Example of how to get all mouse gene coordinates using biomaRt:
{{{
library(biomaRt)

mouse <- useMart("ensembl", dataset="mmusculus_gene_ensembl")

# check out what's available
ma <- listAttributes(mouse)

loci <- getBM(attribute=c("ensembl_gene_id", "chromosome_name", "start_position", "end_position", "strand"), mart=mouse)
}}}

{{{
library(biomaRt)

# what marts are available?
listMarts()

bm <- useMart("ensembl")

# what data sets are available?
listDatasets(bm)

bm <- useDataset("dmelanogaster_gene_ensembl", mart=bm)

# for a given list of entrez gene ids, get the flybase ids
eids <- c("35851", "42737", "34411", "35851", "33196", "35851", "43767", "34085", "41565", "41965", "36382", "32772", "41565", "34411", "37618", "43767", "35851", "41565", "40701", "40701", "37618", "33196", "42737", "42737", "42737")

# filter entrezgene
# attributes entrezgene, flybase_gene_id

eid2fb <- getBM(attributes=c("flybase_gene_id"), filters=c("entrezgene"), values=eids, mart=bm)

}}}