Synthetic Gene DataBase

SGDB Field Description

AAchanges (integer): It indicates whether there are amino acid substitutions in the re-designed synthetic gene (1=Yes, 0=No, -1=Unknown).
Abstract (text): The abstract of a reference.
AssayMethodForRG (text): The assay methods used for analyzing the protein production or function of the re-designed synthetic gene.
AssayMethodForWTGene (text): The assay methods used for analyzing the protein production or function of the natural gene.
Author (text): The names of authors who published the article.
AuthorAddress (text): The mailing address of the corresponding author of a reference.
Comments (text): Additional notes on the sequences published.
ContactAuthor (text): The corresponding author of the article.
ContactEmail (text): The email of the corresponding author of the article.
Discussion (text): The URL (hyperlink) of the webpage where comments on the article can be posted
EntryConfirmation (Yes/No): Whether a particular record has been approved by the administrators of the SGDB.
ExpressionStrains (text): The name of the strain in which the re-designed synthetic gene was expressed.
GeneID (integer): The unique identifier of the natural (wild-type) gene in the SGDB. It is created automatically by MySQL and used as a primary key in the "WTGene" table and a foreign key in the "RecodedGene" table.
GeneLength (integer): The length in base pairs (bp) of a gene.
GeneName (text): The name of a natural gene.
Issue (text): The volume of the journal where a reference was published.
Journal (text): The name of the journal where a reference was published.
Pages (text): The pages that a reference spanned in the journal where it was published.
ProteinFunction (text): The function of the protein that the natural gene encodes.
PublicationDate (text): The date when a reference was published.
PublicationYear (integer): The year when a reference was published.
PubMedID (integer): The unique identifier of a reference in PubMed (NCBI literature database).
RecodingEffect (text): It summarizes (in abbreviations) the consequence of gene re-design (SIE: significantly increased expression, or >=3 fold increase; IE: slightly increased expression, or < 3 fold increase; EE: equal or similar expression; DE: decreased expression; UE: undetectable expression; NR: not reported).
RecodingMethod (text): The method how the natural gene is recoded (re-designed).
RecodingPurpose (text): The reason why a natural gene is recoded (re-designed).
ReferenceID (integer): The unique identifier of a reference in the SGDB. It is created automatically by MySQL and used as a primary key in the "Literature" table and a foreign key in the "WTGene" table.
ReferenceType (text): The type of a reference, such as Journal Article, Book, Lab Manual and Web Publication.
ResultForWTGene (text): A short summary of the experiment results for the natural gene.
ResultsEvaluation (text): An overall evaluation of the results: whether the goal of the recoding has been achieved.
ResultsForRG (text): A short summary of the experiment results for the re-designed synthetic gene.
RG3End (text): The flanking nucleotide sequence downstream (3') of the coding sequence of the re-designed synthetic gene.
RG5End (text): The flanking nucleotide sequence upstream (5') of the coding sequence of the re-designed synthetic gene.
RGAccessionNumber (text): The unique identifier of a synthetic gene in GenBank at NCBI.
RGGI (integer): The unique identifier of a synthetic gene in GenBank at NCBI.
RGID (integer): The unique identifier of the re-designed synthetic gene in the SGDB. It is created automatically by MySQL and used as a primary key in the "RecodedGene" table.
RGLength (integer): The length in base pairs for a synthetic gene.
RGName (text): The name of the re-designed synthetic gene.
RGNote (text): Additional inforamtion on the re-designed synthetic gene.
RGNucSequence (text): The nucleotide sequence (composed of A, T, C and G) of the re-designed synthetic gene.
SourceSpecies (text): The name (usually Latin name) of the species where the natural gene was from.
SubmitterID (integer): The unique identifier of the submitter in the SGDB. It is created automatically by MySQL and used as a primary key in the "Submitter" table and a foreign key in the "Literature" table.
Summary (text): A short description (critic) of the experiments, usually written by the submitter of a reference.
SynthesizedBy (text): Who synthesized the synthetic gene.
TargetSpecies (text): The name (usually Latin name) of the species where the re-designed synthetic gene was expressed.
Title (text): The full title of a reference.
VectorForRG (text): The name of the expression vector that was used to express the re-designed synthetic gene.
VectorForWT (text): The name of the expression vector that was used to express the natural gene.
Volume (integer): The volume of the journal where a reference was published.
WT3End (text): The flanking nucleotide sequence downstream (3') of the coding sequence of the natural gene.
WT5End (text): The flanking nucleotide sequence upstream (5') of the coding sequence of the natural gene.
WTAccessionNumber (text): The unique identifier of a wild-type (natural) gene in GenBank at NCBI.
WTGI (integer): The unique identifier of a wild-type (natural) gene in GenBank at NCBI.
WTNote (text): Additional inforamtion on a wild-type (natural) gene.
WTNucSequence (text): The nucleotide sequence (composed of A, T, C and G) of the natural gene.
WTStrain (text): The name of the strain from which the natural gene was cloned