Isolation and annotation of 10828 putative full length cDNAs from indica rice

Kabin Xie, Jianwei Zhang, Yong Xiang, Qi Feng, Bin Han, Zhaohui Chu, Shiping Wang, Qifa Zhang, Lizhong Xiong

Research output: Contribution to journalArticle

16 Scopus citations

Abstract

We reported the isolation and identification of 10828 putative full-length cDNAs (FL-cDNA) from an indica rice cultivar, Minghui 63, with the long-term goal to isolate all full-length cDNAs from indica genome. Comparison with the databases showed that 780 of them are new rice cDNAs with no match in japonica cDNA database. Totally, 9078 of the FL-cDNAs contained predicted ORFs matching with japonica FL-cDNAs and 6543 could find homologous proteins with complete ORFs. 53% of the matched FL-cDNAs isolated in this study had longer 5′UTR than japonica FL-cDNAs. In silico mapping showed that 9776 (90.28%) of the FL-cDNAs had matched genomic sequences in the japonica genome and 10046 (92.78%) had matched genomic sequences in the indica genome. The average nucleotide sequence identity between the two subspecies is 99.2%. A majority of FL-cDNAs (90%) could be classified with GO (gene ontology) terms based on homology proteins. More than 60% of the new cDNAs isolated in this study had no homology to the known proteins. This set of FL-cDNAs should be useful for functional genomics and proteomics studies.

Original languageEnglish (US)
Pages (from-to)445-451
Number of pages7
JournalScience in China, Series C: Life Sciences
Volume48
Issue number5
DOIs
StatePublished - 2005

Keywords

  • Functional genomics
  • Oryza sativa L.
  • indica

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Environmental Science(all)
  • Agricultural and Biological Sciences(all)

Fingerprint Dive into the research topics of 'Isolation and annotation of 10828 putative full length cDNAs from indica rice'. Together they form a unique fingerprint.

  • Cite this

    Xie, K., Zhang, J., Xiang, Y., Feng, Q., Han, B., Chu, Z., Wang, S., Zhang, Q., & Xiong, L. (2005). Isolation and annotation of 10828 putative full length cDNAs from indica rice. Science in China, Series C: Life Sciences, 48(5), 445-451. https://doi.org/10.1360/062004-90