PI, Joseph R. Ecker, The Salk Institute for Biological Studies, 
10010 N. Torrey Pines Road, La Jolla, CA 92037, Email: [email protected]

Co-PI, Ronald W. Davis, Stanford Genome Technology Center, Stanford University,
855 California Ave, Palo Alto, CA 94304, Email: [email protected]

Co-PI, Athanasios Theologis, Plant Gene Expression Center, U.C. Berkeley, 
800 Buchanan Street, Albany, CA 94022, Email [email protected]



1. Project Summary 

In order to carry out functional genomic and proteomic studies using
the recently completed Arabidopsis genomic sequence, we must be able
to readily manipulate and express each of the genes as proteins.
Unfortunately, current computational approaches for Arabidopsis gene
prediction are unable to precisely predict or, in some cases, even
recognize many of the genes. These limitations prohibit the use of
new emerging technologies for global gene functional analysis. The
aim of our program is to experimentally determine the transcription
units for all Arabidopsis genes  and create a 
gold standard set of
open-reading-frame (ORF) clones. This will provide an accurate
determination of each of the gene structures and allow for the
construction  of full-length cDNAs for each gene. Determining the
full-length sequences for the transcription units will resolve
ambiguities in the computationally annotated genomic sequence,
allowing precise position of introns/exons and 5' transcription start
and 3' polyadenyation addition sites,. The identification of
full-length cDNAs for all Arabidopsis genes is of primary importance
for the entire plant biology community as these clones will be
essential for many future functional genomic and proteomic studies.


2. Deliverables of the SSP Consortium.

Isolation and complete sequencing of full-length cDNAs for 8,000
genes with immediate deposit of cDNA sequences in GenBank.
SSP-sequenced RAFL cDNAs are available through the RIKEN Bioresource
Center
Construction of 8,000 gold standard
 ORF clones in a universal recombination
plasmid vector (pUNI). The ORF clones are fully sequence validated
and are error-free. These clones are deposited in the Arabidopsis
Biological Resource Center (ABRC) at Ohio State University with no
material transfer agreement. Among the 8,000 ORF clones, 7,000 will
be constructed by PCR from full-length cDNAs and 1,000 will be
identified from non-expressed annotated (hypothetical) genes.
Identification of novel Arabidopsis transcription units using
custom Affymetrix genome tiling arrays and mRNA samples prepared from
various plant tissues and conditions.

URL for SSP Consortium Project Deliverables:
http://signal.salk.edu/SSP/index.html

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