Gene_locus Report for: orysj-b9fi05Oryza sativa subsp. japonica subsp. indica (Rice) Os05g0179900 Putative uncharacterized protein Relationship
(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) There are 29 a/b hydrolases in Oryza sativa subsp. japonica view in a: Table
6_AlphaBeta_hydrolase : orysj-q0jhi5Oryza sativa subsp. japonica (Rice) os01g0862000 protein. ABHD18 : orysj-q6h7q9Oryza sativa (Rice) Oryza glaberrima (African rice),. Uncharacterized protein. BD-FAE : orysj-b9eya5Oryza sativa subsp. japonica, Oryza sativa subsp. indica (Rice) Oryza nivara (Indian wild rice); Oryza glumipatula Putative uncharacterized protein. Carboxypeptidase_S10 : orysj-q0dud7Oryza sativa subsp. japonica (Rice) Os03g0192100 protein. Duf_726 : orysj-q7xcx3Oryza sativa subsp. japonica (Rice) subsp. indica Putative uncharacterized protein. Duf_829 : orysj-q0d9a4Oryza sativa subsp. japonica (Rice) Os06g0730300 protein, orysj-q5z419Oryza sativa subsp. japonica (Rice) Integral membrane protein-like (Putative uncharacterized protein), orysj-q6z6i1Oryza sativa subsp. japonica indica (Rice) Putative uncharacterized protein P0030G11.19 (Os02g0133900 protein) (Putative uncharacterized protein P0585B01.4). Duf_1350 : orysj-q7f8x1Oryza sativa subsp. japonica (Rice) OJ000315_02.20 protein. Epoxide_hydrolase : orysj-q0djj0Oryza sativa subsp. japonica subsp. indica (Rice) cDNA clone:001-022-G09, full insert sequence. Glutamyl_Peptidase_S9 : orysj-cgepOryza sativa subsp. japonica (Rice); O. meridionalis; O. glumipatula; O. nivara (Indian wild rice); O. rufipogon (Brownbeard rice); O. glaberrima; O. barthii; O. brachyantha; O. punctata (Red rice). Probable glutamyl endopeptidase, chloroplastic. Haloperoxidase : orysj-b9gbb7Oryza sativa subsp. japonica (Rice) Putative uncharacterized protein. Hydroxynitrile_lyase : orysj-q0d4u5Oryza sativa (Rice), Oryza glaberrima (African rice, os07g0603600 protein (fragment), orysj-q0jga1Oryza sativa subsp. japonica subsp. indica (Rice) Os01g0934600 protein. Monoglyceridelipase_lysophospholip : orysj-b9eub8Oryza sativa subsp. japonica (Rice) Putative uncharacterized protein. NLS3-Tex30 : orysj-b9fn42Oryza sativa subsp. japonica subsp. indica (Rice) Oryza glaberrima (African rice), Oryza brachyantha, Putative uncharacterized protein. Pectinacetylesterase-Notum : orysj-b9fkb0Oryza sativa subsp. japonica (Rice) subsp. indica (Rice), Oryza glaberrima (African rice) Putative uncharacterized protein, orysj-q5jl22Oryza sativa subsp. japonica (Rice) subsp. indica (Rice); Oryza glaberrima (African rice) cDNA clone:002-101-G02, full insert sequence, orysj-q6yvk6Oryza sativa subsp. japonica (Rice) subsp. indica (Rice); Oryza glaberrima (African rice) cDNA clone:J013158P10 Putative uncharacterized protein, orysj-q65xv3Oryza sativa subsp. japonica (Rice) Putative uncharacterized protein P0016H04.15, orysj-q94d71Oryza sativa subsp. japonica (Rice) subsp. indica, Oryza glaberrima (African rice), Putative uncharacterized protein. Plant_carboxylesterase : orysj-q0iq98Oryza sativa subsp. japonica (Rice); Oryza glaberrima (African rice). Os12g0135800 protein, orysj-b9gbs4Oryza sativa subsp. japonica (Rice); Oryza glaberrima (African rice). Os11g0139000 protein, orysj-b9gbs1Oryza sativa subsp. japonica (Rice); Oryza rufipogon (Brownbeard rice) (Asian wild rice). Os12g0135500 protein, orysj-a0a0p0y6l9Oryza sativa subsp. japonica (Rice). Os12g0135500 protein. Plant_phospholipase : orysj-pla4Oryza sativa subsp. japonica (Rice). Phospholipase A1-II 4, orysj-pla1Oryza sativa subsp. japonica ; indica (Rice). Phospholipase A1-II 1. RsbQ-like : orysj-q10j20Oryza sativa subsp. japonica subsp. indica (Rice) High tillering - Dwarf D14 like OsDLK1 Orthologue of KAI2 putative hydrolases Warning: This entry is a compilation of different species or line or strain with more than 90% amino acide identity. You can retrieve all strain data
(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) Oryza sativa Japonica Group: N, E. Oryza sativa subsp. indica: N, E. Oryza sativa Indica Group: N, E.
