How to retrieve exon list for coding and non coding genes?

[Nazia Ahmad]

UCSC Team

I want to retrieve list of all coding and non coding exons for all coding and non coding genes. How to retrieve this?

I downloaded the repeat masked sequence from UCSC. Is all types of repeats are masked in that sequence?

Regards,

Nazia

[Luvina Guruvadoo]

Hello Nazia,

Thank you for your question. You can download the list of coding and non-coding exons using the Table Browser. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables and make the following selections (I will use the human hg19 assembly in my example):

clade: Mammal

genome: Human

assembly: hg19

group: Genes and Gene Predictions

track: RefSeq Genes (or a different gene track)

table: refGene

output format: selected field from primary and related tables

output file: enter a file name to save your results, or leave blank to display output in the web browser

Click "get output". On the following page, select 'name', 'cdsStart', 'cdsEnd', and any other appropriate fields. Click "get output". Alternatively, you can connect to our public MySQL server and perform the same query. More details can be found here: http://genome.ucsc.edu/goldenPath/help/mysql.html.

To answer the second part of your question, yes, all repeats are masked.

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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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[Luvina Guruvadoo]

Hello Nazia,

I should also note, "BED" output gives you the option of breaking it down into exons. On the Table Browser, select output format: BED - browser extensible data.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

[Nazia Ahmad]

UCSC Team

I want to retrieve repeat masked DNA sequence from UCSC directly typing co-ordinates in web  browser.Is any way of doing that?

Regards,

Nazia

[Jonathan Casper]

Hello Nazia,

You can retrieve DNA sequence directly from the UCSC Genome Browser as follows.

1. Open the Genome Browser at http://genome.ucsc.edu/cgi-bin/hgGateway.
2. Select your species and assembly of choice.
3. Enter the region that you would like to obtain DNA from into the search term box and click "submit".
4. On the resulting page, the top menu bar should now include a "View" dropdown. The second item down will be titled "DNA". Click that item.

You should now be presented with a page for fetching DNA from regions of your chosen assembly, with options for various types of masking and the addition of upstream and downstream regions. Make sure the check the box next to "Mask repeats" if that is what you would like to do. If you click the "extended case/color options" button, you will be presented with additional options for modifying the sequence output.

You may also be interested in the resources on our training page at http://genome.ucsc.edu/training/. The OpenHelix video tutorial there presents several methods of getting sequence from the UCSC Genome Browser, including a discussion of the View -> DNA options.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

On Wed, Aug 19, 2015 at 8:22 AM, Nazia Ahmad <naziaa...@gmail.com> wrote:

UCSC Team

I want to retrieve repeat masked DNA sequence from UCSC directly typing co-ordinates in web  browser.Is any way of doing that?

Regards,

Nazia

On Tue, Jul 7, 2015 at 9:41 AM, Nazia Ahmad <naziaa...@gmail.com> wrote:

UCSC Team

I want to retrieve list of all coding and non coding exons for all coding and non coding genes. How to retrieve this?

I downloaded the repeat masked sequence from UCSC. Is all types of repeats are masked in that sequence?

Regards,

Nazia

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