Site Report

Overview

Site Reports contain details about DNA sites bound by transcription factors and RNA sites bound by miRNAs. Protein binding sites fall into the following categories:

Transcription factor binding sites within eukaryotic genes, from yeast to human
Artificial sequences resulting from mutagenesis studies, in vitro selection procedures starting from random oligonucleotidemixtures, or from specific theoretical considerations
Consensus binding sequences given in the IUPAC code, many of which orginate from the compilation of Faisst and Meyer, 1992

The first criterion for a site to be included in TRANSFAC is protein binding, the second is function.

Please note: Site Reports are only available for BKL subscribers who have licensed the TRANSFAC module.

Each Site Report is similarly organized and comprises different blocks for properties curated and references cited in the Report. Other BKL Reports mentioned in the Site Report are hyperlinked to the corresponding Reports. For example, transcription factors that bind the site described in the Site Report are listed, with links to their corresponding Locus Reports.

Site Reports may be accessed through the BKL Tools or through hyperlinks on BKL reports.

Anatomy of a Site Report

The general structure of a Transcription Binding Site Report is described below.

Access help by clicking the help menu and clicking the Site report help link.
Navigate to the desired section of the report by opening the table of contents

Points of navigation within the report are indicated by the following visual cues.

Links to additional reports within the BKL are presented as regular text links.
Links to external resources are indicated by a blue bubble, such as the PubMedID link shown here: .
Links to display additional text within the page are indicated by a yellow bubble, such as the show abstract link shown here: .
Links providing an option to download content are indicated by a green bubble, such as the FASTA link shown here: .

Binding Site Information

Describes the characteristics of the transcription factor binding site.

Gene

Identifies the name of the gene the binding site is associated with, hyperlinked to the corresponding Locus Report.

Gene region

Describes the type of functional region the binding site comprises (promoter or enhancer, for example).

Sequence

Provides the sequence of the binding site, as shown in the scientific literature. When authors emphasize a particular motif within a sequence, the motif is displayed in capital letters, while the rest of the sequence is shown in lower case. In case of diverging site borders on both strands, only the overlapping sequence is given. Click here for information about the symbols used to describe sequences. Conflicts with sequences within the EMBL data library are mentioned in the Comments block.

Sequence Type

mRNA sequences that are targets for miRNA interactions are now included in the BKL. This block identifies whether the sequence described is DNA or RNA.

Reference Point

The reference point typically refers to the transcription start site (TSS) (+1); where this is not the case, the reference point is stated explicitly in this block.

Position

Provides the range of nucleotides the element comprises, relative to the transcription start site unless otherwise indicated in the Reference Point block. Click here for additional details about Element Ranges.

Genomic coordinates

For human, mouse and rat sites, when known, provides the genomic position of the site.

Site denomination

Denomination of this site, e.g. based on its binding factor or function, or just in relation to its gene.

Promoters that the element is mapped to

Provides the promoter that the site overlaps with, when relevant.

Binding Factors

Identifies transcription factors experimentally determined to bind the site, with hyperlinks to the corresponding Locus Reports. Also provides a quality designation that gives information about the reliability of the experiment that identified the binding. Click here for details about the Quality scale.

Experimental source

Describes the cellular source (tissue, cell line) used in the experiment that identified the transcription factor binding site and (if applicable) their treatment.

Method

Lists the methods used to identify the transcription factor binding site. For a list of methods, click here.

Comments

Provides free-text comments added by the curator that include additional information that may be helpful to the researcher, including function of the element or comments about conflicts in the scientific literature. In addition, conflicts with sequences within EMBL are identified in the Comments box.

Matrices

Provides nucleotide distribution matrices derived from alignment of this site and other binding sites of a specific factor, with hyperlinks to the corresponding Matrix Reports.

Identifiers

Displays BIOBASE accession numbers, may display external accessions

BIOBASE accession

Displays the BIOBASE accession number.

External identifiers

Displays external identifiers for the binding site.

References

This block gives the full citations, with titles, that correspond to the PubMed identifiers displayed. When a PubMed identifier is not available, the Medline identifier is displayed. When neither a PubMed nor Medline identifier is available, a BIOBASE-specific number is assigned preceded by a "P". Nearly all of the reference numbers are hyperlinked to the Entrez database where the abstracts may be read. All references cited in the annotations and properties section are listed, and other references known to contain information about the protein may also be listed. The first five references are shown, click [ more ...] to view all references. View abstracts via webservice, by additionally clicking the [+] which appears.