Arabidopsis TSS far away from genes

[Carissa Robyn Bleker]

Hi,


I'm trying to extract TSS sites for Arabidopsis, and merged the file available here https://epd.expasy.org/ftp/epdnew/A_thaliana/current/At_EPDnew.sga with Araport11 GFF from TAIR (after checking the differences to TAIR10 are minimal). I calculated the distance from the TSS to the 5'UTR of the gene (considering strand), and found a few of predicted TSS sites unexpectedly far from the gene, for example (with a threshold of 10 kbp):

AT1G75940, AT1G17440, AT1G31550, AT1G65540, AT2G25050, AT3G08720, AT3G08850, AT3G09260, AT3G59690, AT5G34850, AT5G66620.


When I searched for AT1G75940 (with gene feature start at Chr1:28511142), the result shows a promoter at location Chr1:28334941, more than 150kbp from the query gene (confusingly upstream of gene AT1G75490).


https://epd.expasy.org/cgi-bin/epd/get_doc?db=atEpdNew&format=genome&entry=AT1G75940_1
[cid:54f0d376-92f9-46f7-9e12-f131c5b9f34f]

Are these an artifact? Is it plausible to remove TSS's more that 5 kbp away from the 5'UTR?

Best,
Carissa

[Philipp Bucher]

Dear Carissa,

I looked at one of your examples, AT1G75940, and came to the conclusion that this is an error produced by the automatic TSS calling pipeline of EPD. I therefore assume that the other examples mentioned in your mail are also errors.As we will not be able to fix this in the coming weeks, we apologise for the inconvenience it causes to you.

We are nevertheless very grateful to you for having brought this to our attention. Such feedback is essential for making our resource better in the future. Thank you very much!

Best,
Philipp

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[Carissa Robyn Bleker]

Dear Philipp,

Thank you for your reply and explanation. I look forward to an update. In the meanwhile, is there a threshold to use to filter out such TSSs far away from the 5'UTR? In my examples, I used 10 kbp, but maybe 5 kbp is more plausible?

Best,
C





________________________________
From: Philipp Bucher <phb...@gmail.com>
Sent: 25 April 2024 16:02:32
To: Carissa Robyn Bleker
Cc: ask...@googlegroups.com
Subject: Re: [EPD] Arabidopsis TSS far away from genes

Dear Carissa,

I looked at one of your examples, AT1G75940, and came to the conclusion that this is an error produced by the automatic TSS calling pipeline of EPD. I therefore assume that the other examples mentioned in your mail are also errors.As we will not be able to fix this in the coming weeks, we apologise for the inconvenience it causes to you.

We are nevertheless very grateful to you for having brought this to our attention. Such feedback is essential for making our resource better in the future. Thank you very much!

Best,
Philipp

> On 22 Apr 2024, at 17:49, Carissa Robyn Bleker <CarissaRo...@nib.si> wrote:
>
> Hi,
>
>

> I'm trying to extract TSS sites for Arabidopsis, and merged the file available here https://atpscan.global.hornetsecurity.com/index.php?atp_str=fxe1b2ITaM1VXGpZWiBYi0uwTdNjwIEJessttFPxbhM8etK0b5mQi977VSImsIN6zAoBlH9XW9oL_DLJe3gPzuIHlVsbz3cFLTD0ziEEb7SbPLx7pZPAs9ABGZ_jTmv3kC48e7k1nrGeOZ0L3i_c7vxPrNLWRxfLVRSaIw7eHiASh_xOiibaO-71DCEXZoPYUffEyGuh2h95ZA5wCid7C6SfEAYs1983jRlDMFYey8l32bXiMqfRGDlezKSRlmt8OkfHewylMyUelgVyafwO6DmX-xKNkvNnUXAa2FhluWytlKE4CgD_S-x5c4jqFH5_th6SScTFwbGG-RK-Izo6I7YTbjRZMIVZu9FU-iM6OiNfJycdja1q8No0WmbFBLhZ with Araport11 GFF from TAIR (after checking the differences to TAIR10 are minimal). I calculated the distance from the TSS to the 5'UTR of the gene (considering strand), and found a few of predicted TSS sites unexpectedly far from the gene, for example (with a threshold of 10 kbp):

>
> AT1G75940, AT1G17440, AT1G31550, AT1G65540, AT2G25050, AT3G08720, AT3G08850, AT3G09260, AT3G59690, AT5G34850, AT5G66620.
>
>
> When I searched for AT1G75940 (with gene feature start at Chr1:28511142), the result shows a promoter at location Chr1:28334941, more than 150kbp from the query gene (confusingly upstream of gene AT1G75490).
>
>

> https://atpscan.global.hornetsecurity.com/index.php?atp_str=Fgp4LmZNF7diUTg_aa5cFMUh5hRCfpRokVm8TK0zhYBZY_ixI3fHCvQZ1071qJsUu1Csu04LXZdHamKIxnvezsbfSmvK3QMFVZIeE2fUWLZYv_VwhiQU0UihRYSS0Zb9oBjjDdzFFL7EohX0ztPZrX1-7e83bbIV-jk6hhL0riry6sl1YkMETtPJ_oq4xfYDN8WrznY_AHLMp5SLW3BbNruhviyp6b3H_seBdzY8fpFKnZio_Q4NtjMUMjp1aVlxsi377OVmuhdFaWTcgtCKvBxrlwBNswSiQTR0o6jeUlLK_u-Cq9LRZKxKD05Ma_jIlAqVkvAF6VkzwgJhd1G7561I5HoPefRve36mWprqFO4jOjojAnOmOR6kHOQCy3iHIzo6I06YJQ4QpQ_FdrRx6gUV8EY

> [cid:54f0d376-92f9-46f7-9e12-f131c5b9f34f]
>
> Are these an artifact? Is it plausible to remove TSS's more that 5 kbp away from the 5'UTR?
>
> Best,
> Carissa
>
>
>
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> You received this message because you are subscribed to the Google Groups "Ask EPD" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to ask-epd+u...@googlegroups.com.

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> <pastedImage.png>