Some basic ambiguities making me confused. I downloaded 5'UTR, CDS, 3'UTR, and exon sequences, separately from Biomart for a gene P4HA2 (Homo sapiens) and found some simple sequence repeat (SSR) on them. While there is a repeat x on the exon sequence, it was not located on the 5'UTR, 3'UTR, and coding sequence (or CDS) of gene. As I remember, exon sequences is the same with coding sequence, except for the first and last exon, which are parts of 5'UTR and 3'UTR, respectively, am I right?. Could you please help me out to find how the mentioned event is possible? Thanks
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$\begingroup$ Are your comparing the same splice variant? $\endgroup$– canadianerCommented Sep 7, 2015 at 23:56
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$\begingroup$ As @canadianer said, remember that almost all human genes are interrupted. There are long intronic sequences in the gene that can interrupt your coding sequence. Also alternative splicing can cut out exons that make up the mature mRNA. If you do an alignment you should be able to pick up where the exons are in the splice variant of your gene. $\endgroup$– AMRCommented Sep 8, 2015 at 3:47
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$\begingroup$ Yes Canadianer, I compare the same splice variant. $\endgroup$– MaryCommented Sep 8, 2015 at 5:08
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2 Answers
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As I remember, exon sequences is the same with coding sequence, except for the first and last exon, which are parts of 5'UTR and 3'UTR, respectively, am I right?
Not necessarily. The UTRs can be composed of multiple exons and there can be an exon that spans both sides of the start codon i.e it is both a part of the 5'UTR and CDS. Similarly, an exon can span both sides of the stop codon.
A reason for why you are not able to map your repeat to any of the regions of the mRNA could be that your repeat falls in an exon that spans the start/stop codon. The repeat itself might span these sites. You need to provide additional details such as the location of the repeat, size of the repeat and which exon it maps to. Also mention which reference genome file are you using.
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The coding region is that region of the DNA coding strand that is translated into a product. This is synonomous with the exon region. The 5' untranslated region and the 3'untranslated region are just that and though they may serve some little understood function in replication, they are not translated into a protein. "coding region" is not a term that I have heard widely used although I am a neophyte as a molecular biologist.
