Question: How to get Transcription End site (TES) via ensembl biomart ?
0
gravatar for ZheFrench
7 months ago by
ZheFrench140
France
ZheFrench140 wrote:

Via Biomart you can get TSS coordinates, but I don't see how you can retrieve the TES . I am certainly missing something in biomart...

biomart ensembl • 313 views
ADD COMMENTlink modified 7 months ago by Ben_Ensembl720 • written 7 months ago by ZheFrench140
1
gravatar for Ben_Ensembl
7 months ago by
Ben_Ensembl720
EMBL-EBI
Ben_Ensembl720 wrote:

Hello,

You can't get transcription end site (TES) directly from BioMart, although as you pointed out, you can retrieve transcription start site (TSS) directly as a BioMart attribute. However, you can retrieve 'transcript start (bp)' and 'transcript end (bp)' as attributes from BioMart.

You will have to bear in mind that the start of a transcript is always less than or equal to the end of the transcript, regardless of the strand it is on. For example, a transcript on the reverse strand has a TSS coordinate equal to the coordinate reported for the 'transcript end (bp)'.

In this Biomart query, ENST00000361445 is on the reveres strained, so 'TSS' and 'transcript end (bp)' = 11262507.

I hope this helps but please do get back in touch if you have any further questions.

Best wishes

Ben Ensembl Helpdesk

ADD COMMENTlink written 7 months ago by Ben_Ensembl720
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