RegulonDB RegulonDB 10.7: Operon form Help
Operon form help


Operon

Operon: Set of one or more overlapping transcription units. In RegulonDB, one gene cannot belong to more than one operon.
Name: Operon name, formed by the shortest listing of all genes that constitute an operon. Example: glnALG, nlpD-rpoS.



Transcription unit.
Transcription unit: Set of one or more genes co-transcribed.
Name: TU name formed in the same way as names for operons.
Synonym(s): Alternative names that identify the same TU.
Transcribed Gene(s): Names of genes belonging to the same TU.
+1: First nucleotide transcribed during transcription initiation.
Sigma Factor: Sigma factor used by the RNA polymerase core enzyme to recognize the promoter sequence.
Sequence: Promoter sequence recognized by a sigma factor; it can be of sigma70 or sigma54 type.
Notes: Comments added by curators about a promoter, acknowledging the original sources of information.
Evidence: Experimental or computational methods that support information about a transcription unit.
Reference(s): Original literature source in which a transcription unit was identified.
External database links: Links to other databases that refer to a transcription unit.

Promoter: The DNA sequence that is specifically recognized by the RNA polymerase holoenzyme (with a specific sigma factor bound) to initiate transcription.
Name: Promoter name formed usually by the first transcribed gene, followed by p, or p1, p2. Example: glnAp1
TSS: Transcription start site (TSS) absolute coordinate in the genome. First transcribed nucleotide.
Sigma Factor: Sigma factor used by the RNA polymerase core enzyme to recognize the promoter sequence. Sigmulon link contains a connection to the sigmulon page with all genes transcribed by this sigma factor.
Sequence: Promoter sequence are specific to the sigma factors associated to the RNA polymerase core. A promoter is represented as a stretch of 60 upstream and 20 downstream upper-case nucleotide sequences from the precise initiation TSS (showed in red and capitalized character) of transcription, also called +1. -35 and -10 boxes are indicated for the sigma 70 family of promoters, and -12 and -24 conserved nucleotides for sigma 54 promoters.
Distance to start of the gene: Negative for upstream usual location, and positive if within the gene.
Evidence: Evidence source of information supporting the regulatory interaction of the TF binding to the TFBS and its effect on the regulated promoter.
Reference(s): Original and subsequent literature supporting the evidence behind the regulatory interaction (TF, promoter, function).

Terminator(s): Names of terminator sequences within a TU. Their names are assigned based on the closest upstream gene.
Distance to last transcribed gene: Distance from the central position of the terminator to the last nucleotide of the closest upstream gene.
Type: Type of terminator, Rho-dependent or independent.
Sequence: Sequence of a terminator element, shown as an upper-case segment flanked by 10 nucleotides at both sides.
Notes: Comments added by curators about a terminator with additional information.


TF binding sites (TFBSs):
Regulation: Transcriptional regulation of the promoter that transcribes the TU.
Transcription Factor (TF): Regulatory protein that activates or represses the transcription of a TU upon binding to its specific TF DNA binding sites (TFBSs).
Function: Effect of a TF over the expression of a TU, activation, repression or both (dual).
Promoter: The DNA sequence that is specifically recognized by the RNA polymerase holoenzyme (with a specific sigma factor bound) to initiate transcription.
Binding sites: Physical DNA sites recognized by transcription factors within a genome.
LeftPos: Left absolute position in the genome of a TFBS. Left position is always smaller than RightPos.
RightPos: Right absolute position in the genome of a TFBS. Right position is always larger than LeftPos.
Central Rel-Pos: The central relative position is distance from the transcription start site (+1) of the regulated promoter to the central position of a TFBS. Sites upstream from the promoter are negative, whereas sites downstream from the promoter have positive relative distances. Note that the same physical site can regulate different promoters with different relative distances.
Sequence: Sequence of a transcription factor binding site in the genome.
Evidence (Strong, Weak): Evidence supporting the TFBS. Bold typeface indicates strong or confirmed evidence. For a full list of all evidence codes see: Evidence Classification.
Reference(s): Original literature source supporting knowledge of the TFBS.
Notes: Additional comments about a regulatory interaction.
Regulatory phrases: Collection of TFBSs, usually for the same TF, those participate in a single mechanism of regulation. The TFBSs within a phrase are classified as proximal or remote based on their relative distance to the regulated TSS. Proximal sites are those within the interval from -93 to +20; from where the TF can in principle directly interact with RNA polymerase. All other sites are considered remote, either upstream or downstream.
Type: Sites within a phrase are either proximal or remote (see above ?regulatory phrases?).
Transcription Factor (TF): Regulatory protein that binds to the TFBS.
Function: Activation, repression, both (dual), no effect, or unknown effect in transcription initiation of the regulated promoter by the TF bound to its TFBS.
Promoter: The DNA sequence that is specifically recognized by the RNA polymerase holoenzyme (with a specific sigma factor bound) to initiate transcription.
Binding sites: Physical DNA sites recognized by transcription factors within a genome.
LeftPos: Left absolute position in the genome of a TFBS. Left position is always smaller than RightPos.
RightPos: Right absolute position in the genome of a TFBS. Right position is always larger than LeftPos.
Central Rel-Pos: The central relative position is distance from the transcription start site (+1) of the regulated promoter to the central position of a TFBS. Sites upstream from the promoter are negative, whereas sites downstream from the promoter have positive relative distances. Note that the same physical site can regulate different promoters with different relative distances.
Sequence: Sequence of a transcription factor binding site in the genome.
Evidence (Strong, Weak): Evidence supporting the TFBS. Bold typeface indicates strong or confirmed evidence. For a full list of all evidence codes see: Evidence Classification.
Reference(s): Original literature source supporting knowledge of the TFBS.
Notes: Additional comments about a regulatory interaction.

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