FlyBase:Allele Report

Last Updated: 8 November 2006

The Allele Report contains the information for an individual allele.

An allele is a variant of a gene, often induced by mutagenic means. An allele may be defined by genetic/phenotypic characteristics, e.g. by complementation analysis, or in terms of alterations mapped to the known sequence of that gene, or both.

As well as including allele reports for classical mutant alleles and natural variants, e.g. electrophoretic variants, FlyBase also includes reports for alleles that have been introduced into Drosophila via transgenic constructs. See the Nontraditional alleles documentation for a detailed description of these alleles.

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

FlyBase attributes data to the publication that reported it, so that users can easily refer back to the original publication if they wish. Thus, where possible in the fields below, the publication(s) that are the source of the information are listed, typically in parentheses to the right of the data. The exception in the Allele Report is the GENERAL INFORMATION section which contains a summary of the identity of the allele.

General Information

Symbol	The valid symbol that is used in FlyBase for the allele. 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 allele symbol is used throughout FlyBase. For D.melanogaster alleles, the species prefix is only displayed in the GENERAL INFORMATION section at the top of a Report.
Name	The valid full name that is used in FlyBase for the allele.
Feature type	The type of feature described in the report. In this case, "allele".
Associated gene	The gene which the mutant affects. Clicking on the gene symbol will take you to the relevant Gene Report.
Species	The organism that the allele originates from, with the initial letter of the genus and the full species name listed.
FlyBase ID	The Primary FlyBase identifier number of the allele, used to uniquely identify the allele in the database. An allele may also have any number of Secondary FlyBase identifier numbers, which are listed in the SECONDARY FLYBASE IDs section of the Allele Report.
Created/Updated	The date that the allele was entered into the chado database underlying FlyBase (we migrated to the chado database on 2006-08-22) and the date that the allele report was last updated. The dates are in the format: year-mm-dd.
Allele class	A summary list (without the publications that were the source of the information) of controlled vocabulary terms from the FlyBase controlled vocabulary that describe the class of the allele, e.g. "hypomorph" or "gain of function". For a list of allele class terms together with the associated publications, see the Allele class field in the NATURE OF THE ALLELE section of the Allele Report.
Mutagen	A summary list (without the publications that were the source of the information) of controlled vocabulary terms from the FlyBase controlled vocabulary that describe the origin of the allele, typically the mutagen(s) used to induce the mutant allele or the type of in vitro mutagenesis method used to create it. For a list of mutagen terms together with the associated publications, see the Mutagen field in the NATURE OF THE ALLELE section of the Allele Report.

