Difference between revisions of "FlyBase:Recombinant Construct Report"

From FlyBase Wiki
Jump to navigation Jump to search
(documenting changes in FB2021_06)
 
(34 intermediate revisions by 2 users not shown)
Line 2: Line 2:
  
 
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.
 
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 [[FlyBase:Clone Report|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.
 
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).
 
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).
−
 
−
cDNA clones are described in the [[FlyBase:Clone Report|Clone Report]].
 
  
 
This is a field-by-field guide to the information provided in the '''Recombinant Construct Report'''.
 
This is a field-by-field guide to the information provided in the '''Recombinant Construct Report'''.
Line 18: Line 18:
 
|-
 
|-
 
|'''Feature type''' || A single [[FlyBase:Controlled vocabularies used by FlyBase|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.
 
|'''Feature type''' || A single [[FlyBase:Controlled vocabularies used by FlyBase|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, [http://{{flybaseorg}}/reports/FBms0000495.html pCaSpeR-mcs] represents the multiple cloning site segment of the "engineered_construct" [http://{{flybaseorg}}/reports/FBmc0000168.html pP{CaSpeR}], a cloning vector. The "transgenic_transposon" [http://{{flybaseorg}}/reports/FBtp0000155.html P{CaSpeR}] represents only the transposon portion (bound by transposon ends, lacking bacterial replication and selection sequences) of the "engineered_construct" [http://{{flybaseorg}}/reports/FBmc0000168.html pP{CaSpeR}].
 
For example, [http://{{flybaseorg}}/reports/FBms0000495.html pCaSpeR-mcs] represents the multiple cloning site segment of the "engineered_construct" [http://{{flybaseorg}}/reports/FBmc0000168.html pP{CaSpeR}], a cloning vector. The "transgenic_transposon" [http://{{flybaseorg}}/reports/FBtp0000155.html P{CaSpeR}] represents only the transposon portion (bound by transposon ends, lacking bacterial replication and selection sequences) of the "engineered_construct" [http://{{flybaseorg}}/reports/FBmc0000168.html 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. A maximum of ten case-insensitive synonyms are shown - when synonyms differ only by case, the version associated with most papers is reported. This field is suppressed when there are no other synonyms. A full list of synonyms is reported in the '''synonyms and secondary IDs''' section, below.  
+
|'''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:RefMan F.#FlyBase Identifier Numbers|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.
 
|'''FlyBase ID''' || The '''Primary''' [[FlyBase:RefMan F.#FlyBase Identifier Numbers|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. See the '''Component Alleles''' section, below, for more details.
+
|'''Component Alleles'''|| A list of FlyBase-curated alleles that describe the components of the construct. For example: [http://{{flybaseorg}}/reports/FBtp0000026.html 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.
 
|'''Size''' || Size of the recombinant construct, in kilobases. Additional information is to be found in the '''Segments and Sizes''' section, below.
Line 33: Line 32:
 
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.
 
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. 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.
+
|'''Molecular map''' || If available, map generated by FlyBase of the recombinant construct, based on compiled sequence data curated by FlyBase. [http://{{flybaseorg}}/reports/FBmc0000168.html 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". Detailed information is to be found in the '''Expression Data''' 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: [http://{{flybaseorg}}/reports/FBtp0000026.html P{Thb16-lacZ}]. Detailed information is to be found in the '''Expression Data''' section, below.
 
|}
 
|}
  
Line 44: Line 43:
 
{| class="wikitable" style="width: 100%;"
 
{| class="wikitable" style="width: 100%;"
 
|-
 
|-
−
|'''Species''' || style="width: 80%;" | 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. All others are described as "synthetic construct."
+
|'''Species''' || style="width: 80%;" | 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: [http://{{flybaseorg}}/reports/FBms0000567.html 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, gene trap, mobile activating element, deletion generation component.
 
