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PLACE (http://www.dna.affrc.go.jp/htdocs/PLACE/) is a database of nucleotide sequence motifs found in plant cis-acting regulatory DNA elements. Motifs were extracted from previously published reports on genes in vascular plants. In addition to the motifs originally reported, their variations in other genes or in other plant species in later reports are also(More)
PLACE (http://www.dna.affrc.go.jp/htdocs/PLACE/) is a database of motifs found in plant cis -acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also(More)
An extensive effort of the International Rice Genome Sequencing Project (IRGSP) has resulted in rapid accumulation of genome sequence, and >137 Mb has already been made available to the public domain as of August 2001. This requires a high-throughput annotation scheme to extract biologically useful and timely information from the sequence data on a regular(More)
We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were(More)
A computer-based analysis was conducted to assess the characteristics of microsatellites in transcribed regions of rice and Arabidopsis. In addition, two mammals were simultaneously analyzed for a comparative analysis. Our analyses confirmed a novel plant-specific feature in which there is a gradient in microsatellite density along the direction of(More)
Nicotiana tabacum was transformed with a chemically synthesized gene encoding the human epidermal growth factor (hEGF) under control of the CaMV-35S promoter. The hEGF gene sequence was present at one to several copies in the primary transformant plants (R0), and a transcript with the expected length was produced. Slot blot analysis of total RNAs of the(More)
We report here on the characterization of a putative Dof transcription factor gene in rice (Oryza sativa)--rice Dof daily fluctuations 1 (Rdd1). Daily oscillations in Rdd1 expression were retained after transferring to continuous dark (DD) or light (LL) conditions, indicating circadian regulation. However, Rdd1 showed arrhythmic expression in etiolated(More)
We mapped two loci for ADP-ribosylation factor homologues (ARF1, ARF2) and two loci for cysteine proteinase inhibitors (oryzacystatin-I and -II: OCI, OCII) by linkage analysis of restriction fragment length polymorphism loci in rice (Oryza sativa L.) genomic DNAs using their cDNAs as probes.Oc-1 andArf-2 were found to be closely located to each other on(More)
A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii)(More)
The Rice Proteome Database is the first detailed database to describe the proteome of rice. The current release contains 21 reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments. These reference maps comprise 11 941 identified proteins showing tissue and subcellular(More)