Nature of the Allele

Allele class	A full list (including the publications that were the source of the information) of controlled vocabulary terms from the FlyBase controlled vocabulary that describe the class of the allele, e.g. "hypomorph" or "gain of function".
Mutagen	A full list (including the publications that were the source of the information) of controlled vocabulary terms from the FlyBase controlled vocabulary that describe the origin of the allele, typically the mutagen(s) used to induce the mutant allele or the type of in vitro mutagenesis method used to create it.
Mapped Features and Mutations	A table listing features associated with the allele, that have been mapped to the genome and form part of the annotation of the gene. The table lists the type of feature in the first column. The second column contains the feature's name as well as its location on the genome. The third column lists the evidence type, any associated mapping information, and any comments related to mapping the feature. The fourth column lists the reference used to map the feature.
Associated Sequence Data	A table of sequence accession numbers associated with the allele. Clicking on the accession number will take you to the appropriate entry in the external database from which they are derived. The table contains accession numbers from the following databases: DDBJ/EMBL/GenBank - nucleic acid accession number and associated protein ID number (if applicable). UniProtKB/Swiss-Prot - protein accession number. UniProtKB/TrEMBL - protein accession number. These accession numbers are FlyBase curated links.
Progenitor genotype	For classical alleles, this is the mutant chromosome(s) on which the allele was induced, where the progenitor is relevant to the derivative allele. The progenitor is usually another mutant allele of the same gene, or a transposable element insertion. For non-traditional alleles carried in transgenic constructs, this is typically the allele that was used in vitro as the progenitor. Clicking on the symbol of the progenitor will take you to the relevant Report page.
Nature of the lesion	For classical alleles, this is a free text description of the nature of the mutant lesion. For non-traditional alleles carried in transgenic constructs, this is a free text description of the overall structure of the allele at the end of the cloning process.
Mode of assay	This field is only filled in for non-traditional alleles carried in transgenic constructs. It contains a list of controlled vocabulary terms from the FlyBase controlled vocabulary that describe which assay methods has been used to introduce the allele into Drosophila e.g. Drosophila cell culture, In transgenic Drosophila (intraspecific), for each publication listed.
Caused by insertion	If the allele is caused by an insertion of a transposable element, due to the insertion being within the transcribed extent of the gene and/or resulting in a mutant phenotype due to an effect on the gene, the insertion symbol is displayed in this field. Clicking on an insertion symbol will take you to the relevant Insertion Report. This field is only displayed on an individual Allele Report if it contains data.
Carried in construct	If the allele is carried in a transgenic construct, the transgenic construct symbol is displayed in this field. Clicking on a transgenic construct symbol will take you to the relevant Recombinant Construct Report. This field is only displayed on an individual Allele Report if it contains data.
Tags	This field is displayed in an Allele Report that represents an engineered tag which has been used in a transgenic construct to mark genes or their products. This includes variants of epitope tags such as the EGFP version of "Avic\GFP". The field lists the alleles that contain the tag. Clicking on the symbol will take you to the relevant Allele Report. This field is only displayed on an individual Allele Report if it contains data.
Tagged with	This field is only filled in for non-traditional alleles carried in transgenic constructs. If the allele contains an engineered tag that has been used to mark the gene or its product, the symbol of that tag is displayed in this field. Engineered tags include epitope tags such as "Avic\GFP" and function tags such as nuclear localization signals. Clicking on the tag symbol will take you to the relevant Report. This field is only displayed on an individual Allele Report if it contains data.
Caused by aberration	If the allele is caused by an aberration breakpoint within the locus, the aberration symbol is displayed in this field. Clicking on the aberration symbol will take you to the relevant Aberration Report. This field is only displayed on an individual Allele Report if it contains data.
Carried on aberration	If the allele is carried on an aberration, but separable from the aberration breakpoints, the aberration symbol is displayed in this field. Clicking on an aberration symbol will take you to the relevant Aberration Report. This field is only displayed on an individual Allele Report if it contains data.
Cytology	Free text comments about the cytology of the allele.

Phenotypic Data

Phenotypic Class	A list of statements describing the overall phenotypic class of the mutant allele. Each statement contains a controlled vocabulary term from the phenotypic class section of the FlyBase controlled vocabulary that describes the class of phenotype that is observed in the mutant allele, e.g. visible, lethal, circadian rhythm defective. The phenotypic class term may also be "qualified" with more controlled vocabulary term(s) that further specify the mutant phenotype, for example, describing whether the phenotype is "recessive" or "dominant", or specifying at which stage of development the phenotype is observed, e.g. second instar larval stage. These additional qualifying terms are either from the FlyBase controlled vocabulary or the Development controlled vocabulary. If the mutant phenotype is observed in combination with another allele of the same gene, or a deficiency that affects the same gene, this second allele or deficiency is indicated in parentheses after the controlled vocabulary terms. If the allele is part of a system that requires a driver, such as the UAS-GAL4 system, the driver allele is indicated at the end of the phenotypic class statement, after a comma. Clicking on a controlled vocabulary term will take you to the relevant CV Term Report. Clicking on an allele or deficiency symbol will take you to the relevant Report.
Phenotype Manifest In	A list of the parts of the animal affected by the mutant allele. These terms range from the entire animal to subcellular components and are often specific for a developmental stage. Body part and cell-type terms are from the Anatomy controlled vocabulary, while terms relating to parts of the cell are cellular component terms from the Gene Ontology controlled vocabulary. The body part term may also be "qualified" with more controlled vocabulary term(s) that further specify the mutant phenotype, for example, describing that the body part was affected in an experiment involving a "somatic clone" or is due to a "maternal effect". These additional qualifying terms are from the FlyBase controlled vocabulary. If the mutant phenotype is observed in combination with another allele of the same gene, or a deficiency that affects the same gene, this second allele or deficiency is indicated in parentheses after the controlled vocabulary terms. If the allele is part of a system that requires a driver, such as the UAS-GAL4 system, the driver allele is indicated at the end of the phenotypic class statement, after a comma. Clicking on a controlled vocabulary term will take you to the relevant CV Term Report. Clicking on an allele or deficiency symbol will take you to the relevant Report.
Detailed Description	Free text description of the mutant phenotype. Some of these statements have corresponding controlled vocabulary statements in the Phenotypic class and Phenotype manifest in subsections of the PHENOTYPIC DATA section.

