text: user16622: 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.
  
  user2108: 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.
  
original_text: 16622: <p>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?</p>
  <p>My annotation data source is the assembly of <em>Phaseolus vulgaris</em> <a href="https://ftp.ensemblgenomes.org/pub/plants/release-55/gff3/phaseolus_vulgaris/" rel="nofollow noreferrer">here</a>.</p>
   2108: <p>Assuming that you know the gene name, you would be able to look it up in a <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0883-6" rel="nofollow noreferrer">transcriptome assembly</a> presumably, or perhaps <a href="https://www.ncbi.nlm.nih.gov/nuccore" rel="nofollow noreferrer">NCBI</a> has a full length transcript (search <code>txid3885[Organism:exp]</code> with your gene name).</p>
  <p>For nearby regulatory DNA, you could consult <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3674728" rel="nofollow noreferrer">an ATAC-seq dataset</a> or <a href="https://www.biorxiv.org/content/10.1101/2022.06.15.496248v1.full.pdf" rel="nofollow noreferrer">other similar</a>, though I doubt that causal links of regulatory DNA to your gene will have been directly assayed.</p>
  