Search GFP Database Input Help

Search GFP Database

GFP database search allow you to search for the target genes with a variety of parameters. You can perform a simple search by each parameter, and limit your search to target genes with the parameter combination among parameters of gene and protein.

Name

You can search for proteins by the locus name: For sequenced genes, the locus name corresponds to the orf name determined by AGI orf naming convention. AGI orf names have the format AT(1-5)gXXXXXX. Where the value in parenthesis here corresponds to the chromosome number.

Length

The length of the gene is in nucleotide acids. This is genomic sequence including the intergenic sequence of the gene.

Expression Level

The expression level of the gene is expressed by mean intensity, which generated from ~600 microarray experiments by Arabidopsis. These values can provide a 'rough' idea of level of expression.

EST

Expressed Sequence Tags (ESTs) are short DNA sequences, usually based on a single dideoxy sequencing run, representing sequences expressed in an organism under particular conditions.

Chromosome

This option allows you to restrict your search to target genes on a particular chromosome.

Plant Specificity

Plant-specific genes were defined as the genes having no significant matches (e-value<10e-6 using BLASTP) to non-Virdiplantae sequences in the GenBank non-redundant proteindatabase(808,320 entries).

Molecular Weight

The molecular weight is in Daltons.

Predicated Subcellular Location

The subcellular locations were predicted using TargetP. Refer to the TargetP website, which also contains a detailed description of the output.

Membrane Protein

The number of transmembrane domains were calculated using the HMMTOP program. Input parameters: The ATH1.pep protein fasta file. The HMMTOP program is available from http://www.enzim.hu/hmmtop/. (Older versions of the protein search used TMpred for predicting membrane domains. However, HMMTOP seems to give more accurate results. TMPred is available at www.isrec.isb-sib.ch/ftp-server/tmpred/).

Interpro ID

Interpro ID is an accession number for Interpro database. Accession numbers are of the form IPRxxxxxx where the x's are digits. InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.

Date

Date is expressed by YYYY-MM-DD (2003-06-10). This option allow you to get how many genes were done at certain stage (assigned , PCRed, colned, transformed, or imaged) during some time.

User

This option will let you know what genes were done by researchers in different labs.

Primer Design

Primers were designed by modified Primer3 as followings:

The GFP insersion position was selected at 10 Aa of C-terminus (default gfp insersion position in our project).
Design primer2 and primer3 by the formula: Tm=(delta H/(delta S X ln(c/4))-273.15 + 16.6log[Na+] (Nucleic acids research Vol 18, No. 21 6409. Tables of nearest-neighbor thermodynamics for DNA base were fromtable 2 Breslauer Frank, Bolcker, and Markey PNAS Vol 83, 3748.
Use predesigned primer2 as righprimer and designed primer1 by primer3. Use primer as left primer to design primer 4 by primer3.
If the primers were unacceptable, select another GFP insertion position that there is on specific domain around it, and then repeat the process above.

Product size were determined as followings:

For the upstream intergenic sequence, if the length bigger than 3000bp, the product size is 3000 + the lenght between primer 1 and primer 2. If the length shorter than or eque to 3000bp, the product size is the length of downstream intergenic sequence + the lenght between primer 1 and primer 2.
For the downstream intergenic sequence, if the length bigger than 1000bp, the product size is 1000 + the lenght between primer 3 and primer4. If the length shorter than or eque to 1000bp, the product size is the length of downstream intergenic sequence + the lenght between primer 3 and primer4.