Pipeline Status Explanations

On Hold

The default stage when the request is entered into the database.

Vega: Annotation Requested

The first step in the process of making an allele is to manually annotate the gene. This is carried out by the Havana group and the annotation is made publicly available on the Vega website at the next release.

Vega: Annotation Complete

The gene has been manually annotated by the Havana group and if it is not already present on the Vega site, it will be included in the next Vega release.

Vega: Not Annotated - No Evidence

The gene could not be annotated as there was not enough evidence to do so. Requests are put on hold in this status as annotation is required for the design of an allele.

Vega: Annotation Complete - Design Requested

The gene has been manually annotated by the Havana group and has yet to enter the design process.

Vega: Annotation Complete - Design Complete

The gene has been manually annotated by the Havana group and the design of a conditional allele has been generated.

Vega: Annotation Complete - Conditional Design Not Possible

The gene has been manually annotated by the Havana group. Design of a conditional allele has not been possible. Reasons for design failures include the absence of frame-shifting (critical) exons, introns flanking critical exons are too small, too few exons (our vector design strategy requires the presence of at least two exons), etc. Requests are usually put on hold in this status unless other designs (e.g. deletion alleles) are specified.

Vega: Annotated as Pseudogene

Manual annotation of the gene sequence by the Havana group indicates that this is a pseudogene. Requests are put on hold in this status as the annotation indicates the Ensembl predicted gene is not the intended protein-coding gene.

Vega: Not Annotated - Assembly Problems

The gene could not be manually annotated due to problems with the assembly of the sequence. Requests are put on hold in this status as annotation is required for the design of an allele.

Oligos Ordered

Oligos for recombineering have been ordered for the construction of the targeting vectors.

Intermediate Vector Available

A Gateway-adapted intermediate vector has been constructed and has passed sequenced-based QC. These vectors can be requested from the designated EUCOMM repository.

Intermediate Vector Unsuccessful

The construction of the Gateway-adapted intermediate vector was not successful or did not pass sequence-based QC.

Intermediate Vector Unsuccessful - Alternative Design in Progress

The construction of the Gateway-adapted intermediate vector was not successful or did not pass sequence-based QC. Recombineering will be repeated using an alternative valid conditional design.

Intermediate Vector Unsuccessful – No Alternative Design Possible

The construction of the Gateway-adapted intermediate vector was not successful or did not pass sequence-based QC. No alternative valid conditional designs are possible. Requests are put on hold in this status unless other designs (e.g. deletion allele) are specified.

Targeting Vector Available

A final targeting vector (post Gateway) has been constructed, has passed sequence-based QC, and is available for use in ES cells. These vectors can be requested from the designated EUCOMM repository.

Targeting Vector: Initial Attempt Unsuccessful

The construction of a final targeting construct following the Gateway exchange reaction was not successful or did not pass sequence-based QC, pending second attempt.

ES Cells: Targeting Confirmed

Correctly targeted ES cell clones have passed LRPCR/sequenced-based QC. These ES cell clones can be requested from the designated EUCOMM repository.

ES Cells: Promoterless Targeting Unsuccessful

Electroporation of the final targeting construct containing a promoterless selectable cassette yielded an insufficient number of colonies for analysis. The electroporation may be repeated following the construction of a final targeting vector containing a promoter-driven selectable cassette.

ES Cells: Intial Genotyping Unsuccessful

ES cell clones were picked and screened, but have not passed LRPCR/sequenced-based QC. These ES cell clones may be rescreened with additional genotyping primers. These unverified ES cell clones can be requested from the designated EUCOMM repository.