June 2016 (New):
The Rice Kinase Database was updated to version 7 of MSU rice genome annotation. In this version, changes were made to modify the view and strengthen phylogenomic analysis. Firstly, multiple transcripts of a single gene were eliminated and only RGAP model transcript was used for further analysis and data representation. Secondly, rather than selecting each of the experiment/study from the drop-down box, users are provided with anatomy, abiotic, biotic and hormone datasets. Selecting any or all of these datasets display the corresponding data values or heatmap in a single frame. Thirdly, a few publicly available Rice RNASeq datasets have been included for various rice tissues. We have removed Digital nortern and MPSS datasets in this version.
October 2009 :
The Rice Kinase Database was updated to MSU/TIGR ver 6 rice genome annotation. In this version, there are 1,467 kinase genes (locus) corresponding to 1,934 transcripts (gene model). We provided phylogenetic trees for each subfamily individually. More microarray data were incorporated and heatmap function was also added.
More rice expression data was added in this update, including more MPSS libraries, more Affymetrix microarray data, Agilent and NSF 45K microarray data.
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.
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.
The Rice Kinase Database was created to host functional genomic information gathered as part of a large NSF funded rice kinase proteomics project
. Our goal is to integrate disparate data sets into a logical, user friendly format. To accomplish this, we have developed a platform to display user selected functional genomic data on a phylogenetic tree. The RKD also includes an interactive chromosomal map showing the positions of all rice kinases and an interactive protein-protein interaction maps. Links are provided to navigate between these pages and to the TIGR rice genome annotation database.
We hope this format will make it easier to compare closely related kinases within subfamilies as well as perform global comparisons between sets of related subfamilies. We would greatly appreciate any feedback you may have that would assist us in to continually improve the RKD.
Annotation of the Rice Kinome
Plant receptor kinases (PRK) form one of the largest families of plant proteins. The size and potential redundancy within PRK subfamilies poses a difficult challenge to study PRK functions. Along with our collaborator Mike Gribscov (SDSC), we have identified 1,496 rice kinases from the TIGR rice pseudomolecules release 2. Remarkably, the rice kinome contains 40% more kinases than Arabidopsis and is 3 times larger than the human kinome. These expansions in rice are primarily attributed to large multi-gene families of the membrane bound receptor type, most of which have unknown functions. A phylogenetic tree was constructed using nearest neighbor method and includes 1,508 kinase sequences.
(77 putative kinases could not be aligned because they contain only short kinase domain fragments and an additional 89 alternative spliced products were added.) Additional sequence information can be found on
. Our collaborators at TIGR
(Ouyang Shu and Robin Buell) have provided us detailed sequence information including: complete genomic, cDNA and protein sequences, chromosome # and position of 5' and 3' ends, BAC accession numbers, alternative splicing products and sequence quality data.