−
|-
 
−
|'''Description''' || A  [[FlyBase:Controlled vocabularies used by FlyBase|controlled vocabulary]] term or terms providing more information about the type construct. Examples: plasmid, cosmid, P-element transposon, Tni\piggyBac transposon, transposon modified in vivo.
 
−
|-
 
−
|'''Uses''' || A  [[FlyBase:Controlled vocabularies used by FlyBase|controlled vocabulary]] term or terms providing information about the how the recombinant construct has been used. Examples: cloning vector, enhancer trap, characterization (of a specific gene), mobile activating element, genomic insertion screen.
 
 
|-
 
|-
−
|'''Cloning sites''' || For cloning vectors only: unique restriction sites suitable for use as cloning sites.
+
|'''Description''' || Short textual description. Filled in for recombinant constructs that are designed to be used as an insertional mutagenesis tool (enhancer trap e.g. [http://{{flybaseorg}}/reports/FBtp0000352.html P{GawB}], protein trap e.g. [http://{{flybaseorg}}/reports/FBtp0072593.html Mi{PT-GFSTF.0}], mis-expression element e.g. [http://{{flybaseorg}}/reports/FBtp0001317.html P{EP}], etc.) or a genome engineering tool (docking element e.g. [http://{{flybaseorg}}/reports/FBtp0018807.html P{CaryP}], RMCE target element e.g. [http://{{flybaseorg}}/reports/FBtp0051711.html Mi{MIC}], etc.).
 
|}
 
|}
  
Line 61: Line 54:
 
|'''Sequence (FB)''' || style="width: 80%;" | 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.
 
|'''Sequence (FB)''' || style="width: 80%;" | 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 or comprising a transposable element, the FlyBase sequence initiates at the 5' end of and reads into that element.)
+
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===
 
===Associated Sequence Data===
  
−
For constructs or segments for which the sequence is available directly from the sequence accession databases, the accession number, and extent within that accession that corresponds to the construct or segment being described. Note that orientation may be reversed, in which case the extent will be indicated with the greater coordinate listed first.
+
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==
 
==Segments & Sizes==
Line 74: Line 67:
 
{| class="wikitable" style="width: 100%;"
 
{| class="wikitable" style="width: 100%;"
 
|-
 
|-
−
|'''Total size ''' || style="width: 80%;" |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. If the size is based upon a length reported in the literature, it is attributed to the source.
+
|'''Total size ''' || style="width: 80%;" |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.
 
|'''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.
Line 80: Line 73:
 
|'''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.
 
|'''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.
+
|'''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 [http://{{flybaseorg}}/reports/FBtp0021815.html P{GSV1}].
 
|}
 
|}
−
 
−
==Features==
 
−
 
−
Fields in this section are attributed data fields, meaning they include citations for the sources of the data.
 
  
 
==Component Alleles==
 
==Component Alleles==
Line 93: Line 82:
 
{| class="wikitable" style="width: 100%;"
 
{| class="wikitable" style="width: 100%;"
 
|-
 
|-
−
|'''Molecular data''' || style="width: 80%;" | A free text description of the overall molecular structure of the component allele, as described in the '''Nature of the lesion''' field in the [[FlyBase:Allele Report|Allele Report]].
+
|'''Molecular data''' || style="width: 80%;" | A free text description of the overall molecular structure of the component allele, as described in the '''Nature of the lesion''' field in the [[FlyBase:Allele Report|Allele Report]]. For example: [http://{{flybaseorg}}/reports/FBtp0003488.html P{hsp-torso<sup>4021</sup>-sev}].
 
|-
 
|-
−
|'''Phenotypic class''' || A list of statements describing the overall phenotypic class of the mutant allele. Each statement contains a  [[FlyBase:Controlled vocabularies used by FlyBase|controlled vocabulary]] term describing the class of phenotype that is observed in the mutant allele, e.g. visible, lethal, eye colour defective.
+
|'''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 [[FlyBase:Allele Report|Allele Report]]. This is described using [[FlyBase:Controlled vocabularies used by FlyBase|controlled vocabulary]] terms, like lethal, eye colour defective, etc.
  
