Rice Oligonucleotide Array Database Overview
Download the Rice Oligo Array Database (zip, 2.9M) (Updated Mar 13, 2007).
The oligo sequences for the 45k array are available for download (FASTA format) (zip, 967K).
The oligo sequences for the 20k array are available for download (FASTA format) (zip, 528K).
The data types in the Rice Oligonucleotide Microarray Database are the following:
Rice Oligo ID: a unique identifier generated by TIGR to reference this oligonucleotide. Format: TR######. Oligos numbered TR000001 - TR020440 belong to the 20K array and oligos numbered TR030001 - TR073311 belong on the 45K array set (made up of 2 x 23K arrays). Non-TIGR Oligo IDs include Affymetrix (e.g. Os.10027.1.S1_at), Agilent (e.g. A_71_P104391) and Yale/BGI (e.g. Os049662_01) array identifiers.
Array Platform: The array platform containing this oligo: NSF 20K, NSF 45K (23K A or 23K B), Affymetrix, Agilent or Yale/BGI.
Putative Annotation: The putative gene function assignment is based on either sequence similarity (BLASTP) of the gene model (or in a few cases the full-length cDNA or gene index sequence) with entries in a non-identifical amino acid database or by the presence of Pfam domains within the predicted protein. Click here for more information on the rice gene model annotation process.
Match: The sequence this oligo aligns to at 100% length and identity. Example match IDs include TIGR Rice Genome Annotation release 5 models (e.g. LOC_Os01g01150.1, 11669.m00474), TIGR Plant Transcript Assemblies (e.g. TA58977_4530), or full length cDNAs (e.g. AK109021).
Match Type: The type of matching sequence this oligo was aligned to: TIGR Rice Genome Annotation release 5 models, full length cDNAs, TIGR Plant Transcript Assemblies, or TIGR Rice Genome Annotation pseudomolecules.
A TIGR locus ID is a gene/locus identified in the TIGR Rice Genome Annotation project or a rice full-length cDNA clone in the case the oligo can no longer be mapped to a rice gene model. Gene models are created by running a series of gene prediction programs on the rice genome and improvement of gene model structure with experimental evidence from ESTs and full-length cDNAs. Click here for more information on the gene prediction process.
Plant GO ID: the Gene Ontology identifier(s) assigned to this oligo, if available.
Tm: Calculated melting temperature of the designed oligo, in °C, from PICKY.
Oligo Length: Length in bp of the designed oligo (50-70).
GC Content: GC base content of the designed oligo as a percentage of its total length.
Oligo Sequence: The sequence of the oligo. Clicking 'View oligo alignment' will open the TIGR Rice Annotation Project Genome Browser.
Last modified: Tuesday, 13-Mar-2007 14:46:26 EDT