Frequently Asked Questions:

  1. The space between genes is to small to see the CNEs distinctly. Can I make that space wider?
  2. I initially queried for gene XYZ in dog. How can I change the display so that gene XYZ in mouse is now the reference?
  3. I am only interested in the 5' side of my gene, how can I shift the display to only show the region upstream?
  4. When I "mouse over" a CNE, it does not have orthologous CNEs lighting up in another other species. Why?
  5. I am only interested in comparing a gene between primates and fish, how can I clear the display so that other species are not shown?
  6. My gene of interest has an ortholog in the cat genome but why are there no neighbouring genes in this species?
  7. What does the "A" in a red circle mean?
  8. I typed a well known gene symbol in the entry form but it says that the gene does not exist. Why?
  9. The order of genes from left to right is reversed compared to what I see in Ensembl or UCSC. Why?

The space between genes is to small to see the CNEs distinctly. Can I make that space wider?

You can "zoom in" around the gene in the centre of the display (marked by a vertical black line) by using the cursor on top to specify how many gene you want to see on either side. By default, up to 10 genes are shown on either side of the "query" gene. When zooming in, the genes are redistributed over the width of the display, thus making the intergenic regions "wider". If you want to zoom in on an intergenic region that is not next to the "central" gene, first reset the display around a gene that borders your region of interest (click on "explore the tree of this gene" in the information box) and then zoom in.

I initially queried for gene XYZ in dog. How can I change the display so that gene XYZ in mouse is now the reference?

Click on the name of the species that you want to use as reference on the right hand side of the panel containing the genomic regions. The consequence will be that all the genes in that new species (e.g. mouse) will be coloured, and orthologs in other species will be coloured with reference to the mouse genes.

I am only interested in the 5' side of my gene, how can I shift the display to only show the region upstream?

Use the left and right arrows on either side of the zoom button to shift to the left or the right of the genomic region of interest, while keeping the same gene and same species as reference.

When I "mouse over" a CNE, it does not have orthologous CNEs lighting up in another other species. Why?

There may be two reasons for this:

  1. If a CNE of set 1 (human + mouse + dog) is shown in human for instance, it necessarily exists in the other two species, since this condition is part of the definition of this CNE (see paragraph on CNEs). However in the Synteny Browser we only show "syntenic" CNEs. In order to be syntenic, the three orthologous non-coding regions in their respective genomes must share an orthologous gene within a range of five genes upstream or downstream. Therefore if in mouse for instance the CNE does not verify this condition then it is not shown in mouse.
  2. If a CNE of set 1 (human + mouse + dog) is shown in human, it necessarily exists in the other two species, since this condition is part of the definition of this CNE. Even though in mouse or dog the CNE might be syntenic (see point "a" above) it may not be located in a genomic region that is currently shown on the display. It may lie somewhere "outside" of the display to the left of the leftmost gene or the right of the rightmost gene.

I am only interested in comparing a gene between primates and fish, how can I clear the display so that other species are not shown?

You may hide some extant and ancestral tracks by clicking on the oldest ancestral node of these species (generally a blue circle). The node then becomes underlined to remind you that it is collapsed. Click again to unfold the node again.

My gene of interest has an ortholog in the cat genome but why are there no neighbouring genes in this species?

A number of mammalian species have had their genome sequenced only at low coverage (generally close to 2 X coverage) to provide a first glimpse of the sequence (see the current status of this project at the Broad Institute). Because of the low coverage, the genome assemblies remain fragmented and so we lack long range continuity. The sequence is organised in so-called "scaffolds" and not as chromosomes. A given scaffold may often contain a single gene, hence the reason why it does not have any neighbours on the display.

What does the "A" in a red circle mean?

Strictly speaking, the gene order shown for ancestral species is the order that we predict in the last common ancestor of the extant species located below this node in the tree. We have very little idea of what these last common ancestors looked like and how to represent them graphically. Short of a better idea, we currently use a generic "A" for Ancestor to represent these species.

I typed a well known gene symbol in the entry form but it says that the gene does not exist. Why?

Currently the only genes symbols allowed (other than the Ensembl nomenclature) are human, mouse and zebrafish approved symbols, respectively by the Human Gene Nomenclature Committee, the Mouse Genome Informatics and the ZFIN consortium.

The order of the genes from left to right is reversed compared to what I see in Ensembl or UCSC. Why?

To make comparisons easier, all the chromosome regions on display are oriented using the "root" as reference. In practice, this means that we first determine the orientation of the ancestral version of the query gene (in the root species), then order all the descendent genomic regions with respect to this gene. Sometimes the ancestral and extant genomic regions are in the same orientation and so you don't notice any change compared to Ensembl or UCSC, but sometimes the gene order in the extant species needs to be "flipped" so that it is well aligned with the other genomes. In AlignView, this is indicated by a double arrow under the bloc of genes. Note however that these orders are purely arbitrary and the respective relative gene orders within each regions is obviously unchanged.