RegulonDB RegulonDB 10.6.3: Gene form help
Gene form help



Gene

Name:   Gene name.
Synonyms:   Alternative names that identify the same gene.
Genome position (nucleotides) :  Start and end absolute positions of a gene in a replicon. Strand: Replicon DNA strand in which a gene is coded; it can be forward o reverse.
Nucleotide sequence : Complete nucleotide sequence of the gene.
GC content % : Percentage of guanine and cytosine in the sequence of a gene.
CRI score : Codon-Richness Index (CRI). Quantifies the degree to which individual genes use the most abundant codons in a reference genome.
Notes: Comments added by curators about a gene, acknowledging the original sources of information.
Evidence: Experimental or computational methods that support the definition of a gene.
Reference: Original literature source from where some information about a gene was obtained.
External database links :Links to other databases that refer to a gene.



Shine dalgarno
Sequence: Shine-Dalgarno sequence, shown in capital letters with 10 lowercase flanking nucleotides at both sides.
Notes:  Comments added by curators about a Shine dalgarno sequence, acknowledging the original sources of information.
Evidence:  Experimental or computational methods that support the definition of a Shine-Dalgarno sequence.
Reference:  Original literature source in which a Shine-Dalgarno sequence was identified.
External database links: Links to other databases that refer to the Shine-Dalgarno sequence of a gene.


Product

Product:   Molecule obtained when a gene is expressed, usually a protein or a RNA molecule.
Name:   Product name.
Synonyms:   Alternative names that identify the same product.
Type:   Molecular type of a product, such as regulator or RNA.
Get amino acid sequence : Amino acid sequence of a gene product(protein).
Regulator Family: Evolutionary family to which a regulatory protein belongs, based on sequence similarity.
Cellular location: Location in the cell in which a gene product is functional.
Molecular weight:  Sum of the weights of the atoms of which a gene product is made, usually given in kilodatons (kDa).
Isoelectric point: The pH at which the net charge of a gene product is, on average, zero. Calculated automatically using the EMBOSS parameters.
Motif(s):  Discrete regions of a gene product attached to a particular function.
Type:   Motif type, such as protein motif (for instance Helix-Turn-Helix motif) or RNA motif.
Position within product:   Position of a motif within a gene product.
Sequence:  Complete amino acid/RNA sequence of a motif.
Classification:  Functional classification of a motif based on sequence similarity.
Notes:  Comments added by curators about a gene product, acknowledging the original sources of information.
Evidence:  Experimental or computational methods that support some information about a product.
Reference(s):  Original literature source from where some information about a gene product was obtained.
External database links:   Links to other databases that refer to a gene product.



Operon

Operon: Set of one or more overlapping transcription units which share genes. In RegulonDB, one gene cannot belong to more than one operon.
Name: Operon name, which includes the names of the genes that constitute an operon.
Operon arrangement : Set of transcription units included in the same operon.
Transcription unit (TU) : Set of one or more genes transcribed from a single promoter. A TU may also include regulatory protein binding sites affecting this promoter and a terminator.
Promoters: Names of promoters included in the same operon.
Nebulon NetView : Tool that builds networks of funcional relationships between gene products based on their operon organization in any available genome.





Transcriptional regulation
Transcriptional regulation :  All the known transcriptional regulatory mechanisms that control the expression of a TU.
Activated by :  Names of regulatory proteins that activate or enhance the transcription of a TU.
Repressed by :  Names of regulatory proteins that repress the transcription of a TU.
Undetermined regulation : Names of regulatory proteins whose effects over the transcription of a TU have not been determined.




Growth conditions
Growth condition(s) : Experimental conditions in which a strain was grown affecting gene expression.
Literature based : Growth conditions extracted from literature sources were a few selected genes were studied.
Microarray based : Growth conditions extracted from literature sources reporting microarray experiments in which a whole collection of genes is analyzed.
Reference(s) : Original literature source where some growth condition was reported.




Elements in the selected gene context region unrelated to any object in RegulonDB
Display elements in the gene context region that are not related or linked to any object in RegulonDB.



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