Sequence
References 2 more
Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio BA, Nagamura Y and Sasaki T <4 more author(s)> Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio BA, Nagamura Y, Imanishi T, Ikeo K, Itoh T, Gojobori T, Sasaki T (- 4) Ref: Nucleic Acids Research, 34:D741, 2006 : PubMed ESTHER: Ohyanagi_2006_Nucleic.Acids.Res_34_D741 PubMedSearch: Ohyanagi 2006 Nucleic.Acids.Res 34 D741 PubMedID: 16381971 Gene_locus related to this paper: orysa-Q9FW17, orysa-Q0JK71, orysa-B9EWJ8, orysa-Q5N7L1, orysa-Q5N7J6, orysa-pir7a, orysa-q2qyi1, orysa-q2qyj1, orysa-q2rbb3, orysj-q6yse8, orysa-q6yzk1, orysa-Q8S0U8, orysa-Q84ZY8, orysa-Q0J0A4, orysi-a2z179, orysi-a2zef2, orysi-b8a7e6, orysi-b8a7e7, orysi-b8bfe5, orysi-b8bhp9, orysj-b9fi05, orysj-q0d4u5, orysj-q0djj0, orysj-q0jaf0, orysj-q0jga1, orysj-q0jhi5, orysj-q5jl22, orysj-q5jlw7, orysj-q6h7q9, orysj-q6yvk6, orysj-q7f8x1, orysj-q7xcx3, orysj-q9fwm6, orysj-q10j20, orysj-q10ss2, orysj-q69uw6, orysj-q94d71, orysj-q0iq98, orysj-b9gbs4, orysj-b9gbs1 Abstract With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through http://rapdb.lab.nig.ac.jp/. Title: The map-based sequence of the rice genome. Matsumo T, Sasaki T Ref: Nature, 436:793, 2005 : PubMed ESTHER: Matsumoto_2005_Nature_436_793 PubMedSearch: Matsumoto 2005 Nature 436 793 PubMedID: 16100779 Gene_locus related to this paper: orysa-Q9FRJ0, orysa-Q7XTC5, orysa-Q852M6, orysa-Q8GSE8, orysa-Q9FYP7, orysa-Q5ZBH3, orysa-Q5ZA26, orysa-Q5JLP6, orysa-Q8H5P5, orysa-Q7F1Y5, orysa-Q949C9, orysa-cbp3, orysa-cbpx, orysa-Q6YSZ8, orysa-Q8S5X5, orysa-Q8LIG3, orysa-Q6K7F5, orysa-Q69UB1, orysa-Q9FW17, orysa-Q337C3, orysa-Q84QZ6, orysa-Q84QY7, orysa-Q851E7, orysa-Q851E3, orysa-Q0JK71, orysa-Q8S1D9, orysa-Q5N8V4, orysa-Q8GTK2, orysa-B9EWJ8, orysa-Q8H3K6, orysa-Q6ZDG8, orysa-Q6ZDG6, orysa-Q6ZDG5, orysa-Q658B2, orysa-Q5N7L1, orysa-Q8RYV9, orysa-Q8H3R3, orysa-Q5SNH3, orysa-Q8W0F0, orysa-pir7a, orysa-q2qnj4, orysa-q2qnt9, orysa-q2qx94, orysa-q2qyj1, orysa-q2r051, orysa-q2r077, orysa-Q4VWY7, orysa-q5nbu1, orysa-q5smv5, orysa-q5vnp5, orysa-q5vrt2, orysa-q5w6c5, orysa-q5z5a3, orysa-q5z901, orysa-Q5ZBI5, orysa-q6atz0, orysa-q6ave2, orysa-q6h7i6, orysa-q6i5q3, orysa-q6j657, orysa-q6k3d9, orysa-q6k4q2, orysa-q6l5b6, orysj-q6yse8, orysa-q6yy42, orysa-q6yzk1, orysa-q6z8b1, orysa-q6z995, orysa-q6zjq6, orysa-q7x7y5, orysa-Q7XC50, orysa-q7xkj9, orysa-q7xr62, orysa-q7xr63, orysa-q7xsg1, orysa-q7xsq2, orysa-q7xts6, orysa-q7xv53, orysa-Q8LQS5, orysa-Q8RZ79, orysa-Q8S0U8, orysa-Q8W3C6, orysa-Q9LHX5, orysa-q33aq0, orysa-q53lh1, orysa-q53m20, orysa-q53nd8, orysa-q60e79, orysa-q67iz2, orysa-q67iz3, orysa-q67iz7, orysa-q67iz8, orysa-q67j02, orysa-q67j05, orysa-q67j09, orysa-q67j10, orysa-q67tr6, orysa-q67tv0, orysa-q69j38, orysa-q69k08, orysa-q69md7, orysa-q69me0, orysa-q69pf3, orysa-q69xr2, orysa-q69y17, orysa-q69y21, orysa-q75hy1, orysa-q75hy2, orysa-q75i01, orysa-Q94JD7, orysa-Q0J0A4, orysa-q651a8, orysa-q652g4, orysa-q688m0, orysa-q688m8, orysa-q688m9, orysa-Q6H8G1, orysi-a2z179, orysi-a2zef2, orysi-b8a7e6, orysi-b8a7e7, orysi-b8bfe5, orysi-b8bhp9, orysj-b9fi05, orysj-b9fkb0, orysj-cgep, orysj-q0djj0, orysj-q0dud7, orysj-q0jaf0, orysj-q0jga1, orysj-q0jhi5, orysj-q5jl22, orysj-q5jlw7, orysj-q6h7q9, orysj-q6yvk6, orysj-q7f8x1, orysj-q7xcx3, orysj-q9fwm6, orysj-q10j20, orysj-q10ss2, orysj-q69uw6, orysj-q94d71, orysj-q338c0, orysj-b9gbs1, orysj-a0a0p0y6l9, orysj-pla4, orysj-pla1 Title: The Genomes of Oryza sativa: a history of duplications Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S and Yang H <88 more author(s)> 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 X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren 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, Xiao Y, Bu D, Tan J, Yang L, Ye C, 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, Huang X, Su Z, Tong W, Tong Z, Ye J, Wang L, Lei T, Chen C, Chen H, Huang H, Zhang F, Li N, Zhao C, Huang Y, Li L, Xi Y, Qi Q, Li W, Hu W, 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, Wong GK, Yang H (- 88) Ref: PLoS Biol, 3:e38, 2005 : PubMed ESTHER: Yu_2005_PLoS.Biol_3_e38 PubMedSearch: Yu 2005 PLoS.Biol 3 e38 PubMedID: 15685292 Gene_locus related to this paper: orysa-Q7XTC5, orysa-Q852M6, orysa-Q8GSE8, orysa-Q9S7P1, orysa-Q9FYP7, orysa-Q5ZBH3, orysa-Q5ZA26, orysa-Q5JLP6, orysa-Q8H5P9, orysa-Q8H5P5, orysa-Q7F1Y5, orysa-Q949C9, orysa-cbp1, orysa-cbp3, orysa-cbpx, orysa-Q33B71, orysa-Q8GSJ3, orysa-LPL1, orysa-Q6YSZ8, orysa-Q8S5X5, orysa-Q8LIG3, orysa-Q6K7F5, orysa-Q7F1B1, orysa-Q8H4S9, orysa-Q69UB1, orysa-Q9FW17, orysa-Q337C3, orysa-Q7F959, orysa-Q84QZ6, orysa-Q84QY7, orysa-Q851E3, orysa-Q6YTH5, orysa-Q0JK71, orysa-Q8S1D9, orysa-Q5N8V4, orysa-Q0JCY4, orysa-Q8GTK2, orysa-B9EWJ8, orysa-Q8H3K6, orysa-Q6ZDG8, orysa-Q6ZDG6, orysa-Q6ZDG5, orysa-Q6ZDG4, orysa-Q5NAI4, orysa-Q658B2, orysa-Q5JMQ8, orysa-Q5QMD9, orysa-Q5N7L1, orysa-Q8RYV9, orysa-Q8H3R3, orysa-Q5SNH3, orysa-Q8W0F0, orysa-pir7a, orysa-pir7b, orysa-q2qlm4, orysa-q2qm78, orysa-q2qm82, orysa-q2qn31, orysa-q2qnj4, orysa-q2qnt9, orysa-q2qur1, orysa-q2qx94, orysa-q2qyi1, orysa-q2qyj1, orysa-q2r051, orysa-q2r077, orysa-q2ram0, orysa-q2rat1, orysa-q2rbb3, orysa-Q4VWY7, orysa-q5na00, orysa-q5nbu1, orysa-Q5QLC0, orysa-q5smv5, orysa-Q5VP27, orysa-q5vrt2, orysa-q5w6c5, orysa-q5z5a3, orysa-q5z9i2, orysa-q5z417, orysa-q5z901, orysa-Q5ZAM8, orysa-Q5ZBI5, orysa-Q5ZCR3, orysa-q6atz0, orysa-q6ave2, orysa-q6f358, orysa-q6h6s1, orysa-q6h7i6, orysa-q6i5q3, orysa-q6i5u7, orysa-q6j657, orysa-q6k3d9, orysa-q6k4q2, orysa-q6k880, orysa-q6l5b6, orysa-Q6L5F5, orysa-q6l556, orysj-q6yse8, orysa-q6yy42, orysa-q6yzk1, orysa-q6z8b1, orysa-q6z995, orysa-q6zc62, orysa-q6zia4, orysa-q6zjq6, orysa-q7x7y5, orysa-Q7XC50, orysa-q7xej4, orysa-q7xem8, orysa-q7xkj9, orysa-q7xr62, orysa-q7xr63, orysa-q7xr64, orysa-q7xsg1, orysa-q7xsq2, orysa-q7xts6, orysa-q7xv53, orysa-Q7XVB5, orysa-Q8L562, orysa-Q8LQS5, orysa-Q8RZ40, orysa-Q8RZ79, orysa-Q8S0U8, orysa-Q8S0V0, orysa-Q8S125, orysa-Q8SAY7, orysa-Q8SAY9, orysa-Q8W3C6, orysa-Q8W3F2, orysa-Q8W3F4, orysa-Q8W3F6, orysa-Q9LHX5, orysa-q33aq0, orysa-q53lh1, orysa-q53m20, orysa-q53nd8, orysa-q60e79, orysa-q60ew8, orysa-q67iz2, orysa-q67iz3, orysa-q67iz7, orysa-q67iz8, orysa-q67j02, orysa-q67j05, orysa-q67j07, orysa-q67j09, orysa-q67j10, orysa-q67tr6, orysa-q67tv0, orysa-q67uz1, orysa-q67v34, orysa-q67wz5, orysa-q69j38, orysa-q69k08, orysa-q69md7, orysa-q69me0, orysa-q69pf3, orysa-q69ti3, orysa-q69xr2, orysa-q69y12, orysa-q69y21, orysa-q75hy2, orysa-q75i01, orysa-Q94JD7, orysa-Q0J0A4, orysa-q651a8, orysa-q651z3, orysa-q652g4, orysa-q688m0, orysa-q688m8, orysa-q688m9, orysa-Q6H8G1, orysi-a2wn01, orysi-a2xc83, orysi-a2yh83, orysi-a2z179, orysi-a2zef2, orysi-b8a7e6, orysi-b8a7e7, orysi-b8bfe5, orysi-b8bhp9, orysj-a3b9l8, orysj-b9eub8, orysj-b9eya5, orysj-b9fi05, orysj-b9fkb0, orysj-b9fn42, orysj-b9gbb7, orysj-cgep, orysj-PLA7, orysj-q0d4u5, orysj-q0djj0, orysj-q0jaf0, orysj-q5jl22, orysj-q5jlw7, orysj-q5z419, orysj-q6h7q9, orysj-q6yvk6, orysj-q6z6i1, orysj-q7f8x1, orysj-q7xcx3, orysj-q9fwm6, orysj-q10j20, orysj-q10ss2, orysj-q69uw6, orysj-q94d71, orysj-q338c0, orysi-b8bly4, orysj-b9gbs4, orysi-a2zb88, orysj-b9gbs1, orysi-b8b698, orysj-pla4, orysj-pla1 Abstract We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, 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. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family. 2 less
Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T and Echeverria M <80 more author(s)> Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Souvorov A, Smith-White B, Tatusova T, An S, An G, S OO, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M (- 80) Ref: Nucleic Acids Research, 36:D1028, 2008 : PubMed ESTHER: Tanaka_2008_Nucleic.Acids.Res_36_D1028 PubMedSearch: Tanaka 2008 Nucleic.Acids.Res 36 D1028 PubMedID: 18089549 Gene_locus related to this paper: orysa-Q9FW17, orysa-Q0JK71, orysa-B9EWJ8, orysa-Q5N7L1, orysa-pir7a, orysa-q2qyj1, orysj-q6yse8, orysa-q6yzk1, orysa-Q8S0U8, orysa-q33aq0, orysa-Q0J0A4, orysi-a2z179, orysi-a2zef2, orysi-b8a7e6, orysi-b8a7e7, orysi-b8bfe5, orysi-b8bhp9, orysj-b9fi05, orysj-b9fkb0, orysj-cgep, orysj-q0djj0, orysj-q0dud7, orysj-q0jaf0, orysj-q0jga1, orysj-q5jl22, orysj-q5jlw7, orysj-q6h7q9, orysj-q6yvk6, orysj-q7f8x1, orysj-q7xcx3, orysj-q9fwm6, orysj-q10j20, orysj-q10ss2, orysj-q69uw6, orysj-q94d71, orysj-q0iq98, orysj-b9gbs4, orysj-b9gbs1, orysj-pla4, orysj-pla1 Abstract The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/. Title: Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R and Sasaki T <85 more author(s)> Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T (- 85) Ref: Genome Res, 17:175, 2007 : PubMed ESTHER: Itoh_2007_Genome.Res_17_175 PubMedSearch: Itoh 2007 Genome.Res 17 175 PubMedID: 17210932 Gene_locus related to this paper: orysa-Q7XTC5, orysa-Q852M6, orysa-Q8GSE8, orysa-Q9FYP7, orysa-Q5ZA26, orysa-Q5JLP6, orysa-Q8H5P5, orysa-Q7F1Y5, orysa-cbp3, orysa-cbpx, orysa-Q6YSZ8, orysa-Q9FW17, orysa-Q84QZ6, orysa-Q0JK71, orysa-B9EWJ8, orysa-Q6ZDG6, orysa-Q6ZDG5, orysa-Q658B2, orysa-Q5N7L1, orysa-Q8RYV9, orysa-Q8H3R3, orysa-Q5SNH3, orysa-pir7a, orysa-q2qnj4, orysa-q2qyj1, orysa-q2r077, orysa-Q4VWY7, orysa-q5smv5, orysa-q5z901, orysa-Q5ZBI5, orysa-q6atz0, orysa-q6i5q3, orysa-q6j657, orysa-q6k4q2, orysj-q6yse8, orysa-q6yy42, orysa-q6yzk1, orysa-q6z8b1, orysa-q6z995, orysa-q6zjq6, orysa-q7x7y5, orysa-Q7XC50, orysa-q7xr62, orysa-q7xr63, orysa-q7xsg1, orysa-q7xsq2, orysa-q7xts6, orysa-q7xv53, orysa-Q8LQS5, orysa-Q8RZ79, orysa-Q8S0U8, orysa-Q8W3C6, orysa-Q9LHX5, orysa-q53m20, orysa-q53nd8, orysa-q60e79, orysa-q67iz2, orysa-q67iz3, orysa-q67iz7, orysa-q67iz8, orysa-q67j02, orysa-q67j05, orysa-q67j09, orysa-q67j10, orysa-q67tr6, orysa-q67tv0, orysa-q69j38, orysa-q69y21, orysa-q75hy1, orysa-q75hy2, orysa-Q0J0A4, orysa-q651a8, orysa-q652g4, orysa-q688m8, orysa-Q6H8G1, orysi-a2z179, orysi-a2zef2, orysi-b8a7e6, orysi-b8a7e7, orysi-b8bfe5, orysi-b8bhp9, orysj-b9fi05, orysj-q0djj0, orysj-q0jaf0, orysj-q0jga1, orysj-q0jhi5, orysj-q5jl22, orysj-q5jlw7, orysj-q6h7q9, orysj-q6yvk6, orysj-q7f8x1, orysj-q7xcx3, orysj-q9fwm6, orysj-q10j20, orysj-q10ss2, orysj-q69uw6, orysj-q94d71, orysj-q0iq98, orysj-b9gbs4, orysj-b9gbs1 