FlyBase:Recombinant Construct Report

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Last Updated: 15 December 2017

The Recombinant Construct Report is used to present data on engineered constructs of all types, including transgenic transposons, cloning vectors, and cell culture vectors. A small number of genomic clones are also described using this report, if they were used subsequently to create transposon cloning vectors.

cDNA clones are described in the Clone Report.

For commonly used recombinant constructs, FlyBase has curated detailed descriptions of the component DNA segments. For each individual DNA segment a Recombinant Construct Report has also been created, containing data specific to that segment.

Junction segments: Multiple cloning sites and the resulting small segments between large cloned fragments have been described by FlyBase as "junction" segments. These segments contain the terminal restrictions sites and cloning sites that are likely to change when the larger flanking segments are manipulated. Reports for junction segments typically have very little data: size, sequence if known, and a listing of restriction sites (see Comments section, below).

This is a field-by-field guide to the information provided in the Recombinant Construct Report.

General Information

Symbol The valid symbol that is used in FlyBase for the recombinant construct.
Feature type A single controlled vocabulary term which describes this sequence entity. Three feature types are presented in this report: "transgenic_transposon" for entities bounded by transposon ends and capable of inserting into the genome; "engineered_construct" for other functional constructs, including cloning vectors; and "DNA_segment" for component segments of recombinant constructs.

For example, pCaSpeR-mcs represents the multiple cloning site segment of the "engineered_construct" pP{CaSpeR}, a cloning vector. The "transgenic_transposon" P{CaSpeR} represents only the transposon portion (bound by transposon ends, lacking bacterial replication and selection sequences) of the "engineered_construct" pP{CaSpeR}.

Also known as Symbol synonyms that do not match the current gene symbol or annotation ID but have been used to refer to the gene in at least two papers. This field is suppressed when there are no other synonyms. A maximum of ten case-insensitive synonyms are shown - when synonyms differ only by case, the version associated with most papers is reported. A full list of synonyms is reported in the synonyms and secondary IDs section, below.
FlyBase ID The Primary FlyBase identifier number of the recombinant construct, used to uniquely identify the construct in the database. A construct may also have any number of Secondary FlyBase identifier numbers, which are listed in the synonyms and secondary IDs section, below.
Component Alleles A list of FlyBase-curated alleles that describe the components of the construct. For example: P{Thb16-lacZ}. See the Component Alleles section, below, for more details.
Size Size of the recombinant construct, in kilobases. Additional information is to be found in the Segments and Sizes section, below.
Associated insertions For transgenic transposons only: the number of insertions of this element described in FlyBase, linked to a complete list of those insertions (hyperlinked to the relevant Insertion Reports).

NOTE ABOUT STOCKS: Stocks for a transgenic_transposon are listed under the specific insertions contained in the stocks; they are not indicated in this report.

Molecular map If available, map generated by FlyBase of the recombinant construct, based on compiled sequence data curated by FlyBase. pP{CaSpeR}. For transgenic transposons, the map may show the corresponding plasmid form. Information on compiled sequence is to be found in the Segments and Sizes section, below. Information on the alleles indicated may be found in the Component Alleles section, below.
Expression data For transgenic transposons only: if Ecol\lacZ enhancer trap expression data or Scer\GAL4 reporter/driver data have been curated for this transgenic transposon, it is indicated by "lacZ reporter" or "GAL4 reporter/driver". For example: P{Thb16-lacZ}. Detailed information is to be found in the Expression Data section, below.

Description & Uses

Fields in this section are attributed data fields, meaning they include citations for the sources of the data.

Species For segments that are derived as a continguous extent from a single species, the source species is indicated with the initial letter of the genus and the full species name. For example: lacZ+3.3(-P). All others are described as "synthetic construct."
Location-dependent role For transgenic transposons only: Description of function(s) contained within the inserted element that impact the genomic region of an insertion, or genes within that region. Examples include enhancer trap (e.g., P{lacZ}), gene trap (e.g., PBac{IRES-GFP.GT}), mobile activating element (e.g., P{EP}), deletion generation component (e.g., P{3'.RS5+3.3'}).
Description A controlled vocabulary term or terms providing more information about the type construct. Examples: plasmid (e.g., pBluescript_SK(+)), cosmid (e.g., cosP), P-element transposon (e.g., P{EP}), Tni\piggyBac transposon (e.g., P{Hsp70-PBac\T}).
Uses A controlled vocabulary term or terms providing information about the how the recombinant construct has been used. Examples: cloning vector (e.g., cosP), enhancer trap (e.g., P{lacZ}), characterization of a specific gene (e.g., P{Thb16-lacZ}), mobile activating element (e.g., P{GSV1}, genomic insertion screen (e.g., P{EP}).

Sequence Data

Sequence (FB) This field contains a link to the complete sequence of the construct or segment, as compiled by FlyBase; sequence data are available only for the most commonly used constructs. The compiled sequence is presented in the format of a sequence accession, and is annotated with the extents and sources of component segments. For constructs or segments for which the sequence is available directly from the sequence accession databases, see the Associated sequence data field, below.

If the order or orientation of a FlyBase-compiled sequence differs from that submitted to the sequence accession databases, both are presented. (For constructs containing a transposable element, the FlyBase sequence initiates at the 5' end of and reads into that element.)

Associated Sequence Data

When available, sequence accessions are provided for the construct or segment. The extent of the sequence accession representing the FlyBase construct or segment is indicated in brackets. Note that the orientation of the region in the sequence accession may be reversed, in which case the extent is indicated with the greater coordinate listed first.

Segments & Sizes

Fields in this section are attributed data fields, meaning they include citations for the sources of the data.

Total size Length of the construct or segment, in kilobases. Whenever possible, this is computed by FlyBase based upon the compiled sequence or length of the corresponding extent within a DNA accession, in which case no source is attributed. If the size is based upon a length reported in the literature, it is attributed to the source.
Left end The feature that defines the left end of the construct or segment, if appropriate; typically a transposon terminus or a restriction site. A terminal restriction site is NOT included within the extent of the segment, unless specified. This field is not used for junction segments.
Right end The feature that defines the right end of the construct or segment, if appropriate; typically a transposon terminus or a restriction site. A terminal restriction site is NOT included within the extent of the segment, unless specified. This field is not used for junction segments.
Segments A listing of the component segments of the construct and their orientation; available only for the most commonly used constructs. Each segment listing is hyperlinked to the Recombinant Construct Report for that segment; segments may be composites of further, smaller segments. The FlyBase compiled sequence, assessed from the SEQUENCE DATA section, above, provides an ordered list of each simple segment contained within the described construct. See, for example P{GSV1}.

Features

Features of the construct, such as having a "selectable marker" or being "mobile", are listed here. These features are attributed to publications (citations at the right).

Component Alleles

Alleles curated by FlyBase describing components of the construct (hyperlinked to the relevant Allele Report). The data in this section are derived from the equivalent fields in the Allele Report, where the data are also reported.

Molecular data A free text description of the overall molecular structure of the component allele, as described in the Nature of the lesion field in the Allele Report. For example: P{hsp-torso4021-sev}.
Phenotype Data Links to the allele report where phenotypic data can be found. Data include:

"Phenotypic Class" - the phenotypic class of the mutant allele, as reported in the Phenotypic Class field of the Allele Report. This is described using controlled vocabulary terms, like lethal, eye colour defective, etc.

"Phenotype Manifest In" - a list of anatomical parts affected by the mutant allele, as reported in the Phenotype Manifest In field of the Allele Report. This is described using controlled vocabulary terms. These terms range from the entire animal to subcellular components and are often specific for a developmental stage.

"Detailed Description" - Free text description of the mutant phenotype, as described in the Detailed description field in the Allele Report.

Expression Data

Fields in this section are attributed data fields, meaning they include citations for the sources of the data.

Reporter Expression

A structured description of the expression pattern, broken down into stage and anatomical distribution. Expression statements are sorted by the assay used to detect expression, with the assay listed at the top of each sub-section of expression statements: e.g., "distribution deduced from reporter (Gal4 UAS)".

Additional Information

Free text description of reporter expression pattern.

Statement Free text comments describing the expression pattern of the recombinant construct.
Marker for If the reporter is used as an anatomical marker, the region or body part is specified, using controlled vocabulary anatomical terms.
Reflects expression of If the reporter is described as reflecting the normal expression of an endogeneous gene, the gene is listed, using the FlyBase gene symbol (hyperlinked to the relevant Gene Report). If the expression pattern is described as reflecting a part of the normal expression pattern of that gene, the gene symbol is followed by the term "subset".
Reporter construct used in assay When the construct is a driver, the reporter construct used to detect driver activity is listed (e.g., UAS-GFP).

Progenitors & Descendants

Fields in this section are attributed data fields, meaning they include citations for the sources of the data.

Progenitor(s) Recombinant construct(s) from which the described construct was created. If the progenitor construct is described in FlyBase, the valid FlyBase symbol is indicated and is hyperlinked to the appropriate Recombinant Construct Report.
Descendant(s) Recombinant constructs in FlyBase for which the described construct served as a progenitor. The valid FlyBase symbol is indicated and is hyperlinked to the appropriate Recombinant Construct Report.

Comments

Miscellaneous free-text comments about the recombinant construct. For junction segments, may include a listing of restriction sites.

Stocks Listed in FlyBase

For 'transgenic_transposon' constructs, a list of the stocks from the public Stock Centers that contain this construct; for each Stock Center, stock number and genotype are displayed. Clicking on the genotype will take you to the appropriate Stock report.

External Crossreferences and Linkouts

A complete list of links to external databases for the gene. The Crossreferences sections contain accession numbers which are FlyBase curated links. The Linkouts section contains links maintained by external individuals. Clicking on the accession number or linkout identifier will take you to the appropriate entry in the external database from which they are derived. See, for example, P{VT039046-GAL4}).

Synonyms and Secondary IDs

Reported As

Symbol Synonym A list of symbols that have been used in the literature, or by FlyBase, to describe the recombinant construct.

Secondary FlyBase IDs

A list of Secondary FlyBase identifier numbers of the insertion. If a construct has a secondary identifier number, it generally indicates that at some point it has been merged with or split from other entries in the database.

References

The number in parentheses indicates the number of references listed.

A list of publications that discuss the construct, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual Recombinant Construct Report.