Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice

Suyoung An, Sunhee Park, Dong Hoon Jeong, Dong Yeon Lee, Hong Gyu Kang, Jung Hwa Yu, Junghe Hur, Sung Ryul Kim, Young Hea Kim, Miok Lee, Soonki Han, Soo Jin Kim, Jungwon Yang, Eunjoo Kim, Soo Jin Wi, Hoo Sun Chung, Jong Pil Hong, Vitnary Choe, Hak Kyung Lee, Jung Hee ChoiJongmin Nam, Seong Ryong Kim, Phun Bum Park, Ky Young Park, Woo Taek Kim, Sunghwa Choe, Chin Bum Lee, Gynheung An

Research output: Contribution to journalArticle

185 Citations (Scopus)

Abstract

We analyzed 6,749 lines tagged by the gene trap vector pGA2707. This resulted in the isolation of 3,793 genomic sequences flanking the T-DNA. Among the insertions, 1,846 T-DNAs were integrated into genic regions, and 1,864 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 1,846 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.

Original languageEnglish
Pages (from-to)2040-2047
Number of pages8
JournalPlant physiology
Volume133
Issue number4
DOIs
Publication statusPublished - 2003 Dec 1

Fingerprint

Sequence Analysis
Databases
rice
DNA
Genes
chromosomes
genes
Chromosomes
Chromosomes, Human, Pair 10
Chromosomes, Human, Pair 4
start codon
Intergenic DNA
knockout mutants
Initiator Codon
Centromere
Chromosomes, Human, Pair 1
Base Composition
centromeres
intergenic DNA
Oryza sativa

All Science Journal Classification (ASJC) codes

  • Physiology
  • Genetics
  • Plant Science

Cite this

An, S., Park, S., Jeong, D. H., Lee, D. Y., Kang, H. G., Yu, J. H., ... An, G. (2003). Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice. Plant physiology, 133(4), 2040-2047. https://doi.org/10.1104/pp.103.030478
An, Suyoung ; Park, Sunhee ; Jeong, Dong Hoon ; Lee, Dong Yeon ; Kang, Hong Gyu ; Yu, Jung Hwa ; Hur, Junghe ; Kim, Sung Ryul ; Kim, Young Hea ; Lee, Miok ; Han, Soonki ; Kim, Soo Jin ; Yang, Jungwon ; Kim, Eunjoo ; Wi, Soo Jin ; Chung, Hoo Sun ; Hong, Jong Pil ; Choe, Vitnary ; Lee, Hak Kyung ; Choi, Jung Hee ; Nam, Jongmin ; Kim, Seong Ryong ; Park, Phun Bum ; Park, Ky Young ; Kim, Woo Taek ; Choe, Sunghwa ; Lee, Chin Bum ; An, Gynheung. / Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice. In: Plant physiology. 2003 ; Vol. 133, No. 4. pp. 2040-2047.
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abstract = "We analyzed 6,749 lines tagged by the gene trap vector pGA2707. This resulted in the isolation of 3,793 genomic sequences flanking the T-DNA. Among the insertions, 1,846 T-DNAs were integrated into genic regions, and 1,864 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 1,846 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.",
author = "Suyoung An and Sunhee Park and Jeong, {Dong Hoon} and Lee, {Dong Yeon} and Kang, {Hong Gyu} and Yu, {Jung Hwa} and Junghe Hur and Kim, {Sung Ryul} and Kim, {Young Hea} and Miok Lee and Soonki Han and Kim, {Soo Jin} and Jungwon Yang and Eunjoo Kim and Wi, {Soo Jin} and Chung, {Hoo Sun} and Hong, {Jong Pil} and Vitnary Choe and Lee, {Hak Kyung} and Choi, {Jung Hee} and Jongmin Nam and Kim, {Seong Ryong} and Park, {Phun Bum} and Park, {Ky Young} and Kim, {Woo Taek} and Sunghwa Choe and Lee, {Chin Bum} and Gynheung An",
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An, S, Park, S, Jeong, DH, Lee, DY, Kang, HG, Yu, JH, Hur, J, Kim, SR, Kim, YH, Lee, M, Han, S, Kim, SJ, Yang, J, Kim, E, Wi, SJ, Chung, HS, Hong, JP, Choe, V, Lee, HK, Choi, JH, Nam, J, Kim, SR, Park, PB, Park, KY, Kim, WT, Choe, S, Lee, CB & An, G 2003, 'Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice', Plant physiology, vol. 133, no. 4, pp. 2040-2047. https://doi.org/10.1104/pp.103.030478

Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice. / An, Suyoung; Park, Sunhee; Jeong, Dong Hoon; Lee, Dong Yeon; Kang, Hong Gyu; Yu, Jung Hwa; Hur, Junghe; Kim, Sung Ryul; Kim, Young Hea; Lee, Miok; Han, Soonki; Kim, Soo Jin; Yang, Jungwon; Kim, Eunjoo; Wi, Soo Jin; Chung, Hoo Sun; Hong, Jong Pil; Choe, Vitnary; Lee, Hak Kyung; Choi, Jung Hee; Nam, Jongmin; Kim, Seong Ryong; Park, Phun Bum; Park, Ky Young; Kim, Woo Taek; Choe, Sunghwa; Lee, Chin Bum; An, Gynheung.

In: Plant physiology, Vol. 133, No. 4, 01.12.2003, p. 2040-2047.

Research output: Contribution to journalArticle

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T1 - Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice

AU - An, Suyoung

AU - Park, Sunhee

AU - Jeong, Dong Hoon

AU - Lee, Dong Yeon

AU - Kang, Hong Gyu

AU - Yu, Jung Hwa

AU - Hur, Junghe

AU - Kim, Sung Ryul

AU - Kim, Young Hea

AU - Lee, Miok

AU - Han, Soonki

AU - Kim, Soo Jin

AU - Yang, Jungwon

AU - Kim, Eunjoo

AU - Wi, Soo Jin

AU - Chung, Hoo Sun

AU - Hong, Jong Pil

AU - Choe, Vitnary

AU - Lee, Hak Kyung

AU - Choi, Jung Hee

AU - Nam, Jongmin

AU - Kim, Seong Ryong

AU - Park, Phun Bum

AU - Park, Ky Young

AU - Kim, Woo Taek

AU - Choe, Sunghwa

AU - Lee, Chin Bum

AU - An, Gynheung

PY - 2003/12/1

Y1 - 2003/12/1

N2 - We analyzed 6,749 lines tagged by the gene trap vector pGA2707. This resulted in the isolation of 3,793 genomic sequences flanking the T-DNA. Among the insertions, 1,846 T-DNAs were integrated into genic regions, and 1,864 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 1,846 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.

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