Is there a way to quickly download UTR information?

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Hi Araport team,

I was wondering if there is a tool on Araport11 website that allows us to quickly bulk download 5'UTR or 3'UTR sequences for multiple genes?

Thanks!!! Larry

Yes, you can use ThaleMine queries to extract UTR sequences

Hello Larry,

Thank you for bringing up this question. You can build custom queries in ThaleMine to bulk download the UTR sequences for all genes.

A typical workflow is as follows:
1) Go to the Query Builder page here
2) Copy/Paste one of the following queries, click 'Submit', and the click 'Show results':

This query extracts both 5' and 3'UTR:

<query model="genomic" view="UTR.gene.primaryIdentifier UTR.primaryIdentifier UTR.sequence.residues" sortOrder="UTR.primaryIdentifier ASC" >
</query>

This query extracts only 5' UTR:

<query model="genomic" view="UTR.gene.primaryIdentifier UTR.primaryIdentifier UTR.sequence.residues" sortOrder="UTR.primaryIdentifier ASC" >
  <constraint path="UTR.primaryIdentifier" op="CONTAINS" value="five_prime" code="A" />
</query>

This query extracts only 3' UTR:

<query model="genomic" view="UTR.gene.primaryIdentifier UTR.primaryIdentifier UTR.sequence.residues" sortOrder="UTR.primaryIdentifier ASC" >
  <constraint path="UTR.primaryIdentifier" op="CONTAINS" value="three_prime" code="A" />
</query>

3) In the result page, click on 'Export', choose FASTA format (from the drop-down menu) to download a text file containing the sequences. You may also choose to export to other relevant formats (tsv, csv) for your downstream analysis.

Please let us know if this addresses what you were looking for, and/or you have additional questions. Thank you.