This reference is used to list current 'unspecified' objects in FlyBase, along with metadata describing the type of unspecified entity they represent.

1. 'unspecified' loss of function alleles.

Allele symbol format: gene^unspecified

If a paper describes a loss of function phenotype of a gene, but it is not possible to determine the particular allele (or allele combination) used in the experiment (for example if there not enough information in the paper and there has been no response from authors asking for more details), then as a last resort, FlyBase curators create an 'unspecified' allele so that the phenotypic information can be captured and displayed on the relevant gene page.

Only one allele of this type is generated for each gene, and it is only used for those cases where the context makes it reasonably clear that the phenotype being described is some kind of loss of function.

This means that phenotypic data attached to an unspecified allele may actually correspond to phenotypes of multiple different loss of function alleles or allele combinations. This applies to phenotypes attributed to different publications, but also to phenotypes attributed to the same publication, as the Methods may indicate that multiple loss of function alleles were used in the paper, but an individual Figure may not specify the precise allele(s) used in a given experiment.

Each unspecified loss of function allele is attached to this reference, and the following FlyBase curator comment is added to the description field:

“FlyBase curator comment: this entry is used to capture phenotypic information when the particular allele (or allele combination) used by the author could not be determined but the context of the experiment suggests that the phenotype being described is some kind of loss of function.”

2. 'unspecified' transgenic constructs.

If a paper describes using a transgenic construct, but it is not possible to determine the particular construct used (for example if there not enough information in the paper and there has been no response from authors asking for more details), then as a last resort, FlyBase curators will create an 'unspecified' transgenic construct so that phenotypic information can be captured and displayed (for example on the gene page of the gene expressed by the construct).

A construct of this type is only made when the context makes it clear that the construct was not a new one generated in the paper, and there is enough information from the symbol/description given to be able to determine its basic composition, in particular the nature of the expressed product (e.g. wild-type vs RNAi vs dominant-negative) and the promoter that drives expression.

For each gene, only a single transgenic construct is made for each broad category of construct, e.g. a gene can have only one 'unspecified' construct representing the wild-type gene product expressed under the control of UAS sequences, and only one 'unspecified' UAS-RNAi construct.

This means that phenotypic data attached to such a transgenic construct may actually correspond to phenotypes of multiple different transgenic constructs. This applies to phenotypes attributed to different publications, but also to phenotypes attributed to the same publication, e.g. the Methods may indicate that multiple UAS-RNAi lines were used for a given gene in the paper, but an individual Figure may not specify the particular UAS-RNAi used.

Whenever a new unspecified transgenic construct is made, a description of the category it represents is attributed to this reference, in the relevant description fields (e.g. "UAS sequences regulate expression of geneX", "UAS sequences regulate expression of an RNAi line that targets geneX"). In addition, the following FlyBase curator comment is added to the description field:

FlyBase curator comment: this entry represents a transgenic construct where the particular construct used cannot be determined.