Welcome to the AGRIS tutorial on the ATCISDB

The following tutorial was developed to help guide a new user through conducting a search through the ATCISDB and provides information on using the website as a whole.

AGRIS Homepage-

The header contains links to “HOME” the homepage, the “ATCISDB” a cis-regulatory database consisting of the 5' regulatory sequences of all 25,080 annotated genes with a description of the corresponding cis-regulatory elements. The “ATTFDB” a database of information on almost 1,550 transcription factors (TF) arranged into 39 families. “NSF2010” will provide information about the NSF information of Arabidopsis 2010 project, “DOWNLOADS” will provide information about the data download information for AtcisDB and AtTFDB, “PEOPLE” will provide information about the individuals that have currently contributed to the website, “LINKS” contains links to additional Arabidopsis resources, “NEWS” will provide information about recent updates and events. In addition, there are links to various departments at The Ohio State University that have contributed to the project.

 

Search the ATCISDB

Click on the ATCISDB link

ATCISDB Homepage-

On the ATCISDB homepage, type in a . . .

Gene Symbol: the common gene name

Locus ID: a unique locus name that corresponds to a transcribed region in the Arabidopsis genome. The names were designated as part of the genome sequence annotation and are associated with genes, genetic markers, polymorphic states, or map features. The format of the

LocusID is, AtXgYYYYY. The “At” refers to Arabidopsis thaliana, the “X” number corresponds to the chromosome number, the “g” refers to gene and the 5 following “Y”s correspond to the five-digit code, numbered from top to bottom of the chromosome.

 

Then select the corresponding radio button and click Search.

 

Search Results Page-

Search Results are displayed on the “Search Results” page, each page lists up to 10 records, to view additional records click the “First”, “Next”, “Previous”, or “Last” links. After finding the gene you were looking for you may view a variety of information.

 

Locus ID: by selecting on the locus ID you may view the cis-regulatory elements mapped to the chromosome and a description of each binding site (additional detail in the next section of the tutorial Binding Site Page)

Links: you can view additional information from various Arabidopsis resources TIGR,

MIPS, SALK, and TAIR.

For example, if a search was conducted using MYB15, the following pages would be displayed utilizing the various link.

(M) for MIPS (Munich Institute for Protein Sequences): the MATDB within the

MIPS website contains all Arabidopsis sequences and annotations produced by the

Arabidopsis Genome Initiative plus mitochondrial and chloroplast genomes.

Sequences were consolidated from European sequencing projects, Cold Spring

Harbor Lab, and Washington University. Information obtained from MIPS website includes name, title, function, PROSITE motifs, and Arabidopsis ESTs (as seen in figure below).

(T) for TIGR (The Institute for Genomic Research): An alternative DB of

Arabidopsis sequences and annotations from all AGI labs. The user can view various information about the gene searched on, including Gene Product and Locus name, attributes, gene structure and function (as seen in following figure).

(S) for SALK: Utilizing the SIGnAL Arabidopsis Gene Mapping Tool, it provides a map of the genome area in which the locus is found. On the map, cDNA (full-length cloned copies of mRNA) and T-DNA (sites of insertion of Agrobacterium T-DNA in the Arabidopsis genome) information is displayed in relation to the LocusID entered (as seen in figure below).

(T) for TAIR (The Arabidopsis Information Resource): A genomic data resource collected from a wide variety of sources, with information about genes, markers, polymorphisms, maps, sequences, clones, DNA and seed stocks, gene families and proteins. A link to the TAIR database contains information on TAIR accession number, gene model, description, nucleotide sequence, protein data, and map locations.

Binding Site Page-

If the user clicks on the LocusID from the search page, he/she will be directed to the binding site page, which shows a graphical representation of the Locus with the predicted binding sites, a table with promoter information, and a table listing each of the binding sites with additional information.

Binding Sites Map: The user may slide his/her cursor across the binding sites to see the detail (site name with beginning and ending sites, and the sequence identified) and zoom in or out of the promoter sequence. Zooming in and out will open a new browser and display the new promoter image. Please note if 2 or more transcription factors bind to the same promoter sequence both will not be represented on the image, but both will be listed in the table.

Each box type on the graph is a different color –

1. Blue – promoter motif

2. Red – documented binding sites in a specific promoter

3. Purple – specific binding sites that are found in promoters other than the specific

documented promoter

4. Green – binding sites for a specific transcription factor or transcription factor family

Boxes above the line indicate binding sites in the “+” strand and boxes below the line are binding

sites in the “-“ strand.

The most current list of specific binding sites can be viewed by clicking the “Click here to view the most current list of binding sites and references” link. These are the binding sites that have been documented in various scientific journals and are designated as red on the image.

Promoter Table: In addition to viewing specific binding sites we have included promoter

information. Information includes the promoter Locus ID, description, chromosome location, sequence, and AGRIS type. There are two types of promoters in AtcisDB. Predicted promoters and curated promoters. Predicted promoter sequences were determined by downloading the annotated coding sequences and the chromosomal sequences from TIGR. The coding sequences were mapped to the chromosomal sequences using BLAT. The intergenic region was considered to be the promoter of the next downstream gene, to exclude any coding region of upstream genes. The curated promoters were found by matching 13,181 Full length Arabidopsis cDNAs

from the Riken institute with the predicted promoters from AGRIS. The promoter sequence can be seen by click on the “Get Sequence” link under promoter sequence.

Binding Site Information Table: The user may scroll through the binding sites displayed to find the site of interest to see the gene description and view the promoter sequence by clicking on the “Promoter Sequence” link.

Clicking on the BS name will display the BS on the promoter and binding site information.

BS Genome State and End give the location in the promoter where the motif begins and ends. The sequence shows the user the specific motif found in the promoter. For those binding sites that are associated with a particular TF or TF family, additional information can be obtained by click on the TF family link in the “Binding Site Family/TF” column.