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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?

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  • $\begingroup$ I haven't been able to find that kind of information anywhere. Finding the genomic context is "fairly easy" but the transcription information is much harder to find. You'll probably will have to find transcription elements yourself. $\endgroup$ – Resonating Nov 19 '15 at 14:52
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mRNA specific queries

Add this to your NCBI query: AND mrna[filter]

If it's not available in major databases it may not be known.

However mRNA data can be obscure to find even in those major databases but it should be there. I would be surprised if that is the case, however since you're not working with model organisms there may well be nothing available.

When looking for a transcript gene, NCBI have some tips that you can see here for searching their database. #8 might be relevant to you as it's a way of filtering exclusively mRNA records.

If there is no UniGene cluster for this gene and organism, perform a search in the Nucleotide database with the gene name, product name, or symbol. Include the organism in the search to find the most relevant results and filter for transcript sequences, for example: Cytochrome c AND bullfrog[orgn] AND mrna[filter].

Predicting mRNA

Basic: ExPasy DNA translation tool

Advanced: regrna 2

Assuming that advanced querying doesn't reveal what you need you might be able to make some useful predictions before taking it to the lab. There are a handful of other predictive tools that can maybe help you out if that's the only option available. I can't get my head around exactly what information you have as an input. Assuming you have the DNA sequence, I would start with the obvious choice: the ExPasy DNA translation tool.

I would then say that regrna 2 might be able to steer you in the right direction regarding more subtle translational elements.

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