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Simple Search: This search form allows you to find gene loci and
gene models given basic information (locus name, Gene Model ID, Transcript ID,
Translation ID, Gene symbol, Gene name), including partial names.
More Examples:
lg1,
liguleless1,
Zm00001eb067740,
GRMZM2G036297,
DAA35605,
Zm00001d002005_T001
Search for Gene Models by Sequence Translate Gene Model IDs - download Alternatively, download the full gene model associations list between the B73 assemblies and all other assemblies in our database Download By Region and Annotation Download Sequence for Gene Model List Gene Model DownloadsThe current gene model set for the representative maize genome, m-B73-REFERENCE-NAM-5.0 (B73 v5) is Zm00001eb.1.
Gene model cross-references and pan-genes
Please note that there is not a 1-to-1 correspondence between all
gene models in all annotations. Some gene models are unique to
specific genome assemblies, some have been split or merged
between annotation or assembly versions, some direct associations may be
difficult to calculate, so multiple gene models that are similar in
sequence and position may be listed. And some gene models may be similar in
sequence but do not appear in the same syntenic locations.
Gene model associations across all B73 assemblies. Current pan-gene data
Older gene model downloads
Gene model set Zm00001d.2 corresponds to Gramene release 36. Zm00001d.2 gene model cDNA fasta Zm00001d.2 gene model ncRNA fasta Zm00001d.2 gene model translations fasta Zm00001d.2 gene model GFF3 
Gene model set Zm00001d.1 corresponds to Gramene release 32. (Requires EnsemblPlant login or download as 'Guest') Zm00001d.1 gene model cDNA fasta Zm00001d.1 gene model ncRNA fasta Zm00001d.1 gene model translations fasta Zm00001d.1 gene model GFF3
Gene model set 5b+ for B73 RefGen v3 corresponds to Gramene release 21. 5b+ gene model cDNA fasta 5b+ gene model ncRNA fasta 5b+ gene model translations fasta 5b+ gene model GFF3 B73 RefGen_v3 MAKER-P gene models
Gene model set Zm00001d.provisional holds low confidence gene models that were not included in the Zm00001d.2 annotation. Zm00001d.provisional (low confidence) gene model GFFs Zm00001d.provisional (low confidence) gene model transcripts Zm00001d.provisional (low confidence) gene model proteins Cross reference for 5b+ GRMZM and ZEAMMB73 IDs 5b.60: Filtered Gene Set for B73_RefGen_v2 5a.59: Working Gene Set for B73_RefGen_v2 4a.53: Filtered Gene Set for B73_RefGen_v1 4a.53: Working Gene Set for B73_RefGen_v1 Download all data for a list of gene modelsEnter a list of B73 gene models, separated by newlines, commas, spaces, or semicolons.Note: this can take several minutes, even for a short list of gene models.
B73 Reference Genome Assembly and Gene Model IssuesWe need your help! Please report any assembly or gene model structure problems. This includes misassembled regions, evidence for closing gaps, gene models that should be merged or split, evidence supporting low-confidence gene models, et cetera. All issues will be shared with the maize community and with the team charged with improving the B73 assembly and gene models. About the Current Gene Model Set The current gene model set (i.e. structural assembly annotation) is Zm00001eb.1. See the 2016 Whole-Genome Assembly and Annotation nomenclature document for an explanation of the assembly and annotation identifiers, which was first adopted for the Zm-B73-REFERENCE-GRAMENE-4.0 / Zm00001d assembly and structural annotation and subsequent assemblies and annotation for B73 and other accessions. The Zm00001eb.1 gene model set for Zm-B73-REFERENCE-NAM-5.0 is the current recommended set. Other gene model sets are provided for comparison. Gene model sets and assemblies:
Reference gene model releases
Bold font indicates the current official gene model set.
Gene Model Functional Annotations and Orthologs Zm-B73-REFERENCE-NAM-5.0InterproScan results (Also available in the MaizeGDB downloads for all NAM founder assemblies) Phytozome Download files include functional Annotations for B73 RefGen_v2 ("Ensembl-18") and B73 RefGen_v4, and orthologs for B73 RefGen_v4. (account required) B73 RefGen_v2 Gramene.org: Functional Annotations (B73 RefGen_v2 only) Freeling Lab: Syntenic Orthologs (mapped to RefGen_v2) Gene Models with Associated Genes (B73 RefGen_v3 and Zm-B73-REFERENCE-GRAMENE-4.0, aka B73 RefGen_v4)
Insertion data sets UniformMu About the UniformMu projectW22 to B73 cross-reference: Excel spreadsheet Genomic coordinates for Zm-B73-REFERENCE-NAM-5.0: Release 9 Excel spreadsheet Genomic coordinates for Zm-B73-REFERENCE-GRAMENE-4.0 (aka B73 RefGen_v4): Release 9 Excel spreadsheet Release 9 Excel spreadsheet with gene structure List of gene models from the B73 RefGen_v3 Filtered Gene Set that have UniformMu insertions: Release 8 Excel spreadsheet List of gene models from the B73 RefGen_v2 Filtered Gene Set that have UniformMu insertions including 100 bp upstream or downstream: Release 7 Excel spreadsheet Release 8 Excel spreadsheet List of gene models from the B73 RefGen_v2 Filtered Gene Set that have UniformMu insertions in exons: Release 7 Excel spreadsheet Release 8 Excel spreadsheet Ac/Ds-GFP Abut the Dooner & Du Ac/Ds-GFP projectInsertions validated by Warman et al., 2020 Validation table with B73 v3 and v4 gene model assignments Zm-B73-REFERENCE-NAM-5.0/Zm00001eb.1 Information In-depth metadata for Zm-B73-REFERENCE-NAM-5.0 is available here.See the paper for B73 RefGen_v1 here, and for Zm-B73-REFERENCE-GRAMENE-4.0 here. Counts for each chromosome.
Zm-B73-REFERENCE-NAM-5.0/Zm00001eb.1 Stats
NCBI annotation releases The NCBI B73_v5 annotation release 103 for B73 v5 assembly, the NCBI B73_v4 annotation release 101 and NCBI B73_v4 annotation release 102 for the B73 v4 assembly, and the NCBI B73_v3 annotation release 100 were developed at NCBI using the NCBI Eukaryotic Genome Annotation Pipeline. The final set of annotated features comprises, in order of preference, pre-existing RefSeq sequences and a subset of well-supported Gnomon-predicted models. It is built by evaluating together at each locus the known RefSeq transcripts, the features projected from curated RefSeq genomic alignments and the models predicted by Gnomon.
Nomenclature
To ensure consistency across genomes and to better enable pan-genome analyses,
MaizeGDB is the single naming authority for the assignment of identifiers for
genome assemblies and annotations.
Gene Model Terms Associated Genes: Associated Genes are genes that have been linked to a gene model by hand curation.
Canonical:
The canonical transcript is defined as either the longest CDS, if the
gene has translated transcripts, or the longest cDNA. Note: a
canonical transcript is not always the first transcript (T01) or the
longest transcript.
Evidence Type: The source of evidence to support the gene model.
Model Types:
Protein Coding A gene model with supporting evidence.
Transcript Classes:
WH. With homology to a known non-transposable element in the NR
(non-redundant) database at GenBank. Protein-coding gene.
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Simple gene/gene model search
