LOCUS AAAA02000591 1690 bp DNA linear PLN 21-OCT-2004
DEFINITION Oryza sativa Indica Group cultivar 93-11 chromosome 1 Ctg000591,
whole genome shotgun sequence.
ACCESSION AAAA02000591 AAAA02000000
VERSION AAAA02000591.1
DBLINK BioProject: PRJNA361
BioSample: SAMN02953581
KEYWORDS WGS.
SOURCE Oryza sativa Indica Group (long-grained rice)
ORGANISM Oryza sativa Indica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP
clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
REFERENCE 1 (bases 1 to 1690)
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. and
Yang,H.
TITLE The Genomes of Oryza sativa: a history of duplications
JOURNAL PLoS Biol. 3 (2), E38 (2005)
PUBMED 15685292
REFERENCE 2 (bases 1 to 1690)
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. and Yang,H.
TITLE Direct Submission
JOURNAL 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
REFERENCE 3 (bases 1 to 1690)
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. and Yang,H.
TITLE Direct Submission
JOURNAL Submitted (12-SEP-2003) Beijing Institute of Genomics, Chinese
Academy of Sciences, Beijing Airport Industrial Zone B6, Beijing,
Beijing 101300, P.R.China
REFERENCE 4 (bases 1 to 1690)
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. and Yang,H.
TITLE Direct Submission
JOURNAL Submitted (25-FEB-2011) Beijing Institute of Genomics, Chinese
Academy of Sciences, Beijing Airport Industrial Zone B6, Beijing,
Beijing 101300, P.R.China
COMMENT 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.
FEATURES Location/Qualifiers
source 1..1690
/organism="Oryza sativa Indica Group"
/mol_type="genomic DNA"
/cultivar="93-11"
/db_xref="taxon:39946"
/chromosome="1"
ORIGIN
1 gtactgatgt acttaataat actactagaa ttctagaaat gtgacaatta tctgtggaca
61 catccgtcaa catattagtt ttcactagtg ctactatatg ctggctatta ctagtttaat
121 actccatcta acacatcaac ataaacaaca tctggtatgt aaatccttta gtgattccta
181 ttggttcccc agtatggtat ttatcagttc atcataaggt gaacttatat ttggatatat
241 ttgatatact ccataaccga gttaataaat actgtcacag aacacgtaca aatctgtaaa
301 atggaaattt gaagtcattg tttttttaca ttaattctat ataattattt taggggtaat
361 attatttgtg atgctctgtt taaagttgta taacattaat ttctttgtga tgttcaacag
421 agattgttcc aacaatgttg taataatatt tcgtttagat gtactaatta ttaccacaag
481 aaattatata tgtccgttta tctcgaactc tatatgctga cctaataatg ttctattttc
541 atgagcatcc tatatttcta tgaagacatg ttgtaaagct actctacatt gattggtagt
601 ctttcatgag tagggatttg tattccctcc gtcccaaaat gtcccaaaat ataagtattt
661 ttagcattgc gaaaagtcaa acatttttaa ttttgaccat taataacaaa aaaaaaagat
721 taatcatgta aaattgatgt tagcggattt atcattaaac aaactattat aatatgtaaa
781 tatttttatt taaaatatct cggagaccgt gacgtggttt taaaaatact tatattttga
841 ggcggaggag gtaccttgtt aaccatctgc ttttagtcat tcatataatt tgtttcaact
901 tgttcaccat ccttttcata aactacaaaa tggagtacca atttctgagg catttttttt
961 tctgagacgt cttttctcgg gtgattgcag gtatgcagcc cgtgactaga cagggtctgc
1021 ttgttgagct gcagctctct ctaaaattat tttccgttgc ttgggtcgtt gttttaaaat
1081 tgcctttcag agattttatc tcatcttggg taggtatata tacctactca tcatttatat
1141 atagaggtgc cttgtgtgaa gggagatact aaaactaatc ttttgaatgg gactcgtgag
1201 agtggattgg aaattcatct ttatatctat ttttgagttt tcttcagccc ttgaaaggat
1261 atgtatagga ggtatatata tacctttggg gttattctat atctcaccag aaaattttca
1321 cattgtaaac catgtactta cttttgttct aaacaattta atcggtttaa tttttgattt
1381 actttttttt atcttttaaa taatgtggat atatatatat atatatacct tctcaaggat
1441 aggttacaag ttaattagta caactagttt tttattagca actgacacag gggcttagtt
1501 tttcagatca ttcacataaa tgctactcct aattaagctt gtttaaaata gaatagcacc
1561 gaaagtttgt tgttattggg agagtttacc atcaggagag agagagagag agagagagag
1621 agagagagag agagagaaag aaaatgcagc gtcgctggag ccctatgcgg ccatgtccat
1681 ctattatcat
//