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FLJ Human cDNA Database


NAR Molecular Biology Database Collection entry number 37
Isogai, Takao
Fukushima Medical University, 1 Hikariga-oka, Fukushima, Fukushima 960-1295, Japan

Database Description

FLJ-DB is updated to FLJ Human cDNA Database. In our human full-length cDNA sequencing project, Japan, we obtained about 30,000 of FLJ human full-length sequenced cDNAs and 1,456,213 of 5'-end sequences (EST) of FLJ full-length cDNAs from about 100 kinds of cDNA libraries consist of human tissues and cells constructed by oligo-capping method. And in our next human splicing variant cDNA sequencing project, Japan, we obtained 11,769 of finished grades of full-length sequenced cDNAs. Then we constructed the sequence analysis databases focused on mRNA variations using human genome and cDNA sequences, 55,427 of our FLJ full-length sequenced cDNAs, 1,565,496 of 5' & 3’-ESTs of our FLJ full-length cDNAs, and other public cDNA sequences including human RefSeq and Ensembl, human gene transcripts, sequences. Moreover, the FLJ Human cDNA Database not only contain sequence information on full-length human cDNAs but also contain sequence information on a huge number of human ESTs generated using the oligo-capping method, allowing us to obtain useful information on ESTs mapped on the same genome locus. Because the average length of our EST sequences was about 500 bases, the diversity of mRNAs produced as a result of alternative splicing could be efficiently analyzed by using this information. In addition, every full-length sequenced FLJ human cDNAs is available from NITE Biological Resource Center, National Institute of Technology and Evaluation, Japan (http://www.nbrc.nite.go.jp/e/hflcdna-e.html). The FLJ Human cDNA Database is accessible at http://flj.lifesciencedb.jp/top/

Recent Developments

FLJ Human cDNA Database ver. 3.2 based on the results of an analysis of variable protein coding transcripts produced from a gene by alternative splicing was constructed. The database graphically display mapping of all the full-length cDNAs in the human genome and their open reading frame (ORF) regions, and thus provides a lot of useful information on the mRNA diversity.

Acknowledgements

This work was partly supported by a grant from New Energy and Industrial Technology Developmental Organization (NEDO) project of the Ministry of Economy, Trade and Industry of Japan.

References

1. Ota, T. et. al. (2004). Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat. Genet., 36, 40-45.
2. Kimura, K. et. al. (2006). Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes. Genome Res., 16, 55-65.
3. Wakamatsu, A., Kimura, K., Yamamoto, J., Nishikawa, T., Nomura, N., Sugano, S. & Isogai, T. (2009). Identification and Functional Analyses of 11,769 Full-length Human cDNAs Focused on Alternative Splicing. DNA Res., 16, 371-383.

Subcategory: Human ORFs

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