obtaining genome sequence promoter

[Aditi Kantipuly]

Hi there- I am trying to obtain the first 200 basepairs downstream from the start of the promoter region. I am wondering what settings (what boxes am I supposed to leave checked/unchecked) ? Please seescreenshot below. 

Thank you

aditi 

[Gerardo Perez]

Hello, Adit.

Thank you for your interest in the Genome Browser and your question about obtaining a genome sequence promoter.

Unfortunately, there is no setting on the "Sequence Retrieval Region Options" page that will retrieve the first 200 basepairs downstream from the start of the promoter region. One way would be to create a custom track that has the start coordinate and the end coordinate both be the transcription start site, e.x.

chr17    43044294    43044294    ENST00000352993.7

You can upload the custom track data on the custom tracks page (http://genome.ucsc.edu/cgi-bin/hgCustom), then navigate to the Table Browser and select the following options:

region: genome
output format: sequence

- Click “get output”
- Enter 200 for the extra downstream (3') text box and click “get sequence”

You can refer to this previously asked question for steps on how to create a custom track that contains the chromosome, transcription start site, and gene name: https://groups.google.com/a/soe.ucsc.edu/g/genome/c/RebB1hzAKdA/m/iThBknmYeQIJ

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[Aditi Kantipuly]

Thanks Gerardo. 

Is it possible to obtain more than one gene sequence at one time? if I have a list of 1000+ genes: what would be the quickest way to get the output of the promoter sequence? 

Aditi 

[Luis Nassar]

Hello, Aditi.

Assuming you have a list of gene names/gene symbols, what you can do is follow the same steps my colleague shared before, except when you create the custom track you will paste your gene symbols as identifiers. Then the output will be a custom track with all of your genes in it and the txStart. You will then follow the same steps to extract the sequence and should receive an output of all the genes.

You can refer to this previous question for assistance on pasting identifiers from gene symbols: https://groups.google.com/a/soe.ucsc.edu/g/genome/c/VuFcq6o41Y4/m/gA0Na2jSCAAJ

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAOC5fns%3DszKTzjM9Txutndorm7Sg7LvOEWMPkejKFkpoLL7eAw%40mail.gmail.com.