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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.

(see a sample sequence query)

Examples: bz1, bronze1, GRMZM2G165390, GRMZM2G165390_T01, GRMZM2G165390_P01 , AC195466.3_FG002, AC195466.3_FGT002, AC195466.3_FGP002 .


Download by Chromosome (B73 RefGen_v2)

   Chromosome:       Model type:      Transcript type:      Output type:     

Download by Gene Model List (B73 RefGen_v2)

When downloading sequence please specify which type of input you are entering. For genomic please use the gene model name (e.g. GRMZM2G165390). For cDNA, CDS, and mRNA please use the transcript ID (e.g. GRMZM2G165390_T01). For protein please use the translation ID (e.g. GRMZM2G165390_P01). If you enter only the gene model ID, please choose if you want to see all transcripts or only the canonical transcripts.

   Enter list (one per line) - 8,000 gene model limit:  
   
   (Example list)

   Input type:      Output type:      Model type:  

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

ChromosomeWorking Gene set (WGS) countWGS Transcript countFiltered gene set (FGS) model countFGS 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 FeatureValue
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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Last updated 1:43 pm, Dec 03, 2014.

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