June 2015 (New):
The Rice Kinase Database was updated to MSU ver 7 rice genome annotation.
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 (http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0217312).
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.
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 http://www.tigr.org
(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.