Synteny Tracks

Some JBrowse versions such as the rat RGSC 3.4 JBrowse contain tracks which show blocks of synteny between rat, mouse and human, and between rat v3.4 and rat v5.0.  (For more information about what synteny is, see the Wikipedia page about synteny.)

In the Available Tracks list, click "Synteny", then select the synteny group you are interested in:  Rat v3.4 versus mouse v37 and human v36, Rat v3.4 versus mouse v37 and human v37, or Rat v3.4 versus rat v5.0.  Then choose the track(s) you are interested in.

 

Synteny blocks are shown as colored bars.  The colors denote the matching chromosome in the other species or assembly, in this case, mouse v37, human v37, or rat v5.0.  Chromosome colors are the same as the UCSC chromosome color codes and are as seen below.

An arrow on the end of the synteny block bar denotes the direction of the gene order in the syntenic region in the other species/assembly relative to the gene order in the rat v3.4 chromosome listed in the search box.  For instance, in the example to the left, the gene order on the human chromosome for "Human37Match 66" (the dark olive bar) goes in the opposite direction relative to both the rat chromosome being displayed and the "Mouse37Match 66 block".

Click here to view the RGD Synteny track example in JBrowse.

Chromosome Color Codes (from UCSC):

Chr HTML Hex Code Color Closest Named Color Chr HTML Hex Code Color Closest Named Color
1 #996600 Golden Brown 13 #358000 Napier Green
2 #666600 Fiji Green 14 #0000CC Medium Blue
3 #99991E Citron 15 #6699FF Cornflower Blue
4 #CC0000 Boston University Red 16 #99CCFF Baby Blue Eyes
5 #FF0000 Red 17 #00FFFF Aqua
6 #FF00CC Hot Magenta 18 #CCFFFF Light Cyan
7 #FFCCCC Pink 19 #9900CC Dark Violet
8 #FF9900 Dark Orange 20 #CC33FF Deep Fuchsia
9 #FFCC00 Gold 21 #CC99FF Lilac
10 #FFFF00 Yellow 22 #666666 Dove Gray
11 #CCFF00 Electric Lime X #999999 Dusty Gray
12 #00FF00 Lime Y #CCCCCC Silver

Synteny track popups contain additional information about the syntenic regions in both the "originating" species or assembly (i.e. the species or assembly whose JBrowse you are currently viewing—"originating" does not refer to phylogeny of the species), and the "target" species or assembly.  In the example to the left, the originating species and assembly is rat RGSC v3.4; the target is human build v37.  The information given in the popup includes:

Source:  This is the name of the source file.  For synteny tracks, the source is "synteny".

Class:  Gives the species and assembly of the target.

Genome location:  The full genomic position of the synteny block in the originating species/assembly, shown in the format Chr:Start..Stop.  This value links to the JBrowse view of the entire syntenic region, which could be longer or shorter than the region currently displayed.

Feature length:  The length in base pairs of the syntenic region in the originating species/assembly (in this case, rat v3.4).

Synteny Block ID:  An arbitrary numerical value assigned to the synteny block in the target species/assembly which matches the syntenic region currently viewed.

Corresponding Synteny Block Location:  The genomic position of the synteny block in the target species/assembly, shown in the format Chr:Start..Stop.  This value links to the JBrowse version for the target species/assembly, showing the entire syntenic region in that species or assembly (opens in a new browser window or tab), facilitating comparisons between the syntenic regions in the two species/assemblies.  The synteny tracks in that JBrowse view will also link back to this one.

Synteny Block Length:  The length in base pairs of the syntenic region in the target species/assembly (in this case, human v37.  The syntenic region in this example is human chromosome 2 between 71,305,636 and 71,411,293, having a length of approximately 110 Kb.).  Note that the length of the synteny blocks in the two species are not the same size, possibly because of errors in the sequences, but more likely because the intergenic and intronic regions have been increased, reduced or both through speciation.

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