v1.5
An integrated data warehouse for MaizeGDB. Click here to go to MaizeMine v1.4 (previous release)
Search MaizeMine. Enter names, identifiers or keywords for genes, proteins, pathways, ontology terms, authors, etc. (e.g. Zm00001eb000020, 100037783, GR2b, Zm00001eb000020_T002, Zm00001eb000020_P002, NM_001111367.2, Zm00001d023210, GRMZM2G109674, 708A6_MAIZE, PZE0100000203).
Enter a list of identifiers.
MaizeMine v1.5 (Release-Updates) integrates the Zea mays Zm-B73-REFERENCE-NAM-5.0 genome assembly and genome assemblies of 25 other NAM founder lines with annotation data sets. The tabs below show categories for template queries, which provide simple search menus. The PANGENE template queries are to query for syntelogs among the NAM founder lines. The ALIAS AND DBXREF template queries are for id conversion between the Z. mays Zm00001eb.1 and RefSeq gene sets and between Zm00001eb.1 and the older MaizeGDB/Gramene gene sets (AGPv4_Zm00001d.2 and AGPv3.21_5b+).
Genes |
Pangene |
Expression |
Proteins |
Homology |
Function |
Variation |
Entire Gene Set |
Alias and DBxref |
Community |
MaizeMine v1.5 hosts the Z. mays B73 reference genome assembly (Zm-B73-REFERENCE-NAM-5.0) and genome assemblies of 25 other Z. mays NAM founders. Gene sets include genes from MaizeGDB for all the lines, and NCBI RefSeq for B73. The gene sources for the MaizeGDB gene sets include both the name of the maize line and the MaizeGDB gene set name, e.g. "B73 Zm00001eb.1", to make it easy to select a maize line of interest.
Query for genes:
Pangene data for the Z. mays NAM founders are from MaizeGDB. Pangene groups were assigned identifiers by MaizeMine. Individual genes within pangenes are called "syntelogs". You can search for syntelogs between two Z. mays lines, or you can query entire pangenes containing syntelogs among all the lines.
Query for pangene:
Gene expression levels (FPKM) are from MaizeGDB qTeller. Mean expression levels for tissue samples are provided for the B73 Zm00001eb.1 and RefSeq gene sets.
Query for expression:
MaizeMine includes information about proteins and protein domains from UniProt and InterProt.
Query for proteins:
MaizeMine includes homologue predictions from Ensembl Plants for Zea mays B73, other monocots and Arabidopsis.
Query for homology:
MaizeMine v1.5 includes GO annotation for all Z. mays lines. Pathway information includes KEGG and Plant Reactome for B73, and pathways computed at MaizeGDB using E2P2 for all Z. mays lines.
Query for function:
MaizeMine v1.5 provides SNP information from Ensembl Plants for B73. SNP identifiers are from Panzea.
Query for variation:
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:
The query templates in this category allow you to retrieve gene database crossreference ids for B73 (Zm00001eb.1 <=> RefSeq) and gene alias ids (Zm00001eb.1 <=> AGPv4_Zm00001d.2 and Zm00001eb.1 <=> AGPv3.21_5b+).
Query for alias and dbxref:
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:
Please contact us if you would like any additional template queries or if you have a concern about a query not completing.
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