Rice Phylogenomics Database  


 Rice Kinase Database

 Rice GT Database

 Rice GH Database

 Rice Transporter DB

 Rice TF Database

 Rice Cyt P450 DB

 Database Description


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 Ronald Lab



Database Description

Phylogenetic Tree
Sequence Information
Sequence Quality
Orthologs in Dicots
Interactome Data
Digital Northern Data
MPSS Small RNA Data
Microarray Data

For each family with more than three members, the full protein sequences or domain sequences (Kinase) were aligned using ClustalW Version 2.0 with default options. Then maximum likelihood trees were bulit using PhyML 2.4.4 with JTT model (Kinase, GT, Transporter) or PhyML 3.0 with LG model (GH, TF, Cyt P450).

Family assignment for each gene.
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.
RAP2 Locus
The corresponding locus ID from Rice Annotation Project (RAP) annotation Ver 2.
RAP3 Locus
The corresponding locus ID from Rice Annotation Project (RAP) annotation Ver 3.
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.

Sequences that contain regions matching transposable elements.
Sequences with matching full-length cDNAs or ESTs.
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 gene sequence.

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.

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 byTargetP 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 digital northern data is from MSU/TIGR Rice Genome Annotation Project 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.

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
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

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 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 '*'.

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. Nineteen series corresponding to 104 samples were downloaded from NCBI GEO and EBI ArrayExpress. Then R package marray in Bioconductor was used to do the normalization. Within-array Lowess normalization and between-array MAD scale normalization were used. 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 4 series GSE6533, GSE6552, GSE11712 and GSE13161, corresponding to 251 samples. In the case of multiple oligos that match single loci, the selection method was the same as with the Affymetrix platform.

NSF 20K and 45K 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.
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.
Normalization method and oligo selection are same with Agilent arrays.

Last modified: Wednesday, 01-Apr-2015 11:36:38 PDT
UC Davis Zhejiang University Indica RDA SSAC Last Update: June 2015