Simple Search: This search form allows you to enter basic information (locus name, Gene Model ID, Transcipt ID, Translation ID, Gene symbol, Gene name), including partial names, to search for a gene and/or gene model.
Search for Gene Models by Sequence
Translate Gene Model IDs
Alternatively, download the full gene model associations list between v3 and all other assemblies in our database
Download By Region and Gene Model Set
Download Sequence for Gene Model List
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.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
Gene model cross-reference downloads
Please note that there is not a 1-to-1 correspondence between all v3 and v4
gene models. There are some gene models which are unique to each version of
B73, some have been split or merged, and some do not appear in the same
Complete B73 v1 (4b) gene model cross reference
Complete B73 v2 (5b) gene model cross reference
Complete B73 v3 (5b+) gene model cross reference
Complete B73 v4 (Zm00001d.2) gene model cross reference
Older gene model downloads
Gene model set Zm00001d.1 corresponds to Gramene release 32.
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
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
B73 Reference Genome Assembly and Gene Model Issues
We 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 Zm00001d.2.
See the 2016 Whole-Genome Assembly and Annotation nomenclature document for an explanation of the assembly and annotation identifiers, which has been 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 Zm00001d.2 gene model set for Zm-B73-REFERENCE-GRAMENE-4.0 is the current recommended set. Other gene model sets are provided for comparison. Due to the difficulty of determining when two gene models are the same (or when one represents an alternative splicing of the same genomic material), there are no plans to merge the sets. The next release of the B73 genome (RefGen_v4) is anticipated in 2016 and the new official gene model set will be based on MAKER-P annotations.
Gene model sets and assemblies:
Reference gene model releases
Bold font indicates the current official gene model set.
Gene Model Annotations and Orthologs (B73 RefGen_v3)Gramene.org: Functional Annotations
Phytozome: Functional Annotations (log-in required)
Freeling Lab: Syntenic Orthologs (mapped to RefGen_v2)
Gene Models with Associated Genes (B73 RefGen_v3)
Gene Models with UniformMu insertions (B73 RefGen_v2; versions 7 & 8)List of gene models from the 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 RefGen_v2 Filtered Gene Set that have UniformMu insertions in exons:
Release 7 Excel spreadsheet
Release 8 Excel spreadsheet
Zm-B73-REFERENCE-GRAMENE-4.0/Zm00001d.2 InformationIn-depth metadata for Zm-B73-REFERENCE-GRAMENE-4.0 is available here.
See the paper for B73 RefGen_v1 here, and for Zm-B73-REFERENCE-GRAMENE-4.0 here.
Counts for each chromosome.
Top 20 genes
These are the most searched-for genes in 2017
NCBI B73_v4 annotation release 101The NCBI B73_v4 annotation release 101 was developed independently at NCBI using the NCBI Eukaryotic Genome Annotation Pipeline on B73 RefGen_v4. 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.
The NCBI B73_v3 annotation release 101 is available here.
Gene Model Terms
Associated Genes: Associated Genes are genes that have been linked to a gene model by hand curation.
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
Evidence Type: The source of evidence to support the gene model.
Protein Coding A gene model with supporting evidence.
WH. With homology to a known non-transposable element in the NR
(non-redundant) database at GenBank. Protein-coding gene.