Database Description

Phylogenetic Tree
Sequence Information
Sequence Quality Information
Orthologs in Dicots
Conserved Kinase Motifs
Conserved Domains
Topology
Mutants
Interactome Data
Digital Northern Data
MPSS mRNA Data
MPSS Small RNA Data
Microarray Data

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Phylogenetic Tree:

For each kinase subfamily with more than three members, the kinase domain sequences were aligned using ClustalW Version 2.0 with default options. Then maximum likelihood trees were bulit using PhyML with JTT model.

Sequence Information:

Group
Rice kinases classifications were done according to Shiu SH, Karlowski WM, Pan R, Tzeng YH, Mayer KF, Li WH. and kinase.com. Supertrees were constructed that included the yeast, fly, human, Arabidopsis and rice kinomes. Additional rice kinase classifications were added based on associated clades.
Chromosome
The chromosome on which each kinase gene is located.
5' end
Position of 5?end of kinase coding sequence.
3' end
Position of 3?end of kinase coding sequence.
BAC Name
Name of BAC clone from which each kinase sequence was derived.
GB Accession
The GenBank Accession Number of BAC clone from which each kinase sequence was derived.
RAP2 Locus
The corresponding locus ID from Rice Annotation Project (RAP) annotation Ver 2.
PlantsP Link
Displays a link to the plantsP website http://plantsp.sdsc.edu/. PlantsP has additional annotation information about each kinase.
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.

Sequence Quality:

TE-related
Sequences that contain regions matching transposable elements.
EST/cDNA
Sequences with matching full-length cDNAs or ESTs.
Finished/Unfinished
At the time of TIGR rice pseudomolecule release 5, 98.8 % (3,408 BAC/PAC clones) of the rice genome sequence was "finished" and the remaining "unfinished" regions are from lower quality sequence that requires additional sequencing passes.
PASA Status
The Program to Assemble Spliced Alignments (PASA) was developed and employed towards the incorporation of EST and FL-cDNA alignments into the TIGR Arabidopsis genome annotation. Annotated sequences with exact cDNA matches are listed as "PASA-validated" Sequences with cDNA hits that do not exactly match are listed as "PASA-failed" This information assists with assessing the quality of each kinase sequence.

Orthologs in Dicots

The rice kinase orthologs in selected dicots were identified by InParanoid Version 3 (Remm et al., 2001). The dicots genomes used to scan for orthologs are Arabidopsis thaliana, Medicago truncatula, Populus trichocarpa and Ricinus communis.

Conserved Kinase Motifs:

G-loop
Also called the glycine flap, this motif is found within kinase subdomain I and is involved in binding and orienting ATP. The consensus sequence found in the vast majority of kinases is GXGXXG.
Domain II
Kinase subdomain II contains a highly conserved Lysine that is typically required for catalytic activity. This site is commonly altered to create "catalytically dead" kinases. In many kinases this invariant lysine forms a salt bridge with the invariant glutamic acid in subdomain III. The domain II motif often contains the sequence VAVK.
Domain III
This domain is less well conserved but typically contains a highly conserved glutamic acid residue. Here we list only the presence or absence of the E residue.
Domain VI
This domain contains the RD motif. In most kinases, the highly conserved aspartic acid residue is required for catalytic activity and plays a direct role in the phosphor-transfer reaction. It is found at the center of the kinase active site. The positive charge of the adjacent arginine is thought to inhibit catalysis until activation-loop (situated between subdomains VII and VIII) phosphorylation. Upon activation, negatively charged phospho-amino acids in the activation-loop neutralize the inhibitory arginine resulting in increased kinase catalytic activity (100-1,000 fold). Kinases that lack the conserved arginine are termed Non-RD kinases. These kinases typically are not known to phosphorylate the activation-loop with the exception of the CLK family.
Domain VII
Domain VII contains a highly conserved aspartic acid thought to play a role in orienting the ATP molecule. This residue is also typically required for catalytic activity and is found with the motif DFG.
Domain VIII
Domain VIII commonly contains the motif APE and occurs immediately after the activation-loop.

