Question: 3'UTR of transcript
0
gravatar for joesphzhao2013
2.8 years ago by
joesphzhao20130 wrote:

I use ensemble to get the location of transcript's 3'UTR, but there are multiple location for one transcript. May one transcript have multiple 3UTR region?

sequence • 977 views
ADD COMMENTlink written 2.8 years ago by joesphzhao20130
2

Always helpful if you show an example of what you are seeing. A gene can definitely have multiple 3' UTR locations/annotations, and it's possible to have transcripts with multiple parts of the same UTR (spliced).

But without clear example it's hard to guess what phenomenom you are encountering ;)

ADD REPLYlink written 2.8 years ago by WouterDeCoster40k

['GeneId', 'transcriptID', '3UTR start', '3UTR end'] ['ENSG00000261657', 'ENST00000566782', '66455500', '66456619'] ['ENSG00000261657', 'ENST00000562780', '66449084', '66449105'] ['ENSG00000261657', 'ENST00000562780', '66455382', '66455748'] ['ENSG00000261657', 'ENST00000569579', '66382157', '66382229'] ['ENSG00000261657', 'ENST00000569579', '66424056', '66424100'] ['ENSG00000261657', 'ENST00000569579', '66440552', '66440621'] ['ENSG00000261657', 'ENST00000569579', '66447170', '66447234'] ['ENSG00000261657', 'ENST00000569579', '66448221', '66448294'] ['ENSG00000261657', 'ENST00000569579', '66455382', '66456619'] This is what I get from ensemble. For ENST00000569579, there are multiple 3UTR start and end position

ADD REPLYlink written 2.8 years ago by joesphzhao20130
1

Right, it's a spliced UTR.

ADD REPLYlink written 2.8 years ago by Devon Ryan91k

It's often helpful to have a look at the gene/transcripts in a genome browser such as those from UCSC or Ensembl.

ADD REPLYlink written 2.8 years ago by WouterDeCoster40k
1

Perhaps its 3' UTR is spliced...

ADD REPLYlink written 2.8 years ago by Devon Ryan91k
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