I want to retrieve all the upstream/downstream regions of all the genes in several genomes. Is there a good map that tell you the exact position of the genes in a chromosome/genome fasta file, so you can easily extract them? for example - map of all the predicted positions of ENTREZ genes?
biomart/ensembl used to be able to do it easily , but now it seems to be broken, and I cant get all the flanking regions of genes any more without getting into errors.
answer for particular organisms won't be helpful, since I am looking for general method to retrieve from very different genomes, like sponges, sea anemones, mammals, insects etc.. so UCSC and similar services will not help in this case.