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Protocols

RPG specifications

Information


Unique identifier OMICS_22523
Name RPG
Alternative name Ribosomal Protein Gene database
Restrictions to use Academic or non-commercial use
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Bacteria
    • Escherichia coli
  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens

Maintainer


  • person_outline Naoya Kenmochi

Publication for Ribosomal Protein Gene database

RPG citations

 (9)
library_books

Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage

2016
BMC Genomics
PMCID: 4869280
PMID: 27188984
DOI: 10.1186/s12864-016-2692-4

[…] From this dataset we selected a set of 62 genes that were shared by at least seven tissues.GC-content and codon usage of ribosomal CDSs was determined using a dataset of 80 sequences downloaded from Ribosomal Protein Gene Database (http://ribosome.med.miyazaki-u.ac.jp) []. For each ribosome protein we used only one RefSeq record. When the mRNA of a ribosome protein was annotated with more than on […]

library_books

Comparisons of Ribosomal Protein Gene Promoters Indicate Superiority of Heterologous Regulatory Sequences for Expressing Transgenes in Phytophthora infestans

2015
PLoS One
PMCID: 4696810
PMID: 26716454
DOI: 10.1371/journal.pone.0145612

[…] P. capsici, and P. parasitica genes were extracted from fungidb.org [] using searches for the Gene Ontology term "ribosome" (GO:0005840) and BLASTP queries using proteins from other species from the Ribosomal Protein Gene database []. When hits to conserved genes were not identified within the annotated gene sets, the Phytophthora genomes were searched by TBLASTN. Hits were validated by reciproca […]

library_books

The Impact of Paralogy on Phylogenomic Studies ā€“ A Case Study on Annelid Relationships

2013
PLoS One
PMCID: 3647064
PMID: 23667537
DOI: 10.1371/journal.pone.0062892

[…] d translation into amino acids using ESTwise .As it is crucial for this study, the orthology prediction is outlined in more detail here. First, the 79 human ribosomal proteins were retrieved from the Ribosomal Protein Gene Database and blast searches against the O. fusiformis EST library were conducted. The best hit of each search was kept if the e value was below eāˆ’20. The settings for the ortho […]

library_books

Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to Telo box motif enrichment

2011
BMC Evol Biol
PMCID: 3212954
PMID: 21668973
DOI: 10.1186/1471-2148-11-161

[…] re only proteins with E-value < 10-5 by BLASTP and reliability class ā‰„ 3 by TargetP were selected as RPGs for corresponding organelles, respectively. For C. reinhardtii, euRPGs were obtained from the Ribosomal Protein Gene database [], and cpRPGs were identified using the experimental results [,]. The promoter sequences and expression datasets of ribosomal protein genes for each class in each spec […]

library_books

On the phylogenetic position of Myzostomida: can 77 genes get it wrong?

2009
BMC Evol Biol
PMCID: 2716322
PMID: 19570199
DOI: 10.1186/1471-2148-9-150

[…] We used the published alignments [,] as backbone for our analysis. Human ribosomal protein genes retrieved from the Ribosomal Protein Gene Database [] as search template for local tblastN searches using an e value

library_books

Independent Mammalian Genome Contractions Following the KT Boundary

2009
Genome Biol Evol
PMCID: 2817402
PMID: 20333172
DOI: 10.1093/gbe/evp007

[…] pecies were downloaded from the Ensemble database, whereas those for other species were obtained from sites associated with particular genome projects. As a check on our work, we also referred to the Ribosomal Protein Gene Database (http://ribosome.med.miyazaki-u.ac.jp/) for animal RPs. For the genomes that are not assembled into chromosomes (e.g., the Fugu genome), we integrated the scaffold sequ […]


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RPG institution(s)
Department of Biotechnology, Research Center for Frontier Bioscience, Miyazaki University, Miyazaki, Japan
RPG funding source(s)
Supported by Grants-in-Aid for Scientific Research (168118, 158118, 14035103, and 15310135) and a fund for Research for the Future Program from the Japan Society for the Promotion of Science (JSPS) and Ministry of Education, Culture, Sports, Science and Technology (MEXT).

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