Conserved Domains:

Matching domains listed below are from Pfam and hmmer searches in the PlantsP database. Most commonly occurring domains are listed separately (see below). All other domains are listed together as "all other domains". For graphical displays and more details please visit PlantsP.
Leucine Rich Repeats (LRR)
Leucine-rich repeats (LRRs) are 20-29-residue sequence motifs present in tandem arrays a number of proteins with diverse functions, such as hormone receptor interactions, enzyme inhibition, cell adhesion and cellular trafficking. A number of recent studies revealed the involvement of LRR proteins in early mammalian development, neural development, cell polarization, regulation of gene expression and apoptosis signalling. It was shown that LRRs may be critical to the morphology and dynamics of cytoskeleton. The primary function of these motifs appears to be to provide a versatile structural framework for the formation of protein-protein interactions.
Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel ?sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterized by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the ?strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with -helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions MEDLINE:. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats MEDLINE:.
Lectin Domain (LEC)
Animal lectins display a wide variety of architectures.They are classified according to the carbohydrate-recognition domain (CRD) of which there are two main types, S-type and C-type. C-type lectins display a wide range of specificities. They require Ca2+ for their activity.
PAN/Apple Domains
It has been shown that, the N-terminal N domains of members of the plasminogen/hepatocyte growth factor family, the apple domains of the plasma prekallikrein/coagulation factor XI family, and domains of various nematode proteins belong to the same module superfamily, the PAN module MEDLINE:. PAN contains a conserved core of three disulphidebridges. In some members of the family there is an additional fourth disulphide bridge that links the N and C termini of the domain. The domain is found in diverse proteins, in some the domain mediates protein-protein interactions, in others it mediates protein-carbohydrate interactions.

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 kinases, including 'secretory pathway', 'chloroplast', 'mitochondrion' and 'any other location' as predicted byTargetP Version 1.1.

Mutants:

OryGenesDB was used to map flanking sequence tags (FSTs) from different mutant libraries to the TIGR Version 5 rice pseudomolecules by identifying the highest hit based on a e-10 cut-off. The mapped insertions were then assigned to rice kinase 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.

Interactome Data:

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.

Digital Northern Data:

The digital northern data is from TIGR and provides the tissue specific gene expression evidence for rice loci based on EST data (Jung et al., 2008). The EST evidence was determined using the PASA program which utilizes a number of alignment programs to maximally align transcripts to the genome. The minimal alignment allowed by the PASA program is 95% identity over 90% length of the transcript.

MPSS Data

Massively Parallel Signature Sequencing (MPSS) data was downloaded from the Rice MPSS Database. For the mRNA data, the sum of abundances of 17bp-tag signatures for classes 1, 2, 5, and 7 are listed for each library. mRNA library information is shown below. For more information please visit the Rice MPSS Database website.

Nakano, M., Nobuta, K., Vemaraju, K., Tej, S.S., Skogen, J.W., and B.C. Meyers. (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Research 34, D731-D735. http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D731

