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Nature Genetics
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Complete sequencing and characterization of 21,243 full-length human cDNAs

Nature Geneticsvolume 36, pages40–45 (2004)Cite this article

Abstract

As a base for human transcriptome and functional genomics, we created the “full-length long Japan” (FLJ) collection of sequenced human cDNAs. We determined the entire sequence of 21,243 selected clones and found that 14,490 cDNAs (10,897 clusters) were unique to the FLJ collection. About half of them (5,416) seemed to be protein-coding. Of those, 1,999 clusters had not been predicted by computational methods. The distribution of GC content of nonpredicted cDNAs had a peak at∼58% compared with a peak at∼42%for predicted cDNAs. Thus, there seems to be a slight bias against GC-rich transcripts in current gene prediction procedures. The rest of the cDNAs unique to the FLJ collection (5,481) contained no obvious open reading frames (ORFs) and thus are candidate noncoding RNAs. About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at∼42%, relatively low compared with that of protein-coding cDNAs.

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Figure 1: Flow chart of cDNA categorization.
Figure 2: GC contents of the FLJ cDNAs and the corresponding genomic regions to which they were mapped.

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Acknowledgements

We thank A. Kishimoto, H. Ezoe and T. Matsuo for supporting the project and E. Nakajima for critically reading the manuscript. This project was supported by the Ministry of Economy Trade and Industry of Japan and also in part by Special Coordination Funds for Promoting Science and Technology from the Ministry of Education, Culture, Sports, Science and Technology of Japan. Requests for materials should be addressed to S. Sugano. Requests for physical cDNA clones should be addressed to S.Sugano (flcdna@ims.u-tokyo.ac.jp) or T. Isogai (isogai-t@reprori.jp). For more information on each cDNA clone, visit FLJ-DB. For general information on the FLJ project, please refer to NEDO website.

Author information

Authors and Affiliations

  1. Helix Research Institute, 1532-3 Yana, Kisarazu, 292-0812, Chiba, Japan

    Toshio Ota, Tetsuo Nishikawa, Tetsuji Otsuki, Tomoyasu Sugiyama, Ryotaro Irie, Ai Wakamatsu, Koji Hayashi, Hiroyuki Sato, Keiichi Nagai, Shizuko Ishii, Jun-ichi Yamamoto, Kaoru Saito, Yuri Kawai, Yuko Isono, Yoshitaka Nakamura, Kenji Nagahari, Yasuhiko Masuho & Takao Isogai

  2. Kyowa Hakko Kogyo, Tokyo Research Laboratory, 3-6-6 Asahi-machi, Machida, Tokyo, 194-8533, Japan

    Toshio Ota, Masaya Obayashi, Tatsunari Nishi, Satoshi Nakagawa, Akihiro Senoh, Hiroshi Mizoguchi, Ayako Kawabata, Takeshi Hikiji, Naoko Kobatake, Hiromi Inagaki, Yasuko Ikema, Sachiko Okamoto & Rie Okitani

  3. The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, 108-8639, Japan

    Yutaka Suzuki, Toshikazu Shibahara, Toshihiro Tanaka, Yoshihiro Ohmori, Takuma Kawakami, Saori Noguchi, Tomoko Itoh, Keiko Shigeta, Tadashi Senba, Kyoka Matsumura, Yoshie Nakajima, Takae Mizuno, Misato Morinaga, Masahide Sasaki, Takushi Togashi, Masaaki Oyama, Hiroko Hata, Manabu Watanabe, Takami Komatsu, Junko Mizushima-Sugano, Tadashi Satoh, Yuko Shirai, Yukiko Takahashi, Kiyomi Nakagawa, Riu Yamashita, Kenta Nakai, Tetsushi Yada, Yusuke Nakamura & Sumio Sugano

  4. Hitachi, Central Research Laboratory, 1-280 Higashi-koigakubo, Kokubunj, Tokyo, 185-8601, Japan

    Tetsuo Nishikawa, Kouichi Kimura, Hiroshi Makita, Katsuhiko Murakami, Tomohiro Yasuda, Takao Iwayanagi & Tadashi Satoh

  5. National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo, 151-0066, Japan

    Mitsuo Sekine & Hisashi Kikuchi

  6. Otsuka Pharmaceutical, 463-10 Kagasuno Kawauchi-cho, Tokushima, 771-0192, Japan

    Toshikazu Shibahara, Yoshihiro Goto, Fumio Shimizu, Hirokazu Wakebe, Haretsugu Hishigaki, Takeshi Watanabe, Akira Tanigami, Tsutomu Fujiwara, Toshihide Ono, Katsue Yamada, Yuka Fujii, Kouichi Ozaki, Maasa Hirao, Yoshihiro Ohmori & Takuma Kawakami