Phenotypic Class

Enhanced by

A list of statements describing phenotypes of this allele that are enhanced by a mutation in another gene.

The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic class subsection of the PHENOTYPIC DATA section of the Allele Report, but in addition, the nature of the interaction (in this case "enhanceable by") and the interacting genotype are listed at the end of the statement.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

NOT Enhanced by

A list of statements describing phenotypes of this allele that are NOT enhanced by a mutation in another gene.

The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic class subsection of the PHENOTYPIC DATA section of the Allele Report, but in addition, the nature of the interaction (in this case "non-enhanceable by") and the interacting genotype are listed at the end of the statement.

|Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

Suppressed by

A list of statements describing phenotypes of this allele that are suppressed by a mutation in another gene.

The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic class subsection of the PHENOTYPIC DATA section of the Allele Report, but in addition, the nature of the interaction (in this case "suppressible by") and the interacting genotype are listed at the end of the statement.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

NOT Suppressed by

A list of statements describing phenotypes of this allele that are NOT suppressed by a mutation in another gene.

The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic class subsection of the PHENOTYPIC DATA section of the Allele Report, but in addition, the nature of the interaction (in this case "non-suppressible by") and the interacting genotype are listed at the end of the statement.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

Enhancer of

A list of statements describing phenotypes of a mutation in another gene that this allele enhances.

Each statement starts with the nature of the interaction (in this case "enhancer"), followed by the phenotype that is being enhanced and then the genotype that is being enhanced.

The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic class subsection of the PHENOTYPIC DATA section of the Allele Report.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

NOT Enhancer of

A list of statements describing phenotypes of a mutation in another gene that this allele DOES NOT enhance.

Each statement starts with the nature of the interaction (in this case "non-enhancer"), followed by the phenotype that is not enhanced and then the genotype that is not enhanced.

The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic class subsection of the PHENOTYPIC DATA section of the Allele Report.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

Suppressor of

A list of statements describing phenotypes of a mutation in another gene that this allele suppresses.

Each statement starts with the nature of the interaction (in this case "suppressor"), followed by the phenotype that is being suppressed and then the genotype that is being suppressed.

The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic class subsection of the PHENOTYPIC DATA section of the Allele Report.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

NOT Suppressor of

A list of statements describing phenotypes of a mutation in another gene that this allele DOES NOT suppress.

Each statement starts with the nature of the interaction (in this case "non-suppressor"), followed by the phenotype that is not suppressed and then the genotype that is not suppressed.

The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic class subsection of the PHENOTYPIC DATA section of the Allele Report.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

Other

A list of statements describing phenotypes involving alleles of more than one gene (including this allele), where it is known that there is an interaction between the alleles, but either the nature of the interaction is not known, or each single mutant by itself does not show a mutant phenotype. Each statement lists the phenotype seen in the double mutant genotype, followed by the interacting allele.

