ID CH398139; SV 1; linear; genomic DNA; CON; PLN; 1067259 BP. XX AC CH398139; XX PR Project:PRJNA361; XX DT 21-DEC-2004 (Rel. 82, Created) DT 18-APR-2005 (Rel. 83, Last updated, Version 2) XX DE Oryza sativa Indica Group chromosome 6 scaffold000059 genomic scaffold, DE whole genome shotgun sequence. XX KW . XX OS Oryza sativa Indica Group (long-grained rice) OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa. XX RN [1] RP 1-1067259 RX DOI; 10.1371/journal.pbio.0030038. RX PUBMED; 15685292. RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L., RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., RA Fang L., Lei T., Chen C., Chen H., Xu Z., Li H., Huang H., Zhang F., Xu H., RA Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., RA Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., RA Zheng W., Hao B., Liu S., Wang W., Yuan L., Cao M., McDermott J., RA Samudrala R., Wang J., Wong G.K., Yang H.; RT "The Genomes of Oryza sativa: A History of Duplications"; RL PLoS Biol. 3(2):E38-E38(2005). XX RN [2] RP 1-1067259 RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L., RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., RA Fang L., Lei T., Chen C., Chen H., Xu Z., Li H., Huang H., Zhang F., Xu H., RA Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., RA Zhang B., Hu W., Zhang Y., Zheng W., Hao B., Liu S., Wang W., Yuan L., RA Cao M.L., McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.; RT ; RL Submitted (12-SEP-2003) to the INSDC. RL Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing Airport RL Industrial Zone B6, Beijing, Beijing 101300, P.R.China XX DR MD5; 4100a5accef23d3d0850d07d5c46ac81. DR ENA; AAAA02000000; SET. DR ENA; AAAA00000000; SET. DR ENA-CON; CM000131. DR BioSample; SAMN02953581. XX CC The improved whole-genome shotgun (WGS) sequences for the genomes CC of indica and japonica rice, AAAA02000000 and AACV01000000, CC respectively, have multi-megabase contiguity and are nearly CC 1000-fold improved over the drafts of 2002. Tested against a CC non-redundant collection of 19,079 full-length cDNAs, 98.1% of the CC genes are aligned without fragmentation to the mapped CC super-scaffolds of one or the other genome. Despite having only a CC small variation in gene content, there is an enormous variation in CC intergenic regions. At least a quarter of the two sequences could CC not be aligned, and in the aligned region CC single-nucleotide-polymorphism (SNP) rates varied from as little as CC 3.0 SNP/kb in the coding regions, to 27.6 SNP/kb in the CC transposable elements. XX FH Key Location/Qualifiers FH FT source 1..1067259 FT /organism="Oryza sativa Indica Group" FT /chromosome="6" FT /cultivar="93-11" FT /mol_type="genomic DNA" FT /db_xref="taxon:39946" FT assembly_gap 604..703 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 3764..3863 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 17368..17417 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 18838..18887 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 54883..54932 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 69452..69551 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 73854..73903 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 75031..75080 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 97144..97193 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 101923..101972 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 102937..103036 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 103846..103895 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 105852..105901 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 113678..113727 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 115568..115617 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 117337..117386 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 155589..155638 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 156900..156949 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 160325..170324 FT /estimated_length=10000 FT /gap_type="unknown" FT assembly_gap 179102..179201 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 181341..181390 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 182744..282743 FT /estimated_length=100000 FT /gap_type="unknown" FT assembly_gap 283571..283670 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 298848..298947 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 302740..302789 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 304102..304151 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 306877..306926 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 334362..334411 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 336484..336533 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 337590..337639 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 338582..338631 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 339391..339440 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 356753..356852 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 366216..366265 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 370155..370204 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 371193..381192 FT /estimated_length=10000 FT /gap_type="unknown" FT assembly_gap 401008..401057 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 402487..402536 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 407032..407131 