XDB3 is a web data catalogue of NIBB/NIG/NBRP Xenopus laevis EST project. XDB3 is included the more than 250,000 EST information from the NIBB/NBRP cDNA libraries. EST sequences, assembled contig sequences and their simple annotation by BLAST against nr-aa, X.laevis UniGene (NCBI), Xenopus Gene Index (XGI, TIGR) and Xenopus protein databases (NIH) are presented. The corresponding sequences of Xenopus tropicalis are also presented.

You can use the XDB3 for designing PCR primers and Morpholino oligos to clone genes or to knock out genes of your interest. You can also use the XDB3 for viewing the spatial expression patterns from unfertilized egg to tadpole stage with the high quality photo images of whole mount in situ hybridization from several angles. The full insert sequences, of which are selected as the full-length cDNA clones, are also included.

Concurrent project: We are examining the global transcriptome during early developmental process with 40k macroarray, 4.6k nr-microarray, 20k nr-oligo microarray. We are also carrying out the X3000 global functional analysis. It is composed of global gain/loss of function analysis by means of mRNA overexpression, and antisense techniques (Morpholino oligo, RNAi, maternal depletion etc).

What's NEW ?

DATE: 2010-08-27
    The BLAST result of vs. DFCI X.tropicalis Gene Index is added.
DATE: 2010-08-24
    XDB3.2 each BLAST results has been updated.
DATE: 2005-10-12
    dbEST Summary has been updated.
DATE: 2005-09-09
    XDB3.2 Updated.
    3D Models of gene expression patterns are now available !
DATE: 2004-10-01
    XDB3 is now available!


The cDNA libraryies were constructed by Dr. M. Mochii at NIBB.
The EST sequencing was carried out by NIG, Dr. Y. Kohara and his laboratory.
This web interface was made available in collaboration with Drs. I. Uchiyama and H. Nishide (Computer Laboratory of NIBB)


This project was supported by a grant from the "Research for the Future" program (00L01506) of Japan Society for the Promotion of Science, and by Grant-in-Aid for Scientific Research on Priority Areas "Genome Science" (12201001 and 12202050) from the Ministry of Education, Culture, Sports, Science and Technology of Japan.
We thank Dr. N. Shimizu (Keio University), Dr. S. Asakawa (Keio University), and Dr. M. Kondo (The University of Tokyo) for colony picking.
We thank Dr. K. Cho (University of California, Irvin), Dr. M. Taira ( The University of Tokyo), Dr. K. Tashiro (University of Kyusyu), and Dr. C. Niehrs (Deutsches Krebs-forschungszentrum) for helpful discussion.

We thank Dr. Enrique Amaya and Dr. Mike Gilchrist for Xenopus tropicalis full length clone information.