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I have a partially described gene from a plant with CDS and 3'UTR described but no 5'UTR; if I know the locus and upstream and downstream regions, is there a tool I can use for predicting regulatory DNA and UTRs for a given gene?

My annotation data source is the assembly of Phaseolus vulgaris here.

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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Dec 9, 2022 at 12:44
  • $\begingroup$ I think you need to tell us whether the genome has been sequenced. If not the nearest species with a sequenced genome. $\endgroup$
    – M__
    Dec 9, 2022 at 23:21
  • $\begingroup$ when you say "partially described" what do you mean? what's the name? Do you have any sources of e.g. GFF3 annotation files, a la M__'s question? $\endgroup$ Dec 10, 2022 at 0:24
  • $\begingroup$ Hi, sorry, this is my first post here. So, the plant is Phaseolus vulgaris and is sequenced yet. When I say partially described I mean that I don't have (or can't find) regulatory sequences and in the gff3 file there is not a 5' (the mRNA starts with the first codon). ftp.ensemblgenomes.org/pub/plants/release-55/gff3/… Thank you for the support, I'm new to bioinformatics. $\endgroup$
    – user16622
    Dec 10, 2022 at 11:05
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    $\begingroup$ updating with notes from comments $\endgroup$ Dec 14, 2022 at 20:59

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Assuming that you know the gene name, you would be able to look it up in a transcriptome assembly presumably, or perhaps NCBI has a full length transcript (search txid3885[Organism:exp] with your gene name).

For nearby regulatory DNA, you could consult an ATAC-seq dataset or other similar, though I doubt that causal links of regulatory DNA to your gene will have been directly assayed.

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