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 416191..416290 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 417516..417615 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 423887..423986 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 439186..439235 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 441703..441752 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 442603..452602 FT /estimated_length=10000 FT /gap_type="unknown" FT assembly_gap 476077..476176 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 478612..478661 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 479488..479537 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 481047..481146 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 482783..482832 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 484716..494715 FT /estimated_length=10000 FT /gap_type="unknown" FT assembly_gap 495406..495455 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 497171..497220 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 543616..543665 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 544970..545069 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 546254..546303 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 548234..548283 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 549786..549835 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 550764..550813 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 597039..597088 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 599021..599070 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 601366..601415 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 631219..631268 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 632043..632092 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 641163..641262 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 654886..654935 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 656333..657332 FT /estimated_length=1000 FT /gap_type="unknown" FT assembly_gap 659065..659164 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 677697..677746 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 678495..678544 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 679523..679572 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 685957..686006 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 687731..687780 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 689087..689136 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 690114..690213 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 691845..691894 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 730052..730101 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 731612..731661 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 732699..742698 FT /estimated_length=10000 FT /gap_type="unknown" FT assembly_gap 744379..754378 FT /estimated_length=10000 FT /gap_type="unknown" FT assembly_gap 754986..755035 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 788085..788134 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 803814..803863 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 804700..804749 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 806783..806832 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 807591..807640 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 811337..811386 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 824971..825020 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 827677..827726 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 828652..828701 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 829901..829950 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 831366..831415 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 843612..843711 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 844776..844825 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 845674..845723 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 883636..883685 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 884513..884562 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 885512..885611 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 886656..886705 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 897076..907075 FT /estimated_length=10000 FT /gap_type="unknown" FT assembly_gap 907806..907855 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 955840..965839 FT /estimated_length=10000 FT /gap_type="unknown" FT assembly_gap 970465..970564 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 973507..973556 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 974801..974850 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 976274..976323 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 986375..986474 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 995733..995782 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 996711..996760 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 997987..998086 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 999641..999690 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 1003181..1003230 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 1004271..1004370 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 1006065..1006114 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 1006963..1007062 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 1032261..1032310 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 