|
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. More Examples: lg1, liguleless1, Zm00001d002005, GRMZM2G036297, DAA35605, Zm00001d002005_T001
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 DownloadsGene 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
positions.
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 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.
All open gene model issues
All open assembly issues 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 AnnotationsPhytozome: 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 Information In-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.
Zm-B73-REFERENCE-GRAMENE-4.0/Zm00001d Stats
Top 20 genes These are the most searched-for genes in 2017
NCBI B73_v4 annotation release 101 The 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. Image of gene model frequency for Zm-B73-REFERENCE-GRAMENE-4.0 (Click image for larger view) 
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.
|
|
Simple gene/gene model search
