Hi

I recently asked a question as to whether exons can have different reading frames in the same gene. The answer was, surprisingly to me, yes. In this question I am assuming for simplicity that an exon has the same reading frame in all transcripts it features in.

Lets imagine a gene running from bases 1 to 200. Exon 1 is from bases 50 to 100 and exon 2 is from 125-150 and exon 3 is from 175-200.

Then lets say there is a splice variant (variant 1) containing exons 1 and 2 and another splice variant (variant 2) containing exons 1 and 3.

Then lets imagine there is a SNP in exon 1 at base 60. Could this SNP have a different effect in the different transcripts? For example is it possible that in variant 1 the exon is not translated at base 60 so the SNP is an an upstream untranslated region, but in variant 2 the SNP is in the translated region and causes a synonymous (or non-syn) amino acid change?

So another way of asking the question is this: if an exon appears in multiple transcripts, does it always play the same role in those transcripts? E.g is it always translated or not translated, and if it is translated, does translation start at the same place. I am assuming the answer to this will be 'no' because if an exon can have multiple reading frames in the same gene then all sorts of other scenarios are possible. 

If what I describe does happen, roughly how common or uncommon is it?

Many thanks in advance
I've piped the program I wrote for your previous question and described [here](http://plindenbaum.blogspot.com/2010/10/where-are-alternative-reading-frames-in.html) to cross the data with dbSNP/UCSC:

    java BioStar3034  | head 1000 |  tr ":-" "," |\
    awk -F ',' 'BEGIN { printf("select * from snp130 where chrom=\"_\" ");} {printf(" OR (chrom=\"%s\" and chromStart=%d)\n",$1,int($2)-1);} END {printf(";\n");}' |\
    mysql  -h  genome-mysql.cse.ucsc.edu -A -u genome -D hg18

One of the result is <strong>rs1152725</strong> <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1%3A1209324-1209324">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&amp;position=chr1%3A1209324-1209324</a>

If the alternate base is 'C' instead of ref='T'

 - transcript 1: codon `CTC (L) -> CCC (Proline)` (<strong>non-synonymous</strong>)
 - transcript 2: codon `TCT(Serine) -> TCC (Serine)` (synonymous)

so my answer is YES: it happens :-)