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1 LOCUS AAAA02000000 50231 rc DNA linear PLN 11-MAR-2005
2 DEFINITION Oryza sativa (indica cultivar-group) whole genome shotgun
3 sequencing project.
4 ACCESSION AAAA00000000
5 VERSION AAAA00000000.2 GI:54362548
6 KEYWORDS WGS.
7 SOURCE Oryza sativa (indica cultivar-group)
8 ORGANISM Oryza sativa (indica cultivar-group)
9 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
10 Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
11 clade; Ehrhartoideae; Oryzeae; Oryza.
12 REFERENCE 1 (bases 1 to 50231)
13 AUTHORS Yu,J., Wang,J., Lin,W., Li,S., Li,H., Zhou,J., Ni,P., Dong,W.,
14 Hu,S., Zeng,C., Zhang,J., Zhang,Y., Li,R., Xu,Z., Li,S., Li,X.,
15 Zheng,H., Cong,L., Lin,L., Yin,J., Geng,J., Li,G., Shi,J., Liu,J.,
16 Lv,H., Li,J., Wang,J., Deng,Y., Ran,L., Shi,X., Wang,X., Wu,Q.,
17 Li,C., Ren,X., Wang,J., Wang,X., Li,D., Liu,D., Zhang,X., Ji,Z.,
18 Zhao,W., Sun,Y., Zhang,Z., Bao,J., Han,Y., Dong,L., Ji,J., Chen,P.,
19 Wu,S., Liu,J., Xiao,Y., Bu,D., Tan,J., Yang,L., Ye,C., Zhang,J.,
20 Xu,J., Zhou,Y., Yu,Y., Zhang,B., Zhuang,S., Wei,H., Liu,B., Lei,M.,
21 Yu,H., Li,Y., Xu,H., Wei,S., He,X., Fang,L., Zhang,Z., Zhang,Y.,
22 Huang,X., Su,Z., Tong,W., Li,J., Tong,Z., Li,S., Ye,J., Wang,L.,
23 Fang,L., Lei,T., Chen,C., Chen,H., Xu,Z., Li,H., Huang,H.,
24 Zhang,F., Xu,H., Li,N., Zhao,C., Li,S., Dong,L., Huang,Y., Li,L.,
25 Xi,Y., Qi,Q., Li,W., Zhang,B., Hu,W., Zhang,Y., Tian,X., Jiao,Y.,
26 Liang,X., Jin,J., Gao,L., Zheng,W., Hao,B., Liu,S., Wang,W.,
27 Yuan,L., Cao,M., McDermott,J., Samudrala,R., Wang,J., Wong,G.K. and
28 Yang,H.
29 TITLE The Genomes of Oryza sativa: A History of Duplications
30 JOURNAL PLoS Biol. 3 (2), E38 (2005)
31 PUBMED 15685292
32 REFERENCE 2 (bases 1 to 50231)
33 AUTHORS Yu,J., Hu,S., Wang,J., Li,S., Wong,K.-S.G., Liu,B., Deng,Y.,
34 Dai,L., Zhou,Y., Zhang,X., Cao,M., Liu,J., Sun,J., Tang,J.,
35 Chen,Y., Huang,X., Lin,W., Ye,C., Tong,W., Cong,L., Geng,J.,
36 Han,Y., Li,L., Li,W., Hu,G., Huang,X., Li,W., Li,J., Liu,Z., Li,L.,
37 Liu,J., Qi,Q., Liu,J., Li,L., Wang,X., Lu,H., Wu,T., Zhu,M., Ni,P.,
38 Han,H., Dong,W., Ren,X., Feng,X., Cui,P., Li,X., Wang,H., Xu,X.,
39 Zhai,W., Xu,Z., Zhang,J., He,S., Zhang,J., Xu,J., Zhang,K.,
40 Zheng,X., Dong,J., Zeng,W., Tao,L., Chen,X., He,J., Liu,D.,
41 Tian,W., Tian,C., Xia,H., Li,G., Gao,H., Li,P., Chen,W., Wang,X.,
42 Zhang,Y., Hu,J., Wang,J., Liu,S., Yang,J., Zhang,G., Bao,Q.,
43 Xiong,Y., Li,Z., Mao,L., Zhou,C., Chen,R., Zhu,Z., Hao,B.,
44 Zheng,W., Chen,S., Guo,W., Li,G., Liu,S., Huang,G., Tao,M.,
45 Wang,J., Zhu,L., Yuan,L. and Yang,H.
46 TITLE Direct Submission
47 JOURNAL Submitted (04-JAN-2002) Beijing Genomics Institute/Center of
48 Genomics & Bioinformatics, Institute of Genomics, Chinese Academy