1034081..1034130 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 1035937..1035986 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 1037313..1037362 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 1038009..1038058 FT /estimated_length=50 FT /gap_type="unknown" FT assembly_gap 1040802..1040901 FT /estimated_length=100 FT /gap_type="unknown" FT assembly_gap 1041581..1051580 FT /estimated_length=10000 FT /gap_type="unknown" XX CO join(AAAA02018828.1:1..603,gap(100),AAAA02018829.1:1..3060,gap(100), CO complement(AAAA02018830.1:1..13504),gap(50), CO complement(AAAA02018831.1:1..1420),gap(50),AAAA02018832.1:1..35995,gap(50), CO AAAA02018833.1:1..14519,gap(100),AAAA02018834.1:1..4302,gap(50), CO complement(AAAA02018835.1:1..1127),gap(50),AAAA02018836.1:1..22063,gap(50), CO complement(AAAA02018837.1:1..4729),gap(50),AAAA02018838.1:1..964,gap(100), CO complement(AAAA02018839.1:1..809),gap(50),AAAA02018840.1:1..1956,gap(50), CO complement(AAAA02018841.1:1..7776),gap(50),AAAA02018842.1:1..1840,gap(50), CO complement(AAAA02018843.1:1..1719),gap(50),AAAA02018844.1:1..38202,gap(50), CO AAAA02018845.1:1..1261,gap(50),complement(AAAA02018846.1:1..3375), CO gap(10000),AAAA02018847.1:1..8777,gap(100),AAAA02018848.1:1..2139,gap(50), CO complement(AAAA02018849.1:1..1353),gap(100000),AAAA02018850.1:1..827, CO gap(100),AAAA02018851.1:1..15177,gap(100), CO complement(AAAA02018852.1:1..3792),gap(50), CO complement(AAAA02018853.1:1..1312),gap(50), CO complement(AAAA02018854.1:1..2725),gap(50),AAAA02018855.1:1..27435,gap(50), CO complement(AAAA02018856.1:1..2072),gap(50), CO complement(AAAA02018857.1:1..1056),gap(50), CO complement(AAAA02018858.1:1..942),gap(50),AAAA02018859.1:1..759,gap(50), CO AAAA02018860.1:1..17312,gap(100),complement(AAAA02018861.1:1..9363), CO gap(50),AAAA02018862.1:1..3889,gap(50),AAAA02018863.1:1..988,gap(10000), CO AAAA02018864.1:1..19815,gap(50),AAAA02018865.1:1..1429,gap(50), CO AAAA02018866.1:1..4495,gap(100),complement(AAAA02018867.1:1..9059), CO gap(100),AAAA02018868.1:1..1225,gap(100),AAAA02018869.1:1..6271,gap(100), CO AAAA02018870.1:1..15199,gap(50),complement(AAAA02018871.1:1..2467),gap(50), CO AAAA02018872.1:1..850,gap(10000),AAAA02018873.1:1..23474,gap(100), CO AAAA02018874.1:1..2435,gap(50),complement(AAAA02018875.1:1..826),gap(50), CO AAAA02018876.1:1..1509,gap(100),AAAA02018877.1:1..1636,gap(50), CO complement(AAAA02018878.1:1..1883),gap(10000), CO complement(AAAA02018879.1:1..690),gap(50),AAAA02018880.1:1..1715,gap(50), CO complement(AAAA02018881.1:1..46395),gap(50), CO complement(AAAA02018882.1:1..1304),gap(100), CO complement(AAAA02018883.1:1..1184),gap(50), CO complement(AAAA02018884.1:1..1930),gap(50),AAAA02018885.1:1..1502,gap(50), CO complement(AAAA02018886.1:1..928),gap(50), CO complement(AAAA02018887.1:1..46225),gap(50),AAAA02018888.1:1..1932,gap(50), CO complement(AAAA02018889.1:1..2295),gap(50),AAAA02018890.1:1..29803,gap(50), CO complement(AAAA02018891.1:1..774),gap(50),AAAA02018892.1:1..9070,gap(100), CO AAAA02018893.1:1..13623,gap(50),complement(AAAA02018894.1:1..1397), CO gap(1000),AAAA02018895.1:1..1732,gap(100), CO complement(AAAA02018896.1:1..18532),gap(50), CO complement(AAAA02018897.1:1..748),gap(50),AAAA02018898.1:1..978,gap(50), CO complement(AAAA02018899.1:1..6384),gap(50), CO complement(AAAA02018900.1:1..1724),gap(50), CO complement(AAAA02018901.1:1..1306),gap(50),AAAA02018902.1:1..977,gap(100), CO complement(AAAA02018903.1:1..1631),gap(50), CO complement(AAAA02018904.1:1..38157),gap(50), CO complement(AAAA02018905.1:1..1510),gap(50),AAAA02018906.1:1..1037, CO gap(10000),complement(AAAA02018907.1:1..1680),gap(10000), CO AAAA02018908.1:1..607,gap(50),AAAA02018909.1:1..33049,gap(50), CO complement(AAAA02018910.1:1..15679),gap(50), CO complement(AAAA02018911.1:1..836),gap(50), CO complement(AAAA02018912.1:1..2033),gap(50), CO complement(AAAA02018913.1:1..758),gap(50), CO complement(AAAA02018914.1:1..3696),gap(50),AAAA02018915.1:1..13584,gap(50), CO complement(AAAA02018916.1:1..2656),gap(50), CO complement(AAAA02018917.1:1..925),gap(50), CO complement(AAAA02018918.1:1..1199),gap(50),AAAA02018919.1:1..1415,gap(50), CO complement(AAAA02018920.1:1..12196),gap(100), CO complement(AAAA02018921.1:1..1064),gap(50),AAAA02018922.1:1..848,gap(50), CO complement(AAAA02018923.1:1..37912),gap(50),AAAA02018924.1:1..827,gap(50), CO AAAA02018925.1:1..949,gap(100),complement(AAAA02018926.1:1..1044),gap(50), CO complement(AAAA02018927.1:1..10370),gap(10000), CO complement(AAAA02018928.1:1..730),gap(50), CO complement(AAAA02018929.1:1..47984),gap(10000), CO complement(AAAA02018930.1:1..4625),gap(100), CO complement(AAAA02018931.1:1..2942),gap(50),AAAA02018932.1:1..1244,gap(50), CO complement(AAAA02018933.1:1..1423),gap(50), CO complement(AAAA02018934.1:1..10051),gap(100),AAAA02018935.1:1..9258, CO gap(50),AAAA02018936.1:1..928,gap(50),complement(AAAA02018937.1:1..1226), CO gap(100),AAAA02018938.1:1..1554,gap(50),AAAA02018939.1:1..3490,gap(50), CO AAAA02018940.1:1..1040,gap(100),complement(AAAA02018941.1:1..1694),gap(50), CO AAAA02018942.1:1..848,gap(100),complement(AAAA02018943.1:1..25198),gap(50), CO complement(AAAA02018944.1:1..1770),gap(50), CO complement(AAAA02018945.1:1..1806),gap(50),AAAA02018946.1:1..1326,gap(50), CO AAAA02018947.1:1..646,gap(50),AAAA02018948.1:1..2743,gap(100), CO complement(AAAA02018949.1:1..679),gap(10000), CO complement(AAAA02018950.1:1..15679)) //