The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic class subsection of the PHENOTYPIC DATA section of the Allele Report.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

Phenotype Manifest In

Enhanced by

A list of body parts where the phenotype for this allele is manifest, for which each phenotype is enhanced by a mutation in another gene.

The body part affected is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic manifest in subsection of the PHENOTYPIC DATA section of the Allele Report, but in addition, the nature of the interaction (in this case "enhanceable by") and the interacting genotype are listed at the end of the statement.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

NOT Enhanced by

A list of body parts where the phenotype for this allele is manifest, for which each phenotype is NOT enhanced by a mutation in another gene.

The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic manifest in subsection of the PHENOTYPIC DATA section of the Allele Report, but in addition, the nature of the interaction (in this case "non-enhanceable by") and the interacting genotype are listed at the end of the statement.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

Suppressed by

A list of body parts where the phenotype for this allele is manifest, for which each phenotype is suppressed by a mutation in another gene.

The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic manifest in subsection of the PHENOTYPIC DATA section of the Allele Report, but in addition, the nature of the interaction (in this case "suppressible by") and the interacting genotype are listed at the end of the statement.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

NOT Suppressed by

A list of body parts where the phenotype for this allele is manifest, for which each phenotype is NOT suppressed by a mutation in another gene.

The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic manifest in subsection of the PHENOTYPIC DATA section of the Allele Report, but in addition, the nature of the interaction (in this case "non-suppressible by") and the interacting genotype are listed at the end of the statement.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

Enhancer of

A list of body parts where the phenotype for a mutation in another gene is manifest, for which each phenotype is enhanced by this allele.

Each statement starts with the nature of the interaction (in this case "enhancer"), followed by the phenotype that is being enhanced and then the genotype that is being enhanced.

The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic manifest in subsection of the PHENOTYPIC DATA section of the Allele Report.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

NOT Enhancer of

A list of body parts where the phenotype for a mutation in another gene is manifest, for which each phenotype is NOT enhanced by this allele.

Each statement starts with the nature of the interaction (in this case "non-enhancer"), followed by the phenotype that is not enhanced and then the genotype that is not enhanced.

The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic manifest in subsection of the PHENOTYPIC DATA section of the Allele Report.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

Suppressor of

A list of body parts where the phenotype for a mutation in another gene is manifest, for which each phenotype is suppressed by this allele.

Each statement starts with the nature of the interaction (in this case "suppressor"), followed by the phenotype that is being suppressed and then the genotype that is being suppressed.

The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic manifest in subsection of the PHENOTYPIC DATA section of the Allele Report.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

NOT Suppressor of

A list of body parts where the phenotype for a mutation in another gene is manifest, for which each phenotype is NOT suppressed by this allele.

Each statement starts with the nature of the interaction (in this case "non-suppressor"), followed by the phenotype that is not suppressed and then the genotype that is not suppressed.

The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic manifest in subsection of the PHENOTYPIC DATA section of the Allele Report.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

Other

A list of statements describing phenotypes involving alleles of more than one gene (including this allele), where it is known that there is an interaction between the alleles, but either the nature of the interaction is not known, or each single mutant by itself does not show a mutant phenotype. Each statement lists the body part affected in the double mutant genotype, followed by the interacting allele.

Clicking on a controlled vocabulary term will take you to the relevant CV Term Report.

Clicking on an allele or deficiency symbol will take you to the relevant Report.

This field is only displayed on an individual Allele Report if it contains data.

Additional Comments

Genetic Interactions

Free text description of genetic interactions involving the allele. Genetic interactions are defined in FlyBase as interactions between alleles of genes derived from the same species that the interaction is being assayed in. Some of these statements have corresponding controlled vocabulary statements in the Phenotypic class and Phenotype manifest in subsections of the INTERACTIONS section.