49 of Sciences, Beijing Airport Industrial Zone B6, Beijing, Beijing
50 101300, P.R.China
51 REFERENCE 3 (bases 1 to 50231)
52 AUTHORS Yu,J., Wang,J., Lin,W., Li,S., Li,H., Zhou,J., Ni,P., Dong,W.,
53 Hu,S., Zeng,C., Zhang,J., Zhang,Y., Li,R., Xu,Z., Li,S., Li,X.,
54 Zheng,H., Cong,L., Lin,L., Yin,J., Geng,J., Li,G., Shi,J., Liu,J.,
55 Lv,H., Li,J., Wang,J., Deng,Y., Ran,L., Shi,X., Wang,X., Wu,Q.,
56 Li,C., Ren,X., Wang,J., Wang,X., Li,D., Liu,D., Zhang,X., Ji,Z.,
57 Zhao,W., Sun,Y., Zhang,Z., Bao,J., Han,Y., Dong,L., Ji,J., Chen,P.,
58 Wu,S., Liu,J., Xiao,Y., Bu,D., Tan,J., Yang,L., Ye,C., Zhang,J.,
59 Xu,J., Zhou,Y., Yu,Y., Zhang,B., Zhuang,S., Wei,H., Liu,B., Lei,M.,
60 Yu,H., Li,Y., Xu,H., Wei,S., He,X., Fang,L., Zhang,Z., Zhang,Y.,
61 Huang,X., Su,Z., Tong,W., Li,J., Tong,Z., Li,S., Ye,J., Wang,L.,
62 Fang,L., Lei,T., Chen,C., Chen,H., Xu,Z., Li,H., Huang,H.,
63 Zhang,F., Xu,H., Li,N., Zhao,C., Li,S., Dong,L., Huang,Y., Li,L.,
64 Xi,Y., Qi,Q., Li,W., Zhang,B., Hu,W., Zhang,Y., Zheng,W., Hao,B.,
65 Liu,S., Wang,W., Yuan,L., Cao,M.L., McDermott,J., Samudrala,R.,
66 Wang,J., Wong,G.K.-S. and Yang,H.
67 TITLE Direct Submission
68 JOURNAL Submitted (12-SEP-2003) Beijing Institute of Genomics, Chinese
69 Academy of Sciences, Beijing Airport Industrial Zone B6, Beijing,
70 Beijing 101300, P.R.China
71 COMMENT On Oct 21, 2004 this sequence version replaced gi:19924305.
72 The Oryza sativa (indica cultivar-group) whole genome shotgun (WGS)
73 project has the project accession AAAA00000000. This version of
74 the project (02) has the accession number AAAA02000000, and
75 consists of sequences AAAA02000001-AAAA02050231.
76 The improved whole-genome shotgun (WGS) sequences for the genomes
77 of indica and japonica rice, AAAA02000000 and AACV01000000,
78 respectively, have multi-megabase contiguity and are nearly
79 1000-fold improved over the drafts of 2002. Tested against a
80 non-redundant collection of 19,079 full-length cDNAs, 98.1% of the
81 genes are aligned without fragmentation to the mapped
82 super-scaffolds of one or the other genome. Despite having only a
83 small variation in gene content, there is an enormous variation in
84 intergenic regions. At least a quarter of the two sequences could
85 not be aligned, and in the aligned region
86 single-nucleotide-polymorphism (SNP) rates varied from as little as
87 3.0 SNP/kb in the coding regions, to 27.6 SNP/kb in the
88 transposable elements.
89 FEATURES Location/Qualifiers
90 source 1..50231
91 /organism="Oryza sativa (indica cultivar-group)"
92 /mol_type="genomic DNA"
93 /cultivar="93-11"
94 /db_xref="taxon:39946"
95 WGS AAAA02000001-AAAA02050231
96 WGS_SCAFLD CM000126-CM000137
97 WGS_SCAFLD CH398081-CH401163
98 //