  7. Hitachi, Life Science Group, 1-3-1 Minamidai, Kawagoe, 350-1165, Saitama, Japan

    Masako Wagatsuma, Akiko Shiratori, Hiroaki Sudo, Takehiko Hosoiri, Yoshiko Kaku, Hiroyo Kodaira, Hiroshi Kondo, Masanori Sugawara, Makiko Takahashi, Katsuhiro Kanda, Takahide Yokoi, Takako Furuya, Emiko Kikkawa, Yuhi Omura, Kumi Abe, Kumiko Kamihara, Naoko Katsuta, Kazuomi Sato, Machiko Tanikawa, Makoto Yamazaki & Ken Ninomiya

  8. Hitachi Science Systems, 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan

    Tadashi Ishibashi, Hiromichi Yamashita, Katsuji Murakawa, Kiyoshi Fujimori, Hiroyuki Tanai, Manabu Kimata, Motoji Watanabe, Susumu Hiraoka, Yoshiyuki Chiba, Shinichi Ishida, Yukio Ono, Sumiyo Takiguchi, Susumu Watanabe, Makoto Yosida, Tomoko Hotuta, Junko Kusano & Keiichi Kanehori

  9. Takara Shuzo, 2257 Sunaike, Noji, Kusatu, Shiga, 525-0055, Japan

    Asako Takahashi-Fujii, Hiroto Hara, Tomo-o Tanase, Yoshiko Nomura, Sakae Togiya, Fukuyo Komai, Reiko Hara, Kazuha Takeuchi, Miho Arita, Nobuyuki Imose, Kaoru Musashino, Hisatsugu Yuuki & Atsushi Oshima

  10. Nisshinbo Industries, 1-2-3 Onodai, Midori-ku, Chiba, 267-0056, Japan

    Naokazu Sasaki, Satoshi Aotsuka, Yoko Yoshikawa, Hiroshi Matsunawa, Tatsuo Ichihara, Namiko Shiohata, Sanae Sano, Shogo Moriya, Hiroko Momiyama, Noriko Satoh, Sachiko Takami, Yuko Terashima & Osamu Suzuki

  11. Toyobo, 10-24 Toyo-cho, Tsuruga, 914-0047, Fukui, Japan

    Akio Sugiyama, Makoto Takemoto & Bunsei Kawakami

  12. Fujiya, 228 Soya, Hadano, Kanagawa, 257-0031, Japan

    Masaaki Yamazaki, Koji Watanabe, Ayako Kumagai, Shoko Itakura, Yasuhito Fukuzumi, Yoshifumi Fujimori, Megumi Komiyama & Hiroyuki Tashiro

