<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>

CC BY-SA 4.0
2022-12-14T20:59:08.607Z
2022-12-14T20:59:08.607Z
Maximilian Press
<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>

CC BY-SA 4.0
2022-12-09T12:44:53.667Z
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.
Community
CC BY-SA 4.0
2022-12-09T23:21:55.477Z
I think you need to tell us whether the genome has been sequenced. If not the nearest species with a sequenced genome.
M__
CC BY-SA 4.0
2022-12-10T00:24:15.393Z
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?
Maximilian Press
CC BY-SA 4.0
2022-12-10T11:05:40.393Z
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.
user16622
CC BY-SA 4.0
2022-12-14T20:59:04.603Z
updating with notes from comments
Maximilian Press
<sequence-annotation><functional-annotation><tools>
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?
# 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  

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## 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.


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