Xenogenetic Interactions

Free text description of xenogenetic interactions involving the allele. Xenogenetic interactions are defined in FlyBase as either interactions between alleles of genes not normally found in the same species, or interactions being assayed in a species that is not the one in which either of the interacting genes is normally found. Some of these statements have corresponding controlled vocabulary statements in the Phenotypic class and Phenotype manifest in subsections of the INTERACTIONS section.

Complementation & Rescue Data

Complements	A list of alleles reported to be complemented by this allele, where both are alleles of the same gene. Clicking on an allele symbol will take you to the relevant Allele Report. This field is only displayed on an individual Allele Report if it contains data.
Partially complements	A list of alleles reported to be partially complemented by this allele, where both are alleles of the same gene. Clicking on an allele symbol will take you to the relevant Allele Report. This field is only displayed on an individual Allele Report if it contains data.
Fails to complement	A list of alleles reported NOT to be complemented by this allele, where both are alleles of the same gene. Clicking on an allele symbol will take you to the relevant Allele Report. This field is only displayed on an individual Allele Report if it contains data.
Rescued by	A list of alleles reported to rescue this allele, where both are alleles of the same gene. If the rescue experiment used a system that requires a driver, such as the UAS-GAL4 system, the driver allele is also indicated. Clicking on a symbol will take you to the relevant Report. This field is only displayed on an individual Allele Report if it contains data.
Partially rescued by	A list of alleles reported to partially rescue this allele, where both are alleles of the same gene. If the rescue experiment used a system that requires a driver, such as the UAS-GAL4 system, the driver allele is also indicated. Clicking on a symbol will take you to the relevant Report. This field is only displayed on an individual Allele Report if it contains data.
Not rescued by	A list of alleles reported NOT to rescue this allele, where both are alleles of the same gene. If the rescue experiment used a system that requires a driver, such as the UAS-GAL4 system, the driver allele is also indicated. Clicking on a symbol will take you to the relevant Report. This field is only displayed on an individual Allele Report if it contains data.
Rescues	A list of mutations of the same gene as this allele (typically another allele of the same gene, or a deficiency that affects the same gene) reported to be rescued by this allele. If the allele is part of a system that requires a driver, such as the UAS-GAL4 system, the driver allele is also indicated. Clicking on a symbol will take you to the relevant Report. This field is only displayed on an individual Allele Report if it contains data.
Partially rescues	A list of mutations of the same gene as this allele (typically another allele of the same gene, or a deficiency that affects the same gene) reported to be partially rescued by this allele. If the allele is part of a system that requires a driver, such as the UAS-GAL4 system, the driver allele is also indicated. Clicking on a symbol will take you to the relevant Report. This field is only displayed on an individual Allele Report if it contains data.
Fails to rescue	A list of mutations of the same gene as this allele (typically another allele of the same gene, or a deficiency that affects the same gene) reported NOT to be rescued by this allele. If the allele is part of a system that requires a driver, such as the UAS-GAL4 system, the driver allele is also indicated. Clicking on a symbol will take you to the relevant Report. This field is only displayed on an individual Allele Report if it contains data.
Comments	Free text comments related to complementation and rescue data.

Stocks

Clicking on the "Search for Stocks" button allows you to search for stocks that contain this allele.

Notes on Origin

Discoverer

A list of the individuals who identified or generated the allele. Free text comments about the origin of the allele. For example, information that it was simultaneously induced with another mutation, or information about the genotype of the progenitor which is irrelevant to the derivative.

Comments

Miscellaneous free text comments about the allele.

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 allele.
Name Synonym	A list of names that have been used in the literature, or by FlyBase, to describe the allele.

Secondary FlyBase IDs

A list of Secondary FlyBase identifier numbers of the allele.

If an allele 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. See the FlyBase identifier numbers section for some examples of the cases where identifier numbers are made secondary.

References

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