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Database Description



For each family with more than three members, the full protein sequences or domain sequences (Kinase) were aligned using ClustalW Version 2.1 with default options. Then maximum likelihood trees were bulit using PhyML 3.0 with JTT model


Family
Family assignment for each gene.
Chromosome
The chromosome on which each gene is located.
5' end
Position of 5' end of coding sequence.
3 'end
Position of 3' end of coding sequence.
RAP-DB Locus
The corresponding locus ID from Rice Annotation Project database (RAP-DB).
NCBI Blast Link
Displays a link to the NCBI blastp search. Click on the link and you will be redirected to the current NCBI blastp search result.
Literature information
The published information of the locus is identified from OGRO database and presented.


The orthologs in sequenced plants were identified by
InParanoid Version 4.1 (Remm et al., 2001). The plant genomes used to scan for orthologs are Brachypodium distachyon, Panicum virgatum, Sorghum bicolor, Zea mays, Arabidopsis thaliana, Cucumis sativus, Glycine max, Medicago truncatula, Mimulus guttatus, Populus trichocarpa, Ricinus communis and Vitis vinifera.

Topology:


Transmembrane Domain
TM indicates the presence of one or more predicted transmembrane domains by TMHMM Server Version 2.0.
N-terminal Myristoylation Site
The predicted potential N-terminal myristoylation sites by Plant-Specific Myristoylation Predictor will be indicated as Myrist.
N-terminal Signal Peptide
SignalP indicates presence of predicted N-terminal signal peptide by SignalP Version 3.0.
Chloroplast Transit Peptide
ChloroP indicates presence of predicted chloroplast transit peptide by ChloroP Version 1.1.
Predicted Subcellular Localization
The subcellular localization of rice GTs, including 'secretory pathway', 'chloroplast', 'mitochondrion' and 'any other location' as predicted by TargetP Version 1.1


OryGenesDB was used to map flanking sequence tags (FSTs) from different mutant libraries to the TIGR Version 6 rice pseudomolecules by identifying the highest hit based on a e-10 cut-off. The mapped insertions were then assigned to rice genes based on the insertion map locations relative to the genome annotation. In the OryGenesDB database, a gene was defined as beginning 800 bp 5' of the initiation codon and to the end of the 3'-UTR, where known. The Postech activation lines were obtained from the Postech Rice T-DNA Insertion Sequence Database. We gathered mutant line information from the National Institute of Agrobiological Sciences (NIAS) Tos17 Insertion Mutant Database, UCD Rice Transposon Flanking Sequence Tag Database with Ds KO lines, Oryza Tag Line (OTL) Database with Tos17 and T-DNA KO lines, Rice Mutant Database (RMD) with T-DNA KO lines, Taiwan Rice Insertional Mutants Database (TRIM) with T-DNA KO lines and Postech Rice T-DNA Insertion Seqence Database with T-DNA KO and AC lines.



Yeast Two-hybrid Bait
Displays links to interactive yeast two-hybrid protein-protein interaction maps. Links will be displayed only for kinases that have interactors. Kinases and their interacting proteins are represented by shapes. Protein name and annotation are also included. Clicking on the protein will automatically redirect you to TIGR rice gene annotation. This data is distributed by Song Lab, Department of Plant Pathology, University of Florida and includes 378 interactions with 254 distinct kinase interactors.
Tandem Affinity Purification-tagged Bait
This data is another set of protein-protein interactions generated by tandem affinity purification-tagged experiments. It is distributed by Mike Fromm Lab, University of Nebraska and consists of 364 interactions.


The Affymetrix raw data was downloaded from
NCBI GEO and EBI ArrayExpress. We used the MAS 5.0 method provided by the affy R package to convert probe level data to expression values. The trimmed mean target intensity of each array was arbitrarily set to 500. The data within this database was log transformed. There is a little difference between this MAS 5.0 normalization method that we used and the MAS 5.0 provided by Affmetrix Inc. Affymetrix normalization is usually done after summarization and the normalization we used was carried out before summarization. The Rice Multiple-platform Microarrary Element Search tool was used to get the corresponding Affymetrix probe sets for rice genes and only unique probe sets that match unique rice loci were included in this database. If several unique probe sets are available for one certain rice gene, we only select one probe set with the highest expression and this probe set is indicted by the symbol '*'.


Currently, updated version include anatomy RNASeq data provided in the
CARMO platform and spatio-temporal RNASeq transcriptome data generated for rice phosphate starvation and recovery in root and shoot by Secco et al. (2013).

August 2008:

More rice expression data was added in this update, including more MPSS libraries, more Affymetrix microarray data, Agilent and NSF 45K microarray data.

June 2008:

In June 2008, we updated the RKD again. In this update, we added predicted orthologs in selected four dicots, more mutant lines from different libraries and some available phenotypes, more protein-protein interactions from both yeast two-hybrid and TAP-tagged experiments, etc.

January 2008:

In January 2008, the Rice Kinase Database was updated to TIGR Ver 5 annotation. Because of differences between TIGR Ver 3 and Ver 5 annotation, 34 of the previous 1508 rice kinases were deleted. These kinases are now annotated as 'N/A' in the current Rice Kinase Database. 32 kinases have new locus IDs in the TIGR Ver 5 annotation compared to TIGR Ver 3. The new in TIGR Ver 5 annotation include 346 new kinases. Most of these are newly identified alternative splice products of previous kinases. Click here to see the detailed information about these new kinases. We have also updated the sequence information and sequence quality based on new TIGR Ver 5 annotation. We have added in the latest T-DNA and Tos 17 knockouts information, corresponding RAP2 (Rice Annotation Project Ver 2) locus information, and homozygous knockout line information (from POSTECH).
We have also incorporated new rice expression data including MPSS mRNA and small RNA data, digital northern data and microarray expression data.