Abstract We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene. Title: The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio BA, Nagamura Y and Sasaki T <4 more author(s)> Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio BA, Nagamura Y, Imanishi T, Ikeo K, Itoh T, Gojobori T, Sasaki T (- 4) Ref: Nucleic Acids Research, 34:D741, 2006 : PubMed ESTHER: Ohyanagi_2006_Nucleic.Acids.Res_34_D741 PubMedSearch: Ohyanagi 2006 Nucleic.Acids.Res 34 D741 PubMedID: 16381971 Gene_locus related to this paper: orysa-Q9FW17, orysa-Q0JK71, orysa-B9EWJ8, orysa-Q5N7L1, orysa-Q5N7J6, orysa-pir7a, orysa-q2qyi1, orysa-q2qyj1, orysa-q2rbb3, orysj-q6yse8, orysa-q6yzk1, orysa-Q8S0U8, orysa-Q84ZY8, orysa-Q0J0A4, orysi-a2z179, orysi-a2zef2, orysi-b8a7e6, orysi-b8a7e7, orysi-b8bfe5, orysi-b8bhp9, orysj-b9fi05, orysj-q0d4u5, orysj-q0djj0, orysj-q0jaf0, orysj-q0jga1, orysj-q0jhi5, orysj-q5jl22, orysj-q5jlw7, orysj-q6h7q9, orysj-q6yvk6, orysj-q7f8x1, orysj-q7xcx3, orysj-q9fwm6, orysj-q10j20, orysj-q10ss2, orysj-q69uw6, orysj-q94d71, orysj-q0iq98, orysj-b9gbs4, orysj-b9gbs1 Abstract With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through http://rapdb.lab.nig.ac.jp/. Title: The map-based sequence of the rice genome. Matsumo T, Sasaki T Ref: Nature, 436:793, 2005 : PubMed ESTHER: Matsumoto_2005_Nature_436_793 PubMedSearch: Matsumoto 2005 Nature 436 793 PubMedID: 16100779 Gene_locus related to this paper: orysa-Q9FRJ0, orysa-Q7XTC5, orysa-Q852M6, orysa-Q8GSE8, orysa-Q9FYP7, orysa-Q5ZBH3, orysa-Q5ZA26, orysa-Q5JLP6, orysa-Q8H5P5, orysa-Q7F1Y5, orysa-Q949C9, orysa-cbp3, orysa-cbpx, orysa-Q6YSZ8, orysa-Q8S5X5, orysa-Q8LIG3, orysa-Q6K7F5, orysa-Q69UB1, orysa-Q9FW17, orysa-Q337C3, orysa-Q84QZ6, orysa-Q84QY7, orysa-Q851E7, orysa-Q851E3, orysa-Q0JK71, orysa-Q8S1D9, orysa-Q5N8V4, orysa-Q8GTK2, orysa-B9EWJ8, orysa-Q8H3K6, orysa-Q6ZDG8, orysa-Q6ZDG6, orysa-Q6ZDG5, orysa-Q658B2, orysa-Q5N7L1, orysa-Q8RYV9, orysa-Q8H3R3, orysa-Q5SNH3, orysa-Q8W0F0, orysa-pir7a, orysa-q2qnj4, orysa-q2qnt9, orysa-q2qx94, orysa-q2qyj1, orysa-q2r051, orysa-q2r077, orysa-Q4VWY7, orysa-q5nbu1, orysa-q5smv5, orysa-q5vnp5, orysa-q5vrt2, orysa-q5w6c5, orysa-q5z5a3, orysa-q5z901, orysa-Q5ZBI5, orysa-q6atz0, orysa-q6ave2, orysa-q6h7i6, orysa-q6i5q3, orysa-q6j657, orysa-q6k3d9, orysa-q6k4q2, orysa-q6l5b6, orysj-q6yse8, orysa-q6yy42, orysa-q6yzk1, orysa-q6z8b1, orysa-q6z995, orysa-q6zjq6, orysa-q7x7y5, orysa-Q7XC50, orysa-q7xkj9, orysa-q