Code	Tittle	# 0f Signatures
NYR	14 days - Young Roots	1,944,785
NRA	60 days - Mature Roots - Replicate A	2,675,567
NRB	60 days - Mature Roots - Replicate B	2,617,770
NGD	10 days - Germinating seedlings grown in dark	2,512,579
NST	60 days - Stem	2,095,983
NYL	14 days - Young leaves	2,249,147
NLA	60 days - Mature Leaves - Replicate A	1,073,991
NLB	60 days - Mature Leaves - Replicate B	1,348,557
NLC	60 days - Mature Leaves - Replicate C	1,263,549
NLD	60 days - Mature Leaves - Replicate D	1,254,824
NME	60 days - Crown vegetative meristematic tissue	2,568,641
NPO	Mature Pollen	2,310,574
NOS	Ovary and mature stigma	2,499,264
NIP	90 days - Immature panicle	2,661,421
NGS	3 days - Germinating seed	1,861,571
NCA	35 days - Callus	2,131,255
NSR	14 days - Young roots stressed in 250 mM NaCl for 24h	1,842,226
NSL	14 days - Young leaves stressed in 250 mM NaCl for 24h	2,531,362
NDR	14 days - Young roots stressed in drought for 5 days	2,190,870
NDL	14 days - Young leaves stressed in drought for 5 days	2,613,140
NCR	14 days - Young roots stressed in 4C cold for 24h	2,401,553
NCL	14 days - Young leaves stressed in 4C cold for 24h	2,322,924
XC00	Unwounded Control-Nipponbare Xa21-0hr	1,190,318
XC06	Mock treatment-6hr	1,367,076
XC24	Mock treatment-24hr	1,165,716
XR03	X.oryzae-R-3hr	1,134,269
XR06	X.oryzae-R-6hr	1,269,616
XR12	X.oryzae-R-12hr	1,542,183
XR24	X.oryzae-R-24hr	1,055,586
XR48	X.oryzae- R-48hr	1,248,814
XS03	X.oryzae-S-3hr	1,466,965
XS06	X.oryzae-S-3hr	1,419,178
XS12	X.oryzae- S-12hr	1,444,840
XS24	X.oryzae- S24hr	1,264,383
XS48	X.oryzae-S-48hr	1,175,368
MR03	M. grisea-R-3hr	1,422,272
MR06	M. grisea-R-6hr	1,054,700
MR12	M. grisea-R-12hr	1,331,343
MR24	M. grisea-R-24hr	1,435,098
MR48	M. grisea-R-48hr	1,367,250
MS03	M. grisea-S-3hr	1,584,229
MS06	M. grisea-S-6hr	1,354,948
MS12	M. grisea-S-12hr	1,086,361
MS24	M. grisea-S-24hr	1,022,535
MS48	M. grisea-S-48hr	1,518,407
MS96	M. grisea-S-96hr	1,061,873
MC00	Mock treatment-0hr	1,372,860
MC24	Mock treatment-24hr	1,402,116
I9RO	Roots	2,162,940
I9RR	Roots - Replicate	2,156,164
I9LA	Leaves	1,606,175
I9LB	Leaves - Replicate	1,005,937
I9LC	Leaves	1,144,192
I9LD	Leaves - Replicate	1,146,212
I9ME	Merismatic Tissue	2,112,790
FRO	F1 Hybrid 60days Mature Root	2,436,387
FRR	F1 Hybrid 60days Mature Root-Repl	2,205,884
FLA	F1 Hybrid 60days Mature Leaf Replicate A	1,171,478
FLB	F1 Hybrid 60days Mature Leaf Replicate B	1,040,468
FLC	F1 Hybrid 60days Mature Leaf Replicate C	1,056,621
FLD	F1 Hybrid 60days Mature Leaf Replicate D	1,419,115
FME	F1 Hybrid 60days Meristematic tissue	3,045,290
PSC	rice developing seeds, 6 days old cypress high milling(99-1710)	1,266,713
PSI	rice developing seeds,6 days old, Ilpumbyeo - High Taste	1,201,584
PSL	rice developing seeds, 6 days old, LaGrue-Low Milling	1,082,099
PSN	rice developing seed, 6 days old, Nipponbare-Grain quality control	1,207,914
PSY	rice developing seeds,6 days old, YR15965Acp33 - Low Taste	1,190,250
PLA	rice leaf, beet armyworm damaged, 24 hr(99-1726)	1,150,869
PLW	rice leaf, water weevil damaged, 24 hr	1,012,170
PLC	rice leaf, mechanical damaged, 24 hr	1,213,577

For the small RNA data, the sum of abundances for signatures are listed for each library. Small RNA library information is shown below.

Code	Title	Total Sequences	Genome Matched Reads	Distinct Genome Matched Reads	t/r/sn/snoRNA Matched Reads
STM	Stem	520,676	381,597	50,766	19,113
SNU	Germinating seedlings	701,631	542,567	28,574	18,813
FLR	Nipponbare Immature panicles- 90 days old plants	1,731,548	1,111,811	150,743	49,681
SNM	Germinating seedlings infected with Magnaporthe grisea (strain 70-15)	541,360	428,929	25,596	16,916
ABA	Seedlings treated with ABA	448,763	372,597	30,209	8,367
UNT	Seedling control for ABA treatment	529,886	438,376	48,396	9,956

Microarray Data:

Affmetrix Platform
The Affymetrix array contains probes to query 51,279 transcripts representing two rice subspecies, with approximately 48,564 japonica transcripts and 1,260 transcripts representing indica. The arrays were designed using NCBI UniGene Build #52 (May 7, 2004) incorporating predicted genes from GenBank and the TIGR Os1 v2 data set (ftp.tigr.org FASTA, 89.3 MB). The NCBI GEO platform Accession Number is GPL2025.
The Affymetrix raw data was downloaded from NCBI GEO, including 14 series: GSE4438, GSE4471, GSE6737, GSE6893, GSE6901, GSE6908, GSE7197, GSE7256, GSE7951, GSE8380, GSE9498, GSE10857, GSE10872 and GSE12069. 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 Multi-platform Microarrary Search tool was used to get the corresponding Affymetrix probe sets for rice kinases 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 kinase, we only select one probe set with the highest expression and this probe set is indicted by the symbol '*'.

