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. 2008 Nov 26;8:118.
doi: 10.1186/1471-2229-8-118.

RICD: A Rice Indica cDNA Database Resource for Rice Functional Genomics

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Free PMC article

RICD: A Rice Indica cDNA Database Resource for Rice Functional Genomics

Tingting Lu et al. BMC Plant Biol. .
Free PMC article

Abstract

Background: The Oryza sativa L. indica subspecies is the most widely cultivated rice. During the last few years, we have collected over 20,000 putative full-length cDNAs and over 40,000 ESTs isolated from various cDNA libraries of two indica varieties Guangluai 4 and Minghui 63. A database of the rice indica cDNAs was therefore built to provide a comprehensive web data source for searching and retrieving the indica cDNA clones.

Results: Rice Indica cDNA Database (RICD) is an online MySQL-PHP driven database with a user-friendly web interface. It allows investigators to query the cDNA clones by keyword, genome position, nucleotide or protein sequence, and putative function. It also provides a series of information, including sequences, protein domain annotations, similarity search results, SNPs and InDels information, and hyperlinks to gene annotation in both The Rice Annotation Project Database (RAP-DB) and The TIGR Rice Genome Annotation Resource, expression atlas in RiceGE and variation report in Gramene of each cDNA.

Conclusion: The online rice indica cDNA database provides cDNA resource with comprehensive information to researchers for functional analysis of indica subspecies and for comparative genomics. The RICD database is available through our website http://www.ncgr.ac.cn/ricd.

Figures

Figure 1
Figure 1
Query and display of cDNA clones in Rice Indica cDNA Database. The query parts are in red, while the display parts are in blue.
Figure 2
Figure 2
A example result page of a putative function query. The figure shows the page displaying Pfam search results for query term "bZIP transcription factor".
Figure 3
Figure 3
A typical result display page of a cDNA. The information of an indica cDNA clone includes the clone ID, GenBank Accession, library, genome position, gene annotation, expression atlas, variation report, cDNA sequence, ORF information. SNPs and InDels information and the results of similarity search will be shown after clicking corresponding buttons.

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