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Sequence Set Browser

 

AAAA00000000.2 Oryza sativa Indica Group

Master
# of Contigs: 50,231
# of Proteins: 37,358
# of Scaffolds: 3,095
Total length: 410,679,186 bp
BioProject: PRJNA361
BioSample: SAMN02953581
Keywords: WGS
Annotation: Scaffolds
Organism: Oryza sativa Indica Groupshow lineagehide lineage
Biosource:
/cultivar = 93-11
/mol_type = genomic genomic
WGS: AAAA02000001:AAAA02050231
Scaffolds: CH398081:CH401163, CM000126:CM000137
3,095 scaffolds, 37,358 proteins, total length is 769,683,080 bases
Reference:
The Genomes of Oryza sativa: a history of duplications : PLoS Biol. 3 (2), E38 (2005) – show 117 authorshide authors
Yu,J., Wang,J., Lin,W., Li,S., Li,H., Zhou,J., Ni,P., Dong,W., Hu,S., Zeng,C., Zhang,J., Zhang,Y., Li,R., Xu,Z., Li,S., Li,X., Zheng,H., Cong,L., Lin,L., Yin,J., Geng,J., Li,G., Shi,J., Liu,J., Lv,H., Li,J., Wang,J., Deng,Y., Ran,L., Shi,X., Wang,X., Wu,Q., Li,C., Ren,X., Wang,J., Wang,X., Li,D., Liu,D., Zhang,X., Ji,Z., Zhao,W., Sun,Y., Zhang,Z., Bao,J., Han,Y., Dong,L., Ji,J., Chen,P., Wu,S., Liu,J., Xiao,Y., Bu,D., Tan,J., Yang,L., Ye,C., Zhang,J., Xu,J., Zhou,Y., Yu,Y., Zhang,B., Zhuang,S., Wei,H., Liu,B., Lei,M., Yu,H., Li,Y., Xu,H., Wei,S., He,X., Fang,L., Zhang,Z., Zhang,Y., Huang,X., Su,Z., Tong,W., Li,J., Tong,Z., Li,S., Ye,J., Wang,L., Fang,L., Lei,T., Chen,C., Chen,H., Xu,Z., Li,H., Huang,H., Zhang,F., Xu,H., Li,N., Zhao,C., Li,S., Dong,L., Huang,Y., Li,L., Xi,Y., Qi,Q., Li,W., Zhang,B., Hu,W., Zhang,Y., Tian,X., Jiao,Y., Liang,X., Jin,J., Gao,L., Zheng,W., Hao,B., Liu,S., Wang,W., Yuan,L., Cao,M., McDermott,J., Samudrala,R., Wang,J., Wong,G.K., Yang,H.
Submission:
Submitted (04-JAN-2002) Beijing Genomics Institute/Center of Genomics & Bioinformatics, Institute of Genomics, Chinese Academy of Sciences, Beijing Airport Industrial Zone B6, Beijing, Beijing 101300, P.R.China – show 94 authorshide authors
Yu,J., Hu,S., Wang,J., Li,S., Wong,K.-S.G., Liu,B., Deng,Y., Dai,L., Zhou,Y., Zhang,X., Cao,M., Liu,J., Sun,J., Tang,J., Chen,Y., Huang,X., Lin,W., Ye,C., Tong,W., Cong,L., Geng,J., Han,Y., Li,L., Li,W., Hu,G., Huang,X., Li,W., Li,J., Liu,Z., Li,L., Liu,J., Qi,Q., Liu,J., Li,L., Wang,X., Lu,H., Wu,T., Zhu,M., Ni,P., Han,H., Dong,W., Ren,X., Feng,X., Cui,P., Li,X., Wang,H., Xu,X., Zhai,W., Xu,Z., Zhang,J., He,S., Zhang,J., Xu,J., Zhang,K., Zheng,X., Dong,J., Zeng,W., Tao,L., Chen,X., He,J., Liu,D., Tian,W., Tian,C., Xia,H., Li,G., Gao,H., Li,P., Chen,W., Wang,X., Zhang,Y., Hu,J., Wang,J., Liu,S., Yang,J., Zhang,G., Bao,Q., Xiong,Y., Li,Z., Mao,L., Zhou,C., Chen,R., Zhu,Z., Hao,B., Zheng,W., Chen,S., Guo,W., Li,G., Liu,S., Huang,G., Tao,M., Wang,J., Zhu,L., Yuan,L., Yang,H.
Submission:
Submitted (12-SEP-2003) Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing Airport Industrial Zone B6, Beijing, Beijing 101300, P.R.China – show 112 authorshide authors
Yu,J., Wang,J., Lin,W., Li,S., Li,H., Zhou,J., Ni,P., Dong,W., Hu,S., Zeng,C., Zhang,J., Zhang,Y., Li,R., Xu,Z., Li,S., Li,X., Zheng,H., Cong,L., Lin,L., Yin,J., Geng,J., Li,G., Shi,J., Liu,J., Lv,H., Li,J., Wang,J., Deng,Y., Ran,L., Shi,X., Wang,X., Wu,Q., Li,C., Ren,X., Wang,J., Wang,X., Li,D., Liu,D., Zhang,X., Ji,Z., Zhao,W., Sun,Y., Zhang,Z., Bao,J., Han,Y., Dong,L., Ji,J., Chen,P., Wu,S., Liu,J., Xiao,Y., Bu,D., Tan,J., Yang,L., Ye,C., Zhang,J., Xu,J., Zhou,Y., Yu,Y., Zhang,B., Zhuang,S., Wei,H., Liu,B., Lei,M., Yu,H., Li,Y., Xu,H., Wei,S., He,X., Fang,L., Zhang,Z., Zhang,Y., Huang,X., Su,Z., Tong,W., Li,J., Tong,Z., Li,S., Ye,J., Wang,L., Fang,L., Lei,T., Chen,C., Chen,H., Xu,Z., Li,H., Huang,H., Zhang,F., Xu,H., Li,N., Zhao,C., Li,S., Dong,L., Huang,Y., Li,L., Xi,Y., Qi,Q., Li,W., Zhang,B., Hu,W., Zhang,Y., Zheng,W., Hao,B., Liu,S., Wang,W., Yuan,L., Cao,M.L., McDermott,J., Samudrala,R., Wang,J., Wong,G.K.-S., Yang,H.
Submission:
Submitted (25-FEB-2011) Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing Airport Industrial Zone B6, Beijing, Beijing 101300, P.R.China – show 112 authorshide authors
Yu,J., Wang,J., Lin,W., Li,S., Li,H., Zhou,J., Ni,P., Dong,W., Hu,S., Zeng,C., Zhang,J., Zhang,Y., Li,R., Xu,Z., Li,S., Li,X., Zheng,H., Cong,L., Lin,L., Yin,J., Geng,J., Li,G., Shi,J., Liu,J., Lv,H., Li,J., Wang,J., Deng,Y., Ran,L., Shi,X., Wang,X., Wu,Q., Li,C., Ren,X., Wang,J., Wang,X., Li,D., Liu,D., Zhang,X., Ji,Z., Zhao,W., Sun,Y., Zhang,Z., Bao,J., Han,Y., Dong,L., Ji,J., Chen,P., Wu,S., Liu,J., Xiao,Y., Bu,D., Tan,J., Yang,L., Ye,C., Zhang,J., Xu,J., Zhou,Y., Yu,Y., Zhang,B., Zhuang,S., Wei,H., Liu,B., Lei,M., Yu,H., Li,Y., Xu,H., Wei,S., He,X., Fang,L., Zhang,Z., Zhang,Y., Huang,X., Su,Z., Tong,W., Li,J., Tong,Z., Li,S., Ye,J., Wang,L., Fang,L., Lei,T., Chen,C., Chen,H., Xu,Z., Li,H., Huang,H., Zhang,F., Xu,H., Li,N., Zhao,C., Li,S., Dong,L., Huang,Y., Li,L., Xi,Y., Qi,Q., Li,W., Zhang,B., Hu,W., Zhang,Y., Zheng,W., Hao,B., Liu,S., Wang,W., Yuan,L., Cao,M.L., McDermott,J., Samudrala,R., Wang,J., Wong,G.K.-S., Yang,H.

