Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica Rice

We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.

[1]  T. Gojobori,et al.  The genome sequence and structure of rice chromosome 1 , 2002, Nature.

[2]  Yujun Zhang,et al.  Sequence and analysis of rice chromosome 4 , 2002, Nature.

[3]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[4]  K. Akiyama,et al.  Functional Annotation of a Full-Length Arabidopsis cDNA Collection , 2002, Science.

[5]  D. Barlow,et al.  Quantitative genetics: Turning up the heat on QTL mapping , 2002, Nature Reviews Genetics.

[6]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[7]  Alex Bateman,et al.  The InterPro database, an integrated documentation resource for protein families, domains and functional sites , 2001, Nucleic Acids Res..

[8]  R. R. Samaha,et al.  Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. , 2000, Science.

[9]  K. Nakai,et al.  PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. , 1999, Trends in biochemical sciences.

[10]  Yoshihiro Ugawa,et al.  Plant cis-acting regulatory DNA elements (PLACE) database: 1999 , 1999, Nucleic Acids Res..

[11]  P. Waterhouse,et al.  Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[12]  W R Taylor,et al.  A model recognition approach to the prediction of all-helical membrane protein structure and topology. , 1994, Biochemistry.