During evolution the genome is slowly reorganized due to chromosomal rearrangements. In fact, such chromosomal reorganization probably is a prominent component in speciation. The amount of reshuffling of the genome between two species will be roughly proportional to the time since they shared a common ancestor. Rat and mouse are two species that are quite closely related in the evolutionary sense, and they diverged about 40 million years ago (Kumar and Hedges 1998). As a consequence, the reshuffling of the genome is not extensive between these two species, and in a recent study we were able to identify autosomal ECSs ("evolutionary conserved segments") covering essentially the entire autosomal part of the genome (Gomez-Fabre et al. 2001). This comparative study provides the foundation for accurate transfer of gene map information between the two species ("prediction mapping").

It is reasonable to assume that there are rat counterparts ("orthologs") for most (if not all) mouse genes. Based on the ECSs, the position of a rat gene can be predicted whenever the corresponding mouse ortholog can be assigned to a defined ECS. Since the mouse gene map (at present) is more advanced than that of the rat, we have been able to predict the position of a total of more that 6000 new rat genes based on this concept. In GAPP, rat genes with predicted positions have been indicated by asterisks.

In this step-by-step tutorial you can become acquainted with the possibilities provided by GAPP. GAPP consists of two main parts:

(1) a RAT LOCUS QUERY for known and/or predicted cytogenetic positions of rat loci

(2) a comparative map defining and positioning mouse ECSs on the RAT ECS IDIOGRAM

You make your selection from the Options Menu in the blue bar on the left of the screen.

This query will generate information about known or predicted cytogenetic locations of rat genes. In this option there are several possible combinations. We will explore some of the possibilities.

Rat Chromosome Button

Allows selection of the desired rat Chromosome.
Example:Which genes can we expect to find on Rat Chromosome 15? Try it!

If you select chromosome 15 and submit the query (by clicking "Start Search") the following information will be displayed (in the bottom of the page the TOTAL NUMBER OF GENES on Rat Chr. 15 is shown. There are 25 records per page and via the page indicators you can be transported to any of the pages with a single click).

On green background (to the left) rat information is shown.

Rat Locus Symbol: Linked to RATMAP. When the gene position is predicted the symbol is shown between asterisks.

Band: Rat Chromosome and cytogenetic bands shown.

Alt Chr: Whenever there is ambiguity in the predicted position (it falls between two ECSs) the alternative position is shown.

On blue background (to the right) mouse information is shown.

Mouse Locus Symbol: Linked to MGD.

Chr: Mouse chromosome.

Pos. (cM): CentiMorgan position on the mouse chromosome.

Note! that if a value is entered both with the Rat and the Mouse Chromosome Buttons a list of genes common to the two chromosomes will be returned.

Rat Locus Symbol

This function allows us to search by locus symbol.
Example:
Where is the trans-acting transcription factor 5 (Sp5) located in the rat? Try it!

The predicted position of the gene is shown.

Note that Truncated Rat Symbol Queries can be made (e g to search for members of a gene family).
Example: How many genes containing "Acad" can be found in GAPP? Try it!

A list of genes is displayed.

Gene Description

Any word present in the gene description can be written here.
Example:
Which genes that contain the description "arthritis" are available in GAPP? Try it!

A list of arthritis genes is returned.

Band

Will return all loci situated in a specific cytogenetic band. Enter the chromosome with the Rat Chromosome Button and write in the cytogenetic band.
Example:
Which genes can be expected in Rat Chromosome 1 band q11?Try it!

Note! that the different options can be combined for optimal queries.
Good gene hunting!

This second option allows you to select the desired chromosome from a visual display of the rat idiogram. Selecting a chromosome by clicking on it in the idiogram will return a detailed description of the ECSs present in the selected chromosome. Thus, clicking on Chromosome 1 will return the following picture:

On the left the rat chromosomal idiogram and next to it the alignment of mouse ECS segments. The Table on the right presents information about each ECS (color coded to conform with the diagram on the left).

The Table has four columns defined as follows:

MMU column identifies the mouse chromosome associated with the particular ECS.

The unlabeled narrow column next to it will have an indication if the mouse segment is inverted compared to the rat.

Range column gives the position of genes defining the segment. Between the brackets the outermost genes which have been actually mapped both in the rat and in the mouse are shown in bold print (figures in parenthesis represent cM values in the mouse). Since it is not always certain (or even probable) that the genes at true ends of the conserved segment have been mapped, a gene symbol (between asterisks) representing the outermost locus that may belong to the ECS is shown. Note! that this prediction is sometimes ambiguous.

Genes column shows the number of genes allocated to the particular segment. The bold figure at the top is the total number of genes presently assigned to the segment, below is the number of genes actually mapped to the segment, and below that the number of genes assigned by prediction mapping. The latter fall into three categories: those inside the segment (figure between brackets), and those predicted at either end (sometimes ambiguous).

When studying the idiograms it is possible to generate locus lists of genes situated in each cytogenetic band by clicking on the particular band.