POPcorn Sequence Search Collaborators: Resources
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Affymetrix GeneChip Maize Genome Array (18k)
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Information about the Affymetrix GeneChip Maize Genome Array
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DFCI Maize Gene Index
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The goal of The Gene Index Project is to use available EST and gene sequences, along with reference genomes, to provide an inventory of likely genes and their variants, annotated by their functional role and products.
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Grassius - Grass Regulatory Information Server
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A public web resource composed of databases, computational, and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits.
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Heritable Mu insertions identified by Mu-Illumina in the Photosynthesis Mutant Library
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This database catalogs heritable Mu insertions detected by Mu-Illumina sequencing during mutant cloning efforts involving the Photosynthesis Mutant Library (PML). A pooling strategy is used during this process that associates each insertion with either of two ears. When requests are received for a particular insertion, we will perform gene-specific PCR to identify the single ear harboring that insertion. Seed will then be provided to the individual making the request and to the Maize Coop.
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Maize Assembled Genomic Island (MAGI)
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The MAGI website summarizes the investigations of a diverse group of researchers who are looking at the structure of the maize and sorghum genomes, including assembling gene-enriched and whole genome shotgun genome survey sequences into MAGIs (Maize Assembled Genome Islands) and SAMIs (Sorghum Assembled genoMic Islands) and by assembling maize ESTs into MECs (Maize Expressed Contigs). BLAST is available for these assemblies. The MAGIs have been annotated via a variety of methods. A repeat masker is available.
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Maize Transposable Elements: Discovery, Description, and Functional Characterization
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This website is the home for the project, Maize Transposable Elements: Discovery, Description, and Functional Characterization. This website provides genetic data on transposable elements (TE), information for the scientific community on TE resources, and a source of information for the general public, teachers and students about the history and scientific study of maize.
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MaizeGDB
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MaizeGDB is the community's model organism database for biological information about the crop plant Zea mays ssp. mays. Genetic, genomic, sequence, gene product, functional characterization, literature reference, and person/organization contact information are among the datatypes accessible through this site.
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MaizeSequence.org
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Provides the latest sequence data and primary annotations of the maize genome. Includes genetic and physical map viewers and an Ensembl genome sequence browser. BLAST service is provided.
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NCBI Genbank
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GenBank. is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.
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PLEXdb - PLant EXpression database
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A public resource for gene expression for plants and plant pathogens. PLEXdb. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets.
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Phytozome Zea mays inbred mo17 Genome Browser
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A genome browser from Phytozome, showing data from the Mo17 sequencing effort.
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PlantGDB
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PlantGDB is an NSF-funded project to develop plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities.
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POPcorn Sequence Search Collaborators: Projects
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Maize Assembled Genomic Island (MAGI)
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The MAGI website summarizes the investigations of a diverse group of researchers who are looking at the structure of the maize and sorghum genomes, including assembling gene-enriched and whole genome shotgun genome survey sequences into MAGIs (Maize Assembled Genome Islands) and SAMIs (Sorghum Assembled genoMic Islands) and by assembling maize ESTs into MECs (Maize Expressed Contigs). BLAST is available for these assemblies. The MAGIs have been annotated via a variety of methods. A repeat masker is available.
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B73 Maize Genome Sequencing Project
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The Maize Genome Sequencing Project is a three-year project to sequence the genespace of Zea mays ssp. mays using the public B73 line. Sequencing began in November 2005 as part of a multi-institutional collaboration funded jointly by the NSF, USDA, and DOE. The strategy is to individually sequence a set BAC clones across a minimum-tiling path. Gene space will be identified and sequenced to finished quality.
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NCBI Genbank
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GenBank. is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.
More...
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PlantGDB
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PlantGDB is an NSF-funded project to develop plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities.
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UniformMu - Construction of a sequence-indexed transposon resource for maize based on the UniformMu population
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UniformMu is an inbred transposon population with the following features: 1) a uniform inbred genetic background that facilitates analysis of phenotypes and linkage of phenotypes to insertional mutations in the genome; 2) a facility for genetic control of Mu transposition based on selection of the bz1-mum9 marker for presence of MuDR activity; 3) a steady-state mutagenesis strategy that maintains a consistent average genetic load and moderate average copy number of autonomous MuDR and non-autonomous Mu elements per individual. The goal of this project is to create a resource for reverse genetics based on sequencing genomic DNA flanking germinal Mu insertions in the UniformMu population.
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Genome-wide mutagenesis of maize using Ac/Ds transposons
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A collection of over 2000 near-isogenic (W22) inbred lines each carrying one or two active Ds transposable elements at a precisely defined position.
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Maize TILLING Project
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Targeting Induced Limited Lesions IN Genomes (TILLING) can screen large populations of mutagenized organisms for those individuals that have single base changes in any gene of interest. The Maize TILLING Project (MTP) provides a service for maize researchers to identify and obtain seed for mutant varieties with defects in any gene. In addition, MTP is creating and evaluating new mutagenized lines of the inbreds B73 and W22 to provide the community with a general resource of optimally mutagenized seed.
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Maize Transposable Elements: Discovery, Description, and Functional Characterization
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In addition to identifying all TEs in maize, this project will pay attention to the characterization of TEs such as Pack-MULEs and Helitrons that capture and amplify gene fragments and thereby confound gene annotation. This project will generate an annotated TE database. Computational analysis will serve to identify candidate active TEs whose mobility will be validated using the transposon display technique in conjunction with a spectrum of maize genomic DNAs. This project will extend the analysis of TEs to the pericentromere.
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Palomero toluqueno sequencing project
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The Palomero toluqueño sequencing project is being carried out by Mexican scientists working at CINVESTAV/Langebio who are focusing their research on an ancient landraces with the objective of capturing the genetic diversity of maize.
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Grassius
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A public web resource composed of databases, computational, and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits.
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Facile Production and Efficient Indexing of Transposon-tagged Lines Using Next-generation Sequencing Technology for Maize
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This project will develop and use a general method for generating, sequencing, and indexing Ac/Ds transposable element insertions in maize.
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Use of the Transposon Ac as a Gene-searching Engine in the Maize Genome
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A simple and efficient Ac transposition assay based on the well-studied endosperm markers bz (bronze) and wx (waxy) has been developed. A collection of over 1200 independent Ac transposants has been generated and over one-third of these Ac sites have been mapped relative to the donor locus. In parallel, a panhandle PCR method, originally used in the human genome, has been adapted for the isolation of DNA adjacent to the insertion (tac sites). By sequencing tac sites, insertions have been identified.
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