Can I get a gene's promoter sequence, e.g. AGL20, in Araport?


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Araport offers several ways to get the up to 3kbp upstream from the transcription start site.

  1. Araport -> ThaleMine -> Templates -> Gene-to-FlankingRegion
    The form lets you ask for the 1kb or 3kp upstream of an AGI. The template query form takes an AGI, an amount of flanking sequence, whether upstream or downstream, and the option to leave out the gene sequence. The results come back as a ThaleMine table from which you can use the “export” button to get a file.

  2. Araport -> ThaleMine -> Home
    Search for your AGI and click on the gene report page (example).
    Scroll down to Genomes / Overlapping Features. Click on “Gene Flanking Regions”. In the table that appears, click on “Fasta” in the row for 3bp upstream. This sends FASTA to the browser. ThaleMine pre-computes flanking regions based on the longest transcript, including UTR, for that locus.

  3. Araport -> Science Apps -> Get-Seqeuence App
    You can install this app in one of your workspaces or just preview it using the Araport main menu -> Tools -> App Store -> Preview this app.
    This has tabs for “search by identifier” or “search by location”. Both let you add up to 4kb of flanking sequence. This app will always include the gene sequence and the upstream and downstream flanking sequence.

  4. Araport -> Web Services -> API Explorer -> get_sequence
    The science app above uses two web services that you could call directly from inside a program. These are called get_sequence_by_coordinate and get_sequence_by_identifier. Each web service has documentation and “try it out” buttons within the API Explorer. Use the /search endpoint for each API.