On Oct 21, 2004 this sequence version replaced gi:19924305.

The Oryza sativa Indica Group whole genome shotgun (WGS) project has the project accession AAAA00000000. This version of the project (02) has the accession number AAAA02000000, and consists of sequences AAAA02000001-AAAA02050231.

The improved whole-genome shotgun (WGS) sequences for the genomes of indica and japonica rice, AAAA02000000 and AACV01000000, respectively, have multi-megabase contiguity and are nearly 1000-fold improved over the drafts of 2002. Tested against a non-redundant collection of 19,079 full-length cDNAs, 98.1% of the genes are aligned without fragmentation to the mapped super-scaffolds of one or the other genome. Despite having only a small variation in gene content, there is an enormous variation in intergenic regions. At least a quarter of the two sequences could not be aligned, and in the aligned region single-nucleotide-polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions, to 27.6 SNP/kb in the transposable elements. Annotation was updated on the chromosomes, CM000126-CM000137, in December 2008 Contig AAAA02029393 was suppressed in Feb. 2011 because it may be a contaminant.

Contigs
Download
GenBank:AAAA02.1.gbff.gz 188.6 Mb
FASTA:AAAA02.1.fsa_nt.gz 120.6 Mb
ASN.1:AAAA02.1.bbs.gz 98.8 Mb