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PMID: 12466851 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Nature ·Vol. 420 ·No. 6915 ·2002-12-05 ·Pages 563-73

Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y, FANTOM Consortium, RIKEN Genome Exploration Research Group Phase I & II Team

Abstract

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

MeSH Terms

Alternative Splicing/genetics Amino Acid Motifs Animals Chromosomes, Mammalian/genetics Cloning, Molecular DNA, Complementary/genetics Databases, Genetic Expressed Sequence Tags Genes/genetics Genomics/methods Humans Membrane Proteins/genetics Mice/genetics Physical Chromosome Mapping Protein Structure, Tertiary Proteome/chemistry,genetics RNA, Antisense/genetics RNA, Messenger/analysis,genetics RNA, Untranslated/analysis,genetics Transcription Initiation Site Transcription, Genetic/genetics

Chemicals

DNA, Complementary Membrane Proteins Proteome RNA, Antisense RNA, Messenger RNA, Untranslated

Authors & Affiliations

139 authors, click to expand affiliations / ORCID

Okazaki Y

[1] Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

Furuno M

Kasukawa T

Adachi J

Bono H

Kondo S

Nikaido I

Osato N

Saito R

Suzuki H

Yamanaka I

Kiyosawa H

Yagi K

Tomaru Y

Hasegawa Y

Nogami A

Schönbach C

Gojobori T

Baldarelli R

Hill D P

Bult C

Hume D A

Quackenbush J

Schriml L M

Kanapin A

Matsuda H

Batalov S

Beisel K W

Blake J A

Bradt D

Brusic V

Chothia C

Corbani L E

Cousins S

Dalla E

Dragani T A

Fletcher C F

Forrest A

Frazer K S

Gaasterland T

Gariboldi M

Gissi C

Godzik A

Gough J

Grimmond S

Gustincich S

Hirokawa N

Jackson I J

Jarvis E D

Kanai A

Kawaji H

Kawasawa Y

Kedzierski R M

King B L

Konagaya A

Kurochkin I V

Lee Y

Lenhard B

Lyons P A

Maglott D R

Maltais L

Marchionni L

McKenzie L

Miki H

Nagashima T

Numata K

Okido T

Pavan W J

Pertea G

Pesole G

Petrovsky N

Pillai R

Pontius J U

Qi D

Ramachandran S

Ravasi T

Reed J C

Reed D J

Reid J

Ring B Z

Ringwald M

Sandelin A

Schneider C

Semple C A M

Setou M

Shimada K

Sultana R

Takenaka Y

Taylor M S

Teasdale R D

Tomita M

Verardo R

Wagner L

Wahlestedt C

Wang Y

Watanabe Y

Wells C

Wilming L G

Wynshaw-Boris A

Yanagisawa M

Yang I

Yang L

Yuan Z

Zavolan M

Zhu Y

Zimmer A

Carninci P

Hayatsu N

Hirozane-Kishikawa T

Konno H

Nakamura M

Sakazume N

Sato K

Shiraki T

Waki K

Kawai J

Aizawa K

Arakawa T

Fukuda S

Hara A

Hashizume W

Imotani K

Ishii Y

Itoh M

Kagawa I

Miyazaki A

Sakai K

Sasaki D

Shibata K

Shinagawa A

Yasunishi A

Yoshino M

Waterston R

Lander E S

Rogers J

Birney E

Hayashizaki Y

FANTOM Consortium

RIKEN Genome Exploration Research Group Phase I & II Team

Article Info

Journal

Nature

Abbr.

Nature

ISSN

0028-0836

DOI

10.1038/nature01266

Published

2002-12-05

Pages

563-73

Language

English

Region

England

NLM ID

0410462

Subset

Corrections

CommentIn

PMID: 12466846

CommentIn

PMID: 12511904

CommentIn

PMID: 15495343

External Links

PubMed source DOI: 10.1038/nature01266 View journal details

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Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

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