−
See [[FlyBase:Allele Report|Allele Report]] for a more detailed description of this field.
+
"Phenotype Manifest In" - a list of anatomical parts affected by the mutant allele, as reported in the '''Phenotype Manifest In''' field of the  [[FlyBase:Allele Report|Allele Report]]. This is described using [[FlyBase:Controlled vocabularies used by FlyBase|controlled vocabulary]] terms. These terms range from the entire animal to subcellular components and are often specific for a developmental stage.
−
|-
 
−
|'''Phenotype manifest in''' || A list of the parts of the animal affected by the mutant allele, using [[FlyBase:Controlled vocabularies used by FlyBase|controlled vocabulary]] terms. These terms range from the entire animal to subcellular components and are often specific for a developmental stage.
 
  
−
See [[FlyBase:Allele Report|Allele Report]] for a more detailed description of this field.
+
"Detailed Description" - Free text description of the mutant phenotype, as described in the '''Detailed description''' field in the [[FlyBase:Allele Report|Allele Report]].
−
|-
 
−
|'''Other information''' || Free text description of the mutant phenotype, as described in the '''Detailed description''' field in the [[FlyBase:Allele Report|Allele Report]].
 
 
|}
 
|}
  
Line 112: Line 98:
 
===Reporter Expression===
 
===Reporter Expression===
  
−
A structured description of the expression pattern, broken down into stage and anatomical distribution.
+
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===
 
===Additional Information===
Line 120: Line 106:
 
{| class="wikitable" style="width: 100%;"
 
{| class="wikitable" style="width: 100%;"
 
|-
 
|-
−
|'''Assay mode''' || style="width: 80%;" | Indicates whether expression data is based on assay of reporter gene expression or binary (GAL4) reporter gene expression.
+
|'''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  [[FlyBase:Controlled vocabularies used by FlyBase|controlled vocabulary]] anatomical terms.
+
|'''Marker for''' || style="width: 80%;" | If the reporter is used as an anatomical marker, the region or body part is specified, using  [[FlyBase:Controlled vocabularies used by FlyBase|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 [[FlyBase:Gene Report|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".
 
|'''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 [[FlyBase:Gene Report|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).
 
|}
 
|}
  
Line 141: Line 129:
  
 
Miscellaneous free-text comments about the recombinant construct. For junction segments, may include a listing of restriction sites.
 
Miscellaneous free-text comments about the recombinant construct. For junction segments, may include a listing of restriction sites.
−
 
−
==Synonyms & Secondary IDs==
 
  
 
==Stocks Listed in FlyBase==
 
==Stocks Listed in FlyBase==
  
−
A list of the stocks from the public Stock Centers that contain this strain; for each Stock Center, stock number and genotype are displayed. Clicking on the genotype will take you to the appropriate [[FlyBase:Stock Report|Stock report]].
+
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 [[FlyBase:Stock Report|Stock report]].
  
 
==External Crossreferences and Linkouts==
 
==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 Linkouts. Clicking on the accession number or linkout identifier will take you to the appropriate entry in the external database from which they are derived.
+
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, [http://{{flybaseorg}}/reports/FBtp0093701.html P{VT039046-GAL4}]).
 +
 
 +
==Synonyms and Secondary IDs==
  
 
===Reported As===
 
===Reported As===

Latest revision as of 09:34, 15 December 2021

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."
Description Short textual description. Filled in for recombinant constructs that are designed to be used as an insertional mutagenesis tool (enhancer trap e.g. P{GawB}, protein trap e.g. Mi{PT-GFSTF.0}, mis-expression element e.g. P{EP}, etc.) or a genome engineering tool (docking element e.g. P{CaryP}, RMCE target element e.g. Mi{MIC}, etc.).

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}.

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.

Retrieved from "https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Recombinant_Construct_Report&oldid=171488"