MaizeMine

MaizeMine v1.4 hosts the Z. mays B73 genome assembly (Zm-B73-REFERENCE-NAM-5.0) and two gene sources, Zm00001eb.1 (from MaizeGDB/Gramene) and RefSeq (from NCBI).

Query for genes:

• Gene ID    Database Cross Reference ID
• Gene    Publications
• Gene    Chromosomal location
• Gene    Coding Sequences
• Gene    Transcript + Exon
• Gene Symbol    Gene Source and Chromosomal Location
• RefSeq Gene   Transcript    Protein
• Transcript    Gene

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Gene expression levels (FPKM) are from MaizeGDB qTeller. Mean expression levels for tissue samples are provided for the Zm00001eb.1 and RefSeq gene sets.

Query for gene expression:

• Gene  Gene Expression

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MaizeMine includes information about proteins and protein domains from UniProt and InterProt.

Query for protein:

• All Zea mays proteins (UniProt)
• Gene ID    Protein (UniProt)
• Protein (UniProt)    Gene ID(s)
• Protein (UniProt)    Publications

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MaizeMine includes homologue predictions from EnsemblCompara for Zea mays, other monocots and Arabidopsis.

Query for homology:

• Gene    Homologues
• Organism    Homologues to Zea mays genes

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MaizeMine v1.4 includes GO annotation and pathway information from KEGG and Plant Reactome for Z. mays.

Query for function:

• Gene    GO Terms
• Gene    Pathways
• Gene ID    Gene Symbol and GO Terms
• GO Term    Genes
• Gene source    GO annotations

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MaizeMine v1.4 provides SNP information from Ensembl Plants. SNP identifiers are from Panzea.

Query for variation:

• Maize Panzea SNP ID    Chromosome Location
• Maize Panzea SNP ID     Gene, Transcript and Consequence
• SNP Consequences
• Maize Panzea SNP ID    Transcript and Consequence Details

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The query templates in this category allow you to perform simple queries on an entire gene or protein set for a species.

Query for entire gene set:

• All Zea mays proteins (UniProt)
• All Genes  Database Cross Reference IDs
• Gene Source    Gene ids
• Gene Source    Gene IDs, Symbols, Descriptions
• Genome Assembly    All Genes and Their Locations
• All Transcripts    Gene    Database Cross Reference ID
• Genome Assembly    All miRNAs
• Gene source    GO annotations

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The query templates in this category allow you to retrieve gene database crossreference ids (Zm00001eb.1 <=> RefSeq) and gene alias ids (Zm00001eb.1 <=> AGPv4_Zm00001d.2 and Zm00001eb.1 <=> AGPv3.21_5b+).

Query for alias and dbxref:

• Gene ID    Database Cross Reference ID
• All Genes  Database Cross Reference IDs
• Gene Alias ID    Gene ID
• Gene    Database Cross Reference ID
• All Zm00001eb.1 Gene IDs    Gene Alias IDs
• Gene ID    Gene Alias ID
• Gene    Chromosomal Location and Dbxref Chromosomal Location
• Gene    Alias ID

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Community datasets include published data that were mapped to the Zm-B73-REFERENCE-NAM-5.0 assembly at MaizeGDB. See the Data Source page for a list of datasets.

Query for community:

• Gene ID    Enhancers
• TSS    Gene
• Enhancer ID    Location
• TSS    Location
• Gene ID    TSS
• Gene ID    QTL
• Gene ID    Transposable Element Insertion Sites
• Enhancer ID    Gene

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