The purpose of this database is to organize information about the genes and proteins involved in Arabidopsis initiation, elongation and termination of protein synthesis.
The information is organized by factor. Some factors (eIF2, eIF2B, eIF3 and EF1B) have multiple subunits and the gene(s) for the individual subunits are listed within the factor name. A link is proved ("graphical view of this family") that shows the positions of the genes for a particular factor or its subunits on all five chromosomes. This link was graciously provided by Lukas Mueller of TAIR.
Gene Name. When possible a gene name has been given to the factor or if a gene name already existed, then the previously used gene name is given. There are some factors that have similarity based on protein sequence data, but have not been shown to be a functional member of that family. In these cases, no gene name was assigned.
Source and Publications. The source of the original sequence information is given as a link to the laboratory (when possible) that submited the information or to the Arabidopsis Genome Initiative (AGI) for all gene sequences. In some instances a gene was submitted by an individual laboratory in addition to the AGI information and this is noted as a separate accession number. When possible the PubMed number is linked to publications. The RAFL cDNAs are indicated where available and as this project continues more will be added.
Protein. This column links via the protein accession number to several protein databases. Use the pulldown menu to determine which protein database information you need. BLink provides a graphical alignment to all other similar proteins broken down by species type (plant, mammal, bacteria, etc). Entrez gives sequence information, blastp does a protein search, etc. DART gives information about domains.
mRNA. If a complete or near complete cDNA or a RAFL cDNA is reported for this gene an accession number is given.
Gene. The accession number for the BAC DNA sequence is given.
TC Report. This link gives information about ESTs that match a gene. See also: http://compbio.dfci.harvard.edu/tgi/.
Pub Locus. This column links the unique gene number to several databases via the pull down menu. MIPS reports have information about the # of amino acids, molecular weight, pI, identity, # of ESTs, etc. of the predicted protein in addition to other links. TIGR reports have gene organization (intron/exon) information and sequences for the gene, gene without introns, coding region only and predicted protein. TAIR reports have more detailed information on splice sites, BACs, and a map viewer of BAC location on the chromosome. NCBI reports give detailed map information about chromosome location, BAC information and surrounding genes in addition to MIPS, TIGR and TAIR links for the same gene.
BAC locus. This is the locus that is identified with the gene in the NCBI reports. In some cases there are multiple BACs for a single gene and this information can be found in the TAIR and NCBI reports.
Other links to useful sites. Links to various useful sites, T-DNA Express, GeneVestigator, eFP, AT Gene Express and other sites that use the AT gene identifier have been added as they become available.
Comments. In some cases there is a difference in what is in the databases and what is believed to be the correct sequences. These instances are noted and other useful comments are included.
We welcome comments on this database. If there are suggestions for improvements or errors (or updates) are noted please let us know. We will make every effort to keep the database up to date as more is learned about these genes.
Michael Hoffman--created the programs for gathering, organizing and displaying information on this page while an undergraduate at UT. He is currently a Marshall Scholar at Cambridge studying bioinformatics.
Karen Browning--searched the databases high and low for the genes and maintains the database with occasional advice from Michael.
Research in the Browning lab is supported by NSF, DOE and The Welch Foundation .
This page was created 9-18-2001; last update 01-03-2007