Gene Model Data In MaizeGDB
Simple Gene Model Search | Download by Chromosome | Download by Gene Model List | Gene Model Annotations and Orthologs | Gene Models with Associated Genes | B73 RefGen_v2 information | B73 RefGen_v2 stats | Image of Gene Model frequency | Gene Model Terms
Simple Gene Model Search
This search form allows you to just enter basic info (Gene Model ID, Transcipt ID, Translation ID, Gene symbol, Gene name) to quickly retrieve the desired sequence.
Examples: bz1, bronze1, GRMZM2G165390, GRMZM2G165390_T01, GRMZM2G165390_P01 , AC195466.3_FG002, AC195466.3_FGT002, AC195466.3_FGP002 .
Download by Chromosome (B73 RefGen_v2)
Download by Gene Model List (B73 RefGen_v2)
Gene Model Annotations and Orthologs (B73 RefGen_v2)
MaizeSequence.org: Functional Annotations
Phytozome: Functional Annotations
Freeling Lab: Syntenic Orthologs
Gene Models with Associated Genes (B73 RefGen_v2)
Classical genes (Table, Tab delimited)
MaizeGDB curated genes (Table, Tab delimited)
Combined set (Table, Tab delimited)
B73 RefGen_v2 information
| Chromosome | Working Gene set (WGS) count | WGS Transcript count | Filtered gene set (FGS) model count | FGS Transcript count |
| Chromosome 1 |
16,344
| 20,556
| 6,056
| 9,899
|
| Chromosome 2 |
13,284
| 16,387
| 4,766
| 7,485
|
| Chromosome 3 |
11,613
| 14,383
| 4,197
| 6,650
|
| Chromosome 4 |
12,517
| 15,463
| 4,197
| 6,822
|
| Chromosome 5 |
11,828
| 14,920
| 4,503
| 7,319
|
| Chromosome 6 |
9,207
| 11,458
| 3,293
| 5,263
|
| Chromosome 7 |
8,813
| 10,965
| 3,147
| 5,081
|
| Chromosome 8 |
9,633
| 12,085
| 3,531
| 5,695
|
| Chromosome 9 |
8,347
| 10,313
| 2,920
| 4,690
|
| Chromosome 10 |
7,718
| 9,463
| 2,727
| 4,274
|
| Unmapped |
157
| 170
| 52
| 62
|
| Chromosome total |
109,461
| 136,163
| 39,389
| 63,240
|
| Mitochondria |
171
| 175
| 124
| 127
|
| Chloroplast |
72
| 73
| 57
| 58
|
| Total |
109,704
| 136,411
| 39,570
| 63,425
|
Source: B73 RefGen_v2: Release 5b.60
B73 RefGen_v2 stats
| Gene Feature | Value |
| Average WGS transcript size |
2646 bp
|
| Average FGS transcript size |
4237 bp
|
| Average Exon size |
287 bp
|
| Average Number of exons per gene |
3.6 exons
|
| Maximum exons per gene |
53 exons (GRMZM2G068755_T01)
|
| Average Intron size |
629 bp
|
| Average Coding region size |
210 bp
|
| Average 5' UTR average length |
280 bp
|
| Average 3' UTR average length |
336 bp
|
Image of Gene Model frequency (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:
Canonical. The canonical transcript is the best representative transcript for a given gene model.
Non-canonical. All other transcripts for a gene model that are not the canonical transcript.
Evidence Type:
The source of evidence to support the gene model.
Model Type:
WGS. Working Gene Set. This set merges new annotations performed on RefGen_v2 with 4a gene models mapped onto the new reference. New annotations were achieved by an evidence-based method (Gramene GeneBuilder) and complemented with de novo Fgenesh models performed on masked DNA.
FGS: Filtered Gene Set. The filtered set was generated by screening the working set to remove pseudogenes, TE-encoded genes, and low-confidence hypothetical models.
Transcript Class:
WH. With homology to a known non-transposable element in the NR (non-redundant) database at GenBank. Protein-coding gene.
NH. No homology in the NR (non-redundant) database at GenBank. Hypothetical gene or pseudogene.
TE. With homology to a known transposable element (TE) in the NR (non-redundant) database at GenBank. Transposable element.
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