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Do the transcript nucleotide sequences in nucleotide databases include 3'UTR


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5 replies to this topic

#1 humalog

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Posted 19 August 2010 - 11:12 AM

Hi

I wanted to ask:

When we find a transcript sequence, for example in NCBI nucleotide database, is the 3' UTR regions supposed to be included in this sequence?

Let's take for example the mouse p53 gene variant 2, the one on this link: http://www.ncbi.nlm..../NM_001127233.1). Let's look at it's nucleotide sequence: Does it include the 3' UTR region (i.e. the polyadenylation signal, the stop codon, etc) ?

Please explain me, thanks

#2 pcrman

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Posted 19 August 2010 - 12:09 PM

Yes, 3'UTR is included in mRNA sequence or CDs. In your example, you can find the polyA tail in the sequence.

#3 humalog

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Posted 19 August 2010 - 03:31 PM

Yes, 3'UTR is included in mRNA sequence or CDs. In your example, you can find the polyA tail in the sequence.



Yes. Thanks.

#4 humalog

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Posted 01 September 2010 - 11:29 AM

But what about the cases where there seems to be no poly(A) tail at the end of a transcript?

For example http://www.ncbi.nlm....93?report=fasta

Also, in the example I gave, what is this long AAAAAAAAAAAA.... rich region in its beginning and the long TTTTTTTT... at its end?

thanks

#5 humalog

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Posted 01 September 2010 - 11:42 AM

Another related question I have is this:

Should I expect the end to a transcript sequence that I find in a database to contain the poly(A) signal somewhere near its end? Or could the poly(A) signal be more downstream from its end, and therefore not shown in this sequence?

Edited by humalog, 01 September 2010 - 11:42 AM.


#6 HomeBrew

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Posted 01 September 2010 - 12:26 PM

But what about the cases where there seems to be no poly(A) tail at the end of a transcript?

For example http://www.ncbi.nlm....93?report=fasta

Also, in the example I gave, what is this long AAAAAAAAAAAA.... rich region in its beginning and the long TTTTTTTT... at its end?

thanks



Much of this information is annotated in the GenBank record -- see here.




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