How can I find the mRNA sequence for a specific prokaryotic gene?

Question

What I want to find out is the start of the transcription for a specific gene, how long the UTR is before the actual coding sequence starts.I've looked at various databases like NCBI Gene, Refseq or a specialized one like PRODORIC. But none of them actually contain the mRNA sequence or any information about the untranslated parts of the mRNA. Just the coding sequence itself.Is that kind of information simply not annotated for many bacteria? I'm not looking at model organisms like E. Coli or B. subtilis, but I would have expected some information to be available.Is there a database where I can find the actual transcript sequences for prokaryotic genes?

Answer 1

A good way to find sequence information that is specialized, or specific to your needs, is to find a paper that is relevant to the gene and organism, and have performed sequencing. Such papers, especially related to research submit their raw data or sequences as a part of additional data or appendix information. Reaching out to authors of such papers with a collaboration request and putting your ask that way to them also helps in many cases. USCS Genome Browser is a good tool that encompasses information from all the databases you have mentioned above. They do have the E Coli genome and information on it, but as you said, specific information on UTRs might be difficult to obtain from a database. Good luck!