Agilent Platform
Probes on this array are designed to selections from the extensive rice (japonica) cDNA library of Japan National Institute of Agrobiological Sciences. It contains 22,575 oligos. The NCBI GEO platform Accession Number is GPL892. Twenty one series, GSE4409, GSE5286, GSE5853, GSE5906, GSE6124, GSE6125, GSE6126, GSE6244, GSE6362, GSE6600, GSE7192, GSE7530, GSE7531, GSE7532, GSE8811, GSE9450, GSE9765, GSE10098, GSE11021, GSE11157 and GSE11158, corresponding to 164 samples were downloaded from NCBI GEO. Then all the values in these data sets were converted to log2 scale for comparison. The oligo selection method is same with the Affymetrix platform.

BGI/Yale Platform
Oryza sativa Genome Oligo Set Version 1.0 was used in this dataset, which was designed by the Beijing Genomics Institute (BGI) and contains 60,727 70-mer oligos representing both the indica and japonica genomes. Oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes from the BGI rice genome build and other public resources. The NCBI GEO platform Accession Number is GPL1829. This data was also downloaded from NCBI GEO, including 7 series GSE2211, GSE2360, GSE2619, GSE6533, GSE2691, GSE6552 and GSE11712, corresponding to 97 samples. In the case of multiple oligos that match single loci, the selection method was the same as with the Affymetrix platform.

NSF 20K Platform
The NSF funded rice oligo array version 2 (NSF 20K) developped by the Ronald Lab at UC Davis and the TIGR, contains 20,190 unique probes for rice. The number of total spots including empty and controls is 21,120. The NCBI GEO platform Accession Number is GPL2091. Click here to see the detailed information about this microarray platform.
The NSF 20K microarray data about rice kinases was from an experiment "NSF 20K Oligo Arrays to Dissect Rice Defense Response Pathways " carried out by Guo-liang Wang and Pamela Ronald et al. The NCBI GEO Accession Number is GSE9653. This experiment is a two-condition experiment, 10 mutants vs wild type control with treatment or without treatment, including 114 slides. After obtaining raw data, we performed LOWESS normalization within and between arrays using the R-package, LMGene. In the website, we provide two options: intensity data for either channel (log transformed) and log2 ratio between the two channels. Click here to see the detailed information about the experiment design. In the case of multiple oligos that match single loci, the selection method was the same as with the Affymetrix platform.

NSF 45K Platform
We used the oligonucleotide identification tool, PICKY 2.0, to design the 50- to 70-mer oligos that comprise the NSF45K array. NSF45K arrays contain 43,311 oligonucleotide probes that target 45,116 gene models out of a total of 61,420 target transcript sequences in the TIGR V3 rice gene set release. This array is printed on two slides, NSF45Ka and NSF45Kb. NSF45Ka contains 23,040 oligos including 240 oligos corresponding to the hygromycin phosphotransferase (hph) gene (GenBank Accession: AF354045), a selectable marker used in transgenic rice generation. NSF45Kb contains 20,727 oligos including 216 hph oligos. The hph oligos serve as positive controls for experiments comparing transgenic plants with wild type plants. These show approximately 10-fold induction relative to non-transgenic samples. Alternatively, the hph spots serve as negative controls for non-transgenic samples.
Light and dark responses are fundamental to a plants?biology and produce dramatic differences in gene expression. To verify that the NSF45K array can be used to obtain biologically meaningful data, we performed an experiment to identify rice genes involved in the response of rice to light and dark treatments. For the light vs. dark experiment, we carried out expression-profiling on RNA from leaves of two-week old plants grown in a natural light-dark cycle (light-grown) in comparison to RNA from leaves of plants grown in a natural light dark cycle for a week and then transferred to constant darkness for the second week (dark-grown). In this validation experiment our aim was to identify genes that are universally important to the light/dark response in rice and thus to de-emphasize genotypic differences in the response. Hence, as our biological replicates we employed four different rice varieties with representatives of the two subspecies of rice, japonicas Kitaake, Nipponbare, and Taipei309; and indica, IR24. For statistical purposes, we conducted an additional set of hybridizations with the dyes used to label each sample swapped for each genotype (i.e., technical replicates).