About the Exelixis Collection and FAQ

The Exelixis Collection was generated by Exelixis Inc. and donated to us to be distributed to the academic research community.  In addition, a subset of these stocks were also donated to and may be found at the Bloomington Drosophila Stock Center at Indiana University.

The Bloomington Stock Center also carries several other resources donated by Exelixis which are unavailable from us including:

Since we did not generate the stocks ourselves and have not had the resources to confirm the insertion site of each stock sent to us, we strongly encourage confirming the insertion sites in stocks that you plan on investigating in greater depth.

The following pages will provide you with the means to gather relevant information about the collection:

FAQ

What is the genotype of my stock?

Genotypes would be best determined by consulting FlyBase , then: 1) Enter the Exelixis Stock ID into the “Enter text” of the QuickSearch field. 2) Click on the Exelixis entry (usually the first option, if there is a list). 3) Click on the designation entered into the FlyBase Genotype line. If the transgene has been inserted into a known gene, it will appear in the Affected gene(s) line. If not, then it has not yet been characterized.

 Why do I see multiple eye colors in my stock?

Multiple eye colors can arise for a number of reasons, among which are: 1) Flies continuously produce eye pigments and the eyes will darken with age. Freshly eclosed flies will look much lighter than their parents. 2) The transposons include the white mini-gene, which acts as though it is still on the X chromosome and engages in dosage compensation, even when inserted on an autosome (which is the case for a great majority of the collection). As such, males will most often have more eye color than females of the same age, keeping in mind these males are not hemizygous (as would be the as if the insert was on the X). The mechanisms underlying dosage compensation is still an area of active research, so the rationale as to why the transposons containing the white mini-gene act in such a manner is unclear. 3) Some fly lines are homozygous viable but may still include the balancer over which it was characterized, either CyO or TM6B, in the stock. Here, the homozygous viable flies will have two copies of the transgene, while the ones heterozygous over the balancer will have only one. 4) The line may be in the process of breaking down. If the insertion site is for some reason unstable, the transgene may “hop out” leaving a mixture of homozygous, heterozygous and white eyed flies.

 Why do I see unexpected dominant markers in my stock?

Under construction

Inverse PCR/Insertion Site

 I’d like to confirm the insertion site of a transposon by inverse PCR. Do you have a protocol/primer sequences that I can use?

Please visit our iPCR protocols page for further information.

 I tried to confirm the insertion site in a stock and found that it differs from the annotated site. What’s going on here?

If have found the insertion site to be off by about 200 nt, and you are referring to the data provided in Supplementary Table 3 of Thibault, et. al, you should read the following paragraphs to more fully understand the data.  Otherwise, please Contact Us us and let us know what the problem is.

The keys to reading the data in Supplementary Table 3 are the following:

The first two letters refer to the element type. (XP, PB, RB or WH)
The second entry is the stock number. (one letter followed by five digits)
The third entry indicates the number of flanking sequences are associated with that particular stock.  In some cases this represents multiple inserts per stock, in others this may represent erroneously assigned sequence files (more on this later).
The fourth entry is the R3 coordinate of the insertion site.
The fifth entry is the chromosome arm.  U is unknown.
The sixth entry is the orientation of the element in the chromosome.
Finally, the flanking sequence data completes the set of data.  As a general rule, the first 200 nt precede the transposon while the remaining 201 nt are 3' to the insertion site.

All of this data is in the process of being refined.  Insertion sites should be considered approximate.  In the case of multiple flanking sequences for a given line, one should assume the existence of multiple inserts until proven otherwise.

Exelixis Deficiencies

I’d like to get an Exelixis deficiency, why can’t I find any in your stock list?

We do not carry any of the Exelixis deficiencies, however, they are available from the Bloomington Stock Center at: List of Exelixis Deficiencies.

I’d like to make a deficiency using Exelixis stocks. How do I go about this?

If you'd like to learn more about this, read Parks, et al. for a description of the stocks and crosses involved.

If you'd like to get some of the stocks necessary to generate deficiencies, please visit the Bloomington Stock Center's page that lists some of these stocks.