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Old 01-22-2013, 01:28 AM   #1
lzhdennisdn
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Default A question on Arabidopsis (TAIR10) annotation file

Hey guys,

Below is some part of the annotation file, does any one know why the coordinates of 3'UTR and the last exon are overlapped ? Which should I regard as the real 3'UTR region. (I guess several 3'UTR indicate different isoforms, but why overlap with exon happened?)

Thanks for any kindly help!

Chr2 TAIR10 mRNA 14434339 14436174 . + . ID=AT2G34185.3;Parent=AT2G34185;Name=AT2G34185.3;Index=1
Chr2 TAIR10 protein 14434402 14435302 . + . ID=AT2G34185.3-Protein;Name=AT2G34185.3;Derives_from=AT2G34185.3
Chr2 TAIR10 exon 14434339 14434555 . + . Parent=AT2G34185.3
Chr2 TAIR10 five_prime_UTR 14434339 14434401 . + . Parent=AT2G34185.3
Chr2 TAIR10 CDS 14434402 14434555 . + 0 Parent=AT2G34185.3,AT2G34185.3-Protein;
Chr2 TAIR10 exon 14435036 14435147 . + . Parent=AT2G34185.3
Chr2 TAIR10 CDS 14435036 14435147 . + 2 Parent=AT2G34185.3,AT2G34185.3-Protein;
Chr2 TAIR10 exon 14435233 14435328 . + . Parent=AT2G34185.3
Chr2 TAIR10 CDS 14435233 14435302 . + 1 Parent=AT2G34185.3,AT2G34185.3-Protein;
Chr2 TAIR10 three_prime_UTR 14435303 14435328 . + . Parent=AT2G34185.3
Chr2 TAIR10 exon 14435427 14435520 . + . Parent=AT2G34185.3
Chr2 TAIR10 three_prime_UTR 14435427 14435520 . + . Parent=AT2G34185.3
Chr2 TAIR10 exon 14435814 14436174 . + . Parent=AT2G34185.3
Chr2 TAIR10 three_prime_UTR 14435814 14436174 . + . Parent=AT2G34185.3
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Old 01-22-2013, 10:01 AM   #2
cram
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An exon is defined as any part of the gene that is transcribed - even if it is not translated. UTRs will therefore always overlap exons because they are part of the transcript. Some exons may be entirely UTR and some may contain both CDS and UTR. In this example only one isoform is being described, it has three 3' UTR sections because the 3' UTR accounts for all of the last two exons plus part of a third.
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Old 01-22-2013, 10:14 AM   #3
lzhdennisdn
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Hi cram,

Thanks for your answer, I got one more question based on this, as we can see the three part of 3'UTR, the coordinates are not continuing, does this mean, in the pre-mRNA, even in the UTR region, there are introns exist?
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Old 01-22-2013, 10:34 AM   #4
cram
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Quote:
I got one more question based on this, as we can see the three part of 3'UTR, the coordinates are not continuing, does this mean, in the pre-mRNA, even in the UTR region, there are introns exist?
Yes, there are introns in the UTR. It may help to to take a look at the Gbrowse for this gene. The dark blue boxes are CDS, the light blue is UTR.
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