FlyBase:Insertion Report

Last Updated: 1 December 2006

The insertion report is used to present data on insertions of transgenic constructs, insertions of natural transposons in the sequenced strain, and insertions of natural transposons in strains other than the sequenced strain.

This is a field-by-field guide to the information in the Insertion Report.

General Information

Symbol	The valid symbol that is used in FlyBase for the insertion. If the insertion results in a described allele, the allele symbol is included within the insertion symbol. The first part of the symbol (before the '\') is the standard prefix for the species (from the Species Abbreviations list). For species other than D.melanogaster, the species prefix is displayed wherever the gene symbol is used throughout FlyBase. For D.melanogaster genes, the species prefix is only displayed in the GENERAL INFORMATION section at the top of a report.
Name	This field is not used for insertions of transgenic constructs and transposons.
Feature type	A single controlled vocabulary term from the Sequence Ontology (SO), which describes this sequence entity. The feature type transposable_element_insertion_site is used for two classes: insertions of transgenic constructs and insertions of natural transposons into a strain other than the sequenced strain. If mapping data are available, these insertion classes may be mapped to a single site on the sequenced genome. The feature type transposable_element is used for the third class, natural transposons in the sequenced strain. This class is mapped to an extent (or region) on the sequenced genome, corresponding to a specific individual transposon within the sequenced strain (at the time it was sequenced).
Species	The organism in which this specific insertion exists, with the initial letter of the genus and the full species name listed.
FlyBase ID	The Primary FlyBase identifier number of the insertion, used to uniquely identify the insertion in the database. An insertion may also have any number of Secondary FlyBase identifier numbers, which are listed in the SECONDARY FLYBASE IDs section of the Insertion Report.

Description

Inserted element	The transgenic construct inserted (hyperlinked to the relevant Recombinant Construct Report) or the natural transposon class inserted (natural transposons are described in a specially formatted version of the Gene Report). Detailed information is to be found in the INSERTED ELEMENT section, below.
Affected gene(s)	Gene(s) reported to be affected by insertion; the insertion may within the transcribed extent of the gene, and/or may cause misexpression or a reduction in expression (hyperlinked to the relevant Gene Report). This field includes only genes within the genomic region of the insertion; it does not include genes carried on the inserted element. Detailed information is to be found in the AFFECTED GENE(S) section, below.
Causes allele(s)	Allele(s) created by the presence of the insertion (hyperlinked to the relevant Allele Report). This field includes only alleles of genes within the genomic region of the insertion; it does not include alleles carried on the inserted element. Detailed information is to be found in the ALLELES AND PHENOTYPES section, below.
LINE ID	The line identification number used by one of the large-scale gene disruption projects (eg., the BDGP, the GDP, or DrosDel), if relevant. A line identification number refers to an isolated genetic line, and thus may apply to more than one insertion, if multiple insertions are co-isolated. Additional information is to be found in the DATA ON GENETIC LINE section, below.
Expression data	If Ecol\lacZ enhancer trap expression data or Scer\GAL4 reporter/driver data have been curated for this specific insertion, it is indicated by "lacZ reporter" or "GAL4 reporter/driver". Detailed information is to be found in the EXPRESSION DATA section, below.
Viability/fertility	This field is populated if the homozygous stock has been reported as "viable" and/or "fertile". Lethal or sterile phenotypes are not reported; this information is reported in the ALLELES AND PHENOTYPES section, below.
Stock availability	If stocks of this insertion are available, it is indicated by "publicly available" (if available from one of the public stock centers) or "not publicly available" (if stock may be available from an individual lab). Specific information may be found in the STOCKS section, below.

Genomic Location

Chromosome location	The chromosome arm on which the insertion is located, followed by cytological location in parentheses. See Computed cytological data in FlyBase for a detailed description of how this computed cytological location is calculated. See the DETAILED MAPPING DATA section, below, for sources of these data.
Sequence location	Site of insertion on the genomic sequence, if mapped to the sequenced strain. If the precise point of insertion is not known, this value may be a range. See the DETAILED MAPPING DATA section, below, for source of this data.
Map (GBrowse)	A GBrowse thumbnail graphic showing the location of the insertion in the genome. This map is present only for insertions for which the site of insertion has been mapped to the sequenced genome. Insertions are indicated by blue triangles (which indicate orientation of the insertion) or diamonds (if orientation is not known). See also the GBrowse evidence tiers help document. The "GBrowse" link goes to a fully interactive GBrowse view of the same region. Note that one of the "Data Source" options in GBrowse (one of the upper left menu windows) is "Insertions in Stock Collections."

Detailed Mapping Data

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

Chromosome (arm)	Genomic location as reported, if to level of arm or chromosome.
Sequence Location	Genomic location as reported, if mapped at sequence level to the sequenced genome; expressed in whole-arm coordinates of the current genomic sequence release. Includes orientation of the inserted element (if also reported), indicated in brackets.
Orientation	Orientation of the inserted element (using conventional representation of the element's 5' and 3' ends) relative to the conventional representation of the chromosome, if this information is reported without sequence location.
Cytological location (computed by FlyBase)	Inferred cytological location based on reported sequence location (marked as "inferred by FlyBase from sequence location"); or on report of affected gene for which sequence or cytological location is known (marked as "near gene of known cytology").
Cytological location (reported)	Cytological location as reported; marked as "reported as inferred from sequence location" or "in situ hybridization reported".

Sequence Data

Flanking sequence

DDBJ/EMBL/GenBank accession(s) reporting the sequence of the region flanking the inserted element. Clicking on the accession number will take you to the appropriate entry in the external database from which they are derived. These accession numbers are FlyBase curated links.

Inserted Element

The data in this section are promoted from fields in the relevant Recombinant Construct Report or Gene Report

Construct	The transgenic construct inserted (hyperlinked to the relevant Recombinant Construct Report) or the natural transposon class inserted (natural transposons are described in a specially formatted version of the Gene Report).
Location-dependent role	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.
Size	Size of the inserted element, in kilobases. Refer to the relevant Recombinant Construct Report or specially formatted version of the Gene Report representing natural transposons for details and attribution(s).
Associated alleles	Alleles curated by FlyBase describing components of the inserted element (hyperlinked to the relevant Allele Report).
Molecular map	If available, map generated by FlyBase of the inserted element, based on compiled sequence data curated by FlyBase. Refer to the relevant Recombinant Construct Report for compiled sequence data and attribution(s).

Affected Gene(s)

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

Insertion may affect gene	Gene(s) reported as affected by the insertion (hyperlinked to the relevant Gene Report). The insertion may within the transcribed extent of the gene, and/or may cause misexpression or a reduction in expression, or may be related by other specified criteria. This field includes only genes within the genomic region of the insertion; it does not include genes carried on the inserted element.
Orientation (relative to gene)	Not yet implemented: Reported orientation of the inserted element (using conventional representation of the element's 5' and 3' ends) relative to a specified gene. This information most relevant to insertions with directional location-dependent functions, such as gene trap elements and mobile activating elements.

Alleles and Phenotypes

This section describes only alleles of genes within the genomic region of the insertion; it does not include alleles carried on the inserted element. The data in this section are promoted from fields in the relevant Allele reports.

Causes alleles	Allele(s) created by the presence of the insertion (hyperlinked to the relevant Allele Report).
Lethality	A list of reported lethal/viable phenotypes; see Allele Report for further information.
Sterility	A list of reported sterile/fertile phenotypes; see Allele Report for further information.
Phenotype manifest in	A list of body parts reported to be affected in the mutant alleles using controlled vocabulary anatomical terms; see Allele Report for further information.
Detailed description	Free text descriptions of phenotype.

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.
Additional Information	Free text description of reporter expression pattern.
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".
External Images	Linkout to external database(s) that house reporter expression data. Currently: FlyView, A Drosophila Image Database

Data on Genetic Line

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

Line ID	The line identification number used by one of the large-scale gene disruption projects (eg., the BDGP, the GDP, or DrosDel), if relevant. A line identification number refers to an isolated genetic line, and thus may apply to more than one insertion, if multiple insertions are co-isolated.
Origin as a multiple insertion line	If reported that insertion was originally isolated in a genetic line with multiple insertions, "yes" or "probable" is indicated in this field.

Progenitors within the Genome

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

If the insertion that is subject of report is derived from a previously existing insertion, the FlyBase symbol for the originating insertion is indicated here (hyperlinked to the relevant Insertion Report).

Related Aberration or Balancer

Aberration	If the insertion is on an aberration chromosome, or created an aberration, the FlyBase symbol for the aberration is indicated here (hyperlinked to the relevant Aberration Report).
Balancer	If the insertion is on a balancer chromosome, the FlyBase symbol for the balancer is indicated here (hyperlinked to the relevant Balancer Report).

Stocks

A list of the stocks from the public stocks centers that contain this insertion; genotypes may be provided. If there are a large number of such stocks, the list may be truncated. For participating stock centers, clicking on the stock number will take you to the appropriate stock report.

Linkouts

Contains hyperlinks to relevant 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. These links may also be present in other sections of the Insertion Report, where appropriate.

Linkouts FlyView

Comments

Miscellaneous free text comments about the insertion.

Synonyms & Secondary IDs

Reported As

Symbol Synonym

A list of symbols that have been used in the literature, or by FlyBase, to describe the insertion.

Secondary FlyBase IDs

A list of Secondary FlyBase identifier numbers of the insertion. If an insertion 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 insertion, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual Insertion Report.