v1.4
An integrated data warehouse for MaizeGDB.
Your browser does not have JavaScript enabled. Some parts of this website may require JavaScript to function correctly
Please contact us if you would like any additional template queries or if you have a concern about a query not completing.
Given a gene id, retrieve database cross reference id(s). The input gene id can be from either the Zm00001eb.1 or RefSeq gene set, and the output will be from the other gene set.
Given a gene ID, retrieve mean expression levels with tissue and growth stage information.
Given a Zea mays gene id or symbol, retrieve GO terms.
Given a Zea mays gene id or symbol, retrieve pathways.
Given a Zea mays gene symbol or id, retrieve homologues.
Given a gene id or gene symbol, retrieve publications.
Given a gene source, retrieve all gene ids with their database cross references. Use this to convert between Zm00001eb.1 and RefSeq gene ids, and vice versa. Note that some genes or their cross references may be present in multiple output rows due to split or merged gene models. You can check for this using the Column Summaries above the columns.
Given an organism name, retrieve homologues to Zea mays genes.
Given a gene id, retrieve gene symbol and go terms.
Retrieve all proteins (UniProt) for Zea mays.
Given a gene id from the Zm00001eb.1 or RefSeq gene set, retrieve UniProt proteins.
Given a maize Panzea SNP ID, retrieve chromosome location
Given a gene id, retrieve chromosomal location.
Given a maize Panzea SNP ID, retrieve gene id, transcript id and consequence. No rows will be returned if the SNP is not within a gene.
Given a gene alias ID from an older gene set (GPv4_Zm00001d.2 or AGPv3.21_5b+) retrieve gene id from Zm00001eb.1.
Given a GO term, retrieve Zea mays genes annotated with that GO Term.
Given a gene id, retrieve the coding sequences.
Given the gene source, retrieve all gene ids and gene symbols, if available.
Given a gene id, retrieve transcript ids and locations and exon coordinates.
Given a gene source, retrieve all genes with symbols and descriptions. Currently gene symbols and descriptions are available only for RefSeq.
Given a gene symbol, retrieve gene source and chromosomal location.
Retrieve gene alias identifiers mapping Zm00001eb.1 genes to older gene sets (AGPv4_Zm00001d.2 or AGPv3.21_5b+). Optionally constrain the output to only one older gene set.
Given a Zea mays RefSeq (NCBI) gene id, retrieve transcript ids and protein ids.
Given a Zea mays UniProt id, retrieve gene id(s). Optionally constrain the gene source to Zm00001eb.1 or RefSeq.
Given a gene id or symbol, retrieve database cross reference ids. This is used for the report page.
Retrieve all genes and their chromosomal locations for the specified Zea mays genome assembly.
Given a transcript id, retrieve gene id, symbol and description.
To retrieve publications for a gene
Given a Zea mays UniProt protein identifier, retrieve publications.
Retrieve all Zea mays transcript ids, gene ids and database crossreference ids for an organism. All gene sets will be provided unless the optional gene source constraint is used. Transcripts encoded by genes that do not have a database crossreference will not be provided in the output.
Given a Z. mays gene source, retrieve GO annotations for all genes.
Given a Gene ID from Zm00001eb.1, retrieve alias identifiers from older gene sets (AGPv4_Zm00001d.2 or AGPv3.21_5b+). Optionally constrain the output to only one older gene set.
Retrieve all Zea mays miRNAs and their locations.
Retrieve Transcript , Polypeptide for a gene on report page
Given a Panzea SNP ID, retrieve consequences. This template is used in the SNP report page.
Given a Gene ID from Zm00001eb.1, retrieve alias identifiers from older gene sets (AGPv4_Zm00001d.2 or AGPv3.21_5b+). This template is for the gene report page.
Given an assembly release, retrieve all chromosome identifiers. The column "DB identifier" shows the correct chromosome id format to use in the Regions Search.
Given a gene id, retrieve its chromosomal location and the locations of database cross references. This template will allow you to compare locations between B73_RefGen_v3 and B73_RefGen_v4.
Retrieve all transcripts and proteins for an organism.
Retrieve genes located on a chromosome for the specified Zea mays genome assembly.
Given a gene id, retrieve overlapping QTL. The "QTL" may be a single GWAS SNP. There will be no output if the gene does not overlap a QTL.
Given a gene id, retrieve overlapping transcription start site (TSS). The gene location is also provided. The TSS location is included as part of the TSS identifier. There will be no output if the gene does not overlap a TSS in the database.
Given a Maize Panzea SNP ID, retrieve consequence details, including transcripts if the SNP is located in proximity to a gene.
Given a gene id, retrieve overlapping enhancers. The gene and enhancer locations are also provided. There will be no output if the gene does not overlap an enhancer in the database.
Given a gene id, retrieve overlapping transposable element insertion sites. The gene and insertion site locations are also provided. There will be no output if the gene does not overlap a transposable element insertion site in the database.
Given the id of any sequence feature (e.g. enhancer, TSS, transposable element insertion site, QTL), retrieve its location.
Given a transcription start site (TSS) identifier, retrieve overlapping genes. There will be no output if the TSS does not overlap a gene.
Given an enhancer id, retrieve its location.
Given a transcription start site (TSS) identifier, retrieve its location.
Given an enhancer id, retrieve its location and overlapping gene(s). There will be no output if the enhancer does not overlap a gene.
Given the identifier for a transposable element insertion site, retrieve its location and overlapping gene(s). There will be no output if the insertion site does not overlap a gene.