Answers.Body: <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>
  
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Answers.UserDisplayName: Maximilian Press
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-12-09T12:44:53.667Z
Comments.Text: 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.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-12-09T23:21:55.477Z
Comments.Text: I think you need to tell us whether the genome has been sequenced. If not the nearest species with a sequenced genome.
Comments.UserDisplayName: M__
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Comments.CreationDate: 2022-12-10T00:24:15.393Z
Comments.Text: 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?
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-12-10T11:05:40.393Z
Comments.Text: 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). https://ftp.ensemblgenomes.org/pub/plants/release-55/gff3/phaseolus_vulgaris/                    Thank you for the support, I'm new to bioinformatics.
Comments.UserDisplayName: user16622
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Comments.CreationDate: 2022-12-14T20:59:04.603Z
Comments.Text: updating with notes from comments
Comments.UserDisplayName: Maximilian Press
Tags: <sequence-annotation><functional-annotation><tools>
Title: I have a partially described gene from a plant, which tool may I use for predicting regolatory and UTRs sequences from a single DNA fragment?
ThreadText: # I have a partially described gene from a plant, which tool may I use for predicting regolatory and UTRs sequences from a single DNA fragment?
  
  (Asked by: username_0 on 2022-12-09)
  
  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](https://ftp.ensemblgenomes.org/pub/plants/release-55/gff3/phaseolus_vulgaris/).
  
  **Tags:** sequence-annotation, functional-annotation, tools
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_2**: I think you need to tell us whether the genome has been sequenced. If not the nearest species with a sequenced genome.  
  > **username_3**: 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?  
  > **username_0**: 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). https://ftp.ensemblgenomes.org/pub/plants/release-55/gff3/phaseolus_vulgaris/                    Thank you for the support, I'm new to bioinformatics.  
  > **username_3**: updating with notes from comments  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2022-12-14. Score: 1
  
  Assuming that you know the gene name, you would be able to look it up in a [transcriptome assembly](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0883-6) presumably, or perhaps [NCBI](https://www.ncbi.nlm.nih.gov/nuccore) has a full length transcript (search `txid3885[Organism:exp]` with your gene name).
  
  For nearby regulatory DNA, you could consult [an ATAC-seq dataset](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3674728) or [other similar](https://www.biorxiv.org/content/10.1101/2022.06.15.496248v1.full.pdf), though I doubt that causal links of regulatory DNA to your gene will have been directly assayed.
  
  
  ---
  
  