7xr62, orysa-q7xr63, orysa-q7xsg1, orysa-q7xsq2, orysa-q7xts6, orysa-q7xv53, orysa-Q8LQS5, orysa-Q8RZ79, orysa-Q8S0U8, orysa-Q8W3C6, orysa-Q9LHX5, orysa-q33aq0, orysa-q53lh1, orysa-q53m20, orysa-q53nd8, orysa-q60e79, orysa-q67iz2, orysa-q67iz3, orysa-q67iz7, orysa-q67iz8, orysa-q67j02, orysa-q67j05, orysa-q67j09, orysa-q67j10, orysa-q67tr6, orysa-q67tv0, orysa-q69j38, orysa-q69k08, orysa-q69md7, orysa-q69me0, orysa-q69pf3, orysa-q69xr2, orysa-q69y17, orysa-q69y21, orysa-q75hy1, orysa-q75hy2, orysa-q75i01, orysa-Q94JD7, orysa-Q0J0A4, orysa-q651a8, orysa-q652g4, orysa-q688m0, orysa-q688m8, orysa-q688m9, orysa-Q6H8G1, orysi-a2z179, orysi-a2zef2, orysi-b8a7e6, orysi-b8a7e7, orysi-b8bfe5, orysi-b8bhp9, orysj-b9fi05, orysj-b9fkb0, orysj-cgep, orysj-q0djj0, orysj-q0dud7, orysj-q0jaf0, orysj-q0jga1, orysj-q0jhi5, orysj-q5jl22, orysj-q5jlw7, orysj-q6h7q9, orysj-q6yvk6, orysj-q7f8x1, orysj-q7xcx3, orysj-q9fwm6, orysj-q10j20, orysj-q10ss2, orysj-q69uw6, orysj-q94d71, orysj-q338c0, orysj-b9gbs1, orysj-a0a0p0y6l9, orysj-pla4, orysj-pla1 Title: The Genomes of Oryza sativa: a history of duplications Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S and Yang H <88 more author(s)> 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 X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren 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, Xiao Y, Bu D, Tan J, Yang L, Ye C, 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, Huang X, Su Z, Tong W, Tong Z, Ye J, Wang L, Lei T, Chen C, Chen H, Huang H, Zhang F, Li N, Zhao C, Huang Y, Li L, Xi Y, Qi Q, Li W, Hu W, 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, Wong GK, Yang H (- 88) Ref: PLoS Biol, 3:e38, 2005 : PubMed ESTHER: Yu_2005_PLoS.Biol_3_e38 PubMedSearch: Yu 2005 PLoS.Biol 3 e38 PubMedID: 15685292 Gene_locus related to this paper: orysa-Q7XTC5, orysa-Q852M6, orysa-Q8GSE8, orysa-Q9S7P1, orysa-Q9FYP7, orysa-Q5ZBH3, orysa-Q5ZA26, orysa-Q5JLP6, orysa-Q8H5P9, orysa-Q8H5P5, orysa-Q7F1Y5, orysa-Q949C9, orysa-cbp1, orysa-cbp3, orysa-cbpx, orysa-Q33B71, orysa-Q8GSJ3, orysa-LPL1, orysa-Q6YSZ8, orysa-Q8S5X5, orysa-Q8LIG3, orysa-Q6K7F5, orysa-Q7F1B1, orysa-Q8H4S9, orysa-Q69UB1, orysa-Q9FW17, orysa-Q337C3, orysa-Q7F959, orysa-Q84QZ6, orysa-Q84QY7, orysa-Q851E3, orysa-Q6YTH5, orysa-Q0JK71, orysa-Q8S1D9, orysa-Q5N8V4, orysa-Q0JCY4, orysa-Q8GTK2, orysa-B9EWJ8, orysa-Q8H3K6, orysa-Q6ZDG8, orysa-Q6ZDG6, orysa-Q6ZDG5, orysa-Q6ZDG4, orysa-Q5NAI4, orysa-Q658B2, orysa-Q5JMQ8, orysa-Q5QMD9, orysa-Q5N7L1, orysa-Q8RYV9, orysa-Q8H3R3, orysa-Q5SNH3, orysa-Q8W0F0, orysa-pir7a, orysa-pir7b, orysa-q2qlm4, orysa-q2qm78, orysa-q2qm82, orysa-q2qn31, orysa-q2qnj4, orysa-q2qnt9, orysa-q2qur1, orysa-q2qx94, orysa-q2qyi1, orysa-q2qyj1, orysa-q2r051, orysa-q2r077, orysa-q2ram0, orysa-q2rat1, orysa-q2rbb3, orysa-Q4VWY7, orysa-q5na00, orysa-q5nbu1, orysa-Q5QLC0, orysa-q5smv5, orysa-Q5VP27, orysa-q5vrt2, orysa-q5w6c5, orysa-q5z5a3, orysa-q5z9i2, orysa-q5z417, orysa-q5z901, orysa-Q5ZAM8, orysa-Q5ZBI5, orysa-Q5ZCR3, orysa-q6atz0, orysa-q6ave2, orysa-q6f358, orysa-q6h6s1, orysa-q6h7i6, orysa-q6i5q3, orysa-q6i5u7, orysa-q6j657, orysa-q6k3d9, orysa-q6k4q2, orysa-q6k880, orysa-q6l5b6, orysa-Q6L5F5, orysa-q6l556, orysj-q6yse8, orysa-q6yy42, orysa-q6yzk1, orysa-q6z8b1, orysa-q6z995, orysa-q6zc62, orysa-q6zia4, orysa-q6zjq6, orysa-q7x7y5, orysa-Q7XC50, orysa-q7xej4, orysa-q7xem8, orysa-q7xkj9, orysa-q7xr62, orysa-q7xr63, orysa-q7xr64, orysa-q7xsg1, orysa-q7xsq2, orysa-q7xts6, orysa-q7xv53, orysa-Q7XVB5, orysa-Q8L562, orysa-Q8LQS5, orysa-Q8RZ40, orysa-Q8RZ79, orysa-Q8S0U8, orysa-Q8S0V0, orysa-Q8S125, orysa-Q8SAY7, orysa-Q8SAY9, orysa-Q8W3C6, orysa-Q8W3F2, orysa-Q8W3F4, orysa-Q8W3F6, orysa-Q9LHX5, orysa-q33aq0, orysa-q53lh1, orysa-q53m20, orysa-q53nd8, orysa-q60e79, orysa-q60ew8, orysa-q67iz2, orysa-q67iz3, orysa-q67iz7, orysa-q67iz8, orysa-q67j02, orysa-q67j05, orysa-q67j07, orysa-q67j09, orysa-q67j10, orysa-q67tr6, orysa-q67tv0, orysa-q67uz1, orysa-q67v34, orysa-q67wz5, orysa-q69j38, orysa-q69k08, orysa-q69md7, orysa-q69me0, orysa-q69pf3, orysa-q69ti3, orysa-q69xr2, orysa-q69y12, orysa-q69y21, orysa-q75hy2, orysa-q75i01, orysa-Q94JD7, orysa-Q0J0A4, orysa-q651a8, orysa-q651z3, orysa-q652g4, orysa-q688m0, orysa-q688m8, orysa-q688m9, orysa-Q6H8G1, orysi-a2wn01, orysi-a2xc83, orysi-a2yh83, orysi-a2z179, orysi-a2zef2, orysi-b8a7e6, orysi-b8a7e7, orysi-b8bfe5, orysi-b8bhp9, orysj-a3b9l8, orysj-b9eub8, orysj-b9eya5, orysj-b9fi05, orysj-b9fkb0, orysj-b9fn42, orysj-b9gbb7, orysj-cgep, orysj-PLA7, orysj-q0d4u5, orysj-q0djj0, orysj-q0jaf0, orysj-q5jl22, orysj-q5jlw7, orysj-q5z419, orysj-q6h7q9, orysj-q6yvk6, orysj-q6z6i1, orysj-q7f8x1, orysj-q7xcx3, orysj-q9fwm6, orysj-q10j20, orysj-q10ss2, orysj-q69uw6, orysj-q94d71, orysj-q338c0, orysi-b8bly4, orysj-b9gbs4, orysi-a2zb88, orysj-b9gbs1, orysi-b8b698, orysj-pla4, orysj-pla1 Abstract We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, 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. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family. Other Papers | |||||||||||||||||||||||||||||||||
|
