016-02-15
200 OK2016-02-14
200 OK2016-02-12
200 OK2016-02-10
200 OK2016-02-08
200 OK2016-02-07
200 OK2016-02-05
200 OK2016-02-03
200 OK2016-02-01
200 OK2016-01-31
200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
200 OK2016-01-22
200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

RNA
Bacteria
dedicated protein elongation factor ribosomal protein rna-protein complex tmrna

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Guangyu Wang [2015-06-26]
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