title: Generation and analysis of end sequence database for T-DNA tagging lines in rice.
abstract: We analyzed 6749 lines tagged by the gene trap vector pGA2707. This resulted in the isolation of 3793 genomic sequences flanking the T-DNA. Among the insertions, 1846 T-DNAs were integrated into genic regions, and 1864 were located in intergenic regions. Frequencies were also higher at the beginning and end of the coding regions and upstream near the ATG start codon. The overall GC content at the insertion sites was close to that measured from the entire rice (Oryza sativa) genome. Functional classification of these 1846 tagged genes showed a distribution similar to that observed for all the genes in the rice chromosomes. This indicates that T-DNA insertion is not biased toward a particular class of genes. There were 764, 327, and 346 T-DNA insertions in chromosomes 1, 4 and 10, respectively. Insertions were not evenly distributed; frequencies were higher at the ends of the chromosomes and lower near the centromere. At certain sites, the frequency was higher than in the surrounding regions. This sequence database will be valuable in identifying knockout mutants for elucidating gene function in rice. This resource is available to the scientific community at http://www.postech.ac.kr/life/pfg/risd.
authors: National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea.
authors: Suyoung
authors: S
authors: An
authors: Sunhee
authors: S
authors: Park
authors: Dong-Hoon
authors: DH
authors: Jeong
authors: Dong-Yeon
authors: DY
authors: Lee
authors: Hong-Gyu
authors: HG
authors: Kang
authors: Jung-Hwa
authors: JH
authors: Yu
authors: Junghe
authors: J
authors: Hur
authors: Sung-Ryul
authors: SR
authors: Kim
authors: Young-Hea
authors: YH
authors: Kim
authors: Miok
authors: M
authors: Lee
authors: Soonki
authors: S
authors: Han
authors: Soo-Jin
authors: SJ
authors: Kim
authors: Jungwon
authors: J
authors: Yang
authors: Eunjoo
authors: E
authors: Kim
authors: Soo Jin
authors: SJ
authors: Wi
authors: Hoo Sun
authors: HS
authors: Chung
authors: Jong-Pil
authors: JP
authors: Hong
authors: Vitnary
authors: V
authors: Choe
authors: Hak-Kyung
authors: HK
authors: Lee
authors: Jung-Hee
authors: JH
authors: Choi
authors: Jongmin
authors: J
authors: Nam
authors: Seong-Ryong
authors: SR
authors: Kim
authors: Phun-Bum
authors: PB
authors: Park
authors: Ky Young
authors: KY
authors: Park
authors: Woo Taek
authors: WT
authors: Kim
authors: Sunghwa
authors: S
authors: Choe
authors: Chin-Bum
authors: CB
authors: Lee
authors: Gynheung
authors: G
authors: An
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D004277:DNA, Single-Stranded / Q000235:genetics*; D005091:Exons; D005822:Genetic Vectors; D007438:Introns; D016254:Mutagenesis, Insertional; D012275:Oryza / Q000235:genetics*; D030821:Plants, Genetically Modified / Q000235:genetics; D016133:Polymerase Chain Reaction; D016324:Sequence Tagged Sites
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D004277:DNA, Single-Stranded; C036483:T-DNA