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Help needed about 5' UTR


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6 replies to this topic

#1 kedar

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Posted 17 October 2009 - 09:04 AM

Hi everyone,

I am confused.
I don't know whether everything infront of ATG is considered 5'UTR or not?
for specific example,
http://www.ensembl.o...ENSG00000213927

is 5'UTR CCTCCTCAGCCAGAAGGGCCTGCTCTAGGGACCCATTCCCATCCATTTCTTCTGATAAGA
CAGGCAGGCCAAGCCAGGAAGTGGGGAGGAGAAGGTGAAGGCAAGTTGGTGCTTGCCTGC
CCTCTGCTCCCACCCCACCCACAACTCCCCTGTCAGAATCTGTGTGTGCTAGTGTGAATT
TGCTTGTGATTGGATGACTGTGAAAACACAATTGGGTGGGAGAGGGACTTTGAGTATAAC
CGGGGCTATATAATTTTGTCTACGGTTGTCTGATCATGAGTATGACTTTGTGAGGTTGAC
CAAGTGATTGAGGAGTGACTTTGAATGTGTGGCTATGCGTATTTGAGTGTGAATGTCTAT
CATTAGATGCTGCTGTGGATGCTTGACTGCCCTTACTCACTGTTCCATCAGTCCCTACAT
CACACACTAATCCTTCCCCCAGCTTCACTGCCCAGAGCTTAGGAGCACATGGGAAATGGC
TATCCTAGATGAGGAAGGAGTCTGTGGCAACAGGCCGAGAATTAGGGCCCAGGAGTGTCA
CAGGTTACACAGTACATCTCCAACTGCCTCTGACTCACCTAGTGCCCCAGGTAAAAGGCA
CCCAGATAAAAGGTAGGGGAGGAGGAGAGAGAGAGAAGGAAGAGTCTAGGCTGAGCAAC ?

or just CCCAGATAAAAGGTAGGGGAGGAGGAGAGAGAGAGAAGGAAGAGTCTAGGCTGAGCAAC?

similarly, which is the 3' UTR?


any help would be appreciated.


thanks

#2 kedar

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Posted 17 October 2009 - 09:58 AM

shit, already 14 views and no answer!! :(

#3 zhongmindai

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Posted 17 October 2009 - 10:14 PM

shit, already 14 views and no answer!! :(


I dislike this kind of question.
Its your homework, not ours.
The url you give us is not the gene's mRNA. 5'UTR (5' untranslated region) and 3'UTR is relative to mRNA, not genomic DNA sequences.
Zhong-Min Dai

#4 kedar

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Posted 18 October 2009 - 03:11 AM

I dislike this kind of answer from a rude chinese. If somebody doesn't wanna help, they don't need to reply. Here we help each other, ok.

If somebody else is confused, here is the mRNA. http://www.ncbi.nlm.....2?report=fasta

My confusion is 'should all the sequence (till the very start) before the 1st ATG in the 1st exon be considered 5' UTR or just this part:
CCCAGATAAAAGGTAGGGGAGGAGGAGAGAGAGAGAAGGAAGAGTCTAGGCTGAGCAAC after which there is an inframe ATG.


thanks





shit, already 14 views and no answer!! :(


I dislike this kind of question.
Its your homework, not ours.
The url you give us is not the gene's mRNA. 5'UTR (5' untranslated region) and 3'UTR is relative to mRNA, not genomic DNA sequences.



#5 zhongmindai

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Posted 18 October 2009 - 03:53 AM

I dislike this kind of answer from a rude chinese. If somebody doesn't wanna help, they don't need to reply. Here we help each other, ok.

If somebody else is confused, here is the mRNA. http://www.ncbi.nlm.....2?report=fasta

My confusion is 'should all the sequence (till the very start) before the 1st ATG in the 1st exon be considered 5' UTR or just this part:
CCCAGATAAAAGGTAGGGGAGGAGGAGAGAGAGAGAAGGAAGAGTCTAGGCTGAGCAAC after which there is an inframe ATG.


thanks





shit, already 14 views and no answer!! :(


I dislike this kind of question.
Its your homework, not ours.
The url you give us is not the gene's mRNA. 5'UTR (5' untranslated region) and 3'UTR is relative to mRNA, not genomic DNA sequences.


"shit","rude", who used these words?
An mRNA contains 5'UTR, ORF and 3'UTR.
CCCAGATAAAAGGTAGGGGAGGAGGAGAGAGAGAGAAGGAAGAGTCTAGGCTGAGCAACATGAAGGGGCCCCCAACCTTCTGCAGCCTCCTGCTGCTGTCATTGCTCCTGAGCCCAGACCCTACAGCAGCATTCCTACT
GCCACCCAGCACTGCCTGCTGTACTCAGCTCTACCGAAAGCCACTCTCAGACAAGCTACTGAGGAAGGTCATCCAGGTGGA
ACTGCAGGAGGCTGACGGGGACTGTCACCTCCAGGCTTTCGTGCTTCACCTGGCTCAACGCAGCATCTGCATCCACCCCCA
GAACCCCAGCCTGTCACAGTGGTTTGAGCACCAAGAGAGAAAGCTCCATGGGACTCTGCCCAAGCTGAATTTTGGGATGCT
AAGGAAAATGGGCTGA
AGCCCCCAATAGCCAAATAATAAAGCAGCATTGGATAATAATTTCTGAAAAAAAAAAAAAAAAAAAAAAAA
Zhong-Min Dai

#6 kedar

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Posted 18 October 2009 - 06:42 AM

thanks , that's the spirit. I take back the rude word. :(

My answers are the same but once somebody else tells something else, it becomes a mess, you know. So, i needed to confirm.

thanks

#7 kedar

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Posted 18 October 2009 - 06:49 AM

next question!

if you are asked to count the number of nt in 3' UTR, will you count AGCCCCCAATAGCCAAATAATAAAGCAGCATTGGATAATAATTTCTGA? =48 nucleotides
or AGCCCCCAATAGCCAAATAATA
AAGCAGCATTGGATAATAATTTCTGAAAAAAAAAAAAAAAAAAAAAAAA? because the aaaa... i guess is poly a tail. and i guess you can add more AAAs...

according to me, it's 48..

Edited by kedar, 18 October 2009 - 06:51 AM.





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