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Gene Annotation Overview

    Japonica group cultivar Nip and Indica group cultivar 93-11 are the two main cultivated varieties and parental lines for breeding in Asia. This database provides a vastly improved de novo assembly and annotation of Nip and 93-11 reference genomes using SMRT-seq technique. The newly assembled Nip and 93-11 reference genomes displayed 2.2-fold (contig N50: 16,974kb versus 7,711kb) and 460-fold (9,640kb versus 21kb) higher contiguity than Nip MSU7 (http://rice.plantbiology.msu.edu/index.shtml) and 93-11 BGI (http://rise2.genomics.org.cn/page/rice/index.jsp) genomes, respectively. The new reference assembly has greatly reduced the gap number, from 905 gaps of MSU7 to 18 gaps of BRI for Nip, and 54,600 gaps of BGI to 65 gaps of BRI for 93-11. The new genome assemblies corrected 152 and 8,347 gene annotation errors in Nip and 93-11, respectively, including corrections of gene orientation and gene structure, and identified a number of new genes.

 Locus Search:

Please entry the locus identifier
(e.g. LOC_Os10g07270)

 Function Search:

Please entry the keyword
(e.g. demethylase)
 

Feature

Nip-BRI

93-11-BRI

Genome size (bp)

380,697,840

395,529,940

Contig number

146

195

Gap number

18

65

Gap ratio (%)

0.0005

0.0016

GC content (%)

43.54

43.64

Gene number

39,251

38,504

Gene length (bp)

111,836,585

116,600,764

Average gene length (bp)

2,849.27

3,028.28

CDS length (bp)

42,283,449

43,045,962

CDS length/gene (bp)

1,077.26

1,117.96

Orientation correction

26

1,300

Structure correction

55

1,318

Orientation & structure correction

3

219

New genes

68

5,510

Common genes

38,789

31,458

Improved Nip and 93-11 Genomes
 
 

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