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Maize Oligonucleotide Array Project |
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Maize Oligonucleotide Array Oligo Overview
File Downloads
Download the Maize Oligonucleotide Array Oligo Database v1 (zip, 4.74M).
Download the Maize Oligonucleotide Array Oligo Database v2 (zip, 4.76M).
Download the Maize Oligonucleotide Array Oligo Database v3 (zip, 4.85M).
Download the Maize Oligonucleotide Array Oligo Database v4 (zip, 7.40M).
Download the FASTA sequences of representative genes that oligos map to:
original_genes_submitted_to_operon_57452_fasta.zip (zip, 13.2M)
remapping_version1_57452_fasta.zip (zip, 14.3M)
remapping_version2_57452_fasta.zip (zip, 14.6M)
remapping_version3_57452_fasta.zip (zip, 15.4M)
remapping_version4_57452_fasta.zip (zip, 17.0M)
Visit the Operon/Qiagen Download Center to retrieve the complete 70-mer oligo dataset: http://omad.operon.com/download/index.php
Description of Annotation Fields
The data types stored in the Maize Oligonucleotide Array Design Database are the following:
TIGR Oligo ID: an identifier used by TIGR to identify a particular oligo on the array (~58k oligos). Format (eg. TM00013146).
Operon ID: an identifier used by Operon to identify a particular oligo on the array (~58k oligos). Format (eg. MZ00002633).
Putative Annotation: the annotation associated with this oligo obtained by BLASTing its sequence against one of several databases (TIGR Plant Transcript Assemblies, TIGR Plant Transcript Assemblies (Maize B73), TIGR Maize Database, GenBank, TIGR Gene Index, TIGR Rice Model, Enzyme Nomenclature, TIGR Maize Repeat).
Match Sequence: the accession entries of the matching gene sequence that provided the annotation information for this oligo.
B73 Matches (100%): the Plant Transcript Assembly build for Maize B73 matching EST assemblies that match with 100% identity over 100% length of the oligo sequence.
Other Matches (100%): the accession entries of other matching gene sequences that match with 100% identity over 100% length of the oligo sequence.
Other Matches (95%): the accession entry of other matching gene sequences that match with 95-100% identity over 100% length of the oligo sequence.
Plant GO ID: the Gene Ontology identifier(s) assigned to this oligo, if available.
Plant GO Slim ID: the plant GO slims are cut-down versions of the GO ontologies containing a subset of the terms in the whole GO which are commonly used in plant research.
Rice Model: the feature name of the rice gene model assigned to this oligo, if available.
EC Number: the Enzyme Nomenclature number for the gene associated with this oligo, if available.
Chromosome: the chromosome(s) found to contain this sequence.
Oligo Category: single or multiple letter code designating the source database(s) the oligo was designed from: G Gene Index, A AZM, R Maize Repeat Database, O Organelle, S Special ("pet" genes, root), T Transgenes
Oligo Length: length of the designed oligo in nucleotide bases.
Oligo 5' Coordinate: 5' end position of the oligo within the matching sequence.
Oligo 3' Coordinate: 3' end position of the oligo within the matching sequence.
Oligo Coordinate From 3' End: position of the oligo within the matching sequence from the 3' end.
Tm: the melting temperature of this oligo in °C.
GC Content: the GC content of this oligo expressed as a percentage.
Design Phase: the design classification of the oligo designated by Operon/Qiagen. The Operon/Qiagen design phase criteria are the following:
A. Oligo length = 70mer
B. Tm = 78 +/-5
C. Bases from 3'end <= 1000
D. Cross-hybridization identity <= 70%
E. Contiguous bases in common with another sequence <=20
F. PolyNtractlength < 9
G. Hairpin stem length < 9
| Number of oligos | Phase number | Criteria |
| 41,953 | Phase1 | Criteria A, B, C, D, E, F and G |
| 1,969 | Phase1a | Same as Phase1 except <70mer and/or Tm is not 78+/-5 (its wider) |
| 960 | Phase2 | Same as Phase1 except >1000 bases from 3'end |
| 126 | Phase2a | Same as Phase2 except <70mer and/or Tm is not 78+/-5 (its wider) |
| 12,444 | Phase3 | Oligo does not qualify for previous phases |
Original Sequence: the accession and the sequence of the original gene used to design this oligo. The location of the oligo within the sequence is highlighted in yellow To download the complete oligo sequence dataset, visit the Operon/Qiagen Download Center.
Multi Hits?: if there is more than a single annotation entry for the given oligo sequence at 100% identity and 100% length, this field is 'yes'
Adopted From Original?: if this field is 'yes' it means the oligos failed to map to the new set of the EST, GSS, Repeat database and organelle sequences used to generate the latest version of annotation. Thus, the annotation for those oligos shown in the new version of annotation are adopted from the previous version of annotation.
Annotation Database: the annotation pipeline used to identify and characterize the gene the oligo was designed from. Can be AZM, Gene Index, Repeat, Plant Transcript Assembly for Maize, Plant Transcript Assembly for Maize B73
Annotation Database Version: the version of the database that was BLASTed to provide annotation for this oligo.
Annotation Version: the Maize Oligonucleotide Array Database version.
Version 4 draws from the following databases and their versions:
AZM4 (Assembled Zea Mays 4)
EC
Organelle
GO
GO Slim
Transgene
Organelle
Special
Maize Gene Index 17
Rice pseudomolecule (Version 4)
Plant Transcript Assembly for Maize (Version 3)
Plant Transcript Assembly for Maize B73 (Version 1)
Rice pseudomolecule (Version 4)
Last modified: April 1, 2008Thursday, 15-May-2008 09:10:31 MST