  13. Aisin Cosmos R&D, 1698 Yana, Kisarazu, 292-0812, Chiba, Japan

    Koji Okumura

  14. Kazusa DNA Research Institute, 1532-3 Yana, Kisarazu, 292-0812, Chiba, Japan

    Takahiro Nagase, Nobuo Nomura & Osamu Ohara

  15. BIRC, AIST, 2-41-6 Aomi, Koto-ku, Tokyo, 135-0064, Japan

    Nobuo Nomura & Sumio Sugano

Authors
  1. Toshio Ota
  2. Yutaka Suzuki
  3. Tetsuo Nishikawa
  4. Tetsuji Otsuki
  5. Tomoyasu Sugiyama
  6. Ryotaro Irie
  7. Ai Wakamatsu
  8. Koji Hayashi
  9. Hiroyuki Sato
  10. Keiichi Nagai
  11. Kouichi Kimura
  12. Hiroshi Makita
  13. Mitsuo Sekine
  14. Masaya Obayashi
  15. Tatsunari Nishi
  16. Toshikazu Shibahara
  17. Toshihiro Tanaka
  18. Shizuko Ishii
  19. Jun-ichi Yamamoto
  20. Kaoru Saito
  21. Yuri Kawai
  22. Yuko Isono
  23. Yoshitaka Nakamura
  24. Kenji Nagahari
  25. Katsuhiko Murakami
  26. Tomohiro Yasuda
  27. Takao Iwayanagi
  28. Masako Wagatsuma
  29. Akiko Shiratori
  30. Hiroaki Sudo
  31. Takehiko Hosoiri
  32. Yoshiko Kaku
  33. Hiroyo Kodaira
  34. Hiroshi Kondo
  35. Masanori Sugawara
  36. Makiko Takahashi
  37. Katsuhiro Kanda
  38. Takahide Yokoi
  39. Takako Furuya
  40. Emiko Kikkawa
  41. Yuhi Omura
  42. Kumi Abe
  43. Kumiko Kamihara
  44. Naoko Katsuta
  45. Kazuomi Sato
  46. Machiko Tanikawa
  47. Makoto Yamazaki
  48. Ken Ninomiya
  49. Tadashi Ishibashi
  50. Hiromichi Yamashita
  51. Katsuji Murakawa
  52. Kiyoshi Fujimori
  53. Hiroyuki Tanai
  54. Manabu Kimata
  55. Motoji Watanabe
  56. Susumu Hiraoka
  57. Yoshiyuki Chiba
  58. Shinichi Ishida
  59. Yukio Ono
  60. Sumiyo Takiguchi
  61. Susumu Watanabe
  62. Makoto Yosida
  63. Tomoko Hotuta
  64. Junko Kusano
  65. Keiichi Kanehori
  66. Asako Takahashi-Fujii
  67. Hiroto Hara
  68. Tomo-o Tanase
  69. Yoshiko Nomura
  70. Sakae Togiya
  71. Fukuyo Komai
  72. Reiko Hara
  73. Kazuha Takeuchi
  74. Miho Arita
  75. Nobuyuki Imose
  76. Kaoru Musashino
  77. Hisatsugu Yuuki
  78. Atsushi Oshima
  79. Naokazu Sasaki
  80. Satoshi Aotsuka
  81. Yoko Yoshikawa
  82. Hiroshi Matsunawa
  83. Tatsuo Ichihara
  84. Namiko Shiohata
  85. Sanae Sano
  86. Shogo Moriya
  87. Hiroko Momiyama
  88. Noriko Satoh
  89. Sachiko Takami
  90. Yuko Terashima
  91. Osamu Suzuki
  92. Satoshi Nakagawa
  93. Akihiro Senoh
  94. Hiroshi Mizoguchi
  95. Yoshihiro Goto
  96. Fumio Shimizu
  97. Hirokazu Wakebe
  98. Haretsugu Hishigaki
  99. Takeshi Watanabe
  100. Akio Sugiyama
  101. Makoto Takemoto
  102. Bunsei Kawakami
  103. Masaaki Yamazaki
  104. Koji Watanabe
  105. Ayako Kumagai
  106. Shoko Itakura
  107. Yasuhito Fukuzumi
  108. Yoshifumi Fujimori
  109. Megumi Komiyama
  110. Hiroyuki Tashiro
  111. Akira Tanigami
  112. Tsutomu Fujiwara
  113. Toshihide Ono
  114. Katsue Yamada
  115. Yuka Fujii
  116. Kouichi Ozaki
  117. Maasa Hirao
  118. Yoshihiro Ohmori
  119. Ayako Kawabata
  120. Takeshi Hikiji
  121. Naoko Kobatake
  122. Hiromi Inagaki
  123. Yasuko Ikema
  124. Sachiko Okamoto
  125. Rie Okitani
  126. Takuma Kawakami
  127. Saori Noguchi
  128. Tomoko Itoh
  129. Keiko Shigeta
  130. Tadashi Senba
  131. Kyoka Matsumura
  132. Yoshie Nakajima
  133. Takae Mizuno
  134. Misato Morinaga
  135. Masahide Sasaki
  136. Takushi Togashi
  137. Masaaki Oyama
  138. Hiroko Hata
  139. Manabu Watanabe
  140. Takami Komatsu
  141. Junko Mizushima-Sugano
  142. Tadashi Satoh
  143. Yuko Shirai
  144. Yukiko Takahashi
  145. Kiyomi Nakagawa
  146. Koji Okumura
  147. Takahiro Nagase
  148. Nobuo Nomura
  149. Hisashi Kikuchi
  150. Yasuhiko Masuho
  151. Riu Yamashita
  152. Kenta Nakai
  153. Tetsushi Yada
  154. Yusuke Nakamura
  155. Osamu Ohara
  156. Takao Isogai
  157. Sumio Sugano

Corresponding author

Correspondence toSumio Sugano.

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Ota, T., Suzuki, Y., Nishikawa, T.et al. Complete sequencing and characterization of 21,243 full-length human cDNAs.Nat Genet36, 40–45 (2004). https://doi.org/10.1038/ng1285

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