Similarly the ‘Trait details’ section summarizes all the phenotypic or biochemical traits that have been associated with the selected gene based on experimental data. The page also summarizes the physical interaction data (protein–protein and protein-DNA) for the rice protein as well as any ...
Rice seed nuclear protein database (RSNP-DB) We combined all the information in the form of a database named Rice Seed Nuclear Protein Database (RSNP-DB, https://pmb.du.ac.in/rsnpdb). The web interface of RSNP-DB was designed to include the following components: search, information ...
database (miRbase v. 22.1) to obtain the known miRNA count. Then, rRNAs, tRNAs, snRNAs, and snoRNAs were removed by mapping the remained sRNA tags to Rfam release 1455. Repeat sequences were filtered by using a repeat sequences database56, and tags originating from protein coding genes ...
The protein sequences of PFT/PGGT I-α, PFT-β and PGGT I-β from these species obtained from the Plaza Plant Comparative Genomics Database (http://bioinformatics.psb.ugent.be/plaza/) were queried via BLAST (Fig. S2). The three subunits involved in protein prenylation in rice clustered...
~ 4100 functionally characterized rice genes and ~ 6000 members of different gene families were collected in funRiceGenes, accounting for 22.3% of the 39,045 annotated protein-coding genes in the rice genome. Here, we summarized the update of the funRiceGenes database with new data and new...
Building a protein-protein interaction network forM. grisea The protein sequences ofM. griseawere obtained from theM. griseadatabase (release 5) maintained by the BROAD institute [2], which contains a total of 12,832 sequences. The experimentally identified PPI maps from five model organisms (E...
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has be
Using GFP protein fusions it was shown that SNF1 kinase beta subunits direct the kinase to the nucleus in a glucose-regulated manner [36]. Direct regulatory interaction between signal transduction pathways mediated by the yeast SNF1 kinase and RNA polymerase II holoenzyme has been suggested to ...
Abbreviations cDNA: Complementary DNA GO: Gene Ontology IAA: Indoleacetic acid KMC: K-means clustering PCC: Pearson correlation coefficient PPI: Protein–protein interaction RGAP: Rice Genome Annotation Project WT: Wild type
Eight hundred and thirty-seven experimentally verified protein-protein interaction (PPI) pairs related to Hsps in yeast (Additional file 1: Table S2) were manually selected from the Database of Interaction Proteins (DIPs version 20101010; http://dip.doe-mbi.ucla.edu/dip/). Microarray dataset Gen...