HOW TO GET DNA SEQUENCE

[Shrinka Sen]

Hi

   I am working on Exon-8 (16,774-17,299) of Human SERPING1 Gene.

I want to get 200 bp of DNA sequences after the end of the gene. How can I get that?

Thanks, and Regards

Shrinka Sen

Project Scientist

CDFD, Hyderabad, India

I have tried searching from UCSC by following this method

Get DNA for

Position: chr11:17,299

Add  200 extra downstream (3')

But getting

>hg38_dna range=chr11:17299-17499 5'pad=0 3'pad=200 strand=+ repeatMasking=lower
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
n

[Robert Kuhn]

Hello, Shrinka,

You have done the right thing, but the first 60,000 bases of chr11 in hg38 is annotated as gap, meaning 

that the sequence is, indeed, N at your coordinates.

best wishes,

    --b0b kuhn

Robert Kuhn, PhD

Robert Kuhn Consulting

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[Hiram Clawson]

Good Evening:

Placing the gene name SERPING1 in the hg38 position/search box
sends the browser to the position:

chr11:57,597,685-57,614,848

for the entire length of the gene on chr11.

The exon 8 as at position: chr11:57,614,328-57,614,582
with UTR extending to chr11:57,614,582-57,614,848

Adjust your coordinates 200 bp from those positions

--Hiram

On 7/15/24 9:52 PM, Shrinka Sen wrote:
> Thanks for your response. I am sorry. I am a little confused. I am not
> interested with the 1st bases of Chr11, rather bases after position 22,300,
> where the gene Human SERPING1 Gene (REGION: 5001..22300) is ending.
> Last exon of Human SERPING1 Gene (Exon 8- 16775..17300). I need a 200 bp
> sequence after that.
>
> I hope I am clear to you.

>
> Thanks, and Regards
>
> Shrinka Sen
>
> Project Scientist
>
> CDFD, Hyderabad, India
>

> On Tue, Jul 16, 2024 at 3:54 AM Robert Kuhn <ku...@soe.ucsc.edu> wrote:
>
>> Hello, Shrinka,
>>
>> You have done the right thing, but the first 60,000 bases of chr11 in hg38
>> is annotated as gap, meaning
>> that the sequence is, indeed, N at your coordinates.
>>
>> best wishes,
>>
>> --b0b kuhn
>>
>> Robert Kuhn, PhD
>> Robert Kuhn Consulting
>>
>>
>> On Mon, Jul 15, 2024 at 12:56 PM Shrinka Sen <shrinka....@gmail.com>
>> wrote:
>>
>>> Hi
>>> I am working on Exon-8 (16,774-17,299) of Human SERPING1 Gene.
>>>
>>> I want to get 200 bp of DNA sequences after the end of the gene. How can
>>> I get that?
>>>
>>> Thanks, and Regards
>>>
>>> Shrinka Sen
>>>
>>> Project Scientist
>>>
>>> CDFD, Hyderabad, India
>>>
>>>
>>> I have tried searching from UCSC by following this method
>>> Get DNA for
>>> Position: chr11:17,299
>>>
>>> Add 200 extra downstream (3')
>>>
>>> But getting
>>>

>>>> hg38_dna range=chr11:*17299-17499* 5'pad=0 3'pad=200 strand=+ repeatMasking=lower

>>> nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
>>> nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
>>> nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
>>> nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
>>> n
>>>
>>> --
>>>
>>> ---
>>> You received this message because you are subscribed to the Google Groups
>>> "UCSC Genome Browser Public Support" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an
>>> email to genome+un...@soe.ucsc.edu.
>>> To view this discussion on the web visit
>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAOmkqUCXfJEBxWjHF1Ve7W%3D9s7TX8juJoRneDJHmijpBJFR1kA%40mail.gmail.com

>>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAOmkqUCXfJEBxWjHF1Ve7W%3D9s7TX8juJoRneDJHmijpBJFR1kA%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>>
>
>

[Shrinka Sen]

Thanks for your response. I am sorry. I am a little confused. I am not interested with the 1st bases of Chr11, rather bases after position 22,300, where the gene  Human SERPING1 Gene (REGION: 5001..22300) is ending. 

Last exon of  Human SERPING1 Gene (Exon 8- 16775..17300). I need a 200 bp sequence after that.

I hope I am clear to you.

Thanks, and Regards

Shrinka Sen

Project Scientist

CDFD, Hyderabad, India

On Tue, Jul 16, 2024 at 3:54 AM Robert Kuhn <ku...@soe.ucsc.edu> wrote: