International Mammalian Genome Society

The 14th International Mouse Genome Conference (2000)

D2. RIKEN Mouse Full-Length cDNA Clones as a Common Resource: Full-Length cDNA Sequencing Project (Phase2) with Functional Annotation of the Mouse Clones (FANTOM)

Yasushi Okazaki, Yoshihide Hayashizaki, RIKEN Phase1 group, RIKEN Phase2 group, and FANTOM consortium
Genome Exploration Research Group, RIKEN, Genomic Sciences Center (GSC) and Genome Science Laboratory, RIKEN, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-district, YOKOHAMA, 230-0045 JAPAN

We have been working for mouse encyclopedia project, which consists of three phases, (1) collection of full-length cDNAs, (2) sequencing of full-length cDNAs, and (3) mapping of these clones on a certain chromosome. The phase1 project is to collect mouse full-length cDNA clones from various tissues and developmental stages, classifying them based on their 3'-end sequence tags, and constructing the RIKEN non-redundant cDNA clone set. In the phase2, we rearrayed these clones to construct non-redundant cDNA clone set and applied three sequencing strategies. We performed one pass sequencing from both ends of a clone for the short size clones (less than 0.7kb), primer walking for the middle size clones (0.7 - 2.5kb), and the shotgun sequencing for the long size clones (more than 2.5kb). So far, over 20,000 cDNA clones have been sequenced with their average size around 1.2 kb long.

In order to annotate the function of 20,000 full-length mouse cDNAs sequenced in RIKEN, we held the FANTOM (Functional ANnoTation Of Mouse) meeting through 28th August to 8th September. This meeting was also aimed to discuss and establish the international standard of such annotations. To achieve this goal, we have developed a web-based system, named FANTOM+, for annotating functional information of all clones to be facilitated for functional annotation by human effort in the meeting. FANTOM+ does not only include the gene function itself, but many other informative data describing functional information of the gene. These include supplemental descriptions of gene function (gene symbol and its synonym), the functional classification (Gene Ontology, and TIGR EGAD), chromosomal localization (from genetic mapping and physical mapping if available), expression specificity (organ localization and sub-cellular localization of cDNA), mutation information (disease and knockout mouse information), and so on.

In summary, we will report on RIKEN full-length cDNA clones set with functional annotation as a common resource for the scientific community.


[1] Nature Genetics, 25 (4):371, 2000.

[2] Nature, 407:279. 2000.



[5] The Gene ontology: Nature Genetics, 25 (1): 25-29, 2000.

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