Hi, I have a set of 40 zebrafish genes, and I analyzed the 1000bp upstream of their ATG (accessed through biomart) to look for a specific transcription factor binding site using CLOVER (https://github.com/mcfrith/clover). I have the position of each site as # bp before the ATG and the sequence itself.

gene_site <- data.frame(gene="afg3l2", begin=-123, end=-114,seq="aattgtgta")

I now want to draw each gene (at least 5UTR, introns, and exons) and add a segment to indicate the TF binding site(s). I have managed to do so in R with BiomaRt and gviz:

dr <- useMart("ensembl",dataset="drerio_gene_ensembl")
drTrack <- BiomartGeneRegionTrack(biomart=dr, name="afg3l2", symbol="afg3l2")
plotTracks(drTrack, stackHeight=.1)

resulting in this

But now I have no clue how to add the TF binding site, or even how to expand the line in the 5' direction.

A second issue with this is that it's impossible to plot all the 40 genes one after the other in the same plot, as it tells me that they are in different chromosomes.

Is there a way to do this nicely with biomart and gviz? Is there another, maybe faster, way, even not using R? I can't seem to find good R tools to draw this kind of images.